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INTEGRAL Science Data Centre JEM-X Analysis User Manual

1. JMXi FLUX_1 column is used 2 JMXi FLUX_2 column is used default 0 CATI fluxMin string Low limit for flux selection default gt CAT _LfluxMax string High limit for flux selection default CAT L class string Object class of sources to select default CAT _I_date real IJD for the public data possible values lt 0 all public 0 all private gt 0 according to DAY ID default 1 8 5 jimage bin This script creates shadowgrams in several user defined energy bands calling the j_ima_shadowgram exe cutable once for each band Standard coordinates retain the original detector square grid The shadowgrams are made in a normal coor dinate system when the hidden parameter BIN_I_shdType is equal to 3 The imaging component j_ima_iros requires BIN_I_shdType to be 2 the default value in OSA 5 0 In that case the shadowgram is given with raw event positions i e no on ground correction has been applied Parameters specific to the BIN_I level are given in Table 14 ISDC JEM X Analysis User Manual Issue 10 0 53 8 5 1 ma_shadowgram This executable reads the events from the imaging formats FULL or REST and sorts them according to their position into a 2D histogram the shadowgram The grey filter G and dead time D combined correction factor is evaluated at this step and brought as keyword in the FITS representation of the shadowgram TE
2. 1 Number of phase bins N lt 0 abs N equally spaced bins default 0 Phase bin sizes separated by space e g 0 1 0 2 0 3 default gt 8 10 2 _bin_rate_lc Creates full detector light curve from RATE data Table 22 j_bin_rate_lc parameters specific to the BIN_T level ISDC JEM X Analysis User Manual Issue 10 0 63 Name Name Type Description main script executable LCR timeStep timeStep real Binning time for lightcurve sec default 10 timeStart timeStart real Time in IJD of start of first time bin lt 0 use SWG start default 1 timeStop timeStop real Time in IJD of end of last time bin lt 0 use SWG end default 1 nPhaseBins nPhaseBins integer Number of phase bins N lt 0 abs N equally spaced bins default 0 phaseBins phaseBins string Phase bin sizes separated by space e g 0 1 0 2 0 3 default gt 8 10 3 _bin_bkg_lc Rebin background model data to background lightcurves None of the parameters of j_bin_bkg_lc are included into the main script The behavior of this program is defined by the outputs of j_bin_evts_lc and j_bin_rate_lc 8 11 Observation group level analysis 8 11 1 jima mosaic This executable combines input sky maps produced by j ima_iros to make JEM X mosaic images in a single FITS file named by default jmxi_mosa_ima fits comprising each energy band found in th
3. IMA_userImagesOut boolean Do you want the user defined images to be written default n IMA_pixelFold integer Type of pixelfold O none 1 NL 2 NJW 3 NL 1 D default 1 IMA_useTrace boolean Flag for tracing function calls default no IMA tracestring string Control string for use of trace default 0123456789ABCDEF 8 6 1 j ma_tros The j_ima_iros software package has been developed to provide two main outputs e sky images and corresponding variance maps derived from JEM X shadowgrams e alist of source candidates extracted from the sky images by an Iterative Removal Of Sources IROS algorithm j ima iros processes data shadowgrams from one science window at a time Combining the sky images or the source candidate lists must be done by subsequent software packages j_ima_iros can analyze a maximum of 15 shadowgrams f i 15 separate energy bands from one science window For an initial survey of the observed sources it is best to divide the data into a limited number of energy bands e g four bands j_ima_iros generates its sky images by a simple backprojection algorithm The necessary information for this step is to see if the path from the detector pixel to the sky pixel is free or blocked by e g collimator or mask Since the geometry of the JEM X detector with its collimator is complex the raytracing from shadowgram pixels to sky image pixels is quite time consuming Therefo
4. The correlation gain between the PHA and PI channels varies both in time due to temperature pressure and voltage fluctuations and across the surface of the detector The major part of the spatial gain variation arises from the construction of the microstrip plate and the uniformity of the various strips This variation is stored as percent differences in line ADC positions in data structure JMXi SPAG MOD Table B These values have been determined by pre flight calibrations However there are secondary corrections to these tables determined by in flight monitoring to correct for dead and unstable anode strips This Data Structure contains two 2D arrays along X and Y axes with fractional change for each pixel determined by pre flight calibration in the first slice and secondary corrections determined since launch in the second slice The list of the energy boundaries of the PI channels can be found in JEMXi BDS MOD Data Structure Tables 33 38 Some more details can be also found in Section 3 2 2 In rebinning our events and spectra from PHA channels to PI channels we can expect to introduce some inaccuracy into the energy measurements However the PI channels are carefully chosen to reflect the inherent energy resolution of the detector so this added error is small compared to the detector energy resolution Table 38 Content of JEMXi BDS MOD Data Structures Column Name Description CHANNEL Channel number E_MIN Minimum energ
5. Three upper channel boundaries for shadowgrams for source de tection default 95 134 178 Parameters specific to imaging IMA IMA_makeNewBPL IMA newBackProjFile IMA_detAccLimit IMA_skyImageDim IMA_useDeadAnodes IMA_maxNumSources IMA edgeEnhanceF actor IMA_loopLimitPeak IMA _detSigSingle IMA skyRadiusFactor IMA radiusLimitO IMA_radiusLimitl IMA radiusLimit2 boolean string integer integer boolean integer real real real Do you want to create a new backprojection file default no Base name of new backprojection file default Acceptance limit in JMXi DETE MOD data structure Possible values 1 65535 default 16384 Sky image dimension Possible values 1 255 2 511 default 2 Do you want to include dead anodes areas default no Max number of sources in IROS loop default 10 Edge enhancement factor It is used to convert the sky images to significance maps by amplifying the peaks near the edge relative to those near the center default 1 0 Fractional peak power to stop IROS loop default 0 025 Detection significance for source acceptance default 12 0 Sky radius limit factor default 1 0 Detector radius limit E lt 6 keV mm default 120 0 Detector radius limit 6 lt E lt 12 keV mm default 120 0 Detector radius limit 12 lt E lt 20 keV mm default 1107 0 ISDC JEM X Analysis Use
6. e e 44 Content of JMXi DEAD SCP Data Structure o e e o 45 Content of JMXi SCAL BKG and JMXi SCAL DBG Data Structures 46 Content of JMXi EVTS SEDSTDX n i k e e a e sees ae a 47 Content of JMXi SRCL RES Data Structure e e o 48 Content of JMXi SRCL BSP Data Structure lt e o s o e e 49 Content of JMXi SRCL SPE Data Structure os s ao oo coc awe e 50 Content of JMXi SRCL ARF Data Structure e o 51 Content of JMXi SRC LCR Data Structure lt s ss secde o 52 Content of JMXi FULL DSP JMXi REST DSP and JMXi SPTI DSP Data Structures 53 List of the j_bin_bkg_spectra output Data Structures 54 Content of JMXi DETE LCR IDX Data Structure 55 Content of JMXi DETE LCR Data Structure gt gt so ca ceeded ia roia 56 Content of JMXi DETE FLC IDX Data Structure 57 Content of JMXi DETE FLC IDX Data Structure 58 Content of JMXi MOSA IMA IDK coccion eee e ad 59 Content of JMXi OBS RES Data Structure gt s sss sa s awaa a 60 jema_science_analysis parameters description oso o e 00000 ISDC JEM X Analysis User Manual Issue 10 0 Acronyms and Abbreviations ADC CR DFEE DPE DSRI DXB FRSS FCFOV FOV FULL GTI IC IJD ISOC ISDC ISSW JEM X HURA IROS ISDC JEM X Analysis User Manual Issue 10 0 An
7. n Flag for saving folded image default n Flag for saving array of amplitudes default n Flag for saving array of chi squares default n Prepares for ISDC JEM X Analysis User Manual Issue 10 0 68 saves saveR chatter boolean boolean integer Flag for saving array of significance default n Flag for saving array of local RMS values The save parameters above should only be set to yes is you are working on a single image default n Level of chattiness default 3 ISDC JEM X Analysis User Manual Issue 10 0 69 9 Known Issues and Limitations 1 The JEM X lightcurves are deadtime corrected DEADC in the lightcurve files are set to 1 0 for XRONOS compatibility 2 Due to changes of the on board configuration the detection efficiency has changed significantly several times during the mission history In particular for pointings between revolutions 26 to 45 this means that the measured fluxes of stable sources in particular at low energy will strongly depend on the time when the data was taken These changes are not corrected for in flux units counts cm s in the given energy interval but taken into account in spectral responses 3 The JEM X detector gain varies significantly for a few hours after the instrument has been switched on This mostly affects the beginning of each revolution but can also happen if the
8. ogid equal to GROUP2 WORKING DIR has to be the extensive name of REP_BASE_PROD WARNING make sure that the lightcurve and spectra result files exist for each Science Window you want to co add jmx2_src_lc fits and jmx2 srcl_spe fits files Then give the command that actually builds the fits file from the ASCII file cd REP_BASE_PROD obs txt2idx element dols txt index index_comb_2 fits Then run Ic_pick and spe_pick putting the parameter group equal to index_comb _2 fits cd REP_BASE_PROD obs lc_pick source J180108 2 250445 attach n group index_comb_2 fits 1 1c GX5 1 1c fits emin 3 04 emax 10 08 instrument JMX2 GX5 1 1c fits contains the merged lightcurve of GX 5 1 source ID J180108 2 250445 as can be seen e g in the ISDC reference catalog in the 3 04 10 08 keV band energy range that of course has to exist in the jmx2_src_lc fits original files Using lc_pick without specifying the energy range will produce an output file with multiple extensions one per available energy range cd REP_BASE_PROD obs spe_pick group index_comb_2 fits source GX 5 1 rootname GX5 1 instrument JMX2 GX5 1 sum pha fits the combined spectrum of GX 5 1 and GX5 1 single pha2 fits a file with the four spectra of the initial four Science Windows collected together are created spe_pick also creates an ARF appropriate for your particular dataset This ARF is written to GX5 1_sum_arf fits and GX5 1_sin
