NHSC/PACS Web Tutorials Running the PACS Spectrometer
Contents
1. Addin g pointing pro ducts ChopNodEx RSION py X JG L a 205 Add the pointing information to the Status 206 Uses the pointing horizons product solar system object ephemeries 207 orbitEphemeris products and the SIAM cal file 206 NOTE for SSOs you should contact the HSC helpdesk to check whether the 209 pointing is currently correctly handled for moving objects 210 slicedFrames specAddInstantPointing slicedFrames obs auxiliary pointing callTree calTree orbit a il 212 Extend the Status of Frames with the parameters GRATSCAN CHOPPER CHOPPOS 213 used cal file ChopperThrowDlescription 214 slicedFrames specExtendStatus slicedFrames callTree callTree 215 216 Convert the chopper readouts to an angle wrt focal plane unit and the sky 217 and add this to the Status used cal files ChopperAngle and ChopperSkyAngle 218 slicedFrames convertChopper2Angle slicedFrames calTree calTree 219 220 Add the positions for each pixel Ra and Dec datasets 221 used cal files ArrayInstrument and ModuleArray 222 slicedFrames specAssignRaDec slicedFrames callree callTree e A e 224 if verbose SE show footprint of your observation 2V6 226 slicedPlotPointing slicedFrames S At this point astrometry is added to the data At each pixel a coordinate is assigned and we can check if the pointing was performed correctly page 25 nhsc ipac caltech edu helpdesk PACS 301 her NA2. You should have received a copy of the GNU Lesser General Public License along with HCSS If not see lt http www gnu org licenses gt Te Th YR N SR SR SR TR SR SK HH W war DESCRIPTION Recommen ded for first time users Cd RT page 15 nhsc ipac caltech edu helpdesk PACS 301 hse NASA Herschel Science dl File Edit Run Pipelines Window Tools Help PG Ro WS ei gr Dp i Editor x P e 7 ChopNodLineScan py x 168 have been set 169 if not locals has key multiObs or not multiObs 170 camera blue agin E re eee eee ee er eee eee eee eee eee 173 Set up the calibration tree We take the most recent calibration files 174 for the specific time of your observation obs obs 175 176 This tree contains pointers to all the calibration files that the pip 177 tasks use when calTree calTree is specified in a task s call As YOu click 178 From that calibration tree certain calibration files are used by eac h 179 The Version of the calibration tree can be found from the simple the green arrow 180 print calTree below That version points to a unique set of cali ibratiq the small black 181 IP you print the common or spectrometer branches of the tree you can 182 the version numbers of the individual calibration files this calTree arrow will move down l oF corresponds to V gt calTree getCalTree obs qQbs through the script 187
3. NHSC PACS Web Tutorials Running the PACS Spectrometer pipeline for CHOP NOD Mode PACS 301 Level 0 to 1 processing Line Scan and Short Range Scan Modes Updated Feb 2012 page 1 nhsc ipac caltech edu helpdesk PACS 301 NASA Herschel Science Center This tutorial assumes the following version of HIPE User Build 8 1 or later CIB 8 0 3397 or later There are several improvements over previous versions including calculating the responsivity from the on orbit calibration block taken before the observation instead of using the pre launch nominal response Additional more sophisticated flat fielding is done which also includes refinements to the spectral flat field page 2 nhsc ipac caltech edu helpdesk PACS 301 NASA Herschel Science S Center page 3 Introduction This tutorial will guide you through the interactive spectrometer pipeline from loading raw data into HIPE to obtain calibrated data with astrometry in the case of chop nod mode Pre requisites The following tutorials should be read before this one e PACS 101 How to use these tutorials e PACS 102 Accessing and storing data from the Herschel Science Archive Note that the following tutorial assumes that you have already created a pool in storage with the same name as the obsid of your observation If this is not the case consult PACS 102 nhsc ipac caltech edu helpdesk PACS 301 Overview Step 1 Check HIPE version and
