Home

SURF – SCUBA User Reduction Facility

1. Figure 14 Example despiking of a point source The two outside lines on each diagram indicate the region outside which a spike would be found the clipping envelope The middle line indicates the median of the data in each cell The top two diagrams show the data displayed using Spiral left and Xlinear right modes The x axis indicates that the source is visible for small bin number in spiral mode and for a much larger bin number in xlinear mode The lower two diagrams show the same thing except that hanning smoothing has been applied to the clipping envelope in each case SUN 216 8 Skydips 178 I Skydips The skydip observing mode measures the sky brightness at a range of elevations and uses that data to calculate the zenith sky opacity The absolute value of the sky brightness is required and this values is calculated by interpolating its measured signal from that measured with ambient and cold loads In order to calculate the zenith sky opacity to the sky brightnesses the task fits a theoretical curve to the data The theoretical curve at each wavelength takes the form Jmeas 1 Mitel Jtel ag Mtei Jatm Ditellame 3 where Jmeas is the measured brightness temperature of the sky fte is the transmission of the telescope Ji is the brightness temperature of a black body at the temperature of the telescope Jatm is the brightne
2. f file name of NDF file sdf may be included in the name d file2 name of a second file e g the despiked version of the NDF file The same bolometers will be plotted in a second window or overlaid for comparison s min max Y axis scales for plot can be changed via menu 1 number of bolometers per window bol list of bolometers to plot Type all for 1 37 and alls for 1 91 Can be added via menu if mode r 15 SCUPLOT SUN 216 8 Complete routine descriptions Examples scuplot The user will be asked for a mode and input file before proceeding scuplot m d f 039_lon_ext Interactive despiking on 039_lon_ext sdf see also dspbol scuplot m p f s14_lon_ext 12 13 18 20 25 26 19 Enter p mode and use file s14_lon_ext sdf Plot bolometers 12 13 18 20 25 26 and 19 Notes e If the overlay comes up scrambled delete the agi_xxx files in your home directory and if that does not work also files like linplot sdf in the home you adam subdirectory Related Applications Bugs Freezes when asked to plot a bad bolometer SUN 216 8 Complete routine descriptions 152 SCUQUICK SCUQUICK automate the basic SCUBA data reduction Description This script attempts to automate the first 3 steps of scuba data reduction This script runs change _flat if requested flatfield on the data Then for each sub instrument if a photometry observation if requested and rebin if requeste
3. Before diverging though we should first take a diversion into the question of despiking 9 5 Despiking This section describes the different techniques available for despiking SCUBA data 9 5 1 Manual despiking Manual despiking simply involves examining the data with linplotland identifying bad regions by eye and then running change_quality to turn off the bad points In general this is very 10Note that PHOTOM data array is 3 dimensional use the NDF section 2 with in order to examine these data lt is possible to rebin photometry data although obviously the image will not be fully sampled SUN 216 8 The data reduction process 24 tegration Int 10 15 20 2a BO 355 Bolometer Figure 6 The 3C279 data after processing through extinction and remsky The next stage is to regrid the data using rebin The source can clearly be seen in bolometer 19 H7 The negative stripes are indicating that the chop throw was smaller than the array 25 SUN 216 8 The data reduction process time consuming especially working out the pixel number of a spike so thatichange _ quality can be told the exact location so two interactive techniques are available 1 dspbol This script automates the change _quality cycle bolometers can be plotted in turn with spikes identified and removed all within a few seconds 2 The sclean task allows users to simply click on bad points to remove them This routine has been designed f
4. Usage setbolwt h wtfile filelist filenames Parameters h Return a usage message wtfile file An ASCII text file containing the weights one weight per line corresponding to the order of bolometers stored in the file filelist file An ASCII text file containing a list of files to be processed There must be one file per line and it must be in a form acceptable to rebin ie comments can be included filenames List of filenames to be processed Wild cards can be used eg _lon_ext sdf Examples setbolwt The user will be prompted for a list of input NDFs The weights will be calcu lated by setbolwt setbolwt wtfile weights dat filel Set the weights in filel sdf from the list contained in weights dat setbolwt filel file2 file3 file4 159 SETBOLWT SUN 216 8 Complete routine descriptions Calculate the weights of each bolometer in all four files relative to the central pixel in file1 sdf setbolwt wtfile wt dat filelist rebin inp Set the weights of the files listed in rebin inp to those stored in wt dat same weights for each file Notes e Input files must have been extinction corrected so that only one sub instrument is present per file e When multiple files are used bolometers are compared to the central bolometer of the first file e If source signal is present in any bolometer at a level significantly above the noise the automatic weighting will be skewed in fact the bolometer
5. convert setaxis scuba_image mode delete ndf2fits bitpix 32 profits scuba_image scuba_image fits The PROFITS parameter is there to ensure that all the FITS information in the NDF is propagated to the FITS file With FIGARO we would do figaro delobj scuba_image axis wdfits scuba_image scuba_image fits 13 As of release v1 3 it is no longer necessary to remove the AXIS extension before processing with ndf2fits because rebin now writes WCS information using the AST library SUN 216 8 The data reduction process 34 Note that ee writes integer FITS whereas ndf2fits would by default write REAL FITS ndf2fits bitpix 32 ndf2fits also writes the Variance and Quality arrays to FITS tables in the output file this can be turned off by specifying just the data component with COMP D From Kappa V0 13 the WCS information stored in the header is used when manipulating the NDF As of SURF version 1 4 the astrometry information is no longer stored in IRAS90 or FITS extensions all astrometry information can be found in the AST WCS component which is understood by KAPPA GAIA and 9 7 Photometry For photometry data all that is required after extinction remsky is that the jiggle pattern be processed to determine the signal for each integration and bolometer It is possible to derive the signal by taking the AVERAGE of the jiggle data or by fitting a PARABOLA to the data Parabola fitting probably should not be use
6. e This task does not attempt to create a component if the specified component is missing A Variance array can be created using the KAPPA task setvar if necessary SUN 216 8 Complete routine descriptions 72 CHANGE_DATA e The SECTION parameter is not used if a SCUBA section was given via the IN parameter Related Application SURF change__ quality rebin scuphot 73 CHANGE_FLAT SUN 216 8 Complete routine descriptions CHANGE_FLAT Change the flatfield in a SCUBA datafile Description The flatfield information is stored inside each demodulated data file and this task can be used to change the flatfield that is stored internally The new flatfield is read from a text file Usage change_flat in new_flat Parameters IN NDF Read Name of NDF to change MSG_FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM NEW_FLAT CHAR Read Name of the new flatfield file Examples change_flat test newflat dat This will change the flatfield stored in test sdf to that stored in newflat dat Related Application SURF flatfield SUN 216 8 Complete routine descriptions 74 CHANGE_NACENTRE CHANGE_NACENTRE Shift the Nasmyth centre of the array Description This routine shifts the position of the Nasmyth centre of a SCUBA array It can be used to take out the small difference between the centres of the LONG and SHORT wave arrays Should be run after lextincti
7. Tamb gconst where Tiapse is the temperature drop per kilometre altitude 6 5 K km and Xgconst is a constant determined empirically and has a value of 3 669383 For more information see 35 179 I 1 Calibration SUN 216 8 Skydips I 1 Calibration The choice for T_HOT and T_COLD critically affects the result of the skydip fit The default values for the hot and cold temperatures are usually stored in the data header but occasionally these values are redetermined and the header values must be over ruled As of version 1 6 of SURF the cold load temperature as well as the default telescope efficiency fte for the 850 and 450 ym filters is suggested from a lookup table rather than the data headers Also the hot load temperature is now known to be wavelength dependent and an adjustment of 1K at 850 microns and 3K at 450 microns is now automatically applied to the value stored in the header More details on skydip calibration can be found in Archibald et al 36 I 2 Removing bad skydip data from the fit Occasionally it is necessary to remove bad points from skydip data prior to fitting This is implemented in the same way as it is implemented for other SCUBA data by using change_quality The following extra steps are required 1 Run reduce _ switch to calculate the sky brightness temperature for each integration at each airmass measurement The cold load temperature for each sub instrument will be requested
8. There are also two cookbooks available one dealing with the reduction of photometry data 9 and the other dealing with the reduction of map data 10 Alternatively the JCMT software group can be contacted directly via the World Wide Web Information on known bugs and updates will be available there A mailing list now exists for discussing SCUBA data reduction techniques The list is at scubadr jach hawaii edu To subscribe send an email message to maj ordomo jach hawaii edu with an empty subject and containing the message subscribe scubadr you some email address http www ach hawaii edu JACpublic JCMT software SUN 216 8 What data do I have 3 What data do I have Journal software is available to aid with book keeping of observation files If you are reducing your data at the Joint Astronomy Centre you may need to read Appendix D to find where the data are stored sculog will give a summary of all NDF files in a directory the directory is the current working directory and if set the directory specified by the DATADIR environment variable 7 sculog Enter starting observation number 0 94 Enter final observation number last 95 Log for directory jcmt_sw scuba sun216 scuba observe apr25 dem 94 JUPITER PHOTOM 1997 4 25 17 43 39 99893 RA 21 26 1 54 Dec 15 42 52 0 J2000 Observed centre PLANET Mean airmass 1 2310825 Bolometers H7 Filter 450N 850 Throw 60 arcsec AZ Int
9. e Output file from remdbm now no longer contains CHOP_ keywords 12 7 Changes in Version 1 5 This is a minor update New Tasks e scuba2memlofficially released previously it was available but not advertised e The SURF programming guide SSN 72 now available Changes to existing tasks sculog and related tools rewritten to handle data from multiple UT dates in a single directory Extended support for POLMAP and POLPHOT observing modes e Improve support of external data model in Can now import image of arbri trary coordinates and automatically add chop functions e jadd_dbmjcan now be used to add a triple beam SUN 216 8 Release Notes 48 e Scripts are now compatible with KAPPA version 0 14 Bug fixes e Fix bug in remdbm when using filtering when data have a pixel origin that is not in the middle of the array 12 8 Changes in Version 1 4 The main purpose of this upgrade is to add polarimetry support to SURE New Tasks remip can be used to remove instrumental polarisation e ladd_dbmican be used to generate simulated dual beam images e scusetenv for setting environment variables at the JAC Changes to existing tasks e Units should now be propagated correctly through all tasks ie calibration units are not lost after rebin or scuphot e SURF version number is now written to history information e jscan_rlb Area to use for baseline removal can now be specified as a SCUBA section remdbm The
10. not used not used 2D9 ll 2 00 Oo O I ou ot wou 00 H gt Q e A NN Wee Ep AU A A A O Fs O AS AS tl ooo E2 Rebinned data SUN 216 8 FITS keywords SCUBA instrument being used SCUBA instrument being used SCUBA instrument being used Bol to whose value SW guard ring is set Short wave guard ring on or off Zenith sky optical depth Zenith sky optical depth Zenith sky optical depth Zenith sky optical depth Zenith sky optical depth The ambient air temperature K Effective temperature of cold load K Effective temperature of cold load K Effective temperature of cold load K Effective temperature of cold load K Effective temperature of cold load K The temperature of the hot load K The temperature of the telescope TRUE if dividing chop by cal before rebin Wavelength of map microns Wavelength of map microns Wavelength of map microns Wavelength of map microns Wavelength of map microns The rebinned data files contain the following Note that the astrometry information is not stored in the FITS extension fitslist n59_reb_lon OBJECT 3c279 FILE_1 n59_sky_lon SYSTEM EQUATORIAL 2000 0 LONG 3 3867510541917 LAT 0 10104535223053 TELESCOP JCMT Hawaii INSTRUME SCUBA WAVELEN 0 000862 FREQ 347787074245 94 FILTER 450 SCUPROJ RJ 7 SCUPIXSZ L DATE OBS 08 04 97 DATE 2000 07 06T02 35 4
11. request e a lt CR gt at topic and subtopic prompts to move up one level in the hierarchy and if you are at the top level it will terminate the help session e aCTRL D pressing the CTRL and D keys simultaneously in response to any prompt will terminate the help session e a question mark to redisplay the text for the current topic including the list of topic or subtopic names or e an ellipsis to display all the text below the current point in the hierarchy For example BLOCK displays information on the BLOCK topic as well as information on all the subtopics under BLOCK You can abbreviate any topic or subtopic using the following rules e Just give the first few characters e g PARA for Parameters e Some topics are composed of several words separated by underscores Each word of the keyword may be abbreviated e g Colour_Set can be shortened to C_S e The characters and x act as wildcards where the percent sign matches any single character and asterisk matches any sequence of characters Thus to display information on all available topics type an asterisk in reply to a prompt e Ifa word contains but does end with an asterisk wildcard it must not be truncated e The entered string must not contain leading or embedded spaces Ambiguous abbreviations result in all matches being displayed 137 SCUHELP SUN 216 8 Complete routine descriptions Implementation Status e Uses the portab
12. where we have made the approximation that S Mean S Measured Usage remip in ipfile out Parameters IN NDF Read Input data file IPFILE FILE Read File containing the IP flatfield MSG FILTER CHAR Read Message filter level Options are QUIET NORMAL and VERBOSE Default is NORM OUT NDF Write Output file containing IP removed data Default output filename is _ip 1 for short form Examples remip filel ipfile dat Correct filel sdf using ipfile dat and write IP corrected data to the default output file eg file1_ip Notes e Variance is propagated correctly 119 REMIP SUN 216 8 Complete routine descriptions e This task writes out the waveplate angles and rotation angles The waveplate angle per integration is written to MORE REDS WPLATE The rotation angle waveplate 0 to X pixel axis is written to MORE REDS ANGROT angle per integration The angle between nasmyth and the ra dec frame ie ANGROT 90 degrees is stored in MORE REDS NASMYTH_ANG angle per sample These are written as NDFs and so can be displayed in the normal way The angles are in degrees e Anarray containing the fast axis angle is also written to the REDS extension FAST_AXIS The size of this array matches the number of sub instruments in the file SUN 216 8 Complete routine descriptions 120 REMSKY REMSKY Remove sky noise and constant offsets from SCUBA jiggle data Description This task removes s
13. SUN 216 8 Complete routine descriptions 80 DESPIKE NSIGMA REAL Read The sigma clipping level used for despiking each cell SMODE CHAR Given This parameter controls the mode used for smoothing of the clipping envelope If smoothing is selected the extraction mode DMODE is used to determine the pixels that are adjacent to each other Allowed modes are e NONE No smoothing e HANN Hanning smoothing OUT NDF Write This is the name of the NDF that will contain the despiked data There will be one prompt per input filename assuming spikes were detected OUT_COORDS CHAR Read The coordinate system of the output grid Available coordinate systems are e AZ Azimuth elevation offsets e NA Nasmyth offsets e PL RA Dec Offsets from moving centre eg Planets e RB RA Dec B1950 e RJ RA Dec J2000 e RD RA Dec epoch of observation e GA Galactic coordinates J2000 For RD current epoch is taken from the first input file REF CHAR Read The name of the first NDF to be rebinned The name may also be the name of an ASCII text file containing NDF and parameter values See the notes REF can include a SCUBA section SHIFT_DX REAL Read The pointing shift in X to be applied that would bring the maps in line This is a shift in the output coordinate frame SHIFT_DY REAL Read The pointing shift in Y to be applied that would bring the maps in line This is a shift in the output coordinate frame WEIGHT RE
14. The relative weights associated with each point in the output map are stored in a WEIGHTS NDF in the REDS extension of the output data For WEIGHTS TRUE For spline rebinning each point is equivalent to the number of integrations added into the final data point For weight function regridding the situation is more complicated The actual number of points contributing to each cell can be stored using the TIMES parameter e Bolometer weights will be used if a BOLWT extension is found in the input data file usually set with setbolwt e Astrometry information is stored in the WCS component and not the FITS extension ASCII input files The REF and IN parameters accept ASCII text files as input These text files may contain comments signified by a NDF names values for the parameters WEIGHT SHIFT_DX and SHIFT_DY and names of other ASCII files There is one data file per line An example file is SUN 216 8 Complete routine descriptions 112 REBIN file1 b5 1 0 0 5 0 0 Read bolometer 5 from file1 sdf file2 Read file 2 but you will still be prompted for WEIGHT and shifts file3 i3 1 0 0 0 0 0 Use everything except int 3 test bat Read in another text file Note that the parameters are position dependent and are not necessary Missing parameters are requested This means it is not possible to specify SHIFT_DX position 3 without specifying the WEIGHT If the file has the txt extension the NDF system will attempt to
15. This information along with a standard FITS header is stored as a standard NDF The data array is constructed as follows 3 dimensional N_BOL x N_POS N_BEAM x 2 1 where N_BOL is the number of bolometers N_POS is the number of samples for each bolometer time axis N_BEAM is the number of beams The 3rd dimension contains the actual data value plus positions of every beam associated with the data point Each beam has two positions X offset and Y offset Axis components store bolometer number LST and beam weight Related Applications SURF extract_data rebin DBMEM PIXON Copyright Copyright C 1995 1996 1997 1998 1999 Particle Physics and Astronomy Research Council All Rights Reserved SUN 216 8 Complete routine descriptions 130 SCUCAT SCUCAT Concatenate photometry datasets for further processing Description This routine reads in a list of user specified files and concatenates their data variance and quality arrays so that KAPPA routines like stats and kstest can analyse a complete set of photometry observations scucat can be configured so that either all data are concatenated into one file regardless of bolometer METHOD catall or data for each bolometer is kept separate METHOD separate In the latter case if a file contained data for H7 and H9 then two output files would be created e g test_h7 and test_h9 if the OUT parameter was set to test and for each new bolometer a new file is c
16. BA ae ee oes es ate Se aoe ot A a ee at de es ee 124 AAA A 126 SCUBA2MEM 0 0 0 0 0 a 128 SCUGAIA 5 bts ete i Oe ats eb cies ars E a ae AS 130 ye areas Bee ye ee GE ees eek gee Ge eee oe ee 132 SCUCEKERRY a soria asa ek we ROD A ee ele 134 A ee A es E E es E ee ee es 135 SCULOG I sina woh Bo us ee Ae ee ty Be Ph de Meal hh Boe Oe tee es 138 SCUMAKEWT 0 0 crcscec asesu ekek n aua Gordea 141 Pa a a ae oe A E a 143 Ele Be vee A DA da a Se ee is a 144 OG WPAN a O a is a as sae eae 146 SCUPHO Da a hee e rte a Gk ane a ee te ee teas dat ats 147 blocs aes alee Spek Ge ae es ee ea toda Te Ace se at eo ge da 149 ie ey Reade ok ae Gee a e a a peace Hees a 152 SCUSETENV sa cn cose td gt thn a ah Wee Pa 155 SCUSHIUPIAL 2 dew eater ei Oh dey Pees ke me Ge es SA ha ae 156 Be A ee ve he A wea At E anee eat eae 157 ide oe Asics Sea ees ea ee ie ee ee a a 158 dees aoe Geis Oo See Gee ee ee ee ee ee 160 A as Sore eas be deus ae uae Jose ee 161 Soe Gy awd ee ee eee eo eee oe Se ee ee ee 164 166 fee Ge Gea ek Ee ecg es Hee Roos ye eon ak bak ne 166 CS ae ae ee A e ee ee o A a are 166 167 eee eats A do O Spacey A weeds ea Aa 167 E 2 Structure of RO files ee ee 167 E 3 Structure of demodulated files 2 ee 168 170 Bat ace Heer ee Sou es GD Gets Se ee 170 Sly este er atin te eg Gees Gyan Ge ea ee e 173 174 176 178 Ld Calibration e 6 4 0 84 8 Ge es a ede a Be Bebe Be Be ded 179 I 2 Removing bad skydip dat
17. POLPHOT POLMAP These are PHOTOM or MAP observations observed in polarimetry mode For these observations a measurement is taken usually consisting of one integration for different positions of a half wave plate SURF can be used to reduce these measurements so they can be processed by a specialized polarimetry data reduction package such as POLPACK SCAN MAP In SCAN MAP mode also known as on the fly mapping the telescope is continuously scanned across the sky usually at a Nasmyth position angle of 18 degrees so that the image is fully sampled on a single pass whilst using the secondary mirror to chop so that atmospheric contributions can be minimized Scan rates of up to 24 arcseconds per second are possible in this mode and it is the most efficient SCUBA mapping mode One problem with this mode is that the data is taken in dual beam mode each data point is the difference between the left and the right chop positions This means that sources appear twice in data separated by the chop throw a positive beam and a negative beam this dual beam response must be taken out in software Two forms of data taking are implemented one involves chopping along the scan direction whilst the other involves chopping in a fixed direction on the sky but combining data from many chop configurations 121 13 SKYDIP This mode measures the sky brightness temperature at a range of elevations and uses that data to calculate the zenith sky opacity I
18. SUN 216 8 FITS keywords SWTCH_NO S_PER_E TELESCOP TEL_OPER UTDATE UTEND UTSTART VERSION ALIGN_DX ALIGN_DY ALIGN_X ALIGN_Y AZ_ERR CHOPPING EL_ERR FOCUS_DZ FOCUS_Z SEEING SEE_DATE TAU_225 TAU_DATE TAU_RMS UAZ UEL UT_DATE BAD_LIM CALIB_LG CALIB_PD CHOP_LG CHOP_PD CNTR_DU3 CNTR_DU4 FILT_i FILT_2 FILT_3 FILT_4 FILT_5 FLAT JIG_DSCD L_GD_BOL L_GUARD MEAS_BOL N_BOLS N_SUBS PRE_DSCD PST_DSCD REBIN REF_ADC REF_CHAN SAM_TIME SIMULATE SKY SUB_1 SUB_2 dl 2 JCMT 2 Ned Land 1997 4 8 79 43 49 99992 9 35 09 999847 0 0 414241 0 556058 4 0787 4 16459 0 T 0 0 113297 16 0 316 29704072245 0 096 29704080210 3 0E 03 3 35413 2 04832 gt 8 Apr 1997 32 5 64 02849 4 18 2927 0 0 2450 a 850 gt not used not used gt not used noiseflat dat 1 2H7 2 F not used 128 2 0 0 LINEAR 1 1 123 F gt skydip_startup dat gt SHORT gt LONG 4 a a ns a a es Sa a s s a a es SS ee Se a 172 F1 Demodulated data Switch number at end of observation Number of switch positions per exposure Name of telescope Telescope operator UT date of observation UT at end of observation UT at start of observation SCUCD version MU tables X MU tables Y MU tables X MU tables Y axis S axis S S S Error in the telescope azimuth S E S S alignment offset axis alignment offset axis MU Chopper choppin
19. Setting ANGROT to 70 27795 Setting IMGID to omci_reb I1 Setting FILTER to 850_ 2 5 lt cut intervening information gt Processing omci_reb 1I16 Setting WPLATE to 335 Setting ANGROT to 75 46666 Setting IMGID to omci_reb 1I16 Setting FILTER to 850_335 SURF provides a suitable import table The next stage is to generate the I Q and U images from these individual waveplate images This can be done by the polcal task directly polcal weights 3 ilevel 2 omc1_reb Processing 16 images in single beam mode OUT Output Stokes cube gt omc1_cube Iteration 1 Total number of aberrant input pixels rejected 199 Iteration 2 Total number of aberrant input pixels rejected 219 Iteration 3 Total number of aberrant input pixels rejected 219 Iteration 4 Total number of aberrant input pixels rejected 219 None of the output pixels failed the test specified by parameter MINFRAC In this case we use WEIGHTS 3 to generate the variance information from the fit since the SCUBA variances are unreliable although in many cases these variances are not under estimated polcal can combine images from separate overlapping fields all in one go if desired If the intention is to mosaic separate fields within polcallintrebin should be run with the TRIM parameter set to some non zero value to prevent problems with edge effects during the mosaicing Also expects all the images to be referenced to the
20. The name of the skydip data file or if SCUBA_PREFIX is set the number of the observation raw demodulated data only The input data file can be the output from reduce _ switch or the raw skydip data Can be located in DATADIR The filename will be requested if not specified on the command line Examples sdip 19970623_dem_0008 Reduce the skydip data in 19970623_dem_008 sdf and plots the result Related Applications SURF Skysum Syd Implementation Status e Requires KAPPA e All files created by this task are removed SUN 216 8 Complete routine descriptions 158 SETBOLWT SETBOLWT Calculate or set bolometer weights Description This routine sets the bolometer weights It can do this in two ways 1 Calculate the statistics for each bolometer then generate the weights relative to the central pixel Should not be used when a strong source is present The weights are calculated by using to calculate the standard deviation of each bolometer in turn The weight is defined as the relative variance between this bolometer and the reference bolometer 2 Read the weights from a text file using the wtfile option Writes to the BOLWT extension This extension is then read by rebin Multiple files can be referenced to the first file by specifying multiple files on the command line or by using a rebin style input file and the filelist option In conjunction with the wtfile option all input files are given the same weights
21. b41 52 i3 BAD_QUALITY Set bolometers 41 and 52 as well as integration 3 to bad quality Use of SEC TION here is not recommended given the complication when using commas and square brackets change_quality test SECTION b2 i2 BAD_QUALITY Set everything bad except bolometer 2 and integration 2 Notes Samples are marked bad by setting bit 3 of the quality array The effects of can be removed by changing the value of the bad bit mask with the task or by running change _quality on the entire array section is for entire array but with BAD_QUALITY false so that bit 3 decimal value of 8 is no longer used as a masking bit Related Application SURF rebin scuphot KAPPA 79 DESPIKE SUN 216 8 Complete routine descriptions DESPIKE Despike data by position Description This routine despikes demodulated data by comparing points that lie in the same region of sky Each point is placed in the output grid similar to rebin but without the smoothing depending on its position The points in each cell are then compared with each other and spikes are detected if any points lie more than NSIGMA from the mean Optionally a plot is provided showing the points in each bin along with the clipping level to be used for despiking In order to provide a 2 dimensional plot of 3 dimensional data the grid is unwrapped such that all the cells are plotted in one axis The unwrapping order is governed by the DMODE parameter Mo
22. negative and Right beams NBEAMS 3 writes Middle Left and Right beams OUT NDF Write This parameter specifies the name of the output file to be used to store the positional information The file format is described below OUT_COORDS CHAR Read The coordinate system of the output map Available coordinate systems are e AZ Azimuth elevation offsets e NA Nasmyth offsets e PL RA Dec Offsets from moving centre eg Planets e RB RA Dec B1950 RJ RA Dec J2000 e RD RA Dec epoch of observation 129 SCUBA2MEM SUN 216 8 Complete routine descriptions e GA Galactic coordinates J2000 SHIFT REAL 2 Read The pointing shift X Y to be applied that would bring the map into the correct position This is a shift in the output coordinate frame CHANGE_POINTING should be used to add Az El pointing offsets Examples scuba2mem out_coords GA 034_lon_ext 034_mem nbeams 1 Calculate the coordinates of all bolometer positions in tangent plane offsets from the GA map centre scuba2mem 034_lon_ext nbeams 3 Calculate all chop positions for 034_lon_ext Use RJ coordinates Notes e Can be used on JIGGLE and SCAN data e The coordinates of the selected output frame are written to the output FITS extension in keywords OUT_CRDS OUTLONG and OUTLAT The full FITS header of the observation itself is still available Format of output file SCUBA DBMEM requires the data positions of every beam and the LST for every point
23. or as flag option e It may be necessary to set the HDS_SCRATCH environment variable if files are being logged from directories for which write access is denied e g setenv HDS_SCRATCH tmp Related Applications SURF fculog fmapsun Pointsum bssur Ekysum 103 PLTBOL SUN 216 8 Complete routine descriptions PLTBOL Interactive bolometer display Description pltbol or any p gt link to scuplot is a wrapper around the KAPPA utility linplotand facilitates data inspection It allows plots of a whole series of bolometers one by one optionally overlaying them with the same bolometer from a second file Obvious overlays are despiked on non despiked data or data from different exposures to check the noise The menu items are M H Redisplay menu Q Quit N Next bolometer B Switch to bol X min max X cen X axis from min max or cen 10 Just x activates the cursor R Reset X axis Y min max Y lim Y axis from min max or lim lim U Reset Y axis Option gt Note that a X center defined with the cursor or X cen defaults to a 20 points window around cen the position of the spike Using the CURSOR the Left Mouse button always defines the point the Right Mouse button exits the cursor task while accepting the last point clicked Usage pltbol f sdf_file d sdf_file2 s min max bol bol bol Parameters h elp Print the help information f file name of NDF file
24. reduce_switch 70 SURF Opening 19971115_dem_0070 in scuba observe 19971115 dem SURF run 70 was a SKYDIP observation SURF file contains data for 1 switch es in 1 exposure s in 10 integration s in 10 measurement s OUT Name of output file to contain reduced switch data 070 gt T_COLD Temperature of cold load for SHORT_DC 95 gt T_COLD Temperature of cold load for LONG_DC 55 gt 2 The resulting output file looks just like a file produced by reduce_ switch on map data it contains a 2 dimensional data array of sub instrument bolometer number along the first axis and sample number number of integrations times number of measurements along the second axis You can find the sub instrument corresponding to each bolometer number either by running skydip and noting the order of the listed sub instruments or by using the command fitslist 070 grep SUB_ SUB_1 gt SHORT 7 SCUBA instrument being used SUB_2 LONG SCUBA instrument being used SUB_3 not used SCUBA instrument being used SUB_4 not used SCUBA instrument being used SUB_5 not used SCUBA instrument being used For example the data for the second sub instrument in this case the LONG array can be plotted by using linplot mode 2 device xwindows 070 2 Fig 15 shows an example Note that in contrast with other observing modes the second axis is labelled in measurements rather than integration
25. 9 4 Common data reduction 21 A AA II 23 9 5 1 Manual despiking ddr ii ee ed da A EES 23 9 5 2 Automatic despiking es ds Sk ch eee o e Ee ERE EHS 25 9 6 Map MaKINE ere iced kok eee aS eRe eee ae ee ESE EES 27 9 6 1 Rebinning multiple datasets om A A A A A 31 9 6 2 Output coordinate frames 22 5 G5 ud E Re eS AA 31 9 6 3 Exporting Maps se b eee he eke Bek A AR A 33 9 7 ODO ere bo a RO a A ORS OS ee 34 7 1 SURF photometry and KAPPA s 2 2 6 eh 6 ek awe Oe ew ee ee ses 35 Paer ue oh ues ee ah eu Be ee ee Gee eee ee A 36 9 8 1 Baselineremoval 0 00 cee ee ee ee 37 98 2 STEVE A ee ee eG 37 9 8 3 _ Dual beam deconvolution 0 00000 eee eee 39 9 9 Polarimetry data reduction ots DIARIA RUE e ie ee See 41 10 Citing SURF 44 11 Future Work 45 12 Release Notes 46 12 1 Changes in Version 1 6 11 es cues kee Pee Sow a ee Re 46 SUN 216 8 Contents iv 12 2 Changes in Version 16 10 22142 sea heb babe Phe Shae AA 46 12 3 Changes in Version 1 6 9 2o2 dst tee btad a A EYER 46 124 Changes in Version 1 6 8 2144 niu tee de Sh OE EERE REESE REELS 46 12 5 Changes in Versi n 67 rociar RE RRE ar eS Re ee Re ws 46 12 6 Changes in Version Lol es 4 dee pois oe e ES oR OR ee a AA 47 12 7 Changes i Version Ole sac ee ee ee OE oe OY A eee ee bee es 47 12 8 Changes ifi Version LA as goya ane eee a ee E A RY OE 48 129 Changes in Version L3 e cerei as E EA IDO RA
26. A 11 gal gal 351 jae 37 jsel aol aol 33X rr rra a ays 251 261 271 281 201 301 31 32l 25 A A A pe pepe wa isi ia 201 jan 22 231 24 71 E 1 ae oe oe AAN 1107 19 12 13y 14 15 16 9 10 i IS iJi 1 pr 14 11 Sis 1 2 13 4 5 6 7 l8 1 YLINEAR DIAGI DIAG2 Figure 13 A schematic of the different display modes for despike The start of each scan is represented by the letter S and the end by the letter E SUN 216 8 Quality flags 176 Table 4 Quality bits used by SURF Bit Value Meaning 0 1 Infinity eg division by zero 1 2 Set by flatfield 2 4 Set by if the transputers detected more spikes than specified by the SPIKE_LEVEL parameter is provided This option smooths the clipping envelope the region that determines whether a point is a spike or not across adjacent bins so that fluctuations in the statistics of adjacent bins are reduced This smooth works in one dimension only and the definition of adjacent depends on the method used for transforming the data to 1 D parameter DMODE Figure 14 shows an example of the different modes with and without smoothing Points lying outside the high and low lines are treated as spikes In this example the smoothing has resulted in the detection of two spikes probably too faint on this figure but the spikes are in bins 120 spiral and 2370 x H Quality flags The
27. Iam only interested in raw demodulated data i e files containing _dem_ in their names sculog and obssum supports many more options and these are detailed in Alternatively listings of certain observations can be obtained by using the more specialized listing programs photsum mapsum pointsum and skysun pointsum lists pointing observations photsum lists photometry observations and in fact skydip observations lists map observations and skysumllists skydip observations Using photsum instead er the data used above gives photsum begin 92 end 98 HST Source Meas Int Am Filter SubInst Signal S N Tau Seeing 92 07 33 JUPITER 1 4 1 23 450N 850 LONG 7 85e 00 2841 0 074 0 161 93 07 36 JUPITER 1 4 1 23 450N 850 LONG 6 34e 00 1257 0 074 0 161 94 07 43 JUPITER 1 4 1 23 450N 850 LONG 5 97e 00 936 4 0 074 0 423 SHORT 9 26e 01 164 SK kkk k 95 07 46 SKYDIP 10 20 450N 850 SHORT 1 756 0 074 0 423 LONG 0 310 In this case I specify the range of observations on the command line and the format of the listing has changed from that returned by sculog Note that the signal and signal to noise are now provided this is only the case if RO files are catalogued since the demodulated data files do not contain results the column is left blank if no reduced data is found On the other hand mapsum gives this output mapsum begin 92 end 100 HST Source Meas Int Am Filter Mode Thr Crd PA Tau Seeing kk kkk kk
28. In arcseconds Edge is defined as a radius of 70 arcseconds IN NDF Read The name of the NDF containing to be tested MSG FILTER CHAR Read Message filter level Default is NORM LAG REAL Write The discrepancy between the LST stored in the FITS header and the LST when data acquisition begins This provides a measure of the lag in starting up the observation including slew times The value is stored in seconds MJD DOUBLE Write Modified Julian Date of start of observation corrected for the lag time and the clock error Notes e The calculated clock error is only accurate to about 15 seconds References Jenness T 2000 JCMT Technical Report TR 001 84 135 SCUHELP SUN 216 8 Complete routine descriptions SCUHELP Gives help about SCUBA software Description Displays help about SCUBA software The help information has classified and alphabetical lists of commands general information about SCUBA and related material it describes individual commands in detail Usage scuhelp topic subtopic subsubtopic subsubsubtopic Parameters TOPIC LITERAL Read Topic for which help is to be given SUBTOPIC LITERAL Read Subtopic for which help is to be given SUBSUBTOPIC LITERAL Read Subsubtopic for which help is to be given SUBSUBSUBTOPIC LITERAL Read Subsubsubtopic for which help is to be given Examples scuhelp No parameter is given so the introduction and the top level help index