9. ISGR_FLUX_2 ISGRI flux in the hard ISGRI energy band PICS_FLUX_1 PICsIT flux in the soft PICsIT energy band PICS_FLUX_2 PICsIT flux in the hard PICsIT energy band JEMX_FLUX_1 JEMX flux in the soft JEMX energy band JEMX_FLUX_2 JEMX flux in the hard JEMX energy band E_MIN Lower energy boundaries E_MAX Upper energy boundaries FLUX Flux values FLUX_ERR Flux errors SEL_FLAG Source selection flag DETSIG Source detection significance in JEM X FLAG Generic flag COSX_JMX Direction cosine between X axis and source in instrument coor dinates COSY _JMX Direction cosine between Y axis and source in instrument coor dinates COSZ_JMX Direction cosine between Z axis and source in instrument coordi nates q_identify_sres q identify_src updates the columns in JMXi SRCL RES with source name and identifier C 7 j_src_extract_spectra This script derives JEM X countrate spectra for all sources found in the current Science Window Output is in three data structures JMXi SRCL BSP contains the background spectra at each source location which have been used to correct the source spectrum itself Background spectra are stored in PHA II format JMXi SRCL SPE contains the spectra for each individual found source Spectra are stored in PHA II format JMXi SRCL ARF contains ancillary response for each source The ARFs are stored in the ARF II format The ARF is scaled to the total detector area to correspond to the stored spectra
10. Rr JEM X Analysis User Manual ISDC LO Se September 2012 10 0 ISDC OSA UM JEMX INTEGRAL Science Data Centre JEM X ANALYSIS USER MANUAL Reference ISDC OSA UM JEMX Issue 10 0 Date September 2012 INTEGRAL Science Data Centre Chemin d cogia 16 CH 1290 Versoix Switzerland http isdc unige ch Authors and Approvals ad ISDC JEM X Analysis User Manual LAN September 2012 10 0 Prepared by M Chernyakova P Kretschmar JEM X team A Neronov V Beckmann L Pavan Agreed by CSFerrnenG tata TETE TER YA gee Pt E AREA atone TARA EOS Approved by Te Diels COUTVOLSI A A HERE Se MEAG Se Was Sh ede Bt ISDC JEM X Analysis User Manual Issue 10 0 Document Status Sheet dl ISDC af e JEM X Analysis User Manual 2 April 2003 1 0 First Release 19 May 2003 1 1 Update of the First Release Section 5 9 Tables 60 14 21 and bibliography were up dated 18 July 2003 2 0 Second Release Sections 5 6 9 8 1 Appendix C and bibliography were updated Section 8 11 was added 8 December 2003 3 0 Third Release Part I and the bibliography were updated Section 6 was rewritten 19 July 2004 4 0 Fourth Release Sections 6 9 and the bibliography were updated 6 December 2004 4 2 Update of Fourth Release Sections 6 8 6 9 Table 41 and the bibliography were up dated 3 June 2005 5 0 Fifth Release Descriptions of j_ ima_iros and j_ima_mosaic are
11. default IJD DOL of a bad time interval table default Input Bad Time Interval names to be considered default BAD_RESPONCE BAD CONFIGURATION Accepted attitude variability arc min default 0 5 DOL of table with parameter limits default Names of instrumental GTIs to be included in merged GTI default Names of spacecraft GTIs to be included in merged GTI default Name of merged GTI to be used in analysis default MERGED Used accuracy for OBT to IJD conversion and vice versa possible values any inaccurate accurate default any y Accepted attitude stability tolerance of Z axis arcmin default 3 0 Parameters specific to Dead Time Calculation DEAD DEAD_outputExists boolean Assume already existing output default n Parameters specific to catalog extraction CAT_I CAT LrefCat string DOL of the Reference Catalog default ISDC_REF_CAT ISDC JEM X Analysis User Manual Issue 10 0 93 CAT_I_usrCat CAT I radiusMin CAT I radiusMax CAT IT fluxDef CAT _I_fluxMin CAT_I_fluxMax CAT_I_class CAT Idate string string string string string string string real DOL of the User Catalog Currently not used default Low limit for the position selection Can be multiple limits with separating blank default 0 2 4
12. ANCRFILE File and row of corresponding ARF EXPOSURE Effective integration time for the spectrum TELAPSE Total elapsed time of the data in seconds ONTIME Sum of good time intervals in seconds DEADC Deadtime correction factor TFIRST Start of the integration time interval in IJD TLAST End of the integration time interval in IJD EVT_TYPE Event type Table 50 Content of JMXi SRCL ARF Data Structure Column Name Description ARF_NUM Reference Number of ARF data in this row ENERG_LO Lower energy boundaries of bins ENERG_HI Upper energy boundaries of bins SPECRESP Effective area in cm of the detector for a given source taking all effects into account C 8 4_ src_extract_Ic This application extracts energy binned light curves for each found point source in the FOV Background subtraction is an integral part of the data extraction The only used executable is j_src_lc ISDC JEM X Analysis User Manual Issue 10 0 86 C 8 1 i src_ic Creates binned lightcurves for each found source in FOV The output data structure JMXi SRC LCR see Table 51 contains a countrate light curve for a given source and a given energy range of the JEM Xi instrument Table 51 Content of JMXi SRC LCR Data Structure Column Name Description TIME Time of measurement for the bin TIMEDEL Integration time for the bin RATE Countrate in the given energy band ERROR Countrate error in the the given energy
13. COR _gainModel string integer DOL of the Index Group with gain variation history This data is stored per revolution and thus not accessible via the IC system default Gain history smoothing model to be applied possible values 1 default Let the algorithm choose between the optimal model to be used O Linear interpolation between gain history values 1 This model is obsolete 2 Exponential gain decay with linear segment immediately after switch Models normal time variation of gain in a revolution 3 Non trigger dependent model 4 Hardware trigger dependency in the smoothing If there is no significant trigger variation during the revolution then the program defaults back to model 3 default 1 ISDC JEM X Analysis User Manual Issue 10 0 92 COR_outputExists COR_randPos boolean boolean Assume already existing output default n Should output positions be randomized within the pixel default n Parameters specific to Good Time Intervals GTI GTI_gtiUser GTI_TimeFormat GTI_BTLDol GTI_BTI_Names GTI_attTolerance GTI limitTable GTL gtiJemxNames GTI gtiScNames GTI_MergedName GTI Accuracy GTL AttStability_Z string string string string real string string string string string real DOL of the input user GTI default Time format to be used possible values IJD UTC OBT
14. Table 28 Content of JMXi REST RAW Data Structure Column Name Description REST_PHA Pulse height of the event DELTA_POS Delta position number of the event RAWX X location of the event calculated by PreProcessing RAWY Y location of the event calculated by PreProcessing Table 29 Content of JMXi RATE RAW Data Structure Column Name Description DELTA_COUNT Delta countrate COUNT R ATE Reconstructed count rate calculated by PreProcessing GREY_FILTER Grey filter for first event in the count rate A 1 3 Spectral Timing mode This format provides the timing and spectral capabilities of FULL IMAGING but no imaging In this case raw data are written to the JMXi SPTI RAW data structure Table 30 Content of JMXi SPTI RAW Data Structure Column Name Description PHA Pulse height of the event DELTA_TIME Delta time to previous event A 1 4 Timing mode This format provides only the timing information of the FULL IMAGING In this case raw data are written to the JMXi TIME RAW data structure Table 31 Content of JMXi TIME RAW Data Structure ISDC JEM X Analysis User Manual Issue 10 0 73 Column Name Description DELTA_TIME Delta time to previous event A 1 5 Spectral mode This format provides limited spectral resolution 64 channels with limited time resolution 1 8 s for the whole detector no imaging In this case raw data are w
15. This data structure is also used as the EBOUNDS extension of the redistri bution matrix file RMF See more details in Section B 3 and Table 38 Lists the nominal energy boundaries of the PI channels for energy measure ments obtained with restricted imaging mode See more details in Section B 3 and Table 38 Lists the nominal energy boundaries of the PI channels for spectra obtained in spectrum mode See more details in Section B 3 and Table 38 Data Structure used for position correction see section B 4 JMXi CORX MOD JMXi CORY MOD JMXi PLLX MOD JMXi PLLY MOD JMXi PSIZ MOD JMXi PRED MOD Contains the corrected X positions in mm from the center of detector for Full and Restricted Imaging event modes from the JEM Xi instrument It is a 2D table with axes along X and Y positions where the raw values are used See more details in Section B 4 The same as JMXi CORX MOD but for Y positions Gives the X value mm of the lower left corner of the pixel Gives the Y value mm of the lower left corner of the pixel Gives size of each pixel cm Is the pixel redistribution description from the raw pixels on a regular pixel grid Data Structures used for Dead Time derivation ISDC JEM X Analysis User Manual Issue 10 0 75 JMXi DEAD MOD Contains the dead time model for the read time for different events for both 8MHz and 16 MHz operation of the on board CPU TRIGGERS lists the event counter I
16. default 0 0 Correct for vignetting Forced to yes Vignetting correction is always applied default y Event type 0O FULL 1 REST 1 both possible values 0 FULL 1 REST 1 both default 1 Speed precision level see more details in Section 8 7 1 possible values 20 the only value presently supported default 20 Flux scaling to area possible values 1 Full area open to the illumination 2 100cm 3 lem default 3 Ignore pixels near dead anodes default y Ignore pixels in hotspot area default n ISDC JEM X Analysis User Manual Issue 10 0 97 LCR_tAccuracy LCR_rowSelect LCR_useRaDec LCR_overrideColl Tilt integer string boolean real Time Correlation accuracy possible values O high 1 low 3 any default 3 CFITSIO selection string on events default Use sky coordinates Ra Dec instead of instrument coordinates default y Value of collimator tilt parameter If lt 0 use Instrument Model Group value default 1 0 Parameters specific to detector spectra binning BIN_S BIN_S_timeStep BIN_S_rowSelectEvts BIN_S_rowSelectSpec BIN_S_evtType real string string integer Binning time s for spectra 0 0 bin all data default 0 0 CFITSIO selection string on events default CFITSIO selection string on spectrum mode data default Data forma