4. 13 Information Box What is an Observation Context To use an interactive ipipe scripts the observation context must be defined in a variable named obs e The observation context provides the link to the data and all relevant ancillary and calibration products It is a container holding all this material in one place Documentation References e HIPE user manual Version 1 2 chapter 3 pgs 45 56 PACS data reduction guide Version 3 Section 5 2 pg 145 nhsc ipac caltech edu helpdesk PACS 301 Jet NASA Herschel Science s Center Check 7 The observation context is properly loaded in HIPE Console x Type in console window o HIPE gt print obs Observation ID and data type are identified HIPE gt print ois description ahseryationcontext for PACS data of observation 1342186797 meta type eator creationDate description instrument modelName Output startDate endDate a bsid dNumber cusMode esteMode obsMode processingMode origin slewTime aorLabel aot equinox issionConfig waran Pacha een pMDEC raNominal MaA ra dec posAngle telescope velocityDefinition radialVelocity observer proposal pointingMode missionConfiguration instrumentConfiguration startTime endTime chopAvoidFrom chopAvoidTo chopNod decoff doSlewScience loo ks faintLines fluxUnit lWave lcontFlux lineFlux lineId lineStep lineWidth lines m mapRasterAngle n naifid obsOverhead Sen
5. 168 First we copy the metadata from the ObservationContext to the Level product 169 Then we extract the Level product from the ObservationContext 170 pacsPropagateMetaKeywords obs 9 obs level0 171 lLevel PacsContext obs level0 Lee 173 For your camera extract the Frames scientific data the rawramps raw data 174 for one pixel and the DMC header the mechanisms status information 175 sampled at a high frequency 1 6 slicedFrames SlLicedFrames lLevelO fitted getCamera camera product 177 slicedRawRamp LevelO raw getCamera camera product 178 slicedDmcHead Level O dmc getCamera camera product 179 180 if verbose 181 Get an overview of the basic structure of the data prior to any processing 182 SLicedSummary slicedFrames 183 Plot the grating position amp raw signal of central pixel 184 pO slicedSummaryPLot slicedFrames signal 1 165 4 From now on we will step through the script line by line using the green arrow on the menu bar The first step consists in extracting the O level products from the observation context page 22 nhsc ipac caltech edu helpdesk PACS 301 her ZE Check level 0 Let s check first the basic structure of the data It is important to verify if the observation has been performed correctly Calibration block 2 5 10000 l i 12000 5 It line 3 repeats eet 1000 2000 3000 4000 5000 6000 Signal Det 8 Mod 12 Reset Number RB
6. GRATING POSITION raw B Signal Det 8 Mod 12 In our case after the calibration block we can identify two different lines observed 3 times in the two nod positions page 23 nhsc ipac caltech edu helpdesk PACS 301 nhise L NASA Herschel Science Center 7 ChopNodEx RSION py X i O M mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm mm EN 187 Processing Level 0 gt Level 0 5 166 189 190 191 flag the saturated data in a mask SATURATION and RAWSATURATION this 192 uses the raw data we get for some pixels 193 used cal files RampSatLimits and SignalSatLimits 194 slicedFrames specFlagSaturationFrames slicedFrames rawRamp slicedRawRamp calTree callT ree 195 196 Convert digital units to Volts used cal file Readouts2Volts 197 slicedFrames specConvDigit2VoltsPerSecFrames slicedFrames call ree calTree 198 199 Identify the calibration blocks and fill the CALSOURCE Status entry 200 slicedFrames detectCalibrationBlock slicedFrames 201 202 Add the time information in UIC to the Status 203 slicedFrames addUtc slicedFrames obs auxiliary timeCorreLation 204 z 4 page 24 nhsc ipac caltech edu helpdesk PACS 301 nhse
7. and you wish to measure accurately the equivalent width of the line In most other respects the standard pipeline works well page 8 nhsc ipac caltech edu helpdesk PACS 301 Ui This should look like something like this when read in NASA Herschel Science k HIT HIPE Users apple scripts ChopNodInteractive py Bebo sws RF EC ah A t gt Navigator x L User areas 1 zi Home Folder 7 ChopNodin ctive py x 1p This file is part of Herschel Common Science System HCSS Public License along with p www gnu org licenses gt 7 navigati ng through the E m File System S A Copyright 2001 2010 Herschel Science Ground Segment Consortium 5 HCSS is free software you can redistribute it and or modify 6 IE under the terms of the GNU Lesser General Public License as 7 published by the Free Software Foundation either version 3 of 8 the License or at your option any later version 9 10 HCSS is distributed in the hope that it will be useful 11 but WITHOUT ANY WARRANTY without even the implied warranty of 12 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the 13 GNU Lesser General Public License for more details S 1 b f p 2 Variabl C ro d r O r 15 You should have received a copy of the GNU Lesser General x opNodInteractive py v 1 3 2010 11 19 15 06 02 juergen Exp Deen USER ee EE Purpose 25 PACS Spe
