Home
ORAC-DR – imaging data reduction
Contents
1. 00 00088 3 1 9 Chopping 1 10 Post pre subtraction 3 1 11 FITS headers Qo 3 2 Dark subtraction 0000048 3 2 1 Dark creation 004 3 3 Flat fielding 3 3 1 Flat creation 3 3 2 Object masking 3 6 1 Polarimetry Extraction and Sky Subtraction Automatic Registration 3 7 3 8 1 Polarimetry Resampling 3 10 Near Infra red Aperture Photometry 3 11 Mid infra red Aperture Photometry 3 12 Improving the signal to noise of Mid infra red Data 13 Catalogue Generation Qo 3 7 1 Moving Targets 000 wk ari Pe 3 8 Mosaicking ass BE ek oS eS lS SUN 232 8 Contents SUN 232 8 Contents iv 22 3 15 Tidying 23 23 by Sad Beene de A 23 ta by Se s SS eee Ge dee Gee eS 23 A O we deg ues Gen eon ayaa eka at ae 24 se BH to Hout sw kes Gee en Gn eho Bc a se 24 Se Save Sr eet a en o dies y ee ee 25 HGS e Sie ee a Ge eae Me ee Se ets Se es eee ee a 26 27 28 28 A Processing UKIRT data obtained before 2000 August 29 30 32 37 BR Shae Se 2h ie he oh ee Se a Sh ale a ee Seay os oh ote eh eu ah oe et ce 37 Be ee erie oa eee ss Gea we ee oe eee Ge 48 A eae A de A nae eee a tee eas 08 na aa ee ee 49 ARRAY TESTO 50 o eee ee ee A ee ee 51 Beas A amp sie toe as ee we eo a 53 Sige ee Ss Ba a Owe ae Be es 56 CA AAA Deke AR 58 Sees Gee A A ees oe ee 61 hs bi a Sak A Be et
2. The processing engines are from the Starlink packages and SUN 232 8 Recipes 132 NOD_CHOP_FAINT e Uses the Starlink NDF format and multi NDF HDS container files e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter 133 NOD_CHOP_SCAN SUN 232 8 Recipes NOD_CHOP_SCAN Reduces a chopped and nodded observation in a scan pattern Description This script reduces chopped and nodded observation currently just for Michelle data It takes an imaging observation comprising a multiple of four object frames at a series of scan offset positions to make calibrated untrimmed mosaics at each scan position automatically It performs a null debiassing creation and propagation of data variance difference the integrations for each AB chop beam pair bad pixel masking difference adjacent nodded pairs registers the frames and forms a mosaic at each scan position See the Notes for further information Notes A variance array is created for each beam first using the read noise and once the bias is removed Poisson noise is added A bias frame selected from the calibration system is removed from each beam in CHOP read mode If no bias frame is available in the CHOP mode the recipe subtracts a null bias so the errors will be overestimated in the CHOP read mode the data array will be unaffected once
3. e The processing engines are from the Starlink packages and e Uses the Starlink NDF format and multi NDF HDS container files e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter 127 NOD_CHOP_APHOT SUN 232 8 Recipes NOD_CHOP_APHOT Reduces a chopped and nodded observation and performs aperture photometry Description This script reduces a chopped and nodded observation currently just for Michelle data It takes an imaging observation comprising a multiple of four object frames to make a calibrated untrimmed mosaic automatically It performs a null debiassing creation and propagation of data variance difference the integrations for each AB chop beam pair bad pixel masking difference adjacent nodded pairs registers the frames and forms a mosaic See the for further information The script combines and registers the various chopped and nodded images of the point source and neighbouring background to form to form a single image with four times the signal Photometry of the point source using a fixed 5 arcsecond aperture is then calculated The results appear in 0RAC_DATA_OUT aphot_results txt in the form of a Starlink small text list The analysis of each star is appended to this file Notes e A variance array is created for each beam first using the read noise and once the bias is removed
4. lt waveplate_angle gt is the integer part of the angle e g 22 67 where lt filter gt is the filter name excluding the po1 and lt group_number gt is the frame number of the group For each subsequent cycle of the recipe the recipe makes new flats which have a _c lt cycle_number gt suffix where lt cycle_number gt is the number of the cycle counting from one e The flats are filed in 0ORAC_DATA_0UT index flat Parameters USEVAR LOGICAL Whether or not to create and propagate variance arrays 1 Related Recipes SKY_FLAT_FP SKY_FLAT_MASKED SKY_FLAT_POL_ANGLE Implementation Status e The processing engines are from the Starlink packages CCDPACK FIGARO and EXTRACTOR e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through the intermediate file to the flat e Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 186 SKY_FLAT_POL_ANGLE SKY_FLAT_POL_ANGLE Creates and files flat fields derived from jittered frames at each waveplate angle using object masking to reduce artifacts Description This recipe make a sky flat for UKIRT imaging from a series of sky or object frames combined using one of a selection of statistics It is intended to be used to make flats at each waveplate angle for polarimetry data The data should comprise at least three spatial positions for each waveplate angle 0 45 22 5 and 67 5 degrees in tu
5. F4 F3 F5 F6 F8 F7 Flatfield where Fn is the bad pixel masked and dark subtracted frame n In practice the flat field is applied to each differenced pair such as F4 F3 when the pair becomes available rather than waiting until all eight frames have been observed Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist e The bad pixel mask applied is 0RAC_DATA_CAL bpm 81 EP SUN 232 8 Recipes Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used You should use 5SKY_FLAT_FP to make the flat field Registration is performed using the telescope offsets transformed to pixels There is no resampling merely integer shifts of origin The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of eight the recipe creates a mosaic which is then added into a master mosaic of im
6. by pixel using a broadened median and the combined array normalised to a have a mean of one It is possible to use another statistic for the combination such as a clipped median MAKE_FLAT_FROM_GROUP_ MAKE_FLAT_FROM_NORMALISED_GROUP_ _MASK_DEVIANTS_ There are variants for certain families of recipes which marshall the various required subgroups of frames MAKE_FLAT_CHOP_SKY_ _MAKE_FLAT_FROM_NORMALISED_CHOP_SKY_ _MAKE_FLAT_EXTENDED_ MAKE_FLAT_FROM_NORMALISED_EXTENDED_ _MAKE_FLAT_QUADRANT_JITTER_ Flats are filed with the calibration system _FILE_FLAT_ 3 3 2 Object masking In recipes which make a flat using the frames taken of the targets the so called self flat any sources present can bias the flat field and result in blotchy mosaics The full versions of such recipes as opposed to the _BASIC versions and greatly reduce these artifacts using the following algorithm After the application of the approximate self flat field an EXTRACTOR inventory is made of objects having at least 12 connected pixels above 1 0 g above sky The thresholds can be changed in 0RAC_DATA_CAL extractor_mask sex through the DETECT_MINAREA and DETECT_THRESH parameters The locations shapes orientations and sizes are used to make a mask The mask is applied to the dark subtracted frames and a new flat created As the outer parts of bright objects often leave residual unmasked blobs a circular central occulting mask is used The diameter is no
7. e Error propagation is controlled by the USEVAR parameter 121 MOVING_QUADRANT_JITTER SUN 232 8 Recipes MOVING QUADRANT JITTER Reduces a Quadrant Jitter observation of a moving target including object masking Description This script reduces a quadrant jitter photometry observation with UKIRT imaging data It takes an imaging observation comprising one or more series of four object frames where the target is approximately centred in each quadrant and a dark frame to make automatically a calibrated untrimmed mosaic in the reference frame of the moving target It performs bad pixel masking null debiassing dark subtraction flat field creation and division feature detection and matching between object frames and resampling See the for further information Registration is adjusted to track the motion of the moving target using ephemeris data stored in file target_ephem dat See Ephemeris file Format for details of this file s format This recipe works well for extended moving sources comets whose extent does not exceed 45 arcseconds for UFTI or 10 arcseconds for IRCAM in moderately crowded fields Sources may include those with a comparatively bright core embedded in faint extended emission The object need not be isolated as the recipe masks objects within the other quadrants and hence does not introduce significant artifacts into the flat field This recipe should not be used for frames where the te
8. e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The naming format is slightly different for some non UKIRT instruments The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters NUMBER INTEGER The number of frames in the jitter pattern If not supplied the number of offsets as given by FITS header NOFFSETS minus one is used If neither is available 9 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent Related Recipes ITTER_SELF_FLAT BASIC JITTER SELF FLAT TELE MOVING _JITTER SELF PLAT SUN 232 8 Recipes 118 MOVING_JITTER_SELF_FLAT_ BASIC Implementation Status e The processing engines are from the Starlink packages and e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter Deprecated Variants MOVING_JITTER9_SELF_FLAT_BASIC 119 MOVING_NOD_CHOP SUN 232 8 Recipes MOVING_NOD_CHOP Reduces a chopped and nodded observation of a moving target Description This script reduces a chopped and nodded observatio
9. Recipes DARK_AND_BPM Measures dark current and creates a new bad pixel mask for UIST Description This recipe is used to measure the dark current for UIST using a long exposure DARK frame It first finds and bad pixels in the DARK then measures and reports the dark current The recipe appends to a tabulation of the dark current in an engineering log file S ORAC_DATA_0UT uist_array_tests log which it creates with headings if the log does not exist Notes e The recipe applies thresholds to the dark frame and flags pixels outside these limits as bad The thresholds are derived from 3 standard deviation clipped statistics pixels more than 5 standard deviations above the mean are flagged e The bad pixels detected are added into the current bad pixel mask and then this is filed with the calibration system as a new and current bad pixel mask e The new bad pixel mask is applied to the original dark frame whose unclipped mean scaled by the gain and inverse exposure time is the dark current in electrons per second Output Data e The engineering log 0RAC_DATA_0UT uist_array_tests log Related Recipes ARRAY _TESTS MMEASURE_READNOISE Implementation Status e The processing engines are from the Starlink package KAPPA e Uses the Starlink NDF format e History is recorded within the data files e Error propagation is not used SUN 232 8 Recipes 70 DARK_SUBTRACT DARK_SUBTRACT Subtracts a dark frame Description Th
10. e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter Deprecated Variants MOVING_JITTER9_SELF_FLAT SUN 232 8 Recipes 116 MOVING_JITTER_SELF_FLAT_BASIC MOVING_JITTER_SELF_FLAT_BASIC Reduces a standard jitter photometry observation of a moving target using just the basic operations for speed Description This script reduces a standard jitter photometry observation with UKIRT imaging data It takes an observation comprising jittered object frames of a moving target and a dark frame to make automatically a calibrated untrimmed mosaic in the reference frame of the target It performs a null debiassing bad pixel masking dark subtraction flat field creation and division amd integer shifts of pixel origin to register to fixed sky co ordinates See the Notes for further information The registration is adjusted to track the motion of the moving target using ephemeris data stored in file target_ephem dat See Ephemeris file Format for details of this file s format This recipe aims to keep pace with the pipeline s incoming data It works well for faint moving sources and in moderately crowded fields It should not be used for frames where the telescope guided on the moving object In that case reduction should be performed by ITTER_SELF_FLAT_TELE which registers using the t
11. 0 139 NOD_SELF_FLAT_NO_MASK_APHOT SUN 232 8 Recipes Related Recipes BRIGHT_POINT_SOURCE_APHOT NOD_SELF_FLAT_NO_MASK Implementation Status e The processing engines are from the Starlink packages FIGARO and EXTRACTOR e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter Deprecated Variants NOD4_SELF_FLAT_NO_MASK_APHOT NOD8_SELF_FLAT_NO_MASK_APHOT SUN 232 8 Recipes 140 NOD_SKY_FLAT_THERMAL NOD_SKY_FLAT_THERMAL Reduces a nod jitter observation creating a flat from sky frames Description This script reduces a nod jitter observation with UKIRT imaging data It takes an imaging observation comprising a multiple of eight object frames and a dark frame to make a calibrated untrimmed mosaic automatically It performs a null debiassing bad pixel masking dark subtraction difference adjacent pairs flat field creation and division feature detection and matching between object frames and resampling See the Notes for further information This recipe works well for faint sources in moderately crowded fields Notes A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The
12. 0RAC_DATA_OUT target_ephem dat The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of jittered frames the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic Intermediate frames are deleted except for the flat fielded _ff suffix frames Ephemeris file Format The current format of the ephemeris file is one line per object comprising three space separated fields in the following order the objectname which may contain embedded spaces the motion in the plane of the sky in arcsec second for right ascension then declina tion Note that the right ascension motion is the change in right ascension multiplied by the cosine of the declination The form
13. For each spatial set the recipe performs a null debiassing bad pixel masking dark subtraction pairwise frame differencing flat field division integer shifts of origin to register and mosaicking The wavelength shifted mosaic is given by F1 F2 F4 F3 Flatfield where Fn is the bad pixel masked and dark subtracted frame n In practice the flat field is applied to each differenced pair such as F1 F2 when the pair becomes available rather than waiting until all four frames have been observed Finally the recipe registers all the wavelength mosaics spatially and forms a untrimmed mosaic combined using the median to reduce stellar artifacts Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist e The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used 87 FP_JITTER_NO_SKY SUN 232 8 Recipes You should use SKY_ FLAT _FP to make the flat field Registration is performed using the telescope offsets transformed to pixels e There is no resampling merely integer shifts of origin For each set of four the recipe creates a wavelength mosaic For each cycle of spatial p
14. Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 e Data errors are propagated through all processing steps The initial values are found by applying the nominal ADU conversion and read noise The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used You should use SKY_FLAT POL or SKY FLAT POL ANGLE to make the flat fields The target regions are 10 to 90 of the frame width about the Right ascension centre i e roughly centred on the source The current sky limits are 1 to 99 of the frame width along the Right ascension axis The Declination pixel limits are instrument dependent and are as follows For UFTI o sky 69 264 e sky 320 484 o target 601 764 e target 824 988 For IRCAM o sky 12 52 e sky 67 107 o target 152 192 e target 207 247 SUN 232 8 Recipes 150 POL_EXTENDED The sky subtraction for
15. The polarisation data for each pixel are also stored in catalogues See Output Data The intensity image may be displayed with vectors overlaid Steps are taken to reduce the number of noisy or insignificant pixels as well as clutter First the polarisation catalogue data are averaged in 3 by 3 pixel bins Second a binned pixel is rejected if its polarisation is greater than 50 or is not positive or its polarisation signal to noise less than 3 or its polarisation error is greater 5 The bin size and thresholds can readily be changed by supplying arguments to the CALC _STOKES_NOD_CHOP_ primitive At the end of each cycle the grand mosaics are registered and new polarisation maps and catalogues constructed Intermediate frames are deleted except for the differenced pairs _dp suffix frames Output Data The integrated mosaics in lt m gt lt date gt _ lt group_number gt _p lt angle gt _mos where lt m gt is the instrument s group prefix and lt angle gt is 0 22 45 or 67 A mosaic for each cycle of chopped and nodded frames per waveplate angle in lt m gt lt date gt _ lt group_number gt _p lt angle gt _mos_c lt cycle_number gt where lt cycle_number gt counts from 0 The combined source image and neighbourhoods at each waveplate angle in lt m gt lt date gt _ lt group_number gt _p lt angle gt _cab The differenced pairs in lt i gt lt date gt _ lt obs_number gt _dp where lt i gt is the Polarisation fram
16. There is no rotation to align the Cartesian axes with the cardinal directions e The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of frames the recipe creates mosaics for each chop beam and waveplate angle modulo 180 degrees Each mosaic has its bad pixels filled and after the first SUN 232 8 Recipes 158 POL_NOD_CHOP cycle is then added into its own master mosaic of improving signal to noise The exposure time is also summed and stored in each master mosaic s corresponding header Likewise the end airmass and end UT headers are updated to match that of the last observed frame contributing to the mosaic For each waveplate angle the combined source image is made by taking symmetrical areas about each source such that no pixels are duplicated Thus the divisions occur at midpoints of the chop throw and the nod separations These are registered using the source centroids The polarised intensity is corrected for the statistical bias of the noise by subtracting the variance of Q or U An offset of 0 0 degrees clockwise is applied to the rotation angle for the orientation of the analyser with
17. This frame median is subtracted from the source frames after they have been flat fielded A flat field is created for each row of the grid of target frames and applied only to that row of target frames The sky subtraction comes from linear interpolation of the sky modal values of the two flat fielded sky frames which immediately bracket the target frame Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects it then tries the crosshead offsets If these are null the script resorts to the telescope offsets The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions 73 EXTENDED_3x3 SUN 232 8 Recipes e The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The noise will be greater in the mosaic s peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame Mosaics are made and displayed for each row except the last At the end of each cycle of 19 frames the full mosaic of nine target frames is created and displayed instead On the second and subsequent cycles the full mosaic is added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s c
18. Whether or not to create and propagate variance arrays 0 Related Recipes ITTER_SELF_FLAT_APHOT NOD_SELF_FLAT_NO_MASK_APHOT SKY_AND_JITTER SKY_FLAT SKY_FLAT MASKED Implementation Status The processing engines are from the Starlink packages AND Uses the Starlink NDF format History is recorded within the data files The title of the data is propagated through intermediate files to the mosaic Error propagation is controlled by the USEVAR parameter 177 SKY_AND_JITTER_APHOT SUN 232 8 Recipes Deprecated Variants SKY_AND_JITTER5_APHOT SUN 232 8 Recipes 178 SKY_FLAT SKY_FLAT Creates and files a flat field derived from jittered frames Description This recipe makes a sky flat for UKIRT imaging from a series of sky or object frames which are combined using one of a selection of statistics It expects one dark frame followed by jittered sky frames It performs a null debiassing bad pixel masking and dark subtraction before combining normalised frames pixel by pixel using the median Details of the flat are filed in the index of flats for future selection and use of the flat See the for further details For best results the field observed should contain few stars and no bright ones In contami nated sky regions recipe SKY_FLAT_MASKED will greatly reduce artifacts appearing in the resultant flat Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no W
19. as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used Applies a mask about the Fabry Perot s transmitted circular region on the detector If the centre is not known through the fpcentre calibration it is determined using profiles of the surrounding ring The flat field is created iteratively First an approximate flat field is created by combining normalised sky frames using the median at each pixel This flat field is applied to the sky frames Sources within the flat fielded frames are detected and masked in the dark subtracted frames The first stage is repeated but applied to the masked frames to create the final flat field Intermediate frames are deleted Sub arrays are supported Output Data The created flat field in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent recipe cycles Token lt filter gt is the filter name lt group_number gt is the frame number of the group and lt cycle_number gt is the number of the cycle counting from one The flats are filed in 0RAC_DATA_OUT index flat 181 SKY_ELAT_FP SUN 232 8 Recipes Parameters USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes SKY_FLAT SKY_FLAT_ MASKED Implementation Sta
20. as described in Section 3 3 2 Then it forms a one dimensional profile by masking objects collapsing along rows using the median from which it subtracts a clipped mean of the profile to form a new profile of the bias variations The bias variation profile is then subtracted from each row of the original flat fielded frame ISAAC _BIAS_CORRECT_GROUP_ NACO has alternating positive and negative signals in its columns most noticeable in longer exposures The same filter as ISAAC except it collapses along columns and does not mask SUN 232 8 Features of the Primitives 16 objects is applied to the flat fielded frames NACO _BIAS_CORRECT_GROUP_ _REMOVE_COLUMN_ROW_STRUCTURE_ 3 6 Sky Subtraction In general the recipes do not sky subtract in the literal sense of pixel by pixel subtraction of a sky frame or better of some median of jittered sky or even target frames Such recipes could readily be created if there is a demand Instead the sky signature is usually accounted for in thelflat fielding Therefore the mosaics generally have the sky signature removed but not base level The sky varies rapidly in the thermal and mid infra red so dithered pairs or nodded and dithered pairs respectively are differenced to attempt to remove the sky signature See Sec tion 3 1 9 _DIFFERENCE_PAIR_ Another recipe which performs a pixel by pixel sky subtraction isISKY_AND_JITTER It s hardly used and not recommended because it demands a v
21. in SUN 230 for examples 27 SUN 232 8 Correcting headers 5 Correcting headers There are reasons why you may need to edit some of the FITS headers used by ORAC DR e At the summit of Mauna Kea it s easy to make mistakes One of the common ones is to make an error in the exec or sequence This can cause for example frames to be in the wrong observation groups or be assigned the wrong data reduction recipe While the ORAC Observation Tool has reduced the frequency of such errors they will not be eliminated e You may have made some trial observations before taking making a longer integration through several cycles of a recipe Now you wish to combine all the observations of a target to obtain the best signal to noise The main headers to change are RECIPE the data reduction recipe NOFFSETS the number of offsets OBSNUM the number of the frame starting from 1 on each night GRPNUM the group number and should be given by the frame number OBSNUM of its first member and GRPMEM whether or not the frame participates in group processing For IRCAM Michelle UIST UFTI and converted ISAC files it is possible to edit the NDF s FITS extension using KAPPA s fitsmod command The command is a bit long and the author regrets not defining a fitsupdate synonym The following changes the GRPNUM keyword to have value 36 in the raw NDF frame f19991108_00042 fitsmod 19991108_00042 grpnum u 36
22. including histograms and contour plots if you choose a KAPPA GWM widget Most people prefer a simple scaled image display with GAIA This offers facilities to inspect and analyse the data and both pixel and sky co ordinates of the cursor position are presented The selection of frame types to display where they should appear and how they are scaled are configurable using a simple text file or a special GUI tool oracdisp See SUN 230 for details and examples Processing offline there is less need to see the data displayed in real time If you wish to accelerate the processing switch off the display option oracdr nodisplay If you do want to display a recommendation is to create two GAIA windows displaying images using autoscaled limits This first could be for raw and flat fielded data and the second for the mosaics You are likely to want to interact with the latter using GAIA s toolboxes Your ORAC_DATA_OUT disp dat could look like this Send raw frame to first GAIA window num type image tool gaia region 0 window 0 autoscale 1 zautoscale 1 Send flatfielded frame to first GAIA window ff type image tool gaia region 0 window 0 autoscale 1 zautoscale 1 Send mosaic frame to second GAIA window mos type image tool gaia region 0 window 1 autoscale 1 zautoscale 1 SUN 232 8 Using the pipeline 6 2 6 Calibration Information ORAC DR records calibration information such as dark frames flat fields and the read noise
23. jittering on source Requires a separate flat field and a dark Flat Creates a Fabry Perot sky flat from jittered blank sky exposures FP at on and off line wave lengths Requires a dark SUN 232 8 Recipes 48 D 2 Reference documentation The following recipes apply to both UFTI and IRCAM unless otherwise noted Where there are processing differences for the two instruments they are noted in the reference specification Also there is an ARRAY_TESTS recipe for each instrument of which only UFTI s is presented below for technical reasons In the Configurable Steering Parameters sections the defaults appear at the end of the parame ter s description between The non generic recipes of the original release are not documented here but are still available for reducing pre ORAC 2000 August data They are listed in the Deprecated variants section of their generic counterpart Each behaves as the generic counterpart except the number of jitter points is fixed Thus the JITTER9_SELF_FLAT reduces a nine point jitter 49 ADDWCS SUN 232 8 Recipes ADDWCS Creates the valid WCS in the FITS headers of raw data Description This recipe uses the existing hotpotch of UKIRT and AAT imaging headers of raw data to make a new set of headers which define a valid world co ordinate system using the AIPS convention Notes e For IRCAM old headers are reordered and structured with headings before groups of related k
24. of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 e The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is derived from the sky frames as follows The mode sigma clipped mean is used to offset each sky frame s mode to that of the first sky frame The corrected sky frames are combined pixel by pixel using a median of the values in each frame The resultant frame is normalised by its median to form the flat field This frame median is subtracted from the source frames after they have been flat fielded A flat field is created for each row of the grid of target frames and applied only to that row of target frames e The sky subtraction comes from linear interpolation of the sky modal values of the two flat fielded sky frames which immediately bracket the target frame Registration is performed using the telescope offsets transformed to pixels e There is no resampling merely integer shifts of origin The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongs
25. plus NACO and UIST variants FIXED_APERTURE_PHOTOMETRY_ _MAKE_PHOTOMETRY_TABLE_ _GET_FILTER PARAMETERS _ and several instrument variants _PERSSON_STANDARD_MAGNITUDE_ _UKIRT_STANDARD_MAGNITUDE_ _STANDARD_MAGNITUDE_ and instrument specific variants CLIPPED_STATS_ _FIND_SOURCE_CENTROID_ _GET_FRAME_CENTRE_ 3 11 Mid infra red Aperture Photometry This is similar to near infra red aperture photometry The main difference is the source measured Rather than measuring each positive and negative image NOD_CHOP_APHOT integrates the average flux of the one or two pairs of positive and negative images in the chopped and 21 SUN 232 8 Features of the Primitives nodded mosaic The number of pairs depends on the chop and nod orientations and the nod throw The four or two images are first registered using their centroids extracted with a symmetric neighbouring background but without any duplication of pixels from the original mosaic and finally combined averaging to preserve the flux per unit time The exposure time header therefore remains that of the mosaic The aperture size is 5 arcseconds The background is determined from an annulus with an inner diameter of 7 5 arcseconds and an outer diameter of 15 arcseconds enclosing the source The Michelle chip characteristics and the UKIRT chop throw limit the area of this combined image mosaic normally a 15 arcsecond square leaving comparatively little background Recommended a
26. too quickly SKY_AND_JITTER_APHOT As SKY_AND_JITTER but also per forms aperture photometry of the source SUN 232 8 Recipes 42 Faint point source recipes Recipe Name Type of Data Function and Comments ITTER_SELF_FLAT Faint 1 Z gt 17 JHK gt 15 Standard jitter self flats Normally 9 point jitter Requires a dark ITTER_SELF_FLAT_CATALOGUE As JITTER_SELF_FLAT but pro duces an inventory of the locations and brightnesses of sources within the mosaic BRIGHT_POINT_SOURCE_ CATALOGUE As BRIGHT_POINT_SOURCE but produces an inventory of the loca tions and brightnesses of sources within the mosaic Preferred when a self flat is not appropriate ITTER_SELF_FLAT_BASIC Fastest JITTER_SELF_FLAT recipe as it lacks object masking automatic registration and resampling ITTER_SELF_FLAT_NO_MASKi As JITTER_SELF_FLAT but faster as it lacks object masking It only suit able for uncrowded fields 43 SUN 232 8 Recipes Extended source recipes Recipe Name Type of Data Function and Comments QUADRANT_JITTER QUADRANT_JITTER_BASIC Galaxies quasars and nebulae of small lt 45 arcsec angular extent 4 point jitter masks the quad rant containing the target to make the flat then masks the ob jects Requires a dark QUADRANT_JITTER_NO_MASK As QUADRANT_JITTER but without object masking Fas
27. within index files one for each type of calibration information When the pipeline needs a calibration frame it searches the index file for the best matching entry subject to a set of rules Each recipe reports the calibrations it has used If no suitable calibration exists the pipeline exits with an error message stating this fact For further details see SUN 230 Section 4 3 has an example of an index file You can also select a specific calibration using the calib command line option provided the chosen calibration has an entry in the appropriate index file See the section on in SUN 230 for details and examples 2 6 1 Available calibration methods The following calibration methods are available for imaging recipes e baseshift Use the given comma separated doublet i e 0 0 as the frame s base po sition This is used to locate faint sources in the mid infra red data where centroiding fails when there is some telescope pointing error such as incorrect instrument aper tures It is calibrated within NOD_CHOP_APHOT on a bright standard and used by NOD_CHOP_FAINT For a well tuned system the baseshift is expected to be near 0 0 so the centre of the detector is at the reference position derived from the FITS headers e bias Use the given bias frame e dark Use the given dark frame e fpcentre Use the given Cartesian pixel centre of the Fabry Perot transmitted region UFTI only e flat Use the given
28. 0 The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The naming format is slightly different for some non UKIRT instruments Polarisation frames lt m gt lt date gt _ lt group_number gt _ lt suffix gt each with a differ ent suffix for the each parameter The suffices are I intensity P percentage polarisation PI polarisation intensity Q Stokes Q TH polarisation angle U Stokes U A FITS binary table catalogue of the binned and culled polarisation data called lt m gt lt date gt _ lt group_number gt _1 FIT For each point it tabulates the x y co ordinates the total intensity the Stokes parameters the percentage polarisation the polarisation angle and intensity There are additional columns giving the standard deviation on each of the tabulated values excluding the co ordinates Likewise lt m gt lt date gt _ lt group_number gt _all FIT and lt m gt lt date gt _ lt group_number gt _bin FIT store the full and binned catalogues re spectively Parameters NUMBER INTEGER The number of frames in the jitter pattern per waveplate angle If this is not set the number of offsets as given by FITS header NOFFSETS minus one is used If neither is available 3 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent USEVAR LOGICAL
29. 3 15 Tidying Each recipe has a tidy procedure which removes unnecessary intermediate frames when the recipe no longer requires them Retained are the raw data flat fielded frames differenced pairs for chopped data and the mosaics Most of the intermediate small text files are removed in individual primitives but some registration related files do persist until the tidy script cleans up If you need to retain the intermediate files comment out the final instruction of the recipe which calls the tidy primitive and follow the instructions in Section f to make and use a private version of a recipe or set the 0RAC_KEEP environment variable to 1 lt recipe_family gt _TIDY_ such as EXTENDED_TIDY_ JITTER_SELF_FLAT TIDY_ _NOD_CHOP_TIDY_ _REDUCE_DARK_TIDY_ general _DELETE_A_FRAME_ general _DELETE_INTERMEDIATE_GROUP_FILES_ general _DELETE_TEMP_FILES_ general _DELETE_TEMP_GROUP_FILES_ _IMAGING_GOODBYE_ 4 Customising Recipes If you wish to write your own data reduction recipes you should consult the ORAC DR Program mer s Guide SUN 233 However for most purposes observers wishing to modify existing scripts can get by without this document A easier to use tailoring system to control parameters and primitive arguments from the com mand line and personal style files is under consideration 4 1 Search paths ORAC DR allows you to create your own recipes and primitives or modify those provided as part of the package
30. An offset of 6 3 degrees clockwise is applied to the rotation angle for the orientation of the analyser with respect to north The polarisation data for each pixel are also stored in catalogues See Output Data The intensity image may be displayed with vectors overlaid Steps are taken to reduce the number of noisy or insignificant pixels as well as clutter First the polarisation catalogue data are averaged in 3 by 3 pixel bins Second a binned pixel is rejected if its polarisation is greater than 50 or is not positive or its polarisation signal to noise less than 3 or its polarisation error is greater 5 The bin size and thresholds can readily be changed by supplying arguments to the CALC _STOKES_ primitive At the end of each cycle the grand mosaics are registered and new polarisation maps and catalogues constructed Intermediate frames are deleted except for the flat fielded _ff suffix frames and the mosaics _mos or _mos_c lt cycle_number gt suffix Output Data The integrated mosaics in lt m gt lt date gt _ lt group_number gt _ lt beam gt lt angle gt _mos where lt m gt the instrument s group prefix Token lt beam gt is e or 0 and lt angle gt is 0 22 45 or 67 155 POL_JITTER SUN 232 8 Recipes e A mosaic for each cycle of jittered frames per beam and angle in lt m gt lt date gt _ lt group_number gt _ lt beam gt lt angle gt _mos_c lt cycle_number gt where lt cycle_number gt counts from
31. As a rule of thumb the group prefix is the frame prefix preceded by g Here is a table of the prefixes Instrument Frame Prefix Group Prefix Notes Classic Cam cc gcc Applies to raw frames after processing with cc2oracdr INGRID r gingrid Format is lt prefix gt lt obs_number gt for individual frames Group files use the UKIRT convention IRCAM i gi ro rg Before 2000 August IRIS2 gi Format is lt date gt lt obs_number gt for in dividual frames where lt date gt is in the form ddmmm Group files use the UKIRT convention ISAAC isaac gisaac Applies to raw frames after processing with isaac2oracdr Michelle m gm NACO naco gnaco Applies to raw frames after processing with naco2oracdr NIRI N gN UFTI f gf UIST u gu 31 SUN 232 8 File prefixes ORAC DR converts the FITS data for instruments like INGRID and NIRI note that the naming convention may be different for the raw FITS data compared with their raw NDF counterparts For example NIRI files are named N followed by the eight digit UT date then S and the four digit observation number and have file extension fits SUN 232 8 File suffices 32 Files generated during ORAC DR imaging data reduction have suffices denoting the processing step that created them This appendix contains a list with short descriptions of what they mean Most will be removed once a recipe has finished using them So you will probably only see these files if you list the conte
32. C It s possible to edit many files using a C shell or Perl script to edit a series of files very quickly If you do it s better to specify the values by keyword instead of position like this fitsmod ndf f19991108_00042 edit update keyword grpnum value 36 position comment C because it is better insulated against change to fitsmod If the file being edited is a multi NDF container file you can avoid disconcerting but harmless error messages if you change the fitsmod command to specify the HEADER NDF Here is an example for Michelle data which changes the number of offsets fitsmod m20011107_00079_raw header noffsets u 5 C For Classic Cam IRIS2 INGRID ISAAC NACO NIRI or old UFTI data you can edit the raw FITS files SORAC_DIR bin fitsmod pl is a documented example Perl script to edit FITS headers The intention is for you to make a copy and edit to suit your particular header editing requirements For some of these instruments it may prove easier to edit the FITS headers in the NDF form of the raw data especially the ESO cameras which have hierarchical headers SUN 232 8 Copyright and License 28 6 Acknowledgments ORAC DR was developed at the Joint Astronomy Centre by Frossie Economou and Tim Jenness in collaboration with the UK Astronomy Technology Centre as part of the ORAC project 1 should like to thanks to members of the ORAC team UKIRT staff and observers who made suggestions for new or improved reci
33. If your NACO data do not show this you can form your own mask from a long exposure dark frame looking for the highly deviant pixels See the notes Creating a bad pixel mask below for suggestions _MASK_BAD_PIXELS_ There are two problems First the pre calculated mask only accounts for 95 of UFTT s problem pixels The other 5 are occasionally deviant on timescales of days The variability of IRCAM Michelle UIST and IRIS2 bad pixels is unknown at the time of writing In addition the bad pixel masks have not been regularly monitored prior to 2000 August The result is that non physical values could appear in the processed data some as extreme as 10 causing automatic registration and image display to go awry Therefore after dark subtraction recipes apply thresholding which flags non physical values as bad meaning undefined This is just augmenting the bad pixel mask and no valid data are lost SUN 232 8 Features of the Primitives 10 The upper limit is above the nominal saturation levels 16000 for Classic Cam 30000 for INGRID 20000 for IRCAM in STARE or NDSTARE mode and 33000 using the Deepwell 200000 for IRIS2 and ISAAC 100000 for Michelle 4300 for NACO in FowlerNsamp and Double_RdRstRd modes but 12400 for Uncorrelated reads except for the M band where it is 28000 17000 times the number of coadds for NIRI 15000 for UFTI and 20000 for UIST The lower limit is the 2 3 3 0 clipped mean approximating to t
34. Poisson noise is added e A bias frame selected from the calibration system is removed from each beam in CHOP read mode If no bias frame is available in the CHOP mode the recipe subtracts a null bias so the errors will be overestimated in the CHOP read mode the data array will be unaffected once the beams are differenced The ARRAY_TESTS recipe files a suitable short exposure dark as a bias in the calibration system The integrations of the two beams are differenced the first subtracted from the second in each pair e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist e The bad pixel mask applied is 0RAC_DATA_CAL bpm Registration is performed using the telescope offsets transformed to pixels The resampling applies integer shifts of origin There is no rotation to align the Cartesian axes with the cardinal directions e The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of object frames the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise The SUN 23
35. The errors are internal based on the sky noise Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix A mosaic for each cycle of jittered frames in lt m gt lt date gt _ lt group_number gt _ lt filter gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming format is slightly different for some non UKIRT instruments For ISAAC the individual bias corrected frames in isaac lt date gt _ lt obs_number gt _bc The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters SUN 232 8 Recipes 104 JITTER_SELF_FLAT_NCOLOUR_APHOT NUMBER INTEGER The number of frames in the jitter pattern If not supplied the number of offsets as given by FITS header NOFFSETS minus one is used If neither is available 9 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes BRIGHT