29. SUN 216 8 Complete routine descriptions 164 SKYSUM SKYSUM Produce one line summary of SCUBA skydip observations Description Skysum goes through all the sdf files in the current directory and optionally DATADIR defined in an environment variable and summarizes files containing skydip observations In the absence of the all flag a numeric range is requested This range only has an effect on raw data or reduced files which have the run number embedded into the file name Filenames with no numbers are treated as scan 0 Usage skysum h demod reduced all begin nn end nn Parameters hlelp Return a help message only More help can be obtained by using showme sun216 or scuhelp skysum all List all skydip files in the current directory and DATADIR demod Only list demodulated data files signified by _dem_ file name reduced Only list reduced data files signified by _red_ file name begin nn First scan number to be considered same as begin nn end nn Final scan number to be considered same as end nn Examples skysum Ask for a range of scan numbers and then give a summary of every skydip file matching this criterion in DATADIR and the current directory skysum all Generate a summary of all skydip files in the current and DATADIR directory skysum begin 5 end 100 Generate a summary of all skydip data from scans 5 to 100 inclusive sk
30. SURF software conforms to the NDF standard concerning the processing of quality or bad pixel masks Each method of setting a pixel bad is associated with a bit in the quality masking flag the NDEQUALITY BADBITS component The bad bits and their meaning in SURF are described in table 4 In order to remove the effect of a particular bit i e to ignore a despiking the KAPPA task setbb can be used to change the bad bits mask in the NDF Simply calculate the value related to the bits you are interested in keeping and use this value in setbb Note that care must be taken in deciding which bits are to be used for masking bad data Bits zero and one must always be set whereas the other three bits are optional change _qualitylis the only task that acts on a file rather than producing a processed copy and it is probably better if change _qualitylis used directly if you wish to manipulate the mask associated with bit three Additionally regridded images also use quality flags Bit 0 is used to represent areas where no data were available and bit 1 is used to mask data at the edge of the regridded area via the TRIM parameter 177 SUN 216 8 Quality flags
31. TION and MEASUREMENT For SCAN MAP data the middle of an exposure ie scan is used Default is exposure 1 EXT NDF Read The name of the extinction corrected data from which the bolometer positions should be taken INTEGRATION INTEGER Read Use the bolometer positions at the specified integration Default is measurement 1 MEASUREMENT INTEGER Read Use the bolometer positions at the specified exposure Default is measurement 1 MSG_FILTER CHAR Read Message filter level Default is NORM NDF NDF Read The name of the regridded data set taken from the AGI graphics database NAME LOGICAL Read Label with bolometer name if true else bolometer number The default is true If a null response is given the bolometer label is not drawn STYLE LITERAL Read Plotting style to be used for the bolometers The relevant key to use for adjusting the plotting style is bolometer This is a synonym for curve and can be abbreviated to bol The most useful attribute to change is the colour Explicit control of the style of the text labels is provided using the text attribute If this attribute is not supplied all plotting styles are inherited from the bol style 145 SCUOVER SUN 216 8 Complete routine descriptions Examples scuover The bolometer names will be overlaid using the default colour scuover style colour bol red noname This command will overlay bolometer numbers over the image in red scu
32. Use KAPLIBS rather than private copies of KAPPA routines 12 5 Changes in Version 1 6 7 This is a bug fix release ov V1 6 e Add support for raster skydips e Minor fixes for scuba2mem with EKH scanning e Don t calculate clock correction when using AZ 47 SUN 216 8 Release Notes 12 6 Changes in Version 1 6 This includes important changes to the skydip task relating to default values of fitting parameters and a fix for the SCUVAX clock error problem New Tasks scuclkerr can be used to determine possible clock errors in the acquisition system Changes to existing tasks e Add correction for the SCUVAX clock error problem e Skydips now know the correct values to use as defaults for ETA_TEL T_COLD and T_HOT In remsky the outer ring of bolometers can be specified using R 1 i e it counts from the outside in if you use a negative ring number e scuover is now a little cleverer and the text can be a different color to the circles and uses PGPLOT rather than the old SGS plotting system e scunoiselworks on Windows NT e If the second LST provided to remsky is less than the first LST it is now assumed that the time refers to the following day Bug Fixes e Fixed error when scuphot runs in the pipeline where occasionally the parabola fit of the complete coadd could give incorrect answers e Can now combine data taken at almost the same wavelengths a 20 micron difference is allowed when using rebin
33. Write The name of the NDF to which the flatfielded data are to be written Examples flatfield redsw flat This will flatfield the data from redsw sdf and write it to flat sdf Related Applications SURF SUN 216 8 Complete routine descriptions 92 INTREBIN INTREBIN Generate a separate regridded image for each integration Description This routine rebins the demodulated data from SCUBA MAP observations onto a rectan gular mesh by a variety of methods Currently convolution by weighting functions spline interpolation and median are supported Usage Weighting functions Currently linear Bessel and Gaussian weighting functions are supported The width of the Bessel function is such that it should preserve all spatial information obtained by the telescope at the wavelength of observation but suppress higher spatial fre quencies To minimise edge effects the Bessel function is truncated at a radius of 10 half widths from the centre although this is configurable and apodized over its outer third by a cosine function Viewed in frequency space the method consists of Fourier transforming the input dataset s multiplying the transform by a cylindrical top hat the F T of the Bessel function then transforming back into image space A linear weighting function is also available which works out to one half width this has the advantage that it is much faster to process and is much less susceptible to edge effects The Gaussi
34. all samples to the output file This is necessary for observations where the number of integrations is small and the variance can not be calculated reliably SUN 216 8 Release Notes 50 scan _rlbjnow has two extra modes for baseline removal MEAN and MEDIAN e A Gaussian regridding option has been added to rebin bolrebin intrebin Also the radius and footprint size of the convolution functions can now be configured e A median regridding option is available This option simply calculates the median value of all points in an output cell e A histogram of the distribution of data samples on the output image can be obtained with the TIMES parameter in rebin e Bolometer weighting has been added to rebin This is still in alpha test since it has been shown not to conserve flux for small data sets for larger datasets hours there is a signal to noise gain without turning off bad pixels e skydip now provides an estimate of the errors Minor fixes despike can now be told to write output files automatically via the DEFOUT parameter scuclip now performs an iterative clip by default e Units are propagated through scuphot sdip now resets the linplot colour settings to their original values after use e The size of the IN parameter has been increased in change_qualityland change _ data e A memory leak has been fixed in despike 12 11 Changes in Version 1 1 General changes e Output files are now as
35. are QUIET NORM and VERB Default is NORM There are no verbose messages OUT CHAR Write The name of the HDS output file to contain the NDFs described above This file will have the extension sdf but this should not be specified in the name Examples scuphot o56_lon_ext average o56_lon_pht Process 056_lon_ext by averaging integrations Do not write a text file contain ing the results Notes e ALLBOLS must be false for 2 and 3 bolometer photometry unless you know what you are doing e SCUPHOT can process JIGGLE MAP data The output is the signal for each integra tion for each bolometer This is useful for checking sky removal and should not be used for performing on source photometry on map data This method can not be used for SCAN MAP data Related Applications SURF scucat Implementation Status Ideally scuphot should process MAP data on a per exposure basis Currently only per integration is supported 149 SCUPLOT SUN 216 8 Complete routine descriptions SCUPLOT Interactive display and despiking Description Scuplot is a wrapper script around a number of KAPPA utilities Since it understands the Scuba NDF file format it hides most of the complicated syntax from the user Mode p and r are wrappers around plotting utilities and facilitate the inspection of the data of each bolometer The utility allows change to the plot scales via the menu but will keep the scales the same for all bolometers w
36. can be found in The sdip script can be used to automate the procedure of running skydip and displaying the results with KAPPA s linplot More information on skydipping can be found in Appendix I 9 3 Noise measurements Noise observations are reduced on line and written to an ASCII text file In some cases this text file is not available and the reduce _noise task can be used to recreate it as well as generating an NDF file containing the results from the raw demodulated data file reduce_noise 19981113_dem_0001 SURF Opening 19981113_dem_0001 in scuba observe 19981113 dem SURF run 1 was a NOISE observation OUT Name of container file to hold map and time sequence data o1 gt FILE Name of ASCII file to contain results summary noise_981113_1 dat gt 9 4 Common data reduction Now the data processing can begin We will start by running reduce _switch in order to subtract the off from the on and to split the data array of the raw data into separate components reduce_switch 59 SURF Opening apr8_dem_0059 in scuba observe apr8 dem SURF run 59 was a MAP observation of object 3c279 SURF file contains data for 2 switch es in 4 exposure s in 3 integration s in 1 measurement s OUT Name of output file to contain reduced switch data 059 gt or with the full file specification reduce_switch apr8_dem_0059 SURF Opening apr8_dem_0059 in scuba observe apr8 dem SURF run 59 was a MAP o
37. convert it to NDF format before processing this is probably not what you want Related Applications SURF polea ntrebin Seuquiek extract daia 113 REDUCE_NOISE SUN 216 8 Complete routine descriptions REDUCE_NOISE Process demodulated noise data Description This routine takes raw demodulated noise data and processes it NDF and ASCII results files are generated The output NDF file is a 2 D dataset with a chop signal and calibrator signal per bolometer The text file is similar to the file generated by the real time system Parameters IN NDF Read The name of the raw noise data file A single number can be supplied if SCUBA_PREFIX is set DATADIR is recognised OUT NDF Write Output NDF This file is 2 dimensional The first dimension is bolometer number The second dimension is chop signal and calibrator signal along with variances and quality If no output NDF is required a null value can be given FILE FILENAME Write Output text file Format is almost identical to that generated by the real time system A null value can be supplied to prevent a text file from being written The default output name is the same name as generated by the on line system noise YYMMDD_nr dat MSG_FILTER CHAR Read Message output level Default is NORM Allowed values are QUIET NORMAL and VERBOSE Examples reduce_noise 19981113_dem_0001 out_noise Read in observation 1 and write the output to an NDF names out_noise
38. data reduction scheme is identical to standard reduction except that the remip task must be run after extinction to remove the instrumental polarisation For map observations the ntrebin task must then be used to generate an image for each integration in practice this means an image per wave plate position intrebinfensures that the sky rotation angle and the waveplate angle are stored in the FITS headers using the ANGROT and WPLATE keywords respectively At this point the images can either be processed by scripts to calculate the Q and U we use the POLPACK data reduction system version 2 or higher which fits a sine wave to each pixel in the input images The following example uses POLPACK and is similar to the approach used by the ORAC DR 27 polarimetry recipes 28 Assuming the output of ntrebinlis stored in file onc1_reb sdf remembering that this file will contain an image per waveplate position named i1 i2 etc There are 16 images in this example POLPACK must first be told where to find the rotation angle and waveplate position polimp table SURF_DIR polimp scuba omci_reb 16 input images to process 14 Available from your support scientist if required although the ORAC DR pipeline recipes are now preferred SUN 216 8 The data reduction process Figure 11 Final image of M82 after single beam restoration 42 43 SUN 216 8 The data reduction process Processing omci_reb I1 Setting WPLATE to 2 5
39. environment variable is searched This means that the raw data does not have to be in the working directory In addition IN accepts a number This number is converted to a demod ulated data filename by prepending it with information specified in the SCUBA_PREFIX environment variable This filename expansion only works for demodulated data ie data containing _dem_ The _dem_ is assumed and should not be present in SCUBA_PREFIX SUN 216 8 Complete routine descriptions 116 REMDBM REMDBM Remove dual beam signature from scan maps Description This program should be used to reduce SCAN MAP data taken using the technique described by Emerson 1995 ASP Conf Ser 75 309 The deconvolution is performed using Fast Fourier techniques Usage remdbm h v out noams filter files Parameters h Help message v Version number Also indicates whether ADAM communication is enabled out file Filename of output image Default is final sdf noams Turn off ADAM messaging if available Default is false Ignored if ADAM messaging is not available filter Turns on high frequency filtering When used data at frequencies greater than that to which the telescope is sensitive are set to zero files List of input files to be processed Shell wildcards are allowed See notes for restric tions Examples remdbm x_reb sdf Process all files matching the pattern and write the result to final sdf remdb
40. filter option will filter out high frequencies before inverting the Fourier transform e rebin Add TRIM parameter to trim edge regions from rebinned images useful when trying to mosaic Astrometry information is now entirely contained in the AST WCS component No longer written to FITS or IRAS90 extensions Also the pixel origin is now centred on the specified RA Dec centre of the image and not the bottom left hand corner REFPIX parameter has been added to make it easier to specify the reference pixel location when changing the map size in the past the reference pixel was always the middle of the map when specifying the map size The output file is now propagated from the input when processing a single file keeps history intact Waveplate position and sky rotation angle are now written to the fits headers for polarimetry observations Can process FAST_AXIS polarimetry information correctly Add preliminary support for RASTER mode not yet stable POLMAP and POLPHOT are now supported modes now recognizes measurements as well as integrations required for polarime try observing Now can make a weights image like a reference image ie same size chop throw and position angle See the LIKE parameter 49 SUN 216 8 Release Notes 12 9 Changes in Version 1 3 This is only a minor upgrade All scripts have been updated so that they are compatible with KAPPA VO0 13 New Tasks e Noise data can now be
41. for examining the data before regridding or passing it to an external program for further processing Obviously this task should not be used to simply examine the data KAPPA tasks such as display and can do that this task gives you the position of each bolometer in addition to the data value Additionally the scuba2mem task can be used for finding the chop positions although it would then be necessary to use the CONVERT indf2ascii task to generate a text file scuclip can also be used for despiking jiggle map data as long as sources are weak SUN 216 8 Basic outline of SCUBA data reduction 16 REDUCE_SWITCH CHANGE FLAT FLATFIELD EXTINCTION a SCUCLIP CHANGE QUALITY lt gt aa REMSKY SCUPHOT SCUCAT Figure 2 The SURF data reduction flow diagram for PHOTOM data Optional tasks are indicated by dashed lines Note that map data can follow the photometry path and photometry data can follow the map path if necessary 17 SUN 216 8 Basic outline of SCUBA data reduction REDUCE SWITCH CHANGE_FLAT F FLATFIELD EXTINCTION SCUCLIP CHANGE QUALITY oN Pe lt 5 e CHANGE NACENTRE lt CHANGE_POINTING CALCSKY t Py 3 REMSKY j XN y r
42. in the name d file2 name of a second file e g the despiked version of the NDF file The same bolometers will be plotted in a second window or overlaid for comparison s min max Y axis scales for plot can be changed via menu bol list of bolometers to plot Type all for 1 37 and alls for 1 91 Can be added via menu if mode r Examples scuplot The user will be asked for an input file and bolometer list before proceeding dspbol f 039_lon_ext Interactive despiking on 039_lon_ext sdf A bolometer list will be requested dspbol f s14_lon_ext 12 13 18 20 25 26 19 Use file s14_lon_ext sdf Plot bolometers 12 13 18 20 25 26 and 19 Notes e If the overlay comes up scrambled delete the agi_xxx files in your home directory and if that does not work also files like linplot sdf in the home you adam subdirectory e Figaro s sclean is a more efficient alternative Related Applications SURE KAPPA FIGARO Bugs Freezes when asked to plot a bad bolometer SUN 216 8 Complete routine descriptions 86 EXTINCTION EXTINCTION Remove the effect of atmospheric extinction from a SCUBA observation Description This application extracts from a demodulated data file data for a specified SCUBA sub instrument and corrects it for the effect of atmospheric extinction The airmass at which each bolometer measurement was made is calculated then multiplied by the zenith sky extinction at the time of the mea
43. input string of 015_1on_ext would become an output string of 015_lon_clip i e the trailing _ext has been replaced with _clip This method ensures that the length of the filename does not grow out of control during the data reduction Ad ditionally if the suggested output filename would be the same as the input e g by running scuclip successively a is appended to the string so that the two can be distinguished This is the default method and is used by scuquick VERBOSE In this mode the output filename is constructed by appending the long suffix related to the current task to the input filename This means that the filename becomes longer and longer as the reduction proceeds The method of choice can be selected by setting SCUBA_SUFFIX to one of the above values case independent e g setenv SCUBA_SUFFIX verbose The suffix strings related to each task and mode are detailed in table 2 and typical examples from a data reduction are shown in table Currently modes LONG and VERBOSE share the same suffices but use them in different ways 7 2 Other useful environment variables Three non SURF environment variables can be used to affect the behaviour of SURF HDS_SCRATCH As described in SUN 92 this variable defines the directory in which HDS will create temporary files This variable must sometimes be set when you are accessing data from directories in which you do not have write permission Usually this variabl
44. integrations added into the final data point For weight function regridding the situation is more complicated The actual number of points contributing to each cell can be stored using the TIMES parameter Bolometer weights will be used if a BOLWT extension is found in the input data file usually set with setbolwt Astrometry information is stored in the WCS component and not the FITS extension ASCII input files The REF and IN parameters accept ASCII text files as input These text files may contain comments signified by a NDF names values for the parameters WEIGHT SHIFT_DX and SHIFT_DY and names of other ASCII files There is one data file per line An example file is SUN 216 8 Complete routine descriptions 96 INTREBIN file1 b5 1 0 0 5 0 0 Read bolometer 5 from file1 sdf file2 Read file 2 but you will still be prompted for WEIGHT and shifts file3 i3 1 0 0 0 0 0 Use everything except int 3 test bat Read in another text file Note that the parameters are position dependent and are not necessary Missing parameters are requested This means it is not possible to specify SHIFT_DX position 3 without specifying the WEIGHT If the file has the txt extension the NDF system will attempt to convert it to NDF format before processing this is probably not what you want Related Applications SURF rebin bolrebin extract data 97 MAPSUM SUN 216 8 Complete routine descriptions MAPSUM Prod
45. into your favoured data format The RO file signified by _red_ in the file name contains the reduced data image skydip result photometry result calculated by the on line system These data can be examined either by using or for images a Starlink compatible image display package note that nested NDFs are used see Appendix E Thttp wwwijach hawaii edu JACpublic JCMT Figure 1 The SCUBA arrays uononponur g 9IZ NNS 3 SUN 216 8 Starting up SURF 2 Starting up SURF The SURF environment can be initialised from the C shell using the surf command surf SURF SCUBA User Reduction Facility Commands are now available Version 1 6 0 Type scuhelp for help on SURF commands Type showme sun216 to browse the hypertext documentation Note that the represents the C shell prompt and shouldn t be typed SURF is also available from the ICL command language 2 1 Getting help Help is available in two forms from the command line and via a hypertext version of this document The command line version is available with scuhelp and the hypertext version can be obtained with findme surf or showme sun216 A WWW browser will be started up if necessary It is possible to start the help system when responding to an ADAM prompt Supplying a will give more information on the parameter being requested and supplying will start the interactive help system
46. many cases it is known that the tau value was taken a certain time before or after the observation so this value can simply be added In addition most of the time a constant tau value is used and for the case of a constant tau the LST is irrelevant 23 SUN 216 8 The data reduction process If desired sky noise can now be removed Sky signal can be identified in two ways firstly using bolometers that are known to be looking at sky implemented in remsky and secondly using a model of the source structure to enable the sky signal to be calculated with the source subtracted from the data implemented in calcsky In this section we will examine the first method since this is the simplest and can be used for jiggle observations The more complex approach will be dealt with in 9 8 2 where sky removal from scan map data is discussed remsky works in a very simplistic way Sky bolometers are specified each jiggle is then analysed in turn the average value for the sky bolometers either MEDIAN or MEAN is then removed from the entire array At present it is not possible to specify sky regions only sky bolometers can be specified This may cause problems with extended sources rebin the map in NA coordinates initially to find the sky bolometers remsky should normally be run after rebin in order to choose sky bolometers that are really looking at sky for this example we will skip that step remsky is sufficient for the mapping of compact sources in ji
47. of all photometry files in the current and DATADIR direc tory photsum begin 5 end 100 Generate a summary of all photometry data from scans 5 to 100 inclusive SUN 216 8 Complete routine descriptions 102 PHOTSUM photsum all reduced Produce a one line summary of all reduced _red_ photometry files This will include the photometry results calculated by the on line system photsum all reduced gt log txt Produce a one line summary of all the reduced photometry files and store the output in the text file log txt note this example is shell specific photsum all reduced demod Produce a summary of all reduced _red_ and demodulated _dem_ photome try data files ie not files produced during off line data reduction Notes e If task is run on reduced data _red_ files then the photometry results will be listed e Skydip data is printed for convenience e Files are drawn from the current working directory and the directory indicated by the DATADIR environment variable e Data reduced by the off line system will all be treated as run 0 for the purposes of listing unless numbers are present in the filename e The output can be stored in a file by using unix redirection as long as the search range is fully specified either as all or with begin and end e Command line options can be abbreviated e Options that take values can be used either as flag option
48. processed with the reduce _noise task Changes to existing tasks e scunoiseJhas been modified so that it can read files generated by reduce _ noise e Images produced by rebin now include world coordinate information via the AST library WCS extension e The guard ring has been turned on for LINEAR and GAUSSIAN regridding It had been turned off in v1 2 A new parameter GUARD can be used to turn the bolometer guard ring on or off e Axis information is now written to the output files from REMDBM Minor fixes e rebin can now combine 256 files e sculog now formats the RA field correctly e The documentation has been updated to reflect the addition of reduce _ noiseland the use of AST 12 10 Changes in Version 1 2 New Tasks e Sky removal for SCAN map is now available using the calcsky task e Dual beam images taken using the new SCAN map observing mode can now be reduced using the remdbm task also uses scumakewt e The offset between the arrays can be compensated for by using change_nacentre e Noise data can now be displayed with scunoise e Bolometer weights can be set with setbolwt Changes to existing tasks can now accept a comma separated list of input files or a text file containing a list of files rather than having to supply one at a time Also there is now a METHOD option in scucat to control whether bolometers are treated independently or combined regardless of bolometer name can now propagate
49. rated same as mode 0bs Examples sculog Ask for a range of scan numbers and then give a full listing of every sdf file matching this criterion in DATADIR and the current directory sculog all 139 SCULOG SUN 216 8 Complete routine descriptions Generate a full listing of all sdf files in the current and DATADIR directory sculog begin 5 end 100 Generate a detailed log of all data from scans 5 to 100 inclusive sculog summary all Produce a one line summary of all files see also lobssum sculog summary all reduced Produce a one line summary of all reduced _red_ files sculog summary all reduced gt log txt Produce a one line summary of all the reduced files and store the output in the text file log txt note this example is shell specific sculog summary all reduced demod Produce a summary of all reduced _red_ and demodulated _dem_ data files ie not files produced during off line data reduction sculog summary all mode pointing Produce a one line summary of all pointing observations sculog summary reduced begin 100 end 200 mode photom skydip Produce a one line summary of the photom and skydip observations of reduced files with scan numbers 100 to 200 This is similar to photsumlexcept that the signal and signal to noise will not be displayed even if reduced files are being listed Notes e sculog only uses in
50. same pixel origin This can be achieved using eani but it is easier to do this infintrebin by making sure that all images are regridded relative to the same RA Dec centre the resulting images will all be aligned to the same pixel grid In many cases a more reliable approach to calculating the IQU cubes with satisfactory variance information is to use the polstack task on a set of 16 images and use that to generate 4 images with associated variances These variances are determined directly from the data rather than from the fitting We have found that running polcal on the resulting 4 images with WEIGHTS 1 SUN 216 8 Citing SURF 44 Vector sc 8 743257 Pa al a ee yee f P eel 4 22 00 F VA OS J eae AN OS E IA STE F SYAN LA Eo a Ni Si fy a 23 00 I NS A LZ SOE Vas 7 i 0 o E 5 24 00 F Al A 4 5550018 e 12 i008 Right ascension Figure 12 Polarisation E vectors around OMC 1 at 850 microns since we now wish to use the supplied variance information and then mosaicking the resultant IQU cubes e g via CCDPACK makemos to improve signal to noise gives the most robust results and provides variance information that agrees with theory Once the IQU cube is made polvec can be used to generate the vectors polvec omc1_cube CAT Output catalogue gt omci_cat 2530 vectors written to the output catalogue This catalogue can then be binned using polbin sections selected u
51. small as possible In version 1 0 0 output files were the same size as the input file e Observation numbers rather than the full filename can now be given to tasks that process the raw demodulated data skydip sdip scuquick This feature requires the SCUBA_PREFIX environment variable e All tasks now supply a default output filename The form of this filename is governed by the SCUBA_SUFFIX environment variable e The MAP_X MAP_Y and LOCAL_COORDS observing parameters are now sup ported New tasks e A despiking task has been added for JIGGLE MAP data e An experimental despiking task is available for SCAN MAP data despike2 e The data clipping functionality has been moved from remsky to a stand alone task cuco e There is now a task for extracting flatfield information from data files extract _ flat e Data suffering from the data shift problem mainly Semester 97a can be fixed with the scushift task 51 SUN 216 8 Release Notes e The experimental task scan_rlb can be used to remove linear baselines from SCAN MAP data e The addition of some interactive despiking and data inspection tools dspbol pltbol and rinplot Changes to existing tasks e skysum is now officially released with documentation e SKYDIP data can now be processed with reduce_switch and change_ quality This Th allows bad skydip points to be removed prior to fitting with is required changes to reduce_switch cold loa
52. the data This can be used to make an estimate of the actual number of samples responsible for each point in the output grid Note that in general the number of pixels in the output grid exceeds the number of independent beams in the image The data can be accessed as OUT more reds times Default is FALSE WEIGHT REAL Read The relative weight that should be assigned to each dataset WEIGHTS LOGICAL Read This parameter governs whether the convolution weights array will be stored in the output NDF The default is FALSE i e do not store the weights array WTFENRAD INTEGER Read Size of the weighting function in scale sizes This parameter is irrelevant for LINEAR regridding For Gaussian the default is 3 i e a diameter of 3 FWHM for the footprint 65 BOLREBIN SUN 216 8 Complete routine descriptions Examples and for Bessel it is 10 The smaller the weighting function is a combination of WTENRAD and SCALE the faster the regridding goes bolrebin rebin_method LINEAR out_coords RJ Rebin the maps with LINEAR weighting function in J2000 RA Dec coordinates You will be asked for input datasets until a null value is given bolrebin rebin_method BESSEL out map Rebin the maps with Bessel weighting function Each bolometer is rebinned sep arately and placed in an NDF in the output container file map sdf Bolometer H7 can be accessed by displaying map h7 bolrebin noloop ref test bat Rebin each bolometer using the da
53. time If you supply no data the existing pointing corrections will be removed Corrections will be requested until a negative number is given for the local sidereal time Usage change_pointing in change_point Parameters CHANGE_POINT CHAR Read If true you will be prompted for pointing corrections otherwise the program will exit after listing the current pointing corrections IN NDF Read Name of NDF to change MSG FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM POINT_DAZ REAL Read The Azimuth pointing correction arcsec POINT_DEL REAL Read The elevation pointing correction arcsec POINT_LST CHAR Read The sidereal time of the pointing correction Pointing corrections are asked for repeatedly until a NULL or negative value are given for POINT_LST Notes Pointing corrections are erased when new items are written e Pointing corrections can be removed completely by issuing null in response to POINT_LST when first prompted ie pointing corrections are removed if no corrections are given Use ABORT if you don t want to change the pointing corrections once you have started entering values Pointing corrections must be given in LST order SUN 216 8 Complete routine descriptions 76 CHANGE_POINTING Related Application SURF rebin 77 CHANGE_QUALITY SUN 216 8 Complete routine descriptions CHANGE QUALITY Set SCUBA data quality bad o
54. times with different values of NSIGMA Begin with NSIGMAS5 look at the result to see how effective despiking has been then repeat the process with NSIGMA 4 5 4 0 etc until you start to clip source information Usage restore in out nsigma Parameters IN NDF Read The name of the input file containing demodulated SCUBA data 83 DESPIKE2 SUN 216 8 Complete routine descriptions MSG_FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM No verbose messages are used NSIGMA REAL Read Nsigma from mean at which spikes begin OUT NDF Write The name of the output file to contain the processed data A default output name is suggested that is derived from the input Examples restore 037 o37_des 5 0 Despike 037 sdf at 5 0 sigma restore 037 Despike using the default sigma level and writing to the default output file Notes Care must be taken when despiking bright sources Related Applications SURF despike scucTip Sigclip SUN 216 8 Complete routine descriptions 84 DSPBOL DSPBOL Interactive display and despiking Description Idspbol or any dx link to scuplot can be used to interactively despike bolometers While it is not as fast as a completely integrated routine would be it makes interactive despiking much easier by hiding the cycle between linplot and change_quality for the user The most common use is to zoom in on the region with th
55. to correct for seeing effects measurement A measurement is a group of integrations Most MAP or PHOTOM observations will consist of only one measurement A FOCUS or ALIGN observation consists of five measurements one for each secondary mirror position A SKYDIP observation consists of one measurement at each elevation nod In order to correct for atmospheric variation the telescope is moved off source in each exposure so that sky can be measured ODF The observation definition file ODF is a file containing a list of instructions for an observation with SCUBA sub instrument SCUBA contains bolometer arrays and photometric pixels that can operate at several wavelengths simultaneously Each of these is called a sub instrument They are e SHORT the short wave array containing 91 bolometers e LONG the long wave array containing 37 bolometers e P1100 the single bolometer optimised for 11004m 53 SUN 216 8 Release Notes e P1350 the single bolometer optimised for 1350jm e P2000 the single bolometer optimised for 2000jm switch The switch is the fundamental unit of data taking in an observation For example in a JIGGLE MAP or PHOTOM observation each chunk of jiggle positions measured with the object in the beam of a telescope is a switch Each scan across the source in a SCAN MAP observation is also a switch tau 7 Submillimetre extinction is measured using the zenith optical depth tau or T this is a measure of the a