17. ee Left Overall design of JEM X showing the two units with only one of the two coded masks Right functional diagram of one unit the avalanche charge The orthogonal coordinate of an event is obtained from a set of electrodes deposited on the rear surface of the microstrip plate MSP The X ray window of the detector is composed of a thin 250 um beryllium foil which is impermeable to the detector gas but allows a good transmission of low energy X rays see dashed curve in Fig 1 the Be window imposes an absolute lower limit of 3 keV on the energy of X rays coming into the detector and hence it is meaningless to try to push the data analysis below this limit A collimator structure with square shaped cells is placed on top of the detector entrance window It gives support to the window against the internal pressure and at the same time limits and defines the field of view of the detector The collimator is important for reducing the count rate caused by the cosmic diffuse X ray background However the presence of the collimator also means that sources near the edge of the field of view are attenuated with respect to on axis sources see Fig 3 The materials for the collimator molybdenum copper aluminium have been selected in order to minimize the detector background caused by K fluorescence Four radioactive sources are embedded in each detector collimator in order to calibrate the energy response of the JEM X detectors in orbit Fo
18. ln s directory_of_ic_files_installation__ ic ic ln s directory_of_idx_files_installation__ idx idx ln s directory_of_cat_installation__ cat cat ln s directory_of_local_archive__ scw scw ln s directory_of_local_archive__ aux aux lFor installation of the Instrument Characteristics files OSA_IC package and the Reference Catalogues OSA_CAT package follow the instructions given in Installation Guide for the INTEGRAL Data Analysis System 4 ISDC JEM X Analysis User Manual Issue 10 0 16 JEM X calibration files are continuously produced by the JEM X Team for new revolutions To be sure to have all the latest calibrations update your copy of the Instrument Characteristics each time you want to analyse new data using the rsync command rsync Lzrtv isdcarc unige ch arc FTP arc_distr ic_tree prod directory_of_ic_files_installation_ This command will download the Instrument Characteristics files ic and idx directories to your directory_of_ic_files_installation__ Then just create a file jmx lst containing the 2 lines scw 0102 010200210010 001 swg fits 1 scw 0102 010200220010 001 swg fits 1 which is the list of ScWs you want to analyse technically we call them DOLs Data Object Locators i e a specified extension in a given FITS file This file name jmx lst will be used later as an argument for the og_create program see section 6 5 Alternatively if you do not have any of the above dat
19. or a symbolic link to it section 6 1 See more details on barycent tool in the Data Analysis section of 1 7 7 Timing Analysis without the Deconvolution Read this if you are interested in fast variability studies up to milliseconds In the same way as for ISGRI analysis also for JEM X it is possible to do timing analysis in a non binning way i e starting from the single events This way is suitable for very short time scales up to milliseconds and is less recommended for longer time bins for which the the methods described in Sect 6 8 are suitable In the example we will use one of the Science Windows with Crab data you have already downloaded e g 010200210010 ISDC JEM X Analysis User Manual Issue 10 0 44 In general the table with the events can be very big so if you are interested in only part of the Science Window e g in the case of a burst it is better to define a user good time interval see Section 7 and work within it Create with og_create observational group REP_BASE_PROD obs crab og_jemx2 fits and run analysis from COR to DEAD level prepare the catalog with Crab only cd REP_BASE_PROD obs crab ibis_science_analysis startLevel COR endLevel DEAD jemxNum 2 fcopy infile ISDC_REF_CAT NAME Crab outfile crab_cat fits For the next command you will need to specify the Instrument Model file to be used This is a file located in your REP_BASE_PROD ic folder In your IC tree you will found seve
20. stamping of each event is done relative to the previous event The LOBT of the first event in each data packet is given in the JMXi FULL PRW data structure ISDC JEM X Analysis User Manual Issue 10 0 72 Table 27 Content of JMXi FULL RAW Data Structure Column Name Description RAWX X location of the event RAWY Y location of the event PHA Pulse height of the event DELTA_TIME Delta time to previous event A 1 2 Restricted Imaging mode This format provides all imaging capabilities of FULL IMAGING but provides limited spectral resolution 8 channels and timing resolution 1 8 s for the count rates and up to 32 s for images It is may be used when the source is too bright exceeds 120 cts s and the full information can t be transmitted to the Earth In this case raw data with spatial information are written to the JMXi REST RAW data structure and count rates data are written to JMXi RATE RAW see details in Tables 28 29 As we loose the time information during the accumulation time the events in the packets are ranked according the position of the triggered pixel all the pixels have some conventional number in accordance of their position Note that again only the position of the event with the lowest position number is transmitted you can find it in JMKi RATE PRW and for all others in TM only the relative positions are given Pre Processing calculates the absolute position and add it to the data structure
21. version of this document or the introduction of a new section in this case only the title is marked in blue A more general overview on the INTEGRAL Data Analysis can be found in the Introduction to the INTE GRAL Data Analysis 1 For the JEM X analysis scientific validation report see 3 The JEM X Analysis User Manual is divided into two major parts e Description of the Instrument This part based to some extent on the JEM X User Manual 2 introduces the INTEGRAL on board X Ray Monitor JEM X e Description of the Data Analysis This part starts with an overview describing the different steps of the analysis Then in the Cookbook Section several examples of analysis and their results and the description of the parameters are given Finally the used algorithms are described A list of the known limitations of the current release is also provided In the Appendix of this document you find the description of the Raw and Prepared Data and also the description of the Scientific Products ISDC JEM X Analysis User Manual Issue 10 0 1 Part I Instrument Definition 1 Scientific Performance Summary The Joint European Monitor for X rays JEM X on board INTEGRAL fulfills three roles e It provides complementary data at lower energies for the studies of the gamma ray sources observed by the two main instruments IBIS and SPI Flux changes or spectral variability at the lower energies may provide important elemen
22. 212 30 56 30 92 42 2 72 2 80 128 9 92 10 08 213 30 92 31 28 43 2 80 2 88 129 10 08 10 24 214 31 28 31 64 44 2 88 2 96 130 10 24 10 40 215 31 64 32 00 45 2 96 3 04 131 10 40 10 56 216 32 00 32 36 46 3 04 3 12 132 10 56 10 72 217 32 36 32 72 ISDC JEM X Analysis User Manual Issue 10 0 8 47 3 12 3 20 133 10 72 10 88 218 32 72 33 08 48 3 20 3 28 134 10 88 11 04 219 33 08 33 44 49 3 28 3 36 135 11 04 11 20 220 33 44 33 80 50 3 36 3 44 136 11 20 11 36 221 33 80 34 16 51 3 44 3 52 137 11 36 11 52 222 34 16 34 52 52 3 52 3 60 138 11 52 11 68 223 34 52 34 88 53 3 60 3 68 139 11 68 11 84 224 34 88 36 16 54 3 68 3 76 140 11 84 12 00 225 36 16 37 44 55 3 76 3 84 141 12 00 12 16 226 37 44 38 72 56 3 84 3 92 142 12 16 12 32 227 38 72 40 00 57 3 92 4 00 143 12 32 12 48 228 40 00 41 28 58 4 00 4 08 144 12 48 12 64 229 41 28 42 56 59 4 08 4 16 145 12 64 12 80 230 42 56 43 84 60 4 16 4 24 146 12 80 12 96 231 43 84 45 12 61 4 24 4 32 147 12 96 13 12 232 45 12 46 40 62 432 4 40 148 13 12 13 28 233 46 40 47 68 63 4 40 4 48 149 13 28 13 44 234 47 68 48 96 64 4 48 4 56 150 13 44 13 60 235 48 96 50 24
23. 6 3 Instrument Operations 3 1 Telemetry Formats and Data Compression JEM X data can be transmitted in several different telemetry formats which vary in their information content for position energy or time and the required bandwidth per event In addition a grey filter mechanism exists eliminating a fraction of the incoming events in a randomized way The possible transmission settings range from 32 32 to 1 32 of the incoming events These mechanisms allow the instrument to cope with sources of very different brightness despite its limited telemetry allocation For formats with poor time resolution REST SPEC countrate data packets are also transmitted to provide some data for timing analysis However countrate data is not an independent data format For a given observation a primary and a secondary telemetry format are defined and they can be identical If the observed data rate is too high to be transmitted completely first the grey filtering will be increased to reduce the number of processed events Should this not be sufficient the instrument will autonomously switch to the secondary telemetry format continuing to adapt the grey filter as necessary For decreasing input rates the instrument will reduce the filtering and possibly switch back to the primary format All these changes are driven by the filling status of an on board buffer the mechanism includes a certain hysteresis in order to avoid rapid switching between formats