36. The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used e Intermediate frames are deleted e Sub arrays are supported Output Data e The dark called dark_ lt exposure_time gt _ lt frame_number gt For single frames the group number is the same as the frame number The decimal point in the time is replaced by p e The dark is filed in 0RAC_DATA_OUT index dark Parameters USEVAR LOGICAL Whether or not to create and propagate variance arrays 1 Implementation Status e The processing engines are from the Starlink package KAPPA e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through the intermediate file to the dark SUN 232 8 Recipes 172 REDUCE_FLAT REDUCE_FLAT Reduces an imaging flat field Description This reduces a flat field in the conventional manner consisting of bad pixel masking dark subtraction and normalisation by the mean of the image It also files the normalised flat field frame for use by subsequent flat fielding operations Notes e This recipe will reduce any image passed to it Care must be taken to ensure that a proper flat field image will be reduced e The bad pixel mask applied is 0RAC_DATA_CAL bpm e The flat field is normalised using a clipped mean where the clipping levels are 2 3 and 3
37. a beam uses a constant modal sky level from the correspond ing sky regions Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects for automatic registration the recipe matches the centroid of central source within an 8 arcsecond box Should that fail for the jittered e and o beam sections the recipe resorts to using the telescope offsets transformed to pixels However the final option for registering the e and o beam mosaics at different waveplate angles uses the beam offsets in arcseconds for the current filter converted to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the few pixels in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of twelve frames the recipe creates mosaics for each beam and wave plate angle Each mosaic has its bad pixels filled and after the first cycle is then added into its own master mosaic of improving signal to noise The exposure time is also summed and stored in each ma
38. a mean trimmed of the most extreme tenth of the values gives better results First copy _MAKE_FLAT_FROM_GROUP _ to your primitives directory SUN 232 8 Customising Recipes 26 Y cp 0RAC_DIR primitives imaging _MAKE_FLAT_FROM_GROUP_ O0RAC_PRIMITIVE_DIR Using an editor find the first line in your copy of IMAKE_FLAT_FROM_GROUP_ commencing hidden It should be as follows hidden method median sigmas 2 0 reset accept Change this to hidden method trimmed alpha 0 1 sigmas 2 0 reset accept to effect the change of statistic There is in fact a second line assigning variable hidden depending on argument CLEAN and you should make the same alteration there too If there is demand additional arguments could be provided for primitives to simplify control Please contact the author if you have suggestions for arguments and new recipes or need help customising your ORAC DR scripts 4 3 Index files Once the pipeline has run for a bit you will find text files in 0RAC_DATA_OUT called index flat index dark amongst others These list the calibration frames ORAC DR uses these to find the most recent appropriate calibration For example a flat requires that the filter of the flat matches that of the frame being flat fielded and a dark must have the same exposure time as the target frame and both must have been taken in the same instrument mode Here is an example of a flat index FILTER MODE ORACTIME RDOUT_X1 RDOUT_X2 RDOUT_Y
39. a valid WCS in the FITS headers of raw data This recipe is for all instruments ARRAY_TESTS This is for IRIS2 It calculates and reports the readnoise and dark current using a group of four frames taken in the array tests sequence The readnoise and dark current are logged to a text file and the readnoise is filed with the calibration system DARK_SUBTRACT Subtracts a dark frame from an observation This recipe is meant for a quick look of data that are being taken at a high rate SUN 232 8 Release Notes V3 1 1 204 1 2 Modified recipes Reduction of nodded and chopped data specifically for Michelle It is similar to NOD_CHOP but first removes horizontal and vertical artifacts from the mosaic then forms a single image of the source using a median filter and finally smooths the combined image to enhance the visibility of faint sources NOD_CHOP_SCAN Reduction of nodded and chopped data taken in a scan pattern specifi cally for Michelle It is similar to NOD_CHOP but will create a mosaic from nodded and chopped groups taken in a scan pattern REDUCE_FLAT Reduces a flat field by masking bad pixels subtracting a dark and normalising the result This recipe is for all instruments I 2 Modified recipes e INOD_CHOP_APHOT The photometry aperture has been increased to 5 arcseconds from 3 and inner and outer diameters of the sky annulus have been modified correspondingly The reported photometry uses filter zero points and widt
40. activates two more application engines POLPACK and CATSELECT A new UFTI bad pixel mask Added waveplate angle to flat rules file 5ORAC_DATA_CAL rules flat The angle defaults to zero if it does not have a value in the FITS headers Bug fixes and documentation improvements especially links in the Perl POD
41. and lt angle gt is 0 22 45 or 67 151 POL_EXTENDED SUN 232 8 Recipes e A mosaic for each cycle of jittered frames per beam and angle in lt m gt lt date gt _ lt group_number gt _ lt beam gt lt angle gt _mos_c lt cycle_number gt where lt cycle_number gt counts from 0 e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The naming format is slightly different for some non UKIRT instruments Polarisation frames lt m gt lt date gt _ lt group_number gt _ lt suffix gt each with a differ ent suffix for the each parameter The suffices are I intensity P percentage polarisation PI polarisation intensity Q Stokes Q TH polarisation angle U Stokes U A FITS binary table catalogue of the binned and culled polarisation data called lt m gt lt date gt _ lt group_number gt _1 FIT For each point it tabulates the x y co ordinates the total intensity the Stokes parameters the percentage polarisation the polarisation angle and intensity There are additional columns giving the standard deviation on each of the tabulated values excluding the co ordinates Likewise lt m gt lt date gt _ lt group_number gt _all FIT and lt m gt lt date gt _ lt group_number gt _bin FIT store the full and binned catalogues re spectively Parameters NUMBER INTEGER The number of frames in the jitter pattern per waveplate angle If this is not set the numb
42. and end SUN 232 8 Recipes 134 NOD_CHOP_SCAN UT headers are updated to match that of the last observed frame contributing to the mosaic e Intermediate frames are deleted except for the differenced pairs _dp suffix frames Output Data The integrated mosaics in lt m gt lt date gt _ lt group_number gt _o lt scan gt _mos where lt m gt is the instrument s group prefix lt group_number gt is the number of group and lt scan gt is the index number of the distinct scan position counting from 0 e A mosaic for each cycle of object frames in lt m gt lt date gt _ lt group_number gt _o lt scan gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 e The differenced pairs in lt i gt lt date gt _ lt obs_number gt _dp where lt i gt is the Parameters NUMBER INTEGER The number of frames in the nod pattern If absent the number of offsets as given by header NOFFSETS minus one is used If neither is available 4 is used An error state arises if the number of jittered frames is fewer than 4 and not a multiple of 4 USEVAR LOGICAL Whether or not to create and propagate variance arrays 1 Related Recipes NNOD_CHOP NOD_SELF_FLAT_NO_MASK_APHOT Implementation Status e The processing engines are from the Starlink packages and e Uses the Starlink NDF format and multi NDF HDS container files e History is recorded within the data files e The title of the data is propagated through inter
43. and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 e The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created iteratively First an approximate flat field is created by combining normalised object frames using the median at each pixel This flat field is applied to the object frames Sources within the flat fielded frames are detected and masked in the dark subtracted frames The first stage is repeated but applied to the masked frames to create the final flat field Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects the script resorts to using the telescope offsets transformed to pixels Once the offsets are determined they are SUN 232 8 Recipes 114 MOVING_JITTER_SELF_FLAT adjusted for the motion of the target so that the final mosaic registers the target not the background stars The ephemeris file is specified by environment variable ORAC_EPHEMERIS defaulting to
44. are given by the expression 2 5 log10 abs counts per second exposure time Therefore negative sources can be measured too as presented by the thermal photometry recipe NOD_SELF_FLAT_NO_MASK_APHOT The photometry also yields an internal error determined from the sky variance A case and space insensitive comparison of the object name with the entries in a table provides a catalogue magnitude for a standard star in I Z J H or K for all instruments and in L or M for IRCAM and ISAAC Also a mean extinction is applied for the mean of the start and end airmasses Thus the primitive calculates an approximate zero point Note that ISAAC and NACO standard stars include additional objects not present in the UKIRT faint standard list or Persson s HST list for these the magnitude and derived zero point will not be determined automatically For accurate photometry the actual extinction coefficients should be determined As the output from the photometry is a small text list you can use catphotomfit command of the CURSA package to achieve this The units and meanings of the columns are documented within each small text list The seeing is estimated for each frame and the mosaic by fitting a two dimensional Gaussian to the star although in good seeing the UKIRT images are more centrally concentrated than a Gaussian The full width half maximum so derived is also tabulated in the small text list _APHOT_MAG_ APHOT_MAG_NCOLOUR_ NOD_APHOT_MAG_
45. array_tests log at the AAT compared with UFTI at UKIRT References to NDSTARE are not applicable and so are absent from the documentation The observation mode is DRM The upper limit on the readout noise is 20 electrons compared with 30 electrons for UFTI There are JITTER_SELF_FLAT variants with a higher registration completeness 0 5 from 0 4 giving purer registration but may rely on the telescope offsets more often For a full list of available recipes see the IRIS2 web page 189 E5 ISAAC SUN 232 8 Instrument Recipe Notes E5 ISAAC The observation template and sequence names are converted into matching recipes with a default of QUICK_LOOK Available are CHOP_SKY_JITTER JITTER _SELF_FLAT TER _SELF_FLAT APHOT NOD_SELF_FLAT_NO_MASK INOD_SELF_FLAT NO_MASK APHOT POL_JITTER REDUCE_DARK and SKY_FLAT MASKED Please note that at the time of writing the thermal recipes have yet to be tested with ISAAC data Polarimetry is not available yet Other recipes supplied on the oracdr command line should work provided the observation pattern matches that expected by the recipe The CHOP_SKY_JITTER recipe has no leading sky frame so the recipe subtracts the mode of the first sky frame from the first target frame rather than interpolating between the bracketting sky frames as occurs in the standard version The sequence of frames can also end on the source The spatial distortion correction in the core jitter recipes uses the ATOOLS
46. as follows e Updated and expanded documentation particularly the description of the primitives and lists the main primitives used at each stage mention of and many more hyperlinks SUN 232 8 Release Notes V4 0 202 H 3 Global changes Introduction of environment variable ORAC_KEEP to retain intermediate frames Environment variables ORAC_DATA_IN and ORAC_DATA_OUT can define paths relative to the current working directory xoracdr now knows the default calibrations for all instruments A bug which prevented xoracdr operating on non networked computers is fixed Calibration reference offset added for off centre nod patterns This and the baseshift offset used array references Arrays of values in a calib can be comma separated A bug affecting ORACTIME in calibrations for Michelle fixed it was previously set to 0 in all cases Cater for early Michelle data which had missing metadata affecting six headers Allow for missing undefined or malformed RA_BASE and DEC_BASE headers in UFTI data Allow for old UFTI data with CTYPE1 header set erroneously to Detector Rows to create WCS For IRIS2 modify the header translations for filter name and observation mode correct the airmass calculation and allow alternate frames to have alternate files but still be members of the same group by using different headers for group membership checks There is no longer the assumption of a right handed world co ordinate system in co o
47. at es Pv ve E ep eee Se ee aon ee a abate E 210 Use i oc he Sek es ae oe te a a ete Ate ae os he ch te ok te 210 A E ee oe cee 2 oe ee oe 211 1 SUN 232 8 Using the pipeline 1 Introduction ORAC DR is a data reduction pipeline operating at UKTRT JCMT the It is part of the ORAC The pipeline reduces and displays multi frame observations soon after they are read from the detector This allows observers to assess the quality and suitability of their data in near real time Yet ORAC DR is capable of producing publication quality results ORAC DR is suitable for offline data reduction at your home institution too There are many reasons why you may wish to use ORAC DR in this fashion For instance you may have come back from UKIRT with only the raw observations or there was an error in a telescope sequence formerly an exec mixing the groups of observations or some data were reduced with a basic algorithm for speed at the telescope and now you want to do a more careful job ORAC DR is capable of reducing data from instruments not running the pipeline at their respective telescopes Hence ORAC DR is available on Starlink SUN 230 presents an overview Of ORAC DR general facilities like its display system and it explains the differences between a pipeline and a traditional reduction package Put briefly ORAC DR uses a few data headers to direct the data reduction Amongst these headers is the name of a recipe A recipe is a s
48. bpm Registration is performed using the telescope offsets transformed to pixel adjusted for the motion of the target so that the final mosaic registers the target not the background stars The ephemeris file is specified by environment variable ORAC_EPHEMERIS defaulting to 0RAC_DATA_OUT target_ephem dat The resampling applies integer shifts of origin There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame SUN 232 8 Recipes 120 MOVING_NOD_CHOP e For each cycle of object frames the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass and end UT headers are updated to match that of the last observed frame contributing to the mosaic e Intermediate frames are deleted except for the differenced pairs _dp suffix frames Ephemeris file Format The current format of the ephemeris file is one line per object comprising three space separated fields in t
49. comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created by combining normalised sky frames using the median at each pixel There is no cleaning of extreme outliers Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects the script resorts to using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of object frames the recipe creates a mosaic which has
50. easy to create one oracdr noeng from 1 skip nodisplay NIGHT_LOG This will create a log called 0RAC_DATA_IN lt date gt nightlog for the current UT date For multi mode instruments such as Michelle UIST IRIS2 NACO or ISAAC the log will be called 5 SUN 232 8 Using the pipeline ORAC_DATA_IN lt date gt _im nightlog 2 4 Graphical initialisation and operation You may prefer the ORAC DR graphical interface called xoracdr See SUN 230 It allows you to configure ORAC DR set the instrument UT date raw and reduced directories and to run the pipeline with the various options It permits monitoring of the primitives during execution of a recipe xoracdr offers access to other facilities like display controlland recipe editing The in built documentation does not pertain to the GUI itself but to general ORAC DR information however xoracdr is straightforward to use and explore While xoracdr has some rough edges it is popular with many users To try it enter xoracdr amp Once the tool appears you should select an instrument from the menu on the left a UT date in the top centre and raw and reduced directories to the lower right The From and To refer to the observation numbers to process When you are ready to reduce data click on the Start ORAC DR button 2 5 Display ORAC DR optionally lets you inspect the raw frames and the processed data as they are created There is a variety of graphical methods available
51. fielding Some recipes create their own flats from the observations themselves called a self flat or sky frames within a sequence that dithers to sky or use a separate observation of a jitter on sky There is no support for internal calibrations or dome flats in the recipes Whenever a flat is required recipes access the flat calibration index to find the most recent flat matching the required attributes such as filter The current recipes for Michelle mid infra red observations do not create or use flat fields SUN 232 8 Features of the Primitives 14 Creating a flat can be an iterative procedure involving cleaning making a first guess object masking proper normalisation and making an improved flat There are some primitives to bundle the operations including division by the flat field _FLAT_FIELD_MASKED_GROUP_ _FLAT_FIELD_QUADRANT_JITTER_ _FLAT_FIELD_NCOLOUR_ _DIVIDE_BY_FLAT_ DIVIDE_BY_FLAT_FROM_GROUP_ There are variants for certain families of recipes which marshall the various required subgroups of frames before dividing by the flat field _DIVIDE_BY_FLAT_CHOP_SKY_ _DIVIDE_BY_FLAT_FROM_EXTENDED_ _DIVIDE_BY_FLAT_NOD_PAIRS_ 3 3 1 Flat creation Frames are optionally cleaned to remove extreme outliers 3 or 607 about the mean in 15x15 pixel neighbourhood iterated three times except for thermal recipes NOD_SELF_FLAT_NO_ MASK and variants and NOD_SKY_FLAT_THERMAL The data are then normalised combined pixel
52. flat frame e mask Use the given bad pixel mask polrefang Use the specified polarimetry calibration angle converting measured polari sation vector orientations into position angles It is measured in degrees applied clockwise to the vector direction to allow for the orientation of the analyser with respect to north e readnoise Use the given value for the detector readnoise in electrons referenceoffset Use the comma separated doublet i e 0 0 as the frame s reference offset which is difference between the frame centre and the reference pixel derived from the FITS headers rotation Use the given frame as a rotation matrix This is no longer used in the imaging recipes e sky Use the given sky frame 7 SUN 232 8 Features of the Primitives 2 7 Log files In addition to presenting the progressing data reduction to an ORAC DR X window ORAC DR by default retains a copy of the processing steps and errors in a log file These logs are important if something has gone wrong and you have exited the X window Information from the applications software can be included if you run the pipeline with the verbose command line option Logs also serve as a record of the data processing Yet the log files are often overlooked because they are hidden The log file is called 0RAC_DATA_OUT oracdr_ lt number gt where lt number gt is the current process identification The log f option to the oracdr command enables
53. gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles The catalogue in catalogue_ lt group_number gt txt Parameters NUMBER INTEGER The number of frames in the jitter pattern If not supplied the number of offsets as given by FITS header NOFFSETS minus one is used If neither is available 9 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 99 JITTER_SELF_FLAT_CATALOGUE SUN 232 8 Recipes Related Recipes BRIGHT_POINT_SOURCE_CATALOGUE JITTER_SELF_FLAT ITTER_SELF_FLAT_APHOT Implementation Status e The processing engines are from the Starlink packages FIGARO and EXTRACTOR e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 100 JITTER_SELF_FLAT_NCOLOUR JITTER_SELF_FLAT_NCOLOUR Reduces a multi colour standard jitter photometry observation using object masking Description This script reduces a standard jitter photometry observation with near infrared imaging data observed through one or more filters For each filter it t
54. headers are updated to match that of the last observed frame contributing to the mosaic Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix A mosaic for each cycle of four in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming formatlis slightly different for some non UKIRT instruments The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes QUADRANT JITTER QUADRANT JITTER_NO_MASK EXTENDED_3x3_BASIC EXTENDED_5x5_BASIC Implementation Status The processing engines are from the Starlink packages CCDPACK KAPPA FIGARO and EXTRACTOR Uses the Starlink NDF format History is recorded within the data files The title of the data is propagated through intermediate files to the mosaic Error propagation is controlled by the USEVAR parameter 167 QUADRANT_JITTER_NO_MASK SUN 232 8 Recipes QUADRANT_JITTER_NO_MASK Reduc
55. is controlled by the USEVAR parameter Deprecated Variants SKY_AND_JITTERS 175 SKY_AND_JITTER_APHOT SUN 232 8 Recipes SKY_AND_JITTER_APHOT Reduces a combined jitter photometry observation and performs aperture photometry Description This script reduces a combined jitter photometry observation with UKIRT imaging data It takes an imaging observation comprising one or more sets of frames each set containing a sky frame followed by jittered object frames and a pre determined flat field frame to make a calibrated trimmed mosaic automatically This recipe performs bad pixel masking null debiassing sky subtraction flat field division feature detection and matching between object frames and resampling See the Notes for details Photometry of the point source using a fixed 5 arcsecond aperture is calculated for each jitter frame and the mosaic The results appear in 0RAC_DATA_OUT aphot_results txt in the form of a Starlink small text list The analysis of each star is appended to this file This recipe is suitable for moderately faint point sources Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected S
56. its bad pixels filled and is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass and end UT headers are updated to match that of the last observed frame contributing to the mosaic 141 NOD_SKY_FLAT_THERMAL SUN 232 8 Recipes e Intermediate frames are deleted except for the flat fielded _ f suffix frames Output Data e The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix e A mosaic for each cycle of object frames in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming format is slightly different for some non UKIRT instruments e The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters NUMBER INTEGER The number of frames in the nod pattern If absent the number of offsets as given by header NOFFSETS minus one is used If neither is available 8 is used An error state arises if the number of jittered frames is fewer than 8 and not a multiple of 8 USEVAR LOGICAL Whether or not to create and propag
57. least 3 If NUMBER is absent the number of offsets as given by internal header NOFFSETS minus one is used An error state arises if the resulting number of jittered frames is fewer than 3 and a default of 3 is assumed If neither NUMBER nor NOFFSETS are defined 1 is used USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 85 FP_JITTER SUN 232 8 Recipes Related Recipes FP_JITTER_NO_SKY SKY_FLAT_FP Implementation Status e The processing engines are from the Starlink packages and e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 86 FP_JITTER_NO_SKY FP_JITTER_NO_SKY Reduces a spatially jittered 4 frame Fabry Perot observation Description This script reduces a Fabry Perot observation with UFTI data It takes an imaging obser vation comprising at least three sets of four object frames each set being for a different telescope position The recipe combines these with a dark frame and a separate flat to make a continuum subtracted untrimmed mosaic automatically Each sequence of four frames expected in each spatial position are tabulated below Frame Position Wavelength 1 On source On line 2 On source Off line positive offset 3 On source On line 4 On source Off line negative offset
58. left unchanged unless there is a need to add more steering parameters passed to the steering primitive The steering primitive itself is only modified for such new steering parameters and if the observing pattern or sequence is different from what the recipe is programmed to expect Other primitives not mentioned here are tied closely with single recipes usually to create and file calibrations 3 1 Preparation of Single Frames IMAGING_HELLO_ lt instrument gt _INSTRUMENT_HELLO_ _PREPARE_SINGLE_FRAME_ SUN 232 8 Features of the Primitives 8 3 1 1 Manipulation of Raw Data The first stage makes an NDF or multiple NDFs stored in an container file located in 0RAC_DATA_OUT the actual operation depending on the instrument In some cases like UFTI this is dealt by the ORAC DR infrastructure including conversion from FITS for early UFTI data lt instrument gt _CREATE_RAW_FRAME_ For IRCAM the recipes are merely copying the raw NDF because the original raw files are normally write protected UIST and Michelle both copy all the components of multi NDF container file These container files have a HEADER NDF of the observation wide FITS headers and NDFs of chopped beams or integrations Recipes check that two integrations are present for a chopped observations or one integration for other modes exiting with an error message if either test fails A single integration NDF is merged with the HEADER NDF into a simple NDF 3 1 2 Prel
59. log file creation See SUN 230 for details of the logging options 3 Features of the Primitives Primitives are the Perl scripts which actually call the applications to do most of the data processing All of the imaging recipes are in principle independent of the instrument However some recipes are inappropriate for example the NOD_CHOP family of recipes are intended for mid IR imaging with Michelle but not the JITTER_SELF_FLAT family The generality comes in part from translations of relevant header information into a generic form used by ORAC DR Not all the following steps apply to all recipes Consult the to see summaries for each recipe The steps are presented in normal order of appearance The main primitives pertinent to each step are listed in bracketed italics should you wish to tailor the recipes These are found in 0RAC_DIR imaging tree unless they start with general when they are located in 0RAC_DIR general Note the some may be instrument specific variants either given explicitly or with the lt instrument gt token which means substitute the instrument name in uppercase While those listed form the bulk of the primitives there are many not listed here mostly those for recipe initialisation called lt recipe gt _HELLO_ see Section for more information and for recipe steering which control when to perform certain operations called lt recipe gt _STEER_ see Section 4 2 2 The first of these is normally
60. lt group_number gt _ lt filter gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The naming formatlis slightly different for some non UKIRT instruments The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters NUMBER INTEGER The number of frames in the jitter If absent the number of offsets as given by header NOFFSETS minus one is used If neither is available 5 is used An error state arises if the number of jittered frames is fewer than 3 USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes ITTER_SELF_FLAT Implementation Status The processing engines are from the Starlink packages CCDPACK KAPPA FIGARO and EXTRACTOR Uses the Starlink NDF format History is recorded within the data files The title of the data is propagated through intermediate files to the mosaic Error propagation is controlled by the USEVAR parameter Deprecated Variants JITTER5_SELF_FLAT_NCOLOUR SUN 232 8 Recipes 102 JITTER_SELF_FLAT_NCOLOUR_APHOT JITTER_SELF_FLAT_NCOLOUR_APHOT Reduces a multi colour standard jitter photometry observation using object masking and performs aperture photometry
61. match that of the last observed frame contributing to the mosaic The photometry tabulation includes the file name source name time filter air mass the catalogue magnitude and estimates of the zero point with and without the application of a mean extinction There are headings at the top of each column The photometry uses a multiply clipped 2 2 2 5 3 standard deviations mean to estimate the sky mode in an annulus about the source This is not unduly biased by the presence of the self flat artifact in the pixel histogram The inner annulus diameter is 1 3 times that of the aperture 6 5 arcsec the outer annulus is 2 5 times 12 5 arcsec for UFTI and twice the aperture 10 arcsec for IRCAM and IRIS2 The errors are internal based on the sky noise Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix A mosaic for each cycle of jittered frames in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming format is slightly different for some non UKIRT instruments For ISAAC the individual bias corrected frames in isaac lt date gt _ lt obs_number gt _bc The created flat field
62. performed using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaic by applying offsets in intensity to give the most consis tent result amongst the overlapping regions The mosaic is trimmed to the dimensions of an input frame The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of jittered frames the recipe creates a mosaic which is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass and end UT headers areupdated to match that of the last observed frame contributing to the mosaic SUN 232 8 Recipes 62 BRIGHT_POINT_SOURCE_TELE e Intermediate frames are deleted except for the flat fielded _ f suffix frames e Sub arrays are supported Output Data e The resultant mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the in strument s group prefix e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming format is slightly different for some non UKIRT instruments Parameters NUMBER INTEGER The number of frames in the jitter pattern If this is not set th
63. recipe reduces a bright standard photometry observation It takes an imaging obser vation comprising a series of jittered object frames and a dark frame with a predetermined flat field frame to make a calibrated trimmed mosaic automatically This recipe performs a null debiassing bad pixel masking dark subtraction flat field division feature detection and matching between object frames and resampling See the for details Photometry of the point source using a fixed 5 arcsecond aperture is calculated for each jitter frame and the mosaic The results appear in 0RAC_DATA_OUT aphot_results txt in the form of a Starlink small text list The analysis of each star is appended to this file As the name implies it is intended for bright point sources such as standard stars but also any observation of a point source where using its own frames to make the flat is not appropriate Notes You may use SKY_FLAT or SKY_FLAT_MASKED to make the flat field e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 e The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has th
64. results is reported and logged for each cycle e The NDSTARE readout noise is filed in the calibration system Output Data e The engineering log 0RAC_DATA_0UT ufti_array_tests log Implementation Status e The processing engines are from the Starlink package KAPPA e Uses the Starlink NDF format 51 BRIGHT_POINT_SOURCE SUN 232 8 Recipes BRIGHT_POINT_SOURCE Reduces a bright point source photometry observation Description This recipe reduces a bright standard photometry observation It takes an imaging obser vation comprising a series of jittered object frames and a dark frame and a predetermined flat field frame to make a calibrated trimmed mosaic automatically This recipe performs bad pixel masking null debiassing dark subtraction flat field di vision feature detection and matching between object frames and resampling See the for details As the name implies it is intended for bright point sources such as standard stars but also Notes any observation where using its own frames to make the flat is not appropriate You may use SKY_FLAT or SKY_FLAT_MASKED to make the flat field A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS vi
65. sky frames and applied to all the target frames For ISAAC residual bias variations along the columns are largely removed from each flat fielded frame The recipe first masks the sources then collapses the frame along its rows to form a profile whose clipped mean is subtracted The resultant profile SUN 232 8 Recipes 64 CHOP_SKY_JITTER reflects the bias variations The recipe subtracts this profile from each column of the flat fielded frame The sky subtraction comes from linear interpolation of the sky modal values of the two flat fielded sky frames which immediately bracket the target frame The field distortion of ISAAC is corrected in the target frames using the mappings documented on the ISAAC problems web page Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects it then tries the crosshead offsets If these are null the script resorts to the telescope offsets The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The noise will be greater in the mosaic s peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame A
66. standard deviationss This value is effectively the mode of the image The entire image is divided by this value to normalise it e Intermediate frames are deleted Output Data e The flat is called flat_ lt frame_number gt e The flat is filed in 0RAC_DATA_OUT index flat Implementation Status e The processing engines are from the Starlink packages KAPPA and CCDPACK e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through the intermediate file to the flat e Variance information is not supported 173 SKY_AND_JITTER SUN 232 8 Recipes SKY_AND_JITTER Reduces a combined jitter photometry observation Description This script reduces a combined jitter photometry observation with UKIRT imaging data It takes an imaging observation comprising one or more sets of frames each set containing a sky frame followed by jittered object frames and a pre determined flat field frame to make a calibrated trimmed mosaic automatically This recipe performs bad pixel masking null debiassing sky subtraction flat field division feature detection and matching between object frames and resampling See the Notes for details This recipe is suitable for moderately faint point sources Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and
67. star is appended to this file This recipe works well for faint sources in moderately crowded fields Notes A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 The bad pixel mask applied is 0RAC_DATA_CAL bpm For INGRID the pre and post exposure images are subtracted A non linearity correction is then applied Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created iteratively First an approximate flat field is created by combining normalised object frames using the median at each pixel This flat field is applied to the object frames Sources within the flat fielded frames are detected and masked in the dark subtracted frames The first stage is repeated but applied to the masked frames to create the final flat field For ISAAC residual bias variations along the columns are largely removed from each flat fielded frame The recipe first masks t
68. target and a region of nearby sky Thus the raw data comprise four strips with an aspect ratio of about 6 These partitions are normally separated by a mask but the recipes do not depend on having the mask to extract the various regions say by detecting the edges For each instrument the pixel limits of each region are fixed The current target limits are 30 to 70 of the width of the long axis of each region to allow for some reasonable dithering of point sources since there are usually only three jitter positions while making mosaics with few pixels not derived from all contributing jittered frames For extended sources these limits change to 10 to 90 to include as much object as possible with smaller dithers and alternating to blank sky regions Thus the limits define a section 40 or 80 of the width of the frame roughly centred on the source 17 SUN 232 8 Features of the Primitives The limits on the sky regions are 1 to 99 of the frame width mainly to avoid unreliable and pathological pixels at the detector s edge lt instrument gt _DEFINE_POL_REGIONS_ The recipes extract the target regions into e and o beam frames The modes the means after clipping at 2 3 3 standard deviations of the e and o beam sky regions are subtracted from their corresponding target beam incorporating the uncertainty of each sky level in the corresponding target beam s variance array For an extended source observation the sky levels are deter
69. telescope has tracked the nucleus 209 K 2 K 3 K 2 Modified recipes SUN 232 8 Release Notes V2 1 0 Modified recipes ARRAY TESTS For UFTI the ADU conversion is obtained from the GAIN header rather than being hardwired at 7 0 CHOP_SKY_JITTER This now functions correctly for multiple cycles of the recipe FP Documentation improvements especially in the description Primitive _FP_STEER_ has a new steering parameter NPAIRS and parameter NUMBER has changed to its normal meaning NIGHT_LOG This can start from observation numbers other than 1 A bug has been fixed where the dimensions appeared as zero for UFTI It arose because certain headers no longer existed after 2000 August SKY_FLAT_FP This is no longer limited to eight frames SKY_AND_JITTER A bug has been fixed where some intermediate files were not being removed for this recipe and its variant Global changes The main changes from a user perspective were as follows The aperture for _APHOT recipes is now 5 arcseconds A new photometry catalogue fs2001 dat supplied in original form by Sandy Leggett is used by the _APHOT recipes The new catalogue contains ZLM magnitudes for the first time and the JHK data have been refined to account for recent observations The 2000 edition is accessed for J HK photometry if the 2001 catalogue is unavailable Another new UFTI bad pixel mask Old masks are available on request A bug that affected some rare mixed m
70. the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created by combining normalised object frames using the median at each pixel There is no cleaning of extreme outliers For ISAAC residual bias variations along the columns are largely removed from each flat fielded frame The recipe first masks the sources then collapses the frame along its rows to form a profile whose clipped mean is subtracted The resultant profile reflects the bias variations The recipe subtracts this profile from each column of the flat fielded frame Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects the script resorts to using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear in
71. the beams are differenced The ARRAY_TESTS recipe files a suitable short exposure dark as a bias in the calibration system The integrations of the two beams are differenced the first subtracted from the second in each pair A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist The bad pixel mask applied is 0RAC_DATA_CAL bpm The telescope offsets of the first frame in each multiple of four frames define scan position The recipe creates a mosaic at each distinct pair of offsets Registration is performed using the telescope offsets transformed to pixels The resampling applies integer shifts of origin There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of object frames at each distinct scan position the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise for that scan position The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass
72. to create and propagate variance arrays 0 Related Recipes SKY_FLAT FP SKY_FLAT MASKEDI SKY_FLAT POL Implementation Status e The processing engines are from the Starlink packages CCDPACK and FIGARO e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through the intermediate file to the flat e Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 180 SKY_FLAT_FP SKY_FLAT_FP Creates and files a flat field derived from multiples of four frames using object masking to reduce artifacts Description This recipe make a sky flat for UFTI from a series of four or multiples of four sky or object frames combined using one of a selection of statistics It is intended to be used to make a flat for Fabry Perot data It performs a null debiassing bad pixel and non signal region masking and dark subtrac tion before combining the sky frames pixel by pixel to make the flat See the Notes for further details The parameters of the flat are filed in the index of flats for future selection and use of the flat For best results the field observed should contain few stars and no bright ones Notes A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged
73. to form a flat field 5 NCOL INTEGER The number of target frames in a column of the mosaic Its minimum is 2 5 USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes EXTENDED_3x3_BASICMHEXTENDED_5x5 QUADRANT JITTER BASIC Implementation Status e The processing engines are from the Starlink packages and e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 80 EP FP Reduces an 8 frame Fabry Perot observation Description This script reduces a Fabry Perot observation with UFTI data It takes an imaging observa tion comprising eight object frames and a dark frame to make a continuum subtracted and sky subtracted untrimmed mosaic automatically The sequence of frames expected in the observations are tabulated below Frame Position Wavelength 1 On source On line 2 Off source On line 3 Off source Off line positive offset 4 On source Off line positive offset 5 On source On line 6 Off source On line 7 Off source Off line negative offset 8 On source Off line negative offset It performs a null debiassing bad pixel masking dark subtraction pairwise frame differ encing flat field division integer shifts of origin to register and mosaicking The desired result is given by F1 F2