8. print calTree 188 print calTree common 189 print calTree spectrometer 190 191 nn 192 Show an overview of the uplink parameters of this observation 193 i e the settings during your observation 194 if verbose obsSummary obs e L 69 of 7163 page 16 nhsc ipac caltech edu helpdesk PACS 301 Tite Dies SEI THE VERBOSE LEVEL AND SPECTROMETER D Camera This will govern whether you get a red or blue spectrum analyzed so its important because some calibration needs to know which side is being analysed You will need to repeat the whole exercise for the other channel if you want to analyse both channels VERBOSE 1 turns on diagnostic plots and other useful info SETUP 0 5 updateObservationContext At the end of each level do you want to update the Observation choice a 0 do not update the observation context a l update the observation context See further down the script for simple ways to save your reduct at various steps in the data processing updateObservationContext 0 P athens becca rc ee pics E SETUP I Ca Red or blue camera As before we test for whether this sc Ca being run within a multiObs script in which case the camera al have been set E ae set the band you want red of blue depending on the line You can always execute gt print camera to check later page 17 PACS 301 her HASA Her
9. 0 0 1 2 3 B2B B3A UNDEF 18 25 5536 57 213 88 119 Nb of slices 1 Slice BLINDPIXELS SATURATION RAWSATURATION NOISYPIXELS BADPIXELS UNCLEANCHOP GRATMOVE Slice edges 0 5536 IPE gt KA KA KA O CO k re nhsc ipac caltech edu helpdesk PACS 301 nhse NASA Herschel Science Check before ene TA s Cal Block RT 20 5 6 10 L l i 10 1 8 SA 10 1 6 5 2 10 E O 5 D 1 2 E e 5 0 10 1 s i 0 1 0 E 48 10 D Q e E 0 8 4 6 10 i gt SS O Sts Ojos O 4 410 0 4 4 2 10 10 0 2 0 0 4 0 10 DO 5900 W GRATING POSITION raw EE Wavelength um RB GRATSCAN H E CALSOURCE 0 None 1 CS1 2 CS2 mmm NOD A am NOD B BAND 0 UNDEP 1 R1 2 B2B 3 B24 4 B3A There are two lines two wavelengths in red Grating scans are numbered positive if upscans and negative if downscans page 29 nhsc ipac caltech edu helpdesk PACS 301 her NASA Herschel Science 2 Slicing A Editor x 7 ChopNodE RSION py x 295 Slice the data by Line Range Raster Point nod position nod cycle 96 on off position and per band The parameter removeUndefined is for cleaning purposes 98 Virtually any column in the BlockTable can be used as a SlicingRule but do 99 not modify the SlicingRules if you are not 100 aware of what you are doing 300 rules SlicingRule LineId 1 SlicingRule RasterLineNum 1 SlicingRule RasterColumnNum 1 301 S
10. 0 1460 2479 3498 4517 5536 HIPE gt e nhsc ipac caltech edu helpdesk PACS 301 NASA Herschel Science Cal Block GRAT POS Check after slicing vs ON yy 2 NII 57 90 5 6 10 SS an 4 0 80 10 1 8 5 4 10 70 1 6 5 D 1 2 Sto Hi une 4 8 107 40 5 r r gt N 4 6 10 30 7 5 Line d 4 4 10 20 0 4 4 2 10 10 10 0 2 l 0 0 0 4 0 10 1 000 6000 Reset N r B CRATING POSITION raw BH Wavelength u m E GRATSCAN E E CALSOURCE 0 None 1 CS1 2 CS2 mmm NOD A aus NOD H BAND 0 UNDEF 1 R1 2 B2B 3 B2A4 4 B3A 1 0 0 9 0 8 0 7 0 6 0 5 0 4 0 3 0 2 0 1 0 0 There are four slices calibration nod A and B for the 1 line nod A and B for the 2 line page 32 nhsc ipac caltech edu helpdesk PACS 301 Ia NASA Herschel Science Genter Step 5 Run the 0 5 gt 1 pipeline Glitch detection chop differentiation RSRF flat page 33 nhsc ipac caltech edu helpdesk PACS 301 nhse e Level 0 5 gt 1 Divide by Relative Spectral Response Function RSRF Apply Responsivity Correction derived from Cal Block Convert Data Frame to Cube Apply Flat Field Level 1 Frames to Cubes 5 X 5 xX 16 x ramps page 34 nhsc ipac caltech edu helpdesk PACS 301 her Biewer Y D egl itc h n E ChopNodEx RSION py X LO 3 De activate all masks before running the glitch flagging J slicedFrames activateMasks slicedFrames Stringld exclusive True CH
11. 02 If you have already done this then skip to STEP 4 Otherwise continue page 10 nhsc ipac caltech edu helpdesk PACS 301 nhse NASA Herschel Science weCenter Insert the correct obsid Then just run the following lines of the script if a you already have a pool in the default location hcss Istore and b if the pool has the same name as the obsid recommended will be present if you are running the multiObs script If multi present the obsid will have been set already and if not then t here If you get a NameError then the obsid had not been set if not locals fas keyrsgulitiObs or not multiObs obsid 1342188943 useHsa 0 obs getObservation obsid verbose True useHsa useHsa poolLocation None poolName None if useHsa saveObservation obs poolLocation None poolName None Otherwise either set the poolLocation and poolName variables to the location of your pool before running this part poolLocation mypooldir poolhame mynamepool If this is the first time you have accessed your data i e you have not already created a data pool then please follow the instructions in Pacs tutorial PACS 102 page 11 nhsc ipac caltech edu helpdesk PACS 301 ner NASA Herschel Science Genter Step 4 Check that you have indeed loaded the correct Observational Context page 12 nhsc ipac caltech edu helpdesk PACS 301 nhs ANASA Herschel Science a Center page