24. 6 E z Z E a P 5 E o o v y 0 4 q 0 4 OZ 3 D 2 0 0 00 0 10 20 30 40 0 10 20 30 4D Energy kev Energy kev Figure 7 S Empty field background spectrum measured with the nominal detector gain of 1500 left compared to the background spectrum with the reduced gain of 500 right After these measurements the rejection criteria have been adjusted 2003 02 25 but no blank fields have been observed for a longer period since then The background has increased with about 10 15 at higher energies and with 20 30 below 10 keV after the adjustment ISDC JEM X Analysis User Manual Issue 10 0 11 4 4 Sensitivity The sensitivity achieved for source detection and flux determination also depends on the performance of the deconvolution software Figure 8 shows the 30 detection limit as a function of observation time The changes in gas gain and corresponding changes in signal patterns led to a large fraction of events being classified as background and rejected on board until new selection criteria could be determined and uploaded 2003 03 25 revolution 45 Even with the new optimized selection criteria the detector sensitivity below 5 keV is reduced Source detection limit 3 10 keV TT TT q AAA A A F 141742 294 80 ra L P of T L Oph Cluster 75 SLX 1735 269 479 gs a L oo Me 30273 80 3 10 O 2 gt Feo IGR J17497 2B21 wd 2 ATE 41709287 30 4 o E e IGP 17254 3257 60 4U 1705
25. DEAD_outputExists n GTI_gtiUser user_gti fits 1 GTI_TimeFormat IJD 7 2 Usage of the predefined Bad Time Intervals Read this to know how to make proper selection of the science windows that should be used in your analysis Different things could happen to the instrument during a particular science window To inform the user on any unusual things that she should be aware of the list of time intervals which had some anomalies bad time intervals has been created and is kept in the latest version of the REP_BASE_PROD ic jmxi lim jmxi_gnrl_bti fits file To download the files the user can follow the instructions given to rsync the entire IC structure as explained in section 6 1 For JEM X the BTI are divided into 2 categories e BAD_RESPONSE indicates a problem related to the response of the instrument most typically linked to rapid gain changes following the re activation of the unit after a long dormant period or after a solar flare e BAD CONFIGURATION indicates cases affected by change of configuration or any other problem For the most conservative data analysis use the following value of the hidden GTLBTI_Names parameter GTI_BTI_Names BAD_CONFIGURATION BAD_RESPONSE This is also the default value In case the user wants to analyse data affected by some BTI the parameter should be modified accordingly see section 8 2 5 For instance to analyze periods affected by a solar flare use GTI_BTI_Names BAD
26. Data Structure Data Structure Contains RAW Contains Contains Corrected event spectral data event spectral OBTs event spectral data Full Imaging JMXi FULL RAW JMXi REST RAW JMXi FULL PRP JMXi REST PRP JMXi FULL COR JMXi REST COR Restricted Imaging REST Count Rate for REST JMXi RATE RAW JMXi RATE PRP JMXi RATE COR Spectral Timing JMXi SPTI RAW JMXi SPTI PRP JMXi SPTI COR Timing JMXi TIME RAW JMXi TIME PRP JMXi TIME COR Spectral JMXi SPEC RAW JMXi SPEC PRP JMXi SPEC COR A l Raw Data For each Raw data structure given in the Table 26 there is a data structure with the same name but ending not with RAW but with PRW These data structures contain package raw data with the information on the telemetry package structure and the position and Local On Board Time LOBT of the first event of the package For the FULL REST Spectral and Spectral Timing modes there are also data structures with names finished with SRW these data structure contains secondary raw data with the information on the grey filter changes and various marker events transmitted in telemetry stream A 1 1 Full Imaging mode This is the main JEM X format used for by far the largest part of the data taking In this mode data have the highest imaging spectral and timing resolution The raw data are written to the JMXi FULL RAW data structure see details in Table 27 Note that in an effort to compress the transmitted information the time
27. High limit for the position selection Can be multiple limits with separating blank default 2 4 5 8 Column used for flux selection default o Low limit for flux selection default High limit for flux selection default Object class of sources to select default IJD for the public data possible values lt 0 all public 0 all private gt 0 according to DAY_ID default 1 Parameters specific to shadowgram binning BIN_I BIN_L evt Type BIN_I_shd Type BIN_I_shdRes BIN_I_rowSelect ISDC JEM X Analysis User Manual Issue 10 0 integer integer string string Event type possible values 0 FULL 1 REST 1 both default 1 Type of shadowgram possible values O skew 1 shadowgram based on corrected event positions 2 shadowgram based on raw event positions required for j ima_iros 3 shadowgram based on regularized detector pixels default 2 DOL of the output shadowgrams default CFITSIO selection string on events Ensures removal of all hotspot events and other seriously bad events default amp amp STATUS lt 256 amp amp 94 BIN_I_gtiNames BIN_I_chanLowDet BIN_I_chanHighDet string string string Names of GTI tables to be used default Three lower channel boundaries for shadowgrams for source de tection default 46 96 135
28. Image ovio aa e a ae ee ae 24 6 6 5 Combining JEMX 1 and JEMX 2 mosaic images 28 6 6 6 Finding Sources in the Mosaic Image o o e 28 6 6 7 Making images in arbitrary energy bands aooo 30 6 7 Source Spectra Extraction s c eoin A aaa eee a ee ed ee 30 6 7 1 Spectral Extraction at SPE level ea a e e a 30 6 7 2 Energy binning definition a sa os e aa oeoc e e a e e 30 6 1 0 Spectral response generation 000 eee eee eee 30 6 7 4 Individual Science Windows Spectra 2 0 eee ee 31 6 7 5 Combining Spectra of different Science Windows 33 6 7 6 Extracting Spectra from a given Position in the Sky 33 6 7 7 Spectral Extraction from Mosaic Images ooa 34 6 8 Source Lightcurve Eztra ti n lt sa sameaa o ee 37 6 8 1 Lightcurve extraction at LCR level 0 o o o 37 6 8 2 Individual Science Windows Lightcurves o o 37 6 8 3 Combining Lightcurves from Different Science Windows 37 6 8 4 Displaying the Results of the Lightcurve Extraction 38 6 8 5 Lightcurve extraction from the IMA step o 39 T Useful recipes for JEM X data analysis ee 39 Tal eerie oe hie ee wake bbe oe Mew eae wea ee eee ee a a 39 7 2 Usage of the predefined Bad Time Intervals o 40 Ta Rerunning the Analysis oo 244
29. The scaling will probably be changed so that it corresponds to the source illuminated area ISDC JEM X Analysis User Manual Issue 10 0 85 Table 48 Content of JMXi SRCL BSP Data Structure Column Name Description SPEC_NUM Reference Number of spectrum in this row ROWID Unique identifier of spectrum CHANNEL Array of channel numbers for the countrates RATE Array of countrates in the defined channels STAT_ERR Array of estimated statistical uncertainty of the countrates SYS_ERR Array of estimated systematical uncertainty of the countrates QUALITY Array of quality flags for the channels EXPOSURE Effective integration time for the spectrum TELAPSE Total elapsed time of the data in seconds ONTIME Sum of good time intervals in seconds DEADC Deadtime correction factor TFIRST Start of the integration time interval in IJD TLAST End of the integration time interval in IJD Table 49 Content of JMXi SRCL SPE Data Structure Column Name Description SPEC_NUM Reference Number of spectrum in this row ROWID Unique identifier CHANNEL Array of channel numbers for the countrates RATE Array of countrates in the defined channels STAT_ERR Array of estimated statistical uncertainty of the countrates SYS_ERR Array of estimated systematical uncertainty of the countrates QUALITY Array of quality flags for the channels BACKFILE File and row of corresponding background spectrum BACKSCAL Background scaling factor
30. and five classes of source matches are found e Good matches The found and catalogue source are the best fit to each other alone relative distance between the match sources is much less than 1 16 Additionally sources found with very high significance see section 6 6 2 in only one band will be added to the basic source set ISDC JEM X Analysis User Manual Issue 10 0 58 3000 2000 1009 Figure 24 DNS 050802 NW 0 006 0 004 0 002 0 000 0 002 0 004 0 006 Pixel value in RAW_RECT cts cm2 s The distribution of pixel values in a RECTIFIED image with only one or two weak sources around the center of the FOV thick histogram A Gaussian fit is shown with the dashed curve and it is evident that the wings of the distribution are wider that the fit e Confused Sources Two found sources are equally good fits to a particular catalogue source within the slackness allowed by distFuzz i e fractional difference in two relative distances that can be considered insignificant when making a match and relDist one of them could be a new source e Multiple Identification One found source can be equally well identified with two or more catalogue sources within the slackness allowed by distFuzz and relDist e New Source A found source that cannot be matched to any catalogue source e Not Found Source A catalogue source that couldn t be matched to any of the found sources In the case of the two ambig
31. band BRATE Background countrate in the given energy band BERROR Background countrate error in the given energy band BARYTIME Barycentric time for the bin C 9 4_bin_spectra This script bins events or Spectral Mode data without deconvolution C 9 1 _bin_evts_spectra This executable generates detector spectra for a single JEM X unit from Full Imaging Restricted Imaging or Spectral Timing events by binning the event data The output data structures are JMXi FULL DSP JMXi REST DSP and JMXi SPTI DSP These data structures are compatible with XSPEC Table 52 Content of JMXi FULL DSP JMXi REST DSP and JMXi SPTI DSP Data Structures Column Name Description SPEC_NUM Reference Number of spectrum in this row ROWID Unique descriptive string for each spectrum CHANNEL Array of channel numbers for the countrates RATE Array of countrates in the defined channels STAT_ERR Array of estimated statistical uncertainty of the countrates SYS_ERR Array of estimated systematical uncertainty of the countrates QUALITY Array of quality flags for the channels BACKFILE File and row of corresponding background spectrum BACKSCAL Background scaling factor EXPOSURE Effective integration time s for the spectrum TSTART Start of the integration time interval in IJD TSTOP End of the integration time interval in IJD C 9 2 4_bin_bkg_spectra This executable generates time resolved spectra for a single JEM X detector by rebinni