74. to the flat self flat recipes the mode is now calculated using multiple standard deviation clipping for JITER_SELF_FLAT_APHOT and NOD_SELF_FLAT_NO_MASK_APHOT The previous estimation was from iterative SUN 232 8 Release Notes V2 0 1 212 L 3 Global changes application of Chauvenet s criterion and using the 3 median 2 mean formula and lead to a underestimate of the sky level For typical standard stars this systematic error led to a brightening of 1 2 The latter method is still used for photometric recipes which do not self flat such as jBRIGHT_POINT_SOURCE_APHOT If you create and apply a superflat the artifact is much reduced and therefore the former estimator is appropriate More and better processing status messages For example all floating point numbers are now reported with a sensible number of decimal places and the names of calibration frames are reported Addition of FWHM to the aperture photometry results and small text list The file name column is 3 characters wider to accommodate the positive and negative suffices of recipe NOD_SELF_FLAT_NO_MASK_APHOT The saturation level in the aperture photometry was a constant Now it is set to the appropriate value by instrument and mode It is possible to use versions of KAPPA other than the latest The changed argument lists in various tasks are adjusted for the KAPPA version More intermediate files mostly the text files are removed Pipeline
75. to the steering primitive Suppose that for some reason an observation of a nine point jitter self flat was aborted after seven positions If you try the recipe stored in the headers some processing will occur but it will not include mosaic creation The final steps inclusing mosaic creation occur once all nine frames are dark subtracted Now there are no seven point recipes to substitute on the command line You could make your own seven point recipe to reduce those data First make a new recipe by copying the standard one cd 0RAC_RECIPE_DIR cp ORAC_DIR recipes imaging JITTER_SELF_FLAT JITTER7_SELF_FLAT 25 SUN 232 8 Customising Recipes Next edit JITTER7_SELF_FLAT and alter the line _JITTER_SELF_FLAT_HELLO_ to become _JITTER_SELF_FLAT_HELLO_ NUMBER 7 The recipe will then generate the self flat flat field and make the mosaic once the seventh frame is dark subtracted Recipes are stored in 0RAC_DIR recipes imaging and for a few instrument specific recipes in ORAC_DIR recipes lt instrument gt where lt instrument gt is IRCAM MICHELLE UFTI IRIS2 ISAAC or INGRID See Appendix E for some details 4 2 3 Recipe primitives After the steering primitive we come to the recipe specific scripts that actually perform the recipe The most likely and easiest things you would change are to add arguments or modify argument values of the primitives in the recipes For instance you might wish to change the aperture diame
76. 1 RDOUT_Y2 WPLANGLE flat_Lp98_23 Lp98 STARE 13 3484 1 256 1 256 0 flat_K98_pol10_62 K98 pol NDSTARE 7 971 1 1024 1 1024 0 000 flat_K98_pol122_62 K98 pol NDSTARE 7 971 1 1024 1 1024 22 5 flat_K98_po145_62 K98 pol NDSTARE 7 971 1 1024 1 1024 45 flat_K98_pol167_62 K98 pol NDSTARE 7 971 1 1024 1 1024 67 5 flat_J98_88 J98 flush_read 7 46111E 00 1 1024 1 1024 0 flat_H98_93 H98 flush_read 7 58330E 00 1 1024 1 1024 0 flat_K98_98 K98 flush_read 7 70559E 00 1 1024 1 1024 O flat_H98_133 H98 flush_read 8 99034E 00 1 1024 1 1024 0 flat_H98_138 H98 flush_read 9 07139E 00 1 1024 1 1024 O flat_H98_138_c1 H98 flush_read 9 12074E 00 1 1024 1 1024 0 flat_X98_290_row0 K98 flush_read 1 13094E 01 1 1024 1 1024 0 flat_X98_290_row1 K98 flush_read 1 15080E 01 1 1024 1 1024 0 The first line contains the column headings ORACTIME is the UT in decimal hours and WPLANGLE is the polarisation waveplate angle In general you should not manipulate these files Mis editing can lead to the calibration system breaking down If you must edit this file say to exclude a poor dark or an uneven flat restrict yourself deleting the line corresponding to that calibration file It s safer to remove the calibration file and recreate a new one with the calibration frames you want by running the pipeline If you want to nominate specific calibration frames overriding those selected from the calibration indices there is a calib option for the oracdr command to do this See the section on
77. 2 8 Recipes 128 NOD_CHOP_APHOT exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass and end UT headers are updated to match that of the last observed frame contributing to the mosaic e The combined source image is made by taking symmetrical areas about each source such that no pixels are duplicated Thus the divisions occur at midpoints of the chop throw and the nod separations These are registered using the source centroids e The photometry tabulation includes the file name source name time filter air mass the catalogue magnitude and estimates of the zero point with and without the application of a mean extinction There are headings at the top of each column e The photometry uses a multiply clipped 2 2 2 5 3 standard deviations mean to estimate the sky mode in an annulus about the source The inner annulus diameter is 1 5 times that of the aperture 7 5 arcsec the outer annulus is 3 0 times 15 arcsec for Michelle The errors are internal based on the sky noise e Intermediate frames are deleted except for the differenced pairs _dp suffix frames Output Data e The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instruments group prefix e A mosaic for each cycle of object frames in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 e The combined source image an
78. 3x3_BASIC EXTENDED_3x3_BASIC Basic extended source standard reduction using interpolated sky subtraction Description This recipe reduces an extended source using near infrared imaging data The data comprise alternating blank sky and target frames commencing and ending with a blank sky The target frames are arranged in an overlapping 30 50 grid of 3x3 frames from which the recipe makes a sky subtracted untrimmed mosaic automatically The script performs bad pixel masking null debiassing dark subtraction flat field divi sion sky subtraction registration using telescope offsets and mosaicking The Notes give more details It is suitable for extended objects up to 2 arcminutes across with UFTI 28 arcseconds with IRCAM and 14 arcminutes with IRIS2 Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 e The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above
79. 7 5 degrees in turn and a dark frame to make calibrated polarisation images and vectors automatically See Output Data for a list of these images It performs a null debiassing bad pixel masking dark subtraction and flat field division on all frames Next the sections of the frame representing the e and o beam target and sky regions are extracted and the target frames sky subtracted The resultant frames undergo registration and resampling to form a mosaic for each waveplate angle and beam Once all eight mosaics are formed they are registered and resampled and then combined to form the various polarisation images The polarisation data are binned and noisy data excluded from a final catalogue of vectors See the Notes for details This recipe works well for point sources and for extended sources whose sizes in Right Ascension and Declination are less than about 35 and 15 arcseconds respectively for UFTI or 9 and 4 arcseconds for IRCAM Objects which would appear in both the target and sky regions i e Declination extents south of the centre larger than 35 arcseconds UFTT or 8 arcseconds IRCAM should use recipe POL_EXTENDED for best results Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard for
80. 78 Sh eA oe eed a ee ee otek been oa 6es 180 been adios E E a 182 E A EE One E eee aia ad 184 e A Stic A Bae ae ae 186 188 wee Rae ee Weare ee ee eb eee oe a ee eee s 188 Pa 20 2 heed edad Ghad dg ee DREEERD Che edand dead 188 ESIRCAM em ae bbcenedehs bateas da 188 PA ct atac eb see E E ee eee ade tareea dene 188 o deen Mana tes hoe lo amp Gennes a a 189 Eee Bee oo ad Pe re ee ee 189 SUN 232 8 Contents vi ESE 2 ee te hh Did aa a ee Bom ad 189 EORI ecc o Bou So o oy Se oe e a ds Oe ee 190 F Internal Headers 191 F 1 Translated HeadersS 0 00000 eee ee ee eee 191 EZ Steering Heermann ae rar eae ee OED pui 193 G_Release Notes V4 1 197 Gl New tedipes ei a e E AAA Ke 197 G 2 Modified Rape yh a ie eae ADA e AE A EA 197 G3 ODA Changes lt 2 4 ee ae a DARIA E ee oe See BS 198 H_Release Notes V4 0 201 AHT New rtegipes e oc Ge dg bee awe a ee eee Re AR AN A 201 E e ote PSS ke RENEE S BPE RES CG ES a SHARE 201 H 3 Global changes 20 we be ee VOU ESSE ES SS S P44 As BEES 201 I Release Notes V3 1 1 203 LT New recipes e ne 2 rea REA A ee ek Se 203 IL Modified TECIDES ete See ESR SERED ERS RE ORE Oe EE 204 ES Clopal changes e ss side ree ee ea a eo Re Bes Ow Ewe 204 J Release Notes V3 0 3 205 K_ Release Notes V2 1 0 208 ee es a do es ee ee ee et 208 A ie ee eae 209 Maid a ae ee ee ee ee ee ee ee ee 209 L_ Release Notes V2 0 1 210 Sy Scenes eee ok
81. AIC_ and invoked within several wrappers all with the MAKE_MOSAIC_ prefix tied to various families of recipes 3 8 1 Polarimetry Resampling To permit the calculation of the Stokes parameters polarimetry recipes resamples each frame using non integer Cartesian offsets or merely finds the offsets between frames to the nearest pixel and shifts the origin The mosaic extends to include all pixels in contributing the frames however in practice there should be at most one pixel variation in dimensions _RESAMPLE_MOSAICS_ 3 9 Polarimetry Parameters These are outlined in the Output Data section of the polarimetry recipes such as POL_JITTER and are calculated using standard formulae and the methods of POLPACK A calibration correction polrefang measured in degrees clockwise is applied to the vector direction for the orientation of the analyser with respect to north based upon UKIRT s TRPOL instrument Current values are 24 for Michelle and UIST 9 for UFTI and 96 3 for IRCAM For other instruments the offset can be determined using polarimetric standard star calibrations CALC_STOKES_ MICHELLE _CALC_STOKES_NOD_CHOP_ 3 10 Near Infra red Aperture Photometry The recipes with an _APHOT suffix exceptiNOD_CHOP_APHOT perform aperture photometry on the mosaic and the contributing flat fielded frames The method assumes that the target SUN 232 8 Features of the Primitives 20 usually a standard star is approximately
82. Allow for _bc files in relevant _TIDY_ primitives e Support added to remove electronic ghosting correct residual bias and resample for field distortion all initially for ISAAC The main changes from a programmer perspective were as follows Calibration index files permit user header uhdr to be in expressions for bias dark flat and sky Infrastructure uses perl modules Astro FITS Header for access to FITS headers and Starlink HDSPACK for manipulation of HDS components e Add the internal headers ORAC_TELESCOPE ORAC_X_REFERENCE_PIXEL and ORAC_Y_REFERENCE There is a Grp gt memberindex Frm method which returns the position the supplied frame has in the group starting from 0 This is useful in batch mode processing where the groups are pre populated _CLIPPED_STATS_ has new NUMBER argument returning the number of good pixels e _DIVIDE_BY_FLAT_CHOP_SKY_ and _DIVIDE_BY_FLAT_EXTENDED_ permit flat fielding of sky frames via a new argument FLATSKY e There are some new primitives including _GET_FILTER_PARAMETERS_ to encapsulate filter attributes and _FORM_SKY_LEVELS_ to determine the modal sky level for the sky frames after flat fielding e Script nongeneric_imaging csh is moved from the etc to the new admin directory e Lexical handles rather than global variables are used for accessing files I Release Notes V3 1 1 The main change is the addition of support for IRIS2 I 1 New recipes ADDWCS Adds
83. C A basic faster version of CHOP_SKY_JITTER Reduction of a Fabry Perot observation without jittering JITTER _SELF_FLAT_NCOLOUR Reduction of multi colour standard jitters This will become the new JITTER_SELF_FLAT once the recipes are colour generic POL_ANGLE JITTER Reduces an imaging polarimetry observation in which the waveplate angle iterates at each jitter position POL_EXTENDED Reduces an imaging polarimetry observation of an extended source POL_JITTER Reduces an imaging polarimetry observation in which the spatial is position jittered before moving the waveplate angle SKY_FLAT_FP Creates and files a Fabry Perot flat field derived from eight frames using object masking SKY_FLAT_POL Creates a polarimetry flat field derived from eight frames two at each wave plate angle using object masking It copies the flat for each waveplate angle and files them SKY_FLAT_POL_ANGLE Creates and files polarimetry flat fields derived from jittered frames at each waveplate angle using object masking L 2 Modified recipes Many former recipes had numerous variants for different jitter sizes These have largely been superseded by generic equivalents Only the EXTENDED recipes await conversion The families of recipes changed are listed below e JITTER_SELF_FLAT Six recipes in the family There were three five seven and nine point versions but most were only available for one or two recipe variants e IMOVING_JIT
84. CS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 e The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used e Intermediate frames are deleted e Sub arrays are supported Output Data e The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent recipe cycles Token lt filter gt is the filter name lt group_number gt is the frame number of the group and lt cycle_number gt is the number of the cycle counting from one e The flats are filed in 0RAC_DATA_OUT index flat Parameters 179 SKY_FLAT SUN 232 8 Recipes NUMBER INTEGER The number of frames in the jitter If absent the number of offsets as given by header NOFFSETS minus one is used If neither is available 5 is used An error state arises if the number of jittered frames is fewer than 3 USEVAR LOGICAL Whether or not
85. DF HDS container files History is recorded within the data files The title of the data is propagated through intermediate files to the mosaics The polarisation maps have new titles as follows using the suffices described in Output Data I Intensity P Polarisation PI Polarised Intensity Q Stokes Q TH Polarisation Angle U Stokes U The origins of the generated polarisation maps are set to 1 1 The WCS current frame is unchanged The units are set for the frames with suffices see Output Data P to and TH to degrees Error propagation is controlled by the USEVAR parameter 163 QUADRANT_JITTER SUN 232 8 Recipes QUADRANT _JITTER Reduces a Quadrant Jitter observation including object masking Description This script reduces a quadrant jitter photometry observation with near infrared imaging data It takes an imaging observation comprising one or more series of four object frames where the target is approximately centred in each quadrant and a dark frame to make a calibrated untrimmed mosaic automatically It performs bad pixel masking null debiassing dark subtraction flat field creation and division feature detection and matching between object frames and resampling See the for further information This recipe is suitable for faint objects or objects within a comparatively bright core embed ded in faint extended emission e g a quasar or extended objects less than 45 arcseconds across wit
86. Description This script reduces a standard jitter photometry observation with near infrared imaging data observed through one or more filters For each filter it takes an imaging observation comprising jittered object frames and a dark frame to make a calibrated untrimmed mosaic automatically It performs a null debiassing bad pixel masking dark subtraction flat field creation and division feature detection and matching between object frames and resampling See the for further information Photometry of the point source using a fixed 5 arcsecond aperture is calculated for each jitter frame and the mosaic The results appear in 0RAC_DATA_OUT aphot_results txt in the form of a Starlink small text list The analysis of each star is appended to this file This recipe works well for faint sources in moderately crowded fields Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS e The bad pixel mask applied is 0RAC_DATA_CAL bpm For INGRID the pre and post exposure images are subtracted A non linearity correction is then applied e Each dark subtracted frame has thresholds app
87. FLAT_APHOT ITTER_SELF_FLAT BASIC JITTER SELF FLAT TELE QUADRANT_JITTER_NO_MASK Implementation Status e The processing engines are from the Starlink packages and e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter Deprecated Variants JITTER5_SELF_FLAT_NO_MASK JITTER9_SELF_FLAT_NO_MASK 107 JITTER_SELF_FLAT_TELE SUN 232 8 Recipes JITTER_SELF_FLAT_ TELE Reduces a standard jitter photometry observation using object masking and telescope offsets for registration Description This script reduces a standard jitter photometry observation with near infrared imaging data It takes an observation comprising jittered object frames and a dark frame to make a calibrated untrimmed mosaic automatically It performs a null debiassing bad pixel masking dark subtraction flat field creation and division registration using telescope offsets and resampling See the Notes for further information This recipe works well for faint sources and for moderately crowded fields It is also used for observations that track a moving object Notes A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keyw
88. First the readnoise variance for the instrument is applied It is currently a constant for all pixels which takes the gain the number of exposures and the number of array reads per exposure into account For more than one read n the noise scales by the following factor y n n 1 12 n 1 which is derived from linear regression theory The read noise reduces by the factor 1 number of exposures _ADD_READNOISE_VARIANCE_ The raw read noise in units of electrons comes from the readnoise calibration set within the SENEE recipe or should one not exist ORAC DR selects a representative default The and IRCAM defaults come from the instrument Web pages such as http www jach hawaii edu JACpublic UKIRT instruments ufti PARAMETERS html and depend on speed gain and read type Typical values are as follows A0e INGRID 25e 47e7 15e7 18 5e7 NACO 53e7 50e7 26e7 and 4027 reductions merely use an estimate of 1000e lt instrument gt _GET_READNOISE_ The gain the number of electrons per analogue to digital unit comes from the data headers If for some unusual reason the header is absent the recipe subsitutes suitable time dependent defaults The gain is 7 5e for Classic Cam 4 1e for INGRID 6e for UFTI and IRCAM 5 2e for IRIS2 4 6e for ISAAC 500e for Michelle 10e for NACO 12 3e7 for NIRI and 15e for UIST lt instrument gt _GET_GAIN_ e The second step is to add the Poisson variance This simply
89. HT_POINT_SOURCEJJITTER_SELF_FLAT_APHOT SKY_FLAT SKY_FLAT_MASKED Implementation Status e The processing engines are from the Starlink packages CCDPACK KAPPA FIGARO and PHOTOM 55 BRIGHT_POINT_SOURCE_APHOT SUN 232 8 Recipes e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 56 BRIGHT_POINT_SOURCE_CATALOGUE BRIGHT_POINT_SOURCE_CATALOGUE Reduces a bright point source photometry observation producing a catalogue of all sources in the field Description This recipe reduces a bright standard photometry observation It takes an imaging obser vation comprising a series of jittered object frames and a dark frame and a predetermined flat field frame to make a calibrated trimmed mosaic automatically This recipe performs bad pixel masking null debiassing dark subtraction flat field di vision feature detection and matching between object frames and resampling See the for details Source extraction is performed only on the reduced mosaic and uses EXTRACTOR The results appear in 0RAC_DATA_OUT catalogue_ lt group_number gt txt No zero point or airmass corrections are applied to the instrumental magnitudes As the name implies it is intended for bright point sources such as standard stars but also any observation where usi
90. ITTER_SELF_FLAT_APHOT ITTER_SELF_FLAT_BASIC ITTER_SELF_FLAT_NO_MASK JITTER_SELF_FLAT_TELE MOVING_JITTER_SELF_FLAT QUADRANT_JITTER 91 JITTER_SELF_FLAT SUN 232 8 Recipes Implementation Status e The processing engines are from the Starlink packages FIGARO and EXTRACTOR e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter Deprecated Variants JITTER3_SELF_PLAT JITTER5_SELF_FPLAT JITTER9_SELF_FLAT SUN 232 8 Recipes 92 JITTER_SELF_FLAT_APHOT JITTER_SELF_FLAT_APHOT Reduces a standard jitter photometry observation using object masking and performs aperture photometry Description This script reduces a standard jitter photometry observation with near infrared imaging data It takes an imaging observation comprising jittered object frames and a dark frame to make a calibrated untrimmed mosaic automatically It performs a null debiassing bad pixel masking dark subtraction flat field creation and division feature detection and matching between object frames and resampling See the for further information Photometry of the point source using a fixed 5 arcsecond aperture is calculated for each jitter frame and the mosaic The results appear in 0RAC_DATA_OUT aphot_results txt in the form of a Starlink small text list The analysis of each
91. In either case you must tell ORAC DR where your recipes and or primitives are stored This is achieved through two environment variables 0RAC_RECIPE_DIR should equate to the directory containing your recipes ORAC_PRIMITIVE_DIR specifies the directory containing your primitives Here s an example setenv ORAC_RECIPE_DIR home user drmoan recipes setenv ORAC_PRIMITIVE_DIR home user drmoan primitives Once these environment variables are defined ORAC DR first looks in 0RAC_RECIPE_DIR or O0RAC_PRIMITIVE_DIR to find a recipe or primitive respectively If the script is absent ORAC DR looks in the standard 0RAC_DIR directories 4 2 Anatomy of an imaging recipe There are documentation modules a Starlink style between and delimiters at the head and a Perl POD Plain Old Documentation at the foot Between these is the code This consists of calls to primitives sometimes with arguments Primitives have uppercase names preceded and terminated by underscores such as _DIVIDE_BY_FLAT_ SUN 232 8 Customising Recipes 24 4 2 1 Hello primitives The first of these primitives is IMAGING_HELLO_ It contains instrument specific code and initialisation It is best left alone See Section for a description of what this primitive does for each instrument Second there is a recipe specific primitive such as _JITTER_SELF_FLAT_HELLO_ This sets up CCDPACK when to perform certain operations optionally create variances removes any bia
92. LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes EXTENDED_3x3 EXTENDED_5x5_BASIC QUADRANT_ JITTER Implementation Status e The processing engines are from the Starlink packages and e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 78 EXTENDED_5x5_BASIC EXTENDED_5x5_BASIC Basic extended source standard reduction using interpolated sky subtraction Description This recipe reduces an extended source using near infrared imaging data The data comprise alternating blank sky and target frames commencing and ending with a blank sky The target frames are arranged in an overlapping 30 50 grid of 5x5 frames from which the recipe makes a sky subtracted untrimmed mosaic automatically The script performs bad pixel masking null debiassing dark subtraction flat field divi sion sky subtraction registration using telescope offsets and mosaicking The Notes give more details It is suitable for extended objects up to 3 arcminutes across with UFTI 42 arcseconds with IRCAM and 20 arcminutes with IRIS2 Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups
93. ORAC DR for which instrument you wish to reduce data the observation date and the directory containing the raw data and wher you want the processed data to be written There are two options SUN 232 8 Using the pipeline 2 e The first needs your data to conform to the directory naming convention of the instrument at UKIRT This will be the case if you simply unpack the archive written by the uktape utility In this case enter setenv ORAC_DATA_ROOT lt root_data_directory gt oracdr_ lt instrument gt lt date gt where lt root_data_directory gt is the directory in which you unpacked the data from the tape lt instrument gt is either ufti or ircam and lt date gt is the UT date in the format YYYYMMDD Note that each 7 represents the UNIX shell s prompt which you do not type The commands must be entered in the above order For example the standard location for raw UFTI data is raw ufti YYYYMMDD and reduced ufti YYYYMMDD for the corresponding reduced data So if your data are stored in home users abc data UKIRT raw ufti you should enter the following setenv ORAC_DATA_ROOT home users abc data UKIRT oracdr_ufti 20001108 to enable the pipeline for UFTI data taken on 2000 November 8 Data taken from the AAT is handled differently as there is no unified directory structure for both raw and reduced data directories For IRIS2 INGRID ISAAC NACO NIRI or Classic Cam data the best option is specifying where the ra
94. OURCE NOD_SELF_FLAT_NO_MASK_APHOT Implementation Status e The processing engines are from the Starlink packages and e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter Deprecated Variants NOD4_SELF_FLAT_NO_MASK NOD8_SELF_FLAT_NO_MASK 137 NOD_SELF_FLAT_NO_MASK_APHOT SUN 232 8 Recipes NOD_SELF_FLAT_NO_MASK_APHOT Reduces a nod jitter photometry observation and performs aperture photometry Description This script reduces a nod jitter photometry observation with UKIRT imaging data It takes an imaging observation comprising a multiple of four object frames and a dark frame to make a calibrated untrimmed mosaic automatically It performs a null debiassing bad pixel masking dark subtraction difference adjacent pairs flat field creation and division feature detection and matching between object frames and resampling See the Notes for further information Photometry of the point source using a fixed 5 arcsecond aperture is calculated for each jitter frame and the mosaic The results appear in 0RAC_DATA_OUT aphot_results txt in the form of a Starlink small text list The analysis of each star is appended to this file This recipe works well for faint sources in moderately crowded fields Notes A World Co ordinate System WCS using
95. RK frames and files that measurement with the calibration system It also determines the readnoise variance The readnoise result is compared with the nominal value you are notified whether or not the value is within acceptable limits The recipe appends a tabulation of the readnoise and its variance in a log file SORAC_DATA_0UT uist_array_tests log which it creates with headings if the log does not exist Notes e The first dark frame is used to clean up the array before statistics are done on the remaining frames e The recipe calculates the readnoise as follows It first derives the population variance estimate PVE of the dark frames calculated on a per pixel basis It then finds the square root of the mean of this PVE image If the images were taken before UT 2002 December 2 the readnoise is calculated as the product of the square root of the mean of the PVE the number of reads minus one the read interval and the the gain divided by the number of multiple reads Otherwise the readnoise is formed by multiplying the gain by the square root of the mean e The readnoise is nominal if it falls between 38 and 45 e second Output Data e The engineering log 0RAC_DATA_OUT uist_array_tests 1log Parameters DARK_FRAMES INTEGER The number of dark frames to combine The maximum allowed is 9 5 Related Recipes AARRAY_TESTS DARK_AND_BPM Implementation Status e The processing engines are from the Starlink packa
96. SUN 232 8 Starlink Project Starlink User Note 232 8 Malcolm J Currie Brad Cavanagh Joint Astronomy Centre Hilo Hawaii 2004 June Copyright 2004 Particle Physics and Astronomy Research Council ORAC DR imaging data reduction 4 1 User Guide SUN 232 8 Abstract ii Abstract ORAC DR is a general purpose automatic data reduction pipeline environment This document describes its use to reduce imaging data collected at the United Kingdom Infrared Telescope UKIRT with the UFTI UIST IRCAM and Michelle instruments at the Anglo Australian Telescope AAT with the IRIS2 instrument at the Very Large Telescope with ISAAC and NACO from Magellan s Classic Cam at Gemini with NIRI and from the Isaac Newton Group using INGRID It outlines the algorithms used and how to make minor modifications to them and how to correct for errors made at the telescope Copyright 2004 Particle Physics and Astronomy Research Council Contents 1 Introduction 2 2 Raw Data Formats and Conversions 2 5 Displa lt 2 6 1 _Available calibration methods 2 7 Log files e lt sewed eean ee a 3 Features of the Primitives 3 1 Preparation of Single Frames 3 1 1 Manipulation of Raw Data 3 1 2 Preliminaries 3 1 3 Non linearity Correction 3 1 4 Electronic Ghosting 3 1 5 Bad pixels 3 1 6 _Data Variance 3 1 7 _Biassubtraction 0 3 1 8 Biascreation
97. T NOD_SKY_FLAT_THERMAL Bright L lt 10 or all M faint L gt 10 Nod jitter self flats of differ enced pairs of frames Has su perior and fast sky subtraction No object masking Requires a dark Use 4 point jitter for L lt 10 and 8 point for fainter L and all M As the previous recipe but also performs aperture pho tometry of the positive and negative sources Nod jitter interspersed sky frames Sky subtraction flat field created from sky frames only Requires a dark 4 point jitter 8 point sequence Aa HE SUN 232 8 Recipes Bright point source recipes Recipe Name Type of Data Function and Comments ITTER_SELF_FLAT 13 lt 1Z lt 17 9 lt JHK lt 15 Standard jitter self flats Normally 5 point jitter Requires a dark ITTER_SELF_FLAT_APHOT As JITTER_SELF_FLAT but also per forms aperture photometry of the source ITTER_SELF_FLAT_NO_MASKi ITTER_SELF_FLAT_NCOLOUR_ APHO As JITTER_SELF_FLAT but faster as it lacks object masking It only suit able for uncrowded fields As JITTER_SELF_FLAT_APHOT but produces filenames that include filters for easier identification for multi colour observation sequences SKY_AND_JITTER A sky frame and jitter on target The sky is subtracted from the target frame before flat fielding Requires a separate flat as the background is too low to self flat and a dark No longer recommended as sky varies
98. TER_SELF_FLAT Two recipes These were limited to nine point jitters e INOD_SELF_FLAT_NO_MASK Four recipes There were limited to fixed sizes of four and eight point jitters e SKY_AND_JITTER Two recipes Only five point jitters were available 211 L 3 Global changes SUN 232 8 Release Notes V2 0 1 In addition certain recipes had a fixed jitter size but no longer These families are as follows L 3 RIGHT_POINT_SOURCE Two recipes These were formerly restricted to five point jitters Global changes The main changes from a user perspective were as follows Recipes and primitives are instrument generic Improved registration allowing mixed solutions There is a new offset type beam separa tions for combining polarimetry mosaics Thresholding of dark subtracted data to prevent bizarre values affecting the pipeline processing In addition JITTER_SELF_FLAT and 5KY_FLAT recipes and their variants which use object masking to make a flat now have the deviant pixels of the initial flat field frame reflagged as bad Editing of the FITS headers to create a world co ordinate system which GAIA and KAPPA recognise Also pre ORAC IRCAM data have their headers structured and comments edited to bring them closer towards the UKIRT FITS standard and to make the headers easier to read and comprehend The names of flats have changed The filter name is included for easy identification Certain characters have s
99. TEST_STATISTICS_ FILE BIAS _ Likewise the UIST ARRAY_TESTS recipe averages a group of bias frames and sets its variance to a population variance estimate The mean bias frame filed with the calibration system includes the group number in its name UIST _BIAS_GROUP_ 3 1 9 Chopping In the thermal and mid infra red regimes the sky is varying so rapidly normal reduction methods are inappropriate Instead sky subtraction is achieved either by frequently oscillating the secondary mirror between two beams mid infra red called A and B or moving the telescope offsets thermal after a short exposure The generic term is chopping The former are reduced by the NOD_CHOP recipes and the latter by the NOD_SELF_FLAT_NO_MASK recipes Both methods produce frames with the target image at different positions on the detector The aforementioned recipes difference these pairs of frames so that the result has both a positive and negative image and a background level close to zero The sense of the subtraction is always the same ORAC DR subtracts the B beam from the A beam and the normal sequence is ABBA For the thermal data the chopped beam is only notional but the same terminology and subtraction sense is used _DIFFERENCE_PAIR_ _DIFFERENCE_PAIR_SIMPLE_ _DIFFERENCE_CHOP_BEAMS_ If the telescope is further offset nodded the final mosaic of the differenced frames can have two positive and two negative representations of the source In pr
100. The UIST ARRAY_TESTS calculates the dark current and readnoise in four regions equally divided along the X axis The recipe reports the quality of each statistic compared with normal operating parameters FP_JITTER and FP_JITTER_NO_SKY May allow scaling of the various components in the formula to create the reduced data if other external calibrations are available defaulting to the previous behaviour e MAKE BPM No longer applies an existing bad pixel mask and creates unwanrted variance SUN 232 8 Release Notes V4 1 198 G 3 Global changes e REDUCE DARK Permits averaging of darks of the same exposure time The dark frame name now includes the exposure time This does not apply to instruments whose darks only have a group identifier of 0 namely IRCAM UFTI and UIST e SKY_FLAT and SKY_FLAT_MASKED These can now process multi coloured observa tions e SKY_FLAT_FP Applies a mask beyond the etalon s transmitted circular region on the detector The circle s centre is either determined through the new fpcentre calibration or it is determined using profiles of the surrounding ring G 3 Global changes The main changes from a user perspective were as follows Updated and expanded documentation featuring the new recipes and instrument data supported more on the Features of the Primitives and a new appendix listing the file e Added support for Magellan imager and the ESO NACO instrument in imaging
101. VING_QUADRANT _JITTER which registers using the telescope offsets alone Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created iteratively First the quadrant containing the object is masked in each object frame Second an approximate flat field is created by combining the normalised and masked object frames using the clipped median at each pixel This flat field is applied to the object frames Sources within the flat fielded frames are detected and masked in the dark subtracted frames The second stage is repeated but applied to the masked frames to create the final flat field Registration is performed using the telescope offsets transformed to pixels SUN 232 8 Recipes 170 QUADRANT_JITTER_TELE The resampling applies non integer shifts
102. Whether or not to create and propagate variance arrays 1 Related Recipes POL_ANGLE_JITTER POL_EXTENDED SKY_FLAT POL SKY_FLAT_POL_ANGLE Implementation Status e The processing engines are from the Starlink packages CCDPACK KAPPA FIGARO FIGARO POLPACK and CURSA e Uses the Starlink NDF format e History is recorded within the data files SUN 232 8 Recipes 156 POL_JITTER e The title of the data is propagated through intermediate files to the mosaics The polarisation maps have new titles as follows using the suffices described in Output Data I Intensity P Polarisation PI Polarised Intensity Q Stokes Q TH Polarisation Angle U Stokes U e The origins of the generated polarisation maps are set to 1 1 The WCS current frame is unchanged e The units are set for the frames with suffices see Output Data P to and TH to degrees Deprecated Variants POL_JITTERS 157 POL_NOD_CHOP SUN 232 8 Recipes POL_NOD_CHOP Reduces a chopped and nodded polarimetry observation nodded at each angle Description This script reduces a chopped and nodded single beam polarimetry observation currently just for Michelle data The imaging observation should comprise a multiple of four object frames nodded and chopped and integrated at the four waveplate angles 0 45 22 5 67 5 degrees in turn For each waveplate angle the recipe makes automatically a calibrated untrimmed mosaic The recipe combines th
103. _POINT_SOURCE_APHOT JITTER_SELF_FLAT ITTER_SELF_FLAT_BASIC JITTER_SELF_FLAT_NO_MASK QUADRANT_JITTER Implementation Status e The processing engines are from the Starlink packages and PHOTOM e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter 105 JITTER_SELF_FLAT_NO_MASK SUN 232 8 Recipes JITTER_SELF_FLAT_NO_MASK Reduces a standard jitter photometry observation without object masking Description This script reduces a standard jitter photometry observation with near infrared imaging data It takes an imaging observation comprising jittered object frames and a dark frame to make a calibrated untrimmed mosaic automatically It performs a null debiassing bad pixel masking dark subtraction flat field creation and division feature detection and matching between object frames and resampling See the for further information This recipe works well for faint sources and sparse fields Notes A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious
104. a a E 63 Siete O ee aie arden ey ete E a a es E ae 66 Se Ut Gite feet ee Bah cys he aay A Gee dee te os ae 69 jolie le dnd 4 Reale ay ate eds eB Bh pow ek AA a de 70 O Be dodged wade wie Greets dow a b eee tee weak eee and 71 A aoa ame Qu a a e a eda ee duets ae a 72 hoch a eee i Ge oes ee Gh teak a clans wo yee ee 74 E eaten 76 be este pe ae th Be Me eh Yay tee ts he ee os ee ee a a 78 O see ak ewe shh ae ae ee E ete 80 a e a eats a pee tuned et Sera eo aie doe eae oon ees co 83 Eps Ae ie Ae oe aes a ee ee ee a 86 a Gots Be ea we ee GS Ae ee Oe a 89 Pe ao es ek ee ee ee 92 pide Juice ly Ea Beh eet ae he ree oe 95 JITTER _SELF_FLAT CATALOGUE 0 0 97 v SUN 232 8 Contents A AO 100 ea dea 102 eat das et 105 e a ee es 107 a o do 109 ea rs oats Ae eens oe ee 111 ee eos US a pra ia sa Ol 112 A eee ee eee ea ee 113 oye oes oak bene ee ee 116 o TOE ee oa oe ees 119 EERE TENET PEES AEE ER 121 e a pe pea 124 A O be meee a 125 A A 127 is e a ees en 130 e ese oun e ia ak seca os 133 A thd hath T 135 OO 137 a o tas ee eee ree 140 o ta aa 142 A hee ae bee eae ae 146 a oon a oa wees 149 Sos be OS se a ee ee Ae es oy 153 eid eee os a eee OER ad oe ee os 157 O 160 A a ee ne ao 163 A ace eee ae aes 165 E eens eee 167 Ook oA So Gules GR ed ae ee cda 169 es ae aaa eee Cokes eet 171 dite ada Bake bet patead ot boda sete ees 17 a a e e A E E e aa 173 o as pee dd eee 175 AP A ate ae a eeace ens 1
105. a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of jittered frames the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic The catalogue includes the right ascension and declination instrumental apparent magnitude calculated as 2 5 x log counts and the error in the magnitude Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix A mosaic for each cycle of jittered frames in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming formatlis slightly different for some non UKIRT instruments For ISAAC the individual bias corrected frames in isaac lt date gt _ lt obs_number gt _bce The created flat fields in flat_ lt filter
106. actice the thermal reductions register and co add the nodded frames to compensate for flat field errors in IRCAM 3 1 10 Post pre subtraction Raw INGRID data comprise a pre exposure image and a post exposure integration The pipeline subtracts the former from the latter to give the measured signal INGRID _DIFFERENCE_PRE_POST_ 3 1 11 FITS headers For historical reasons IRCAM headers prior to were somewhat jumbled disorganised FITS standard and some violated the The pipeline corrects orders and structures the headers to help the human reader locate information quickly and allow complete conversion to FITS 13 SUN 232 8 Features of the Primitives For IRCAM and even since ORAC came online the raw headers do not provide a sky co ordinate system also has an incomplete sky co ordinate system supplied in the raw headers Using information in the raw headers the pipeline creates a FITS world co ordinate system using a tangent plane projection in the AIPS convention this is quite adequate given the small fields of view which it imports into the NDF s WCS component Thus GAIA and KAPPA can display these co ordinates on overlay grids and axes For all these such as KAPPA S display with axes you may need to select the appropriate astrometric Frame like this wcs rame lt your_NDF gt frame sky where you substitute your NDF s name for lt your_NDF gt The mosaics from the pipeline should already have the sky domain
107. ad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used e Intermediate frames are deleted e Sub arrays are supported Output Data e The created flat field in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent recipe cycles Token lt filter gt is the filter name lt group_number gt is the frame number of the group and lt cycle_number gt is the number of the cycle counting from one e The flats are filed in 0RAC_DATA_OUT index flat Parameters NUMBER INTEGER The number of frames in the group If absent the number of offsets as given by header HIERARCH ESO TPL NEXP If neither is available 6 is used An error state arises if the number of jittered frames is fewer than 6 or is odd numbered USEVAR LOGICAL Whether or not to create and propagate variance arrays 1 References ISAAC Data Reduction Guide 1 5 P Amico et al 2002 Implementation Status SUN 232 8 Recipes 110 LAMP_FLAT e The processing engines are from the Starlink packages CCDPACK and KAPPA e Uses the Starlink NDF format e History is recorded within the data files e The tit
108. adds the data array to the variance component taking into account the gain of the detector and the number of exposures For read modes where the bias level is not removed such as CHOP or STARE a bias frame must be subtracted first If no suitable bias is found the bias is deemed to be zero ORAC DR issues a warning that the variance is wrong likely overestimated The calculations also derive the ratio of the read noise to the Poisson noise and reports the percentage of background limited pixels i e those where the Poisson noise is greater than the read noise ADD_POISSON_VARIANCE 3 1 7 Bias subtraction In most cases there is no bias to subtract Recipes attempt to remove a bias frame only if the data have variance information and were taken using a non ND mode i e where the bias has not SUN 232 8 Features of the Primitives 12 already been subtracted in the instrument data system whereupon a bias frame if available is subtracted if however there is no bias calibration the recipe issues a warning issued that the computed variances may be wrong This step occurs between the creation of the readnoise variance and adding the Poisson variance _REMOVE_BIAS_ 3 1 8 Bias creation The Michelle ARRAY_TESTS recipe averages two bias frames sets the observation type to BIAS for the result and files the mean bias frame in the calibration system The filed frame includes the observation number in its name MICHELLE _ARRAY_