12. ER EE EE EE E SD ER GESA E SSTA ER rt ER EE ER ttt e Masked glitch s SS E j p ee e N ER OFF signal REES ican page 36 nhsc ipac caltech edu helpdesk PACS 301 ON signal _ nhse NASA Herschel Science we Center More masks It is possible to explore MM masked unmasked other masks _ selected LS step time index Select unclean chop Row H Column 12 we h e 4 A e KK e e ia ep w m f d r aa S alias e m mo a l geb DE In this case it is clear why there is a second group of points for the ON and OFF positions These corresponds to signals obtained when the chopper was not yet in the correct position page 37 nhsc ipac caltech edu helpdesk PACS 301 NASA Herschel Science Center Convert signal levels to standard capacitance Except for very strong signals this would normally be the standard capacitance used LL CO C L T LUA Z TZ LUA e TJ Inspect signal vs wavelength wavelengths frame wa pwave PlotxY waveleng del frame wavelengths e ZZ TXL e LCAL LCAL CAL CA CT E L CC TO CL TL E 7 ULLA LCAL CA CA L LE E LUUL e detector module flux line Style NONE titleText Slice t str slice subtitleText Ye Sk TR HS Activate all masks for all slices SlicedFrames activateMasks slicedFrames slicedFrames get 0 getMaskTypes Derive detectors response from calib
13. ITION raw B E Wavelength Lu m E H CALSOURCE 0 None 1 CS1 2 CS2 mmm NOD A BAND 0 UNDEFPF 1 R1 2 B2B 3 B2A 4 B3A page 40 nhsc ipac caltech edu helpdesk Wavelength PACS 301 nhise Chop differentiation The data are only on the ON position OFF being subtracted Slice 0 Detector 8 Module 12 Signal arb A i bo o h a oo o HM b Eo 0 6 63 19 63 20 63 21 63 22 63 23 63 24 63 25 63 26 Wavelength u m page 41 nhsc ipac caltech edu helpdesk PACS 301 NASA Herschel Science Center Apply RSRF 453 Used ca tiles rsrfR1 rsrfB2A rsrfB2B r rsrrB7 454 slicedFrames rsrfCal slicedFrames cal Pree calTreey 455 a from specDiffCs csResponseAndDark 458 6licedFrames specRespCal slicedFrames csResponseAndDark csResponseAndDark EES Wed EEN if verbose slicedSummary slicedCube s Convert data from frames to cube page 42 nhsc ipac caltech edu helpdesk PACS 301 Apply Flat field This is a more involved process involving several tasks from the Level 1 2 pipeline which are used here for quickly identify where a bright line is and remove it for the purpose of the flat field processing We will not describe in detail all the tasks here since you will learn more about then in the next tutorial PACS 302 If you have a bright line in your dataset you can pretty much just run this section with the defaults prov
14. SA Herschel Science Check footprint PACS WE alag esight positions 69 47 00 69 46 00 69 45 00 wein ree 69 43 00 69 42 00 69 4 1 00 Dec 69 40 00 69 39 00 69 38 00 69 36 00 69 35 00 69 34 00 LL E 2 09 56 30 09 56 20 09 56 10 09 56 00 09 55 50 09 55 4 09 55 30 09 55 20 i RA Aon Herschel boresight page 26 nhsc ipac caltech edu helpdesk PACS 301 her Masks and wav calibration ChopNodEx RSION py X 228 Add the wavelength for each pixel Wave dataset used cal file WavePolynomes a 229 slicedFrames waveCalc slicedFrames calTree calTree 230 231 Correct the wavelength for the spacecraft velocity 232 Uses the pointing orbitEphemeris and timeCorrelation product 233 slicedFrames specCorrectHerschelVelocity slicedFrames obs auxiliary orbitEphemeris obs auxiliar 234 235 Find the major logical blocks of this observation and organise them in the 236 Blocklable attached to the Frames used cal file ObcpDescription 237 slicedFrames findBlocks slicedFrames calTree calTree 238 239 Flag the known bad or noisy pixels in the masks BADPIXELS and NOISYPIXELS 240 used cal files BadPixelMask and NoisyPixelMask 241 gt by default the bad pixels will be excluded later when final cubes are built the noisy pixel 242 slicedFrames specFlagBadPixelsFrames slicedFrames calTree calTree 243 244 Flag the data a
15. Science ae Center Step 2 Load in the correct script for processing your data page nhsc ipac caltech edu helpdesk PACS 301 In this example we assume you are not using your own Center Specialist script Here we take the script from the pipeline pulldown menu NASA Herschel Science File Edit R Ti eo 4 Pipelines Wim dow Tools Help ZS Photometer_ Spectrometer Chopped line scan amp short range scan LSC P Chopped large range scan SED Unchopped line scan amp short range s aE Golt On O From the Pipeline Menu select Unchopped range scan Wavelength switching 7 get savobs_prep py E PACS Spectrometer Chopped line scan amp short range scan lineScan Note that there are several options in the Chop Nod mode HSC Pipeline are the scripts used by the HSC pipeline and are intended to be non interactive Split ON OFF allows the user to make separate ON and OFF maps and SHOULD NOT BE USED FOR DATA ANALYSIS Its purpose is to allow the user to inspect the chop off positions for contamination by a source if suspected Background Normalization is an alternative way to calibrate your data using the telescope background from the chop off observation to calibrate these data The standard scrip uses the calibration block This alternative method is only recommended when the observer is interested in measuring accurately a faint continuum level for example if you have a faint absorption line