32. be set through the outfile parameter It is convenient to create an RMF before the spectral analysis so that one can just pass the rebinned RMF to the analysis scripts In this way the fits files with the spectra will automatically contain a link to the correct RMF 6 7 4 Individual Science Windows Spectra Let us first proceed with the spectral extraction using the source positions found at the IMA step In our example only the Crab was found by the imaging analysis so the spectral analysis will generate only the spectrum of the Crab if you run the script with default values assuming you run j rebin rmf in your REP_BASE_PROD directory cd REP_BASE_PROD obs crab jemx_science_analysis startLevel SPE endLevel SPE jemxNum 2 response REP_BASE_PROD jemx_rebinned_rmf fits The results of the spectral analysis data are in the file scw RRRRPPPPSSSF 001 jmx2_srcl_spe fits Look on the result of the spectral analysis of the Science Window 010200210010 cd scw 010200210010 001 fv jmx2_srcl_spe fits ISDC JEM X Analysis User Manual Issue 10 0 31 In this file you find the spectra for all sources that were found at the IMA level Note that the correspondence between source name and source ID can be found in the file jmx2_srcl_res fits data and folded model data and folded model mx2_srol_spe fitsf1 crob_sum_pha fits 01 Pp AL 4 0 1 F 4 a
33. cece ea hbeaa da waa Bee HHS Ga Ga eae e ES 2 2 The Delator 6 ke e Rh a a eR ESO oA a a 2 3 Coded MESE nec kee ad a SRE a MRR Rae eee a ae ia Es Instrument Operations x o 0662 4 a R 2444 D445 a a ee ee ES deL Telemetry Formats and Data Compression e 3 2 Energy Binning casa N Tee E A ad 3 21 PHA Binning sricu etad dinaa aa RR a ad bs 3 2 2 PP Binning o aces ia piina ma PA A A D Peake bate Performance of the Instrument lt os sco coeg ee os ae ee a a e 4 1 Position Resolution 2622 6 646404 44 44 0a eee ee Pa ee o a 4 2 Energy Resolutiom o au eie oga Be a a Gate Bern ee dB ek eh ad 4 3 MAG a i at ee Se Ee ee ins E hw ee 4 4 DOMSITIVILY 4d aan o a iu II Data Analysis 5 6 Overview 644 2504 05 rra Peed ned ae ee ee bhed bees DOME EE Cookbook for JEM X analysis exceso soii wee ek ek A oe A 6 1 Setting Up the Analysis Data lt ee xe aR ee 6 2 Downloading Your Dala 2 466 24 ssc eb bbw eee Ree Oa DA ee ee 6 3 Setting the SWVITONMERE e K m ta k bera Ee ee ae R Gow a RS 6 4 Useful te howl 228544454 e booed ee abe baa teen R bbd Beda 6 5 A Walk Through the JEM X Analysis o ee ee ee ee 6 6 Examples of Image Creation ee 6 6 1 Results from the Image Step ss sa acca saaara e ee ee 6 6 2 Weak Sources and Sources at the Edge of the FOV ISDC JEM X Analysis User Manual Issue 10 0 iii 6 6 3 PIF cleaning of images around strong Sources 24 6 6 4 The Mosaic
34. detector gain from spectrum 1 RESOL_1 Energy resolution for spectrum 1 PKINT_1 Peak intensity in counts for spectrum 1 PKCHAN_1 ADC channel of line peak for spectrum 1 G_ZERO_2 Zero channel detector gain from spectrum 2 G_CAL_2 First order detector gain from spectrum 2 RESOL_2 Energy resolution for spectrum 2 PKINT_2 Peak intensity in counts for spectrum 2 PKCHAN_2 ADC channel of line peak for spectrum 2 G_ZERO_3 Zero channel detector gain from spectrum 3 G _CAL3 First order detector gain from spectrum 3 RESOL_3 Energy resolution for spectrum 3 PKINT_3 Peak intensity in counts for spectrum 3 PKCHAN_3 ADC channel of line peak for spectrum 3 G_ZERO_4 Zero channel detector gain from spectrum 4 G_CAL 4 First order detector gain from spectrum 4 RESOL 4 Energy resolution for spectrum 4 PKINT_4 Peak intensity in counts for spectrum 4 PKCHAN_4 ADC channel of line peak for spectrum 4 ISDC JEM X Analysis User Manual Issue 10 0 79 Table 37 Content of JMXi GAIN CAL Index Column Name Description RESID_1 Residual counts of calibration spectrum 1 RESID_2 Residual counts of calibration spectrum 2 RESID_3 Residual counts of calibration spectrum 3 RESID_4 Residual counts of calibration spectrum 4 No useful values of the gain parameters can be found if there is a problem processing the calibration spectra This problem only arises when housekeeping packets are missing and is relatively rare Using either linear in
35. different Science Win dows belonging to the same group In that case the file og jmx2 fits points to all the Science Win dows and it is possible to launch the collecting merging tools Ic_pick and spe_pick directly on the group group og_jmx2 fits 1 14Please note that the images that you intend to merge MUST have the same energy boundaries i e all the ScW maps must have been analysed in the same way You cannot merge a 3 10 keV map with a 7 18keV one ISDC JEM X Analysis User Manual Issue 10 0 42 If you have Science Windows belonging to different groups you need an intermediate step Basically you need to create a file an index that points to all the Science Windows you want to co add similarly to the case seen in the previous section Then this file will be given as input via the group parameter at the place of og_jmx2 fits To create the index make a list of the Science Window groups you want to combine and save it as e g dols txt under REP_BASE_PROD obs To ensure a proper work of the software give the full path i e your file should look like WORKING DIR obs GROUP1 scw 011901060010 001 swg jmx2 fits WORKING DIR obs GROUP1 scw 011901070010 001 swg jmx2 fits WORKING DIR obs GROUP2 scw 012000360010 001 swg_jmx2 fits WORKING DIR obs GROUP2 scw 012000370010 001 swg_jmx2 fits The first 2 files belong to a run with the og_create parameter ogid equal to GROUP1 while the latter two to a run with
36. divided by the positions at a reference time and then multiplied by the overall gain of the entire detector at that time determined from the Xe fluorescence lines in blank field observations at the reference time This gives the time corrected gain conversion factor that is used to convert individual event or spectral PHA values to PI values In theory the detector ADC offset GO can be non zero but since an offset factor is already subtracted from the measured energy value by the on board software this value will in practice usually be zero The value of the zero energy ADC channel is determined by the electronic calibration procedure at the beginning of every revolution Currently this corresponds to the value subtracted on board If the zero point ADC value changes an on board patch can be used to return the offset value seen in the telemetry to zero again G is the gain slope or linear calibration parameter See the lower part of figure 26 In practice GO is zero and typical values of G1 are 0 07 KeV per ADC channel for JEM X1 and 0 05 KeV per ADC channel for JEM X2 Table 36 Content of JMXi GAIN CAL IDX Index Column Name Description REVOL Revolution number OBT_ACQ OBT acquisition time in the middle of the integration INT_TIME Effective integration time TSTART Start time of interval covered by this file TSTOP End time of interval covered by this file G_ZERO_1 Zero channel detector gain from spectrum 1 G_CAL_1 First order
37. energy bands see Fig 11 In the file jmx2_srcl_res fits you find a list of all found sources the energy bands and the derived flux values and in the file jmx2_srcl_cat fits the list of the sources in the input catalog You can see that most of the catalog sources were not found as they are too weak When you run the lightcurve and spectra extraction steps the results would be produced for all sources listed in jmx2_srcl_res fits Please note that with OSA10 the count rates are scaled to one cm while until OSA9 the count rates were scaled to one dm There is a nice way to locate the found sources as well as the catalog sources on the sky image To do it use the utility cat2ds9 cat2ds9 jmx2_srcl_res fits 1 found reg symbol box color red cat2ds9 jmx2_srcl_cat fits 1 cat reg symbol circle color white to find out more about this program type cat2ds9 h in the command line With the help of the above two commands the two files found reg and cat reg are created They contain the lists of all the found sources and all the catalog sources respectively Several types of images may be produced the vignetting corrected intensity image called RECONSTRUCTED the variance image VARIANCE RECTIFIED raw intensity image RESIDUAL residuals left after removing all found sources and EXPOSURE the exposure map ISDC JEM X Analysis User Manual Issue 10 0 22 O I fv Summary of jmx2_sky ima fits in unsaved_data neron
38. in flight calibration based on on the Xe 30 Kev fluorescence lines which can be observed over the whole detector Unusual gain fluctuations hidden from the calibration sources e g hidden gain suppression on the plate and rare telemetry procedure changes that can t be dealt with automatically are handled by having the instrument team deliver instrument characteristics gain history tables JMXi GAIN OCL to ISDC These are used automatically by the OSA software instead of the usual gain history tables if one exists for a given revolution All the revolutions after 948 have an IC table because of aging and occasionally eccentric behaviour of the instruments Some revolutions prior to 948 also have IC tables due to odd behaviour Delivery of these files is constantly ongoing and users should always check that they have the latest IC IMOD files before beginning an analysis For a complete overview of the gain calibration of every revolution see http www spacecenter dk oxborrow sdast GAINresults html The j_correction script will automatically fill this parameter with the DOL of an available IC gain history table if one is available for the revolution to which the SCW belongs More details can be found in Section 3 2 and Appendix B 3 j_cor_gain parameters included into the main script are given in Table 7 For the quality of gain corrections of JEM X all users should look at the web page http www spacecenter dk oxborrow sdast GAINresults h
39. in the 3 10 keV energy band obtained in AIToff Hammer projection 6 6 5 Combining JEMX 1 and JEMX 2 mosaic images j_ ima_mosaic can combine JEM X mosaics provided that they have been obtained in the same energy bands for the same sky area and in the same projection As for the simple mosaic image the user may specify the coordinates of the center of the image RAcenter and DECcenter parameters as well as its size and resolution diameter and cdelt parameters when creating the mosaics Any mix however of JEMX 1 and JEMX 2 mosaics is allowed As an example let us create a mosaic image of the Galactic Center region which combines the JEMX 2 mosaic see previous sub section with the JEMX 1 To combine mosaics these must be attached in a group so the first step is to create an empty group dal_create obj_name jemx_mosaics fits template This uses the default template which is a standard group Next we need to attach the mosaics dal_attach jemx_mosaics fits obs1 jmx1_mosa_ima fitsX obs2 jmx1_mosa_ima fits obs3 jmx2_mosa_ima fits The final is necessary to signal to dal_attach that there are no more data structures to attach Up to five data structures can be attached with a single dal_attach commands Additional extensions can be added by issuing another dal_attach command The combination of the mosaic is then very easily performed using the command j_ima_mosaic inObsGrp jemx_mosaics fits outfile combined_mosaic fits mo