109. ages and CURSA e Uses the Starlink NDF format and multi NDF HDS container files e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaics The polarisation maps have new titles as follows using the suffices described in Output Data I Intensity P Polarisation PI Polarised Intensity Q Stokes Q TH Polarisation Angle U Stokes U e The origins of the generated polarisation maps are set to 1 1 The WCS current frame is unchanged The units are set for the frames with suffices see Output Data P to and TH to degrees Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 160 POL_QU_FIRST_NOD_CHOP POL_QU_FIRST_NOD_CHOP Reduces a chopped and nodded polarimetry observation where waveplate angle iterates in pairs at each jitter position Description This script reduces a chopped and nodded single beam polarimetry observation currently just for Michelle data The imaging observation should comprise chopped object frames at the angles 0 45 degrees for each of a multiple of two pairs of nod positions followed by frames at waveplate angles 22 5 67 5 degrees also for each of a multiple of two pairs of nod positions For each waveplate angle the recipe makes automatically a calibrated untrimmed mosaic The recipe combines the multiple images of the source within each of these mosaics into new frames and uses those four combine
110. akes an observation com prising jittered object frames and a dark frame to make a calibrated untrimmed mosaic automatically It performs a null debiassing bad pixel masking dark subtraction flat field creation and division feature detection and matching between object frames and resampling See the for further information This recipe works well for faint sources and for moderately crowded fields Notes A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created iteratively First an approximate flat field is created by combining normalised object frames using the median at each pixel This flat field is applied to the object frames Sources within the flat fielded frames are detected and masked in the dark subtracted frames The first stage is repea
111. applied to the masked frames to create the final flat field Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects it matches the centroid of the central source If this fails the script resorts to using the telescope offsets transformed to pixels SUN 232 8 Recipes 164 QUADRANT_JITTER The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame Thus the noise will be greater in the peripheral areas having received less exposure time The full signal will be in the central ninth containing the main object The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of four the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data The integrat
112. ar infrared photometry uses the latest standards list which also includes standards for the IZ HKLM wavebands e In photometry recipes the sky units are now reported as counts s pixel e Scripts have improved error detection and reporting after accessing text files e The default display suffices have been augmented These are for Michelle _cab _scab _cpc and _rpc and _dk for IRCAM e The calibration called mask should be used to specify other than the default bad pixel mask rather than the bpm calibration The main changes from a programmer perspective were as follows e There is better structuring of the preliminary steps to permit instrument specific variants such as correcting the world co ordinate system headers e The waveplate angle header values are standardised to a single format e The preliminary operation includes the removal of axes after a rearrangement in ORAC Convert e The registration was modified to allow for changes to CCDPACK e The COMBINE_CHOPPED_FRAME_ primitive as used by the NOD_CHOP family of recipes has new options These comprise centroiding with validation the method by which the individual chopped and nodded images are combined the ability to apply block smoothing for faint sources and the removal of pickup and bias variations The removes column then row patterns by subtracting the median of each column or row from all the values in that column or row J Release Notes V3 0 3 The main c
113. arget is a faint or low surface brightness galaxy at low galactic latitude brighter stars relegate the galaxy toa high identification number So the code now checks for a common denominator object between all the frames with a higher identification number The mosaic making primitive has been partly restructured to make the code more obvious and it also rationalises the naming Gone is the _mu file The mosaic with bad pixels filled has its own _fb suffix All individual cycle mosaics are retained The only disadvantage is that for a single cycle observation there are two copies of the same mosaic one with suffix _mos and the other with suffix _mos_0 the recipe cannot know if there is a second cycle to come The mosaics have the world co ordinate system domain set to sky so that displays with GAIA and KAPPA have sky co ordinates The start and end UT times for mosaics are updated to that of the first and last contributing frames The photometry results file now reports the sky in counts per second previously just counts and the exposure time The alignment of the columns is thus slightly altered The recipe tidying has been improved to remove all unwanted files Some of the registra tion text files certain suffices and later cycle frames were being missed In the polarimetry calculations the chip position angle is added to the offset of north with respect to the analyser so that the vectors are also measured with respect to no
114. arisation error is greater 5 The bin size and thresholds can readily be changed by supplying arguments to the CALC _STOKES_ primitive At the end of each cycle the grand mosaics are registered and new polarisation maps and catalogues constructed Intermediate frames are deleted except for the flat fielded _ff suffix frames and the mosaics _mos or _mos_c lt cycle_number gt suffix Output Data SUN 232 8 Recipes 144 POL_ANGLE_JITTER e The integrated mosaics in lt m gt lt date gt _ lt group_number gt _ lt beam gt lt angle gt _mos where lt m gt the instrument s group prefix Token lt beam gt is e or o and lt angle gt is 0 22 45 or 67 e A mosaic for each cycle of jittered frames per beam and angle in lt m gt lt date gt _ lt group_number gt _ lt beam gt lt angle gt _mos_c lt cycle_number gt where lt cycle_number gt counts from 0 e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The naming formatlis slightly different for some non UKIRT instruments Polarisation frames lt m gt lt date gt _ lt group_number gt _ lt suffix gt each with a differ ent suffix for the each parameter The suffices are I intensity P percentage polarisation PI polarisation intensity Q Stokes Q TH polarisation angle U Stokes U e A FITS binary table catalogue of the binned and culled polarisation data called lt m gt lt date gt _ lt grou
115. arrays 0 Related Recipes SKY_FLAT_FP FP_JITTER FP JITTER NO_SKY SUN 232 8 Recipes 82 EP Implementation Status e The processing engines are from the Starlink packages and e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter 83 FP_JITTER SUN 232 8 Recipes FP_JITTER Reduces spatially jittered sets of 8 frame Fabry Perot observations Description This script reduces a Fabry Perot observation with UFTI data It takes an imaging obser vation comprising at least three sets of eight object frames each set being for a different telescope position The recipe combines these with a dark frame and a separate flat to make a continuum subtracted and sky subtracted untrimmed mosaic automatically Each sequence of eight frames expected in each spatial position are tabulated below Frame Position Wavelength 1 On source On line 2 Off source On line 3 Off source Off line positive offset 4 On source Off line positive offset 5 On source On line 6 Off source On line 7 Off source Off line negative offset 8 On source Off line negative offset For each spatial set the recipe performs a null debiassing bad pixel masking dark subtraction pairwise frame differencing flat field division integer shifts of origin to register and mosaicking The wavelength sh
116. as having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame Mosaics are made and displayed for each row except the last At the end of each cycle of 51 frames the full mosaic of 25 target frames is created and displayed instead On the second and subsequent cycles the full mosaic is added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic e Intermediate frames are deleted except for the flat fielded _ f suffix frames Output Data e The full mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instru ment s group prefix e A mosaic for each row in lt m gt lt date gt _ lt group_number gt _mos lt row_number gt where lt row_number gt is 0 to 3 e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming formatlis slightly different for some non UKIRT instruments Parameters NROW INTEGER The number of target frames in a row of the mosaic Its minimum is 3 because this number of blank skies are needed to form a flat field 5 NCOL INTEGER The number of target frames in a column of the mosaic Its minimum is 2 5 USEVAR
117. ast three jittered positions the telescope is moved before the waveplate An appro priate dark and flat fields at each waveplate angle must be obtained POL_NOD_CHOP ize OL_QU_FIRST_NOD_ HOP O Polarimetry of point or small lt 10 arcsec extended sources in mid infra red As POL_ANGLE_ NOD_CHOP but the tele scope is nodded before the waveplate is moved Polarimetry of point or small lt 10 arcsec extended sources in mid infra red It is a hybrid of POL_ANGLE_NOD_CHOP and POL_NOD_CHOPias the waveplate an gle iterates in pairs at each jitter position SKY_FLAT_POL Flat Obtain a master polarimetry flat field from the median average of eight jittered frames the waveplate is cycled after every second frame Makes a copy of the flat for each waveplate angle Requires a dark 47 SUN 232 8 Recipes Fabry Perot recipes Recipe Name Type of Data Function and Comments SKY_FLAT_FP Fabry Perot Uses a sequence of eight frames object sky pairs at on line off line blue on line and off line red FP settings to make a mosaic Requires a separate flat field made by SKY_FLAT_FP and a dark FP_JITTER_NO_SKY On Off line images with nodding to blank sky as EP and spatial jittering on source Requires a separate flat field and a dark On Off line images without nodding to blank sky i e sequence of four frames and spatial
118. at will change to include UT and possibly date Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix A mosaic for each cycle of jittered frames in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The naming format is slightly different for some non UKIRT instruments The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters 115 MOVING_JITTER_SELF_FLAT SUN 232 8 Recipes NUMBER INTEGER The number of frames in the jitter pattern If not supplied the number of offsets as given by FITS header NOFFSETS minus one is used If neither is available 9 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes ITTER_SELF_FLAT JITTER_SELF_FLAT_TELE MOVINGJITTER_SELF_FLAT_BASIC Implementation Status e The processing engines are from the Starlink packages FIGARO and EXTRACTOR e Uses the Starlink NDF format
119. ata files The title of the data is propagated through intermediate files to the mosaic Error propagation is controlled by the USEVAR parameter 169 QUADRANT_JITTER_TELE SUN 232 8 Recipes QUADRANT_JITTER_TELE Reduces a Quadrant Jitter observation using object masking and telescope offsets for registration Description This script reduces a quadrant jitter photometry observation with near infrared imaging data It takes an imaging observation comprising one or more series of four object frames where the target is approximately centred in each quadrant and a dark frame to make a calibrated untrimmed mosaic automatically It performs bad pixel masking null debiassing dark subtraction flat field creation and division registration using telescope offsets and resampling See the Notes for further information This recipe is intended for extended moving sources comets tracked by the telescope The source extent should not exceed 45 arcseconds for UFTI or 10 arcseconds for IRCAM in moderately crowded fields Sources may include those with a comparatively bright core embedded in faint extended emission The object need not be isolated as the recipe masks objects within the other quadrants and hence does not introduce significant ar tifacts into the flat field This recipe should not be used for frames where the telescope has not guided on the moving object In that case reduction should be performed by MO
120. ate variance arrays 0 Related Recipes BRIGHT_POINT_SOURCE NOD_SELF_FLAT_ NO_MASK Implementation Status e The processing engines are from the Starlink packages and e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 142 POL_ANGLE_JITTER POL_ANGLE_JITTER Reduces an imaging polarimetry observation where waveplate angle iterates at each jitter position Description This script reduces a polarimetry observation with UKIRT imaging data It takes an imaging observation comprising object frames at the four waveplate angles 0 45 22 5 67 5 degrees for each of of a series of jitter positions offset in Right Ascension and a dark frame to make calibrated polarisation images and vectors automatically See Output Data for a list of these images It performs a null debiassing bad pixel masking dark subtraction and flat field division on all frames Next the sections of the frame representing the e and o beam target and sky regions are extracted and the target frames sky subtracted The resultant frames undergo registration and resampling to form a mosaic for each waveplate angle and beam Once all eight mosaics are formed they are registered and resampled and then combined to form the various polarisation images The polarisation data are b
121. ated suffices The following frame suffices were present prior to version 3 0 of ORAC DR Suffix Stands for Description _dg De Glitched Bad pixels replaced by median of neighbours _sbp Substitute Bad Pixels Bad pixels replaced needed for PISA sc SCaled Data scaled to lie within the range of values allowed by PISA for the object masking The following mosaic suffices were present prior to version 3 0 of ORAC DR Suffix Stands for Description mu Mosaic Unfiltered Intermediate mosaic could contain bad hot pixels 37 SUN 232 8 Recipes D Recipes The original set of recipes and names were prescribed in G S Wright amp S K Leggett 1997 Scripts for UFTI orac009 ufts v01 D 1 Classified Recipes In hindsight you may decide that there was a better recipe for your data than stored in the RECIPE header Also you may have used a faster variant of a recipe at the telescope but now want the full reduction Here is a classified list so that you can select an alternative Magnitudes and dimensions apply to UFTI except for the NOD_SELF_FLAT_NO_MASK recipes whose magnitude ranges are for IRCAM and the NOD_CHOP recipes which are applicable to For dimensions are 10 smaller for TRIS2 dimensions are 6 8x larger for UIST they are either 33 smaller or 22 larger depending on the camera The magnitude ranges are courtesy of Sandy Leggett and apply to UKIRT SUN 232 8 Recipes 38 Calibration Recipes Recip
122. be changed by supplying arguments to the CALC _STOKES_NOD_CHOP_ primitive At the end of each cycle the grand mosaics are registered and new polarisation maps and catalogues constructed Intermediate frames are deleted except for the differenced pairs _dp suffix frames Output Data The integrated mosaics in lt m gt lt date gt _ lt group_number gt _p lt angle gt _mos where lt m gt is the instrument s group prefix and lt angle gt is 0 22 45 or 67 A mosaic for each cycle of chopped and nodded frames per waveplate angle in lt m gt lt date gt _ lt group_number gt _p lt angle gt _mos_c lt cycle_number gt where lt cycle_number gt counts from 0 The combined source image and neighbourhoods at each waveplate angle in lt m gt lt date gt _ lt group_number gt _p lt angle gt _cab The differenced pairs in lt i gt lt date gt _ lt obs_number gt _dp where lt i gt is the Polarisation frames lt m gt lt date gt _ lt group_number gt _ lt suffix gt each with a differ ent suffix for the each parameter The suffices are SUN 232 8 Recipes 148 POL_ANGLE_NOD_CHOP I intensity P percentage polarisation PI polarisation intensity Q Stokes Q TH polarisation angle U Stokes U e A FITS binary table catalogue of the binned and culled polarisation data called lt m gt lt date gt _ lt group_number gt _I FIT For each point it tabulates the x y co ordinates the total intensity the Stokes parameters the percentage p
123. bias is removed Poisson noise is added e A bias frame selected from the calibration system is removed from each beam in CHOP read mode If no bias frame is available in the CHOP mode the recipe subtracts a null bias so the errors will be overestimated in the CHOP read mode the data array will be unaffected once the beams are differenced The ARRAY_TESTS recipe files a suitable short exposure dark as a bias in the calibration system The integrations of the two chop beams are differenced the first subtracted from the second in each pair e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist e The bad pixel mask applied is 0RAC_DATA_CAL bpm e Registration is performed using the telescope offsets transformed to pixels e The resampling applies integer shifts of origin There is no rotation to align the Cartesian axes with the cardinal directions e The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of frames the recipe creates mosaics for each chop beam and waveplate angle modulo 180 degrees Each mosaic has its bad pixels filled a
124. bs_number gt _dp where lt i gt is the Polarisation frames lt m gt lt date gt _ lt group_number gt _ lt suffix gt each with a differ ent suffix for the each parameter The suffices are 159 POL_NOD_CHOP SUN 232 8 Recipes I intensity P percentage polarisation PI polarisation intensity Q Stokes Q TH polarisation angle U Stokes U e A FITS binary table catalogue of the binned and culled polarisation data called lt m gt lt date gt _ lt group_number gt _I FIT For each point it tabulates the x y co ordinates the total intensity the Stokes parameters the percentage polarisation the polarisation angle and intensity There are additional columns giving the standard deviation on each of the tabulated values excluding the co ordinates Likewise lt m gt lt date gt _ lt group_number gt _all FIT and lt m gt lt date gt _ lt group_number gt _bin FIT store the full and binned catalogues re spectively Parameters NUMBER INTEGER The number of frames in the nod pattern If absent the number of offsets as given by header NOFFSETS minus one is used If neither is available 4 is used An error state arises if the number of jittered frames is fewer than 4 and not a multiple of 4 USEVAR LOGICAL Whether or not to create and propagate variance arrays 1 Related Recipes POL_ANGLE_NOD_CHOP POL_QU_FIRST_NOD_CHOP NOD_CHOP_APHOT POL_JITTER Implementation Status e The processing engines are from the Starlink pack
125. ceived less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of object frames the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass and end UT headers are updated to match that of the last observed frame contributing to the mosaic Intermediate frames are deleted except for the differenced pairs _dp suffix frames Output Data SUN 232 8 Recipes 126 NOD_CHOP e The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instruments group prefix e A mosaic for each cycle of object frames in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 e The differenced pairs in lt i gt lt date gt _ lt obs_number gt _dp where lt i gt is the Parameters NUMBER INTEGER The number of frames in the nod pattern If absent the number of offsets as given by header NOFFSETS minus one is used If neither is available 4 is used An error state arises if the number of jittered frames is fewer than 4 and not a multiple of 4 USEVAR LOGICAL Whether or not to create and propagate variance arrays 1 Related Recipes NOD_CHOP_APHOT NOD_SELF_FLAT_NO_MASK Implementation Status
126. centrally located after allowing for the jitter offsets If you have data where the star lies outside the aperture it is possible to apply an offset See the RAOFF and DECOFF arguments of primitive _FIXED_APERTURE_PHOTOMETRY_ in _APHOT_MAG_ to adjust the aperture s position The thermal chopped data have sources displaced from the centre but the reductions allow for the symmetric offsets about the mean jitter position For UIST thermal data the search algorithm does not assume a central or centrally symmetric distribution of the positive and negative signals Residual bad pixels usually in the individual flat fielded frames are removed by median filtering This does leave a bias in the wings of stars but certainly the underestimate is far less than ignoring the bad pixels and is typically far less than the other photometric errors The photometry is through a circular aperture located at the centroid of the source with the sky measured from a concentric annulus outside the aperture The default aperture size is 5 arcseconds 3 arcseconds for NACO The annulus diameters are 6 5 to 10 arcseconds all instruments but UFTI and NACO 6 5 to 12 5 arcseconds for UFTI and 3 9 to 6 arcseconds for The default estimator of the sky flux is the mode calculated from 3 x median 2 mean and Chauvenet s rejection criterion The photometry accounts for fractional pixels at the aperture edge but without allowance for the local gradient The magnitudes
127. ch cycle of four the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix A mosaic for each cycle of four in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming formatlis slightly different for some non UKIRT instruments The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes QUADRANT_JITTER QUADRANT_JITTER_BASIC EXTENDED_3x3_BASIC EXTENDED_5x5_BASIC Implementation Status The processing engines are from the Starlink packages and Uses the Starlink NDF format History is recorded within the d
128. cipe iterations Fixed a bug where exposure time was not integrated in the grand mosaic of EXTENDED recipes The the start and end times and airmasses are also updated in the grand mosaic s headers The mosaic s WCS is set to the SKY by default Allow polarimetry recipes to work with angles of 0 45 90 and 135 degrees This permits the circular polarisation to be determined from the Stokes images Appropriately named flats for 90 and 135 degrees are created where necessary There is a new polrefang calibration to correct the measured polarisation angles to position angle allowing for instrumental alignment The index file may be created manually to overide the default calibrations The default near infrared polarisation selection criteria have changed The maximum polarisation threshold is increased from 50 to 75 The standard deviation is relaxed to 10 There is a new criterion where the minimum intensity must be at least three standard deviations above zero The binning size is increased from 3 to 5 and its value is reported The polarimetry parameter images now have their world co ordinates set to SKY so plots will be annotated with equatorial co ordinates More intermediate frames are tidied at the end of recipes notably in CHOP_SKY_JITTER Improved header translations for such as offering fallback translations if the primary keyword is absent setting cumulative offsets to zero for the first jitter position recognising differ
129. comprising one or more series of four object frames where the target is approximately centred in each quadrant and a dark frame to make a calibrated untrimmed mosaic automatically It performs bad pixel masking null debiassing dark subtraction flat field creation and division and registration using telescope offsets See the Notes for further information This recipe aims to keep pace with the pipeline s incoming data and many options which improve the final mosaic are omitted This recipe is suitable for faint objects or objects within a comparatively bright core embedded in faint extended emission e g a quasar or extended objects less than 45 arcseconds across with UFTI 10 arcseconds with IRCAM and 2 arcminutes with IRIS2 If the object is not isolated there will be artifacts introduced into the flat field These arise from the contribution of sources outside the quadrant containing the primary object This variant of QUADRANT _JITTER is best for isolated objects or where speed is critical Use QUADRANT_JITTER itself if object masking is required instead Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instr
130. cted by the initial flat field creation restored after object masking _fpm Fabry Perot Masked After a mask is applied to exclude regions be yond the circle transmitted by the Fabry Perot etalon md Masked Deviants Deviant pixels from the neighbourhood usually 3 0 in 15x15 pixel region flagged as bad nl Non Linearity The standard non linearity correction has been applied IRCAM only _nm Normalised to Mode Normalised masked frames combined to make the flat field _om Objects Masked This has sources masked with bad values so that they do not bias the self flat field oss O beam Sky Subtracted Polarimetry target o beam after sky subtraction SUN 232 8 File suffices 34 Suffix Stands for Description _qm Quadrant Masked One of the quadrants is masked with bad pixels cre ated in QUADRANT_JITTER _pov POisson Variance Poisson variance added raw Raw copy Copy of the raw data but in output directory and has history recording enabled rnv Read Noise Variance Variance created containing the readnoise _ss Sky Subtracted Global or local sky subtraction applied _th THresholded Non physical values set to bad trn TRaNsform The transformed or resampled data immediately prior to making a mosaic xpr X PRofile Median of each row ISAAC _ypr Y PRofile Median of each column ISAAC 35 Group suffices SUN 232 8 File suffices Suffix Stands for Description _An A beam Negative Extracted negative A beam source and r
131. d frames to calculate automatically calibrated polarisation images and vectors of the source See Output Data for a list of these images It performs a null debiassing creation and propagation of data variance difference the integrations for each AB chop beam pair bad pixel masking difference adjacent nodded pairs registers the frames and forms a mosaic See the Notes for further information Notes e A variance array is created for each chop beam first using the read noise and once the bias is removed Poisson noise is added A bias frame selected from the calibration system is removed from each beam in CHOP read mode If no bias frame is available in the CHOP mode the recipe subtracts a null bias so the errors will be overestimated in the CHOP read mode the data array will be unaffected once the beams are differenced The ARRAY_TESTS recipe files a suitable short exposure dark as a bias in the calibration system The integrations of the two chop beams are differenced the first subtracted from the second in each pair e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist e The bad pixel mask applied is 0RAC_DATA_CAL bpm Registration is performed using the telescope offsets transformed to pixels The resampling applies integer shifts of origin There is no rotation to align the Cartesian axes with the cardinal directions e The recipe makes the m
132. d neighbourhoods in lt m gt lt date gt _ lt group_number gt _cab e The differenced pairs in lt i gt lt date gt _ lt obs_number gt _dp where lt i gt is the Parameters NUMBER INTEGER The number of frames in the nod pattern If absent the number of offsets as given by header NOFFSETS minus one is used If neither is available 4 is used An error state arises if the number of jittered frames is fewer than 4 and not a multiple of 4 USEVAR LOGICAL Whether or not to create and propagate variance arrays 1 Related Recipes NOD_CHOP NOD_SELF_FLAT_NO_MASK_APHOT BRIGHT_POINT_SOURCE_APHOT JITTER_SELF_FLAT_APHOT Implementation Status e The processing engines are from the Starlink packages FIGARO and PHOTOM e Uses the Starlink NDF format and multi NDF HDS container files e History is recorded within the data files 129 NOD_CHOP_APHOT SUN 232 8 Recipes e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 130 NOD_CHOP_FAINT NOD_CHOP_FAINT Reduces a chopped and nodded observation of a faint source combining images and smoothing Description This script reduces a chopped and nodded observation of a faint point or compact source currently just for Michelle data It takes an imaging observation comprising a multiple of four object frames to make a calibrated smoothed combined image of the source au
133. d to the dimensions of a single frame thus the noise will be greater in the few pixels in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of twelve frames the recipe creates mosaics for each beam and wave plate angle Each mosaic has its bad pixels filled and after the first cycle is then added into its own master mosaic of improving signal to noise The exposure time is also summed and stored in each master mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic The polarised intensity is corrected for the statistical bias of the noise by subtracting the variance of Q or U An offset of 6 3 degrees clockwise is applied to the rotation angle for the orientation of the analyser with respect to north A non null value will be applied once it is determined The polarisation data for each pixel are also stored in catalogues See Output Data The intensity image may be displayed with vectors overlaid Steps are taken to reduce the number of noisy or insignificant pixels as well as clutter First the polarisation catalogue data are averaged in 3 by 3 pixel bins Second a binned pixel is rejected if its polarisation is greater than 50 or is not positive or its polarisation signal to noise less than 3 or its pol
134. der SUN 232 8 Recipes 106 JITTER_SELF_FLAT_NO_MASK Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic e Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix e A mosaic for each cycle of jittered frames in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming formatlis slightly different for some non UKIRT instruments The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters NUMBER INTEGER The number of frames in the jitter pattern If not supplied the number of offsets as given by FITS header NOFFSETS minus one is used If neither is available 9 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent 1 USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes ITTER_SELF_FLAT JITTER_SELF_
135. e Name Type of Data Function and Comments Array check Calculates read noise and dark current Dark and Mask Measures dark current and creates a new bad pixel mask for UIST Array Check and Mask Calculates statisticd for Michelle darks in a pairwise manner Mask Creates and files imaging flat fields derived from a calibration lamp for ESO instruments Mask Creates a bad pixel mask by standard deviation thresholding Array check Measures and files the readnoise for UIST from a set of dark frames Dark Averages and files observations as the cur rent dark Flat Reduces an imaging flat field Flat Creates and files a flat field derived from five jittered frames Mostly for use with BRIGHT_POINT_SOURCE recipes Requires a dark Flat Creates a Fabry Perot sky flat from jittered blank sky exposures FP at on and off line wavelengths Requires a dark SKY_FLAT_MASKED Flat As SKY_FLAT but masks objects to give a better flat field Flat Obtain a master polarimetry flat field from the median average of eight jittered frames the waveplate is cycled after every second frame Makes a copy of the flat for each wave plate angle Requires a dark SKY_FLAT_POL_ANGLE Flat Obtain four polarimetry flat fields one for each waveplate angle from the median aver age of jittered frames Requires a dark QU NO Miscellaneo
136. e The processing engines are from the Starlink packages FIGARO and EXTRACTOR e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 124 NIGHT_LOG NIGHT_LOG Produces a text file log of a night s observations Description This recipe takes a night s observations and creates a text file containing a headed tabula tion of parameters for each frame The parameters are observation number object name observation type UT start time exposure time number of coadds read mode and speed filter start airmass frame dimensions in pixels base equatorial co ordinates and data reduction recipe name Notes e Run with oracdr noeng nodisplay from 1 skip for efficiency e The lt date gt comes from the header keyword DATE e Specification provided by Sandy Leggett Output Data e The text log file SORAC_DATA_IN lt date gt nightlog where lt date gt is the UT date 125 NOD_CHOP SUN 232 8 Recipes NOD_CHOP Reduces a chopped and nodded observation Description This script reduces a chopped and nodded observation currently just for Michelle data It takes an imaging observation comprising a multiple of four object frames to make a calibrated untrimmed mosaic automatically It performs a null debiassing creation and propagation of data va
137. e contributing to the mosaic Intermediate frames are deleted except for the flat fielded _ff suffix frames Ephemeris file Format The current format of the ephemeris file is one line per object comprising three space separated fields in the following order the objectname which may contain embedded spaces the motion in the plane of the sky in arcsec second for right ascension then declina tion Note that the right ascension motion is the change in right ascension multiplied by the cosine of the declination The format will change to include UT and possibly date Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix A mosaic for each cycle of four in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is f for UFTI and i for IRCAM and u for UIST The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles 123 MOVING_QUADRANT_JITTER SUN 232 8 Recipes Parameters USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes MOVING JITTER SELF_FLAT QUADRANT JITTER IQUADRANT_ JITTER TELE Implementation Status
138. e corrected Spurious instrument names are changed to IRCAMS3 The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created iteratively First an approximate flat field is created by combining normalised sky frames using the median at each pixel This flat field is applied to the sky frames Sources within the flat fielded frames are detected and masked in the dark subtracted frames The first stage is repeated but applied to the masked frames to create the final flat field Intermediate frames are deleted Sub arrays are supported Output Data The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent recipe cycles Token lt filter gt is the filter name lt group_number gt is the frame number of the group and lt cycle_number gt is the number of the cycle counting from one 183 SKY_FLAT_MASKED SUN 232 8 Recipes e The flats are filed in 0RAC_DATA_OUT index flat Parameters NUMBER INTEGER The number of frames in the jitter If absent the number of offsets as given by header NOFFSETS minus one is used If neithe
139. e full mosaic is added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic e Intermediate frames are deleted except for the flat fielded _ f suffix frames Output Data e The full mosaic in lt m gt lt date gt _ lt group_number gt _mos Where lt m gt is the instru ment s group prefix e A mosaic for each row in lt m gt lt date gt _ lt group_number gt _mos lt row_number gt where lt row_number gt is 0 or 1 e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The naming format is slightly different for some non UKIRT instruments Parameters NROW INTEGER The number of target frames in a row of the mosaic Its minimum is 3 because this number of blank skies are needed to form a flat field 3 NCOL INTEGER The number of target frames in a column of the mosaic Its minimum is 2 3 USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes EXTENDED_3x3 EXTENDED_5x5_BASIC QUADRANT_JITTER_BASIC Implementation Status e The processing engines are from the Starlink packages and e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagat
140. e is 0 RA_OFFSET DIFFERENCE F The right ascension displacement between a nodded pair of frames REFERENCE_FRAME B A true value specifies the reference frame for normalisa tion of the masked frames It is true for the first frame and false for all subsequent frames in the observation REFERENCE LEVEL F The reference modal level used when combining masked frames to form a flat REFERENCE_SKY The reference sky level used for sky subtraction REGISTER_IMAGES B Whether or not to register and resample the polarimetric e and o beam mosaics SUN 232 8 Internal Headers Name Type 196 F2 Steering Headers Meaning TARGET_NUMBER I USE_VARIANCE WAVEPLATE_FLAT When TARGET_OR_SKY is target this counts the target frames starting from zero It is used for interpo lation between sky measurements Whether or not variance processing is to occur Whether or not to make a flat for each polarimeter wave plate angle For non polarimetric data the value is im material For polarimetric data false means combine all waveplate angles to make the flat there should be an equal number of each angle 197 SUN 232 8 Release Notes V4 1 G Release Notes V4 1 The main changes are improvements to polarimetry aperture photometry and Fabry Perot reductions several new recipes and support for Magellan VLT NACO and Gemini NIRI instruments G 1 New recipes BRIGHT_POINT_SOURCE_NCOLOUR Reduces a multi colour bright po
141. e multiple images of the source within each of these mosaics into new frames and uses those four combined frames to calculate automatically calibrated polarisation images and vectors of the source See Output Data for a list of these images It performs a null debiassing creation and propagation of data variance difference the integrations for each AB chop beam pair bad pixel masking difference adjacent nodded pairs registers the frames and forms a mosaic See the Notes for further information Notes A variance array is created for each chop beam first using the read noise and once the bias is removed Poisson noise is added e A bias frame selected from the calibration system is removed from each beam in CHOP read mode If no bias frame is available in the CHOP mode the recipe subtracts a null bias so the errors will be overestimated in the CHOP read mode the data array will be unaffected once the beams are differenced The ARRAY_TESTS recipe files a suitable short exposure dark as a bias in the calibration system The integrations of the two chop beams are differenced the first subtracted from the second in each pair e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist e The bad pixel mask applied is 0RAC_DATA_CAL bpm e Registration is performed using the telescope offsets transformed to pixels e The resampling applies integer shifts of origin
142. e number of offsets as given by FITS header NOFFSETS minus one is used If neither is available 5 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes BRIGHT_POINT_SOURCE BRIGHT_POINT_SOURCE_APHOT ITTER_SELF_FLAT SKY_FLAT SKY_FLAT_MASKED Implementation Status e The processing engines are from the Starlink packages and e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter 63 CHOP_SKY_JITTER SUN 232 8 Recipes CHOP_SKY_JITTER Reduction of alternating sky target jitters using interpolated sky subtraction Description This recipe reduces a moderately extended source using near infrared imaging data The data comprise alternating blank sky and target frames commencing and ending with a blank sky Both the sky and target frames are jittered The recipe makes a sky subtracted untrimmed mosaic automatically The script performs bad pixel masking null debiassing dark subtraction flat field divi sion sky subtraction registration resampling and mosaicking The Notes give more details It is suitable for extended objects where the ob
143. e offsets and mosaicking The Notes give more details It is suitable for extended objects where the object fills or nearly fills the frame so sky estimation within the frame is impossible or unreliable but the extended mapping of the target is not required Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 e The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is derived from the sky frames as follows The mode sigma clipped mean is used to offset each sky frame s mode to that of the first sky frame The corrected sky frames are combined pixel by pixel using a median of the values in each frame The resultant frame is normalised by its median to form the flat field This frame median is subtracted from the source frames after they have been flat fielded A flat field is created from all
144. e pixel histogram The inner annulus diameter is 1 3 times that of the aperture 6 5 arcsec the outer annulus is 2 5 times 12 5 arcsec for UFTI and twice the aperture 10 arcsec for IRCAM The errors are internal based on the sky noise Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix A mosaic for each cycle of object frames in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The naming format is slightly different for some non UKIRT instruments For ISAAC the individual bias corrected frames in isaac lt date gt _ lt obs_number gt _bc The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters NUMBER INTEGER The number of frames in the nod pattern If absent the number of offsets as given by header NOFFSETS minus one is used If neither is available 4 is used An error state arises if the number of jittered frames is fewer than 4 and not a multiple of 4 USEVAR LOGICAL Whether or not to create and propagate variance arrays
145. e previous recipe but also performs aper ture photometry of the combined four images after extraction and centroid registration As NOD_CHOP but removes column and row artifacts from the mosaic then it combines each chopped and nodded image using a median filter to form an image of the source with four times the signal This image is then smoothed to enhance the visibility of faint sources NOD_CHOP_SCAN As NOD_CHOP but for chopped and nodded observations that are taken in a scan pattern A mosaic is formed at each scan position 45 SUN 232 8 Recipes Moving non sidereal source recipes Recipe Name Type of Data Function and Comments MOVING_JITTER_SELF_FLAT MOVING_JITTER_SELF_FLAT_BASIC JITTER_SELF_FLAT_TELE Minor planets comets As JITTER_SELF_FLAT but uses ephemeris data to track the non sidereal source As JITTER_SELF_FLAT_BASIC but uses ephemeris data to track the non sidereal source Standard jitter using telescope off sets This is needed when the telescope has tracked on the non sidereal target Requires a dark MOVING_NOD_CHOP As NOD_CHOP but uses ephemeris data to track the non sidereal source in the mid infra red MOVING QUADRANT _JITTER Compact comets As QUADRANT JITTER but uses ephemeris data to track the non sidereal source QUADRANT_JITTER_TELE As QUADRANT JITTER but uses telesco