56. two SECTIONS of b3 and i2 Only b3 will be used if the square brackets are not used Care must also be taken when using commas in SCUBA sections the parameter system will split multiple entries on commas unless the entire section is quoted SECTION gt b3 5 i2 If necessary the negation character should come after a section ie after the closing curly bracket and that negation applies to the combined section and not just the string containing the negation character SECTION gt b3 i2 implies that the section consists of everything except bolometer 3 and integration 2 This parameter is only used when no SCUBA section was specified via the IN param eter SUN 216 8 Complete routine descriptions 78 CHANGE_QUALITY Examples change_quality ndf BAD_QUALITY false Select the entire array and unset bit 3 change_quality ndf b2 BAD_QUALITY Select the second bolometer and mark it bad change_quality ndf b2 i3 BAD_QUALITY Select the third integration of bolometer two but set all other data points bad by inverting the section change_quality ndf b16 i2 BAD_QUALITY Select all of bolometer 16 and the whole of integration 2 change_quality ndf e5 16 18 MSG_FILTER quiet Select exposure 5 and 16 through 18 Messaging is turned off change_quality ndf Since no section has been specified the user will be prompted for a section later change_quality test SECTION
57. upon completion of each observation Both the demodulated and reduced data are written to a directory in jcmtarchive Usually the directory name is constructed from the UT date in YYYYMMDD format i e on June 27th 1997 the directory will be called 19970627 The data should not be copied into the working directory primarily to save disk space and can be accessed by setting DATADIR setenv DATADIR jcmtarchive 19970627 This can be automated by using the scusetenv command scusetenv Setting up SURF for UT date 19990618 SCUBA_PREFIX set to 19990618 DATADIR has been set to jcmtarchive 19990618 ORAC_DATA_IN has also been set to this value D 2 Hilo SCUBA data is transferred to Hilo every afternoon This data is stored in scuba in semester directories eg scuba m99a for data taken during semester M99A containing a UT directory and an ro UT directory Data can be accessed by setting DATADIR setenv DATADIR scuba m99a 19990615 or setenv DATADIR scuba m98b ro 19980927 Note that unlike at the summit the demodulated and reduced data are in separate directo ries The directories containing the demodulated data also contain index and log files which summarise the observations This can be automated by using the scusetenv command scusetenv 19990205 Setting up SURF for UT date 19990205 SCUBA_PREFIX set to 19990205 DATADIR has been set to scuba m99a 19990205 ORAC_DATA_IN has also been set to this value 167 SU
58. y e SETBOLWT DESPIKE XN y REBIN BOLREBIN INTREBIN EXTRACT_DATA Figure 3 The SURF data reduction flow diagram for Jiggle map data Optional tasks are indicated by dashed lines Note that map data can follow the photometry path and photometry data can follow the map path if necessary SUN 216 8 Basic outline of SCUBA data reduction 18 REDUCE SWITCH CHANGE_FLAT J A l FLATFIELD e A ET al DESPIKE2 l EXTINCTION SCAN_RLB _ ke SCUCLIP f CHANGE QUALITY CHANGE NACENTRE Go i a gt CHANGE POINTING CALCSKY X T Y x A AM a qa DESPIKE SETBOUWT asee u RESTORE 2 BOL INTREBIN HR A EXTRACT_DATA REBIN NA A a gt x REMDBM Figure 4 The SURF data reduction flow diagram for Scan map data Optional tasks are indicated by dashed lines Tasks annotated with a single asterisk can not process EKH scan data ie chopping along the scan direction Conversely tasks annotated with a double asterisk can not process Emerson II data chopping in a fixed direction 19 SUN 216 8 The data reduction process 9 The data reduction process This section will describe the steps needed to process SCUBA data For more detailed examples please consult the two cookbooks 9 10 For this example I will use map and photo
59. 16 8 Complete routine descriptions ADAM parameters Any Any parameters accepted by the individual routines as long as they use PARAM VALUE format Examples scuquick When run this way will ask for the input file name and for the output root name will then run followed by extinction on each sub instrument Each task will ask questions as needed scuquick quick Same as scuquick except that defaults will be assumed for all parameters that have defaults scuquick rebin Process as for scuquick except that rebin is run on each sub instrument scuquick quick jun02_dem_0002 Process the input file jun02_dem_0002 sdf accepting all defaults scuquick quick jun02_dem_0003 MSG_FILTER QUIET Process jun02_dem_0003 sdf accepting all defaults and turning off all but the most important messages from the SURF tasks scuquick quick notau rebin temp OUT root Process temp sdf with zero extinction correction accept all defaults use root as the default filename and regrid scuquick remsky change_flat sub long Run the and tasks in addition to the standard tasks but only process the LONG sub instrument scuquick rebin quick MSG_FILTER QUIET PIXSIZE_OUT 1 test OUT temp Process test sdf Accept all defaults Use temp as the filename root Regrid all data onto a 1 arcsecond grid Hide all messages from the SURF tasks Notes Given a rootname specified with OUT root or by acceptin
60. 7az98_red_0001 M_970308_50 lt SCUDR_MAP gt LONG lt NDF gt image from long wave array SHORT lt NDF gt image from short wave array HEADER lt NDF gt Qbservation parameters in FITS extension The image from the long wave array would be displayed in Kappa with display clear axes m97az98_red_0001 long SUN 216 8 File naming and data structures 168 E 3 Structure of demodulated files and the FITS information would be displayed with fitslist m97az98_red_0001 header In addition to one NDF per sub instrument there is also one NDF per measurement For example the RO file from a FOCUS observation would contain an NDF for each FOCUS position names MEAS_1 MEAS 2 etc this is the case for FOCUS and ALIGN observations Skydip data is slightly different since the names of the NDFs are of the form SUB_WAVELENGTH i e SHORT_450 and LONG_850 If an observation is only using a particular bolometer eg a FLATFIELD or PHASE observation there will be an NDF for the bolometer eg H7 rather than for the array as a whole E 3 Structure of demodulated files Demodulated data files are much more complicated as they have to contain a full description of the state of SCUBA for each observation Here is an example trace the map of 3C279 used in the example hdstrace apr8_dem_0059 STRUCT lt gt MORE lt EXT gt structure FIGARO lt FIGARO_EXT gt structure structure is empty SCUCD lt SCUCD_ST gt str
61. 82 fullwcs NDF structure m82 Title SURF remdbm Label Extinction corrected Shape No of dimensions 2 Dimension size s 256 x 256 Pixel bounds 127 128 127 128 Total pixels 65536 Axes Axis 1 Label R A offset Units arcsec Extent 127 5 to 128 5 Axis 2 Label Declination offset Units arcsec Extent 127 5 to 128 5 Data Component Type _REAL Storage form SIMPLE Bad pixels may be present Quality Component Storage form SIMPLE Bad bits mask 3 binary 00000011 World Coordinate Systems Number of coordinate Frames 4 Index of current coordinate Frame 4 Frame index 1 Title Data grid indices first pixel at 1 1 Domain GRID Frame index 2 Title Pixel coordinates first pixel at 127 5 1 Domain PIXEL Frame index 3 Title Axis coordinates first pixel at 127 127 Domain AXIS Frame index 4 Title FK5 equatorial coordinates mean equinox J20 Domain SKY 33 SUN 216 8 The data reduction process Extensions FITS lt _CHAR 80 gt REDS lt SURF_EXT gt History Component Created 1999 Feb 07 17 34 41 No records 9 Last update 1999 Jun 16 17 00 07 MATHS KAPPA 0 13 6 Update mode NORMAL In the above example the SKY frame is the current frame this will be used by KAPPA display and is set to FK5 J2000 The AXIS frame contains arcsecond offsets from the regrid centre The PIXEL frame uses pixel indices and rebin ensures that the
62. 9 ORIGIN OBSRA 194 04654166665 OBSDEC 5 7894722222218 name of object name of input datafile sky coordinate system centre longitude radians centre latitude radians name of telescope name of instrument Wavelength of the observation metres Frequency of observation Hz Filter name SCUBA output coordinate system Pixel size arcsec Date of first observation file creation date YYYY MM DDThh mm ss UTC gt SCUBA User Reduction Facility SURF Origin of the FITS file RA of map centre degrees deprecated Dec of map centre degrees deprecated SUN 216 8 Description of despiking method used by despike 174 G Description of despiking method used by despike The despike routine works in the following way e Create an output grid with a cell of size one quarter of the beamwidth A 4D Calculate the position of every data point in the output coordinate frame and place it in the corresponding cell of the output grid For each cell bin calculate statistics mean median and standard deviation If neither smoothing nor a plot are required simply remove spikes from each cell Spikes are found if a point in a given cell is further than NSIGMA from the mean of the data in the cell Spikes are marked bad Write the despiked data to disk one output file for each input file Displaying the data in 3 dimensions x y grid and n data points for each bin would be far too cluttered so the 2 dimens
63. A Dec epoch of observation e GA Galactic coordinates J2000 For RD current epoch is taken from the first input file OUT_OBJECT CHAR Read The name of the object ie the NDF title PIXSIZE_OUT REAL Read Size of pixels in the output map Units are arcsec REBIN_METHOD CHAR Read The rebin method to be used A number of regridding methods are available e LINEAR Linear weighting function e GAUSSIAN Gaussian weighting function e BESSEL Bessel weighting function e SPLINE1 Interpolating spline PDA_IDBVIP e SPLINE2 Smoothing spline PDA_SURFIT e SPLINES Interpolating spline PDA_IDSFFT e MEDIAN Median regridding SUN 216 8 Complete routine descriptions 110 REBIN Please refer to the PDA documentation SUN 194 for more information on the spline fitting algorithms REF CHAR Read The name of the first NDF to be rebinned The name may also be the name of an ASCII text file containing NDF and parameter values See the notes REF can include alSCUBA section REFPIX 2 INTEGER Read The coordinate of the reference pixel in the output data array This corresponds to the pixel associated with the specified RA Dec centre Default is to use the middle pixel if a size is specified or the optimal pixel if the default size is used see the SIZE parameter TRIM INTEGER Read This parameter determines the amount of good data that should be trimmed from the final image to correct for edge effects The supplied valu
64. ADIR The filename will be requested if not specified on the command line Examples scupa 19970623_dem_0012 Reduce the data with scuquick displays the image and overlays the array using Notes Only JIGGLE MAP POINTING and PHOTOM observations can be used Related Applications SURF Seuquick euover Implementation Status e Requires KAPPA e All files created by this task are removed 147 SCUPHOT SUN 216 8 Complete routine descriptions SCUPHOT Reduce SCUBA PHOTOM data Description This routine reduces the data for a single sub instrument from a PHOTOM observation For each bolometer used to look at the source the data will be analysed as follows e An ndf called lt bolname gt _map e g h7_map will be created in the OUT file to hold the coadded data from all the integrations If the jiggle pattern points fit a 2 d rectangular pattern then these data will be arranged as a 2 d map suitable for plotting as an image A 2 d parabola will be fitted to the coadded image and the results written in ASCII form to FILE If an irregular jiggle pattern is used the map will take the form of a 1 D strip Second an ndf called lt bolname gt _peak e g h7_peak will be created in the OUT file to hold the fitted results to the data for each integration The results stored are the fit peak its variance and quality and they are held as a 1 d array suitable for plotting as a graph The fit results are also written in ASCII form to F
65. AL Read The relative weight that should be assigned to each dataset XRANGE INTEGER Read The X range of the plot This parameter loops indefinitely until a null response is provided Examples despike out_coords RJ smode none device Despike the maps by placing points onto an RJ grid Do not plot the data points before despiking and do not smooth the clipping envelope You will be asked for input datasets until a null value is given 81 DESPIKE SUN 216 8 Complete routine descriptions despike device out_coords RB smode hann dmode sp nsigma 4 0 Despike on a RB grid with hanning smoothing Use a 4 0 sigma clip and do not display Note that the smoothing uses the spiral mode for grid unwinding despike device xwindows dmode x nsigma 3 0 Unwind with XLINEAR mode and display the data before despiking despike noloop accept ref test bat Despike the files specified in test bat using an RJ grid Notes For each file name that is entered values for the parameters WEIGHT SHIFT_DX and SHIFT_DY are requested e The application can read in up to 100 separate input datasets e The output grid will be large enough to include all data points e SCUBA sections can be given along with any input NDF ASCII input files The REF and IN parameters accept ASCII text files as input These text files may contain comments signified by a NDF names values for the parameters WEIGHT SHIFT_DX and SHIFT_DY and names of other ASCII
66. AN is worth a try although extremely complicated regions e g OMC 1 may cause problems In order to overcome this problem it is also possible to specify specific scans that can be used for calculating the offset level since the DC level appears to be fairly constant during an integration When the SECTION baseline removal method is selected a SCUBA section 6 can be used to specify exposure scan numbers or actual positions in the data stream Usually the first and last exposures are used since these are most likely to be off source The appendix on scan_rlb contains some examples on the use of SCUBA sections to select baseline regions 9 8 2 Sky removal remsky can not be used to calculate the sky contribution for scan map data because it is no longer possible to select bolometers that are guaranteed to be on sky since most bolometers will see source at some point during the observation In order to overcome this problem the source signal must be removed from the data before attempting to calculate the sky This is achieved with the task For each point in the input datasets calcsky finds the expected flux at that position by comparison with a model of the source and removes that flux from the input data The source model can be calculated internally by calcskyJor an external image can be supplied usually generated from the same input data using rebin The source model is calculated in exactly the same way as for MEDIAN
67. CHOP_COORDS SC Related Applications SURF rebin CMTDR restore SUN 216 8 Complete routine descriptions 124 RLINPLOT RLINPLOT Interactive display Description rlinplot or any rx link to scuplot is a wrapper around the KAPPA utility mlinplot and y PP y facilitates data inspection It provides plots of sets of bolometers in a single window with optionally data from a second file in a second window Obvious files are despiked and non despiked data or data from different exposures to check the noise The menu items are M H Redisplay menu Q Quit N Next bolometer s Y min max Y lim Y axis from min max or lim lim U Reset Y axis Option gt Usage rlinplot f sdf_file d sdf_file2 s min max 1 bol bol bol Parameters h elp Print the help information f file name of NDF file sdf may be included in the name d file2 name of a second file e g the despiked version of the NDF file The same bolometers will be plotted in a second window or overlaid for comparison s min max Y axis scales for plot can be changed via menu 1 number of bolometers per window bol list of bolometers to plot Type all for 1 37 and alls for 1 91 Can be added via menu if mode r Examples rlinplot The user will be asked for an input file before proceeding to the menu 125 RLINPLOT SUN 216 8 Complete routine descriptions rlinplot f 039_lon_ext Plot bolome
68. CT_DATA SUN 216 8 Complete routine descriptions SHIFT_DY REAL Read The pointing shift in Y to be applied that would bring the maps in line This is a shift in the output coordinate frame WEIGHT REAL Read The relative weight that should be assigned to each dataset Notes For each file name that is entered values for the parameters SELECT_INTS WEIGHT SHIFT_DX and SHIFT_DY are requested e The application can read in up to 256 separate input datasets e No data is returned if the DATA or positions are bad Data is still returned if Variance is bad ASCII input files The REF and IN parameters accept ASCII text files as input These text files may contain comments signified by a NDF names values for the parameters WEIGHT SHIFT_DX and SHIFT_DY and names of other ASCII files There is one data file per line An example file is file1 b5 1 0 0 5 0 0 Read bolometer 5 from filel sdf file2 Read file 2 but you will still be prompted for WEIGHT and shifts file3 i3 1 0 0 0 0 0 Use everything except int 3 test bat Read in another text file Note that the parameters are position dependent and are not necessary Missing parameters are requested This means it is not possible to specify SHIFT_DX position 3 without specifying the WEIGHT Also note that SCUBA sections can be specified with any input NDF Related Applications SURF rebin change quality SUN 216 8 Complete routine descriptions 90 EXT
69. DIR and SCUBA_PREFIX for the current UT date scusetenv 19980201 Set DATADIR and SCUBA_PREFIX for the data observed on date 19980201 Notes e Currently this routine only works for the JAC and JCMT systems This is because the data are stored in standard directories and indexed by YYYYMMDD UT date e ORAC_DATA_IN environment variable is also set only relevant for users of the ORAC DR pipeline e If this routine is run from a non JAC JCMT site DATADIR will not be set but SCUBA_PREFIX will be set Parameters UTdate YYYYMMDD format string Optional The UT date of the data to be processed in YYYYMMDD format The default value is to use the current UT date Implementation Status This script should be sourced not executed since the environment variables should be set after the script has been read SUN 216 8 Complete routine descriptions 156 SCUSHIPT SCUSHIFT Correct for data shift error in demodulated data files Description This script corrects for the DAQ communications error and shifts the data from ADC cards along by a specified amount Since all channels are read from a particular ADC card but only some of them are actually stored in the demodulated data file the shift may result in fewer bolometers being stored for a given sub instrument Usage scushift h NDF card shift Parameters h Help information NDF Given The input files to be modified card The letter identifying the A to D card allowed val
70. Dec chopping and 90 degrees RA chopping in a coordinate frame fixed on the sky This will give 37 SUN 216 8 The data reduction process the best coverage of spatial frequencies but reasonable maps can also be obtained by combining four of the chop configurations This mode also has the advantage that the deconvolution occurs after the images have been regridded this means that data can be salvaged even if a scan did not go completely off source by combining with data that does and small spikes will be averaged out During commissioning it has been shown that the new method can result in a substantial improvement in signal to noise over the EKH method 13 9 8 1 Baseline removal The EKH method guarantees that the mean of every scan should be zero the transputers remove the mean on line In the absence of spikes the data would not need baseline removal but in some cases a large spike can adjust the mean of the scan and the baseline should be recalculated after spike removal with despike2 For the Emerson II method the situation is more complicated since the mean of each scan is now not guaranteed to be zero and in fact the transputers do not attempt to remove a baseline in this case scan_rlb must be run in order to remove the baseline each bolometer sees a slightly different background For data where the scans are long enough to be off source LINEAR baseline removal can be used For more complicated source structure MEDI
71. FIT LOGICAL Write Flag to indicate whether the fit was good TRUE or bad FALSE MODEL_OUT CHAR Write The name of the output file that contains the fitted sky temperatures MSG_FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM There are no verbose messages SUN 216 8 Complete routine descriptions 162 SKYDIP OUT CHAR Write The name of the output file that contains the measured sky temperatures RESIDUAL REAL Write Absolute difference between the model and the data in Kelvin i e abs Data Model SIGMA REAL Write Standard deviation of the residuals of the fit Kelvin SUB_INSTRUMENT CHAR Read The name of the sub instrument whose data are to be selected from the input file and fitted Permitted values are SHORT LONG P1100 P1350 and P2000 TAUZ_ERR REAL Write Error in the fitted value of TAUZ Set to bad if the fit has failed TAUZ_FIT REAL Write The fitted sky opacity for the selected sub instrument T_COLD REAL Read Temperature of the cold load The default value is taken from the input file This parameter is not required for data that has been processed by reduce _ switch T_HOT REAL Read Temperature of the hot load The default value is taken from the input file This parameter is not required for data that has been processed by reduce _ switch WAVELENGTH REAL Write The wavelength of the selected sub instrument XISQ REAL Wri
72. I 1994 MNRAS 270 L75 12 12 33 Meyerdierks H M Berry D Draper P Privett G Currie M J 1997 PDA Public Domain Algorithms Starlink User Note 194 34 Berry D S 1996 GRP Routines for Managing Groups of Objects Starlink User Note 150 35 Duncan W D SCUBA project documentation SCU WDD 31 1 1093 36 Archibald E Wagg J W Jenness T 2000 Calculating Sky Opacities a re analysis for SCUBA data SCUBA Calibration Database System Note 002 37 Wall L Christiansen T Schwartz R L 1996 Programming Perl 2nd edn O Reilly 38 Jenness T Bly M J 1998 NDFPERL Perl interface to NDF Starlink User Note 222 SUN 216 8 An alphabetical summary of SURF commands 56 A An alphabetical summary of SURF commands ADD_DBM Generate simulated dual beam images page 60 BOLREBIN Generate a separate regridded image for each bolometer page 62 CALCSKY Calculate sky variation independent of source structure page 67 CHANGE_DATA Change data or variance values in a dataset page 70 CHANGE _ FLAT Change the stored flatfield information page 73 CHANGE_NACENTRE Shift Nasmyth centre of array page 74 CHANGE_POINTING Change Az and El pointing offsets for map data page 75 CHANGE_QUALITY Change data quality page 77 DESPIKE Despike JIGGLE MAP data page 79 DESPIKE2 Despike SCAN MAP data page 82 DSPBOL Interactive despiking and data inspection Requires KAPPA page 84 EXTINCT
73. ILE as is the coadd of all the individual fits to the data Usage scuphot in analysis out file Parameters ALLBOLS LOGICAL Read By default only the observed bolometers are processed i e if you observed with H7 only H7 data will be stored If ALLBOLS is set to true then all middle beam data is processed This is useful for examining sky noise Note that for 2 and 3 bolometer photometry ALLBOLS must be false to avoid weighting problems for the bolometers that were observed in the left or right beams ANALYSIS CHAR Read The method used to determine the peak for each integration Either average or parabola Parabola is not recommended at this time Alternatively all the samples can be propagated without processing samples this will give the same result for the signal as average since average returns a smoothing of all the data but for small datasets may give a more accurate measure of the error The discrepancy is especially noticeable for calibration measurements where N_INTEGRATIONS may only be 6 the noise statistics on 6 averaged numbers are less reliable than those of 6 x 9 numbers assuming 9 samples per integration FILE FILENAME Write The name of the ASCII output file IN NDF Read The name of the input file containing demodulated extinction corrected SCUBA data SUN 216 8 Complete routine descriptions 148 SCUPHOT MSG FILTER CHAR Read Message output level Allowed values
74. ION Corrects demodulated data for atmospheric extinction page 86 EXTRACT_DATA Write bolometer positions and data to text a file page 88 EXTRACT_FLAT Write flatfield information to text file page 90 FLATFIELD Multiply the data array by the flatfield volumes page 91 INTREBIN Generate a separate regridded image for each integration page 92 MAPSUM Generate a summary of map observations page 97 OBSSUM Summarize all observations page P9 PHOTSUM Generate a summary of photometry observations page 101 PLTBOL Interactive data inspection Requires KAPPA page 103 POINTSUM Generate a summary of pointing observations page 105 QDRAW Plot photometry data requires KAPPA page 107 REBIN Rebin all data onto a rectangular grid page 108 REDUCE_NOISE Process raw noise data files page 113 REDUCE_SWITCH Convert raw demodulated data to standard format and process individ ual switches page 114 REMDBM Remove dual beam signature from SCAN MAP images requires K APPA page 116 57 SUN 216 8 An alphabetical summary of SURF commands REMIP Remove instrumental polarisation from polarimetry data page 118 REMSKY Remove sky contribution from each jiggle page 120 RESTORE Remove dual beam response from SCAN MAP data page 123 RLINPLOT Interactive data inspection via mlinplot Requires KAPPA page 124 SCAN_RLB Remove linear baselines from SCAN MAP data page 126 SCUBA2MEM Calculates bolometer positions wit
75. L Read Value to which all selected data points should be set A value of bad will set the data point to VAL__BAD Starlink bad data value For COMP Quality only numbers 0 to 255 are allowed numbers outside this range are assumed to be bad values Examples change_data ndf b2 bad changed Copy all data in ndf sdf to changed sdf and change all data in bolometer 2 to bad change_data ndf comp variance value 0 0001 Copy ndf sdf to the output file asked for explicitly and set all variance values to 0 0001 change_data test section b47 i3 value 1 02 Select data from bolometer 47 and integration 3 in test sdf and set this to a value of 1 02 This method of selecting a section is not recommended given the complication using commas and square brackets change_data test2 section b2 5 i2 value 0 2 comp err Select everything except integration 2 and bolometers 2 and 5 Set the error for this section to 0 2 change_data phot i2 6 b3 comp quality value 8 Explicitly set the quality array to 8 for integrations 2 through 6 and bolometer 3 The task change _ quality is recommended in this case since then only bit 3 is affected change_data map i2 5 value 0 0 Set everything except integrations 2 and 5 to zero Notes e This software sets the actual value in the specified component and so unlikelchange quality is not reversible For this reason a new output file is created
76. LOGICAL Read This parameter governs whether the convolution weights array will be stored in the output NDF The default is FALSE i e do not store the weights array WTFENRAD INTEGER Read Size of the weighting function in scale sizes This parameter is irrelevant for LINEAR regridding For Gaussian the default is 3 i e a diameter of 3 FWHM for the footprint 111 REBIN SUN 216 8 Complete routine descriptions and for Bessel it is 10 The smaller the weighting function is a combination of WTENRAD and SCALE the faster the regridding goes Examples rebin rebin_method LINEAR out_coords RJ Rebin the maps with LINEAR weighting function in J2000 RA Dec coordinates You will be asked for input datasets until a null value is given rebin rebin_method BESSEL out map out_coords NA Rebin the maps with Bessel weighting function in Nasmyth coordinates rebin noloop accept ref test bat out rebin Rebin the files specified in test bat onto a rectangular grid using linear interpola tion 3 arcsecond pixels and RJ coordinates Notes For each file name that is entered values for the parameters WEIGHT SHIFT_DX and SHIFT_DY are requested e The application can read in up to 256 separate input datasets e The output map will be large enough to include all data points e Spline regridding may have problems with SCAN MAP since integrations contain lots of overlapping data points e SCUBA sections can be given along with any input NDF
77. N 216 8 File naming and data structures E File naming and data structures Unless instructed otherwise in the observation definition file ODF the SCUBA software writes a demodulated data file essentially the raw data and a reduced observation RO file to disk E 1 Naming Conventions SCUBA data files have the following naming convention string_obs type_run number sdf Where string is either the UT date of the observation in YYYYMMDD format or the PATT ID for the observation Therefore the first data from 23rd June 1997 will be in files de LE 19970623_dem_0001 sdf 19970623_red_0001 sdf for the demodulated and reduced data respectively The RO file contains the reduced data calculated by the telescope during the observation and supplies a first look at the data At present the on line system does not produce calibrated publishable quality images the data should be re processed using the demodulated data and SURF E 2 Structure of RO files Since SCUBA can produce data from more than one sub instrument simultaneously and yet only one file is wanted for each observation the RO files are in fact HDS container files containing NDFs In general there is one NDF for each sub instrument used plus one NDF containing all the observation parameters it is a blank NDF containing a FITS extension For example a map observation with the LONG and SHORT wave array would produce an RO file with the following structure hdstrace m9
78. Privett G J Chipperfield A J 1995 CONVERT A format conversion package Starlink User Note 55 8 Currie M J 1994 HDSTRACE HDS data file listing Starlink User Note 102 9 Stevens J A Ivison R J Jenness T 1997 The SCUBA photometry cookbook Starlink Cookbook 102 18 10 Sandell G 1997 The SCUBA mapping cookbook A first step to proper map reduction Cookbook 11 2 1 9 11 Emerson D T Klein U Haslam C G T 1979 ApJ 76 92 12 Emerson D T A S P Conf Ser 75 309 13 Jenness T Lightfoot J F Holland W S 1998 Removing Sky contributions from SCUBA data in Advanced Technology MMW Radio and Terahertz Telescopes Philips T G ed Proc SPIE 3357 548 14 Matthews H E Jenness T 1997 The Specx cookbook Starlink Cookbook 8 6 15 Chipperfield A J 1999 ADAM Starlink User Note 144 16 Richer J S 1992 MNRAS 254 165 17 Eaton N 1995 AGI Applications Graphics Interface Starlink User Note 48 18 Rees P C T Chipperfield A J 1995 MERS MSG and ERR Message and Error Reporting Systems Starlink User Note 104 19 Greisen E W Calabretta M 2002 Representations of celestial coordinates in FITS AGA 395 1077 55 SUN 216 8 References 20 Warren Smith R F Berry D S 1998 AST A Library for Handling World Coordinate Systems in Astronomy Starlink User Note 210 21 Warren Smith R F Lawden M D 1995 HDS Hiera
79. RA AR E 49 12 10Changes in Version 12 RA A AA 49 12 11Changes in Version Lll ir 4G ew ne 6 Re ew ew ORS Oe Bw ew 50 12 12Version 10 0 2 2 2 ee 51 52 54 56 B_ Classified SURF commands 58 59 A ss e odon ee 60 A eee ee eee ee ees E od a 62 Se eS Bee ee ee es ee ae ee eee 2 67 foe eee ee ee a a a es A 70 CHANGE FLAT ee 73 aie oe Re ee ay Beh ES Othe A eS ee 74 A ON 75 big ois asha deb nad oes oxo 4 eran 77 Seah hilo We a a Sst a Se ava ae ws ps a T 79 We east A enon Ge eo TA ie alee nea ee ee pun ee ay 82 moet use oie ates es endear a ace aude eis Ape ies wes ee Gs NA 84 pedis ul Sp oe ES ea a oe Gee 86 A Bede aio le Ads dow a kes neath da ars ans 88 O E 90 Bet adh dae Sedo Mth et ae Meo D a Ga ee a 91 eg eee ee a pow a oe eee See ae 92 Ett AA oa Se Pe es eee oe 97 Sete dale Boe oo Bee a asas de ea ee a ee O A Be a 99 oe le Oe es ee eee ee 2 ee ee eee eee 101 Ca ee ee ae ee eee Re amas ia Gs 103 beh needy unk Gol ee Soe a ee A Y Gre ne ee 105 Sc Bt eee a ee eee GS GS Set ok eat eo 107 ou ek ee ee eee eee eee eee ee eee ee ees 108 a AG a Soa nese Ge ee es SG ede ees 113 as o e o Gow tne y te Bod Seen oe aaa 114 po ons a Se hg Sees a Sete ee Os See 116 atts OH Ae abe Geter Weel ards setae yt ee areal aes aes Gait we ue a a eee 118 REMSK Yie e scr id Riedie bh OR ee OE ae OS ee Bee ee as ob 120 Vv SUN 216 8 Contents eh Ge Sides Gas he Deke As Ges ete Oo See Pa ee ae A R 123
80. RACT_ELAT EXTRACT_FLAT Extract a flatfield from a SCUBA demodulated data file Description This routine extracts the flatfield information from a SCUBA demodulated data file and writes it out in a format suitable for use by CHANGE_FLAT The full flatfield is extracted Bolometer positions and relative responsivities Usage extract_flat in file Parameters IN NDF Read The name of the NDF containing the demodulated data with the required flatfield MSG_FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM There are no verbose messages FILE FILE Write The name of the ascii file to which the flatfield information will be written Examples extract_flat 19971017_dem_0002 oldflat dat This will read the flatfield from 19971017_dem_0002 sdf and write it to a text file Related Applications SURF 91 FLATFIELD SUN 216 8 Complete routine descriptions FLATFIELD Flatfield demodulated SCUBA data Description This routine flatfields SCUBA demodulated data The data must previously have been processed by peduce switch Usage flatfield in out Parameters IN NDF Read The name of the NDF containing the demodulated data to be flatfielded This file should already have been run through the reduce_switch application MSG_FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM There are no verbose messages OUT NDF
81. REBIN_METHOD CHAR Read The rebin method to be used A number of regridding methods are available e LINEAR Linear weighting function e GAUSSIAN Gaussian weighting function e BESSEL Bessel weighting function e SPLINE1 Interpolating spline PDA_IDBVIP e SPLINE2 Smoothing spline PDA_SURFIT e SPLINES Interpolating spline PDA_IDSFFT e MEDIAN Median regridding SUN 216 8 Complete routine descriptions 94 INTREBIN Please refer to the PDA documentation SUN 194 for more information on the spline fitting algorithms REF CHAR Read The name of the first NDF to be rebinned The name may also be the name of an ASCII text file containing NDF and parameter values See the notes REF can include alSCUBA section REFPIX 2 INTEGER Read The coordinate of the reference pixel in the output data array This corresponds to the pixel associated with the specified RA Dec centre Default is to use the middle pixel if a size is specified or the optimal pixel if the default size is used see the SIZE parameter TRIM INTEGER Read This parameter determines the amount of good data that should be trimmed from the final image to correct for edge effects The supplied value should be in arcseconds All pixels closer to a bad pixel than this distance will be set to bad in the output image by setting bit 1 in the quality array Default is 0 0 SCALE REAL Read Radius of one scale size in arcsec This effectively governs the size
82. SUN 216 8 Complete routine descriptions 142 SCUMAKEWT Examples scumakewt 20 90 3 256 256 ft wt Generate the FT and weight of a 20 arcsec RA chop using 3 arcsec pixels and a 256 square output image The weight is written to wt sdf and the FT to ft sdf scumakewt chop 20 size 256 512 ftchop fft wtchop weights Generate the weight and ft of a chop of size 20 arcseconds on a 256 x 512 image The pixel scale will be requested Related Applications SURF 143 SCUNOISE SUN 216 8 Complete routine descriptions SCUNOISE Display SCUBA noise data Description Scunoise can read in a directory of noise summaries the dat files produced by the real time system and plot them A date must be supplied so that SCUNOISE can pick up the correct file associated with a given run number Once the noise data are displayed the pointer can be moved over a point to determine the associated bolometer name Double on the window will bring up a diagram of the array with all bolometers above the specified noise level specified by the position of the pointer for the double click highlighted in a different colour Usage scunoise h v d obsdate runnr Parameters h Return a help message only y Return the version number of scunoise d Switch on debug output obsdate Observation directory date e g 19980210 runnr SCUBA observation number of noise measurement Examples scunoise Prompt for date and run numb
83. SUN 216 8 Starlink Project Starlink User Note 216 8 T Jenness J F Lightfoot Joint Astronomy Centre Hilo Hawaii 3 April 2003 Copyright 1997 2000 2003 Particle Physics and Astronomy Research Council SURF SCUBA User Reduction Facility 1 6 User s manual SUN 216 8 Abstract ii SURF is a set of ADAM tasks necessary for reducing demodulated Submillimetre Common User Bolometer Array SCUBA data obtained from the James Clerk Maxwell Telescope The tasks allows one to completely re reduce your SCUBA data This document describes how to reduce SCUBA data and includes detailed descriptions of each task Copyright 1997 2000 2003 Particle Physics and Astronomy Research Council ii SUN 216 8 Contents he Contents 1 2 Starting up SURF 3 2 1 Getting help oie AAA RA RA 3 3 What data do I have 4 Supported Observing Modes Message filtering 7 j 6 SCUBA sections 8 7 _ Environment variables 9 7 1 SURF environment variables 0 0 0000 eee eee ee eee 9 ZA DATADIR 2 2 2464 44 4 icy Boe gb SA ai eet ete Ex 9 712 SCUBA PREFIX 0 000000 eee ee ee 10 7 1 3 SCUBA SUFFIX szed asamada re pira reaR OREAREN 10 7 2 Other useful environment variables 12 8 Basic outline of SCUBA data reduction 13 9 The data reduction process 19 9 1 Preliminaries oaaae a 19 A 20 9 3 Noise measurements 0 0 0 0 a a ee 21