40. in the given energy band BARYTIME Barycentric time for the bin C 11 Observation group level analysis C 11 1 jima mosaic This executable creates the mosaic images of all the science windows used in the analysis The output is written to the J MOSAIC_ fits files where the number indicates the energy band In these files you find the mosaic images JMXi MOSA IMA data structures for each kind of IMATYPE mosaic maps However only some of the included keywords are relevant as shown in the following table Table 58 Content of JMXi MOSA IMA IDX Column Name Description IMATYPE NAXIS1 NAXIS2 EXTNAME INSTRUMENT TSTART TSTOP TELAPSE BUNIT CTYPE1 CTYPE2 CRVAL1 CRVAL2 CD1_1 CD2_2 CD1_2 CD2 1 CRPIX1 CRPIX2 E_MIN E_MEAN E MAX IMATYPE Type of image Size of the mosaic image in axis 1 Size of the mosaic image in axis 2 Extension name of the template JEM X instrument JMX1 or JMX2 Start time of the observation IJD End time of the observation IJD Total elapsed time s Pixel units Projection name RA TAN 1962 Projection name DEC TAN 1962 Sky coord ref 1 axis deg Sky coord ref 2 axis deg Transformation deg Transformation deg Transformation deg Transformation deg Sky pixel ref 1 axis pixel Sky pixel ref 2 axis pixel Lower Energy limit keV Mean Energy keV Upper Energy limit keV Type of sky map shown C 11 2
41. instrument was shut down e g for solar flares The pattern is very similar each time and modeled in the gain correction step even in complicated cases Nevertheless it could in principle fail in which case linear interpolation gain correction values would be used which could lead to distorted spectra Users are advised to check this possibility in case of highly unusual source spectra e g by consulting http www spacecenter dk oxborrow sdast GAINresults html 4 If the gain correction step fails then take a look at the gain history table Gain correction failure is often signaled by all corrected events having a non zero STATUS value due to bad gain determination 64 If the gain history for your revolution shows multiple switch on offs this may be confusing j cor_gain Then remove all gain history values up to the switch on off just before your SCW being analyzed For help fitting data in these complicated revolutions contact Dr Carol Anne Oxborrow at oxborrow space dtu dk 5 The source coordinates found by j ima iros may deviate a little from the true positions and this can occasionally cause inaccurate flux reconstructions from j_src_spectra or j_src_lc If a good source position is available it is better to force these coordinates by use of a user catalogue An example is given in the cookbook but see also point 8 below 6 Lightcurves from weak sources may be contaminated by counts from stronger sources in the FOV This happens b
42. is created and you can look at it with fv In the first extension you have 4 rows each row has the link to a given swg_jmx2 fits file What you need to do now is to let the software know that it has to use this particular set of Science Windows for the analysis You do this by pointing og_jmx2 fits to this file This has to be done because no matter what level of the scientific analysis you are performing the software will analyse the Science Windows pointed to by og_jmx2 fits Replace the first row of og_jmx2 fits with cd REP_BASE_PROD obs GROUP1 ftedit og_jmx2 fits MEMBER_LOCATION 1 index_comb fits You may check with fv that actually the first row of og_jmx2 fits is indeed index_comb fits At this point you are ready to launch the analysis and to create a joint mosaic cd REP_BASE_PROD obs GROUP1 jemx_science_analysis ogDOL 0g_jmx2 fits startLevel IMA2 endLevel IMA2 See 6 6 for a description of the main parameters of the mosaic step The above command is valid in case you have just run the ScW analysis part so that you indeed keep the same energy boundaries Otherwise if your parameter file has changed in between you should add in the above the definition of nChanBins chanLow and chanHigh according to the energy boundaries of the single ScW maps you want to merge 7 4 2 Combining spectra and lightcurves from different observation groups In sections 6 7 5 and 6 8 3 you have seen how to merge lightcurves and spectra from
43. l1st ogid crab_usrcat baseDir instrument JMX2 copy the user catalog created as explained above into the observation group cp user_cat fits obs crab_usrcat 12Please note that if your analysis ends with a really weird looking spectrum it can be related to the problem of gain coefficients modelling See section 8 1 1 for a discussion ISDC JEM X Analysis User Manual Issue 10 0 32 and run the analysis till SPE level in this group cd obs crab_usrcat jemx_science_analysis startLevel COR endLevel SPE jemxNum 2 CAT_I_usrCat user_cat fits A nChanBins 4 response REP_BASE_PROD jemx_rebinned_rmf fits The obtained spectra can be analysed with XSPEC as it was done above To convince yourself that the spectral extraction with and without fixing the source position gives slightly different results you can com pare the two spectra REP_BASE_PROD obs crab scw 010200210010 001 jmx2_srcl_spe fits and REP_BASE_PROD obs crab_usrcat scw 010200210010 001 jmx2_srcl_spe fits by entering them simul taneously in XSPEC With this OSA release and until the flux determination algorithm in j_ima_iros is duplicated in a dedicated spectral extraction tool it is not possible anymore to generate several spectra in a single analysis with a given time step The user must define her his own GTIs for the specific time period 6 7 5 Combining Spectra of different Science Windows With the help of the spe_pick program described in the Intro
44. largest possible output mosaic in equatorial coordinates the parameters radiusSelect and di ameter must both be set to 1 A better way available with OSA v 10 0 is to use the Aitoff Hammer projection in galactic coordinates by setting the option AITproj The latter enables the mosaicking of large parts of the sky such as for the Galactic Plane Scans without distortion of the map an example is in Fig 16 This new feature can be activated setting the parameter IMA2_AITproj yes The command should be therefore as follows jemx_science_analysis startLevel IMA2 endLevel IMA2 jemxNum 2 IMA2_AITproj yes The resulting AIToff mosaics are expected to be mapped in the Galactic plane and are therefore oriented in galactic rather than equatorial coordinates To produce a mosaic over the whole sky you will need to decrease the resolution of the image by increasing the pixel size cdelt at least to 0 075 degree The computation in AIToff Hammer projection can take approximately 10 more CPU time and the resulting file can have a rather large dimension for example 1G In this case a simple solution can be to compress the file e g with gzip and to work directly with the compressed file ds9 as well as other HEASOFT tools are able to work directly with the compressed file ISDC JEM X Analysis User Manual Issue 10 0 27 Figure 16 The mosaic image of the Galactic Plane Scan observation of revolution 399
45. maps with default pixel size 1 5 arcmin 12 Part II Data Analysis 5 Overview The scientific analysis performed by the user on the data collected by the three high energy instruments on board INTEGRAL has a lot of commonality despite the various differences in detail In a certain step for example events are corrected for instrumental fingerprints in another one events are binned into detector maps and in yet another step sky images are derived by image deconvolution In order to make this more transparent for scientists working with data from several instruments so called Analysis Levels were identified by the ISDC and designated with unique labels The order of these levels the detailed processing and the details of the outputs may differ across instruments but in general a given level will mean similar tasks and similar outputs for JEM X IBIS and SPI The list of all levels is given in the Introduction to the INTEGRAL Data Analysis 1 For JEM X the following levels have been defined Table 4 Overview of the JEM X Scientific Analysis Levels Tasks Description COR Data Correction GTI Good Time definition and handling DEAD Dead Time derivation CATI Catalogue source selection for Imaging BINI Event binning for Imaging IMA Image reconstruction source flux determination SPE Source spectra and response extraction for XSPEC LCR Source light curves extraction BIN_S Event binning fo
46. one dm this can be set with LCR fluxScaling 2 with OSA10 we decided to scale it to one cm default value LCR fluxScaling 3 As a result for each found source a lightcurve is produced in each energy band The results are written into the file scw RRRRPPPPSSSF 001 jmx2_src_lc fits 6 8 3 Combining Lightcurves from Different Science Windows Similar to the spectral case there is the tool Ic_pick see 1 for details to combine the lightcurves from the single Science Windows lc_pick group 08_jmx2 fits 1 source J053432 0 220052 lc crab_lc fits The resulting file contains two lightcurves one for each energy band One of the obtained lightcurves is shown in Figure 21 It is also possible to sum up lightcurves from different observation groups The method to do this is the same as in the spectral case and is explained in section 7 4 2 ISDC JEM X Analysis User Manual Issue 10 0 37 Bintime 100 0 s dl Hh l H 1 Lh ty Count sec 0 5 L L L 4000 5000 6000 7000 Time s Start Time 12866 15 58 21 925 Stop Time 12866 17 06 41 925 Figure 21 Crab lightcurve first energy band The vignetting by the collimator and mask support structure of JEM X has a more complex structure than originally thought Therefore source fluxes can vary significantly of the order of 10 from one Science Window to the next At off axis angles of 5 degrees this can even reach 30 in bad cases The modeling of vignetting a