16. absorption lines will not be treated correctly PACS 301 NASA Herschel Science Center Lets assume that all is well and a line is bright and identified correctly in each slice we will explain the alternative in a moment Next look again at the spectra produced Is there a significant spectral slope to the continuum If so then accept the default for slopelnContinuum 1 True If not you might consider setting to O false but it will still work with 1 Then apply the flatfield correction The rest is just clean up afterwards 3 Actual spectral flatfielding slopeInContinuum is a boolean St it to true for lines existing on a continuum SZ with a significant spectral slope For more information print specFlatFieldLine doe or consult the help SlopeInContinuum 1 rcedcubes slicedSpecFlatFieldLine slicedCubesMask scaling l1 copy l maxrange 50 230 slopeInCon i 4 Rename mask OUTLIERS to OUTLIER specFlagoOutiiers would refuse to overwrite OUTLIERS amp deactivate 1 slicedCubes renameMask OUTLIERS OUTLIERS 1 slicedCubes deactivateMasks slicedCubes Stringld INLINE OUTLIERS 1 if verbose maskSummary slicedCubes slice 0 5 Remove intermediate results del waveGrid slicedRebinnedCubes slicedCubesMask End of Spectral Flat Fielding if verbose maskSummary slicedCubes slice 0 page 45 nhsc ipac caltech edu helpdesk PACS 301 NASA Herschel Science Center What i
17. bes activateMasks slicedCubes Stringld GLITCH UNCLEANCHOP NOISYPIXELS RAWSATURATION 92 slicedRebinnedCubes specWaveRebin slicedCubes waveGrid 94 2 Mask the spectral lines 95 First the spectral lines are automatically detected in every slice widthDetect expressed in FWHM and threshold expressed in local RMS of the continuum are used to detect the spectral lines in contrast with the local continuum SZ widthMask expressed in FWHM is used to mask the relevant wavelength ranges d For more information print maskLines doc Or consult the help JO It is recommended to work with verbose True and carefully inspect the plots J1 for what is accepted as a spectral line J2 If necessary tune the parameters and relaunch slicedMaskLines 3 Via the parameter lineList it is possible to skip the automatic detection 14 of lines and instead force the list of lines to be masked 15 e This is necessary e g for absorption lines 5 widthDetect 2 5 J7 threshold 10 8 slicedCubesMask _slicedMaskLines slicedCubes slicedRebinnedCubes lineList TI widthDetect widthDetect ENEE DPS ee ee os Gem 8 emp mg mp P fr yaa SATU SATU NASA Her Center schel Science 2 Mask the spectral lines First the spectral lines are automatically detected in every slice widthDetect expressed in FWHM and threshold expressed in local RMS of the continuum are used to d
18. ctrometer interactive chopped Line and Range Spect pipeline processing from level 0 to level 2 for pscopy observations WARNING Do not edit this file This 1 the reference copy for your current c Outline x from herschel pacs SlicedFrames from herschel pacs signal context import from herschel pacs spg common port from herschel pacs spg spec import from herschel pacs cal import from herschel ia numeric impor HIPE gt from herschel ia jconsole import HIPE gt obsids 1342186797 HIPE gt login_usr hcss ia pal pool Jhsa haio login_usr HIPE gt Login pwd hcss ia pal pool shsa haio login_pwd HIPE gt Configuration setProperty logjn_usr jsmith01 HIPE gt Configuration setProperty logiin_pwd k ngfish pooldir Configuration getPropPrty hcss ia pal pool lstore dir print pooldir ChopNodinteractive py CS Jython Interpreter 100 351 of 7496 M I e The file you have selected should be named in the script page 9 nhsc ipac caltech edu helpdesk PACS 301 nhse NASA Herschel Science Ces Center Step 3 Execute the first few lines of the script to load up your observational context obs from a pool Unlike previous versions the script now includes steps which will load obs from a pre existing pool NOTE If you prefer you can skip these first few lines and read obs into your session using PACS tutorial PACS 2