84. SUN 216 8 The data reduction process Once the source has been removed a sky signal is calculated from the residual signal by finding the average signal across the array for each time In addition the time series can be smoothed since scan data are sampled much faster approx 8 Hz than the sky emission is expected to vary a few seconds These time series are then stored in an extension inside the file stored in MORE REDS SKY Once the sky has been calculated it can be removed by using remsky recognises the presence of a SKY extension and removes this signal from the main data array Fig 9 shows the sky signal for some of the M82 data In general the sky noise on scan data is below the noise but correlations are visible in the smoothed time series This technique is not limited to scan map data Jiggle maps can benefit from using calcsky in cases where sky bolometers can not be identified or when the sky removal needs to be automated One caveat is that the quality of the sky removal depends critically on the quality of the sky model For extreme cases of sky noise in jiggle data where the individual switches are visible as hexagonal patterns across the image calcsky can not disentangle the source from the hexagonal pattern no other data are available for that position on the sky and sky removal will fail More information on sky removal for jiggle and scan data can be found in Jenness et al 13 9 8 3 Dual beam deconvolution Chopp
85. TART 62 2 4 3 1 lt _INTEGER gt 20 19 18 18 18 18 18 15 14 13 14 13 14 16 22 23 31 41 0 0 0 0 NPIX 62 2 4 3 1 lt _INTEGER gt 2 5 12 13 28 29 29 32 33 34 34 35 37 36 34 32 30 24 23 14 3 0 0 0 0 POINTER 62 2 4 3 1 lt _INTEGER gt 2 4 9 21 34 62 91 120 152 185 52804 52807 52807 52807 52807 FITS 164 lt _CHAR 80 gt ACCEPT not used J Craan WAVE_5 a END DATA_ARRAY 5 128 384 lt _REAL gt 0 011504 0 000014 0 029308 0 000015 0 0 006727 0 000003 0 022551 0 000003 0 00 0 050 0 0 0 0 0 0 5151 0505 051 1 End of Trace From this we can see that there is a 3 dimensional data array and 4 NDF extensions Each will be described in turn DATA_ARRAY The data array contains three dimensions The first dimension is a vector of size 5 and relates to the chop data the chop error the calibrator data the calibrator error and the quality respectively The second dimension is the bolometers and the third is the number of measurements ie number of jiggle positions x number of integrations x 2 number of nods These data can be displayed to examine each component in turn for example checking whether the OFF position contains a source by using NDF sections FIGARO extension The FIGARO extension is not used by the SURF package SCUCD extension The SCUCD extension contains information on the position of the telescope for each sample along with the local sidereal time of each sample SCUBA extension T
86. _reb_lon WTFN_REGRID Entering second rebin phase T 0 9061 seconds WTFN_REGRID Entering third rebin phase T 3 682912 seconds WTFN_REGRID Regrid complete Elapsed time 4 055644 seconds If more than one map is available the extinction corrected data with or without sky removal can all be added into a single map at this stage The parameter IN can be supplied with one new map at a time or via a text file 9 6 1 Each input data set can be shifted by setting SHIFT_DX and SHIFT_DY this shift is in arcseconds on the output grid cf pointing corrections which are in Az El offsets and assigned a relative weight with the WEIGHT parameter rebin does understand SCUBA sections 6 so it is possible to select part of an observation for regridding at this time In addition to rebin there are three closely related tasks in fact they all use the same code bolrebin will regrid each bolometer individually intrebin will regrid each integration into a separate file and will write the data to a text file before regridding Note that the output file for and is an HDS container rather than a simple NDF For example if the OUT file is test sdf the images will be accessible as NDFs via test h7 test h8 etc or test il test i2 for intrebin At this point the map can be displayed with say Fig 7 shows the 850 micron image of 3C279 rebinned in RJ coordinates with the long wave bolometer array overlaid note that displays the array at zer
87. a from the fit o o ooo oo 179 181 K Notes on scripts 185 SUN 216 8 List of Figures vi List of Figures e and photometry data can follow the map path if necessary 4 The SURF data reduction flow diagram for Scan map data Optional tasks are indicated by dashed lines Tasks annotated with a single asterisk can not process EKH scan data ie chopping along the scan direction Conversely tasks annotated with a double asterisk can not process Emerson II data chopping in a fixed 5 The Skydip result for scan 54 The crosses are the measured sky temperatures and the line is the fitted model A 850 micron image of 3C279 rebinned in RJ coordinates with the long wave array 11 Final image of M82 after single beam restoration 42 12 Polarisation E vectors around OMC 1 at 850 microns 13 A schematic of the different display modes for despike The start of each scan is represented by the letter S and the end by the letter E 14 Example despiking of a point source The two outside lines on each diagram indicate the region outside which a spike would be found the clipping envelope diagrams show the data displayed using Spiral left and Xlinear right modes The x axis indicates that the source is visible for small bin number in spiral mode The middle line indicates the median of the data in each cell The top two and for a mu
88. able e Changing header parameters Tasks are available to change header parameters such as flatfield information change _ flat applying pointing corrections change _ pointing or setting pixels bolometers and integra tions to bad values change quality e Changing data values Data can be changed using the task This task can be used to change Data Variance or Quality arrays and should be used with care e Sky noise removal Instrumental variations and sky noise can be removed either by using the task when sky bolometers can be identified or by using in combination with for more complicated sources and scan map data e Despiking Occasionally spikes get through the transputers and into the demodulated data Tasks are provided for despiking jiggle map data despike scan map data despike2 and photome cuci try data e IP Correction Polarimetry observations need to be corrected for instrumental polarisation The remip task can be used for this e Array overlay If the rebinned images are displayed using a program that writes to the graphics database 17 such as display the array can be overlaid on the image using the task This is very useful for identifying noisy bolometers or bad pixels e Display data values The tasklextract _datalis similar to the rebin tasks except that the X Y and data values are written to an ASCII text file instead of being regridded into a final output image This is useful
89. adds of lots of observations These images must have the same map centre the same pixel scale the same dimensions and must be regridded in the same coordinate frame as the chop RJ for RJ RB and GA data PL or RD for moving sources Fig 10 shows examples of four dual beam images of M82 Once these images have been generated they can be processed by remdbm remdbm o8 _lon_reb sdf out m82 Starting monoliths Done Loop number 1 Chop PA 90 THROW 20 SUN 216 8 The data reduction process 40 Figure 10 4 dual beam images of M82 The chop throws are 20 arcsec RA chopping 30 arcsec RA chopping 20 arcsec dec chopping and 30 arcsec dec chopping 41 SUN 216 8 The data reduction process Doing forward transformation Loop number 2 Chop PA 90 THROW 30 Doing forward transformation Loop number 3 Chop PA 0 THROW 20 Doing forward transformation Loop number 4 Chop PA 0 THROW 30 Doing forward transformation Maximum difference between estimates of the same Fourier component is 0 02414273 Doing inverse transformation Result stored in m82 Note the use of shell wildcards The final image can be seen in Fig 9 9 Polarimetry data reduction Polarimetry observations are similar to map and photometry observations except that they are broken into measurements of a number of integrations usually 1 for different positions of a half wave plate The wave plate normally steps in 22 5 degree increments The initial
90. ameter SUN 216 8 Complete routine descriptions 132 SCUCLIP SCUCLIP Simple sigma clipping for each bolometer Description Each bolometer is analysed independently the mean and standard deviation are calculated any points greater than NSIGMA sigma from the mean are treated as spikes and removed Note that for mapping this despiking algorithm is only useful for very weak sources bright sources will be removed since a bolometer jiggles on and off bright sources Photometry observations do not suffer from this problem as the bolometers are always on source Usage scuclip in out nsigma Parameters IN NDF Read This is the name of the input demodulated data file MSG FILTER CHAR Read Message output level Allowed values are QUIET NORM and VERB Default is NORM If MSG_FILTER is set to VERBOSE the number of spikes removed from each bolometer is reported NSIGMA DOUBLE Read Number of sigma beyond which data are thought to be spikes If this number is positive an iterative clip will be performed ie the standard deviation is recalculated after clipping and points lying outside the new range are removed If it is negative then iterative clipping is switched off OUT NDF Write Output data file Examples scuclip infile outfile 5 Clip any data points that are further than 5 sigma from the mean The clipping is done on a per bolometer basis and is iterative scuclip infile outfile 5 Clip any data points th
91. an weighting function is probably the best compromise between the Bessel slow and prone to edge effects and Linear fast but the point spread function is non trivial for modeling The radius and size of footprint for the weighting functions are configurable using the WTFNRAD and SCALE parameters Splines Additionally spline interpolation and smoothing routines are also available Note that the spline routines work on each integration in turn whereas the weighting function routines work on all the input data in one go At present the spline routines are experimental and comments are welcomed Median A regridding option derived from despikelis available This method simply puts all data points in an output grid and calculates the median of each output cell Small pixel scales require large datasets since not all cells in a 1 arcsecond grid will contain data points although the KAPPA commands fillbad and glitch can be used to smooth over bad pixels intrebin ref Parameters GUARD LOGICAL Read Controls whether the bolometer guard ring should be used during the regridding process The guard ring enforces zero flux at the edge of the regridded image Should be turned off if flux is present at the edge Default is to use the guard ring for LINEAR BESSEL and GAUSSIAN rebin modes 93 INTREBIN SUN 216 8 Complete routine descriptions IN CHAR Read The name of the input file to be rebinned This parameter is reques
92. ar baseline to the ends of the scan SECTION Use a SCUBA section to specify regions of each integration that are thought to be flux free Remove the median of the specified section from the associated integration Default is LINEAR MSG FILTER CHAR Read The messaging level Allowed values are QUIET NORM and VERB Default is NORM There are no verbose messages OUT NDF Write The name of the output file to contain the processed data RLB INTEGER Read This parameter governs whether the baseline fit is removed from the input data or stored instead of the data If RLB is TRUE the corrected data are returned If RLB is FALSE the fit is returned SECTION CHAR Read This array parameter can be used to specify SCUBA sections to be used for baseline calculation It is requested when METHOD SECTION In general the SCUBA section should include scan exposure or position p specifiers which will be applied to each bolometer and integration It is possible to be more specific and to provide multiple sections singling out certain bolometers or integrations If entire integrations are selected no baseline removal will occur on unselected integrations this will be stated The median of the section supplied for each integration is subtracted from every exposure in that integration remember that if no integration is specified all integrations are assumed 127 S Examples scan CAN_RLB SUN 216 8 Complete routine descriptions C
93. arcsec Default is to use the value of SCUPIXSZ from the FITS header if present Examples add_dbm gaussian O 30 dbm_out Generate a dual beam image from the single beam gaussian input NDF using a 30 pixel chop at 0 degrees Write the resulting image to dbm_out sdf 61 ADD_DBM SUN 216 8 Complete routine descriptions add_dbm image 90 45 3bm_out nbeams 3 Generate a triple beam image with throw 45 and position angle 90 degrees Notes e The output images are compatible with REMDBM e All extensions and AST WCS information are propogated to the output image e A variance array is created if present in the input image e If a quality array is present in the input image it is used to generate a bad pixel mask in the output image and is removed e Bad pixels in the input image are treated as zeroes for the dual beam calculation Related Applications SURF SUN 216 8 Complete routine descriptions 62 BOLREBIN BOLREBIN Generate a separate regridded image for each bolometer Description This routine rebins the demodulated data from SCUBA MAP observations onto a rectan gular mesh by a variety of methods Currently convolution by weighting functions spline interpolation and median are supported Usage e Weighting functions Currently linear Bessel and Gaussian weighting functions are supported The width of the Bessel function is such that it should preserve all spatial information obtained by the telescope at
94. ask to find any offset A number of questions need to be asked before regridding the data What rebin method should be used Currently three methods are available The data can be regridded with a weighting function interpolated using spline fitting or by calculating the median data value in each cell of the output grid Bessel Gaussian and linear weighting functions are available in theory the Bessel function interpolation should give the best results but in practice the Gaussian or linear functions should be used they are much faster and less affected by edge effects The Gaussian function should be used if you are interested in beam shape since it is easier to work out what is going on when you convolve a JCMT beam with a Gaussian than when you convolve it with a cone The MEDIAN regridding technique can be used if many data points are available since for small output grids at least one input data point preferably many more must be available in each cell in the output to avoid bad pixels If fewer points are available only a few integrations consider using larger cells or use the KAPPA routines fillbad or to interpolate over the holes The spline fitting algorithms are experimental and have not been thoroughly tested please use with care What coordinate system should be used The data can be rebinned in the following coordinate systems SUN 216 8 The data reduction process 28 NA Nasmyth SCUBA coordi
95. at are further than 5 sigma from the mean The clipping is done on a per bolometer basis and only one pass of clipping is performed Notes e The despiking routine is very primitive and should not be used with jiggle map data of bright sources It can be used on PHOTOM data since the jiggle pattern never moves off source although sigclip can be used once the data has been processed by Bcuphot 133 SCUCLIP SUN 216 8 Complete routine descriptions Related Applications SURF cuqui rebin Eeuphol KAPPA Implementation Status The despiking routine sets QUALITY bit 5 to bad It does not affect the data The effects of despiking can be removed by using the KAPPA task setbb to unset quality bit 5 SUN 216 8 Complete routine descriptions 134 SCUCLKERR SCUCLKERR Determine the possible error in the times stored in the data header Description This routine calculates the error in the times stored in the data header It performs a self consistency check to determine the local sidereal time from the Azimuth and elevation information that comes directly from the telescope and compares this to the LST stored in the header Usage scuclkerr filename Parameters CLOCKERR REAL Write On exit the clock error in seconds determined from the header DANG REAL Write Error in the array rotation angle due to the clock error degrees DR REAL Write Positional error at the edge of the array for this particular observation
96. ation for each measurement will be marked bad rather than the nth integration of the mth measurement 181 SUN 216 8 Correcting shifted data wt i em A O a ES E Le ae 35 3 0 2 5 2 0 1 5 10 AIRMASS Figure 16 Skydip plus model without measurement 5 eta 0 87 0 00 b 0 86 0 01 tau 0 667 0 007 Standard Deviation of fit residual 0 81 K X 0 9 N 7 The fit is shown in Fig is the only task that can process raw demodulated data and data processed with J Correcting shifted data Between early 1997 and 15th September 1997 there was an intermittent fault with the SCUBA data acquisition system DAQ that led to a particular form of data corruption The problem is most serious in MAP JIGGLE observations but can also affect PHOTOM The DAQ fault was identified and fixed on 15th September 1997 and checking routines were added to the data taking software to warn of any such data synch problems that occur in the future Observers with data taken after that date need read no further Those with data taken in the problem period may remember that the SCUBA bolometer channels are collected into 9 groups of 16 with each 16 channel group being handled by a different A D card in the DAQ The name of each bolometer reflects the A D card and channel number on that card which handles the signal for example B12 will be routed through channel 12 on card B The 9 A D cards have single letter identifiers ru
97. ative clip is used so that the mean is recalculated each time a point lies NSIGMA from the mean until no points are removed No knowledge of SCUBA is required by this task except that it knows which quality bit to use for the despiking Disadvantages For JIGGLE MAPS on source bolometers jiggle on and off the source and therefore have a large change in signal if the source signal is well above the noise level the mean and standard deviation calculations therefore have a tendency to remove peak signals from the data this can be partly overcome by setting the source bolometer bad clipping the remaining bolometers and then setting the source bolometer to good SUN 216 8 The data reduction process 26 Advantages Can be used for PHOTOM data and weak signals since each bolometers always sees approximately the same signal Can be used for detecting large spikes on strong sources if a sufficiently large value is chosen for NSIGMA This task places each point into a grid cell corresponding to the actual position of the datum on the sky Each cell is then analysed in turn any point further than NSIGMA from the mean for a given cell is then treated as a spikg All modes are supported with the caveat that SCAN MAP data should not have been restored spikes must be removed before the single beam restoration phase also EKH data can not strictly be processed in this way beacause the chop angle is not fixed on the sky Disadvantages For s
98. average This mean value is iterative i e The mean and standard deviation are calculated any points greater than the given distance from the mean are removed and the mean and standard deviation are calculated This process is repeated until no bolometers are dropped from the mean MSG FILTER CHAR Read Message output level Allowed values are QUIET NORM and VERB Default is NORM In VERBOSE mode a list of the selected bolometers is returned along with the value of the sky offset removed for each jiggle OUT NDF Write Output data file Examples remsky ndf sky_removed bolometers g1 g2 g3 g 4 g5 mode median SUN 216 8 Complete routine descriptions 122 REMSKY Use the median of bolometers g1 g2 g3 g4 g5 not necessarily the best choice to calculate the sky signal and write the output to sky_removed sdf remsky 012_lon_ext bolometers all mode median Use the median of all the bolometers for each jiggle and write the output to the default output file e g 012_lon_sky remsky 025_sho_ext bolometers r5 mode mean iter_sigma 4 Use the outer ring of the short wave array as the sky bolometers Calculate the sky contribution by using a clipped mean of each jiggle and remove any points from the calculation of the mean that are more than 4 sigma from the mean Write the output to the default output file Notes e Source rotation is not accounted for so use only those bolometers that always observe sky This
99. be used to subtract the baseline from the input data at a later stage if RLB is true Related Applications SURE KAPPA SUN 216 8 Complete routine descriptions 128 SCUBA2MEM SCUBA2MEM Calculate bolometer positions as tangent plane offsets Description This routine reads in SCUBA demodulated data and writes it out along with the positions of the bolometers on the sky for each sample The positions of the chop beams can be requested as well as the positions of the tracking centre Returns tangent plane offsets from the map centre in arcseconds Additionally the LST of each sample is stored as axis information Usage scuba2mem in out Parameters IN CHAR Read The name ofthe input files to be processed This is a demodulated data file RESTORE should not have been run on it Multiple file names can be specified see the docu mentation on GRP All the input files are referenced to the same output coordinate frame LAT CHAR Read The latitude of the output map centre The supplied default value is that of the map centre of the observation in the output coordinates LONG CHAR Read The longitude of the output map centre The supplied default value is that of the map centre of the observation in the output coordinates MSG _FILTER CHAR Read Message filter level Default is NORM NBEAMS INTEGER Read Number of output beams to be written to file NBEAMS 1 just writes the Middle beam NBEAMS 2 writes the Left
100. bservation of object 3c279 SURF file contains data for 2 switch es in 4 exposure s in 3 integration s in 1 measurement s OUT Name of output file to contain reduced switch data 059 gt SUN 216 8 The data reduction process 22 In this example the calibrator signal has not been used and any datum from which more than 5 spikes were removed by the transputers is marked bad these are the default settings The processed data are then written to file 059 sdf In this case we need to change the flatfield file since the flatfield was updated after the data were taken using change _ flat change_flat IN Name of input file containing demodulated map data 059 gt SURF run 59 was a MAP observation of 3c279 NEW_FLAT The name of the file containing the new flat field gt photflati dat The next task is to flatfield the data flatfield 059 059_flat SURF run 59 was a MAP observation of 3c279 SURF applying flatfield from photflati dat If the input and output files are not specified on the command line they will be requested The data can now be corrected for airmass elevation and sky opacity by using According to the skydip observation taken prior to the map the tau at 850 um is 0 220 and a skydip taken after the map shows it was 0 187 Iflextinction is given two T values from different times then the actual 7 for each jiggle will be calculated by linear interpolation obviously this assumes that the T vari
101. can be checked by using scuover to overlay the bolometer positions on a NAsmyth regridded image since NA shows the signal measured by each bolometer throughout the observation without source rotation e For weak sources ie sources that are not obvious in a single integration itis probably sufficient to choose BOLOMETERS all and MODE median Related Applications SURF Seuquick rebin cuphot Souove 123 RESTORE SUN 216 8 Complete routine descriptions RESTORE remove the chopped beam response from SCAN MAP observations Description This routine removes the chopped beam response from SCAN MAP observations Usage restore in out chop Parameters CHOP INTEGER Read Chop throw in arcseconds The default chop throw is read from the FITS header of the input file IN NDF Read The name of the input file containing demodulated SCUBA data MSG_FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM There are no verbose messages OUT NDF Write The name of the output file to contain the processed data Examples restore input output Restore input sdf to output sdf using the default chop throw restore resw restore 40 2 Restore resw sdf to restore sdf using a chop throw of 40 2 arcseconds Notes Uses the Emerson Klein and Haslam algorithm 1979 A amp A 76 92 This routine can only be used on SCAN MAP data taken whilst chopping along the scan direction
102. can be used either as flag option or as flag option Related Applications SURF feulog photsum paintsum ma psum kysu 101 PHOTSUM SUN 216 8 Complete routine descriptions PHOTSUM Produce one line summary of SCUBA photometry observations Description Photsum goes through all the sdf files in the current directory and optionally DATADIR defined in an environment variable and summarizes files containing photometry obser vations In the absence of the all flag a numeric range is requested This range only has an effect on raw data or reduced files which have the run number embedded into the file name Filenames with no numbers are treated as scan 0 Usage photsum h demod reduced al1 begin nn end mn Parameters hlelp Return a help message only More help can be obtained by using showme sun216 or scuhelp photsum all List all photometry files in the current directory and DATADIR demod Only list demodulated data files signified by _dem_ file name reduced Only list reduced data files signified by _red_ file name begin nn First scan number to be considered same as begin nn end nn Final scan number to be considered same as end nn Examples photsum Ask for a range of scan numbers and then give a summary of every PHOTOM file matching this criterion in DATADIR and the current directory photsum all Generate a summary
103. ce pixel in the output data array This corresponds to the pixel associated with the specified RA Dec centre Default is to use the middle pixel if a size is specified or the optimal pixel if the default size is used see the SIZE parameter TRIM INTEGER Read This parameter determines the amount of good data that should be trimmed from the final image to correct for edge effects The supplied value should be in arcseconds All pixels closer to a bad pixel than this distance will be set to bad in the output image by setting bit 1 in the quality array Default is 0 0 SCALE REAL Read Radius of one scale size in arcsec This effectively governs the size of the weighting function For LINEAR one scale size corresponds to the zero of the cone for BESSEL it is the first zero of the Bessel function 71 and for Gaussian it is the half width half maximum HWHM SIZE 2 INTEGER Read This array parameter sets the size of the output grid in pixels nx ny The default values are the minimum dimensions required to display the entirety of the mapped area SHIFT_DX REAL Read The pointing shift in X to be applied that would bring the maps in line This is a shift in the output coordinate frame SHIFT_DY REAL Read The pointing shift in Y to be applied that would bring the maps in line This is a shift in the output coordinate frame TIMES LOGICAL Read Store an extra NDF in the output map containing the 2 D histogram of
104. ch larger bin number in xlinear mode The lower two diagrams show the same thing except that hanning smoothing has been applied to the clipping has been removed with change quality right 16 Skydip plus model without measurement 5 17 The standard calibrator signal solid line with an overlay of a shifted calibrator signal dashed The A D cards are indicated and a shift is clearly seen on card B 183 1 SUN 216 8 Introduction 1 Introduction The Submillimetre Common User Bolometer Array SCUBA is a continuum instrument on the James Clerk Maxwell Telescopd Mauna Kea Hawaii SCUBA has two arrays and can observe simultaneously at two wavelengths three wavelengths when using the photometry pixels the layout of the SCUBA arrays is shown in Fig The on line system produces data in the Starlink NDF format 3 Both the raw demodulated data signified by _dem_ in the file name and a reduced image RO file can be stored This package is designed to take the demodulated data stored in the dem directory on line and remove SCUBA dependent effects In the case of MAP data a rectangular gridded image is produced for PHOTOM observations a set of photometry data Packages such as GAIA 4 or for MAP and Kappallinplot and drawsig for PHOTOM can be used for further processing Calibration via planet observations can be determined using the FLUXES 6 package The CONVERT 7 package can also be used to export the data
105. corrected or sky removed data so that any bad bolometers and integrations can be turned off using change _quality and SCUBA sections rebin can be used to test a section before committing the change different sky bolometers chosen or new pointing corrections added Once complete the data can be calibrated planet fluxes can be obtained using the FLUXES package and work is progressing on a list of secondary calibrators see e g 24 9 6 1 Rebinning multiple datasets On many occasions it is necessary to combine multiple observations into one regridded image to attain the desired signal to noise for a source map One way of doing this is to enter into rebin or related task each map in turn along with the WEIGHT SHIFT_DX and SHIFT_DY Fora small number of input sets this approach is fine but for large numbers n gt 2 this approach becomes tedious and error prone In order to overcome this problem the rebin tasks can accept an ASCII text file as input as well as an NDF This text file contains information on one input set per line This line must contain either a space separated list of with the NDF weight shift_dx and shift_dy or the name of another text file Regrid text file for 3c279 Format of text file should be NDF WEIGHT SHIFT_DX SHIFT_DY n59_reb_lon 1 0 0 0 0 0 Map 59 n60_reb_lon 1 0 1 0 0 0 Shift 1 0 relative to n59 n61_reb_lon i2 1 02 Only want the second integration from this shifts will be re
106. d are used The output name for each task is related to the task and current sub instrument see Notes Usage scuquick quick tau notau NDF PARAM value Parameters help Print the help message quick This flag makes all of the SURF tasks run with the accept flag see SUN 95 so that default values are accepted for all parameters unless specified on the command line quiet Hide all messages generated by the script note this is not the same as using MSG_FILTER quiet which hides messages from the tasks tau value Run extinction with a tau of value the LST range is set automatically since we are using a constant tau Note that this is dangerous when processing multiple sub instruments Same as tau value notau Run extinction with a zero value of tau the LST range is set for you This is equivalent to using the tau 0 0 option sub sub_instrument Only process the specified sub instrument This is equivalent to setting the SUB_INSTRUMENT parameter explicitly same as sub sub_instrument change_flat Invoke the change_flat task after reduce _ switch clip Invoke the scuclip task after extinction remsky Invoke the remsky task after extinction or scuclip rebin Invoke the rebin package after extinction or remsky NDF The required dataset This parameter is optional reduce_switch will ask for an input file if no value is given 153 SCUQUICK SUN 2
107. d as star Per1 bin perl on Starlink sites is distributed by Starlink and can also be obtained A The sdip scuplot and scupa scripts are written in C shell scunoiselis written in perl Tk version 800 001 or newer available from CPAN a Additionally and require that is installed http wwwach hawaii edu JACpublic JCMT software perl http www cpan org
108. d as a function of time to find the correction that should be applied to each jiggle Since the extinction correction is different for each array it is at this point that the two arrays must be dealt with independently the output of this task will contain data for one sub instrument Single beam restoration The dual beam SCAN MAP data must be restored to a single beam map at some stage For data taken whilst chopping along the scan this is achieved by using the EKH algorithm 11 as implemented in the restore task In this case the restoration must occur before regridding For data taken whilst chopping in a fixed direction on the sky the so called Emerson I1 technique 12 individual chop configurations must be rebinned independently and then combined using the remdbmitask In future it is hoped that a maximum entropy algorithm can be implemented for both chopping techniques At this stage the data reduction path diverges depending on the observation type Map data must be regridded onto a rectangular grid using the rebin task followed by for SCAN MAP scuphot data if necessary whereas photometry data must be processed using the scuphot task 15 SUN 216 8 Basic outline of SCUBA data reduction The data reduction process can be automated to a certain extent by using the scuquick script This script can take as arguments any parameter that is expected by the SURF tasks A number of optional tasks are also avail
109. d temperatures are requested and skydip e reduce _switch now creates axis information instead of extinction e For SCAN MAP data scuover now displays the position of the array at the start of a scan e skydip now reads default values for ETA_TEL from the observation header and allows the T_HOT value to be modified Additionally the fit results are stored as output parameters e extinction now reads default values for FIRST_TAU from the observation header and supplies a default for SECOND_TAU the value accepted for FIRST_TAU e remsky now adds the mean sky level back onto the data in order to minimise the removal of flux from the image e remsky no longer despikes the data This facility is now provided by the tasks Bolometer groups e g ring 1 ring 2 all can now be used to specify bolometer lists for remsly The size of the output map can now be specified in rebin e The filenaming system used by has been modified slightly so that it conforms with the SCUBA_SUFFIX long mode now also recognizes SKYDIPs 12 12 Version 1 0 0 First public release of SURF SUN 216 8 Release Notes 52 Glossary chopping The secondary mirror is continuously moved on and off source at approximately 7 Hz in order to remove the sky to zeroth order This is done in addition to standard jiggling demodulation Removal of the chop signal by the transputers At this time the raw data can not be accessed only the demodulated data are s
110. d unless the sky was exceptionally stable the individual jiggle maps rarely look like they can be fitted by a parabola For this example I will use photometry data on 3C279 taken just before the example used for mapping The data have been processed in the same way as scan 59 scuphot n56_sky_lon SURF run 56 was a PHOTOM observation of 3c279 SURF file contains data for 1 exposure s in 10 integrations s in 1 measurement s ANALYSIS Which reduction method AVERAGE gt OUT Name of container file to hold map and time sequence data gt n56_pht_lon FILE Name of ASCII file to contain results summary gt n56 txt In this example n56_sky_lon sdf is processed with scuphot This observation consisted of 10 integrations and used a 9 point jiggle pattern The value of each integration was determined by taking the average of the jiggle pattern In some cases a better signal to noise can be achieved by processing the individual two second samples rather than averaging over the nine samples that comprise an integration For these cases usually short observations where the scatter on the averaged data is not representative of the standard deviation of the raw data small number statistics ANALYSIS SAMPLE is recommended Information on samples or integrations is written to a text file n56 txt in this case and also to n56_pht_lon sdf Since photometry observations can use multiple bolometers n56_pht_lon sdf is in fact a HDS con
111. e The name of the ASCII file used for storing the data IN CHAR Read The name of the input file to be rebinned This parameter is requested repeatedly until a NULL value is supplied LOOP must be TRUE IN can include aJSCUBA Like the REF parameter this parameter accepts a text file LAT_OUT CHAR Read The latitude of the output map centre The supplied default value is that of the map centre of the first map LONG_OUT CHAR Read The longitude of the output map centre The supplied default value is that of the map centre of the first map LOOP LOGICAL Read Task will ask for multiple input files if true Only REF is read if noloop MSG FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM There are no verbose messages OUT_COORDS CHAR Read The coordinate system of the output map Available coordinate systems are e AZ Azimuth elevation offsets e NA Nasmyth offsets e PL RA Dec Offsets from moving centre e g Planets e RB RA Dec B1950 e RJ RA Dec J2000 e RD RA Dec epoch of observation e GA Galactic coordinates J2000 REF CHAR Read The name of the first NDF to be rebinned The name may also be the name of an ASCII text file containing NDF and parameter values See the notes REF can include alSCUBA section SHIFT_DX REAL Read The pointing shift in X to be applied that would bring the maps in line This is a shift in the output coordinate frame 89 EXTRA