47. particular region of the mosaic you can zoom on a given position in the sky running jemx_science_analysis with additional parameters IMA2_RAcenter IMA2_DECcenter and IMA2_diameter which will specify the position of the center and the diameter in degrees of the resulting mosaic image To do so first move the existing images mv jmx2_mosa_ima fits jmx2_mosa_ima_original fits mv jmx2_obs_res fits jmx2_obs_res_original fits Remember that the images have to be also removed from the observation group This can be done by the following command 8 t j 7 3 ISDC JEM X Analysis User Manual Issue 10 0 26 1A SLX 742 1 294 1E 140 7 2942 1744 2898 IGR J17391 3021 GRS 1747 312 GX 354 0 Figure 15 S The mosaic image of the Galactic Center region for revolution 0053 in the 7 11 keV energy band sig nifcance map dal_clean og_jmx2 fits 1 Now re run the analysis script jemx_science_analysis startLevel IMA2 endLevel IMA2 jemxNum 2 IMA2_diameter 5 0 IMA2_RAcenter 266 4 IMA2_DECcenter 29 0 we have chosen to center the image on the Galactic Center position here If you want to produce a mosaic image only for a specific energy band you can pass the minimal and maximal energies of the selected energy band to the jemx_science_analysis through the parameters IMA2_eminSelect and IMA2_emaxSelect Note that the energies have to be the same as defined previously in chanLow and chanHigh To get the
48. sensitivity had been observed in both JEM X units due to the erosion of the microstrip anodes inside the detector By lowering the operating voltage and thereby the gain of the detectors the anode damage rate has now been reduced to a level where the survival time of the detectors seems to be assured for a further five year period Only 6 anodes have been lost on JEM X1 in all of 2006 Another 7 anode strips have been lost on JEM X1 in the first 8 months of 2007 For the complete updated list of dead anodes see http www spacecenter dk oxborrow sdast InstrConfig JC BadAnodes txt 2 2 The Detector Each JEM X detector is a microstrip gas chamber with a sensitive geometric area of 500 cm per unit The gas inside the steel pan shaped detector vessel is a mixture of xenon 90 and methane 10 at 1 5 bar pressure The incoming photons are absorbed in the xenon gas by photo electric absorption and the resulting ionization cloud is then amplified in an avalanche of ionizations by the strong electric field near the microstrip anodes Significant electric charge is picked up on the strip as an electric impulse The position of the electron avalanche in the direction perpendicular to the strip pattern is measured from the centroid of ISDC JEM X Analysis User Manual Issue 10 0 3 B BB B RRR _ H Coded M 3 4m Collimat window Detector Xenon Methane Gas Miemstrip Detector Front End Electronics Electronics Fi 2
49. source areas It operates horizontally and vertically since the systematics are strongest in these directions However adding many images can amplify the effect of an unnoticed source since the distribution of position angles is quite narrow in particular for the sources near the galactic center which is also where the ISDC JEM X Analysis User Manual Issue 10 0 70 11 12 13 14 15 probability to find a source in the depression caused by a neighboring source is highest If a source is situated in such an indentation its peaksize is reduced accordingly whereas there is no change for the source causing the feature This is solely an image feature so j_tma_iros flux determinations are unaltered A count limiting mechanism the grey filter is actived when sources corresponding to more than 0 75 Crab on axis are in the field of view The grey filter is adjusting itself automatically according to the rate of events accepted as X rays and the filling level of the onboard telemetry buffer Ideally a grey filter should randomly reject events However the mechanism implemented is only pseudo random Therefore some care should be taken in interpreting power spectra of arrival times of events from very bright sources with a very significant grey filter as QPO artifacts may show up Normally the automatic grey filter is varying over a science window This fortunately has the effect of averaging out power spectra artifacts
50. src_collect This executable combines source data obtained by the imaging analysis for individual Science Windows into a single table covering an Observation Group It is possible to retrieve only selected results e g just for a given source The result is written to jemxi jmxi_obs _res fits file The description of JMXi OBS RES data structure is given in the Table 59 Table 59 Content of JMXi OBS RES Data Structure Column Name Description SWID Science Window identifier ISDC JEM X Analysis User Manual Issue 10 0 89 SOURCE_ID NAME RA_OBJ DEC_OBJ ERR_RAD DETSIG OFFANGLE EBIN_NUM E_MIN E_MAX FLUX FLUX_ERR DEADC EXPOSURE TSTART TSTOP SEL FLAG FLAG COSX_JMX COSY_JMX COSZ_JMX ISDC unique source identifier One commonly used name for the source Source right ascension in degrees Source declination in degrees Error radius in degrees Source detection significance in JEM X Off axis angle in degrees Number of used elements in E_MIN E MAX FLUX FLUX_ERR Lower energy boundaries Upper energy boundaries Flux values in counts 100cm 71571 Flux errors in counts 100cm 71571 Mean deadtime amp greyfilter correction factor Mean exposure time over the detector plane in seconds Start time of the observation 1JD End time of the observation 1JD Source selection flag Generic flag Direction cosine between X axis and source in instrum coordinates Direction cosine between
51. the main changes 21 December 2006 6 0 Sixth Release Significant changes in the COR level spectral extraction from mosaic images added 06 February 2007 6 0 1 Update of the Sixth Release RMF Calibration instances updated a new known issue added 14 September 7 0 Seventh Release j ima_iros updates new tool 2007 j ima src locator 25 February 2008 7 0 minor corrections 31 August 2009 8 0 Significant changes in sections 7 6 7 7 26 April 2010 9 0 Several fixes in the cook book Correction of Table 5 in Section 7 6 1 Update of known limitations and URLs 12 July 2010 9 1 Update of binning parameters example in cookbook rebin_rmf 03 September 9 2 Remove IMA2_viewVar parameter setting in example of sec 2010 tion 7 6 6 Spectral extraction of the cookbook minor typo 26 November 2010 9 3 Update of Figure 8 detection limit 18 September 10 0 Several updates in the cook book known limitations and 2012 URLs Added new sections Useful to know and Useful recipes for JEM X data analysis adapted from IBIS UM j ima_mosaic updates 19 SEP 2012 Printed ISDC JEM X Analysis User Manual Issue 10 0 ii Contents Acronyms and Abbreviations o s c seci newe ee bee a ee eo ee Ao or MOVIE EE Introduction I Instrument Definition Scientific Performance Summary 624 262 4 pea N ee RY RAR HERG eee eee Sen Description e ac end beck i a a MRS bale ee aa Le ee Es 2 1 The Overall Design c u
52. the processing instead for each generated JEM X ISDC JEM X Analysis User Manual Issue 10 0 62 lightcurve a corresponding background lightcurve is produced by binning of the background model informa tion using the same binning as the measured lightcurves It calls the following executables e j_bin_evts_lc e j_binrate_lc e j bin_bkg_lc 8 10 1 _bim_evts_lc Bins JEM X event data to lightcurves Table 21 j_bin_evts_Ic specific to the BIN_T level Name main script Name executable Type Description BIN_T_rowSelect BIN_T_evtType nChanBins chanLow chanHigh LCR_timeStep timeStart timeStop nPhaseBins phaseBins rowSelect evtType nChanBins chanLow chanHigh timeStep timeStart timeStop nPhaseBins phaseBins string integer integer string string real real real integer string CFITSIO selection string on events default gt Data format to bin possible values 1 all o FULL 2 SPTI 3 TIME default 1 Number of channel bins default 4 Lower channel bins numbers separated by spaces default 46 83 129 160 Upper channel bins numbers separated by spaces default 82 128 159 223 Binning time for lightcurve sec default 10 Time in IJD of start of first time bin lt 0 use SWG start default 1 Time in IJD of end of last time bin lt 0 use SWG end default
53. time values for each polling cycle 8 seconds for a given JEM X detector calling a single executable jdead_time_calc There are no parameters specific to this level in jemx science analysis par file 8 3 1 j_dead_time_calc The dead time used in standard scientific analysis is calculated from the housekeeping counters that keep track of the fate of every event processed by the on board software The time to read in all the detector signals for a single event depends on how quickly the event is discarded due to grey filtering buffer loss or particle rejection The time taken for each sort of processing is stored in JMXi DEAD MOD see Table 33 in Appendix B The read in time is summed up for all the events to give DEADTIME in JMXi DEAD SCP this deadtime only measures the time that the hardware is occupied with event handling and cannot take in new events and dead time due to buffer losses A further dead time DEAD_EFF is calculated that includes the effect of grey filter This factor can be used to correct fluxes and countrates for all detector processing losses These values however have only 8 secs resolution since this is the frequency of housekeeping packets therefore very rapidly varying strong sources must be treated offline for dead time Most analysis tools use the DEADTIME value in JMXi DEAD SCP and then add the effect of grey filter losses by looking up the grey filter value in the the JMXi_INST STA instrument status table These grey fi
54. to keep the VARIANCE extension in the output of mosaic step IMA2_viewVar Y which is set to yes by default since the variance value at the source location is the error of the flux determination in a given energy band Now you can find the spectrum of any of the sources and even extract a spectrum or energy dependent upper limit of the flux from any position on the sky from the sky images in each ScW using the mosaic_spec script E g the command cd scw 005300410010 001 mosaic_spec DOL_idx jmx2_sky_ima fits DOL_spec spectrum_scw fits JMX2 PHA1 SPE tpl EXTNAME JMX2 SKY IMA ra 261 89 dec 30 80 posmode 0 widthmode 2 Intensity RECONSTRUCTED will extract the spectrum from the position on the sky RA 261 89 DEC 30 80 corresponding to the position of 4U 1722 30 The spectrum will be written in the file spectrum scw fits using the template specified in the template file JMX2 PHA1 SPE tp1 A number of parameters of the mosaic spec script specify the way in which the source flux and error are extracted from the sky image In general the script attempts to fit a Gaussian to the excess of intensity at the position of the source The parameter posmode 0 specifies that the source position always should be left free 1 would freeze the source coordinates as the user may prefer to do with relatively weak sources The parameter widthmode 2 specifies that the width of the fitted Gaussian should be read from the JEM X image T