146. ector in the mode used The flat field is created by combining normalised object frames using the median at each pixel There is no cleaning of extreme outliers For ISAAC residual bias variations along the columns are largely removed from each flat fielded frame The recipe first masks the sources then collapses the frame along its rows to form a profile whose clipped mean is subtracted The resultant profile reflects the bias variations The recipe subtracts this profile from each column of the flat fielded frame Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects the script resorts to using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame SUN 232 8 Recipes 136 NOD_SELF_FLAT_NO_MASK e For each cycle of object frames the recipe creates a mosaic is then added into a master mosaic of improving signal to noise The exposure
147. ed mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix A mosaic for each cycle of four in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The jaming formatlis slightly different for some non UKIRT instruments The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes QUADRANT_JITTER BASIC QUADRANT_JITTER_NO_MASK J EXTENDED_3x3 EXTENDED_5x5 Implementation Status The processing engines are from the Starlink packages FIGARO and EXTRACTOR Uses the Starlink NDF format History is recorded within the data files The title of the data is propagated through intermediate files to the mosaic Error propagation is controlled by the USEVAR parameter 165 QUADRANT_JITTER_BASIC SUN 232 8 Recipes QUADRANT_JITTER_BASIC Reduces a Quadrant Jitter observation using just the basic operations for speed Description This script reduces a quadrant jitter photometry observation with near infrared imaging data It takes an imaging observation
148. ed sources specifically for Michelle The data are expects to iterate over waveplate angle before the telescope is nodded The recipe forms integrating mosaics as NOD_CHOP for each of four waveplate angles For each mosaic it combines the two positive and two negative images of the source The recipe then calculates polarisation frames and catalogues of vectors from these as earlier recipes like POL_JITTER POL_NOD_CHOP As POL_ANGLE_NOD_CHOP except the data are ordered such that the telescope performs its nodding pattern before the waveplate is turned J 2 Modified recipes e ARRAY_TESTS Instrument specific versions for UFTI and IRCAM Both record the read noise in the calibration system J 3 Global changes The main changes from a user perspective were as follows e Correct data variance creation for UKIRT infra red data The previous calculations were for CCD data Easier to switch on data variance processing This combined with handling of chopped data has caused some reordering of the early steps for instance the editing of the world co ordinate system WCS occurs just before dark subtraction rather than immediately after the IMAGING_HELLO_ preliminaries Thus a few of the early frames such as _db and _bp now do not have a WCS defined e More efficient masking using EXTRACTOR instead of PISA Some of the acceleration is because some of the steps to sweeten the data for PISA such as the removal of the bad pixels are now unnec
149. ed through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 76 EXTENDED_5x5 EXTENDED_5x5 Extended source standard reduction using interpolated sky subtraction Description This recipe reduces an extended source using near infrared imaging data The data comprise alternating blank sky and target frames commencing and ending with a blank sky The target frames are arranged in an overlapping 30 50 grid of 5x5 frames from which the recipe makes a sky subtracted untrimmed mosaic automatically The script performs bad pixel masking null debiassing dark subtraction flat field divi sion sky subtraction registration resampling and mosaicking The Notes give more details It is suitable for extended objects up to 3 arcminutes across with UFTI 42 arcseconds with IRCAM and 20 arcminutes with IRIS2 Notes A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 s
150. egion from chopped and nodded mosaic _Ap A beam Positive Extracted positive A beam source and region from chopped and nodded mosaic _Bn B beam Negative Extracted negative B beam source and region from chopped and nodded mosaic _Bp B beam Positive Extracted Positive B beam source and region from chopped and nodded mosaic _cab Combined A amp B beams Combined positive and negative images ex tracted from chopped and nodded mosaic cpc Column Profile Corrected Removed column pattern likely arising from pickup _fb Filled Bad pixels Bad pixels in the mosaic are filled using smooth function of the neighbouring good pixels ul Intensity Polarisation intensity mos Mosaic Final mosaic _P Percentage Percentage polarisation PI Polarisation Intensity _Q Stokes Q Stokes Q parameter _qcab Quality Combining A amp Bbeams Quality map from combining positive and neg ative images extracted from chopped and nod ded mosaic rpc Row Profile Corrected Removed row pattern say due to bias varia tions _scab Smoothed Combined A amp Bbeams_ Block smoothed combined positive and nega tive images extracted from chopped and nod ded mosaic _sp Stokes Parameters Data cube of Stokes parameters _TH THeta Polarisation angle _U Stokes U Stokes U parameter W Wavelength Fabry Perot mosaic from different wavelengths xpr X PRofile Median of each row of the mosaic _ypr Y PRofile Median of each column of the mosaic SUN 232 8 File suffices 36 Deprec
151. elescope offsets alone Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 e The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created by combining normalised object frames using the median at each pixel Registration is performed using the telescope offsets transformed to pixels Once the offsets are determined they are adjusted for the motion of the target so that the final mosaic registers the target not the background stars e There is no resampling merely integer shifts of origin The ephemeris file is specified by environment variable ORAC_EPHEMERIS defaulting to 0RAC_DATA_OUT target_ephem dat 117 MOVING_JITTER_SELF_FLAT_ BASIC SUN 232 8 Recipes e The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping region
152. ensity Q Stokes Q TH Polarisation Angle U Stokes U e The origins of the generated polarisation maps are set to 1 1 The WCS current frame is unchanged e The units are set for the frames with suffices see Output Data P to and TH to degrees SUN 232 8 Recipes 146 POL_ANGLE_NOD_CHOP POL_ANGLE_NOD_CHOP Reduces a chopped and nodded polarimetry observation where waveplate angle iterates at each jitter position Description This script reduces a chopped and nodded single beam polarimetry observation currently just for Michelle data The imaging observation should comprise chopped object frames at the four waveplate angles 0 45 22 5 67 5 degrees for each of a multiple of two pairs of nod positions For each waveplate angle the recipe makes automatically a calibrated untrimmed mosaic The recipe combines the multiple images of the source within each of these mosaics into new frames and uses those four combined frames to calculate automatically calibrated polarisation images and vectors of the source See Output Data for a list of these images It performs a null debiassing creation and propagation of data variance difference the integrations for each AB chop beam pair bad pixel masking difference adjacent nodded pairs registers the frames and forms a mosaic See the Notes for further information Notes A variance array is created for each chop beam first using the read noise and once the
153. ent observation type values and improved the test for the source to be a standard for ESO data More headers are tested for a waveplate angle leading to greater robustness when the polarimetry recipes are released These improvements were based upon experience of more data from a longer range of epochs ORACUT now set for selection of calibrations of INGRID and ESO data Michelle s ORACTIME is now in decimal UT days SUN 232 8 Release Notes V4 1 200 G 3 Global changes The changed Michelle headers are supported Michelle reductions adapted to handle the nod iterator used in observation preparation e UIST uses separate flat calibrations for imaging and spectroscopy The KAPVIEW display recognises a boolean key keyword If set to true 1 it places a key such as the colour table besides the graphic The main changes from a programmer perspective were as follows Much of the ISAAC code applies generally to ESO instruments There are new ESO di rectories for recipes and primitives These directories are ahead of the instrument specific directories in the search path for the recipe and primitive source code ORAC Frame ESO and ORAC Group ESO modules from which instrument specific frame and group meth ods are sub classed Sigma clipping is allowed for certain combination methods during mosaic formation via a new SIGMA argument There is also a new ZERO argument to permit optional zero point shifts between contributing f
154. er of offsets as given by FITS header NOFFSETS minus one is used If neither is available 3 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent USEVAR LOGICAL Whether or not to create and propagate variance arrays 1 Related Recipes POL_ANGLE_JITTER SKY_FLAT_POL SKY_FLAT_POL_ANGLE Implementation Status e The processing engines are from the Starlink packages and CURSA e Uses the Starlink NDF format e History is recorded within the data files SUN 232 8 Recipes 152 POL_EXTENDED e The title of the data is propagated through intermediate files to the mosaics The polarisation maps have new titles as follows using the suffices described in Output Data I Intensity P Polarisation PI Polarised Intensity Q Stokes Q TH Polarisation Angle U Stokes U e The origins of the generated polarisation maps are set to 1 1 The WCS current frame is unchanged e The units are set for the frames with suffices see Output Data P to and TH to degrees 153 POL_JITTER SUN 232 8 Recipes POL_JITTER Reduces an imaging polarimetry observation jittered at each angle Description This script reduces a polarimetry observation with UKIRT imaging data It takes an imaging observation comprising object frames jittered in Right Ascension at the four waveplate angles 0 45 22 5 6
155. er of the cycle a cycle being a set of frames to complete a pass through the recipe The first cycle is 0 DEC_OFFSET_DIFFERENCE F The declination displacement between a nodded pair of frames DIFFERENCE_PAIR B Whether or not to subtract pairs It is normally true every second frame DO_APHOT B Whether or not perform aperture photometry Photom etry is performed once the mosaic is made EXTENDED_ROW I The row number of the frame for EXTENDED _nxm recipes FLAT_DIVIDE Whether or not to apply a flat field JITTER_FIRST This selects the ordering of polarimetry frames If true the jittering occurs at all positions before the waveplate is turned If false all waveplate angles are observed at a given offset JITTER_NUMBER I The number of frames in the jitter MAKE_FLAT Whether or not to make a flat field MAKE_GRAND_MOSAIC Whether or not register the frames and make the full mosaic for EXTENDED_n xm recipes MAKE MOSAIC B Whether or not register the frames and make the mosaic For EXTENDED_n xm recipes it is the time to make a row mosaic MASK_OBJECTS B Whether or not to mask the objects Masking occurs when all the jittered frames in a cycle are available PAIR ORDER B Pair subtraction order true means take second from the first and false means take the first from the second POL_CYCLE_NUMBER B Number of the polarimetry cycle a cycle being a set of frames to complete a pass through the recipe for all waveplate angles The first cycl
156. ered object frames and a dark frame to make a calibrated untrimmed mosaic automatically It performs a null debiassing bad pixel masking dark subtraction flat field creation and division feature detection and matching between object frames and resampling See the for further information Source extraction is performed only on the reduced mosaic and uses EXTRACTOR The results appear in 0RAC_DATA_OUT catalogue_ lt group_number gt txt No zero point or airmass corrections are applied to the instrumental magnitudes This recipe works well for faint sources and for moderately crowded fields Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 The bad pixel mask applied is 0RAC_DATA_CAL bpm For INGRID the pre and post exposure images are subtracted A non linearity correction is then applied e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The fla
157. eries of high level instructions such as make a mosaic or divide by a flat that reduces an observation comprising one or more data frames The implementation of each of these instructions is through a Perl script called a primitive which calls Starlink packages such as CCDPACK and KAPPA to actually do the processing of the bulk data This document describes how to use ORAC DR software on Starlink to reduce data from the UKIRT imaging instruments UFTI UIST IRCAM and Michelle the AAT imaging instrument IRIS2 the ISAAC and NACO instruments on the Very Large Telescope VLT NIRI from Magellan from Gemini and INGRID from the Isaac Newton Group on La Palma It outlines the various algorithms used in the recipes and includes detailed recipe documentation in the appendix Besides the standard reduction recipes this manual describes how you can customise recipes to suit your preferences and how to correct errors in the headers of your data frames There are complementary documents SUN 236 describes the ORAC DR for spectroscopy from CGS4 Michelle and UIST SUN 246 describes the ORAC DR for integral field spectroscopy from UIST and SUN 231 addresses the reduction of SCUBA data with ORAC DR Those wishing wishing to write their own recipes from scratch or wanting to apply ORAC DR to new instruments should consult SUN 233 2 Using the pipeline 2 1 Setting up ORAC DR Before you can run the pipeline you have to tell
158. ervation comprising jittered object frames and a dark frame to make a calibrated untrimmed mosaic automatically It performs a null debiassing bad pixel masking dark subtraction flat field creation flat field division integer shifts of origin to register and mosaicking See the Notes for further information This recipe aims to keep pace with the pipeline s incoming data and is intended for faint sources and for moderately crowded fields Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 e The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created by combining normalised object frames using the clipped median at each pixel Registration is performed using the telescope offsets transformed to pixels e There is no resampling merely integer shifts of origin The recipe mak
159. ery stable sky since only one sky frame is observed at the start of the observation and a region of sky devoid of objects to avoid holes appearing in the subtracted target frames _SUBTRACT_SKY_SKY_AND_JITTER_ Another form of sky subtraction is to remove a representative sky level This benefits imaging of extended sources whose scale exceeds the dither pattern or even the detector s field of view The normal procedure is to alternate between dithered integrations on target and a region of sky The representative statistic is a multiply clipped mean at 2 2 5 3 then 3 standard deviations which effectively gives the mode and so is not biased by resolved sources At present the CHOP_SKY_JITTER and EXTENDED_n xmjrecipes take the average of the modes of bracketted sky frames For offline processing it would be possible to fit a spline say to the modes and provide a better subtraction Under normal conditions where the sky level is not varying rapidly or suddenly because of cirrus the algorithm works well especially over longer integrations _FORM_SKY_LEVELS_ NORMALISE_TO_MODE_EXTENDED_ _CLIPPED_STATS_ _SUBTRACT_SKY_CHOP_SKY_ ESO _SUBTRACT_SKY_CHOP_SKY_ _SUBTRACT_SKY_EXTENDED_ 3 6 1 Polarimetry Extraction and Sky Subtraction The polarimetry recipes are designed to work with a Wollaston prism This divides the signal into four partitions These are ordinary and extraordinary beams usually abbreviated to e and o beams for the
160. es lt m gt lt date gt _ lt group_number gt _ lt suffix gt each with a differ ent suffix for the each parameter The suffices are SUN 232 8 Recipes 162 POL_QU_FIRST_NOD_CHOP I intensity P percentage polarisation PI polarisation intensity Q Stokes Q TH polarisation angle U Stokes U e A FITS binary table catalogue of the binned and culled polarisation data called lt m gt lt date gt _ lt group_number gt _1 FIT For each point it tabulates the x y co ordinates the total intensity the Stokes parameters the percentage polarisation the polarisation angle and intensity There are additional columns giving the standard deviation on each of the tabulated values excluding the co ordinates Likewise lt m gt lt date gt _ lt group_number gt _al1 FIT and lt m gt lt date gt _ lt group_number gt _bin FIT store the full and binned catalogues re spectively Parameters NUMBER INTEGER The number of frames in the nod pattern If absent the number of offsets as given by header NOFFSETS minus one is used If neither is available 4 is used An error state arises if the number of jittered frames is fewer than 4 and not a multiple of 4 USEVAR LOGICAL Whether or not to create and propagate variance arrays 1 Related Recipes POL_NOD_CHOP POL_ANGLE_NOD_CHOP NOD_CHOP_APHOT Implementation Status The processing engines are from the Starlink packages FIGARO and CURSA Uses the Starlink NDF format and multi N
161. es a Quadrant Jitter observation without object masking Description This script reduces a quadrant jitter photometry observation with near infrared imaging data It takes an imaging observation comprising one or more series of four object frames where the target is approximately centred in each quadrant and a dark frame to make a calibrated untrimmed mosaic automatically It performs bad pixel masking null debiassing dark subtraction flat field creation and division feature detection and matching between object frames and resampling See the for further information This recipe is suitable for faint objects or objects within a comparatively bright core embedded in faint extended emission e g a quasar or extended objects less than 45 arcseconds across with UFTI 10 arcseconds with IRCAM and 2 arcminutes with IRIS2 If there are other objects of comparable brightness to the principal target in other quadrants they will introduce artifacts into the flat field Use QUADRANT_JITTER for those Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 The bad pixel mask a
162. es the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of jittered frames the recipe creates a mosaic which is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic SUN 232 8 Recipes 96 JITTER_SELF_FLAT_BASIC e Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data e The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix e A mosaic for each cycle of jittered frames in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming formatlis slightly different for some non UKIRT instruments e The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt
163. esent this option is currently disabled by default The easiest way to switch it on is to change the the default value of the SKYREG argument primitive_GENERATE_OFFSETS_ to 1 See Section f for generic instructions to make a private_GENERATE_OFFSETS_ NACO has a tiny plate scale even with adaptive optics the tolerances minimum number of pixels and the percentile threshold searching for fiducial sources are increased and by default the sky registration is enabled NACO _GENERATE_OFFSETS_ 3 7 1 Moving Targets For a moving target it is possible to permit the telescope to track at sidereal rate and adjust the telescope offsets for the motion of a slowly moving target i e one that stays within the field within an observation group Registration uses the revised offsets and in the mosaic the stars trail while the object does not and so can be seen and measured more easily At present the ephemeris is via a pre prepared text file given by environment variable SUN 232 8 Features of the Primitives 18 ORAC_EPHEMERIS if defined otherwise 0RAC_DATA_OUT target_ephemeris dat See one of the moving target recipes say MOVING_JITTER_SELF_FLAT for more details Once the ephemeris is available as a web service the file could become merely a backup this would automate the process and so the observer would not have to prepare the file at altitude just before the epoch of observation _ADJUST_OFFSETS_TO_MOVING_TARGET_ 3 7 2 Polari
164. essary Flat field creation now uses an unweighted median to give approximately equal weighting to the contributing frames The previous version of was supposed to weight the values but had bugs The corrected task weights by the data value in the absence of a variance array assuming pure Poisson statistics which is in appropriate for infra red data The unweighted median gives similar results to earlier ORAC DR versions There is a beneficial exception where the earlier MAKEFLAT biassed towards certain contributing frames and the unweighted median gives a more equitable division 207 J 3 Global changes SUN 232 8 Release Notes V3 0 3 An improved option for registration is available although it is not the default It uses the WCS to only compare sources in the overlap regions and permits a match using a single source provided it is within 12 pixels of the nominal WCS position For moving target registration and the ephemeris file a bug affecting object names con taining spaces is fixed Better formatting of output with blank lines to block related output and some of the commentary contain more details The historical and unnecessary Orac says prefix was removed from the commentary The nearest neighbour registration immediately prior to forming a mosaic had assumed that the brightest object with identification number 1 would be present in all the offset files In rare cases this may not be true For instance if the centred t
165. ethod registrations has been fixed The y offset had the wrong sign Allow for a special case in the mosaicking registration when the nearest neighbour method is used to align the various images and an automatic multiple object registration was found It was possible not to find a common object identifier in all the fields when the target is a low surface brightness galaxy While this is still possible it is far less likely than before The IRCAM saturation level was refined upwards to 20000 or 33000 if header SPD_GAIN is Deepwe11 SPD_GAIN is created by the recipe when it is absent based upon the value of the detector bias The message concerning an AST SKY Frame creation which could be confused with a data frame of blank sky has been clarified The same script allows for a missing CROTA2 header in old data when inserting world co ordinate system headers Various minor improvements and corrections to the documentation such as correcting the former prefix for UFTI mosaics in the reference section and excluding references to IRCAM in the FP recipes SUN 232 8 Release Notes V2 0 1 210 L Release Notes V2 0 1 The major changes are the move to generic recipes and the introduction of many new recipes especially for polarimetry and Fabry Perot data L 1 New recipes CHOP_SKY_JITTER Reduction of alternating sky target jitters for extended objects of size comparable to the detector s field of view CHOP_SKY_JITTER_BASI
166. except for the flat fielded _ f suffix frames e Sub arrays are supported Output Data e The resultant mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the in strument s group prefix e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming format is slightly different for some non UKIRT instruments Parameters NUMBER INTEGER The number of frames in the jitter pattern If this is not set the number of offsets as given by FITS header NOFFSETS minus one is used If neither is available 5 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes BRIGHT_POINT_SOURCE_APHOT JITTER_SELF_FLAT SKY_FLAT SKY_FLAT MASKED Implementation Status e The processing engines are from the Starlink packages and e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter 53 BRIGHT_POINT_SOURCE_APHOT SUN 232 8 Recipes BRIGHT_POINT_SOURCE_APHOT Reduces a bright point source photometry observation and performs aperture photometry Description This
167. eywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 Output Data e The corrected frame in lt i gt lt date gt _ lt obs_number gt _raw where lt i gt is prefix For IRIS2 the corrected frame is in lt date gt lt obs_number gt where lt date gt is in the form ddmmn If the file already exists it s only updated Implementation Status e The processing engines are from the Starlink package KAPPA e Uses the Starlink NDF format e History is recorded within the data files SUN 232 8 Recipes 50 ARRAY_TESTS ARRAY TESTS Calculates the readout noises and dark current for UFTI Description This script calculates for UFTI the NDSTARE readout noise and the dark current from a series of four engineering frames taken with the sequence called array_tests The results are compared with the nominal values and you are notified whether or not the values obtained are within limits At UKIRT the results are also logged to an engineering file for archival purposes Notes e Intermediate frames are deleted e The engineering log contains the UT date and time the NDSTARE readout noise and the dark current The results are normally appended to the log If for some reason it does not exist a new log is created containing the column headings e Multiple array tests are permitted A new set of
168. f the initial processing SUN 232 8 Instrument Recipe Notes 190 E 10 UIST E 10 There is no ARRAY_TESTS recipe Instead there are DARK_AND_BPM and MEASURE_READNOISE There are JITTER_SELF_FLAT variants with a higher registration completeness 0 5 from 0 4 giving purer registration but may rely on the telescope offsets more often Measurement of the full array statistics avoids the outer 5 border in order to avoid aberrant pixels which can still bias the clipped mean Raw polarimetric data are flipped along the second axis to counter a bug in POLPACK computing vector orientations for left handed co ordinates 191 SUN 232 8 Internal Headers F Internal Headers E1 Translated Headers The ORAC DR infrastructure translates instrument metadata stored in FITS headers into inter nal headers An internal header offers a common name meaning and units independent of the instrument thereby makes most recipe code portable between instruments and in creases code reuse a major theme of ORAC DR The internal headers are accessed through the ORAC Frame uhdr and ORAC Group uhdr methods see Frame headers in SUN 233 Below is a list of these translated internal headers and their meanings and units Here are some notes pertaining to the table In a primitive these header names have an ORAC_ prefix for example ORAC_DEC_SCALE e The abbreviations for data type are B boolean F floating point I integer and S stri
169. filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters NUMBER INTEGER The number of frames in the jitter pattern If not supplied the number of offsets as given by FITS header NOFFSETS minus one is used If neither is available 9 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes ITTER SELF _FLAT JITTER SELF FLAT APHOT ITTER_SELF_FLAT NO_MASK JITTER SELF FLAT TELE MOVING _JITTER SELF FLAT BASIC QUADRANT_JITTER_ BASIC Implementation Status e The processing engines are from the Starlink packages CCDPACK FIGARO e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter Deprecated Variants JITTER5_SELF_FLAT_BASIC JITTER9_SELF_FLAT_BASIC 97 JITTER_SELF_FLAT_CATALOGUE SUN 232 8 Recipes JITTER_SELF_FLAT_CATALOGUE Reduces a standard jitter photometry observation using object masking and produces a catalogue of all sources in the field Description This script reduces a standard jitter photometry observation with near infrared imaging data It takes an imaging observation comprising jitt
170. g the exposure time of a single frame 57 BRIGHT_POINT_SOURCE_CATALOGUE SUN 232 8 Recipes e For each cycle of jittered frames the recipe creates a mosaic which is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass and end UT headers areupdated to match that of the last observed frame contributing to the mosaic e The catalogue includes the right ascension and declination instrumental apparent magnitude calculated as 2 5 x log counts and the error in the magnitude e Intermediate frames are deleted except for the flat fielded _ff suffix frames e Sub arrays are supported Output Data e The resultant mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the in strument s group prefix e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming formatlis slightly different for some non UKIRT instruments e The catalogue in catalogue_ lt group_number gt txt Parameters NUMBER INTEGER The number of frames in the jitter pattern If this is not set the number of offsets as given by FITS header NOFFSETS minus one is used If neither is available 5 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS wil
171. g the signal to noise of Mid infra red Data The Michelle electronics can leave an uneven mosaic with vertical banding from bias variations and horizontal ripple patterns from electronic pickup Therefore Michelle NOD_CHOP recipes subtract the median along each column of the mosaic then subtracts the median along each row This cleaning aids the visibility of faint sources In the mid infra red the sky signal is vastly greater than the signal than even the brightest sources While the nodding removes the bulk of the sky signal the sky noise remains still swamping the signal from a faint source Integrating over many nod chop cycles is needed and the real time display of ORAC DR does permit interactive review of the signal to noise in GAIA so observers can curtail data collection when the required contrast is achieved Averaging the positive and negative signals and neighbourhoods into a combined signal cf Section 3 11 only helps by a factor of two or V2 for a single positive and negative pair Recipe NOD_CHOP_FAINT smooths the combined quadrant with a 4 by 4 pixel neighbourhood running average filter to help reveal faint sources Note that the source centroids are not used for registration as the signal is usually too weak SUN 232 8 Features of the Primitives 22 While smoothing reveals the sources it is not sufficient There is also a confusion issue The chopping can bring positive and negative sources actually located beyond the f
172. ges KAPPA and CCDPACK e Uses the Starlink NDF format e History is recorded within the data files e Error propagation is not used 113 MOVING_JITTER_SELF_FLAT SUN 232 8 Recipes MOVING_JITTER_SELF_FLAT Reduces a standard jitter photometry observation of a moving target using object masking Description This script reduces a standard jitter photometry observation with UKIRT imaging data It takes an observation comprising jittered object frames of a moving target and a dark frame to make automatically a calibrated untrimmed mosaic in the reference frame of the target It performs a null debiassing bad pixel masking dark subtraction flat field creation and division feature detection and matching between object frames and resampling See the FNotes for further information Registration is adjusted to track the motion of the moving target using ephemeris data stored in file target_ephem dat See Ephemeris file Format for details of this file s format This recipe works well for faint moving sources and in moderately crowded fields It should not be used for frames where the telescope guided on the moving object In that case reduction should be performed by JITTER_SELF_FLAT_TELE which registers using the telescope offsets alone Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered
173. h UFTI 10 arcseconds with IRCAM and 2 arcminutes with IRIS2 The object need not be isolated as the recipe masks objects within the other quadrants and hence does not introduce significant artifacts into the flat field For isolated objects use or where speed is critical use ADART IEIS instead Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAM3 e The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created iteratively First the quadrant containing the object is masked in each object frame Second an approximate flat field is created by combining the normalised and masked object frames using the clipped median at each pixel This flat field is applied to the object frames Sources within the flat fielded frames are detected and masked in the dark subtracted frames The second stage is repeated but
174. hanges are the addition of recipes for Michelle nodded and chopped observations and a rearranged directory structure for new and multi mode instruments J 1 New recipes ARRAY_TESTS This is for Michelle It derives a mean bias file and calculates and reports the read noise using the latter pair of minimum exposure frames in the array tests sequence Both the bias frame and readnoise are recorded in the calibration system Reduction of nodded and chopped data specifically for Michelle Each recipe cycle comprises four frames located at two nod positions and the A and B beams The individual beams are differenced and then so are successive pairs of observations The differenced images are then combined into a mosaic On successive cycles the mosaics are co added SUN 232 8 Release Notes V3 0 3 206 J 2 Modified recipes As NOD_CHOP but it also extracts registers and combines the two positive and two negative images of the source Then it performs 3 arcsecond aperture photometry on the combined image logging to a small text list It compares the object name against a file of N Q standards to determine the zero point No extinction correciton is currently applied as the coefficients have yet to be determined MOVING_NOD_CHOP As NOD_CHOP but mosaic registration is adjusted to track the motion of an asteroid or compact comet using ephemeris data Reduces chopped and nodded poliarmetry data of point and small lt 10 arcsec extend
175. he following order e the objectname which may contain embedded spaces e the motion in the plane of the sky in arcsec second for right ascension then declina tion Note that the right ascension motion is the change in right ascension multiplied by the cosine of the declination The format will change to include UT and possibly date Output Data e The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix e A mosaic for each cycle of object frames in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 e The differenced pairs in lt i gt lt date gt _ lt obs_number gt _dp where lt i gt is the frame Parameters NUMBER INTEGER The number of frames in the nod pattern If absent the number of offsets as given by header NOFFSETS minus one is used If neither is available 4 is used An error state arises if the number of jittered frames is fewer than 4 and not a multiple of 4 USEVAR LOGICAL Whether or not to create and propagate variance arrays 1 Related Recipes NOD_CHOPI MOVING_JITTER SELF_FLAT MOVING_QUADRANT_JITTER Implementation Status e The processing engines are from the Starlink packages and e Uses the Starlink NDF format and multi NDF HDS container files e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic
176. he mode less five times the clipped standard deviation While a positive threshold looks attractive small negative values while appearing non physical can arise through noise Therefore to avoid a bias mainly in the J band a further constraint is that the lower limit lies in the range 100 to 1 _SUBTRACT_DARK_ lt instrument gt _GET_SATURATION_LEVEL_ Recipes issue warnings if the dark subtracted frame s mode is negative allowing for the error in the mode It aborts with an error message if the modal dark subtracted signal is more than one standard deviation negative These states usually arise because of an aberrant dark Creating a bad pixel mask The easiest way to create your own bad pixel mask for use with the calibration system is to run the MAKE_BPM recipe on a long exposure dark at least 20 seconds integration It is possible to change the symmetric o clipping bounds in the recipe see primitive _MAKE_BPM_BY_SIGMA_THRESHOLDING_ You can tailor this primitive if you want more control say to have asymmetric rejection or more sophisticated definitions _MAKE_BPM_BY_SIGMA_THRESHOLDING_ For better results use the average of long dark frames taken across two or three nights First produce QUICK_LOOK versions of the long exposure dark to flatten the NDF structure or convert the FITS file Flag all pixels that are 5 standard deviations 0 above and below the 3 7 clipped mean of the dark as bad then multiply the resu
177. he mosaic is that of one individual frame The recipes assume that you have used their corresponding execs or sequences and hence have not changed the exposure time during a jitter The exposure time header EXP_TIME UFTI UIST Michelle EXPOSED IRIS2 EXPTIME Classic Cam INGRID ISAAC NACO NIRI or DEXPTIME IRCAM is propagated from the first frame to the mosaic Where multiple frames combined to create a mosaic pixel the signal to noise ratio corresponds to the combined integration time The integration time keyword INT_TIME UFTI TOTALEXP IRIS2 or EXPOSED IRCAM is the number of coadds times the exposure time per coadd Depending on the recipe the mosaic may be trimmed to the dimensions of a raw frame Mosaicking removes virtually all the bad pixels for standard stars where the jitter offsets are small A mosaic forms for each cycle of the recipe e g all four frames in aQUADRANT_JITTER For multiple cycles an integrated grand mosaic forms of improving signal to noise To avoid the build up of bad pixels from cosmic rays bad pixels are interpolated before the addition This may result in some strange stripes in the top left corner of UFTI frames where no interpolation can occur Those pixels are bad in all frames and should be ignored The exposure time header for the integrating mosaic is the sum of the exposure times of the contributing mosaics Again the signal is not divided by the exposure time _MAKE_MOS
178. he sources then collapses the frame along its rows to form a profile whose clipped mean is subtracted The resultant profile reflects the bias variations The recipe subtracts this profile from each column of the flat fielded frame 93 JITTER_SELF_FLAT_APHOT SUN 232 8 Recipes The field distortion of ISAAC is corrected in the target frames using the mappings documented on the ISAAC problems web page Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects the script resorts to using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time the exposure time of a single frame For each cycle of jittered frames the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to
179. headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created iteratively First an approximate flat field is created by combining normalised sky frames using the median at each pixel This flat field is applied to the sky frames Sources within the flat fielded frames are detected and masked in the dark subtracted frames The first stage is repeated but applied to the masked frames to create the final flat field Intermediate frames are deleted Sub arrays are supported Output Data There are flats for each waveplate angle and also for 90 and 135 degrees made by copying the original flat frame This is to permit both flats made at each angle SKY_FLAT_POL_ANGLE or with the angles combined as here Each flat is called flat_ lt filter gt _pol lt waveplate_angle gt _ lt group_number gt The 185 SKY_FLAT_POL SUN 232 8 Recipes
180. here lt m gt is the instrument s group prefix e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming formatlis slightly different for some non UKIRT instruments e Results tabulation to 0RAC_DATA_OUT aphot_results txt Parameters NUMBER INTEGER The number of frames in the jitter pattern If this is not set the number of offsets as given by FITS header NOFFSETS minus one is used If neither is available 5 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes BRIGHT_POINT_SOURCE BRIGHT_POINT_SOURCE_APHOT ITTER_SELF_FLAT SKY_FLAT SKY_FLAT_MASKED Implementation Status e The processing engines are from the Starlink packages and e Uses the Starlink NDF format SUN 232 8 Recipes 60 BRIGHT_POINT_SOURCE_NCOLOUR_APHOT e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter 61 BRIGHT_POINT_SOURCE_TELE SUN 232 8 Recipes BRIGHT_POINT_SOURCE_TELE Reduces a bright point source photometry observation using telescope offsets for registration Description This script reduces a b
181. his expression are either read from the headers or taken verbatim from an IRAF script cited in the user manual CLASSICCAM _CORRECT_NONLINEARITY_ IRCAM _CORRECT_NONLINEARITY_ INGRID _CORRECT_NONLINEARITY_PRE_POST_ 3 1 4 Electronic Ghosting For ISAAC there is a correction applied for electronic ghosting The ghosts consist of an additional signal which on one row is proportional to the sum of the intensity along this row and the row 512 rows away according to the ISAAC Data Reduction Guide Recipes combine the two halves adding the bottom half to the top and vice versa collapse this image along rows scale by the documented correction factor of 1 35E 5 to form the ghost flux per row which is then subtracted from the original image ISAAC _REMOVE_ELECTRONIC_GHOSTING_ 3 1 5 Bad pixels The recipes apply a predetermined bad pixel mask with the aim of removing the bulk of hot and cold pixels The approximate percentages of pixels masked for each instrument is as follows Classic Camil 1 INGRID 1 0 IRCAM 0 1 IRIS2 0 1 ISAAC 0 4 UFTI 0 7 and VISTO The Michelle bad pixel mask is time dependent initially 12 aberrant pixels were identified but when the new detector returned on UKIRT in 2004 the mask merely ignored the top sixth of the array For the test data available NACO had large numbers of very noisy pixels to the foot and sides of the detector hence the default bad pixel mask has 9 9 bad pixels