112. e a summary of all reduced _red_ and demodulated _dem_ pointing files ie not files produced during off line data reduction Notes e pointsumjonly displays pointing data e Files are drawn from the current working directory and the directory indicated by the DATADIR environment variable e Data reduced by the off line system will all be treated as run O for the purposes of listing unless numbers are present in the filename e The output can be stored in a file by using unix redirection as long as the search range is fully specified either as all or with begin and end e Command line options can be abbreviated e Options that take values can be used either as flag option or as flag option Related Applications SURF culog photsur fmapsum Sbssur Skysum 107 QDRAW SUN 216 8 Complete routine descriptions QDRAW Draw a data set with plus or minus 5 sigma range Description This program uses KAPPA routines to calculate mean and standard deviation of an NDF It then uses linplot to display the data with a range of plus or minus 5 sigma Optionally drawsig can be used to overlay 3 sigma lines Usage qdraw noline NDF Linplot Stats Drawsig parameters Parameters noline A Unix type switch which controls whether the 3 sigma lines are displayed or not NDF Given The required dataset ADAM parameters Any Any parameters accepted by the individual routines as long as
113. e contains data for 20 integration s in 10 measurement s T_HOT Temperature of hot load K 278 gt T_COLD Temperature of cold load for LONG_DC 73 6 gt ETA_TEL Telescope efficiency 0 91 gt B_VAL B parameter 1 gt SCULIB fit for filter 850 and sub instrument LONG_DC eta 0 91 0 00 b 0 86 0 00 tau 0 220 0 002 Standard Deviation of fit residual 0 74 K X 1 0 N 9 The results of the fit are displayed in figure 5 Points worth noting are that the local sidereal time of the observation is printed this is useful later when running extinction a fixed ye and 21 SUN 216 8 The data reduction process a floating value of B the default value for e is read from the file header were used and the tau agrees with the on line system which is not surprising since the same code is used on line as in SURF The errors derived for the fit can sometimes be suspect since the parameters are not completely independent The standard deviation of the fit residual gives a measure of the scatter in the points about the model fit Note also that the X indicates the reduced x of the fit forced to be approximately 1 0 by the program when it determines the errors and the N indicates the number of iterations required to converge on the fit Occasionally it is necessary to remove some points from the fit This can be achieved by using reduce_switch and change _quality before running skydip An example of this
114. e regions are handled by removing points from the coadd that lie further than 3 sigma from the mean then redoing the calculation recursively until no further points need be removed The first criterion for a spike is that it s diff value should be further from the mean of diff by NSIGMA times the sigma derived from the endpoints The problem with this simple approach is that bright sources in the scan themselves lead to excursions in diff that can be wrongly identified as spikes To prevent this happening a second criterion is used In this the scan values are convolved with a 3 sample wide box so that each box point is the average of the point itself and the points on either side of it Box is expected to increase faster for real sources than for spikes because in them the increase will be spread over all 3 averaged points rather than just 1 The second criterion for a spike is met therefore if a point s diff is further from the diff mean than the value of box at that point Fixed up values for points that have been identified as spikes are calculated by interpolat ing between the closest healthy points on either side The second spike criterion also means unfortunately that the technique is less sensitive to spikes on bright sources than elsewhere In addition it is still possible to clip bright sources if too low a value for NSIGMA is used It is recommended to run despike several
115. e should be in arcseconds All pixels closer to a bad pixel than this distance will be set to bad in the output image by setting bit 1 in the quality array Default is 0 0 SCALE REAL Read Radius of one scale size in arcsec This effectively governs the size of the weighting function For LINEAR one scale size corresponds to the zero of the cone for BESSEL it is the first zero of the Bessel function 71 and for Gaussian it is the half width half maximum HWHM SIZE 2 INTEGER Read This array parameter sets the size of the output grid in pixels nx ny The default values are the minimum dimensions required to display the entirety of the mapped area SHIFT_DX REAL Read The pointing shift in X to be applied that would bring the maps in line This is a shift in the output coordinate frame SHIFT_DY REAL Read The pointing shift in Y to be applied that would bring the maps in line This is a shift in the output coordinate frame TIMES LOGICAL Read Store an extra NDF in the output map containing the 2 D histogram of the data This can be used to make an estimate of the actual number of samples responsible for each point in the output grid Note that in general the number of pixels in the output grid exceeds the number of independent beams in the image The data can be accessed as OUT more reds times Default is FALSE WEIGHT REAL Read The relative weight that should be assigned to each dataset WEIGHTS
116. e should be set to a local scratch disk setenv HDS_SCRATCH tmp This has the additional advantage that NFS traffic can be reduced when accessing data on remote disks as the scratch files can be written locally ADAM_ABBRV Another useful environment variable is ADAM_ABBRV If this envrionment variable is set parameter abbreviation is turned on e g PIXSIZE_OUT can be referenced as PIX 13 SUN 216 8 Basic outline of SCUBA data reduction Table 3 Filenames generated from a typical data reduction Each row demonstrates how the filename is constructed from the previous row An observation number of 15 is used in this example Task Short Long Verbose 015 015 015 flatfield o15f o15_flat o15_flat o15f_lon_x o15_lon_ext 015 flat_lon ext o15f_ lon_xc o15_lon_clip 015_flat_lon_ext_clip o15f_lon_xcs o15_lon_sky 015_flat_lon_ext_clip_sky o15f_lon_xcsd 015_lon_dsp o15_flat_lon_ext_clip_sky_dsp o15f_lon_xcsdd 015_lon_dsp 015_flat_lon_ext_clip_sky_dsp_dsp rebin 30279 3c279 3c279 ADAM_EXIT If this environment variable is set when an ADAM task terminates the calling process will exit with system status set to 1 if the ADAM status was set or 0 if the ADAM status was okay This is useful when writing shell scripts All the ADAM environment variables are listed in SUN 144 151 8 Basic outline of SCUBA data reduction The SCUBA transputers take data at a rate of 128 Hz but data are only kept every second unti
117. e spike via the X menu option either typing the input or using the cursor and subsequently to flag the offending point just type the coordinate of the point a range or use the cursor in general the coordinate is to the right of the plotted point The routine will overlay the despiked data prompt the user to accept the new set and de zoom to the original scale To reset a previously flagged point flag the point again but do not accept it the point will be set to GOOD again Please read the note below the description of the menu on the use of the mouse The menu consists of M H Redisplay menu Q Quit N Next bolometer B Switch to bol X min max X cen X axis from min max or cen 10 Just x activates the cursor R Reset X axis Y min max Y lim Y axis from min max or lim lim U Reset Y axis Despike point or range of points Just p activates the cursor Option gt Note that a X center defined with the cursor or X cen defaults to a 20 points window around cen the position of the spike Using the CURSOR the Left Mouse button always defines the point the Right Mouse button exits the cursor task while accepting the last point clicked Usage dspbol f sdf_file d sdf_file2 s min max bol bol bol Parameters 85 DSPBOL SUN 216 8 Complete routine descriptions h elp Print the help information f file name of NDF file sdf may be included
118. ed linearly with time For this example we will assume the T variations are correct in order to demonstrate the principle extinction IN Name of NDF containing demodulated data 059_flat gt SURF run 59 was a MAP observation with JIGGLE sampling of object 3c279 SURF file contains data for 4 exposure s in 3 integration s in 1 measurement s SURF observation started at sidereal time 12 19 59 and ended at 12 28 40 SURF file contains data for the following sub instrument s SHORT with filter 450 LONG with filter 850 SUB_INSTRUMENT Name of sub instrument to be extinction corrected SHORT gt 1 FIRST_TAU First zenith sky opacity measured 0 gt 0 22 FIRST_LST Sidereal time of first opacity measurement hh mm ss ss 0 0 gt 11 54 SECOND_TAU Second zenith sky opacity measured 0 22 gt 0 187 SECOND_LST Sidereal time of second opacity measurement hh mm ss ss 11 54 gt 16 10 OUT Name of output NDF 059_lon_ext gt The arrays are separated at this point since the extinction correction would be different In this case the LONG wave array was selected extinction would have to be re run to select the SHORT wave array the question is not asked if only one sub instrument is present Some comment is probably required for the use of LST for the tau measurements this is not as bad as it sounds The skydip task prints the LST of the skydip and extinction prints the LST of the observation in
119. egrations 4 Measurements 1 Accept not used DATA_KPT DEMOD Gain 1 Observation file jupiter_h7 obs Data file apr25_dem_0094 95 SKYDIP 1997 4 25 17 46 26 99799 Bolometers SHORT_DC LONG_DC Filter 450N 850 Max EL 80 Min EL 15 Integrations 20 Measurements 10 Accept NO DATA_KPT DEMOD Gain 1 Observation file scuba_skydip obs Data file apr25_dem_0095 In most cases sculog provides far too much information and a one line summary is more desirable lobssund is provided for this purpose obssum demod Enter starting observation number 0 92 Enter final observation number last 98 Log for directory jcmt_sw scuba sun216 scuba observe apr25 dem HST Obsmode Source Meas Int Airmass Filter 92 07 33 PHOTOM JUPITER 1 4 1 229 450N 850N 93 07 36 PHOTOM JUPITER 1 4 1 229 450N 850N 94 07 43 PHOTOM JUPITER 1 4 1 231 450N 850N 95 07 46 SKYDIP SKY 10 20 450N 850N 96 07 54 POINTING uranus 1 2 1 337 450N 850N 97 OV 57 MAP uranus 1 1 1 407 450N 850N 98 08 45 POINTING uranus 1 2 1 488 450N 850N fou available if ndfperl is installed on your system see Appendix K is simply an alias for sculog summary Bolometers H7 SHORT_DC LONG_DC LONG SHORT LONG LONG 5 SUN 216 8 What data do I have In this example a summary listing has been requested for observations 92 through 98 from the DATADIR directory there were no demodulated data files in my current directory The demod flag indicated that
120. ents mm 171 F1 Demodulated data GAIN HSTEND HSTSTART HUMEND HUMSTART INSTRUME INT_NO JIGL_CNT JIGL_NAM J_PER_S J_REPEAT LAT LAT OBS LAT2 LOCL_CRD LONG LONG OBS LONG2 MAP_HGHT MAP_PA MAP_WDTH MAP_X MAP_Y MAX_EL MEANDEC MEANRA MEAS_NO MIN_EL MJD1 MJD2 MODE N_INT N_MEASUR OBJECT OBJ_TYPE OBSDEF OBSERVER PROJ_ID RUN SAM_CRDS SAM_DX SAM_DY SAM_MODE SAM_PA SPK_NSIG SPK_RMVL SPK_WDTH START_EL STATE STEND STRT_AZD STRT_ELD STSTART SWTCH_MD i SUN 216 8 FITS keywords Programmable gain HST at end of observation HST at start of observation Humidity 4 at end of observation Humidity at start of observation Name of instrument used Integration number at end of observation Number of offsets in jiggle pattern gt JCMIDATA_DIR tile_64_3p09 JIG File containing jiggle offsets 10 223 43 50 003365 23 35 09 999847 22 23 SCUBA 4 3 64 16 1 005 31 08 40 19 8258323669 not used RB 2 012 53 35 84 204 520278931 not used 180 0 180 0 0 1 5 790909 194 0517 dl 1 1 1 gt MAP 3 1 230279 2 PLANET 3c279_map obs Captain Nemo scuba 59 NA 2 1 1 JIGGLE 1 0 T 0 1 Terminating 12 28 40 78857 161 247 63 081 12 19 59 36714 gt BMSW Ser a Ss O AS A US A a na aM a O an M ee a a Aas MS SS TS M SA Number of jiggles per switch position No jiggle pat
121. er scunoise 19980210 5 Display the noise data for observation 5 on 19980210 scunoise 19980315 Prompt user for observation number using data from 19980315 Notes SCUNOISE has been developed for use at the JAC and therefore knows where to find the archived data The current directory and DATADIR are searched for files when the program is run outside of JAC SUN 216 8 Complete routine descriptions 144 SCUOVER SCUOVER Routine to overlay the bolometer names onto a rebinned image Description This routine is used to overlay the array layout onto a rebinned SCUBA image The displayed image is read from the graphics database unless a command line value is given In order to calculate the bolometer positions it is also necessary to read in the extinction corrected data file that was used to regrid the data in fact any extinction corrected file can be used possibly with strange results By default the position of the bolometers at the start of the first integration and zero jiggle offset is plotted Optionally it is possible to plot the bolometer positions at any point during the observation still with zero jiggle offset Usage scuover Parameters DEVICE DEVICE Read The graphics device on which the bolometers are to be drawn The global default set with KAPPA gdset will be used unless specified otherwise EXPOSURE INTEGER Read Ues the bolometer positions at the specified exposure within the specified INTEGRA
122. es will display the source in the middle of the range Sometimes spikes skew the statistics of an individual bin to such an extent that a spike lies within the NSIGMA cutoff region i e the spike makes the standard deviation so large that it lies within NSIGMA of the mean In an effort to overcome this problem a smoothing option 175 SUN 216 8 Description of despiking method used by despike A A eee E lr ra E 49 50 51 52 53 54 55 sel a9 50 tst 52 53 54 55 56 i H 1 Se 1 Baines ar AS AA A eel a ai 42 43 Jaa 45 46 ar as m 42 43 44 45 46 Jar 48 g i i i iar ree 1 I AS AE i i a a il pee 331 34 ast 36 37 3si 39 40 33 34 3536 37 38 39 40 T t r 1 i E 1 AA pS a opos e eed PA ae m te a 251 26 27i 28 29 30 31 32 25 26 27 28 29 30 31 32 T T s 1 ies A ae oe aie aie ee E 0 PE a ic ee azi rel 198 20 21 22 23 24 17 18 19 20 21 22 23 24 r T a i AR E TAS a ENE A A la cag cs aa 9 10 11 12 13 14 15 161 9 10 14 12 13 J14 15 16 i I rl 1 EET ssl isa ne i St ss Ela tsa ne 1 2 3 a 5 6 7 le 1 2 13 4 5 16 7 le SPIRAL XLINEAR E aoh sol 514 52 534 sah ssl se 49 T E i Lit iit I a al aol al al asl lali 471 asl 41 y Ko E E A A
123. ets e NA Nasmyth offsets e PL RA Dec Offsets from moving centre e g Planets e RB RA Dec B1950 e RJ RA Dec J2000 e RD RA Dec epoch of observation e GA Galactic coordinates J2000 For RD current epoch is taken from the first input file REF CHAR Given The name of the first NDF to be processed The name may also be the name of an ASCII text file containing NDF and parameter values REF can include a SCUBA section See rebin for more information on the format of the ASCII input file SHIFT_DX REAL Read The pointing shift in X to be applied that would bring the maps in line This is a shift in the output coordinate frame SHIFT_DY REAL Read The pointing shift in Y to be applied that would bring the maps in line This is a shift in the output coordinate frame WEIGHT REAL Read This parameter does nothing in calcsky It must be present when using text file input Any value is allowed Examples calcsky test_rlb model Al Calculate sky for test_rlb sdf Only read in one file and don t use an external source model calcsky list inp model m82 noloop Read in the files specified in list inp and use m82 sdf as a model of the source calcsky file nosrc nosrc boxsz 10 0 Al Calculate sky for file sdf Store the source subtracted image in nosrc sdf Use a smoothing size of 10 seconds Notes e The model itself is only an approximation to the data since the data points can fall anywhere within a give
124. evant for LINEAR regridding For Gaussian the default is 3 i e a diameter of 3 FWHM for the footprint 95 INTREBIN SUN 216 8 Complete routine descriptions Examples and for Bessel it is 10 The smaller the weighting function is a combination of WTENRAD and SCALE the faster the regridding goes intrebin rebin_method LINEAR out_coords RJ Rebin the maps with LINEAR weighting function in J2000 RA Dec coordinates You will be asked for input datasets until a null value is given intrebin rebin_method BESSEL out map Rebin the maps with Bessel weighting function Each integration is rebinned separately and placed in an NDF in the output container file map sdf Integration 2 can be accessed by displaying map i1 intrebin noloop ref test bat Rebin each integration using the data specified in the file test bat Notes For each file name that is entered values for the parameters WEIGHT SHIFT_DX and SHIFT_DY are requested The application can read in up to 256 separate input datasets The output map will be large enough to include all data points Spline regridding may have problems with SCAN MAP since integrations contain lots of overlapping data points SCUBA sections can be given along with any input NDF The relative weights associated with each point in the output map are stored in a WEIGHTS NDF in the REDS extension of the output data For WEIGHTS TRUE For spline rebinning each point is equivalent to the number of
125. files There is one data file per line An example file is file1 b5 1 0 0 5 0 0 Read bolometer 5 from filel sdf file2 Read file 2 but you will still be prompted for WEIGHT and shifts file3 i3 1 0 0 0 0 0 Use everything except int 3 test bat Read in another text file Note that the parameters are position dependent and are not necessary Missing parameters are requested This means it is not possible to specify SHIFT_DX position 3 without specifying the WEIGHT If the file has the txt extension the NDF system will attempt to convert it to NDF format before processing this is probably not what you want Related Applications SURF rebin despike2 SUN 216 8 Complete routine descriptions 82 DESPIKE2 DESPIKE2 Remove spikes from SCAN MAP observations Description This routine removes spikes from SCAN MAP observations The scan map differential despiking algorithm uses 2 criteria to decide which points are spikes First for each bolometer used a pass is made through each scan calculating for each point point i 1 point i 1 diff i point i 20 Values of diff for the first and last points in the scan are calculated in a similar way but subtracting the mean of points 2 and 3 and points n 1 and n 2 respectively The mean and standard deviation of diff are calculated by coadding the 10 points at each end of the scan where hopefully there is no source emission Spikes in thes
126. formation stored in the FITS header of reduced and raw data files and does not provide summaries of reduced RO data such as photometry results essentially for reasons of clarity must be used to generate a summary of photometry observations that includes reduced data e Files are drawn from the current working directory and the directory indicated by the DATADIR environment variable e Data reduced by the off line system will all be treated as run 0 for the purposes of listing unless numbers are present in the filename SUN 216 8 Complete routine descriptions 140 SCULOG e The output can be stored in a file by using unix redirection as long as the search range is fully specified either as all or with begin and end e Command line options can be abbreviated e Options that take values can be used either as flag option or as flag option Related Applications SURF assum photsum pointsum mapsom sun 141 SCUMAKEWT SUN 216 8 Complete routine descriptions SCUMAKEWT Create weights array for dual beam deconvolution Description Construct an NDF holding the weights array for a particular chop throw and the Fourier Transform FT of the chop function a sine wave Usage scumakewt chop pa pixsize size ftchop wtchop Parameters CHOP REAL Read Chop throw in arcseconds There is no default FTCHOP NDF Write Output NDF containing fourier transform of the chop
127. function The size of the output array matches the dimensions supplied by parameter SIZE LIKE NDF Read This parameter may be used to supply an NDF which is to be used as a template If such a template is supplied then its origin its lower pixel index bounds and extent will be read used for the output NDFs By default no template will be used and the size information will be read from the SIZE parameter Additionally the PA PIXSIZE and CHOP parameters are searched for in the FITS extension if one is present using keywords of CHOP_PA SCUPIXSZ and CHOP_THR respectively These parameters values are requested if not found in the FITS extension MSG FILTER CHAR Read Message filter level Default is NORM OUTCHOP REAL Write Chop throw angle actually used OUTPA REAL Write Position angle actually used OUTPIXSZ REAL Write Actual pixel size used arcsec PA REAL Read Position angle of chop throw Positive is anti clockwise starting from North The angle should be specified in degrees PIXSIZE REAL Read Pixel size to be used for output images Should be in arcseconds ie same units as used for the CHOP parameter SIZE 2 INTEGER Read Array parameter containing the number of pixels X Y in the output images WTCHOP NDF Write Output NDF containing the weights contributed by this chop configuration This is FTCHOP squared The size of the output array matches the dimensions supplied by parameter SIZE
128. g state rror in the telescope elevation MU tables Z axis focus offset MU tables Z axis SAO atmospheric seeing Date and time of SAO seeing CSO tau Date and time of CSO tau CSO tau rms User azimuth pointing offset User elevation pointing offset UT date at start of observation No spikes before quality set bad Lag of internal calibrator in samples Period of internal calibrator in samples Chop lag in samples Chop period in samples Nasmyth dU3 coord of instrument centre Nasmyth dU4 coord of instrument centre Filter name Filter Filter Filter Filter name Name of flat field file No samples discarded after jiggle movement Bol to whose value LW guard ring is set Long wave guard ring on or off Bolometers actually measured in observation Number of bolometers selected name name name Number of sub instruments used No of samples discarded before chop movement No samples discarded after chop movement Rebinning method used by SCUIP A D card of FLATFIELD reference bolometer Channel of FLATFIELD reference bolometer A D sample period in ticks 64musec True if data is simulated Name of sky opacities file SCUBA instrument being used SCUBA instrument being used 173 F 2 Rebinned data SUB_3 SUB_4 SUB_5 S_GD_BOL S_GUARD TAUZ_1 TAUZ_2 TAUZ_3 TAUZ_4 TAUZ_5 T_AMB T_COLD_1 T_COLD_2 1 T_COLD_3 1 T_COLD_4 1 T_COLD_5 1 T_HOT T_TEL USE_CAL WAVE_1 WAVE_2 WAVE_3 WAVE_4 WAVE_5 END not used
129. g the default value offered by SCUQUICK produces the following files identical to the files produced SUN 216 8 Complete routine descriptions 154 SCUQUICK with SCUBA_SUFFIX long root sdf from reduce_ switch root_flat sdf from flatfield root_ lt sub gt _ext sdf from extinction one for each sub root_ lt sub gt _sky sdf from remsky with the remsky switch root_ lt sub gt _reb sdf from rebin with the rebin switch root_ lt sub gt _pht sdf from scuphot if processing a PHOTOM observation root_ lt sub gt _pht dat from scuphot if processing a PHOTOM observation Where lt sub gt is the first three letters of the sub instrument name Using the tau switch is dangerous when processing multiple sub instruments since the extinction changes with wavelength Command line options can be abbreviated Skydip observations are recognised Options that take values can be used either as flag option or as flag option Prior requirements e The NDF perl module must exist this should be installed by your system administra tor if it is missing Related Applications SURF educe switch hange Mat rebin Seuphot cuca 155 SCUSETENV SUN 216 8 Complete routine descriptions SCUSETENV Set the startup environment variables for SURF Description This script sets the standard DATADIR and SCUBA_PREFIX environment variables given a UT date Usage scusetenv UTdate Examples scusetenv Set DATA
130. ggle mode and for photometry if the source structure is complex then calcsky should be considered 89 8 2 remsky IN Name of input file containing demodulated map data w48_newrebin gt 059_lon_ext SURF run 59 was a MAP observation with JIGGLE sampling of object 3c279 OUT Name of output file 059_lon_sky gt BOLOMETERS The Sky bolometers al a2 for an array all h7 gt SURF Using 36 sky bolometers MODE Sky removal mode median gt Adding mean background level onto data value 1 5316721E 6 In this example we have used all the bolometers except for the central pixel H7 and then used median sky removal for each jiggle The average background level has also been added back onto the data The output of extinction or remsky can be displayed using say KAPPA display to see whether some integrations or bolometers should be marked bad Sometimes bad bolometers can only be identified after a rebin phase The output so far can be seen in figure 6 the axes are labeled with bolometer number along the X axis and integration number up the Y axis Now that the data have been extinction corrected and optionally processed with the data reduction path diverges according to the type of observation Map sional jiggle and scan and photometry will be dealt with separately Note that scuquick can be used to automate some of the more repetitive tasks during this stage of the data reduction process
131. gnal from the raw demodulated data i e before running me The simplest way to extract the signal is to use the command 17The files can be found in SURF_DIR 18for the calibrator signal prior to April 1997 or for different filters please contact your SCUBA support scientist for more advice 183 SUN 216 8 Correcting shifted data 0 050 0 040 F o ee ee am gt Calibrator signal o Oo ee o A 0 020 0 010 0 20 40 60 80 100 120 Bolometer Figure 17 The standard calibrator signal solid line with an overlay of a shifted calibrator signal dashed The A D cards are indicated and a shift is clearly seen on card B SUN 216 8 Correcting shifted data 184 manic INPUT Input image calsig_450_850_map gt 19971008_dem_0039 Array is 3 dimensional Dimensions are 5 128 384 ONDIM Dimensionality of output image 3 gt 1 ELINE2 Axis of the input data array that will be used to form the output data array Y gt Y YLIMITS Window limits for the Y axis of the input data array 1 37 gt XRANGE Range for summation over the X axis of the input data array 1 5 gt 3 3 ZRANGE Range for summation over the Z axis of the input data array 1 384 gt OUTPUT Output image gt calsig LOOP Produce another output IMAGE structure and data array NO gt The dimensions of the data array in the demodulated file should be 5 n_bols n_jiggles SE 3
132. gration 3 Note that this is different to b2 i3 which would only select the second bolometer from integration 3 test p50 100 b32 select samples 1 through 49 and 101 through to the end and all bolometers except number 32 The tasks rebin change _quality and extract_data understand the concept of SCUBA sections 7 Environment variables The behaviour of SURF can be modified by the use of environment variables 7 1 SURF environment variables This section describes environment variables that are spcific to SURF SURF has variables for determining the location of the data DATADIR and SCUBA_PREFIXf land the behaviour of the automatic filenaming system SCUBA_SUFFIX 7 1 1 DATADIR DATADIR can be used to specify an alternative location for the raw data This means that users do not need to make multiple copies of the demodulated data files for example at the JAC support scientists access the data archive directly and never take their own copies and saves disk space As an example at the JAC to access demodulated data taken on the 30th October 1997 all that is needed is SThese variables are directly comparable with the SpECx 14 use of the DATADIR environment variable and the set gsd filename command SUN 216 8 Environment variables 10 setenv DATADIR scuba observe 19971030 dem DATADIR is supported by all routines that access demodulated data sculogletc but is not recognised by routines that deal with part
133. h chops page 128 SCUCAT Concatenates photometry results into a single NDF page 130 SCUCLIP Perform sigma clipping of each bolometer page 132 SCUCLKERR Determine potential inconsistency in the SCUBA time headers page 134 SCUHELP Interactive help system page 135 SCULOG Provide detailed descriptions of all observation data page 138 SCUMAKEWT Generate fourier weights of chop function page 141 SCUNOISE Display SCUBA noise data page 143 SCUOVER Overlay bolometer array on image page 144 SCUPA Show position angle of array Requires KAPPA page 146 SCUPHOT Reduces photometry data to a single point per integration page 147 SCUPLOT Interactive despiking and data inspection Requires KAPPA page 149 SCUQUICK Semi automated data reduction pipeline page 152 SCUSETENV Set SCUBA environment variables JAC only page 155 SCUSHIFT Shift bolometers on A to D card page 156 SDIP Script to reduce and display skydip data requires KAPPA page 157 SETBOLWT Calculate and set bolometer weights requires KAPPA page 158 SIGCLIP Remove spikes from photometry data requires KAPPA page 160 SKYDIP Calculate sky opacity from skydip data page 161 SKYSUM Generate a summary of skydip observations page 164 SUN 216 8 Classified SURF commands 58 B Classified SURF commands SURF applications may be classified in terms of their function as follows Observation summaries Provide detailed descriptions of a
134. he SCUBA extension contains the flatfield information position of the bolometers sub intrument of bolometers quality of bolometers and A to D card There are also arrays to aid in the location of each jiggle in the data array DEM_PNTR FITS extension The FITS Extension is described in the next appendix SUN 216 8 FITS keywords 170 In addition a new extension is created by the SURF package itself This extension called REDS for historical reasons contains beam weights for chopping and pointing corrections In general this extension is created for PHOTOMetry observations and by the change _ pointingltask A more detailed description of the file format can be found in Starlink System Note 72 F FITS keywords FITS information is stored in the NDF FITS extension of all SCUBA NDFs This information can be accessed by using the command or less conveniently with hdstrace This appendix gives a full listing of all the information stored in the FITS header F1 Demodulated data All observation parameters are stored in the NDF FITS extension They can be accessed using the KAPPA task fitslistl The same information is stored in the reduced files but in the HEADER component fitslist apr8_dem_0059 ACCEPT not used accept update PROMPT YES or NO ALIGN_AX not used Alignment measurements in X or Y axis ALIGN_SH 1 Distance between successive alignment offsets ALT OBS 4092 Height of observatory above sea
135. hich makes is easy to compare bolometers Mode d allows for interactive despiking Please read the note below the description of the menu on the use of the mouse Mode p or or any px link to scuplot is a wrapper around the KAPPA utility It allows plots of a whole series of bolometers one by one optionally overlaying them with the same bolometer from a second file Obvious overlays are despiked on non despiked data or data from different exposures to check the noise Mode r or or any rx link to scuplot is a wrapper around the KAPPA utility It provides plots of sets of bolometers in a single window with optionally data from a second file in a second window Obvious files are despiked and non despiked data or data from different exposures to check the noise Mode d or or any dx link to scuplot can be used to interactively despike bolometers While it is not as fast as a completely integrated routine would be it makes interactive despiking much easier by hiding the cycle between linplot and change _ quality for the user The most common use is to zoom in on the region with the spike via the X menu option either typing the input or using the cursor and subsequently to flag the offending point just type the coordinate of the point a range or use the cursor in general the coordinate is to the right of the plotted point The routine will overlay the despiked data prompt the user to accept the new se
136. ic JCMT software bin scuba_wish pl SUN 216 8 Release Notes 46 in SSN 72 30 12 Release Notes 12 1 Changes in Version 1 6 11 e Now includes a new version of the scunoise application e A small error was found and fixed in the equation used by Essentially the flux at all waveplate angles should have been reduced by a further small constant fraction determined by the level of instrumental polarization at the observing wavelength The net result is that source polarizations will have been very slightly underestimated For example a source polarization of 1 00 at 850 microns should in fact have been 1 01 and a source polarization of 1 00 at 450 microns should have been 1 03 This effect is smaller than measurement errors unless the source polarization exceeds 10 A bug was fixed to allow 256 maps to be coadded in rebin previously the limit was 256 but another limit was reached after 173 maps 12 2 Changes in Version 1 6 10 Fix problem in on linux unintialized pointer Fix remip problem with aborted polarimeter observations 12 3 Changes in Version 1 6 9 e Fix more problems with scuba2mem when using SC EKH scanning Correctly rebin photometry observations taken with AZ jiggling previously AZ offsets were simply ignored unless pointing corrections were being applied 12 4 Changes in Version 1 6 8 e New version of the mapping cookbook SC 11 now includes scan mapping Update remdbm to support V0 18
137. ication of the data to be changed Usually of the form ndf specl spec2 where ndf is the filename and specl n are the section specifications The section can be read from the SECTION parameter if the SCUBA section is omitted MSG _FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM There are no verbose messages OUT NDF Write Name of the NDF that stores the modified data SECTION CHAR Read This parameter can be used to specify SCUBA sections Curly brackets must still be given Since this is an array parameter square brackets must be used to specify more than one component SECTION gt b3 i2 would supply two SECTIONS of b3 and i2 Only b3 will be used if the square brackets are not used Care must also be taken when using commas in SCUBA sections the parameter system will split multiple entries on commas unless the entire section is quoted SECTION gt b3 5 i2 If necessary the negation character should come after a section ie after the closing curly bracket and that negation applies to the combined section and not just the string containing the negation character 71 CHANGE_DATA SUN 216 8 Complete routine descriptions SECTION gt b3 i2 implies that the section consists of everything except bolometer 3 and integration 2 This parameter is only used when no SCUBA section was specified via the IN param eter VALUE LITERA
138. ifferent secondary mirror position JIGGLE MAP This is the main imaging mode for sources which are smaller than the array i e less than about 2 arcmin All JIGGLE MAP observations including ALIGN FOCUS and POINTING are reduced in the same way using rebin to make the final image info on how a JIGGLE MAP is taken reference exposures and switches NOISE This is the mode used to measure the noise behaviour of the array Data are reduced using Noise data can be inspected with scunoise PHOTOM This mode is used to measure the flux of a point source In its simplest guise the observation involves pointing a single bolometer at the source measuring the signal chopping and SUN 216 8 Message filtering nodding to reduce the effect of sky emission and integrating to build up the signal to noise SCUBA also allows for 2 or 3 bolometer photometry chopping on the array simultaneous photometry using the long and short wave arrays and jiggling on source to reduce the effects of seeing The scuphot task is used to reduce photometry observations to a simpler form one data point per integration for further analysis POINTING This mode is used to check the pointing of the telescope by observing a bright source with a known position A single pixel observing mode is available and is not supported by SuRF The JIGGLE MAP implementation can be processed as a standard JIGGLE MAP The pointing offset can be checked by using say the task
139. in the NDF extensions that must correspond to data in the main DATA_ARRAY none of the SURF tasks can accept NDF sections 3 On many occassions it is desirable to work on a subset of the observation e g data from a specific exposure integration or measurement and the SURF package supports this via the concept of a SCUBA section A SCUBA section is indicated by using curly brackets after the file name c f round brackets for NDF sections The brackets then contain a specification that selects a certain part of the input data using the format shown in table 1 Note that SCUBA data is organised with bolometer number along the X axis and time eg jiggle along the Y axis so that the b specifier simply selects out bolometer data but the p s e i and m specifiers select data by time Here are some example SCUBA sections test select all points good for resetting change _quality mask test i3 means select all bolometers in integration 3 for all measurements 9 SUN 216 8 Environment variables test b3 5 select bolometers 3 to 5 for all points test e3 select everything except the 3rd exposure in each integration test e3 i4 select the third exposure in integration 4 test b5 p500 600 select points 500 to 600 for bolometer 5 test b5 7 19 select bolometers 5 through 7 and bolometer 19 test i1 4 7 b3 select integrations 1 2 3 4 and 7 and all data for bolometer 3 test b2 i3 select bolometer 2 and inte