19. etect the spectral lines in contrast with the local continuum widthMask expressed in FWHM is used to mask the relevant wavelength ranges For more information print maskLines doe or consult the help It is recommended to work with verbose True and carefully inspect the plots for what is accepted as a spectral line If necessary tune the parameters and relaunch slicedMaskLines SZ Via the parameter lineList it is possible to skip the automatic detection of lines and instead force the list of lines to be masked This is necessary e g for absorption lines widthDetect threshold slicedCubesMask slicedMaskLines slicedCubes slicedRebinnedCubes lineList widthDetect widthDetect widthMask 2 5 threshold threshold copy l1 verbose verbose maskType INLINE page 44 y axis 500 460 440 420 400 380 360 2 5 10 0 OO Herschel PlotXY 900 57 25 57 63 05 63 10 63 15 63 63 25 63 30 Dot means the algorithm found a line peak 63 35 63 40 nhsc ipac caltech edu helpdesk For each slice you will get a plot of the spectrum and the black dot indicates that the software has detected a line at that point It will then mask out an area of the spectrum around that point of widthdetect FWHM and use whats left to form the flat field If the black dot has not found a peak or its in the wrong place then you should consider treating the spectrum as a non detection Also
20. f you have 1 No obvious line or a very weak one not well identified 2 A known absorption line In this case you circumvent the automatic line identification by simply specifying the central wavelength of the expected line in the lineList parameter to the call See Section 3 3 of the Pacs Data Reduction Guide accessed through the help in HIPE wv V LA LZ C Yat CUG L CL L LZ CJ L ei L P Lt Lo E M LAL L ijt ost weg LZ CZ GAUL GULMIGA LLU UCG L CZ Ka LLULL of lines and instead force the list of lines to be masked This is necessary e g for absorption lines idthDetect 2 5 threshold sSlicedCubesMask slicedMaskLines slicedCubes slicedRebinnedCubes lineList 63 24 widt idthMask 2 5 threshold threshold copy 1 verbose verbose maskType INLINE By adding a line or list of lines e g 63 24 70 23 as parameter the pipeline will automatically ignore the automatic line ID and will mask around the line position you have given It will then proceed as normal through the rest of the pipeline page 46 nhsc ipac caltech edu helpdesk PACS 301 NASA Herschel Science Genter Congratulations You have reached Level 1 You may now proceed to web tutorial PACS 302 page 4 nhsc ipac caltech edu helpdesk PACS 301
21. ffected by the chopper movement in the mask UNCLEANCHOP 245 Uses the high resolution Dec Mec header and the cal files ChopperAngle and ChopperJitterThreshold 246 slicedFrames flagChopMoveFrames slicedFrames dmcHead slicedDmcHead calTree calT ree 247 248 Flag the data effected by the grating movement in the mask GRATMOVE 249 Uses the high resolution Dec Mec header and the cal file GratingJitterThreshold 250 slicedFrames flagGratMoveFrames slicedFrames dmcHead slicedDmcHead calTree calT ree Sal 252 if verbose 253 Summary of the slices 254 hgyr6 45454te sLicedSummary slicedFrames SE Summary of the active 1 and inactive 0 status of every Mask 256 maskSummary sLicedFrames Paik Plot the instrument movements without the signal included 258 pl slicedSummaryPLot slicedFrames signal 0 di d page 2 nhsc ipac caltech edu helpdesk PACS 301 her NASA Herschel Science T Center Only 1 slice page 28 Check before slicing El console x AIPE gt if verbose DEER Summary of the slices ches SlLicedSummary slicedFrames owes Summary of the active 1 and inactive 0 status of every Mask x maskSummary slicedFrames Plot the instrument movements without the signal included slicedSummaryPlot slicedFrames signal 0 noSlices noCalSlick noScienceShices 0 Slice isScience nodPosition nodCycle rasterId lineld band dimensions waveLengths 0 false KERGER S 0
22. ge pointStep raoff redshiftType redshiftValue refSelected repeatLine source throw userNODcycles widthUnit subType compVersion algoNumber algorithm a a compNumber compMode dxid datasets history None S l m l I a r refs auxiliary calibration level0 level0 5 levell level2 logObsContext quality qualitySummary HIPE gt to one shown here page 14 nhsc ipac caltech edu helpdesk PACS 301 her NASA Herschel Science HAG HIPE Users babar apps hcss hcss dp pacs 6 0 149 scripts pacs spg pipeline ipipe phot L05_frames py File Edit Run Pipeline Window Tools Help homes e 97 8 Pr All se Applicable By Category Lei LOS_frames ys d This file is part of Herschel Common Science System HCSS Copyright 2001 2010 Herschel Science Ground Segment Consortium Click on the single green arrow to step through the commands in the script SRCSfile L05 frames py v Z lt do not touch This field is changed by CSS HCSS is free software you can redistribute it and or modify t under the terms of the GNU Lesser General Public License as published by the Free Software Foundation either version 3 of the License or at your option any later version Q D J On UA WN HCSS is distributed in the hope that it will be useful but WITHOUT ANY WARRANTY without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE See the GNU Lesser General Public License for more details