182. hs the latter to find and report the broadband N equivalent magnitude and flux for narrowband N filters Extinctions are now included The recipe now determines the baseshift calibration which measures the displacement of the source images from the nominal locations e ARRAY_TESTS For Michelle the estimated readout noise is no longer reported 13 Global changes The main changes from a user perspective were as follows Undefined or nonsense headers used by the recipes are replaced internally to pipeline but not in the physical files This usually permits the pipeline to complete Recipes report the names of modified headers for manual checking and correction of the raw data e Further sanity checks are included for Michelle The waveform header is validated and incorrect combinations reported The mean data value must lie between 25000 and 48000 counts to prevent a warning message from appearing Recipes make an on the fly night log in 0RAC_DATA_OUT Night logs contain the group number The file name has an _im suffix for Michelle The default UFTI gain reflects the gain s changing values arising from the use of a different controller NDF blank titles are removed The UFTI bad pixel mask has changed now having 0 3 more bad pixels Centroiding is protected against data comprising all bad values e The hybrid registration has a further improvement for a special case 205 SUN 232 8 Release Notes V3 0 3 e The ne
183. ices see Output Data P to and TH to degrees Error propagation is controlled by the USEVAR parameter 149 POL_EXTENDED SUN 232 8 Recipes POL_EXTENDED Reduces an imaging polarimetry observation of an extended source Description This script reduces a polarimetry observation with UKIRT imaging data It takes an imaging observation comprising alternating object and sky frames at the four waveplate angles 0 45 22 5 67 5 degrees in turn then jittered to at least three positions and a dark frame to make calibrated polarisation images and vectors automatically See Output Data for a list of these images It performs a null debiassing bad pixel masking dark subtraction and flat field division on all frames Next the sections of the target frame representing the e and o beam target regions are extracted and sky subtracted The sky levels are determined from the two corresponding regions for each beam in the following sky frame The resultant frames undergo registration and resampling to form a mosaic for each waveplate angle and beam Once all eight mosaics are formed they are registered and resampled and then combined to form the various polarisation images The polarisation data are binned and noisy data excluded from a final catalogue of vectors See the Notes for details This recipe is intended for extended sources whose sizes are more than about 35 arcseconds respectively for UFTI or 8 arcseconds for IRCAM
184. ied is 0RAC_DATA_CAL bpm Registration is performed using the telescope offsets transformed to pixels e The resampling applies integer shifts of origin There is no rotation to align the Cartesian axes with the cardinal directions e The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame 131 NOD_CHOP_FAINT SUN 232 8 Recipes For each cycle of object frames the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass and end UT headers are updated to match that of the last observed frame contributing to the mosaic Pickup and bias variation patterns evident as ripples in the rows or bands in the columns respectively are removed by subtracting the median along each column or row from the pixels in that column or row The combined source image is made by taking symmetrical areas about the expected position of each source derived from the chop throw and the nod separations corrected for a shift of the base location from its nominal positio
185. iers about the frame such as whether it is of a target or sky They use header information and membership index within a group The names of steering headers should be longer than eight characters to avoid confusion with FITS keywords Most steering headers are per frame and are accessed by ORAC Frame uhdr see headers in SUN 233 Steering headers which must persist between frames such as those which define groups of related raw or processed frames like differenced chopped pairs must be stored in the group internal headers accessed by ORAC Group uhdr While programmers can create their own steering headers as needed it is silly to invent new names for ones which already exist and are accessed by many primitives which the programmers would then not be able to use directly Here is a list of the common steering headers used in the imaging recipes Not all headers SUN 232 8 Internal Headers 194 F2 Steering Headers are pertinent to all recipes The headers used exclusively by specialist recipes such as for Fabry Perot or nod chop in a scan mode are not listed below The abbreviations for data type are B boolean 1 for true 0 for false I integer F floating point and S string Note that some of the timing headers may in fact switch on for the same frame 195 F2 Steering Headers SUN 232 8 Internal Headers Name Type Meaning CREATE_CATALOGUE B Whether or not to create an object catalogue CYCLE_NUMBER I Numb
186. ifted mosaic is given by F1 F2 F4 F3 F5 F6 F8 F7 Flatfield where Fn is the bad pixel masked and dark subtracted frame n In practice the flat field is applied to each differenced pair such as F4 F3 when the pair becomes available rather than waiting until all eight frames have been observed Finally the recipe registers all the wavelength mosaics spatially and forms a untrimmed mosaic combined using the median to reduce stellar artifacts Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist SUN 232 8 Recipes 84 FP_JITTER The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used You should use 5SKY_FLAT_FP to make the flat field Registration is performed using the telescope offsets transformed to pixels There is no resampling merely integer shifts of origin For each set of eight the recipe creates a wavelength mosaic For each cycle of spatial positions the wavelength mosaics are registered to form a spatial mosaic For repeat cycles the spatial mosaic is then added into a master mosaic of improving signal to noise The exposure time is a
187. iminaries There are a few operations applied to all frames First the raw frame may be displayed general _DISPLAY_FRAME_IMAGE_ Recipes remove any AXIS and blank TITLE components the latter to preserve the object name when NDFs are exported to FITS Next they set the origin of the frame so that frame pixels retain the detector pixel indices It then becomes possible to use a full sized bad pixel mask or flat field on any subset of a detector s pixel grid _REMOVE_AXES_ REMOVE_BLANK_TITLE_ SET_ORIGIN_ Then recipes determine the displacements of the reference pixel with respect to the centre of the frame and stores the displacements in the referenceoffset calibration system The reference pixel is where a star would be placed for photometry or the centre of a chopped and nodded pattern _SET_REFERENCE_PIXEL_OFFSET_ GET_FRAME_CENTRE_ The next step is to switch on history recording It is recommended to leave this enabled since it provides a record of the processing steps of your final mosaics Otherwise the pipeline becomes something of a black box Use the KAPPA command hislist to list the history records _TURN_ON_HISTORY_ For Michelle there is a validation check of the waveform used comparing the waveform name given in the headers with other metadata and recipes issue a warning if there is an inconsistency Also the data range is validated to be between 25000 48000 MICHELLE _CHECK_WAVEFORM_ MICHELLE _VALIDATE_RAW_DATA_ Fo
188. inal quadrant to within it There is an option of the COMBINE_CHOPPED_SOURCE_ primitive called by recipe NOD_CHOP recipes which attempts to clarify which sources are actually present in the quadrant by forming a quality map Each quality pixel is the sum of the four corresponding pixel values divided by their absolute values after changing sign for the quadrants containing the negative images In the map 4 indicates that a pixel had positive contributions from the positive quadrants and negative signals from the negative quadrants A quality of 4 strongly implies that the signal is really at the sky location indicated Thus it helps to discriminate from sources which have been chopped into view for which there are no positive or negative counterparts values 2 or noise 0 2 Around the sky which should be near zero noise randomises the quality measurement therefore smoothing should be used in conjunction with the quality map COMBINE_CHOPPED_SOURCE_ _REMOVE_COLUMN_ROW_STRUCTURE_ _REMOVE_COLUMN_ROW_STRUCTURE_SCAN_ FIND_SOURCE_CENTROID_ _GET_CHOP_OFFSETS_ GET_FRAME CENTRE To create a quality map at each cycle you should set argument QMAP 1 and SMOOTH gt 1 For example in NOD_CHOP_FAINT append QMAP 1 to the line _COMBINE_CHOPPED_SOURCE_ METHOD median CENTROID 0 SMOOTH 4 CLEAN 1 3 13 Catalogue Generation The recipes with a CATALOGUE suffix create a source catalogue from the mosaic using EXTRACTOR The catalogue inc
189. ing common point sources in the overlap regions If the recipe cannot identify sufficient common objects it matches the centroid of the central source If this fails the script resorts to using the telescope offsets transformed to pixels Once the offsets are determined they are adjusted for the motion of the target so that the final mosaic registers the target not the background stars The ephemeris file is specified by environment variable ORAC_EPHEMERIS defaulting to 0RAC_DATA_OUT target_ephem dat The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame Thus the noise will be greater in the peripheral areas having received less exposure time The full signal will be in the central ninth containing the main object The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of four the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed fram
190. inned and noisy data excluded from a final catalogue of vectors See the Notes for details This recipe works well for point sources and for extended sources whose sizes in Right Ascension and Declination are less than about 35 and 15 arcseconds respectively for UFTI or 9 and 4 arcseconds for IRCAM Objects which would appear in both the target and sky regions i e Declination extents south of the centre larger than 35 arcseconds UFTT or 8 arcseconds IRCAM should use recipe POL_EXTENDED for best results Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 e Data errors are propagated through all processing steps The initial values are found by applying the nominal ADU conversion and read noise e The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used You should use SKY_ FLAT POL or SKY FLAT POL _ANGLE to ma
191. instrument names are changed to IRCAMS3 The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created by combining normalised object frames using the clipped median at each pixel Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects the script resorts to using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of jittered frames the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding hea
192. int source photom etry observation BRIGHT_POINT_SOURCE_NCOLOUR_APHOT Reduces a multi colour bright point source photometry observation and performs aperture photometry BRIGHT_POINT_ SOURCE CATALOGUE Reduces a bright point source photometry obser vation producing a catalogue of all sources in the field BRIGHT_POINT SOURCE _TELE Reduces a bright point source photometry observation using telescope offsets for registration BRIGHT_POINT_SOURCE_TELE_APHOT Reduces a bright point source photometry obser vation using telescope offsets for registration and performs aperture photometry DIFFERENCE_STATS Calculates statistics for Michelle darks in a pairwise manner JITTER_SELF_FLAT_CATALOGUE Reduces a standard jitter photometry observation using object masking and produces a catalogue of all sources in the field JITTER _SELF_FLAT_NCOLOUR_APHOT Reduces a multi colour standard jitter photome try observation using object masking and performs aperture photometry LAMP_FLAT Creates and files imaging flat fields derived from a calibration lamp for ISAAC and NACO POL_QU_FIRST_NOD_CHOP Reduces a Michelle chopped and nodded polarimetry obser vation where waveplate angle iterates in pairs at each jitter position Its purpose is to form the Q U Stokes parameters as quickly as possible hence offer more accurate polarimetry than integrating at four waveplate angles before nodding G 2 Modified recipes e
193. is flat which produces the flat field frames for mosaicking Systematic errors in the sky a major uncertainty in infra red point source photometry are also reduced significantly by this algorithm EXTRACTOR on occasions underestimate the sizes of objects so there is an enlargement factor from 1 0 1 5 defaulting to 1 0 applied in primitive_MAKE_OBJECTS_MASK_ If at high contrast you find residual dark rings in your flat fielded images try adjusting the ENLARGE argument either in the recipe or the primitive default See Section and in particular Section on how to tailor primitives 3 4 Field distortion Correction The ISAAC instrument exhibits field distortion amounting to 2 5 pixels in the corners of the detector If not corrected mosaics with large dithers have multiple images in the overlap regions Therefore recipes resample the image applying the published polynomial mapping This correction also improves the registration The sky co ordinates are also corrected for the distortion ISAAC _DEFINE_DISTORTION_TRANSFORMATION_ ISAAC _APPLY_DISTORTION_TRANSFORMATION_ 3 5 Bias variation The bias in the ISAAC short wavelength camera depends upon the detected flux Thus in target frames there is a residual bias not fully corrected by bias subtraction evident as two steepening ramps downwards to rows 1 and 513 An ISAAC variant recipe corrects for this as follows First within a flat fielded frame they locate sources and mask them
194. is recipe subtracts a corresponding dark calibration frame then displays the result Implementation Status e The processing engines are from the Starlink package KAPPA e Uses the Starlink NDF format e History is recorded within the data files 71 DIFFERENCE_STATS SUN 232 8 Recipes DIFFERENCE_STATS Calculates statistics for Michelle darks in a pairwise manner Description This recipe is meant to be used in an array tests suite It takes a group of observations subtracts successive pairs then calculates and reports the standard deviation for each resulting differenced frame in a central 200 pixel square region and in the four channels of the detector It finally provides the average of these statistics for the group as a whole Notes e The frames must be in the same group Parameters NUMBER INTEGER The number of frames in the group The default is used if the number of frames is fewer than 2 or is not even 20 Implementation Status e The processing engines are from the Starlink package KAPPA e Uses the Starlink NDF format SUN 232 8 Recipes 72 EXTENDED_3x3 EXTENDED_3x3 Extended source standard reduction using interpolated sky subtraction Description This recipe reduces an extended source using near infrared imaging data The data comprise alternating blank sky and target frames commencing and ending with a blank sky The target frames are arranged in an overlapping 30 50 grid of 3x3 frames f
195. ived from the number of offsets as given by header NOFFSETS The formula is NOFFSETS 2 1 An error results should NOFFSETS be odd If neither is available 9 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent 65 CHOP_SKY_JITTER SUN 232 8 Recipes USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes CHOP_SKY_JITTER_BASIC EXTENDED_3x3 QUADRANT_JITTER Implementation Status e The processing engines are from the Starlink packages FIGARO and EXTRACTOR e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 66 CHOP_SKY_JITTER_BASIC CHOP_SKY JITTER_BASIC Basic reduction of alternating sky target jitters using interpolated sky subtraction Description This recipe reduces a moderately extended source using near infrared imaging data The data comprise alternating blank sky and target frames commencing and ending with a blank sky Both the sky and target frames are jittered The recipe makes a sky subtracted untrimmed mosaic automatically The script performs bad pixel masking null debiassing dark subtraction flat field divi sion sky subtraction registration using telescop
196. ject fills or nearly fills the frame so sky estimation within the frame is impossible or unreliable but the extended mapping of the target is not required Notes A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 The bad pixel mask applied is 0RAC_DATA_CAL bpm For INGRID the pre and post exposure images are subtracted A non linearity correction is then applied Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is derived from the sky frames as follows The mode sigma clipped mean is used to offset each sky frame s mode to that of the first sky frame The corrected sky frames are combined pixel by pixel using a median of the values in each frame The resultant frame is normalised by its median to form the flat field This frame median is subtracted from the source frames after they have been flat fielded A flat field is created from all the jittered
197. ke the flat fields The target regions are 30 to 70 of the frame width about the Right ascension centre i e roughly centred on the source The current sky limits are 1 to 99 of 143 POL_ANGLE_JITTER SUN 232 8 Recipes the frame width along the Right ascension axis The Declination pixel limits are instrument dependent and are as follows For UFTI o sky 69 264 e sky 320 484 o target 601 764 e target 824 988 For IRCAM o sky 12 52 e sky 67 107 o target 152 192 e target 207 247 The sky subtraction for a beam uses a constant modal sky level from the correspond ing sky region Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects for automatic registration the recipe matches the centroid of central source within an 8 arcsecond box Should that fail for the jittered e and o beam sections the recipe resorts to using the telescope offsets transformed to pixels However the final option for registering the e and o beam mosaics at different waveplate angles uses the beam offsets in arcseconds for the current filter converted to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimme
198. l be absent USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes BRIGHT_POINT_SOURCE_APHOTBRIGHT_POINT_SOURCE ITTER_SELF_FLAT CATALOGUE SKY_FLAT SKY_FLAT_MASKED Implementation Status The processing engines are from the Starlink packages FIGARO and EXTRACTOR Uses the Starlink NDF format History is recorded within the data files The title of the data is propagated through intermediate files to the mosaic Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 58 BRIGHT_POINT_SOURCE_NCOLOUR_APHOT BRIGHT_POINT_SOURCE_NCOLOUR_APHOT Reduces a multi colour bright point source photometry observation and performs aperture photometry Description This recipe reduces a bright standard photometry observation observed through one or more filters For each filter it takes an imaging observation comprising a series of jittered object frames and a dark frame with a predetermined flat field frame to make a calibrated trimmed mosaic automatically This recipe performs a null debiassing bad pixel masking dark subtraction flat field division feature detection and matching between object frames and resampling See the for details Photometry of the point source using a fixed 5 arcsecond aperture is calculated for each jitter frame and the mosaic The results appear in 0RAC_DATA_OUT aphot_results txt in the form of a Starlink small text list The analysis of each
199. le of the data is propagated through the intermediate file to the flat e Error propagation is controlled by the USEVAR parameter 111 MAKE_BPM SUN 232 8 Recipes MAKE_BPM Creates and files abad pixel mask from a long exposure dark Description This recipe reduces a long exposure dark frame observation of infrared imaging data to create a bad pixel mask It files the mask in the mask index file Reduction comprises only thresholding the pixel values about a clipped mean using a multiple of the clipped standard deviation Notes e The dark must have a minimum exposure of 20 seconds e Clipping is at 2 3 3 standard deviations e Bad values are deemed to be those beyond the range of the clipped mean 5 standard deviations e Intermediate frames are deleted e Sub arrays are supported Output Data e The bad pixel mask is called bpm_ lt frame_number gt e The bad pixel mask is filed in ORAC_DATA_0UT index mask Related Recipes DARK_AND_BPM Implementation Status e The processing engines are from the Starlink package KAPPA e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is bpm_ lt frame_number gt e Error propagation is not used SUN 232 8 Recipes 112 MEASURE_READNOISE MEASURE_READNOISE Measures and files the readnoise for UIST from a set of dark frames Description This recipe measures the readnoise for a group of five short exposure UIST DA
200. lescope guided on the moving object In that case reduction should be performed by QUADRANT_JITTER_TELE which registers using the telescope offsets alone Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAM3 The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created iteratively First the quadrant containing the object is masked in each object frame Second an approximate flat field is created by combining the normalised and masked object frames using the clipped median at each pixel This flat field is applied to the object frames Sources within the flat fielded frames are SUN 232 8 Recipes 122 MOVING_QUADRANT_JITTER detected and masked in the dark subtracted frames The second stage is repeated but applied to the masked frames to create the final flat field Registration is performed us
201. lied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created iteratively First an approximate flat field is created by combining normalised object frames using the median at each pixel This flat field is applied to the object frames Sources within the flat fielded frames are detected and masked in the dark subtracted frames The first stage is repeated but applied to the masked frames to create the final flat field For ISAAC residual bias variations along the columns are largely removed from each flat fielded frame The recipe first masks the sources then collapses the frame along its rows to form a profile whose clipped mean is subtracted The resultant profile reflects the bias variations The recipe subtracts this profile from each column of the flat fielded frame 103 JITTER_SELF_FLAT_NCOLOUR_APHOT SUN 232 8 Recipes The field distortion of ISAAC is corrected in the target frames using the mappings documented on the ISAAC problems web page Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects the script resorts to using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no r
202. lso summed and stored in the master mosaic s corresponding header Likewise the end airmass and end UT headers are updated to match that of the last observed frame contributing to the mosaic The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions No mosaic is trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas of the spatial having received less exposure time Each mosaic is not normalised by its exposure time that being the exposure time of a single frame Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data The integrated mosaic in gf lt date gt _ lt group_number gt _mos where lt date gt is the UT date in yyyymmdd format A mosaic for each cycle of eight in gf lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 The individual flat fielded frames in f lt date gt _ lt obs_number gt _ff Parameters NPAIRS INTEGER The number of frame pairs to be differenced It must be a multiple of 2 otherwise 4 is assumed A value of four or more is assumed to indicate sky subtraction 4 NUMBER INTEGER The number of spatial jitter positions For each spatial position there are NPAIRS pairs of frames A value of 1 also dictates that no jittering has occurred To make a master mosaic combining spatial positions NUMBER should be at
203. lting frame by zero so that the resulting bad pixel mask has data values of 0 and bad only You can choose your own thresholds Here is an example using data from two nights of UFTI data and Starlink software oracdr_ufti 20010101 setenv ORAC_DATA_OUT pwd oracdr list 4 4 QUICK_LOOK nodisplay oracdr_ufti 20010102 setenv ORAC_DATA_OUT pwd oracdr list 4 4 QUICK_LOOK nodisplay sf sf sf Sf Sf oe kappa add 20010101_00004_raw 20010102_00004_raw add_darks cmult add_darks 0 5 av_darks stats av_dark clip 3 thresh av_darks av_darks_thresh 49 58 bad bad cmult av_darks_thresh 0 avbpm title UFTI bpm January 20011 In the above example the 3 c clipped mean was 4 27 and the standard deviation was 10 727 resulting in 49 and 58 as the lower and upper thresholds Then you specify the bad pixel mask on the command line oracdr calib mask avbpm UIST has its own slightly different formula see DARK_AND_BPMIfor details UIST _FIND_BAD_PIXELS_ UIST _FILE_BAD_PIXELS_ _FILE_MASK_ 11 SUN 232 8 Features of the Primitives 3 1 6 Data Variance There is optional data variance creation for all instruments By default only the polarimetry and mid infra red NOD_CHOP family of recipes have variance processing enabled To switch on variance calculations for the other recipes is a simple edit of the recipe See Section 4 2 1 for instructions The initial variance is calculated as follows e
204. ludes objects having at least 12 connected pixels above 1 0 7 above sky The catalogue is written in ARK Cluster format with a field ID in column 0 this value is typically zero an object ID in column 1 right ascension in columns 2 3 and 4 declination in columns 5 6 and 7 x and y positions in columns 8 and 9 uncalibrated magnitude in column 10 the error in magnitude in column 11 and a quality flag in column 12 this value is typically zero The magnitudes are given by the expression 2 5 log10 counts per second exposure time As the final mosaic has varying noise characteristics with higher noise regions at the edges the detection limit varies across the mosaic Fainter objects can be detected in the central region than near the edges and corners _CREATE_SOURCE_CATALOGUE_ _GET_CATALOGUE_NAME_ 3 14 eSTAR Integration ORAC DR is also integrated with the eScience Telescopes for Astronomical Research eSTAR project which is designed to automatically detect and follow up on transient astronomical objects using manned and robotic telescopes Using the catalogue generated in Section ORAC DR will automatically send a trigger to the eSTAR network containing a FITS file of the final mosaic and the catalogue This step is only done when an observation is taken as part of an eSTAR project i e there is a RMTAGENT header and its value is ESTAR general _TRIGGER_ESTAR_ SET_REMOTE_AGENT_HEADER_ 23 SUN 232 8 Customising Recipes
205. mat Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 e Data errors are propagated through all processing steps The initial values are found by applying the nominal ADU conversion and read noise The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used You should use SKY_ FLAT POLlor SKY_ FLAT POL_ANGLE to make the flat fields The target regions are 30 to 70 of the frame width about the Right ascension centre i e roughly centred on the source The current sky limits are 1 to 99 of the frame width along the Right ascension axis The Declination pixel limits are instrument dependent and are as follows For UFTI o sky 69 264 e sky 320 484 o target 601 764 e target 824 988 For IRCAM o sky 12 52 e sky 67 107 o target 152 192 e target 207 247 SUN 232 8 Recipes 154 POL_JITTER The sky subtraction for a beam uses a constant modal sky level from the correspond ing sky region Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects for automatic registration the recipe matches the centroid of central sou
206. mbers and the number of offsets in the grouped observation into the headers to assist ORAC DR 2 3 Running the pipeline To run the pipeline you use the oracdr command This has a number of qualifiers described fully in SUN 230 There is online help too enter oracdr h for a list of the options Unlike using ORAC DR at UKIRT you are unlikely to need the looping 1oop option for offline processing as all the data exist Thus the most important qualifiers are 1ist and from which specify the frames to process and the recipe name oracdr from 42 will process frames 20001108_00042 until the end of the night s data assuming the earlier oracdr_ufti command running the recipes given by each frame s header RECIPE keyword More likely is that you provide a list of selected observations The following example oracdr list 41 49 51 59 JITTER_SELF_FLAT processes frames from 41 to 49 inclusive and 51 to 59 inclusive invoking the JITTER_SELF_FLAT recipe and overriding the RECIPE header oracdr list 5 7 23 33 would reduce the frames 5 6 7 23 and 33 This is most likely to be applicable to a series of dark frames There is a hazard with the 1ist option Take care to select a complete set of frames associated with an observation A common error is to include accidently a dark frame not part of the group Check the log in the raw data directory it has file extension nightlog If you do not have a log it is
207. mediate files to the mosaic e Error propagation is controlled by the USEVAR parameter 135 NOD_SELF_FLAT_NO_MASK SUN 232 8 Recipes NOD_SELF_FLAT_NO_MASK Reduces a nod jitter observation Description This script reduces a nod jitter observation with UKIRT imaging data It takes an imaging observation comprising a multiple of four object frames and a dark frame to make a calibrated untrimmed mosaic automatically It performs a null debiassing bad pixel masking dark subtraction difference adjacent pairs flat field creation and division feature detection and matching between object frames and resampling See the Notes for further information This recipe works well for faint sources in moderately crowded fields Notes A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the det
208. metry Registration Registration involves both the dithered observations as normal but also the e and o beams at each waveplate angle must align To aid the latter an approximate pixel displacement between the e and o beams from empirical data is set for each filter as the displacement is wavelength dependent Even an approximate offset almost invariably leads to successful registration using the central source _GENERATE_OFFSETS_JITTER_POL_ _GENERATE_OFFSETS_POL_ 3 8 Mosaicking This is fully automated No longer do you have to measure painstakingly centroids and manually tile to form mosaics from the jittered frames The jitter offsets are sufficiently small to permit shift of Cartesian co ordinates to register The offsets are derived from the automatic registration No correction for the detector orientation is applied since it degrades the quality of the data despite the small rotation 1 normally involved Allowance for this misalignment with the cardinal directions will be through the FITS world co ordinate system In the meantime should you need the rotation angle pipe the output of KAPPA s fitslist function into grep fitslist lt your_frame gt grep CROTA2 The flat fielded frame can either be resampled to give sub pixel registration or to the nearest pixel The latter is much faster and is adequate for most uses of thermal IRCAM and Michelle It also has the advantage of not smoothing the data and introducing covaria
209. mined from the two corresponding regions for each beam in the following sky frame _SUBTRACT_SKY_POL SUBTRACT_SKY_POL_EXTENDED_ 3 7 Automatic Registration This makes an inventory of the sources above a threshold in each frame It then performs a pattern recognition to identify common features in jittered frames If the fraction of common objects is under 40 or the total is fewer than three the registration fails and so the script resorts to reading the telescope offsets stored in the FITS headers or matching a central bright object in certain recipes Using telescope offsets can lead to trailed sources as occurred with the The improved registration leads to the detection of fainter sources and more accurate measurement thereof _GENERATE_OFFSETS_ invoked within several wrappers tied to various families of recipes FIND_APPROX_OFFSETS _TELE_OFFSETS_ _GENERATE_TELE_OFFSETS_ _GET_CARTESIAN_TELESCOPE_OFFSETS_ To make use of the best information registration using more than one of the above methods is permitted There is also a new but not extensively tested option in which matching is performed only within overlapping regions as specified from the approximate world co ordinate system and a single match within 12 pixels is allowed to define the offsets between frames This modification should allow more registrations using sources than from telescope offsets which merely assist in the process Since the robustness is unknown at pr
210. mode These have only processed a few nights data exercising a few recipes The NACO pipeline would certainly benefit from more data e Upgraded support for the Gemini instrument from pre alpha to alpha through more thorough header translations adjusting the nominal WCS to an actual one setting the saturation levels tested aperture photometry within a 3 arcsec aperture of thermal data It s still a work in progress but it should be possible to process non thermal data too given a sequence of frames matching a standard sequence Incorporated eStar intelligent agent calls in in five recipes including the two new recipes which make an inventory of the sources such as BRIGHT_POINT_SOURCE_CATALOGUE The IRIS2 ARRAY_TESTS has been improved The mode speed and readnoise are written to the calibration log and reported Several recipes in the BRIGHT_POINT_SOURCE JITTER_SELF_FLAT families and CHOP_SKY_JITTER have two additional steps one to correct for residual bias variations along columns and the other to correct for field distortion For most instruments these are null but not for ISAAC where both are applied and NACO where the bias striping is removed The ISAAC sky co ordinate system is tied to the undistorted grid co ordinates rather than than the distorted grid This means that measured sky positions for sources will not be misplaced by the distortion IRIS2 now corrects its world co ordinate system for spatial distortion but the pi
211. n The shift comes from centroiding on bright sources with recipe NOD_CHOP_APHOT The areas extend such that no pixels are duplicated Thus the divisions occur at midpoints between the four images The combined source image is smoothed using a 4 by 4 pixel block average filter Intermediate frames are deleted except for the differenced pairs _dp suffix and the bias and pickup corrected frames _cpc and _rpc suffices Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix A mosaic for each cycle of object frames in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 The combined source image and neighbourhoods in lt m gt lt date gt _ lt group_number gt _cab The smoothed combined image in lt m gt lt date gt _ lt group_number gt _scab The differenced pairs in lt i gt lt date gt _ lt obs_number gt _dp where lt i gt is the Parameters NUMBER INTEGER The number of frames in the nod pattern If absent the number of offsets as given by header NOFFSETS minus one is used If neither is available 4 is used An error state arises if the number of jittered frames is fewer than 4 and not a multiple of 4 USEVAR LOGICAL Whether or not to create and propagate variance arrays 1 Related Recipes NOD_CHOP NOD_CHOP_APHOT NNOD_SELF_FLAT_NO_MASKi Implementation Status
212. n There are headings at the top of each column The photometry uses the mode calculated from 3 median 2 mean and Chau venet s rejection criterion to estimate the sky level in an annulus about the source The inner annulus diameter is 1 3 times that of the aperture 6 5 arcsec the outer annulus is 2 5 times 12 5 arcsec for UFTI and twice the aperture 10 arcsec for IRCAM Michelle and IRIS2 The errors are internal based on the sky noise e Intermediate frames are deleted except for the flat fielded _ff suffix frames e Sub arrays are supported Output Data e The resultant mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the in strument s group prefix e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The jaming formatlis slightly different for some non UKIRT instruments e Results tabulation to log 0RAC_DATA_OUT aphot_results txt Parameters NUMBER INTEGER The number of frames in the jitter pattern If this is not set the number of offsets as given by FITS header NOFFSETS minus one is used If neither is available 5 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes BRIG
213. n currently just for Michelle data It takes an imaging observation comprising a multiple of four object frames to make automatically a calibrated untrimmed mosaic in the reference frame of a moving target It performs a null debiassing creation and propagation of data variance difference the integrations for each AB chop beam pair bad pixel masking difference adjacent nodded pairs registers the frames and forms a mosaic See the Notes for further information Registration is adjusted to track the motion of the moving target using ephemeris data stored in file target_ephem dat See Ephemeris file Format for details of this file s format Notes A variance array is created for each beam first using the read noise and once the bias is removed Poisson noise is added A bias frame selected from the calibration system is removed from each beam in CHOP read mode If no bias frame is available in the CHOP mode the recipe subtracts a null bias so the errors will be overestimated in the CHOP read mode the data array will be unaffected once the beams are differenced The ARRAY_TESTS recipe files a suitable short exposure dark as a bias in the calibration system The integrations of the two beams are differenced the first subtracted from the second in each pair A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist The bad pixel mask applied is 0RAC_DATA_CAL
214. nce into the data errors For older undersampled IRCAM3 data 0 286 per pixel and for INGRID 07235 resampling has some merit The mosaicking uses the CCDPACK algorithm of its makemos command Only zero point shifts of intensity are applied to the resampled frames to create the mosaic For most cases the comparison is of the sky levels as sky pixels dominate This comparison is repeated for all pairs makemos then finds the most mutually consistent set of additive corrections weighting appropriately to make the smoothest mosaic given the data The first frame which for the UFTI execs is the central offset 0 0 frame has no additive correction applied The mosaic generation adjusts the zero point of the jittered frames Another way of looking at it is that mosaicking attempts to remove the sky variations The additive corrections are normally quite small like a few tenths of a count to a few counts However over longer integrations or in the thermal regime they can amount to a few score A mosaic pixel value is the mean of all the adjusted contributing 19 SUN 232 8 Features of the Primitives pixel values at that location It is possible to select other statistics for the contributing pixels such as the median through the METHOD argument of the MAKE MOSAIC_ family of primitives There is no normalisation to counts per second in the mosaic The mosaic s signal corresponds to that of the first frame thus the exposure time of t
215. nd after the first 147 POL_ANGLE_NOD_CHOP SUN 232 8 Recipes cycle is then added into its own master mosaic of improving signal to noise The exposure time is also summed and stored in each master mosaic s corresponding header Likewise the end airmass and end UT headers are updated to match that of the last observed frame contributing to the mosaic For each waveplate angle the combined source image is made by taking symmetrical areas about each source such that no pixels are duplicated Thus the divisions occur at midpoints of the chop throw and the nod separations These are registered using the source centroids The polarised intensity is corrected for the statistical bias of the noise by subtracting the variance of Q or U An offset of 0 0 degrees clockwise is applied to the rotation angle for the orientation of the analyser with respect to north A non null value will be applied once it is determined The polarisation data for each pixel are also stored in catalogues See Output Data The intensity image may be displayed with vectors overlaid Steps are taken to reduce the number of noisy or insignificant pixels as well as clutter First the polarisation catalogue data are averaged in 3 by 3 pixel bins Second a binned pixel is rejected if its polarisation is greater than 50 or is not positive or its polarisation signal to noise less than 3 or its polarisation error is greater 5 The bin size and thresholds can readily
216. ng Of the floating point only the RA_BASE and DEC_BASE warrant double precision but the recipes impose no restriction Units are in brackets e Some headers retain instrument specific values like ORAC_SPEED until a common set of instrument independent names is compiled SUN 232 8 Internal Headers 192 F1 Translated Headers Name Type Meaning AIRMASS_START F Airmass at the start of the observation AIRMASS_END F Airmass at the end of the observation DEC_BASE F Declination J2000 at reference position and offset 0 0 deg DEC_SCALE F Pixel scale along declination axis arcsec DEC_TELESCOPE_OFFSET F Telescope declination offset with respect to the DEC_BASE position arcsec DETECTOR_BIAS F Detector bias only used by IRCAM V DETECTOR_MODE S Such as STARE NDSTARE CHOP EQUINOX F Equinox of co ordinates fix at 2000 0 y EXPOSURE_TIME F Exposure time for each co add s FILTER S Filter name GAIN F Conversion factor electrons data number INSTRUMENT S Name of instrument such as IRCAM UFTI UIST Michelle ISAAC but its use is deprecated NUMBER_OF_EXPOSURES I Number of exposures in the integration NUMBER_OF_OFFSETS I Number of jitter offset positions NUMBER_OF_READS I Number of reads per exposure OBJECT S Name of the object preferably adhering to IAU standard OBSERVATION_MODE S Operating mode of multi mode instrument OBSERVATION_NUMBER OBSERVATION_TYPE RA_BASE imaging spectroscopy or ifu Obser
217. ng convention and there were different default paths for SORAC_DATA_IN and 0RAC_DATA_OUT IRCAM s NDFs were copied to 0RAC_DATA_OUT and UFTT s raw FITS files were converted to NDFs in that directory To process data from this era follow the instructions of Section 2 1 except you should invoke oracdr_ lt instrument gt _old lt date gt instead of oracdr_ lt instrument gt lt date gt to set up the necessary environment variables The rest is the same You can use modern jitter generic recipes too provided they know how many frames to process The easiest way to do that is make your own copy of the recipe and set the number frames as an argument to the steering primitive See Section for details The standard raw and reduced directories prior to 2000 August were lt instrument gt _data YYYYMMDD raw and lt instrument gt _data YYYYMMDD reduced respec tively where lt instrument gt was either ufti or ircam Details of the former naming convention for IRCAM frames is given under the Output Data headings in the reference section SUN 232 8 File prefixes 30 B File prefixes The UKIRT style naming convention comprises a prefix followed by the eight digit UT date underscore the group or observation number depending on whether it is a file associated with the group like a mosaic or a single frame and finally if it has undergone processing a suffix Section C discusses and lists the last of these