140. ing whilst scanning results in an image that contains two beams a plus and minus image of the source To restore the source profile we must deconvolve the chop from the measured map The problems associated with this step can best be appreciated by considering the Fourier transform FT of the chop function which is a sine wave with zeroes at the origin and at harmonics of the inverse chop throw Deconvolving the chop function is equivalent to dividing the FT of the measured map by the FT of the chop and then transforming back to image space Clearly problems arise at spatial frequencies where the sine wave of the chop FT has a low value or is zero Noise at these frequencies is blown up and significantly reduces the signal to noise of the restored map 11 EKH method The restore task must be used to remove the dual beam response whilst chopping in the scan direction This must be run before rebinning Since the chop direction rotates slowly on the sky since it is dependent on the scan direction which is in Nasmyth coordinates and not the sky orientation tasks that try to map the chopped data onto a sky plane rebin can not be used before the dual beam has been removed despikelis useless after restoration since spikes propagate through the entire scan and show up as sine waves after restore Emerson II method To remove the dual beam signature from Emerson II data rebinned images of each chop configuration must be generated they can be co
141. ional grid is transformed to a 1 dimensional strip before plotting The plot shows data value against bin number for all the bins The transformation from 1 to 2 dimensions can be achieved in many ways but only 5 methods have been implemented in The supported methods presented graphically in figure 13 and with reference to the bin numbers used in the figure are e SPIRAL A Spiral outwards from the reference bin the pointing centre of the map Using the example presented in the figure the bin order used by the plotting task becomes 28 20 21 29 37 36 35 27 etc This means that data from the centre of the array is displayed before the sparse data at the edges of the array e XLINEAR unfold each X strip in turn for each Y In this case the bin order becomes 1 2 3 4 5 6 7 8 9 10 11 etc A source in the centre of the array will be displayed in the middle of the default range provided e YLINEAR unfold each Y strip in turn for each X In this case the bin order becomes 1 9 17 25 33 41 49 2 10 etc e DIAG1 diagonal strips starting at position 1 1 The bin order in the example becomes 1 2 9 3 10 17 4 11 18 25 5 etc e DIAG2 diagonal strips starting at positions nx 1 The bin order in the example becomes 8 7 16 6 15 24 5 etc In general this means that in the case where the source lies in the centre of the array the spiral display mode will show the source in the first few bins whereas the other mod
142. ions where in lis contains the names of the 3 filenames to be processed a comma separated list is also allowed If you do not want to process different bolometers independently the METHOD parameter can be set to CATALL in which case all data will be concatenated together regardless of bolometer and the output filename will match that specified in OUT rather than being OUT bolometer name 9 7 1 SURF photometry and KAPPA The photometry data reduction system produces one flux measurement per integration per bolometer Further analysis simply involves finding a self consistent mean of the merged data set multiple measurements with a given bolometer can be concatenated together using scucat The SURF package supplies two KAPPA scripts to aid with this step of the analysis lgdraw displays the data with a 50 range calculates and draws the 3 sigma lines and reports the mean and error in the mean of the supplied data set This script uses the KAPPA routines stats and drawsig Figure 8 shows the data from the previous section as displayed with SUN 216 8 The data reduction process 36 dE e T Integratior Figure 8 Photometry data of 3C279 This is the concatenated data from three separate observa tions e If the data contains large spikes which are having a significant effect on the standard deviation calculation then can be used to mark bad all data that are outside a given n
143. is displayed scuhelp application topic This gives help about the specified application or topic scuhelp application topic subtopic This lists help about a subtopic of the specified application or topic The hierar chy of topics has a maximum of four levels scuhelp Hints This gives hints for new and intermediate users scuhelp summary This shows a one line summary of each application SUN 216 8 Complete routine descriptions 136 SCUHELP scuhelp classified classification This lists a one line summary of each application in the given functionality clas sification Notes The environment variable SURF_HELP should be set to point to the help file This variable is usually set as part of the Starlink login Navigating the Help Library The help information is arranged hierarchically You can move around the help information whenever SCUHELP prompts This occurs when it has either presented a screen s worth of text or has completed displaying the previously requested help The information displayed by SCUHELP on a particular topic includes a description of the topic and a list of subtopics that further describe the topic At a prompt you may enter e a topic and or subtopic name s to display the help for that topic or subtopic so for example block parameters box gives help on BOX which is a subtopic of Parameters which in turn is a subtopic of BLOCK e a lt CR gt to see more text at a Press RETURN to continue
144. is used Linear interpolation should be fast less than 10 seconds for most reasonable pixel sizes The map can now be made with rebin in this case using linear interpolation J2000 coordinates 1 arcsec pixels and default map centre looping is turned off since I am only regridding one map rebin noloop REBIN_METHOD Rebinning method to be used LINEAR gt SURF Initialising LINEAR weighting functions OUT_COORDS Coordinate sys of output map PL AZ NA RB RJ RD or GA RJ gt SURF output coordinates are FK5 J2000 0 REF Name of first data file to be rebinned n59_sky_lon gt SURF run 59 was a MAP observation of 3c279 with JIGGLE sampling SURF file contains data for 4 exposure s in 3 integrations s in 1 measurement s WEIGHT Weight to be assigned to input dataset 1 gt SHIFT_DX X shift to be applied to input dataset on output map arcsec 0 gt SHIFT_DY Y shift to be applied to input dataset on output map arcsec 0 gt 29 SUN 216 8 The data reduction process SURF Input data name weight dx dy 1 n59_sky_lon 1 0 0 LONG_OUT Longitude of output map centre in hh or dd mm ss ss format 12 56 11 1777 gt LAT_OUT Latitude of output map centre in dd mm ss ss format 05 47 22 1 gt OUT_OBJECT Object name for output map 3c279 gt PIXSIZE_0UT Size of pixels in output map arcsec 3 gt 1 OUT Name of file to contain rebinned map gt n59
145. iting for input e g 4 obssum all gt summary txt Supported Observing Modes The SURF package supports the following SCUBA observing modes ALIGN This is the mode used for setting the X and Y alignment of the secondary mirror This mode usually consists of 5 measurements one for each secondary mirror position Currently the standard observing mode uses a single pixel to calculate the best secondary mirror position since it is the most efficient method for determining the alignment this is similar to the heterodyne X and Y focus observations and this mode is not supported by SURF Alternatively it is possible to ALIGN using the entire array and since these data are simply 5 JIGGLE MAPS this mode can be reduced with SURF Care must be taken to make sure that each measurement is rebinned independently switch off the measurements that are not required by using change_ quality otherwise you will end up with the average of all the measurements at all secondary mirror positions the unfocussed images will dominate Note that no special processing is perfomed on these data and SURF does not provide a way of calculating the secondary mirror offset FOCUS This is the mode used for focussing the Z axis of telescope This mode is similar to ALIGN in that five measurements are taken and that the single pixel mode is not supported The same care must be taken when reducing the unfocussed images since each measurement will be from a d
146. k K 95 07 46 SKYDIP 10 20 450N 850 SHORT 1 756 0 074 0 423 LONG 0 310 97 07 57 uranus 1 1 1 41 450N 850 RASTER 40 SC O 0 074 0 423 pointsumican be used to list pointing data pointsum begin 50 end 98 E LST Source Meas Int Az El Filter Inst Uaz Uel Tau Seeing Hum 51 19 32 jupiter 1 1 140 45 450N 850 LONG 1 6 9 5 0 074 0 344 14 62 20 06 jupiter 1 1 150 49 450N 850 LONG 2 1 10 0 074 0 351 14 83 20 56 jupiter 1 1 168 53 450N 850 LONG 1 8 11 0 074 0 242 15 96 21 47 uranus 1 2 203 48 450N 850 LONG 2 7 11 0 074 0 423 14 98 22 38 uranus 1 2 218 42 450N 850 LONG 3 0 9 6 0 074 0 984 20 5Note that HDS creates temporary files when mapping the reduced data If the files are in a directory in which you do not have write permission this operation will fail and photsum will return an error message This can be overcome by forcing HDS to write temporary files to another directory by setting the HDS_SCRATCH environment variable to a writeable directory e g setenv HDS_SCRATCH tmp SUN 216 8 Supported Observing Modes 6 Note that UAZ and UEL indicate the offsets before the pointing observation and that the time is now quoted as LST instead of HST since this is the format expected by change _ pointing In all cases the output can be stored in a file using standard unix redirection so long as the search path is fully specified either with the a11 flag or with begin and end so that the programs are not wa
147. ky noise and constant offsets from SCUBA jiggle data It does this by requesting sky bolometers calculating an average value for each jiggle and then subtracting this off the jiggle Each jiggle is analysed in turn The average value can be calculated in two ways either MEDIAN or MEAN After the calculation the mean value removed from each jiggle can be added back onto the data this should protect against removing flux from MAP data If a SKY NDF is found in the REDS extension it is assumed that the sky variation has already been determined eg by calcsky and this sky signature is removed The ADD parameter is ignored in this case Usage remsky in out Parameters ADD LOGICAL Read This parameter governs whether the average value removed from the data should be added back after sky removal The default is for ADD to be true for MAPs and false for other modes the assumption being that sky bolometers in PHOTOM observations are guaranteed to be on sky BOLOMETERS CHAR Read List of sky bolometers The following options are now recognised for the BOLOME TERS parameter Code Description Example nn A number 5 or 19 id Bolometer id h7 or c14 rn Ring number r1 for the first ring r5 for the outer ring of the SHORT array r 1 for the outer ring r 2 one ring in from outer ring all All bolometers all select the entire array Each value must be comma separated but can be preceded by a minus sign to remo
148. l scales require large datasets since not all cells in a 1 arcsecond grid will contain data points although the KAPPA commands fillbad and glitch can be used to smooth over bad pixels bolrebin ref Parameters GUARD LOGICAL Read Controls whether the bolometer guard ring should be used during the regridding process The guard ring enforces zero flux at the edge of the regridded image Should be turned off if flux is present at the edge Default is to use the guard ring for LINEAR BESSEL and GAUSSIAN rebin modes 63 BOLREBIN SUN 216 8 Complete routine descriptions IN CHAR Read The name of the input file to be rebinned This parameter is requested repeatedly until a NULL value is supplied LOOP must be TRUE IN can include a SCUBA Like the REF parameter this parameter accepts a text file LAT_OUT CHAR Read The latitude of the output map centre The supplied default value is that of the map centre of the first map LONG_OUT CHAR Read The longitude of the output map centre The supplied default value is that of the map centre of the first map LOOP LOGICAL Read Task will ask for multiple input files if true Only REF is read if noloop MSG_FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM There are no verbose messages OUT NDF Write This is the name of the HDS container file that will contain the rebinned images The map for each bolometer is s
149. l the high speed data link is installed Each second of data therefore is the mean of 128 measurements and the standard deviation gives the error The transputers also detect fast transient spikes which are removed from the calculation of the mean The number of spikes detected in each measurement is stored for use by the off line system Note that the effects of cosmic rays may last significantly longer than 1 128 second and the transputers would probably not detect a spike As the SCUBA arrays are not fully sampled and not on a rectangular grid images can not be taken in the same way as for an optical CCD array At least 16 individual secondary mirror or jiggle positions each of 1 second are required to make a fully sampled image 64 jiggles are required if both the long and short wave arrays are being used simultaneously The SURF data reduction package must take these data combine them and regrid them onto a rectangular grid The data file produced by the on line system contains all the information necessary to reduce the observations As well as the raw data the file contains information on the jiggle pattern SUN 216 8 Basic outline of SCUBA data reduction 14 the coordinates of the bolometers relative to the central pixel flatfield information internal calibrator signal and general observation parameters All SCUBA data reduction must include the following stages see Figs and 4 for flow diagrams 1 Nod compensatio
150. le help system SUN 216 8 Complete routine descriptions 138 SCULOG SCULOG Produce summary of SCUBA observations Description Sculog goes through all the sdf files in the current directory and optionally DATADIR defined in an environment variable and extracts information from any FITS entries that may be present If a HISTORY record is present i e the data have been partially reduced the most recent application to manipulate the data is reported In the absence of the all flag a numeric range is requested This range only has an effect on raw data or reduced files which have the run number embedded into the file name Filenames with no numbers are treated as scan 0 Usage sculog h summary demod reduced mode all begin nn end nn Parameters hlelp Return a help message only More help can be obtained by using showme sun216 or scuhelp sculog summary Return a one line summary of each observation file No HISTORY information is reported all List all files in the current directory and DATADIR demod Only list demodulated data files signified by _dem_ file name reduced Only list reduced data files signified by _red_ file name begin nn First scan number to be considered same as begin nn end nn Final scan number to be considered same as end nn mode obs Select only specified observation modes for listing The list should be comma sepa
151. le should be marked bad if the transputers detected more than 5 spikes during a 1 second sample SWITCH INTEGER Read Parameter to indicate which switch to extract A value of 0 means that all switches should be reduced Default is 0 TARRAY LOGICAL Read Controls whether the T_COLD parameters are read as an array of values true or read as a sequence of scalars false This parameter is useful if the command is to be run in batch mode Default is false T_COLD REAL Read Temperature of the cold load when processing skydip data The default value is taken from the input file T_HOT REAL Read Temperature of the hot load when processing skydip data The default value is taken from the input file USE_CALIBRATOR LOGICAL Read Yes if you want the data for each bolometer measurement divided by the correspond ing internal calibrator signal The default is not to use the calibrator 115 REDUCE_SWITCH SUN 216 8 Complete routine descriptions Examples reduce_switch All parameters will be requested reduce_switch test nosw This will reduce the switch from input file test sdf without dividing by the cali brator signal and tolerating up to 5 spikes in a 1 second sample The output data will be written to nosw sdf reduce_switch test nosw SWITCH 2 This will select switch 2 from test sdf and write it to nosw sdf Notes If the input file is not found in the current directory the directory specified by the DATADIR
152. level metres AMEND 1 117139 Airmass at end of observation AMSTART 1 123245 Airmass at start of observation APEND 625 0427 Air pressure at end of observation mbar APSTART 624 7985 Air pressure at start of observation mbar ATEND 0 158733 Air temp at end of observation C ATSTART 0 305252 Air temp at start of observation C BOLOMS SHORT LONG Names of bolometers measured CALIBRTR T Internal calibrator is on or off CAL_FRQ 1 984 Calibrator frequency Hz CENT_CRD RB CHOP_CRD AZ Centre coordinate system Chopper coordinate system CHOP_FRQ 6 94444 Chopper frequency Hz CHOP_FUN SCUBAWAVE Chopper waveform CHOP_PA 90 Chopper P A 0 in lat 90 in long CHOP_THR 60 Chopper throw arcsec DATA_DIR apr8 DATA_KPT DEMOD RESAMPLED Sub directory where datafile was stored The type of data stored to disk SS S ag US aa I aa O A Tas A TR VS A A END_AZD 165 715 Azimuth at end of observation deg END_EL 1 Elevation of last SKYDIP point deg END_ELD 63 6382 Elevation at end of observation EQUINOX 2000 Equinox of mean coordinate system EXPOSED 3 022848 Exposure per pixel seconds EXP_NO 4 Exposure number at end of observation EXP_TIME 1 007616 Exposure time for each basic measurement sec E_PER_I 4 Number of exposures per integration FILTER 450N 850N Filters used FOCUS_SH 1 Shift between focus measurem
153. ll observation data Summarize all observations Summarize mapping observations Summarize photometry observations Summarize pointing observations Summarize skydip observations Miscellaneous Write the flatfield information to a text file Process demodulated noise data Calculate bolometer positions Determine potential inconsistency in the SCUBA time headers Interactive help system Show position angle of array requires KAPPA Set SCUBA environment variables JAC only Semi automated data reduction pipeline Shift data along an A to D card Script to reduce and display skydip data requires KAPPA Calculate sky opacity from skydip data Initial Processing REDUCE SWITCH Convert raw demodulated data to standard format and process individual switches Multiply the data array by the flatfield volumes Correct the data for atmospheric extinction Calculate sky signal Processing JIGGLE data DESPIKE Despike JIGGLE data REMSKY Remove sky contribution from each jiggle SCUCLIP Sigma clip photometry data and maps of weak sources Processing SCAN MAP data 59 SUN 216 8 Complete routine descriptions Add dual beam to single beam data Despike SCAN MAP data Remove dual beam response from SCAN MAP images requires KAPPA Remove dual beam response from SCAN MAP data EKH method Remove baselines from scans Generate Fourier weights used by remdbm Polarimetry REMIP Remove instrumental polarisati
154. ly finds the signal detected at each pixel by looking at the difference between the pixels nearest to each chop beam This calculates a middle beam response ie the response at each pixel is the difference between the L and the R beams For the triple beam response the signal is the difference between the middle pixel and half the values measured in the negative beams Set NBEAMS to 3 to use triple beam response This task can be used to generate test data for remdbm Usage add_dbm in chop pa out Parameters CHOP REAL Read Chop throw in pixels of the input image There is no default The range of this parameter should lie between 1 and the size of the input image IN NDF Read Input single beam image MSG FILTER CHAR Read Message filter level Options are QUIET NORMAL and VERBOSE Default is NORM NBEAMS INTEGER Read When NBEAMS 2 a dual beam response is calculated When NBEAMS 3 a triple beam response is calculated Default is 3 OUT NDF Write Output Dual beam image Default output name is input name plus _dbm_int pa _int chop PA REAL Read Position angle of chop throw Positive is anti clockwise starting from North The angle should be specified in degrees PIXSIZE REAL Read Pixel size in arcseconds This is required for compatibility with remdbm since the CHOP_THR FITS keyword has to be in arcseconds rather than pixels and REMDBM requires SCUPIXSZ FITS keyword A null value will be treated as 1
155. ly processed data Note that use of DATADIR is equivalent to setting a unix style path of DATADIR i e the current working directory is always chosen in preference to DATADIR 7 1 2 SCUBA_PREFIX In general the initial stages of data reduction involve data taken on the same night Typing in the full name of demodulated data files every time an observation is to be analysed is somewhat tedious and it would be much simpler if only the observation number was required Two pieces of information are required to spcify the file associated with a particular observation 1 The observation number 2 The constant prefix of the data file The SCUBA_PREFIX environment variable can be used to inform SURF of the form of the fixed prefix Data files of the form prefix_dem_nnnn can be accessed by observation number nnn so long as SCUBA_PREFIX is set to prefix the _dem_ is added automatically Also if the full path name is specified for SCUBA_PREFIX DATADIR is not required As an example data in scuba observe 19971015 dem can be accessed by number either by setting setenv DATADIR scuba observe 19971015 dem setenv SCUBA_PREFIX 19971015 or by just setting SCUBA_PREFIX setenv SCUBA_PREFIX scuba observe 19971015 dem 19971015 Note that the current directory is not searched in the second case since the software adds the prefix before trying to load the file The scusetenv command can be used to set this variable this command i
156. m out m82 o66_lon_reb o67_lon_reb o68_lon_reb 069_lon_reb Process the four input images The output filename is set to m82 sdf remdbm filter noams _reb sdf Process the supplied files with high frequency filtering Do not use the messag ing system Notes The following restrictions apply 117 REMDBM SUN 216 8 Complete routine descriptions e Each image should contain a single chop configuration e Each image must have identical dimensions and pixel size they do not need to be square e The images must be rebinned in the same coordinate system as the chop throw Related Applications SURF add _dbm KAPPA fourier SUN 216 8 Complete routine descriptions 118 REMIP REMIP Remove instrumental polarisation from SCUBA pol data Description This task calculates and removes the instrumental polarisation signal from SCUBA po larimeter data For a fractional instrumental polarisation P e at angle 0 e and elevation e the instrumen tal polarisation is elevation dependent the correction to the measured flux at waveplate angle W is S Actual S Measured NN SmeanPr e 1 ES cos 4W B 20 e 1 For SCUBA we can not trivially measure the mean flux level since each bolometer is jiggling to different areas on the sky so this task uses an approximate form of the above equation to correct for instrumental polarisation that is valid for IPs of a few percent S Actual x S Measured 1 a Pr e 1 T cos 4W D 20 e 2
157. mall data sets the number of points per bin is not sufficient to perform accurate statistics calculations Advantages Small spikes can be detected in the presence of strong sources since the actual location on the sky is used for the calculation This task is designed specifically for SCAN MAP data Each scan for each bolometer is analysed in turn and spikes are detected using a running mean calculation Advantages Finds the large spikes in SCAN MAP data Disadvantages Care must be taken when despiking bright sources e g planets In summary each mode should probably use different despiking techniques photom can be used before and should be used after or Seucat scan maps should be used initially For Emerson II data it is also possible to use despike since the chop angle is fixed on the sky only despike data that were taken with the same chop configuration Jiggle maps of strong sources Initially scuclip can be used with a large NSIGMA to remove the obvious spikes Then despike should be used for the smaller spikes i e those comparable with the source signal Jiggle maps of weak sources Can probably run scuclip as for PHOTOM observations Here weak source means data where the source is not far above the noise level BM ore details on despike can be found in appendix G 27 9 6 SUN 216 8 The data reduction process Map making All that is required now is that the data be rebinned ont
158. med you are referring to the following day SECOND_TAU REAL Read The zenith sky opacity after the observation The default value is that of FIRST_TAU SUB_INSTRUMENT CHAR Read The name of the sub instrument whose data are to be selected from the input file and 87 EXTINCTION SUN 216 8 Complete routine descriptions extinction corrected Permitted values are SHORT LONG P1100 P1350 and P2000 This parameter is only used if more than one sub instrument is present in the file Examples extinction flat long 0 24 01 00 00 0 3 02 00 00 corr Process the LONG sub instrument from flat sdf using the knowledge that the 850 tau assuming LONG refers to the 850 micron filter was 0 24 at 1h LST and 0 3 at 2h LST The output is written to corr sdf extinction test short 0 6 0 0 6 O test2 Process the SHORT sub instrument from test sdf assuming a constant tau of 0 6 since FIRST_LST SECOND_LST and write the result to test2 sdf Related Applications SURF rebin Seuphot Skydip Beuquick SUN 216 8 Complete routine descriptions 88 EXTRACT_DATA EXTRACT_DATA Write bolometer positions and values to text file Description This routine writes the value variance and position of each data point to a ASCII file The interface is the same as that used in the rebin task The data and variance are in volts The positions are in radians The data are written out as columns RA DEC DATA VAR Parameters FILE FILENAME Writ
159. meric range is requested This range only has an effect on raw data or reduced files which have the run number embedded into the file name Filenames with no numbers are treated as scan 0 Usage obssum h demod reduced mode all begin nn end nn Parameters hlelp Return a help message only More help can be obtained by using showme sun216 or scuhelp obssum all List all files in the current directory and DATADIR demod Only list demodulated data files signified by _dem_ file name reduced Only list reduced data files signified by _red_ file name begin nn First scan number to be considered same as begin nn end nn Final scan number to be considered same as end nn mode obs Select only specified observation modes for listing The list should be comma sepa rated same as mode obs Examples obssum Ask for a range of scan numbers and then give a summary of every sdf file matching this criterion in DATADIR and the current directory obssum all Generate a summary of all sdf files in the current and DATADIR directory obssum begin 5 end 100 SUN 216 8 Complete routine descriptions 100 OBSSUM Generate a summary of all data from scans 5 to 100 inclusive obssum all reduced Produce a one line summary of all reduced _red_ files obssum all reduced gt log txt Produce a one line summary of all the reduced file
160. metry observation of 3C279 from a commissioning nigh 9 1 Preliminaries The data is not in the work directory so DATADIR should be set setenv DATADIR scuba observe apr8 dem assuming a C shell type environment I can now make a log of a subset of the nights data to find out which observations should be processed sculog summary begin 54 end 63 Log for directory home timj scuba maps sun216 scuba observe apr8 dem HST Obsmode Source Meas Int Airmass Filter Bolometers 54 23 02 SKYDIP SKY 10 20 450N 850 SHORT_DC LONG_DC 55 23 13 POINTING 3c279 1 2 1 14464 450N 850 LONG 56 23 17 PHOTOM 3c279 1 10 1 13858 450N 850 H7 57 23 22 PHOTOM 3c279 1 10 1 13217 450N 850 H7 58 23 28 PHOTOM 3c279 1 10 1 12641 450N 850 H7 59 23 35 MAP 3c279 1 3 1 12019 450N 850 SHORT LONG 60 23 44 MAP 3c279 1 3 1 11481 450N 850 SHORT LONG 61 23 53 MAP 3c279 1 3 1 11101 450N 850 SHORT LONG 62 00 02 MAP 3c279 1 3 1 10965 450N 850 SHORT LONG 63 00 03 POINTING 3c273 1 4 1 05483 450N 850 SHORT 98 03 18 SKYDIP SKY 10 20 450N 850 SHORT_DC LONG_DC In order to save time typing in the filename every time we wish to access demodulated data we also set the SCUBA_PREFIX environment variable setenv SCUBA_PREFIX apr8 This variable allows demodulated data to be referenced by observation number It is also possible to set the style for the default output filename provided by the individual tasks In this example we will use the default conventio
161. mount of water vapour present in the atmosphere For a tau T at a given airmass A the attenuation due to the atmosphere is given as e 47 Note that tau is wave length dependent and that the value quoted by the Caltech Submillimetre Observatory CSO is the t at 225 GHz and will therefore be different at the other wavelengths used by SCUBA see for details of the variation with SCUBA filters or for details on the variation seen with UKT14 SUN 216 8 References 54 References 1 Holland W S Cunningham C R Gear W K Jenness T Laidlaw K Lightfoot J F Rob son E 1 1998 SCUBA A submillimetre camera operating on the James Clerk Maxwell Telescope in Advanced Technology MMW Radio and Terahertz Telescopes Philips T G ed Proc SPIE 3357 305 2 Holland W S Robson E I Gear W K Lightfoot J F Jenness T Ivison R J Stevens J A Cunningham C R Ade P A R Griffin M J Duncan W D Murphy J A Naylor D A 1999 MNRAS 303 659 3 Warren Smith R F 1995 NDF Routines for Accessing the Extensible N Dimensional Data Format Starlink User Note 33 1 6 4 Draper P W 1997 GAIA Graphical Astronomy and Image Analysis Tool Starlink User Note 5 Currie M J 1997 KAPPA Kernel Application Package Starlink User Note 95 6 Privett G J Jenness T Matthews H E 1997 FLUXES JCMT Position and Flux Density Calibration Starlink User Note 213 7 Currie M J
162. n Found data for the following bolometers h7 This is a PHOTOM observation of 3c279 There are 10 integrations N Name of input file containing photometry data gt ag gS y yw E ML G 26 Es as Hot y S Es T 538382258238 es T scucat continues to request input data until a null value is given for the IN parameter Since different bolometers should be processed independently a new file is created for each bolometer In this example scucat produces one file called 3c279_h7 sdf if this data was taken with 2 bolometer chopping there would have been another file called 3c279_h9 sdf for example These files can now be analysed with standard statistics packages e g Kappa stats and kstest An alternative to the above for scucatlis to use a text file to contain the list of filenames to be processed useful for scripts scucat noloop METHOD Concatenation method SEPARATE gt OUT Rootname of files to contain concatenated data gt 3c279 IN Name of input file containing photometry data n56_pht_lon gt in lis SURF Found data for the following bolometers h7 SURF This is a PHOTOM observation of 3c279 There are 10 integrations SURF Found data for the following bolometers h7 SURF This is a PHOTOM observation of 3c279 There are 10 integrations SURF Found data for the following bolometers h7 SURF This is a PHOTOM observation of 3c279 There are 10 integrat
163. n LONG More information on the SURF environment variables can be found in Note that the naming convention has now changed to YYYYMMDD instead of MMMDD as used at the time the data were taken SUN 216 8 The data reduction process 20 180 0 160 0 Pa 4 a se a 140 0 A J S ae A E 120 0 LO A KO l 100 0 4 80 0 y oy y 1 y 1 ii 1 y f y ol y f j i jii j i y ly ii M 1 0 1 5 2 0 2 5 3 0 3 5 4 0 AIRMASS Figure 5 The Skydip result for scan 54 The crosses are the measured sky temperatures and the line is the fitted model 9 2 Skydips From the listing in the previous section we can see that Skydip data was taken at scans 54 and 98 From the RO either by using mapsum or photsum on the ro data or by using hdstrace file we can see that the fitted taus were 1 140 short and 0 220 long for scan 54 and 1 042 short and 0 187 long In most cases these numbers will be sufficient for use by extinction but it is possible to recalculate the tau by using the skydip task As an example here is the result of skydip on scan 54 skydip 54 SURF Opening apr8_dem_0054 in scuba observe apr8 dem SURF run 54 was a SKYDIP observation SURF observation started at sidereal time 11 47 24 and ended at 11 54 07 SURF file contains data for the following sub instrument s SHORT with filter 450 LONG with filter 850 SUB_INSTRUMENT Name of sub instrument to be analysed SHORT gt 1 SURF fil
164. n wa na a The task reduce _switch takes the raw beam switched data and subtracts the off position from the on position nods If required this task also divides the data with the internal calibrator signal this is stored in the demodulated data file as well as the switch informa tion and sets the level at which spikes detected by the transputers become significant Flatfielding Thefflatfield task takes the output of reduce_switch and flatfields the array by multiplying each bolometer by the volume flatfield value these are the volumes relative to a reference pixel the reference bolometers are usually from the array centres H7 and C14 The flatfield file itself is actually stored in the demodulated data file In order to apply a different flatfield the internal file must be changed with the task before running flatfield The change_ flat task changes the bolometer positions as well as the volumes To move flatfield information between files a combination of extract_flatjand should be used It is not necessary to flatfield PHOTOM data unless sky removal is to be used or in some cases multiple bolometers are to be analysed together Extinction correction Thefextinction task takes the flatfielded data and applies an extinction correction to each pixel one jiggle at a time The zenith sky opacity tau should have been obtained from skydips or estimated from photometry The optical depth is linearly interpolate
165. n cell so some source signal will remain after source subtraction 69 CALCSKY SUN 216 8 Complete routine descriptions e If a model is supplied externally via MODEL parameter the cell size of the model is used for the source subtraction e The sky signal is stored in an NDF extension MORE REDS SKY The file must be processed by remsky to actually remove the sky contribution Related Applications SURF remsky SUN 216 8 Complete routine descriptions 70 CHANGE_DATA CHANGE_DATA Set SCUBA data to any value Description This application is used to set SCUBA data to any value by using SCUBA sections to specify a subset of the full data Data Variance and Quality arrays can be modified Once the data specification has been decoded the application will read from parameter VALUE the value of the data that should be used All data specified by the section or by the inverse of this section if specified will be set to this value Usage change_data ndf spec1i spec2 specn value out Parameters COMP LITERAL Read The name of the NDF array component which should be changed Data Error Quality or Variance where Error is the alternative to Variance and causes the square root of the variance values to be taken The default component is always DATA If Quality is specified then the quality values are treated as numerical values in the range 0 to 255 IN CHAR Read Name of data set and the specif
166. n most cases the values found in the RO file should be sufficient and skydip data should not need to be reanalysed The skydip task can be used to re reduce the data if necessary see also sdip A summary of the skydip Bosa observations in a given directory can be produced with the skysum command Message filtering All of the tasks print messages to standard output On some occasions it is desirable for more or less information to be displayed to the user For this reason the verbosity of all the tasks can be modified by use of the MSG_FILTER parameter This parameter controls the messaging level of the tasks and can take values of NORM normal messaging level VERB verbose or QUIET 18 Note that warning messages such as forgetting to flatfield are always displayed whereas the general messages can be turned off by using QUIET mode SUN 216 8 SCUBA sections 8 Specifier Definition Begins a SCUBA section Ends a SCUBA section b indicates that the following numbers describe bolometer numbers ie X axis p indicates data position ie Y axis Can not be used in conjunction with s e i or m s switches e exposures i integrations m measurements Separates components Separates numbers indicates a range of values negates the section when placed after the last curly bracket Table 1 Special characters used to describe SCUBA sections 6 SCUBA sections Since all the tasks rely on information