23. ided If you suspect that your line is faint we will explain how to turn off the automatic line identification process If you are unsure just run the default pipeline and look carefully at the plots A more extensive discussion of the full flat fielding process is found in Sect 3 3 of the PACS data reduction guide found from the welcome screen of HIPE under documentation ry Aub hh BBR Dh Hh Hh AB A e a d bi ae 6516 019 91 E IR 9 i a First we build a preliminary wavegrid flag outliers and do a quick rebinning of the data The aim of this is to allow any bright lines in each spectral slice to be identified for spectral masking The flat fielding process needs to identify and mask any bright lines in the spectrum before performing the flat field calculations If there are no bright lines there is an option to avoid this process Note also that if your spectrum contains absorption lines this step must also be avoided Note that this preliminary rebinning will be superseded later by the actually rebinning However its your first contact with your binned spectra and is usually an exciting moment ele 1 Flag outliers and rebin gt gt waveGrid wavelengthGrid slicedCubes oversample 2 upsample 3 calTree SR 9 slicedCubes activateMasks slicedCubes Stringld GLITCH UNCLEANCHOP NOISYPIXELS RAWSATURATION 90 slicedCubes specFlagOutliers slicedCubes waveGrid nSigma 5 niter 1 91 slicedCu
24. licingRule NoddingPosition 1 SlicingRule NodCycleNum 1 SlicingRule IsOutOfField 1 302 SlicingRule Band 1 303 slicedFrames pacsSliceContext slicedFrames slicingRules rules removeUndefined 1 The slicing of the data is performed according to rules made explicit in the pipeline In our example two lines are observed in two nodding positions So we expect 4 slices plus an initial slice containing the calibration block page 30 nhsc ipac caltech edu helpdesk PACS 301 hse NASA Herschel Science Center 5 slices Line1 B amp A Line2 B amp A nodes page 31 A e 18 25 1019 E Console x LIVES rules SlicingRule LineId 1 SlicingRule RasterLineNum 1 SlicingRule RasterColumnNum 1 Slici ngRule NoddingPosition 1 SlLicingRule NodCycleNum 1 SlicingRule IsOutOfField 1 Slicing Rule Band Di HIPE gt slicedFrames pacsSliceContext slicedFrames slicingRules rules HIPE gt if verbose cess slLicedSummary slicedFrames slicedSummaryPlot slicedFrames signal 0 b 1 i ices 4 Slice isScience nodPosition nodCycle rasterId lineld band dimensions wavelengths 0 false Bd De eg 0 00 0 1 B2B B34 UNDEF 18 25 1460 57 213 88 119 B 1 00 2 B3A 63 093 63379 A 1 00 2 B3A 18 25 1019 63 379 3 true B 1 00 3 BSA 18 25 1019 57 213 57 648 A 1 00 3 B3A 548 Slice edges
25. memory Step 2 Setup Script and load data Step 3 Read in data from script optional Step 4 Check Observation Context and set verbose levels etc Step 5 Run the 0 0 5 pipeline Step 6 Run the 0 5 1 pipeline page 4 nhsc ipac caltech edu helpdesk PACS 301 nhse NASA Herschel Science Genter Step 1 Check that you are running the appropriate version of HIPE for this Tutorial and check the memory page 9 nhsc ipac caltech edu helpdesk PACS 301 GUUS How To DETERMINE YOUR BUILD NUMBER AND i HOW MUCH MEMORY IS ALLOCATED Always allocate less than the RAM capacity of your machine this example is an 8GByte Laptop so allocated 7 5GBtyes okolo HIPE Users apple scrig File Edit Run Pipeline Window Tools a gt SELECT ABOUT FROM DROP DOWN HELP PG E gt H w off E d User areas ip KI 8 Home Fold 2 This file is part of Hersc P File System o Copyright 2001 2010 Hersc 5 ROSS is free software yo 6 LL under the terms of the 7 published by the Free Soft HIPE the License or at your 8 4 gt Herschel Interactive Processing Environment R LS Console x ai E eer Developer build from CIB HIPE gt No outli formatic Build number 8 0 3271 ilable AN OK eC eg oF 7496 mg o gt Memory used and available Allocate in File gt Preferences gt general gt Start up and Shut Down restart HIPE page 6 nhsc ipac caltech edu helpdes PP 301 ner NASA Herschel