218. ng its own frames to make the flat is not appropriate Notes You may use SKY_FLAT or SKY_FLAT_MASKED to make the flat field e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 e The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used e Where automatic registration is not possible the recipe matches the centroid of central source and should that fail it resorts to using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions e The recipe makes the mosaic by applying offsets in intensity to give the most consis tent result amongst the overlapping regions The mosaic is trimmed to the dimensions of an input frame The mosaic is not normalised by its exposure time that bein
219. nts of directory 0RAC_DATA_OUT while the pipeline is running or you interrupt the pipeline with CTRL C or something has gone wrong with the the recipe and pipeline has aborted or you have commented out the _TIDY primitive from the recipe or you have set the ORAC_KEEP environment variable to 1 33 Frame suffices SUN 232 8 File suffices Suffix Stands for Description _adu ADU Multiplied by the exposure time to convert the units to ADU Michelle _bc Bias Corrected Residual bias variations removed ISAAC _bgl BackGround Limited Whether or not each pixel is background limited i e Poisson noise exceeds the read noise _bp Bad Pixel Co added with the bad pixel mask _bpc Bad Pixel Cumulative Cumulative bad pixel mask UIST bpd Bad Pixel Data Thresholded bias or dark frame for bad pixel mask creation UIST sel CLone Modifiable copy of IRCAM raw data _db De Biassed The bias is actually zero but it sets up various CCDPACK ancillary data for later processing dcb Differenced Chop Beams The difference of the A and B beam signals of nodded data as used by NOD_CHOP recipes _dk DarK Dark subtracted _dp Differenced Pair The difference of successive frames in a NOD recipe _dta Distortion Transfomation Applied Resampled for field distortion _ess E beam Sky Subtracted Polarimetry target e beam after sky subtraction EX Flat Field Divided by the flat field _fm Flat Masked This has the flagged deviant pixels dete
220. o noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic SUN 232 8 Recipes 174 SKY_AND_JITTER e Intermediate frames are deleted except for the flat fielded _ f suffix frames e Sub arrays are supported Output Data e The resultant mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the in strument s group prefix e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming format is slightly different for some non UKIRT instruments Parameters NUMBER INTEGER The number of frames in the jitter excluding the sky frame If absent the number of offsets as given by header NOFFSETS minus two is used If neither is available 5 is used An error state arises if the number of jittered frames is fewer than 3 USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes ITTER_SELF_FLAT NOD_SELF_FLAT_NO_MASK SKY_AND_JITTER_APHOT SKY_FLAT SKY_FLAT MASKED Implementation Status e The processing engines are from the Starlink packages and e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation
221. of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame Thus the noise will be greater in the peripheral areas having received less exposure time The full signal will be in the central ninth containing the main object The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of four the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix A mosaic for each cycle of four in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The jaming formatlis slightl
222. olarisation the polarisation angle and intensity There are additional columns giving the standard deviation on each of the tabulated values excluding the co ordinates Likewise lt m gt lt date gt _ lt group_number gt _all FIT and lt m gt lt date gt _ lt group_number gt _bin FIT store the full and binned catalogues re spectively Parameters NUMBER INTEGER The number of frames in the nod pattern If absent the number of offsets as given by header NOFFSETS minus one is used If neither is available 4 is used An error state arises if the number of jittered frames is fewer than 4 and not a multiple of 4 USEVAR LOGICAL Whether or not to create and propagate variance arrays 1 Related Recipes POL_NOD_CHOP POL_QU_FIRST_NOD_CHOP NOD_CHOP_APHOT POL_ANGLE _ JITTER Implementation Status e The processing engines are from the Starlink packages CCDPACK KAPPA POLPACK FIGARO and CURSA e Uses the Starlink NDF format and multi NDF HDS container files e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaics The polarisation maps have new titles as follows using the suffices described in Output Data I Intensity P Polarisation PI Polarised Intensity Q Stokes Q TH Polarisation Angle U Stokes U e The origins of the generated polarisation maps are set to 1 1 The WCS current frame is unchanged The units are set for the frames with suff
223. olating headers are corrected Spurious instrument names are changed to IRCAMS3 The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used Where automatic registration is not possible the recipe matches the centroid of central source and should that fail it resorts to using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaic by applying offsets in intensity to give the most consis tent result amongst the overlapping regions The mosaic is trimmed to the dimensions of an input frame The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of jittered frames the recipe creates a mosaic which is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass and end UT headers areupdated to match that of the last observed frame contributing to the mosaic SUN 232 8 Recipes 52 BRIGHT_POINT_SOURCE e Intermediate frames are deleted
224. on and matching between object frames and resampling See the for further information This recipe works well for faint sources and for moderately crowded fields Notes A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS The bad pixel mask applied is 0RAC_DATA_CAL bpm For INGRID the pre and post exposure images are subtracted A non linearity correction is then applied The dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created iteratively First an approximate flat field is created by combining normalised object frames using the median at each pixel This flat field is applied to the object frames Sources within the flat fielded frames are detected and masked in the dark subtracted frames The first stage is repeated but applied to the masked frames to create the final flat field For ISAAC residual bias variations along the columns are largely rem
225. ords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created iteratively First an approximate flat field is created by combining normalised object frames using the median at each pixel This flat field is applied to the object frames Sources within the flat fielded frames are detected and masked in the dark subtracted frames The first stage is repeated but applied to the masked frames to create the final flat field Registration is performed using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its expo
226. orresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic e Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data e The full mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instru ment s group prefix e A mosaic for each row in lt m gt lt date gt _ lt group_number gt _mos lt row_number gt where lt row_number gt is 0 or 1 e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The naming formatlis slightly different for some non UKIRT instruments Parameters NROW INTEGER The number of target frames in a row of the mosaic Its minimum is 3 because this number of blank skies are needed to form a flat field 3 NCOL INTEGER The number of target frames in a column of the mosaic Its minimum is 2 3 USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes EXTENDED_3x3_BASIC EXTENDED_5x5 QUADRANT_ JITTER Implementation Status e The processing engines are from the Starlink packages and e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 74 EXTENDED_
227. osaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame 161 POL_QU_FIRST_NOD_CHOP SUN 232 8 Recipes For each cycle of frames the recipe creates mosaics for each chop beam and waveplate angle modulo 180 degrees Each mosaic has its bad pixels filled and after the first cycle is then added into its own master mosaic of improving signal to noise The exposure time is also summed and stored in each master mosaic s corresponding header Likewise the end airmass and end UT headers are updated to match that of the last observed frame contributing to the mosaic For each waveplate angle the combined source image is made by taking symmetrical areas about each source such that no pixels are duplicated Thus the divisions occur at midpoints of the chop throw and the nod separations These are registered using the nominal chop throws and telescope offsets The polarised intensity is corrected for the statistical bias of the noise by subtracting the variance of Q or U An offset of 0 0 degrees clockwise is applied to the rotation angle for the orientation of the analyser with respect to north A non null value will be applied once it is determined
228. ositions the wavelength mosaics are registered to form a spatial mosaic For repeat cycles the spatial mosaic is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the master mosaic s corresponding header Likewise the end airmass and end UT headers are updated to match that of the last observed frame contributing to the mosaic The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions No mosaic is trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas of the spatial having received less exposure time Each mosaic is not normalised by its exposure time that being the exposure time of a single frame e Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data e The integrated mosaic in gf lt date gt _ lt group_number gt _mos where lt date gt is the UT date in yyyymmdd format e A mosaic for each cycle of eight in g lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 e The individual flat fielded frames in lt date gt _ lt obs_number gt _ff Parameters NPAIRS INTEGER The number of frame pairs to be differenced It must be a multiple of 2 otherwise 4 is assumed A value of four or more is assumed to indicate sky subtraction 2 NUMBER INTEGER The number of spatial jitte
229. otation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time the exposure time of a single frame For each cycle of jittered frames the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic The photometry tabulation includes the file name source name time filter air mass the catalogue magnitude and estimates of the zero point with and without the application of a mean extinction There are headings at the top of each column The photometry uses a multiply clipped 2 2 2 5 3 standard deviations mean to estimate the sky mode in an annulus about the source This is not unduly biased by the presence of the self flat artifact in the pixel histogram The inner annulus diameter is 1 3 times that of the aperture 6 5 arcsec the outer annulus is 2 5 times 12 5 arcsec for UFTI and twice the aperture 10 arcsec for IRCAM and IRIS2
230. oved from each flat fielded frame The recipe first masks the sources then collapses the frame along its rows to form a profile whose clipped mean is subtracted The resultant profile reflects the bias variations The recipe subtracts this profile from each column of the flat fielded frame The field distortion of ISAAC is corrected in the target frames using the mappings documented on the ISAAC problems web page SUN 232 8 Recipes 90 JITTER_SELF_FLAT Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects the script resorts to using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of jittered frames the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Like
231. p_number gt _I FIT For each point it tabulates the x y co ordinates the total intensity the Stokes parameters the percentage polarisation the polarisation angle and intensity There are additional columns giving the standard deviation on each of the tabulated values excluding the co ordinates Likewise lt m gt lt date gt _ lt group_number gt _al11 FIT and lt m gt lt date gt _ lt group_number gt _bin FIT store the full and binned catalogues re spectively Parameters NUMBER INTEGER The number of frames in the jitter pattern per waveplate angle If this is not set the number of offsets as given by FITS header NOFFSETS minus one is used If neither is available 3 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent USEVAR LOGICAL Whether or not to create and propagate variance arrays 1 Related Recipes POL_EXTENDED POL_JITTER SKY_FLAT _POL SKY_FLAT_POL_ANGLE Implementation Status e The processing engines are from the Starlink packages and CURSA 145 POL_ANGLE_JITTER SUN 232 8 Recipes e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaics The polarisation maps have new titles as follows using the suffices described in Output Data I Intensity P Polarisation PI Polarised Int
232. package in addition to those engines listed in the generic documentation Aperture photometry accesses both the UKIRT Faint standard and Persson HST lists E 6 Michelle DIFFERENCE_STATS POL_ANGLE_NOD_CHOP POL_QU_FIRST_NOD_CHOP and POL_NOD_CHOPlonly apply to Michelle ARRAY_TESTS calculates and files both an average bias frame and the read noise in the calibra tion system There is no logging Checks are made that appropriate waveforms are selected The scope of the recipes is similar to that for ISAAC No attempt has been made to reduce any coronographic data with the standard recipes Registration is critical for such small point spread functions to match well Therefore the minimum number of contiguous pixels above the threshold to be counted as a fiducial source for automatic registration is increased from 9 to 15 and the percentile detection threshold raised from 98 to 99 These may need further adjustment as a wider selection of observations are processed The sky co ordinates are used to aid registration by default Aperture photometry accesses both the UKIRT Faint standard and Persson HST lists E 8 NIRI Tests with 2004 data are limited to thermal data and REDUCE_DARK recipes The prelminaries fudge the WCS headers to give a consistent set A 3 arcsecond aperture is used by default for the thermal imaging aperture photometry E9 The FP family of recipes only applies to UFTI The sky counts are validated as part o
233. pdated to match that of the last observed frame contributing to the mosaic The photometry tabulation includes the file name source name time filter air mass the catalogue magnitude and estimates of the zero point with and without the application of a mean extinction There are headings at the top of each column The photometry uses the mode calculated from 3 median 2 mean and Chau venet s rejection criterion to estimate the sky level in an annulus about the source The inner annulus diameter is 1 3 times that of the aperture 6 5 arcsec the outer annulus is 2 5 times 12 5 arcsec for UFTI and twice the aperture 10 arcsec for IRCAM The errors are internal based on the sky noise Intermediate frames are deleted except for the flat fielded _ff suffix frames Sub arrays are supported Output Data The resultant mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the in strument s group prefix The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The naming format is slightly different for some non UKIRT instruments Parameters NUMBER INTEGER The number of frames in the jitter excluding the sky frame If absent the number of offsets as given by header NOFFSETS minus two is used If neither is available 5 is used An error state arises if the number of jittered frames is fewer than 3 USEVAR LOGICAL
234. pe offsets for registration This is needed when the telescope has tracked on the non sidereal tar get SUN 232 8 Recipes 46 Polarimetry recipes Recipe Name Type of Data Function and Comments POL_ANGLE_JITTER Polarimetry of point or small lt 35 arcsec extended sources Makes a polarisation map from frames at the four waveplate angles at each of at least three jittered positions the waveplate is moved before the telescope An appropri ate dark and separate flat fields at each waveplate angle using SKY_FLAT_POL or SKY_FLAT_POL_ANGLE must be ob tained POL_ANGLE_NOD_CHOP Polarimetry of point or small lt 10 arcsec extended sources in mid infra red Makes a polarisation map from chopped and nodded frames at the four waveplate an gles at two nod positions the waveplate is moved before the telescope is nodded There is no object masking or flat fielding Requires a bias in CHOP mode e g from recipe AR RAY_TESTS POL_EXTENDED Polarimetry of extended sources Makes a polarisation map of an extended source from frames nodded between object and blank sky The object sky pairs must be taken at each of the four waveplate angles Requires an appropriate dark and separate flat fields at each waveplate angle POL_JITTER Polarimetry of point or small lt 35 arcsec extended sources Makes a polarimetry map from frames at the four waveplate angles at each of at le
235. pecial meaning to HDS therefore are removed and a decimal point becomes a p in the flat s name The _cycle suffix is shortened to _c and all _subgrp strings removed from the group number Flats are are not combined over multiple cycles over recipes SKY_FLAT and SKY_FLAT_MASKED are limited to jitters between three to five points for compatibility with other ORAC tools It is still possible to make private variants of these recipes in which the number of jitter positions is set by the NUMBER steering parameter Mosaics are combined using the mean at each pixel This was formerly the median The change was made to correct the photometry Poor registration from telescope offsets due to sparse fields leads to multiple peaks in the mosaic s grid and given the steep point spread function s profile the median preferentially selects pixels not at a peak This resulted in a typical underestimate of the flux of standard stars by 1 3 The _MAKE_MOSAIC_ primitive now has an argument to select various estimators should you prefer not to use the mean For the aperture photometry the default sky annulus radii have been increased This reduces the error estimating the sky level both statistically and from the extend low level pedestal in the point spread function The area is increased 2 9x for IRCAM and 5 6x for UFTL To counteract the spike artifact in the histogram of sky values of flat fielded frames where the pre flattened frame itself contributed
236. pertures and background regions may change in the light of experience with Michelle Already in below average seeing it s evident that a 6 arcsecond circle will leave some signal in the background The object name is compared with a 28 member catalogue of 10 and 20 micron standards a handful of which are known optical semi regular variable stars In addition to deriving magnitudes the recipe calculates an approximate flux in Janskys It is approximate because being an absolute measurement it does require a magnitude zero point to be applied to the relative instrumental magnitude At the time of writing this zero point is only roughly known so the default fluxes should be taken with a pinch of salt The flux is not yet written to the results file If you have determined the zero point from standards you can rerun the pipeline for your target observations with that zero point assigned to argument ZP of primitive _NOD_CHOP_APHOT_MAG_ invoked within recipe NOD_CHOP_APHOT See Section for instructions to make and use a private version of a recipe There is an approximate extinction correction applied using a coeeficient of 0 18 because the coefficients for all but one of the various N and Q filters have yet to be determined _NOD_CHOP_APHOT_MAG_ _FIXED_APERTURE_MIDIR_PHOTOMETRY_ _MAKE_PHOTOMETRY_TABLE_ _GET_FILTER_PARAMETERS_ _UKIRT_MIDIR_STANDARD_MAGNITUDE_ MICHELLE _STANDARD_MAGNITUDE_ _FIND_SOURCE_CEN CLIPPED _SIATS_ 3 12 Improvin
237. pes Special thanks go to Gillian Wright and Sandy Leggett for defining the initial specifications of the UFTI scripts and for subsequent discussions Chris Davis kindly supplied the specifications of the polarimetry and Fabry Perot recipes Paul Hirst wrote the original versions of the primitives which create the data variance Stuart Ryder was instrumental in getting ORAC DR commissioned and installed for use at the AAT Thanks also to Frossie Economou and Tim Jenness for answering my ORAC DR and Perl questions and for incorporating my requested enhancements into ORAC DRinfrastructure The application engines used in ORAC DR were supplied by the Starlink Project which is run by CCLRC on behalf of PPARC I should like to thank the Starlink programmers for their excellent support especially for quickly providing enhancements to tasks 7 Copyright and License ORAC DR is copyright 1998 2003 PPARC the UK Particle Physics and Astronomy Research Council Itis distributed by Starlink under the GNU General Public License as published by the Free Software Foundation Whenever you have used ORAC DR as part of a publication please give an acknowledgment to ORAC DR in the paper This will help us assess the usage of ORAC DR 29 SUN 232 8 Processing UKIRT data obtained before 2000 August A Processing UKIRT data obtained before 2000 August Before the introduction of on 2000 August 1 UFTI raw data were in format IRCAM data had a different nami
238. pplied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created in two steps The quadrant containing the object is masked in each object frame Then the recipe combines the normalised and quadrant masked object frames using the median at each pixel Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects it matches the centroid of the central source If this fails the script resorts to using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions e The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to SUN 232 8 Recipes 168 QUADRANT_JITTER_NO_MASK the dimensions of a single frame Thus the noise will be greater in the peripheral areas having received less exposure time The full signal will be in the central ninth containing the main object The mosaic is not normalised by its exposure time that being the exposure time of a single frame For ea
239. pplied on the command line or the data s FITS headers edited See Section B for instructions Actual testing has been performed on the core recipes JITTER_SELF_FLAT _APHOT BRIGHT_POINT_SOURCE _APHOT REDUCE_DARK Other near infra red plain imaging recipes should work provided the observation pattern matches that expected by the recipe Aperture photometry accesses the Persson HST lists By default the infrastructure uses information in the headers to assign recipe names to DUCE_DARK for a dark and JITTER_SELF_FLAT for jittered target frames Otherwise it defaults to QUICK_LOOK Other recipes supplied on the oracdr command line should work provided the observation pattern matches that expected by the recipe ES ARRAY_TESTS uses eight frames and derives both the STARE and ND_STARE readout noises which are both filed with the calibration system The range of acceptable dark current is 0 10 electrons sec compared with 1 1 for UFTI and the nominal ND_STARE readout noise is 20 50 electrons compared with 8 30 electrons for UFTI The STARE mode readout noise should be 30 70 electrons to be nominal The log file goes to ORAC_DATA_0UT ircam3_array_tests log E 4 IRIS2 The four EXTENDED_n x m recipes cope with missing offset information and a lower complete ness 0 25 from 0 4 for automatic registration thus a smaller fraction of detected objects need match ARRAY_TESTS logs to a different location inst2_soft iris2red logs
240. proving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass and end UT headers are updated to match that of the last observed frame contributing to the mosaic Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data The integrated mosaic in gf lt date gt _ lt group_number gt _mos where lt date gt is the UT date in yyyymmdd format A mosaic for each cycle of eight in gf lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 The individual flat fielded frames in f lt date gt _ lt obs_number gt _ff Parameters NPAIRS INTEGER The number of frame pairs to be differenced It must be a multiple of 2 otherwise 4 is assumed A value of four or more is assumed to indicate sky subtraction 4 NUMBER INTEGER The number of spatial jitter positions For each spatial position there are NPAIRS pairs of frames A value of 1 also dictates that no jittering has occurred To make a master mosaic combining spatial positions NUMBER should be at least 3 If NUMBER is absent the number of offsets as given by internal header NOFFSETS minus one is used An error state arises if the resulting number of jittered frames is fewer than 3 and a default of 3 is assumed If neither NUMBER nor NOFFSETS is defined 1 is used 1 USEVAR LOGICAL Whether or not to create and propagate variance
241. purious instrument names are changed to IRCAMS3 You may use SKY_FLAT or SKY_FLAT_MASKEDI to make the flat field The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The most recent sky frame is used for the sky subtraction e Where automatic registration is not possible the recipe matches the centroid of central source and should that fail it resorts to using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions e The recipe makes the mosaic by applying offsets in intensity to give the most consis tent result amongst the overlapping regions The mosaic is trimmed to the dimensions of an input frame The mosaic is not normalised by its exposure time that being the exposure time of a single frame SUN 232 8 Recipes 176 SKY_AND_JITTER_APHOT For each cycle of jittered frames the recipe creates a mosaic which is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are u
242. r UFTI there is data validation such that a warning is issued if the clipped mean sky level is below 24 counts per second in K band and 32 counts per second in H UFTI _CHECK_SKY_COUNTS_ UFTI _VALIDATE_RAW_DATA_ For UIST data taken before 2002 December 2 and Michelle raw data units are converted from ADU per second to the UKIRT standard of total ADU per exposure lt instrument gt _INSTRUMENT_HELLO_ UIST _DATA_UNITS_TO_ADU Alnight log is created or appended in 0RAC_DATA_OUT for each frame processed This tabulates the main parameters of the observation having first corrected defective or undefined headers _NIGHT_LOG_ UIST _NIGHT_LOG_ lt instrument gt _FIX_HEADERS_ for Classic Cam IRCAM MICHELLE NIRI and UFTI 9 SUN 232 8 Features of the Primitives 3 1 3 Non linearity Correction Detector non linearity corrections are applied to IRCAM and INGRID For IRCAM the correction is 3 3 x 10 times the square of the bias subtracted signal For INGRID the measured to actual counts is given by the expression 1 0 1 2247 x 1076 M 7 68045 x 1071 x M where M is the measured ADU count although it is actually applied after the pre exposure readout is subtracted from the post exposure integration For Classic Cam the correction is 1 625x10 x 1 overhead exposure_time where the overhead is 2 x speed number of pre exposure reads speed readout time x number of post exposure reads The various parameters in t
243. r is available 5 is used An error state arises if the number of jittered frames is fewer than 3 USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes SKY_FLAT Implementation Status e The processing engines are from the Starlink packages CCDPACK FIGARO and EXTRACTOR e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through the intermediate file to the flat e Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 184 SKY_FLAT_POL SKY _FLAT_POL Creates and files a flat field derived from eight frames using object masking to reduce artifacts Description This recipe make a sky flat for UKIRT imaging from a series of eight sky or object frames combined using one of a selection of statistics It is intended to be used to make a flat for polarimetry data The data should comprise two spatial positions at the waveplate angles 0 45 22 5 and 67 5 degrees It performs a null debiassing bad pixel masking and dark subtraction before combining the sky frames pixel by pixel to to make the flat See the Notes for further details The parameters of the flat are filed in the index of flats for future selection and use of the flat For best results the field observed should contain few stars and no bright ones Notes A World Co ordinate System WCS using the AIPS convention is created in the
244. r positions For each spatial position there are NPAIRS pairs of frames A value of 1 also dictates that no jittering has occurred To make a master mosaic combining spatial positions NUMBER should be at least 3 If NUMBER is absent the number of offsets as given by internal header NOFFSETS minus one is used An error state arises if the resulting number of jittered frames is fewer than 3 and a default of 3 is assumed If neither NUMBER nor NOFFSETS are defined 1 is used USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes SKY_FLAT_FP FP_JITTER Implementation Status SUN 232 8 Recipes 88 FP_JITTER_NO_SKY e The processing engines are from the Starlink packages and e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter 89 JITTER_SELF FLAT SUN 232 8 Recipes JITTER_SELF_FLAT Reduces a standard jitter photometry observation using object masking Description This script reduces a standard jitter photometry observation with near infrared imaging data It takes an imaging observation comprising jittered object frames and a dark frame to make a calibrated untrimmed mosaic automatically It performs a null debiassing bad pixel masking dark subtraction flat field creation and division feature detecti
245. rames While the default continues to apply intensity offsets Fabry Perot wavelength mosaics set ZERO to false There is anew POLARIMETRY argument for some of the registration primitives In aperture photometry primitives the centroid search boxsize is now decoupled from the aperture size via a BOXSIZE argument LAMP is a new value for internal header ORAC_OBSERVATION_TYPE to support internal lamps used to make flats The handling of the filters and standards catalogues has been redesigned in the photome try primitives to be be more transparent and to make it easier to use multiple catalogues of standards A waveband is interchanged rather than a column index _CALC_STOKES_ has a boolean DEBIAS argument to control the application of the statistical bias correction _CALC_STOKES_NOD_CHOP_ has a new boolean CENTROID argument whose valued is passed to _COMBINE_CHOPPED_SOURCE_ 201 SUN 232 8 Release Notes V4 0 H Release Notes V4 0 The main changes are the addition of support for UIST ISAAC and INGRID instruments H 1 New recipes The design of the data handling system means a traditional ARRAY_TESTS is not possible for Thus there are two recipes to perform the equivalent steps for darks not in the same observation group This recipe uses a long exposure DARK frame to locate bad pixels then creates and files a bad pixel mask It then measures and reports the dark current from a long exposure DARK frame If this recipe is
246. rce within an 8 arcsecond box Should that fail for the jittered e and o beam sections the recipe resorts to using the telescope offsets transformed to pixels However the final option for registering the e and o beam mosaics at different waveplate angles uses the beam offsets in arcseconds for the current filter converted to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the few pixels in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of twelve frames the recipe creates mosaics for each beam and wave plate angle Each mosaic has its bad pixels filled and after the first cycle is then added into its own master mosaic of improving signal to noise The exposure time is also summed and stored in each master mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic The polarised intensity is corrected for the statistical bias of the noise by subtracting the variance of Q or U
247. rdinate transformations benefitting UIST and future instruments with an extra reflection in the optical train There are additional checks for significantly negative frame means after dark subtraction Depending on the severity this may stop the pipeline or merely issue a warning This is to ensure that valid darks are observed The broadened mean method has been reinstated for combining frames into a flat This avoids the artefact in self flat fielding where in an n point jitter pattern 1 n pixels divide by themselves giving rise to a false peak at the normalisation factor in the histogram of values in a flat fielded frame A possible cause of cause of a negative mode in is given in the warning announnced by _NORMALISE_TO_MODE _ _GENERATE_OFFSETS_EXTENDED_ now uses the 98 percentile the same as the other _GENERATE_OFFSETS_ primitives Centroiding now has a default smoothing option to make object location more robust for fainter sources A double pass median filtering of bad pixels now occurs just prior to the near infra red photometry to reduce bias from unmeasured flux It particulalry helps the flat fielded images as the mosaics almost invariably lose their bad pixels in the region of interest during their formation If variance information is available the aperture photometry uses it to estimate photomet ric errors 203 SUN 232 8 Release Notes V3 1 1 e Tidying correctly erases NDF components within HDS container files
248. reate the final flat field e Intermediate frames are deleted e Sub arrays are supported Output Data e The flats are called flat_ lt filter gt _pol lt waveplate_angle gt _ lt group_number gt The lt waveplate_angle gt is the integer part of the angle e g 22 67 lt filter gt is the fil ter name excluding any pol and lt group_number gt is the frame number of the group For each subsequent cycle of the recipe the recipe makes new flats which have 187 SKY_FLAT_POL_ANGLE SUN 232 8 Recipes a _c lt cycle_number gt suffix where lt cycle_number gt is the number of the cycle counting from one e The flats are filed in ORAC_DATA_0UT index flat Parameters USEVAR LOGICAL Whether or not to create and propagate variance arrays 1 Related Recipes SKY_FLAT_FP SKY_FLAT_MASKED SKY_FLAT_POL Implementation Status e The processing engines are from the Starlink packages CCDPACK FIGARO and FIGARO e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through the intermediate file to the flat e Error propagation is controlled by the USEVAR parameter SUN 232 8 Instrument Recipe Notes 188 E Instrument Recipe Notes This appendix summarises the modifications of instrument specific variants of the recipes and the restricted availability of certain recipes by instrument E1 There is no recipe name in the headers therefore recipes must be su
249. resholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used Where automatic registration is not possible the recipe matches the centroid of central source and should that fail it resorts to using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions e The recipe makes the mosaic by applying offsets in intensity to give the most consis tent result amongst the overlapping regions The mosaic is trimmed to the dimensions of an input frame The mosaic is not normalised by its exposure time that being the exposure time of a single frame SUN 232 8 Recipes 54 BRIGHT_POINT_SOURCE_APHOT For each cycle of jittered frames the recipe creates a mosaic which is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass and end UT headers are updated to match that of the last observed frame contributing to the mosaic The photometry tabulation includes the file name source name time filter air mass the catalogue magnitude and estimates of the zero point with and without the application of a mean extinctio
250. respect to north A non null value will be applied once it is determined The polarisation data for each pixel are also stored in catalogues See Output Data The intensity image may be displayed with vectors overlaid Steps are taken to reduce the number of noisy or insignificant pixels as well as clutter First the polarisation catalogue data are averaged in 3 by 3 pixel bins Second a binned pixel is rejected if its polarisation is greater than 50 or is not positive or its polarisation signal to noise less than 3 or its polarisation error is greater 5 The bin size and thresholds can readily be changed by supplying arguments to the CALC _STOKES_NOD_CHOP_ primitive At the end of each cycle the grand mosaics are registered and new polarisation maps and catalogues constructed Intermediate frames are deleted except for the differenced pairs _dp suffix frames Output Data The integrated mosaics in lt m gt lt date gt _ lt group_number gt _p lt angle gt _mos where lt m gt is the group prefix and lt angle gt is 0 22 45 or 67 A mosaic for each cycle of chopped and nodded frames per waveplate angle in lt m gt lt date gt _ lt group_number gt _p lt angle gt _mos_c lt cycle_number gt where lt cycle_number gt counts from 0 The combined source image and neighbourhoods at each waveplate angle in lt m gt lt date gt _ lt group_number gt _p lt angle gt _cab The differenced pairs in lt i gt lt date gt _ lt o
251. riance difference the integrations for each AB chop beam pair bad pixel masking difference adjacent nodded pairs registers the frames and forms a mosaic See the Notes for further information Notes A variance array is created for each beam first using the read noise and once the bias is removed Poisson noise is added A bias frame selected from the calibration system is removed from each beam in CHOP read mode If no bias frame is available in the CHOP mode the recipe subtracts a null bias so the errors will be overestimated in the CHOP read mode the data array will be unaffected once the beams are differenced The ARRAY_TESTS recipe files a suitable short exposure dark as a bias in the calibration system The integrations of the two beams are differenced the first subtracted from the second in each pair A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist The bad pixel mask applied is 0RAC_DATA_CAL bpm Registration is performed using the telescope offsets transformed to pixels The resampling applies integer shifts of origin There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having re
252. right standard photometry observation with UKIRT imaging data It takes an imaging observation comprising a series of jittered object frames and a dark frame and a predetermined flat field frame to make a calibrated trimmed mosaic automatically This recipe performs bad pixel masking null debiassing dark subtraction flat field divi sion registration using telescope offsets and resampling See the Notes for details As the name implies it is intended for bright point sources such as standard stars or any observation where using its own frames to make the flat is not appropriate and where automatic registration fails Notes You may use SKY_FLAT or SKY_FLAT_ MASKED to make the flat field A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used Registration is
253. rmally 7 arcseconds but it can be adjusted through the OCCULT argument of primitive MAKE OBJECTS_MASK_ In the QUADRANT _JITTER recipe the central mask s diameter equals the length of the shorter side of a quadrant The disadvantage is that the noise is higher within the occulted circle and its variance is non uniform across the central ninth of the mosaic You can modify the the central mask size and shape see primitives _FLAT_FIELD_QUADRANT_JITTER_ and _MAKE_OBJECTS_MASK_ 15 SUN 232 8 Features of the Primitives MAKE_OBJECTS_MASK_ MASK _OBJECTS_ DEFINE_QUADRANT_MASKS_ _MASK_QUADRANT_ After masking biases can be introduced as the objects or masks move to different locations on the detector each with a different response in the flat field This is most pronounced for QUADRANT_JITTER where a quadrant of the detector is masked and IRCAM2 which had a strongly sloping response in which the mean flat is considerably different from the remaining quadrants Merely taking a median at each pixel will preferentially select values from certain frames Thus there has to be an allowance for these systematic differences before the data are combined to give representative relative intensities The first frame becomes a reference frame against which the recipes scales the modal values of the other frames NORMALISE_TO_MODE_ NORMALISE_TO_MODE_EXTENDED_ CLIPPEDOSTATS The improved flat typically shows a uniformity at 0 02 of the sky It is th
254. rn It performs a null debiassing bad pixel masking and dark subtraction before combining the sky frames pixel by pixel to to make the flat See the Notes for further details The parameters of the flat are filed in the index of flats for future selection and use of the flat For best results the field observed should contain few stars and no bright ones Notes e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 e The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created iteratively First an approximate flat field is created by combining normalised sky frames using the median at each pixel This flat field is applied to the sky frames Sources within the flat fielded frames are detected and masked in the dark subtracted frames The first stage is repeated but applied to the masked frames to c
255. rom which the recipe makes a sky subtracted untrimmed mosaic automatically The script performs bad pixel masking null debiassing dark subtraction flat field divi sion sky subtraction registration resampling and mosaicking The Notes give more details It is suitable for extended objects up to 2 arcminutes across with UFTI 28 arcseconds with IRCAM and 14 arcminutes across with IRIS2 Notes A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 The bad pixel mask applied is 0RAC_DATA_CAL bpm Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is derived from the sky frames as follows The mode sigma clipped mean is used to offset each sky frame s mode to that of the first sky frame The corrected sky frames are combined pixel by pixel using a median of the values in each frame The resultant frame is normalised by its median to form the flat field