167. n raw data or reduced files which have the run number embedded into the file name Filenames with no numbers are treated as scan 0 Usage pointsum h demod reduced all begin nn end nn Parameters hlelp Return a help message only More help can be obtained by using showme sun216 or scuhelp pointsum all List all pointing files in the current directory and DATADIR demod Only list demodulated data files signified by _dem_ file name reduced Only list reduced data files signified by _red_ file name begin nn First scan number to be considered same as begin nn end nn Final scan number to be considered same as end nn Examples pointsum Ask for a range of scan numbers and then give a summary of every pointing file matching this criterion in DATADIR and the current directory pointsum all Generate a summary of all pointing files in the current and DATADIR directory pointsum begin 5 end 100 Generate a summary of all pointing data from scans 5 to 100 inclusive SUN 216 8 Complete routine descriptions 106 POINTSUM pointsum all reduced Produce a one line summary of all reduced pointing _red_ files pointsum all reduced gt log txt Produce a one line summary of all the reduced pointing files and store the out put in the text file log txt note this example is shell specific pointsum all reduced demod Produc
168. nate frame AZ Azimuth Elevation offsets PL Moving source e g planet RB RA Dec B1950 RJ RA Dec J2000 RD RA Dec epoch of observation GA Galactic coordinates J2000 The first two coordinate systems are fixed on the telescope so that the source rotates during long observations They are most useful for taking beam maps AZ or examining the properties of the SCUBA bolometers NA Obviously AZ and NA contain no astrometry information The PL coordinate system should be used for moving sources e g planets or comets where the RA and Dec of the source is changing with time offsets from this moving centre are calculated and no astrometry information is stored The remaining coordinate systems correct for source rotation and do have associated FITS World Coordinate Systems WCS astrometry information 19 2O Map centre The default map centre will be the map centre of the first map entered into rebin modified to the epoch of the output map if necessary coordinates used as the map centre of the This question is not asked if a NA AZ or PL coordinate system is being used Pixel size The regridded image can be in any pixel size The main point is that account is taken of the beam sizes approximately 7 arcsec at 450 microns and 14 arcsec at 850 microns The on line system regrids with 3 arcsec pixels Obviously the regridding takes longer the smaller the pixel size that is requested but only becomes a real problem if BESSEL regridding
169. nced Technology MMW Radio and Terahertz Telescopes Philips T G ed Proc SPIE 3357 548 The recommended reference for the Emerson 2 deconvolution algorithm as implemented in SURF is Jenness T Holland W S Chapin E Lightfoot J F Duncan W D 2000 Dual beam rastering and deconvolution techniques for SCUBA in Astronomical Data Analysis Software and Systems X ASP Conf Ser 216 559 The recommended reference for the ORAC DR SCUBA data reduction pipeline is Jenness T Economou F 1999 The SCUBA Data Reduction Pipeline ORAC DR at the JCMT in Astronomical Data Analysis Software and Systems VIII ASP Conf Ser 172 171 The SURF software package is registered with the Astrophysics Source Code Library as asc1 1403 008 11 Future Work The SURF software is now in maintenance mode at the Joint Astronomy Centre Bugs are fixed but new features are only added if there is a strong demand New releases will be announced on the JCMT software web pages and through Starlink Upgrades currently on the work list but which may not be completed due to other developments at the JAC are e Upgrades to the sky removal software to allow removal of planes e Support for heterodyne receiver beam maps If you wish to suggest new tasks or write your own extensions to the software please consult the SCUBA software wish lisf Additional information on writing SURF extensions can be found http wwwijach hawaii edu JACpubl
170. nning from A to I the channel numbers on each run from 1 to 16 Roughly once or twice a night the fault would insert a spurious number into the data stream from one or more of the A D cards to the transputer system that does the digital demodulation The system design is such that until the system was reloaded a spurious shift would be applied to the data Thus if the fault occurred in the B card then after that point the system would see the data from that card as shifted up by one channel number data for channel B5 would appear in channel B6 B7 in B8 etc The end channels wrap around so that channel B16 would appear in SUN 216 8 Correcting shifted data 182 channel B1 of the next dataset The effect is cumulative so that if 2 faults occurred on the B card then the data would then be shifted by 2 channels If the fault occurs for a card whose bolometers are measuring source signal then the image of the source will be reconstructed incorrectly by both the real time display and the SURF package In fact the problem was first noticed when jiggle map images of Uranus showed an apparent double source Faulty data can be patched up using the scushift utility The difficulty is in finding when and where in your data the problem has occurred since without a high signal to noise signal to judge by you cannot go on the appearance of the final image The situation is saved by SCUBA s internal calibrator During all jiggle type observatio
171. ns a sinusoidal signal from a source inside the cryostat is superimposed on the astronomical data The digital demodulation recovers the amplitudes of both the calibrator and astronomical signals The pattern of the calibrator signal from the SCUBA bolometers forms a signature that is constant over long periods and can be used to detect shifts in the data To illustrate this point there are four data files distributed with this packagel These files contain the calibrator signal for this period for the 450 and 850 ym filter The files are e calsig_850_map sdf Calibrator signal for the long wave array with the 850 micron filter e calsig_450_map sdf Calibrator signal for the short wave array with the 450 micron filter e calsig_450_850_map sdf Calibrator signal for the short and long wave arrays at 450 and 850 microns e calsig_450_850_photom sdf Calibrator signal for the short and long wave arrays at 450 and 850 microns but for a photom observation The _map files are intended for comparison with JIGGLE MAP data whereas the _photom file is intended for use with PHOTOM data there are two extra bolometers in this case In addition there is also a file containing shifted data calsig_450_850_bp2 sdf where the signal from the B card has been shifted by 2 channels Fig 17 shows this file overlaid on the correct unshifted calibrator signal Demodulated data can be checked as follows 1 Extract the calibrator si
172. o a rectangular grid with the rebin task If necessary it is possible to enter Az El pointing corrections by using change _ pointing change_pointing n59_sky_lon SURF run 59 was a MAP observation of 3c279 SURF observation started at LST 12 19 59 and ended at 12 28 40 SURF no pointing corrections found CHANGE_POINT Do you want to change the pointing correction data gt y POINT_LST The sidereal time of the pointing offset hh mm ss ss gt 12 00 POINT_DAZ The azimuth pointing correction to be added arcsec gt 0 POINT_DEL The elevation pointing correction to be added arcsec gt 0 POINT_LST The sidereal time of the pointing offset hh mm ss ss gt 12 50 POINT_DAZ The azimuth pointing correction to be added arcsec gt 1 1 POINT_DEL The elevation pointing correction to be added arcsec gt 0 9 POINT_LST The sidereal time of the pointing offset hh mm ss ss gt The time for the pointing corrections must be in LST they also must be entered in chronological order The pointing offset is assumed to vary linearly with time Here I have assumed good pointing at an LST of 12h the pointing observation before the map and a small shift 50 minutes later when another pointing observation was taken the shift can be found by using pointsum It is probably best that the pointing offset is measured directly from the image by first regridding the data in Az El coordinates and then using for example the t
173. o jiggle offset Fig 7 was made as follows note that this requires in addition to KAPPA s display display n59_reb_lon axes lut KAPPA_DIR bgyrw_lut device epsfcol_p MODE Method to define the scaling limits SCALE gt LOW Low value for display 0 01095889788121 gt HIGH High value for display 0 022901531308889 gt scuover prompt MSG_FILTER Messaging level NORM gt DEVICE Name of graphics device xwindows gt epsfcol_p Current picture has name DATA comment KAPPA_DISPLAY Using scuba maps sun217 n59_reb_lon as the input NDF EXT Name of extinction corrected demodulated data file n59_sky_lon gt SURF file contains data for 4 exposure s in 3 integration s in 1 measurement s INTEGRATION Integration number 1 gt EXPOSURE Exposure number 1 gt COL Colour of annotation red gt white NAME Display bolometer name else number TRUE gt psmerge e gks74 ps gks74 ps 1 gt 3c279 eps SUN 216 8 The data reduction process 30 et arcsec S D Declination of 80 60 40 20 O 20 40 60 30 R A offset arcsec Figure 7 A 850 micron image of 3C279 rebinned in RJ coordinates with the long wave array overlaid The two negative sources indicate the nodding and chopping that are part of a SCUBA jiggle map 31 SUN 216 8 The data reduction process In general for faint sources it would now be necessary to go back to the extinction
174. of the weighting function For LINEAR one scale size corresponds to the zero of the cone for BESSEL it is the first zero of the Bessel function 71 and for Gaussian it is the half width half maximum HWHM SIZE 2 INTEGER Read This array parameter sets the size of the output grid in pixels nx ny The default values are the minimum dimensions required to display the entirety of the mapped area SHIFT_DX REAL Read The pointing shift in X to be applied that would bring the maps in line This is a shift in the output coordinate frame SHIFT_DY REAL Read The pointing shift in Y to be applied that would bring the maps in line This is a shift in the output coordinate frame TIMES LOGICAL Read Store an extra NDF in the output map containing the 2 D histogram of the data This can be used to make an estimate of the actual number of samples responsible for each point in the output grid Note that in general the number of pixels in the output grid exceeds the number of independent beams in the image The data can be accessed as OUT more reds times Default is FALSE WEIGHT REAL Read The relative weight that should be assigned to each dataset WEIGHTS LOGICAL Read This parameter governs whether the convolution weights array will be stored in the output NDF The default is FALSE i e do not store the weights array WTFENRAD INTEGER Read Size of the weighting function in scale sizes This parameter is irrel
175. om file1 sdf file2 Read file 2 but you will still be prompted for WEIGHT and shifts file3 i3 1 0 0 0 0 0 Use everything except int 3 test bat Read in another text file Note that the parameters are position dependent and are not necessary Missing parameters are requested This means it is not possible to specify SHIFT_DX position 3 without specifying the WEIGHT If the file has the txt extension the NDF system will attempt to convert it to NDF format before processing this is probably not what you want Related Applications SURF rebin jintrebin extract data 67 CALCSKY SUN 216 8 Complete routine descriptions CALCSKY Calculate sky contribution from median image Description This routine calculates the sky contribution by attempting to remove the source from the input data stream The source signal can either be calculated by this routine or by reading in a model of the source from a file When calculating the source structure internally a similar method to that used by DE SPIKE is employed The input data are placed into bins of size one quarter beamwidth The median of each bin is calculated and this is treated as the source model cf RE BIN_METHOD MEDIAN in rebin Once the source model is available it is removed from all of the input data The source removed data are then analysed with the sky emission derived from the mean of the signal across the array for all the sample times Since the sk
176. on Usage change_nacentre h v infile dx dy Parameters h Return a help message only v Return the version number of scunoise infile Input file name The file is modified in place dx Shift in Nasmyth X du3 direction dy Shift in Nasmyth Y du4 direction Examples change_nacentre Will prompt for input file name and shift change_nacentre file 5 3 Will move the array centre of file sdf by 5 3 arcsec Notes This command can only be reversed by running change _ nacentre with minus the previous X Y shift extinction must have been run on the input file otherwise the file will contain more than 1 array this is not checked for explicitly Related Applications SURF rebin 75 CHANGE_POINTING SUN 216 8 Complete routine descriptions CHANGE_POINTING Change the pointing corrections to map data Description This application is used to change the pointing corrections to map data If the observing mode of the input datafile is MAP the application will search for pointing corrections in the file and if it finds any report them You will be asked if you wish to change the pointing correction data in the file No will result in the data remaining unaltered yes will then ask you for the time of the pointing offset LST in hh mm ss ss format and the azimuth and elevation correction in arcseconds that would have to be added to the observation position to correct the pointing at that
177. on from polarimetry data Data inspection Interactive bolometer display requires KAPPA Interactive display via mlinplot requires KAPPA Plot SCUBA noise data Interactive display and despiking requires KAPPA Data modification Change data or variance values in a dataset Change the stored flatfield information Change Nasmyth coordinates of array centre Change Az and El pointing offsets for map data Change data quality Interactive despiking requires KAPPA Mapping Rebin all data onto a rectangular grid Generate a separate regridded image for each bolometer Generate a separate regridded image for each integration Write bolometer positions and data to text file Overlay bolometer array on image Calculate and set bolometer weights Requires KAPPA Photometry SCUPHOT Reduces photometry data to a single point per integration SCUCAT Concatenate photometry results into a single NDF ODRAW Plot photometry data requires K APPA SIGCLIP Remove spikes from photometry data requires KAPPA C Complete routine descriptions The SURF routines are described in the following pages SUN 216 8 Complete routine descriptions 60 ADD_DBM ADD_DBM Generate a chopped image from a single beam map Description Create a chopped image from a single beam input map Can be used to create a dual beam e g a simlated scan map image or a triple beam map e g a simulated jiggle map image For dual beam it simp
178. or SCUBA despiking and therefore understands SCUBA quality provides an integrated despiking environment showing the 2 D image and a 1 D slice allowing points to be marked bad or good in either window More information can be found in the documentation Additionally the command a wrapper for the command and the pltbol command a wrapper for the command can be used to identify spikes and noisy bolometers rapidly without having knowledge of NDF sections or the specifics of each command 9 5 2 Automatic despiking At first sight the automatic despiking of SCUBA data may seem somewhat daunting since there are 4 different tasks provided for this despike2 scuclip and Detailed information on these can be found in the appendix C but a direct comparison of the four is provided below Originally intended for the final clipping of photometry data this task finds the statistics of the entire data file and clips any point lying more than SIGMA from the mean This task knows nothing about SCUBA data Disadvantages Should not be used where bolometers see differing signals i e most of the time since the clipping is then invalid Advantages Will clip any data file Can be used on reduced photometry data output of for clipping since only data for a single bolometer will be present This task processes each bolometer in turn finding the mean and removing any points lying more than NSIGMA from the mean for the current bolometer An iter
179. over style colour bol yellow font text 3 colour text cyan Draw yellow circles but draw the labels in cyan using font 3 italics scuover integration 2 name Overlay the bolometer positions at the start of the second integration but do not label them Notes e Animage must have already been displayed before using SCUOVER e The image must have been displayed using an AST aware application such as KAPPA display Otherwise the alignment will not occur e The array position is always shown with zero jiggle offset e This routine does not take into account the use of SHIFT_DX or SHIFT_DY in rebin the relevant information is not stored in the rebinned image e Pointing shifts are taken into account e It is assumed that the displayed image id regridded to the default map centre scuover aligns the image using AXIS coordinates and not SKY coordinates therefore there will be an error if incorrect sky coordinates are assumed Related Applications SURF rebin scupa KAPPA display gdset IGARO lima PT 09 oO SUN 216 8 Complete routine descriptions 146 SCUPA SCUPA Show position angle of array Description This script reduces the specified demodulated data file displays the image using Az El coordinates and overlays the array in order to show the position angle of the array during the observation Usage scupa NDF Parameters NDF NDF Read Name of raw data file Can be located in DAT
180. quested when the text file is included n62_reb_lon 0 98 1 0 2 0 3c279_old bat Include previous 3c279 data via a text file From this example we can see that blank line are ignored and a indicates the start of a comment all text on the line after the is ignored Not all the parameters need to be specified on the input line if they are missing the software will simply ask for the values from the user The order of these parameters is important so it is not possible to specify map shifts without specifying a weight similarly SHIFT_DY can not be given without SHIFT_DX Also note that the NDF name can include SCUBA sections Even though text files can include other text files a recursion depth of 5 has been hard wired into the code to prevent abuse it was felt that this should be sufficient in most cases With the default messaging level rebin tasks always show a summary of all the input data before proceeding to the final regridding this can be used to check that the correct files and associated parameters have been read in 9 6 2 Output coordinate frames The output map generated by rebin will contain at least 3 output coordinate frames They are the GRID PIXEL and AXIS coordinate frames For maps regridded in RJ RB GA or RD coordinates there will be an additional SKY coordinate frame SUN 216 8 The data reduction process 32 They can be listed with the ndftrace command lapaki M82 short gt ndftrace m
181. r good Description This application is used to set SCUBA data quality bad or good by using SCUBA sections to specify a subset of the full data Once the data specification has been decoded the application will read from parameter BAD_QUALITY whether quality should be set good or bad A yes answer will mark the area bad a no answer will mark the area good an area will only be good if no other QUALITY bits are set change _quality only uses QUALITY bit 3 The section can be inverted by using the negation character at the end of the section Usage change_quality ndf speci specn bad_quality Parameters BAD_QUALITY LOGICAL Read Set quality to BAD Answering this question with a yes will mean that the selected data will be set to BAD no will set them to good IN CHAR Read Name of data set and the specification of the data to be changed Usually of the form ndf specl spec2 where ndf is the filename and specl n are the section specifications The section can be read from the SECTION parameter if the SCUBA section is omitted MSG_FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM SECTION CHAR Read This array parameter can be used to specify SCUBA sections Curly brackets must still be given Since this is an array parameter square brackets must be used to specify more than one component SECTION gt b3 i2 would supply
182. rces zero flux at the edge of the regridded image Should be turned off if flux is present at the edge Default is to use the guard ring for LINEAR BESSEL and GAUSSIAN rebin modes 109 REBIN SUN 216 8 Complete routine descriptions IN CHAR Read The name of the input file to be rebinned This parameter is requested repeatedly until a NULL value is supplied LOOP must be TRUE IN can include a SCUBA Like the REF parameter this parameter accepts a text file LAT_OUT CHAR Read The latitude of the output map centre The supplied default value is that of the map centre of the first map LONG_OUT CHAR Read The longitude of the output map centre The supplied default value is that of the map centre of the first map LOOP LOGICAL Read Task will ask for multiple input files if true Only REF is read if noloop MSG_FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM There are no verbose messages OUT NDF Write This is the name of the NDF that will contain the rebinned map A null value can be supplied to shut down rebin without error This can be used to determine the size of the output map without creating it OUT_COORDS CHAR Read The coordinate system of the output map Available coordinate systems are e AZ Azimuth elevation offsets e NA Nasmyth offsets e PL RA Dec Offsets from moving centre e g Planets e RB RA Dec B1950 e RJ RA Dec J2000 e RD R
183. rchical Data System Starlink User Note 22 Terrett D L 1993 PSMERGE Encapsulated Postscript handling utility Starlink User Note 23 Berry D S Gong W Parsons D C 1995 IRAS90 IRAS Survey and PO Data Analysis Package Reference Guide Starlink User Note 163 24 Jenness T Stevens J A Archibald E N Economou F Jessop N E Robson E I MNRAS 336 14 25 Shortridge K Meyerdierks H M Currie M J Clayton M FIGARO A general data reduction system Starlink User Note 86 26 Hughes D H 1993 JCMT UKIRT Newsletter 4 32 27 Economou F Bridger A Wright G S Rees N P Jenness T 1998 The future of data reduc tion at UKIRT Astronomical Data Analysis Software and Systems VII Albrecht R Hook R N Bushouse H A eds ASP Conference Series 145 195 28 Jenness T Economou F 1999 The SCUBA Data Reduction Pipeline ORAC DR at the JCMT in Astronomical Data Analysis Software and Systems VIII Mehringer D M Plante R L Roberts D A eds ASP Conf Ser 172 171 29 Berry D S Gledhill T M 1999 Polpack An imaging polarimetry reduction package User Note 223 30 Jenness T Lightfoot J F 1999 The SURF Programming Interface Starlink System Note 72 31 Archibald E N Jenness T Holland W S Coulson I M Jessop N E Stevens J A Rob son E L Tilanus R P J Duncan W D Lightfoot J F 2002 MNRAS 336 1 12 12 32 Stevens J A Robson E
184. re details on despike can be found in appendix G Usage despike Parameters DEFOUT LOGICAL Read Determines whether output files should be written automatically using the default output names or whether the user should be prompted Default is FALSE DEVICE DEVICE Read The device on which to display the binned data Can be null DMODE CHAR Given For display purposes the points in each cell are plotted sequentially on a 1 dimensional plot This parameter governs the way in which the cells are extracted from the grid Allowed values are e SPIRAL A Spiral outwards from the reference pixel e XLINEAR unfold each X strip in turn for each Y e YLINEAR unfold each Y strip in turn for each X e DIAGI diagonal strips starting at position 1 1 e DIAG2 diagonal strips starting at positions nx 1 This parameter is also required if SMODE is not equal to NONE since the smoothing depends on the order that the points are extracted from the grid IN CHAR Read The name of the input file to be despiked This parameter is requested repeatedly until a NULL value is supplied LOOP must be TRUE IN can include aJSCUBA Like the REF parameter this parameter accepts a text file LOOP LOGICAL Read Task will ask for multiple input files if true Only REF is read if noloop MSG FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM In VERBOSE mode the positions of detected spikes are listed
185. reated existing files are overwritten and data is appended to these files when more data for these bolometers is supplied Usage scucat out in Parameters BOL CHAR Read If the input file is an NDF and not an HDS container as expected then this parameter should be given to tell the software the bolometer that should be associated with this data IN NDF Read The input dataset s This parameter is requested repeatedly until a NULL value is given The input dataset can either be output from scuphot or an NDF file A comma separated list of files is allowed A text file containing a list of files can be specified using the up carat symbol in front of the text file name LOOP LOGICAL Read Turns the looping on default is true or off false METHOD CHAR Read Governs whether data from different bolometers are combined regardless CATALL or written to separate files GEPARATE Default is SEPARATE The choice of this parameter governs the behaviour of the OUT parameter MSG FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM There are no verbose messages OUT CHAR Write If METHOD separate this parameter governs the root name of the output NDF i e lt OUT gt _bol If METHOD catall this parameter can be used to specify the actual output file name Examples scucat test phot This routine will copy the data from phot to test_ lt bol gt reducing m
186. rebinning and despike the input data are placed in bins related to position on the output image the median of each bin is then taken to be a good measure of the flux in that region of sky This approach is an approximation since the bin size quarter beam width can accommodate large gradient changes towards point sources but in general these errors are smoothed out by the average taken over the whole array An alternative approach is to rebin the input data on a fine grid e g 1 arcsec or finer and use that as the input model this is especially useful for scan maps since calcsky can add the dual beam response to the data when calculating the model SUN 216 8 The data reduction process 38 4 0 2 0 Signal mV 1 i f 0 0 20 0 40 0 Time s 60 0 Figure 9 Sky noise calculated by calcsky for a short interval of the M82 data 39
187. regrid centre is always at pixel coordinate 0 0 unlike the GRID frame where the pixel origin is always at the bottom left hand corner The PIXEL frame is used by all KAPPA commands that combine images and also the makemos command in For more information on coordinate frames please see Using World Coordinate Systems in SUN 95 9 6 3 Exporting maps After the data have been regridded with rebin the image can then be analysed with an image analysis tool Obviously or GAIA can be used immediately since they support the NDF standard In order to use packages such as IRAF AIPS or MIRIAD the data must first be converted to FITS format by using either the CONVERT task ndf2fits or the FIGARO task wdfits The ndf2fits task is recommended since it can understand FITS tables floating point FITS and the new AST extension PO For images rebinned with an older version of SURF pre 1 3 or if using wdfits or a version of CONVERT that does not understand AST pre 1 1 it is necessary to remove the AXIS components from the NDF before converting since the axis information arcsec offsets from the map centre takes priority In order to propagate WCS astrometry information from the NDF FITS array into the FITS file the axis information must first be removed by using FIGARO s or KAPPA s For example if the image is stored in file scuba_image sdf and we wish to convert this to an integer FITS file scuba_image fits with we would do kappa
188. s SUN 216 8 Skydips 180 I 2 Removing bad skydip data from the fit HHH Measurements Measurements Figure 15 Skydip data after processing with reduce_ switch left and after measurement 5 has been removed with change quality right 3 Once a bad measurement has been identified it can be switched off using change quality change_quality o70 b2 m5 yes SURF run 70 was a SKYDIP observation of not used SURF file has data for 2 bolometers measured at 100 positions there are data for 1 exposure s in 10 integration s in 10 measurements The main thing here is that the m identifier should be used to specify measurement and that only bolometer i e sub instrument 2 should be affected 4 NowJ skydip or sdip can be run on the file skydip 070 SURF run 70 was a SKYDIP observation SURF observation started at sidereal time 1 10 41 and ended at 1 16 38 SURF file contains data for the following sub instrument s SHORT with filter 350 LONG with filter 750 SUB_INSTRUMENT Name of sub instrument to be analysed SHORT gt long SURF file contains data for 10 integration s in 10 measurement s ETA_TEL Telescope efficiency 0 87 gt B_VAL B parameter 1 gt SCULIB fit for filter 750 and sub instrument LONG_DC 16Of course it is still possible to specify an integration to be marked bad but remember to specify also the measurement otherwise the nth integr
189. s and store the output in the text file log txt note this example is shell specific obssum all reduced demod Produce a summary of all reduced _red_ and demodulated _dem_ data files ie not files produced during off line data reduction obssum all mode pointing Produce a one line summary of all pointing observations obssum reduced begin 100 end 200 mode photom skydip Produce a one line summary of the photom and skydip observations of reduced files with scan numbers 100 to 200 This is similar to photsum except that the signal and signal to noise will not be displayed even if reduced files are being listed Notes obssum only uses information stored in the FITS header of reduced and raw data files and does not provide summaries of reduced RO data such as photometry results essentially for reasons of clarity must be used to generate a summary of photometry observations that includes reduced data Files are drawn from the current working directory and the directory indicated by the DATADIR environment variable Data reduced by the off line system will all be treated as run 0 for the purposes of listing unless numbers are present in the filename The output can be stored in a file by using unix redirection as long as the search range is fully specified either as all or with begin and end Command line options can be abbreviated Options that take values
190. s especially useful when reducing data at the Joint Astronomy Centre as DATADIR is also set correctly 7 1 3 SCUBA_SUFFIX Most SURF tasks automatically constructs a default output filename based on the input filename rebin bases the output filename on the object name In this way it is possible for the filename to reflect the data reduction history The SCUBA_SUFFIX environment variable can be used to select the preferred method to use for constructing the output name Three modes are available 7The KaPPa command hhislist provides an explicit data reduction history for a file 11 SUN 216 8 Environment variables Table 2 Output file suffices for each task Task Suffix SHORT LONG VERBOSE flatfield f _ flat r _res ms _ 2 _ext 1 _ip s _sky d _dsp d _des c _clip b _rlb p pht a _cdata 2 thr pd _dbm_thr_pa nn observation number b first three letters of the selected sub instrument e g lon sho p20 p11 p13 These include the throw and position angle of the chop to be added to the data SUN 216 8 Environment variables 12 SHORT In this mode the output filename is constructed by appending the short suffix related to the current task to the input filename LONG In this mode the output filename is constructed as follows 1 Remove everything from the last underscore to the end of the input string 2 Append the long task suffix For example for scucliplan
191. sdf Do not write a text file reduce_noise 3 accept Process observation 3 but do not write an NDF output file Use the default file name for the text file Notes Noise observations containing multiple measurements are condensed into a single mea surement SUN 216 8 Complete routine descriptions 114 REDUCE_SWITCH REDUCE_SWITCH reduce the switch sequence for a SCUBA observation Description This application takes a SCUBA demodulated data file and splits the data array up into its various planes data variance and quality In addition the application reduces the component switches of an exposure to give the exposure result Optionally the routine will divide the internal calibrator signal into the data before doing either of these things It is also possible to select a single switch from the input data For skydip data this routine calculates the sky temperature for each integration and sub instrument Usage reduce_switch in out Parameters IN NDF Read The name of the demodulated data file If SCUBA_PREFIX is set this can be the number of the observation rather than the full filename MSG_FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM There are no verbose messages OUT NDF Read The name of the file to contain the output data SPIKE_LEVEL INTEGER Read Number of spikes tolerated before marking data point bad The default is that the samp
192. sdf may be included in the name d file2 name of a second file e g the despiked version of the NDF file The same bolometers will be plotted in a second window or overlaid for comparison s min max Y axis scales for plot can be changed via menu SUN 216 8 Complete routine descriptions 104 PLTBOL bol list of bolometers to plot Type all for 1 37 and alls for 1 91 Can be added via menu if mode r Examples pltbol The user will be asked for an input file before proceeding to the menu pltbol f 039_lon_ext Plot bolometers from 039_lon_ext sdf and ask for the bolometer list pltbol f s14_lon_ext 12 13 18 20 25 26 19 Use file s14_lon_ext sdf Plot bolometers 12 13 18 20 25 26 and 19 Notes e If the overlay comes up scrambled delete the agi_xxx files in your home directory and if that does not work also files like linplot sdf in the home you adam subdirectory Related Applications SURF dspbol rlinplot KAPPA linplot Bugs Freezes when asked to plot a bad bolometer 105 POINTSUM SUN 216 8 Complete routine descriptions POINTSUM Produce one line summary of SCUBA pointing observations Description Pointsum goes through all the sdf files in the current directory and optionally DATADIR defined in an environment variable and summarizes files containing pointing observa tions In the absence of the all flag a numeric range is requested This range only has an effect o
193. sigma threshold This script uses the KAPPA routines thresh and stats The routine can also be used to check the self consistency of the photometry data by performing a Kolmogorov Smirnov test on the data e g 26 9 8 Scan maps Scan map data can be taken using two techniques both based on chopping The first technique is to chop in the direction of the scan and deconvolve each scan independently the EKH method 11 This technique must be used for single pixel mapping although it can also be used for array scan mapping Problems with this technique are that it is very sensitive to spikes every scan must be completely off source at both ends and correlations with adjacent scans pixels are ignored For array scan maps we scan the array across the source whilst chopping in a fixed direction on the sky Following the work of Emerson 12 we take data using a number of different chop configurations in order to sample as many spatial frequencies as possible we are not sensitive to structure that is larger than the chop throw Multiple chop throws in 2 orthogonal directions are used with chop amplitudes chosen so that except at the origin the zeroes in the Fourier transform of one do not coincide with the zeroes in the FT of the other up to the spatial frequency limit of the telescope beam For SCUBA it is recommended that 6 different chop configurations should be used Chop throws of 20 30 and 65 arcsec each with chop position angles of 0
194. sing part of CURSA and plotted using polplot An example image of OMC 1 can be seen in Fig For more information on POLPACK see SUN 223 29 For photometry observations the output from scuphot can be exported to a single pixel data reduction system or alternatively processed as under sampled images and reduced through as described above 10 Citing SURF If you wish to cite SCUBA in a paper the recommended reference is Holland W S Robson E I Gear W K Lightfoot J F Jenness T Ivison R J Stevens J A Cunningham C R Ade P A R Griffin M J Duncan W D Mur phy J A Naylor D A 1999 MNRAS 303 659 45 SUN 216 8 Future Work If you wish to cite this manual the recommended reference is Jenness T Lightfoot J F 2000 Starlink User Note 216 Starlink Project CLRC although an alternative more recognizable reference to SCUBA data processing can be found at Jenness T Lightfoot J F 1998 Reducing SCUBA Data at the James Clerk Maxwell Telescope in Astronomical Data Analysis Software and Systems VII ASP Conf Ser 145 216 The recommended reference for the sky removal algorithm is now Archibald E N Jenness T Holland W S Coulson I M Jessop N E Stevens J A Robson E L Tilanus R P J Duncan W D Lightfoot J F 2002 MNRAS 336 1 and this supercedes the original paper Jenness T Lightfoot J F Holland W S 1998 Removing Sky contributions from SCUBA data in Adva