26. oC oC st d CHE BL f Ba if verbose maskSummary slicedFrames slice 0 JE 03 Detect and flag glitches GLITCH mask 504 slicedFrames specFlagGlitchFramesQTest slicedFrames 505 BAG B07 if verbose SD SlicedSummary slicedFrames Bag Summary plot including the signal p10 p3 slicedSummaryPLlot slicedFrames signal 1 B11 Plot of signal vs wavelength for the central pixel for a single slice YOU can chose any B12 Detector signal you will see the on and off chop spectral data together B13 on this plot as they have not been subtracted from each other yet 514 compare this plot to p6 below B15 Slice 1 B16 p4 plotSignalBasic slicedFrames slice slice p17 Inspect timeline of signals and masked signals via a viewer B18 MaskViewer sLicedFrames get slice R10 E At this point a deglitching code creates a glitch mask Sometimes this deglitching can be too aggressive It is therefore possible to ignore this mask and detect outliers using data redundancy see tutorial level 1 gt level 2 page 35 nhsc ipac caltech edu helpdesk PACS 301 nhse Glitch detection You can check manually the points flagged as glitch or masked for other reasons using the maskviewer Select a pixel by clicking on it Select a mask Select a frame time index Cu rre nt fra me Row 8 Column 12 LEE E E SESA ER ER E ER SEA ER ESEA E E ER SESA SES E ER E ER EE ER E ER ER E E E E
27. ration block used cal files observedResponse calSourceFlux calBlock selectSlice dF rames aei eal Gal csResponseAndDa specDiffCs calBlock calTree T Use the calibration block to calculate an observation specific responsivity and dark current map for your observations This will be applied later Note this is a change from HIPE 7 and earlier where a ground based value was used The new corrections lead to better absolute calibration page 38 nhsc ipac caltech edu helpdesk PACS 301 nhse Chop differentiation ChopNodEx RSION py A 348 a 349 Compute the differential signal of each on off pair of datapoints for each chopper cycle 350 The calibration block is cut out of the slicedFrames so only the scientific slices remain 351 slicedFrames specDiffChop slicedFrames scical sci keepall False normalize False JR 353 if verbose 354 Data Structure Only science blocks are left 355 SLicedSummary slicedFrames 356 p5 slicedSummaryPLot slicedFrames signal 0 KLE Detector signal signal is now differential with the offs having Deen 358 subtracted from the ons compare to p4 above 359 p6 plotSignalBasic slicedFrames slice 0 After chop differentiation the calibration block is excluded from the data page 39 nhsc ipac caltech edu helpdesk PACS 301 nhse Chop differentiation GRAT POS 500 U 500 1000 1500 2000 2500 3000 3500 4000 Reset Number E E CRATING POS
28. schel Science D 8 L t fnome i adds Zi Cs ST ek Ai Eee 3282 SCr we ZER Dis L d MISE Spec cno i X File Edit Run Pipelines Window Tools Help Editor x Finally we set the calibration tree Unchog d 18 calTree getCalTree obs obs EE Read the time stamp of our 185 print calTree common ei print calTree spectrometer L obs and apply the o Gene calibration from the used distribution console x Show an overview of the uplink parameters of this observation o a i e the settings during your observation PACS Calibration Tree Model EM Scape version Branches amon porters t x H nsctrometer PacsCalCommon Calibration Products chopperAngle FM 3 chopperAngleRedundant FM 3 rem chopperJLitterThreshold FM chopperSkyAngLle FM csReslstanceTemerature FM filterwheel Gand FM obcpDescription FM siam FM timedep FM Version 32 and later ones consider the calibration block and include improved flat WD ENQ on PacsCalSpec Calibration Products absoluteCapacitance FM arraylnstrument Z P badPa velas k FM cal SourceFlux FM ane aL e C H Vin C E E lython Interpreter line 187 100 372 of 6567 MB T page 18 nhsc ipac caltech edu helpdesk PACS 301 NASA Herschel Science M H page 19 Now print a summary of your data This command will print out a lot of useful information about your obser
29. vation Note that since you have already set the camera to either red or blue then only the scans observed in that band are shown If you made a mistake and meant to analyze data from the other band then now is the time to go back and start over with the correct camera selected The command assumes verbose 1 if verbose obsSummary obs Note that you can just type obsSummary obs in the console window at any time in your session to get the summary nhsc ipac caltech edu helpdesk PACS 301 Ia NASA Herschel Science Genter Step 5 Run the 0 gt 0 5 pipeline Basic calibration pointing wavelength calibration slicing page 20 nhsc ipac caltech edu helpdesk PACS 301 nhse a Level 0 gt 0 5 R PACS data Wavelength Data flagging Permanently Bad pixels When grating or chopper moving Saturated data Open and dummy channels Assign RA Level 0 5 Grating to Dec to pixels Sliced Frames wavelength DNs to Volts s conversion 16 x 25 x ramps Assign observing block labels e g Nod positions grating scan direction calibration block scan mode page 21 nhsc ipac caltech edu helpdesk PACS 301 nhse Bech Extractin 8 level 0 data ChopNodEx RSION py X 164 eg 165 166 Extract the level products from the ObservationContext DBZ Get and prepare the Level product that you will pipeline on
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