256. rth This omission had been giving vector orientations approximately 89 degrees too high for IRCAM More allowance for occasional problems with the headers in the raw data e g the base R A in degrees not hours and defunct instrument read modes In earlier versions there were fatal errors which the recipes reported but allowed the pipeline to continue These are now corrected so that the recipe ends its processing Expanded tutorial documentation particularly of the description of algorithms used by the primitives and more hyperlinks and updated for the new directory structure Various minor improvements new hyperlinks and corrections to the recipe documentation SUN 232 8 Release Notes V2 1 0 208 The main changes from a programmer perspective were as follows e The primitives access user headers for steering e The FITS header information is accessed through generic user headers with the prefix ORAC_ This insulation permits common code for multiple instruments e There were upgrades for the latest versions of KAPPA and ARD notably for further use of the world co ordinate system In general recipes use the pixel domain for tasks like CENTROID and recording the former domain and then resetting WCS frame after using the KAPPA task There is a reorganised directory structure for the recipes and primitives These are divided into instrument specific general or by topic such as imaging or spectroscopy The topic directorie
257. run at the dark current is stored in an engineering log file MAKE_BPM Creates and files a bad pixel mask from a long exposure dark by thresholding 5 clipped standard deviations about the clipped mean MEASURE_READNOISE This is the second UIST specific recipe replacing ARRAY_TESTS This recipe measures the readnoise for a group of UIST DARK frames and files that measurement with the calibration system If this recipe is run in a UKIRT environment it will create or append to a log file located at ukirt_sw logs uist_array_tests log NOD_SKY_FLAT_THERMAL This is like NOD_SELF_FLAT_NO_MASK but it expects that the nod throws alternate to sky The sky frames alone make the flat H 2 Modified recipes e ARRAY_TESTS The log file is now called lt instrument gt _array_tests log where lt instrument gt is the lowercase instrument name e INOD_CHOP_FAINT There is now an option to create and display a quality map of the combined source images e NOD_SELF_FLAT_NO_MASK This recipe and NOD_SELF_FLAT_NO_MASK_APHOT now do not clean deviant pixels from the individual frames contributing to the flat Bad pixels in the mosaic are not filled The difference pair frames suffix _dp are no longer removed upon recipe completion e REDUCE_DARK This now supports variance creation and propagation by default There is a new steering parameter USEVAR to disable this H 3 Global changes The main changes from a user perspective were
258. s The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of jittered frames the recipe creates a mosaic which is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic e Intermediate frames are deleted except for the flat fielded _ff suffix frames Ephemeris file Format The current format of the ephemeris file is one line per object comprising three space separated fields in the following order e the objectname which may contain embedded spaces and e the motion in the plane of the sky in arcsec second for right ascension then declina tion Note that the right ascension motion is the change in right ascension multiplied by the cosine of the declination The format may change to include UT and possibly date Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix e A mosaic for each cycle of jittered frames in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0
259. s and edits the FITS headers Two things you might wish to change in the recipe _HELLO script are listed below e Change the extent of the images If there is an instrumental defect in some peripheral rows you might not want to use the full bounds as given by headers ORAC_X_LOWER_BOUND ORAC_X_UPPER_BOUND ORAC_Y_LOWER_BOUND ORAC_Y_UPPER_BOUND Suppose you wanted to trim off the top three rows you could change the line my y2 Frm gt uhdr ORAC_Y_UPPER_BOUND to my y2 Frm gt uhdr ORAC_Y_UPPER_BOUND 3 e Switch on error propagation To save time at the telescope the pipeline does not keep track of the errors per pixel except for the polarimetry recipes with names starting POL and the NOD_CHOP series If you wish to know realistic errors for your data in the recipe switch on the USEVAR argument for the recipe s _HELLO primitive Here is an example for the BRIGHT_POINT_SOURCE recipe _BRIGHT_POINT_SOURCE_HELLO_ USEVAR 1 4 2 2 Steering primitive Within a recipe s _HELLO primitive a steering primitive is invoked These are best left well alone They control when the various operations are performed See Appendix for more details What you can safely adjust are the configurable steering parameters listed in the recipe documentation In the main these parameters set the number of frames processed in a cycle through the recipe The parameters are passed by argument through the recipe s _HELLO script
260. s also have subdirectories for specific instruments This restructuring permits code reuse for current and new instruments It is also now possible to have recipes and primitives with the same name for different topics or instrument Such scripts do have similar functions but the exact processing depends on the data topic or some instrument attribute K Release Notes V2 1 0 The main changes are the addition of spatially jittered Fabry Perot recipes and recipes for compact comets K 1 New recipes FP_JITTER Reduction of a Fabry Perot observation comprising eight frames on and off the source and on and off the spectral line both to the blue and to the red This is repeated for a series of spatial positions of the source FP_JITTER_NO_SKY Reduction of a Fabry Perot observation comprising four frames all on the source and on and off the spectral line both to the blue and to the red This is repeated for a series of spatial positions of the source MOVING _QUADRANT JITTER As QQUADRANT JITTER but registration is adjusted to track the motion of a comet using ephemeris data The comet should lt 45 arcsec diameter for UFTI or lt 10 arcsec for IRCAM Compared with MOVING_JITTER_SELF_FLAT this recipe avoids cometary artifacts appearing in the flat field QUADRANT_JITTER_TELE As QUADRANT_JITTER but registers using the telescope off sets This is used for observing compact comets limiting angular sizes as above when the
261. s in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters SUN 232 8 Recipes 94 JITTER_SELF_FLAT_APHOT NUMBER INTEGER The number of frames in the jitter pattern If not supplied the number of offsets as given by FITS header NOFFSETS minus one is used If neither is available 9 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes BRIGHT_POINT_SOURCE_APHOT JITTER_SELF_FLAT ITTER_SELF_FLAT_BASIC JITTER_SELF_FLAT_NO_MASK QUADRANT_JITTER Implementation Status e The processing engines are from the Starlink packages and PHOTOM e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter Deprecated Variants JITTER5_SELF_FLAT_APHOT 95 JITTER_SELF_FLAT_BASIC SUN 232 8 Recipes JITTER_SELF_FLAT_BASIC Reduces a standard jitter photometry observation using just the basic operations for speed Description This script reduces a standard jitter photometry observation with near infrared imaging data It takes an imaging obs
262. set INGRID headers are also revised by the pipeline into an AIPS system lt instrument gt _CREATE_WCS_ lt instrument gt _GET_PLATE_SCALE_ Note that the reference pixel of the equatorial co ordinates in the raw headers was until recently only known to a few arcseconds but now should be of the order of 0 5 arcseconds The pipeline sets empirical reference pixels now matched by the telescope control system see primitive _CREATE_WCS_ for details For critical work you should tie in your frames with online catalogues as available through GAIA 3 2 Dark subtraction This is as simple as it sounds The dark frame selected through the calibration system must have the same exposure time and read type as the object frames There is no dark subtraction for chopped data as processed by the NOD_CHOP collection of recipes as the differencing of nodded pairs of frames makes the operation unnecessary _SUBTRACT_DARK_ _GET_DARK_NAME_ 3 2 1 Dark creation After the preliminary steps including addition of variance the dark is merely filed in the calibration system using the frame number and the exposure time in the name When multiple darks of the same exposure time form part of the same grouped observation these darks are averaged before filing with the calibration system Such averaged darks have the group number instead of the observation number in their names _AVERAGE_DARKS_ and IRCAM UFTI and UIST variants _GET_DARK_NAME_ 3 3 Flat
263. sis tent result amongst the overlapping regions The mosaic is trimmed to the dimensions of an input frame The mosaic is not normalised by its exposure time that being the exposure time of a single frame 59 BRIGHT_POINT_SOURCE_NCOLOUR_APHOT SUN 232 8 Recipes e For each cycle of jittered frames the recipe creates a mosaic which is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass and end UT headers areupdated to match that of the last observed frame contributing to the mosaic The photometry tabulation includes the file name source name time filter air mass the catalogue magnitude and estimates of the zero point with and without the application of a mean extinction There are headings at the top of each column The photometry uses the mode calculated from 3 median 2 mean and Chauvenet s rejection criterion to estimate the sky level in an annulus about the source The inner annulus diameter is 1 3 times that of the aperture 6 5 arcsec the outer annulus is 2 5 times 12 5 arcsec for UFTI and twice the aperture 10 arcsec for IRCAM and Michelle The errors are internal based on the sky noise e Intermediate frames are deleted except for the flat fielded _ff suffix frames e Sub arrays are supported Output Data e The resultant mosaic in lt m gt lt date gt _ lt group_number gt _ lt filter gt _mos w
264. star is appended to this file As the name implies it is intended for bright point sources such as standard stars but also any observation of a point source where using its own frames to make the flat is not appropriate Notes You may use SKY_FLAT or SKY_FLAT_MASKED to make the flat field e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 e The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used e Where automatic registration is not possible the recipe matches the centroid of the central source and should that fail it resorts to using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions e The recipe makes the mosaic by applying offsets in intensity to give the most con
265. ster mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic The polarised intensity is corrected for the statistical bias of the noise by subtracting the variance of Q or U An offset of 6 3 degrees clockwise is applied to the rotation angle for the orientation of the analyser with respect to north The polarisation data for each pixel are also stored in catalogues See Output Data The intensity image may be displayed with vectors overlaid Steps are taken to reduce the number of noisy or insignificant pixels as well as clutter First the polarisation catalogue data are averaged in 3 by 3 pixel bins Second a binned pixel is rejected if its polarisation is greater than 50 or is not positive or its polarisation signal to noise less than 3 or its polarisation error is greater 5 The bin size and thresholds can readily be changed by supplying arguments to the CALC _STOKES_ primitive At the end of each cycle the grand mosaics are registered and new polarisation maps and catalogues constructed Intermediate frames are deleted except for the flat fielded _ff suffix frames and the mosaics _mos or _mos_c lt cycle_number gt suffix Output Data The integrated mosaics in lt m gt lt date gt _ lt group_number gt _ lt beam gt lt angle gt _mos where lt m gt the instrument s group prefix Token lt beam gt is e or 0
266. structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers are corrected Spurious instrument names are changed to IRCAMS3 You may use SKY_FLAT or SKY_FLAT_MASKED to make the flat field e The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used e The most recent sky frame is used for the sky subtraction e Where automatic registration is not possible the recipe matches the centroid of central source and should that fail it resorts to using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaic by applying offsets in intensity to give the most consis tent result amongst the overlapping regions The mosaic is trimmed to the dimensions of an input frame The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of jittered frames the recipe creates a mosaic which is then added into a master mosaic of improving signal t
267. sure time that being the exposure time of a single frame SUN 232 8 Recipes 108 JITTER_SELF_FLAT_TELE e For each cycle of jittered frames the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic e Intermediate frames are deleted except for the flat fielded _ f suffix frames Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s e A mosaic for each cycle of jittered frames in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The naming formatlis slightly different for some non UKIRT instruments The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters NUMBER INTEGER The number of frames in the jitter pattern If not supplied the number of offsets as given by FITS header NOFFSETS minus one is used If neither is available 9 is the default An error s
268. t _mos lt cycle_number gt where lt cycle_number gt counts from 0 The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The naming format is slightly different for some non UKIRT instruments The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters NUMBER INTEGER The number of target frames in the jitter pattern If this is not set a value is derived from the number of offsets as given by header NOFFSETS The formula is NOFFSETS 2 1 An error results should NOFFSETS be odd If neither is available 9 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent 1 USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes CHOP_SKY_JITTER_BASIC EXTENDED_3x3_BASIC QUADRANT_JITTER_BASIC Implementation Status The processing engines are from the Starlink packages and Uses the Starlink NDF format SUN 232 8 Recipes 68 CHOP_SKY_JITTER_BASIC e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter 69 DARK_AND_BPM SUN 232 8
269. t field is created iteratively First an approximate flat field is created by combining normalised object frames using the median at each pixel This flat field is applied to the object frames Sources within the flat fielded frames are detected and masked in the dark subtracted frames The first stage is repeated but applied to the masked frames to create the final flat field For ISAAC residual bias variations along the columns are largely removed from each flat fielded frame The recipe first masks the sources then collapses the frame along its rows to form a profile whose clipped mean is subtracted The resultant profile reflects the bias variations The recipe subtracts this profile from each column of the flat fielded frame SUN 232 8 Recipes 98 JITTER_SELF_FLAT_CATALOGUE The field distortion of ISAAC is corrected in the target frames using the mappings documented on the ISAAC problems web page Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects the script resorts to using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of
270. t the end of each cycle of sky and object frames the full mosaic of target frames is created and displayed The mosaic has its bad pixels filled by interpolation On the second and subsequent cycles the full mosaic is added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass and end UT headers are updated to match that of the last observed frame contributing to the mosaic Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix A mosaic for each cycle of jittered target frames in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming formatlis slightly different for some non UKIRT instruments For ISAAC the individual bias corrected frames in isaac lt date gt _ lt obs_number gt _bce The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters NUMBER INTEGER The number of target frames in the jitter pattern If this is not set a value is der
271. t the overlapping regions The noise will be greater in the 79 EXTENDED_5x5_BASIC SUN 232 8 Recipes mosaic s peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame e Mosaics are made and displayed for each row except the last At the end of each cycle of 51 frames the full mosaic of 25 target frames is created and displayed instead On the second and subsequent cycles the full mosaic is added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic e Intermediate frames are deleted except for the flat fielded _ f suffix frames Output Data e The full mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instru ment s group prefix e A mosaic for each row in lt m gt lt date gt _ lt group_number gt _mos lt row_number gt where lt row_number gt is 0 to 3 e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming formatlis slightly different for some non UKIRT instruments Parameters NROW INTEGER The number of target frames in a row of the mosaic Its minimum is 3 because this number of blank skies are needed
272. tandard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is derived from the sky frames as follows The mode sigma clipped mean is used to offset each sky frame s mode to that of the first sky frame The corrected sky frames are combined pixel by pixel using a median of the values in each frame The resultant frame is normalised by its median to form the flat field This frame median is subtracted from the source frames after they have been flat fielded A flat field is created for each row of the grid of target frames and applied only to that row of target frames The sky subtraction comes from linear interpolation of the sky modal values of the two flat fielded sky frames which immediately bracket the target frame Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects it then tries the crosshead offsets If these are null the script resorts to the telescope offsets The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions 77 EXTENDED_5x5 SUN 232 8 Recipes e The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The noise will be greater in the mosaic s peripheral are
273. tate arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent 1 USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes ITTER_SELF_FLAT JITTER_SELF_FLAT_APHOT ITTER SELF_PLAT BASIC JITTER SELF_FLAT NO_MASK MOVING _JITTER SELF _FLAT QUADRANT_JITTER Implementation Status e The processing engines are from the Starlink packages FIGARO and EXTRACTOR e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through intermediate files to the mosaic e Error propagation is controlled by the USEVAR parameter Deprecated Variants JITTER9_SELF_FLAT_TELE 109 LAMP_FLAT SUN 232 8 Recipes LAMP_FLAT Creates and files imaging flat fields derived from a calibration lamp Description This recipe makes one or more flats for ESO infrared imaging from a series of internal flat frames with the calibration lamp alternating on then off A new flat is made for each combination of filter It performs a null debiassing bad pixel masking then differences each pair of frames Once all pairs have been so processed these are then treated like sky flats normalised frames are combined pixel by pixel using the median Details of each flat are filed in the index of flats for future selection and use of the flat See the for further details Notes e The b
274. ted but applied to the masked frames to create the final flat field Registration is performed using common point sources in the overlap regions If the recipe cannot identify sufficient common objects the script resorts to using the telescope offsets transformed to pixels The resampling applies non integer shifts of origin using bilinear interpolation There is no rotation to align the Cartesian axes with the cardinal directions The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time 101 JITTER_SELF_FLAT_NCOLOUR SUN 232 8 Recipes e For each cycle of jittered frames the recipe creates a mosaic which has its bad pixels filled and is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic e Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix A mosaic for each cycle of jittered frames for each filter in lt m gt lt date gt _
275. ter for the aperture photometry To alter to a 4 arcsecond aperture change the APERTURE argument s value of the APHOT_MAG_ primitive like below _APHOT_MAG_ APERTURE 4 To obtain details of a primitive s arguments use the oracman or perldoc command Thus oracman _MAKE_MOSAIC_ will display the documentation for primitive MAKE MOSAIC_ Space does not permit inclu sion of the documentation of the many primitives in this manual Most of primitives source code is stored in 0RAC_DIR primitives imaging the instrument specific ones are situated within 0RAC_DIR primitives lt instrument gt where lt instrument gt is UFTI UIST MICHELLE IRCAM IRIS2 ISAAC or INGRID and there are a few general scripts in ORAC_DIR primitives general While the simplest primitives just invoke a Starlink task and updates just that and are amenable to customisation some are quite complex especially for the registration They may invoke other primitives manipulate parameters and small data files so that the various tasks connect to cope with a variety of circumstances The most likely change you will want to make is to change the parameter values of a Starlink task Armed with the reference documentation for the application say with a findme lt application gt it is easy to change values or append further parameters Here is an example Let us suppose you wanted to combine frames to make a self flat not with the median since you have heard that
276. ter over NFS served drives can also lead to erroneous results crashing of the pipeline or computer lockups 3 SUN 232 8 Using the pipeline 2 2 Raw Data Formats and Conversions Raw data take the form of multiple NDFs within an for UKIRT data or individual FITS files for AAT INGRID ISAAC and data For UFTI and IRCAM they comprise one NDF for the data array and dynamic headers such as the start time of the exposure and another for static headers Each container file is converted to a single NDF in 0RAC_DATA_OUT with a merged set of headers The Michelle HDS container file also has NDFs for the individual chop beams However these cannot be merged until the data variance is calculated from the individual beams Michelle reduced chopped data become simple NDFs once the recipe takes the difference of the two beams ORAC DR automatically converts AAT FITS files into single NDFs in 0RAC_DATA_OUT which retain the original FITS headers For INGRID and NIRI ORAC DR converts a multi extension FITS file into a multi NDF HDS container file following UKIRT conventions 2 2 1 ISAAC and NACO Preliminary Conversion Since ORAC DR as yet cannot cope with ESO file naming which uses the UT epoch instead of a sequence number there is a special C shell script which must be invoked once normally before the first ORAC DR initialisation If you enter isaac2oracdr in a directory containing ISAAC FITS files the command converts them into NDFs
277. terpolation There is no rotation to align the Cartesian axes with the cardinal directions SUN 232 8 Recipes 138 NOD_SELF_FLAT_NO_MASK_APHOT The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to the dimensions of a single frame thus the noise will be greater in the peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of object frames the recipe creates a mosaic is then added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic The photometry tabulation includes the file name source name time filter airmass the catalogue magnitude and estimates of the zero point with and without the appli cation of a mean extinction To discriminate between the various results the positive images have suffix _pos after the frame name and the negative images have a _neg suffix There are headings at the top of each column The photometry uses a multiply clipped 2 2 2 5 3 standard deviations mean to estimate the sky mode in an annulus about the source This is not unduly biased by the presence of the self flat artifact in th
278. test QUADRANT_JITTER variant as it lacks object mask ing automatic registration and resampling MOVING _QUADRANT_JITTER Compact comets lt 45 arcsec As QUADRANT JITTER but uses ephemeris data to track the non sidereal source QUADRANT_JITTER_TELE As QUADRANT_JITTER but uses telescope offsets for regis tration Telescope tracks object Galaxies and nebu lae with angular ex tent lt 2 arcminutes Sky subtracted 3x3 grid mosaic on target Frames alternate be tween sky and target Requires a dark EXTENDED_3x3_BASIC As EXTENDED_3x3 but lacks resampling and registers using telescope offsets Galaxies and nebu lae with angular ex tent lt 3 arcminutes Sky subtracted 5x5 grid mosaic of the target Frames alternate between sky and target Re quires a dark EXTENDED_5x5_BASIC As EXTENDED_5x5 but lacks resampling and registers using telescope offsets SUN 232 8 Recipes 44 Point source recipes mid infra red Recipe Name Type of Data Function and Comments Bright N and Q limits to be determined Chopped and nodded observations to remove sky background and telescope contributions dif ferences both chopped beams and nodded pairs of frames giving a mosaic with two positive and two negative images There is no masking or flat fielding Requires a bias in CHOP mode e g from recipe ARRAY_TESTS NOD_CHOP_APHOT As th
279. the jittered sky frames and applied to all the target frames e The sky subtraction comes from linear interpolation of the sky modal values of the two sky frames which immediately bracket the target frame Registration is performed using the telescope offsets transformed to pixels There is no resampling merely integer shifts of origin 67 CHOP_SKY_JITTER_BASIC SUN 232 8 Recipes The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The noise will be greater in the mosaic s peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame At the end of each cycle of sky and object frames the full mosaic of target frames is created and displayed On the second and subsequent cycles the full mosaic is added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix A mosaic for each cycle of jittered frames in lt m gt lt date gt _ lt group_number g
280. the saturation limit for the detector in the mode used The flat field is derived from the sky frames as follows The mode sigma clipped mean is used to offset each sky frame s mode to that of the first sky frame The corrected sky frames are combined pixel by pixel using a median of the values in each frame The resultant frame is normalised by its median to form the flat field This frame median is subtracted from the source frames after they have been flat fielded A flat field is created for each row of the grid of target frames and applied only to that row of target frames e The sky subtraction comes from linear interpolation of the sky modal values of the two flat fielded sky frames which immediately bracket the target frame Registration is performed using the telescope offsets transformed to pixels e There is no resampling merely integer shifts of origin The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The noise will be greater in the 75 EXTENDED_3x3_BASIC SUN 232 8 Recipes mosaic s peripheral areas having received less exposure time The mosaic is not normalised by its exposure time that being the exposure time of a single frame e Mosaics are made and displayed for each row except the last At the end of each cycle of 19 frames the full mosaic of nine target frames is created and displayed instead On the second and subsequent cycles th
281. time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic e Intermediate frames are deleted except for the flat fielded _ f suffix frames Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix A mosaic for each cycle of object frames in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 e The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The naming format is slightly different for some non UKIRT instruments For ISAAC the individual bias corrected frames in isaac lt date gt _ lt obs_number gt _bc The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters NUMBER INTEGER The number of frames in the nod pattern If absent the number of offsets as given by header NOFFSETS minus one is used If neither is available 4 is used An error state arises if the number of jittered frames is fewer than 4 and not a multiple of 4 USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes BRIGHT_POINT_S
282. tomatically It performs a null debiassing creation and propagation of data variance difference the integrations for each AB chop beam pair bad pixel masking difference adjacent nodded pairs registers the frames and forms a mosaic containing positive and negative images of the source Column and row patterns are filtered The script extracts the various chopped and nodded images of the source and neighbouring background from the mosaic It combines them using a median filter at each pixel to form to form a single image of the source with four times the signal This combined frame is smoothed to enhance the visibility of faint sources See the for further information Notes e A variance array is created for each beam first using the read noise and once the bias is removed Poisson noise is added e A bias frame selected from the calibration system is removed from each beam in CHOP read mode If no bias frame is available in the CHOP mode the recipe subtracts a null bias so the errors will be overestimated in the CHOP read mode the data array will be unaffected once the beams are differenced The ARRAY_TESTS recipe files a suitable short exposure dark as a bias in the calibration system The integrations of the two beams are differenced the first subtracted from the second in each pair e A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist The bad pixel mask appl
283. tus e The processing engines are from the Starlink packages CCDPACK FIGARO and EXTRACTOR e Uses the Starlink NDF format e History is recorded within the data files e The title of the data is propagated through the intermediate file to the flat e Error propagation is controlled by the USEVAR parameter SUN 232 8 Recipes 182 SKY_FLAT_MASKED SKY _FLAT_MASKED Creates and files a flat field derived from jittered frames using object masking to reduce artifacts Description This recipe makes a sky flat for UKIRT imaging from a series of sky or object frames which are combined using one of a selection of statistics It expects one dark frame followed by jittered sky frames It performs a null debiassing bad pixel masking and dark subtraction before combining the sky frames pixel by pixel to make the flat See the Notes for further details The parameters of the flat are filed in the index of flats for future selection and use of the flat For best results the field observed should contain few stars and no bright ones In sparse fields recipe SKY_FLATHis a faster alternative Notes A World Co ordinate System WCS using the AIPS convention is created in the headers should no WCS already exist For IRCAM old headers are reordered and structured with headings before groups of related keywords The comments have units added or appear in a standard format Four deprecated headers are removed FITS violating headers ar
284. ument names are changed to IRCAMS3 The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad The lower limit is 5 standard deviations below the mode but constrained to the range 100 to 1 The upper limit is 1000 above the saturation limit for the detector in the mode used The flat field is created in two steps The quadrant containing the object is masked in each object frame Then the recipe combines the normalised and quadrant masked object frames using the median at each pixel Registration is performed using the telescope offsets transformed to pixels e There is no resampling merely integer shifts of origin The recipe makes the mosaics by applying offsets in intensity to give the most consistent result amongst the overlapping regions The mosaic is not trimmed to SUN 232 8 Recipes 166 QUADRANT_JITTER_BASIC the dimensions of a single frame Thus the noise will be greater in the peripheral areas having received less exposure time The full signal will be in the central ninth containing the main object The mosaic is not normalised by its exposure time that being the exposure time of a single frame For each cycle of four the recipe creates a mosaic which is added into a master mosaic of improving signal to noise The exposure time is also summed and stored in the mosaic s corresponding header Likewise the end airmass header and end UT
285. us recipes SUN 232 8 Recipes Recipe Name Type of Data Function and Comments ADDWCS Creates the valid WCS in the FITS headers of raw data NIGHT_LOG Generates a text file log of a series of observations Very bright point source recipes Recipe Name Type of Data Function and Comments BRIGHT_POINT_SOURCE IZ lt 13 JHK lt 9 and bright 13 lt IZ lt 17 9 lt JHK lt 15 Normally a 5 point jitter but would be usable as 3 point Re quires a separate flat as the back ground is too low to self flat and a dark BRIGHT_POINT_SOURCE_APHOT As BRIGHT_POINT_SOURCE but also performs aperture photometry of the source BRIGHT_POINT_SOURCE_ NCOLOUR As BRIGHT_POINT_SOURCE but produces filenames that include filters for easier identifica tion for multi colour observations BRIGHT_POINT_SOURCE_ NCOLOUR_APHOT As BRIGHT_POINT_SOURCE_ APHOT but produces filenames that include filters for easier iden tification for multi colour observa tions BRIGHT_POINT_SOURCE_TELE As BRIGHT_POINT_SOURCE but uses telescope offsets for registration BRIGHT_POINT_SOURCE_TELE_ APHOT As BRIGHT_POINT_SOURCE_ APHOT but uses telescope offsets for registration SUN 232 8 Recipes 40 Point source recipes thermal Recipe Name Type of Data Function and Comments NOD_SELF_FLAT_NO_MASK NOD_SELF_FLAT_NO_MASK_APHO
286. vation number starting at 1 each night BIAS DARK FLAT LAMP OBJECT SKY Right Ascension J2000 at reference position and offset 0 0 h 193 F2 Steering Headers SUN 232 8 Internal Headers RA_SCALE F Pixel scale along right ascension axis arcsec RA_TELESCOPE_OFFSET F Telescope right ascension offset with respect to the RA_BASE position arcsec READMODE S Such as STARE NDSTARE CHOP ROTATION F Angle of the Declination axis with respect to the frame s y axis measured counter clockwise SPEED_GAIN S Speed and type of readout e g Normal Fast Higain for UFTI Standard Fast Deepwell for IRCAM TELESCOPE S The PAL palObs telescope name STANDARD B Whether or not the observation is of a standard UTDATE S UT date of the observation in yyyymmdd format UTEND F UT of the end of the observation h UTSTART F UT of the start of the observation h WAVEPLATE_ANGLE F Polarimetry waveplate position angle deg X_LOWER_BOUND I Start column of array readout X_REFERENCE_PIXEL F The pixel index of the x reference position for RA_BASE and DEC_BASE X_UPPER_BOUND I End column of array readout Y_LOWER_BOUND I Start row of array readout Y_REFERENCE_PIXEL F The pixel index of the y reference position for RA_BASE and DEC_BASE Y_UPPER_BOUND I End row of array readout F2 Steering Headers Headers which direct a recipe are called steering headers These can include timing information such as when a flat should be made qualif
287. w and reduced data directories are as shown below Those with ISAAC and NACO data should see Section 2 2 1 for a necessary preliminary naming conversion step for each instrument Classic Cam users need to read Section concerning renaming raw data files for the respective instruments The second option is where your raw and reduced data are to be in arbitrary directories Type the following oracdr_ lt instrument gt lt date gt setenv ORAC_DATA_IN lt raw_data_directory gt setenv ORAC_DATA_OUT lt reduced_data_directory gt The directories can either be given as full paths or as relative paths to the current working directory Here is an example for IRCAM data using full paths oracdr_ircam 19990328 setenv ORAC_DATA_IN export data mjc asteroid night1 setenv ORAC_DATA_OUT home scratch mjc reduced In the first case 0ORAC_DATA_IN and 0RAC_DATA_OUT are still defined but in terms of the root directory For instance re using the earlier example with UFTI for UT date 2000 November 8 S ORAC_DATA_IN points to 0RAC_DATA_ROOT raw ufti 20001108 ORAC DR operates in 0RAC_DATA_OUT irrespective of what your current directory is when you invoke it Your current directory remains unchanged It is highly recommended to work in directories on discs local to the computer running the pipeline Processing over NFS served drives can many times slower and degrades the perfor mance seen by other users Running ORAC DR on a Linux compu
288. wise the end airmass header and end UT headers are updated to match that of the last observed frame contributing to the mosaic Intermediate frames are deleted except for the flat fielded _ff suffix frames Output Data The integrated mosaic in lt m gt lt date gt _ lt group_number gt _mos where lt m gt is the instrument s group prefix A mosaic for each cycle of jittered frames in lt m gt lt date gt _ lt group_number gt _mos lt cycle_number gt where lt cycle_number gt counts from 0 The individual flat fielded frames in lt i gt lt date gt _ lt obs_number gt _ff where lt i gt is the frame prefix The aming formatlis slightly different for some non UKIRT instruments For ISAAC the individual bias corrected frames in isaac lt date gt _ lt obs_number gt _bce The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters NUMBER INTEGER The number of frames in the jitter pattern If not supplied the number of offsets as given by FITS header NOFFSETS minus one is used If neither is available 9 is the default An error state arises if the number of jittered frames is fewer than 3 For observations prior to the availability of full ORAC header NOFFSETS will be absent USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes
289. with names adhering to the UKIRT convention The prefix is isaac The earliest file has observation number 1 and the observation number increments for each FITS file in time order The script copes with files names in either the raw or archive nomenclature It also writes observation and group number headers to assist ORAC DR It copes with data from more than one night in a given directory assigning each night its own sequence of observation numbers and it uses a common UT date for observations in a single night spanning midnight UT You should put all both the calibration and target files for a given night in the same directory Likewise in a directory of NACO FITS files you should first enter naco2oracdr to create a set of NDF files whose names adhere to the UKIRT convention with a naco prefix 2 2 2 Classic Cam Preliminary Conversion The Magellan raw FITS data have a sequence number but no UT date in their names There is a preprocessor C shell script which must be invoked once normally before the first ORAC DR initialisation If you enter cc2oracdr SUN 232 8 Using the pipeline 4 in a directory containing Classic Cam FITS files the command converts them into NDFs with names adhering to the UKIRT convention The prefix is cc The earliest file has observation number 100 a Classic Cam convention and the observation number increments for each FITS file in sequence number order It also writes the observation and group nu
290. xel grid is not resampled Improved central source registration and corrected the world co ordinate system associ ated with polarimetry products The latter includes allowance for the bifurcation in the Wollaston prism and the left handed sky co ordinates of UIST by flipping the raw data and WCS headers Enlarged the extracted target and sky regions for UIST 199 G 3 Global changes SUN 232 8 Release Notes V4 1 Combining sources in NOD_CHOP recipes revamped using the chop and nod offsets to decide upon the visibility of an image Thus it can now cope with just one positive negative image pair Centroid hunting allows for the source to be just outside the initial search box and should lead to better registration of single sources and photometry when the source is not placed at the nominal location such as shifted instrument apertures at UKIRT The option to clean small blemishes using a 15x15 box filter during flat creation is now accessible from recipes say when invoking _FLAT_FIELD_MASKED_GROUP_ Object masking reports the detection threshold read from the EXTRACTOR parameter file rather than a hardwired value For ESO data CHOP_SKY_JITTER allows the last frame to be of the target Fixed a bug where the normalised sky frames were flat fielded prior to object masking instead of flattening the frames with masked deviant pixels Fixed a bug in determining a consistent set of sky levels for CHOP_SKY_JITTER in multiple re
291. y different for some non UKIRT instruments The created flat fields in flat_ lt filter gt _ lt group_number gt for the first or only cycle and flat_ lt filter gt _ lt group_number gt _c lt cycle_number gt for subsequent cycles Parameters USEVAR LOGICAL Whether or not to create and propagate variance arrays 0 Related Recipes ITTER_SELF_FLAT _TELE IMOVING_JITTER_SELF_FLAT MOVING QUADRANT JITTER QUADRANT _JITTER Implementation Status The processing engines are from the Starlink packages FIGARO and EXTRACTOR Uses the Starlink NDF format History is recorded within the data files The title of the data is propagated through intermediate files to the mosaic Error propagation is not used 171 REDUCE_DARK SUN 232 8 Recipes REDUCE_DARK Averages and files observations as the current dark Description This recipe reduces dark frame observations with infrared imaging data Multiple darks of the same exposure time are averaged It files the single or averaged dark in the dark index file Other reduction steps comprise bad pixel masking optional creation of data errors This recipe reduces a dark frame observation with infrared imaging data It files the dark in the dark index file Reduction comprises bad pixel masking and optional creation of data errors Notes e The bad pixel mask applied is 0RAC_DATA_CAL bpm e Each dark subtracted frame has thresholds applied beyond which pixels are flagged as bad
Download Pdf Manuals
Related Search
Related Contents
uC/Trace User`s Manual - Doc Handbuch - Wincor Nixdorf 6428 User Manual RevA Philips Blu-ray Disc player BDP9100 Theory and Troubleshooting Copyright © All rights reserved.