195. ss temperature of the atmosphere b is the bandwidth factor of the filter being used 1 b is the fraction of the filter bandwidth that is opaque due to atmospheric absorption and like T it is a function of water vapour content T is the zenith sky optical depth and A is the airmass of the measurement Of these parameters Jmeas Jte and A are known Jatm can be estimated from the ambient air temperature at ground level using a model for the behaviour of the observing layer above the telescope as described below fte may be fitted to the data for every skydip and because it does not vary with atmospheric conditions a reliable average value can be derived from many observations Thus there are two remaining free parameters T and b that must be derived from the fit three if fitting Mtei Jatm is calculated from Tamp the ambient air temperature by assuming that the sky emission is dominated by a single absorber emitter whose density falls exponentially and temperature linearly with height In this case it can be shown that a h h h Jatm Jamo A kexp 5 exp Aldo exp 1 3 dh 4 where h is Jamb 6 5 to give a 6 5 K fall in temperature per km height hz is the scale height of the absorbers 2 km A is the airmass and k the extinction per km If we approximate the result of the integral by Jatm T Jamb Xg 1 exp Akhyz 5 it can be shown that X has the form MmT X 1 aaa i exp AT 6
196. surement to give the extinction optical depth along the line of sight The data point in question is then multiplied by the exponential of the optical depth to give the value that would have been measured in the absence of the atmosphere The zenith optical depth is assumed to vary linearly with time between the values input in parameters FIRST_TAU and LAST_TAU If the measurement was taken at a time outside the range covered by FIRST_TAU and LAST_TAU then the value closest in time will be used Usage extinction in sub_instrument first_tau first_lst second_tau second_lst out Parameters FIRST_LST CHAR Read The local sidereal time at which FIRST_TAU was the zenith sky opacity in hh mm ss ss format FIRST_TAU REAL Read The zenith sky opacity before the observation The default value is the zenith tau value accepted by the on line system before the observation IN NDF Read The name of the input file containing demodulated SCUBA data MSG_FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM There are no verbose messages OUT NDF Write The name of the output file to contain the extinction corrected data for the specified sub instrument SECOND_LST CHAR Read The local sidereal time at which SECOND_TAU was the zenith sky opacity in hh mm ss ss format The default value is that of FIRST_LST usually the case for a constant tau If this value is less than FIRST_LST it is assu
197. t and de zoom to the original scale To reset a previously flagged point flag the point again but do not accept it the point will be set to GOOD again Please read the note below the description of the menu on the use of the mouse For each mode the menu items are a subset of SUN 216 8 Complete routine descriptions 150 SCUPLOT M H Redisplay menu Q Quit N Next bolometer B Switch to bol X min max X cen X axis from min max or cen 10 Just x activates the cursor R Reset X axis Y min max Y lim Y axis from min max or lim lim U Reset Y axis Despike point or range of points Just p activates the cursor Option gt Note that a X center defined with the cursor or X cen defaults to a 20 points window around cen the position of the spike Using the CURSOR the Left Mouse button always defines the point the Right Mouse button exits the cursor task while accepting the last point clicked Usage scuplot m mode f sdf_file d sdf_file2 s min max 1 bol bol bol J Parameters h elp Print the help information m mode Select usage mode p plot bolometers one by one optionally overlaid with data from the second input file equivalent to pltbol d interactively despike the data for the bolometers in specified file equivalent to dspbol r same as p except that a whole set of bolometers is plotted in a window equivalent to rlinplot
198. t model_out Parameters IN NDF Read The name of the skydip data file or if SCUBA_PREFIX is set the number of the observation raw demodulated data only The input data file can be the output from reduce_switchlor the raw skydip data The file can be located in DATADIR B_ERR REAL Write Error in the fitted value of B Set to bad if the fit has failed B_FIT REAL Write The fitted value of the B parameter Filter transmission Set to bad if the fit has failed B_VAL REAL Read The B parameter filter transmission This efficiency factor must be between 0 and 1 A negative value allows this parameter to be free CVAR LOGICAL Read This parameter governs whether the points are fitted with a constant variance for all points true or the variance derived from the scatter in the individual integrations false The value used for the fixed variance is the mean of all the calculated variances ETA_TEL REAL Read The telescope efficiency If available the current telescope value is used as the default Values must be between 0 and 1 0 A negative value allows this parameter to be free For data taken before 26 April 2000 the default values supplied for 850 and 450 are provided by the routine rather than being read from the FITS header ETA_TEL_ERR REAL Write Error in the fitted value of ETA_TEL Set to bad if the fit has failed ETA_TEL_FIT REAL Write The fitted value of ETA_TEL Set to bad if the fit has failed GOOD
199. ta specified in the file test bat Notes For each file name that is entered values for the parameters WEIGHT SHIFT_DX and SHIFT_DY are requested The application can read in up to 256 separate input datasets The output map will be large enough to include all data points Spline regridding may have problems with SCAN MAP since integrations contain lots of overlapping data points SCUBA sections can be given along with any input NDF The relative weights associated with each point in the output map are stored in a WEIGHTS NDF in the REDS extension of the output data For WEIGHTS TRUE For spline rebinning each point is equivalent to the number of integrations added into the final data point For weight function regridding the situation is more complicated The actual number of points contributing to each cell can be stored using the TIMES parameter Bolometer weights will be used if a BOLWT extension is found in the input data file usually set with setbolwt Astrometry information is stored in the WCS component and not the FITS extension ASCII input files The REF and IN parameters accept ASCII text files as input These text files may contain comments signified by a NDF names values for the parameters WEIGHT SHIFT_DX and SHIFT_DY and names of other ASCII files There is one data file per line An example file is SUN 216 8 Complete routine descriptions 66 BOLREBIN file1 b5 1 0 0 5 0 0 Read bolometer 5 fr
200. tainer which contains two NDFs per bolometer lt BOL gt _peak contains the photometry data for each integration and lt BOL gt _map contains the integrated jiggle pattern assuming the jiggle pattern was on a regular grid irregular jiggle patterns are written as 1 D images and no map is written for zero offset jiggles In this example the bolometer used was H7 so that n56_pht_lon h7_peak would be the NDF containing the integration data the ascii version of which can be found in n56 txt and n56_phot_lon h7_map which would contain the integrated jiggle pattern Since many photometry observations are usually combined to give the final result the scucat task can be used to concatenate data files that have been produced with scuphot scucat knows about the _peak NDFs In this case we have combined the three photometry observations listed in 9 1 35 SUN 216 8 The data reduction process scucat METHOD Concatenation method SEPARATE gt OUT Rootname of files to contain concatenated data gt 3c279 N Name of input file containing photometry data n56_pht_lon gt Found data for the following bolometers h7 This is a PHOTOM observation of 3c279 There are 10 integrations Name of input file containing photometry data gt n57_pht_lon Found data for the following bolometers h7 This is a PHOTOM observation of 3c279 There are 10 integrations Name of input file containing photometry data gt n58_pht_lo
201. taset s multiplying the transform by a cylindrical top hat the F T of the Bessel function then transforming back into image space A linear weighting function is also available which works out to one half width this has the advantage that it is much faster to process and is much less susceptible to edge effects The Gaussian weighting function is probably the best compromise between the Bessel slow and prone to edge effects and Linear fast but the point spread function is non trivial for modeling The radius and size of footprint for the weighting functions are configurable using the WTFNRAD and SCALE parameters Splines Additionally spline interpolation and smoothing routines are also available Note that the spline routines work on each integration in turn whereas the weighting function routines work on all the input data in one go At present the spline routines are experimental and comments are welcomed Median A regridding option derived from despikelis available This method simply puts all data points in an output grid and calculates the median of each output cell Small pixel scales require large datasets since not all cells in a 1 arcsecond grid will contain data points although the KAPPA commands fillbad and glitch can be used to smooth over bad pixels rebin ref Parameters GUARD LOGICAL Read Controls whether the bolometer guard ring should be used during the regridding process The guard ring enfo
202. te The reduced x of the fit The nature of the error determination forces the reduced x to be approximately 1 The SIGMA parameter provides a better guide to the goodness of fit Examples skydip jun1i0_dem_0002 short Process the short sub instrument using the default value for T_COLD and allow ing ETA_TEL and B to be free parameters No output files are written skydip 19970610_dem_0003 long eta_tel 0 9 out sky model_out model Process the long wave sub instrument with ETA_TEL fixed at 0 9 and B free Write the sky temperature to sky sdf and the fitted model to model sdf Notes If the input file is not found in the current directory the directory specified by the DATADIR environment variable is searched This means that the raw data does not have to be in the working directory In addition IN accepts a number This number is converted to a demod ulated data filename by prepending it with information specified in the SCUBA_PREFIX environment variable This filename expansion only works for demodulated data ie data containing _dem_ The _dem_ is assumed and should not be present in SCUBA_PREFIX If the CVAR parameter is true the reduced x value can not be used to compare the goodness of fit between datasets 163 SKYDIP SUN 216 8 Complete routine descriptions Both RASTER and DISCRETE skydips are supported See Appendix for more information on skydips Related Applications SURF extinction Edip kyu
203. ted repeatedly until a NULL value is supplied LOOP must be TRUE IN can include a SCUBA Like the REF parameter this parameter accepts a text file LAT_OUT CHAR Read The latitude of the output map centre The supplied default value is that of the map centre of the first map LONG_OUT CHAR Read The longitude of the output map centre The supplied default value is that of the map centre of the first map LOOP LOGICAL Read Task will ask for multiple input files if true Only REF is read if noloop MSG_FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM There are no verbose messages OUT NDF Write This is the name of the HDS container file that will contain the rebinned images The map for each integration is stored in an NDF inside this NDF container The maps can be accessed as out name where name is the integration name i e i1 i2 i3 etc OUT_COORDS CHAR Read The coordinate system of the output map Available coordinate systems are e AZ Azimuth elevation offsets e NA Nasmyth offsets e PL RA Dec Offsets from moving centre e g Planets e RB RA Dec B1950 e RJ RA Dec J2000 e RD RA Dec epoch of observation e GA Galactic coordinates J2000 For RD current epoch is taken from the first input file OUT_OBJECT CHAR Read The name of the object ie the NDF title PIXSIZE_OUT REAL Read Size of pixels in the output map Units are arcsec
204. tern repeats in a switch Object latitude Latitude of observatory degrees Object latitude at MJD2 Local offset coordinate system Object longitude East longitude of observatory degrees Object Longitude at MJD2 Height of rectangle to be mapped arcsec P A of map vertical ve towards ve long Width of rectangle to be mapped arcsec Map X offset from telescope centre arcsec Map Y offset from telescope centre arcsec Max elevation of sky dip deg 5 47 27 27173 approx mean Dec deg 194 03 06 053467 approx mean R A deg Measurement number at end of observation Min elevation of sky dip deg Modified Julian day planet at RA DEC Modified Julian day planet at RA2 DEC2 The type of observation No integrations in the observation No measurements in the observation Name of object Type of object The observation definition file The name of the observer The project identification Run number of observation Coordinatesystem of sampling mesh Sample spacing along scan direction arcsec Sample spacing perp to scan arcsec Sampling method Scan P A rel to lat line O lat 90 long N sigmas from fit of spike threshold Automatic spike removal Assumed width of spike Elevation of first SKYDIP point deg RECORD_DATA RESET_DATA_SIZE RECORD_DATA SC ST at end of observation Azimuth at observation start deg Elevation at observation start deg ST at start of observation Switch mode of observation
205. ters from 039_lon_ext sdf and ask for a bolometer list rlinplot f 039_lon_ext l 5 Plot 5 bolometers at a time rlinplot f 039_lon_ext 6 5 8 20 Plot bolometers 5 6 8 and 20 Notes e If the overlay comes up scrambled delete the agi_xxx files in your home directory and if that does not work also files like linplot sdf in the home you adam subdirectory Related Applications SURF KAPPA mlinplot cursor Bugs Freezes when asked to plot a bad bolometer SUN 216 8 Complete routine descriptions 126 SCAN_RLB SCAN_RLB Remove baselines from SCAN MAP data Description This routine removes a baseline from each scan The baseline is determined in a number of ways For removal of a linear baseline a fit is made to the scan ends before removing this from the entire scan Usage scan_rlb in out Parameters CHOP INTEGER Read The linear baseline fit is calculated over regions CHOP arcseconds from the scan ends This region should be as large as possible but should only include baseline regions any scan that includes a source detection within CHOP arcseconds of the scan ends will be rendered useless The default value is the chop throw IN NDF Read The name of the input file containing demodulated SCUBA data METHOD CHAR Read Governs the method to be used for calculating the baseline Options are MEDIAN Remove the median from each scan MEAN remove the mean level from each scan LINEAR fit a line
206. the wavelength of observation but suppress higher spatial fre quencies To minimise edge effects the Bessel function is truncated at a radius of 10 half widths from the centre although this is configurable and apodized over its outer third by a cosine function Viewed in frequency space the method consists of Fourier transforming the input dataset s multiplying the transform by a cylindrical top hat the F T of the Bessel function then transforming back into image space A linear weighting function is also available which works out to one half width this has the advantage that it is much faster to process and is much less susceptible to edge effects The Gaussian weighting function is probably the best compromise between the Bessel slow and prone to edge effects and Linear fast but the point spread function is non trivial for modeling The radius and size of footprint for the weighting functions are configurable using the WTFNRAD and SCALE parameters Splines Additionally spline interpolation and smoothing routines are also available Note that the spline routines work on each integration in turn whereas the weighting function routines work on all the input data in one go At present the spline routines are experimental and comments are welcomed e Median A regridding option derived from despikelis available This method simply puts all data points in an output grid and calculates the median of each output cell Small pixe
207. they use PARAM VALUE format Examples qdraw test Draws test sdf with a scale of 5 sigma and draws lines at 3 sigma qdraw noline test Same as above but without the 3 sigma lines qdraw mode 2 test Plot the data using symbols linplot mode 2 qdraw mode 2 sigcol red test Plot with symbols and use red lines to show the 3 sigma lines Notes The KAPPA_DIR environment variable must point to the location of the KAPPA binaries this is usually done during a Starlink login Related Applications SURF Seucat scuphol SUN 216 8 Complete routine descriptions 108 REBIN REBIN Rebin demodulated SCUBA data onto output map Description This routine rebins the demodulated data from SCUBA MAP observations onto a rectan gular mesh by a variety of methods Currently convolution by weighting functions spline interpolation and median are supported Usage Weighting functions Currently linear Bessel and Gaussian weighting functions are supported The width of the Bessel function is such that it should preserve all spatial information obtained by the telescope at the wavelength of observation but suppress higher spatial fre quencies To minimise edge effects the Bessel function is truncated at a radius of 10 half widths from the centre although this is configurable and apodized over its outer third by a cosine function Viewed in frequency space the method consists of Fourier transforming the input da
208. tions 16 and 31 Enter required shift lt 14 2 Before 123456789 10 11 12 13 14 15 16123456789 10 11 12 13 185 SUN 216 8 Notes on scripts 14 15 16 1 lt cut gt Bolchan 123456789 10 11 12 13 14 15 1615161234567 849 10 11 12 13 14 1 lt cut gt scushift is very verbose The before and bolchan entries simply tell the user the form of the correction used If you look carefully you will see that the 17th number in the list has changed from a 1 to a 15 indicating that the shift was successful This command works inplace and in fact will not run on the raw data file instead it should be run on the file produced by reduce switchlorfflatfield 5 The data should now be corrected but note that PHOTOM data will still need more work see the note in the scushift documentation for more details There is one last wrinkle to the process of extracting calibrator data PHOTOM observations after 3rd June 1997 store signals from 2 channels in addition to the arrays if the arrays were being used Thus n_bols for a PHOTOM demodulated data array will be 130 rather then 128 In this case you should compare the calibrator signature with that in the file calsig_450_850_photom sdf K Notes on scripts Eg Eon the xp nai ie angered anno Perl NDF not form part of the SURF monolith and are all written in perl 37 They all use the and therefore require at least version 5 003 of perl The perl NDF binary will be installe
209. tored exposure An exposure is the result from a complete set of switches For example in a JIG GLE MAP or PHOTOM observation where the telescope is nodding the source between left and right beams the data from each nod position is a switch and the reduced result left switch right switch say is an exposure In a SCAN MAP observation there is no beam switching so in this case an exposure is the same as a switch integration An integration means different things for different observations For one of the mapping modes it means the data from one fully sampled coverage of the map area In a JIGGLE MAP where full sampling is achieved by jiggling the secondary mirror an integration is generally the results from one pass through the complete jiggle pattern An integration is made up of one or more exposures Similarly an integration fora SCAN MAP observation is made up of data from the raster scans that cover the map area once For PHOTOM observations an integration is usually the average of a 9 point mini jiggle For a SKYDIP observation an integration is the data from a single revolution of the sector chopper in front of the cryostat window jiggle In order to sample an image fully the secondary mirror is moved once a second whilst chopping to move the position of the array on the sky this is called jiggling There are a complete set of jiggle positions for each integration A PHOTOM observation can also jiggle in order
210. tored in an NDF inside this NDF container The maps can be accessed as out name where name is the bolometer name e g H7 or G1 etc OUT_COORDS CHAR Read The coordinate system of the output map Available coordinate systems are e AZ Azimuth elevation offsets e NA Nasmyth offsets e PL RA Dec Offsets from moving centre e g Planets e RB RA Dec B1950 e RJ RA Dec J2000 e RD RA Dec epoch of observation e GA Galactic coordinates J2000 For RD current epoch is taken from the first input file OUT_OBJECT CHAR Read The name of the object ie the NDF title PIXSIZE_OUT REAL Read Size of pixels in the output map Units are arcsec REBIN_METHOD CHAR Read The rebin method to be used A number of regridding methods are available e LINEAR Linear weighting function e GAUSSIAN Gaussian weighting function e BESSEL Bessel weighting function e SPLINE1 Interpolating spline PDA_IDBVIP e SPLINE2 Smoothing spline PDA_SURFIT e SPLINES Interpolating spline PDA_IDSFFT e MEDIAN Median regridding SUN 216 8 Complete routine descriptions 64 BOLREBIN Please refer to the PDA documentation SUN 194 for more information on the spline fitting algorithms REF CHAR Read The name of the first NDF to be rebinned The name may also be the name of an ASCII text file containing NDF and parameter values See the notes REF can include alSCUBA section REFPIX 2 INTEGER Read The coordinate of the referen
211. uce a one line summary of all reduced _red_ map files mapsum all reduced gt log txt Produce a one line summary of all the reduced map files and store the output in the text file log txt note this example is shell specific mapsum all reduced demod Produce a summary of all reduced _red_ and demodulated _dem_ map data files ie not files produced during off line data reduction Notes e mapsumJonly displays map data e Files are drawn from the current working directory and the directory indicated by the DATADIR environment variable e Data reduced by the off line system will all be treated as run O for the purposes of listing unless numbers are present in the filename e The output can be stored in a file by using unix redirection as long as the search range is fully specified either as all or with begin and end e Command line options can be abbreviated e Options that take values can be used either as flag option or as flag option Related Applications SURF sculog photsur po misurn ebssur Ekysum 99 OBSSUM SUN 216 8 Complete routine descriptions OBSSUM Produce one line summary of SCUBA observations Description lobssum goes through all the sdf files in the current directory and optionally DATADIR defined in an environment variable and extracts information from any FITS entries that may be present In the absence of the all flag a nu
212. uce one line summary of SCUBA map observations Description Mapsum goes through all the sdf files in the current directory and optionally DATADIR defined in an environment variable and summarizes files containing map observations In the absence of the all flag a numeric range is requested This range only has an effect on raw data or reduced files which have the run number embedded into the file name Filenames with no numbers are treated as scan 0 Usage mapsum h demod reduced al1 begin nn end nn Parameters hlelp Return a help message only More help can be obtained by using showme sun216 or scuhelp mapsum all List all map files in the current directory and DATADIR demod Only list demodulated data files signified by _dem_ file name reduced Only list reduced data files signified by _red_ file name begin nn First scan number to be considered same as begin nn end nn Final scan number to be considered same as end nn Examples mapsum Ask for a range of scan numbers and then give a summary of every MAP file matching this criterion in DATADIR and the current directory mapsum all Generate a summary of all map files in the current and DATADIR directory mapsum begin 5 end 100 Generate a summary of all map data from scans 5 to 100 inclusive mapsum all reduced SUN 216 8 Complete routine descriptions 98 MAPSUM Prod
213. ucture JIGL_X 64 lt _REAL gt 5 3457 0 5 3457 8 033999 0 5 3457 8 033999 2 6883 2 6883 JIGL_Y 64 lt _REAL gt 12 36 12 36 12 36 10 815 10 815 9 27 10 815 10 815 10 815 DEC1 lt _REAL gt 0 DEC2 lt _REAL gt 0 LST_STRT 2 4 3 1 lt _DOUBLE gt 3 23079147492436 3 2322998582771 3 26511400298336 3 26350802081885 RA1 lt _REAL gt 0 RA2 lt _REAL gt 0 SCUBA lt SCUBA_ST gt structure BOL_CALB 16 9 lt _REAL gt 0 858 0 9311 0 9499 1 002 0 9585 1 22130 928 1 304 4 dod od ot oO BOL_DU3 16 9 lt _REAL gt 57 08 45 9 36 15 24 64 14 55 3 62 15 78 9 047 54 65 0 0 0 0 0 0 BOL_DU4 16 9 lt _REAL gt 28 14 35 91 41 46 49 62 63 89 17 16 11 16 0 0 050 0 0 BOL_QUAL 16 9 lt _INTEGER gt 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 050 05050 0 0 0 03051 1 05050 151 BOL_TYPE 16 9 lt _CHAR 20 gt gt SHORT SHORT SHORT SHORT rad Pere s PlS50 DC P1100 DC BAD BOL_ADC 128 lt _INTEGER gt a Ds A ae alta E Pe E O Pals a ade ide eg Hyd ad Sala 848 8 0 9 8 0 0 9 9 9 9 9 9 9 9 9 169 E 3 Structure of demodulated files SUN 216 8 File naming and data structures BOL_CHAN 128 lt _INTEGER gt 1 2 3 4 5 6 7 0 9 10 11 12 13 14 ae 12 13 14 15 16 1 2 9 4 5 6 15859 FLAT_ADC lt _INTEGER gt 0 FLAT_CHN lt _INTEGER gt 0 FLAT_IND lt _INTEGER gt 0 PHOT_BB lt _INTEGER gt 0 DEM_PNTR 2 4 3 1 lt _INTEGER gt 1 17 49 33 65 81 113 97 129 145 257 273 305 289 321 337 369 353 IS
214. ues are A to I shift The number of bolometers to shift by A negative shift moves D1 to D16 for example and a positive shift D1 to D2 In most cases a negative shift is required usually 1 Examples scushift test i 2 Move the I card data of test sdf by minus 2 bolometers scushift test2 h 1 Move the H card data by plus 1 bolometer Notes extinction must not have been run on the input NDF e Arguments are requested if they are missing from the command line e If the system stores channels 1 2 3 6 7 8 10 but we know that we have a shift of 1 in the system ie an extra byte is present This implies that we have actually stored channels 16 1 2 5 6 7 9 and if only bolometers 1 2 6 7 are from the required sub instrument we have to throw away data from channels 15 5 and 9 e The DAQ hardware fault always introduced extra bytes and therefore a negative shift should be used in scushift Currently photometry data is not corrected properly the PHOT_BB extension is not modified so the correct bolometer will not be extracted by scuphot This can be overcome by using the ALLBOLS parameter in scuphot 157 SDIP SUN 216 8 Complete routine descriptions SDIP Reduces and displays skydip data Description This script first runs the skydip task in order to fit the sky parameters to the data The sky data and model are written to files and are then displayed using KAPPA s Usage sdip NDF Parameters NDF NDF Read
215. ultiple bolometers 131 SCUCAT SUN 216 8 Complete routine descriptions to individual files If the input set contained data for bolometer H7 the output file will be test_h7 sdf The program will then ask for another data set scucat test ext_long noloop This will copy all the data from ext_long sdf to test_ lt bol gt sdf and will then exit without asking further questions scucat outfile filel file2 file3 noloop method separate Concatenate the data from filel file2 and file3 into output files containing the rootname of outfile scucat outfile in input lis noloop method catall This will copy all the data contained in the files listed in input lis and write it to a file called outfile sdf Notes e SCUCAT can process output data from scuphot e g file sdf as an HDS container containing NDF files with the names lt bol gt _peak or NDF files e If given an NDF the data array is vectorized so that the output is 1 dimensional regardless of the shape of the input file e This task can also be used to simplify further processing of the photometry data even if no data is to be concatenated in this case the task would be identical to the KAPPA task ndfcopy Related Applications SURF scuphot Implementation Status e NDF sections can not be used e All input pixels are propagated to the output file e See the GRP documentation 34 for more information on specifying multiple input files for the IN par
216. urly brackets must still be given Since this is an array parameter square brackets must be used to specify more than one component SECTION gt e1 e4 b2 would select exposure one from each integration along with exposure 4 for bolometer 2 be used if the square brackets are not used Care must also be taken when using commas in SCUBA sections the parameter system will split multiple entries on commas unless the entire section is quoted SECTION gt e1 4 If necessary the negation character should come after a section ie after the closing curly bracket and that negation applies to the combined section and not just the string containing the negation character SECTION gt e3 implies that the section consists of everything except exposure 3 _rlb infile method linear Remove linear baselines from each scan using baseline regions the same size as the chop Write the results to the default output file scan _rlb infile rlb method linear chop 30 Calculate the linear baseline for each scan using the specified baseline region Write the results to the default output file scan _rlb infile norlb method median Calculate the fit using the median of each scan but do not remove the baseline from the data Store the baseline determination for later analysis scan _rlb method section rlb section e1 4 Calculate the baseline using the first and 4th exposures of each integration Notes The command can
217. ve the bolometer s from the list The definitions of ring number and all are dependent on the selected sub instrument Here are some example values for BOLOMETERS 121 REMSKY SUN 216 8 Complete routine descriptions 17 18 19 20 Bolometers 17 18 19 and 20 h6 h7 h8 h9 Bolometers H6 H7 H8 H9 all Whole array r0 Ring zero central pixel r0 19 No bolometers bol 19 of LONG is RO H7 h7 r1 inner ring and H7 r1 h8 inner ring without H8 r1 18 inner ring without bolometer 18 all r1 h7 all pixels except the inner ring H7 all r3 1 all pixels except ring 3 but with G1 which happens to be in r3 all 11 12 13 14 15 Selects the central pixel all r 1 Selects all except outer ring Note that the bolometer sum is calculated sequentially so that all all h7 would leave you with bolometer H7 IN NDF Read This is the name of the input demodulated data file ITER_SIGMA REAL Read When using MEAN to calculate the average this is the sigma clipping level used This is an iterative value points will be removed from the mean until the spread of data points is smaller than this value Supplying a negative value will turn off clipping MODE CHAR Read Method to be used for calculating the average sky There are two methods available e Median the median value for all the sky bolometers is taken from each bolome ter signal e Mean the mean of the sky bolometers is used as the
218. where n_bols is the total number of bolometers measured 128 for both short and long arrays and n_jiggles is the total number of jiggle positions measured in the observation In summary should be given the following parameters ONDIM 1 ELINE2 Y YLIMITS default XRANGE 3 3 and ZRANGE default where default is the default value sug gested for the parameter Alternatively it should be possible to use ndfcopy to extract the NDF section using the TRIM parameter to reduce the resultant section to 2 dimensions ndfcopy 19971008_dem_0039 3 TRIM TRIMWCS 2 Normalise the calibrator signal by using cdiv to divide the result from manic by n_jiggles 384 in this example cdiv IN Input NDF data structure calsig gt SCALAR Division constant 1280 gt 384 OUT Output NDF gt calsig_div 3 Plot the standard calibrator and overlay the calibrator signal derived above linplot SURF_DIR calsig_450_850_map linplot calsig_div noclear lincol some colour where some colour is a different colour to that used to display the first calibrator signal 4 Once you have identified a data shift this must be corrected with the scushift command Since the shift is usually caused by adding extra bytes to the data stream a negative shift must be applied to correct the problem scushift Input NDF no sdf r95 Which A to D card a single letter B Using the NDF r95 Card 2 starts and ends at posi
219. with the source signal will be down weighted relative to all the others since the standard deviation on the bolometer will be much higher The weights must be set via an external file in this case Related Applications SURF rebin KAPPA SUN 216 8 Complete routine descriptions 160 SIGCLIP SIGCLIP Clip a dataset at n sigma Description This ee to calculate mean and standard deviation of an NDF It then uses to set the values at n sigma to BAD The clipped data are written to NDF _clip sdf Usage sigclip NDF SIGMA Parameters NDF Given The required dataset SIGMA REAL Given The clipping level Examples sigclip test 3 0 Clips test sdf at 3 0 sigma and writes the data to test_clip sdf Notes The KAPPA_DIR environment variable must point to the location of the KAPPA binaries this is usually done during a Starlink login Related Applications SURF scucat scuphot KAPPA stats thresh Implementation Status e The program must have two arguments Parameters are not requested if an argument is omitted from the command line 161 SKYDIP SUN 216 8 Complete routine descriptions SKYDIP calculate sky properties from SCUBA skydip data Description This application takes raw SKYDIP data and calculates tau eta_tel and B by fitting Sky brightness temperatures are calculated for different airmasses and then fitted with a model of the sky Usage skydip in sub_instrument t_cold eta_tel b_fit ou
220. y signal is expected to vary on timescales of the order of one second an option is included for smoothing the sky signal This is especially useful for scan map data where samples are taken at 7 8 Hz Usage calcsky ref Parameters BOXSZ INTEGER Given Size of smoothing box in seconds This is used to smooth the time series Default is 2 0 seconds IN CHAR Read The name of the input file to be processed This parameter is requested repeatedly until a NULL value is supplied LOOP must be TRUE IN can include a SCUBA section Like the REF parameter this parameter accepts a text file LOOP LOGICAL Read Task will ask for multiple input files if true Only REF is read if noloop MODEL NDF Read NDF containing the model of the source The astrometry is read from this file The model must have been generated by SURF since it relies on the presence of certain FITS keywords MSG FILTER CHAR Read Message filter level Allowed values are QUIET NORM and VERB Default is NORM NOSRC NDF Write File to store source removed data This can be used to check the source removal Note that this output file can not be used directly by SURF for further processing since the header is incomplete No file is written by default SUN 216 8 Complete routine descriptions 68 CALCSKY OUT_COORDS CHAR Read The coordinate system to be used for the model determination Available coordinate systems are e AZ Azimuth elevation offs
221. ysum all reduced 165 SKYSUM SUN 216 8 Complete routine descriptions Produce a one line summary of all reduced skydip _red_ files skysum all reduced gt log txt Produce a one line summary of all the reduced skydip files and store the output in the text file log txt note this example is shell specific skysum all reduced demod Produce a summary of all reduced _red_ and demodulated _dem_ skydip files ie not files produced during off line data reduction Notes e skysum only displays skydip data e Files are drawn from the current working directory and the directory indicated by the DATADIR environment variable e Data reduced by the off line system will all be treated as run 0 for the purposes of listing unless numbers are present in the filename e The output can be stored in a file by using unix redirection as long as the search range is fully specified either as all or with begin and end e Command line options can be abbreviated e Options that take values can be used either as flag option or as flag option Related Applications SURF sculog photsur mapsun sbssum poison yap SUN 216 8 Reducing data at the Joint Astronomy Centre 166 D Reducing data at the Joint Astronomy Centre This section describes the location of SCUBA data at the Joint Astronomy Centre D 1 During Observing At the JCMT the SCUBA data is written to a unix disk

SURF – SCUBA User Reduction Facility

Contents

Download Pdf Manuals

Related Search

Related Contents

SURF &ndash; SCUBA User Reduction Facility

Contents

Download Pdf Manuals

Related Search

Related Contents

SURF – SCUBA User Reduction Facility