55. two Scws we are interested in i e 010200210010 and 010200220010 Press the Save SCW list for the creation of Observation Groups button at the bottom of that table and save the file with the name jmx I st The file name jmx st will be used later as an argument for the og_create program see section 6 5 In this file you should find the 2 lines When an analysis script asks you to specify the DOL you should specify the path of the corresponding FITS file and the corresponding name or number of the data structure in square brackets do not forget that numbering starts with 0 See more details in the Introduction to the INTEGRAL Data Analysis 1 ISDC JEM X Analysis User Manual Issue 10 0 17 scw 0102 010200210010 001 swg fits 1 scw 0102 010200220010 001 swg fits 1 You should then download the data pressing the Request data products for selected rows button In the Public Data Distribution Form provide your e mail address and press the Submit Request button You will be e mailed the required script to get your data and the instructions for the settings of the IC files and the reference catalogue Just follow these instructions 6 3 Setting the environment Before you run any OSA software you must also set your environment correctly The commands below apply to the csh family of shells i e csh and tcsh and should be adapted for other families of shells In all cases you have to set th
56. 00 0 05 0 109 X direction cosine Figure 25 Simplified version of the vignetting array 8 9 j_bin_spectra This script bins events or Spectral Mode data without deconvolution It calls the following executables e j_bin_evts_spectra e j_bin_spec_spectra e j_bin_bkg_spectra The j bin spectra deals with background issues in a different fashion than the image reconstruction processes There is no attempt at subtracting the background during the processing instead for each generated JEM X spectrum a corresponding background spectrum or lightcurve is produced by binning of the background model information using the same binning as the measured spectra 8 9 1 j_bin_evts_spectra This executable generates detector spectra for a single JEM X unit from Full Imaging Restricted Imaging or Spectral Timing events by binning the event data A series of spectra resolved in time or phase over a given period can be produced Table 18 j_bin_evts_spectra specific to the BIN_S level Name Name Type Description main script executable BIN_S rowSelectEvts rowSelect string CFITSIO selection string on events default ISDC JEM X Analysis User Manual Issue 10 0 61 BIN_S_evtType evtType integer Data format to bin possible values 1 all 0 FULL 1 REST 2 SPTI 4 SPEC default 1 8 9 2 j_bin_spec_spectra This executable generates time resolved spectra for a sin
57. 1 Figure 4 Collimator layout In this diagram the 4 calibration sources are situated on the upper side The dimensions are in mm i e collimator length 57 mm radius 130 mm ISDC JEM X Analysis User Manual Issue 10 0 5 ye 3 Es B mS ee 75 S 2 052 ame C Fi i igure 5 Illustration of the JEM X coded mask pattern layout without the mechanical interface The diameter of the coded mask is 535 mm The mask has a transparency of 25 2 3 Coded Mask The mask is based on a Hexagonal Uniformly Redundant Array HURA For JEM X a pattern composed of 22501 elements with only 25 open area has been chosen The 25 transparency mask actually achieves better sensitivity than a 50 mask particularly in complex fields with many sources or in fields where weak sources should be studied in the presence of a strong source A mask with lower transparency also has the advantage of reducing the number of events to be transmitted while at the same time increasing the information content of the remaining events Considering the telemetry allocation to JEM X this means an improved overall performance for the instrument particularly for observations in the plane of the Galaxy The mask height above the detector 3 4 m and the mask element dimension 3 3 mm define together the angular resolution of the instrument in this case 3 Figure 5 illustrates the JEM X coded mask pattern ISDC JEM X Analysis User Manual Issue 10 0
58. 300680010 001 swg fits 1 scw 0053 005300740010 001 swg fits 1 scw 0053 005300750010 001 swg fits 1 scw 0053 005300760010 001 swg fits 1 scw 0053 005300820010 001 swg fits 1 Save the above list to the file mos 1st To produce the mosaic image of these pointings you have first to create the corresponding observation group mos using the og_create tool as has been explained above and run the jema_science_analysis up to the IMA level cd REP_BASE_PROD og_create idxSwg mos lst ogid mos baseDir instrument JMX2 cd obs mos jemx_science_analysis startLevel COR endLevel IMA jemxNum 2 Next to produce the mosaic from the intensity images for each energy band as obtained at the IMA level you have to run the jemz_science_analysis script at IMA2 level only jemx_science_analysis startLevel IMA2 endLevel IMA2 jemxNum 2 Again do not forget to specify which of the JEM X instruments you are interested in jemxNum 2 in our case By default intensity RECONSTRUCTED variance significance and exposure mosaic images will be produced The same result can be obtained calling jemx_science_analysis only once from startLevel COR to ISDC JEM X Analysis User Manual Issue 10 0 25 E fv Binary Table of mx2_ohs_res fits 1 in Aisdc scratch2 neronow OSA 5obs crab 1 File Edit Tools _ SWID _ SOURCE_ID _ RA_OBJ DEC OBJ _ ERR_RAD 16A 1E 1E 1E deg deg deg 75900002 005300560010 131574 33500
59. 310 311 312 313 314 315 46 8 Basic Data Reduction In the previous cookbook chapter Section 6 several examples of the JEM X data scientific analysis along with the description of the results were given There you have seen that in order to run Scientific Analysis you should just launch the main script jemz_science_analysis with a desired set of parameters As it was discussed in the Overview Section 5 processing of the main script consists mainly of a loop over the pointings in the Observation Group calling the script jemx_scw_analysis which in turn consists of smaller scripts unifying the executables with the similar tasks see Figure 22 In the present chapter we describe these small scripts in more details in order to explain how the main script works and what parameters you have to enter for a proper analysis Describing the executables we mention all the parameters that were included as a parameter to the main script All other parameters are set internally To know about them type the name of the desired executable with v option Non hidden parameters of the main script are marked with a bold font Usually names of the main script parameters are derived from the corresponding name of the executable parameters by adding as prefix the name of the OSA level at which they are called e g parameter diameter of the executable jima_mosaic called at IMA2 level of OSA is named IMA2 diameter in the main script In the rare case when thi
60. 32 3h S IGR J17200 3116 50 4 E si R a TE J1710 281 40 Y A mtb A GRS 1741 8 2853 60 211 10 Era cido cl AA 10 104 105 105 Figure 8 ISDC JEM X Analysis User Manual Issue 10 0 Effective Observation Time s Source detection capabilities in the 3 to 10 keV resp Sx 10 25 kev erg cms 10719 107 1072 10 Source detection limit 10 25 kev qq mn TTT e a r 1a1 14204 30 20273 301 SLX 1735 268 270 ad e 4U 1705 32 30 y 2400 Oph 30 IGR 4174972821 8c IGR ea id 309 E s GR J17200 3118 3a XTE 417102281 30 rasot s sss 104 10 10 Effective Observation Time s 10 to 25 keV band as function of effective accumulated observation exposure time in JEM X mosaic images corrected for dead time grey filter and vignetting effects The thick solid curve is obtained from simulations where an isolated source must be detected at 30 in the deconvolved image The dashed line represents the case where there are additional sources in the field of view giving a background corresponding to a total of 1 Crab Examples of actual observations are given the source 3C 273 and the other empty circles are instances of isolated sources while the crossed circles represent sources observed in the crowded Galactic Centre region The o values given in parentheses are obtained from a measure of the highest source pixel in significance mosaic
61. 5 0a Fak dana e PEE eee Eee ee 40 7 3 1 Creating a second mosaic in the Observation Group 41 7 4 Combining results from different observation groups 2004 41 TAA Creating a mosaic from different observation groups Al TAQ Combining spectra and lightcurves from different observation groups 42 7 5 Create your own user catalog e e esa bbe nas ee a ee Ee e 43 7 6 IBaryCentrisation i 54 4 5 44 ub BARRO EEE Dae ee Oe ded N 9 44 Tete Timing Analysis without the Deconvolution o e 44 8 Basic Dats Reduction lt lt ai as ee ew eR Re ee a ee ey ga 47 8 1 na it aa ove ha a be A RE AO a he Oe a ee Se ek he 47 8 L 1 MOE cd as 2 A a NA PA a ok A 47 ISDC JEM X Analysis User Manual Issue 10 0 iv 8 1 2 eO E ai eiga ae E Rae EE Ree ed 50 8 2 EOU raae he RAN 50 8 2 1 pa ie S Gs oe A a Be a ee es Hee oe He es 50 8 2 2 GUA L A dirk R R eae de Sa BR ee A A ES 51 8 2 3 GUGA DDS e o ale a ce ee pa A a Eek eR a ay AG De N 51 8 2 4 GOTO vd ok ee BA ol ee ee ed Re a o 51 8 2 5 E a i iie ele hae e ia aa 4 T E ee Taa A E Sea Rie be 52 8 3 PO RR ena A PR eee ee ee ay AA A we e da 52 8 3 1 eE GE 2 Bg se eRe ele Beh be eh ste ws HO ee ee we FE 52 8 4 A a T heats E chat de day rare Be Le ee ean Oe ge Bk h 53 8 5 SMODE E a a a Re ena ea wD pee a a mg A ENE A hw e 53 8 5 1 PIO SRGUOWGTONY lt lt se we Bo A eh ses KO ee ee ee HE 54 8 6 PAGING oS ne A ee Re ee ee A 55 8 6 1 JAOTUS y o
62. 5 RTS 005300590010 005300510010 3174756 0 263349 2 669834E 02 2 655886 01 3 539000 02 005300650010 3174605 5 293055 1a 1742 294 2 665311E 02 2 951624E 01 3 539000 02 Goto Edess Figure 14 The content of jmx2_obs_res fits file endLevel IMA2 eventually skipping the intermediate levels with the command skipLevels LCR SPE BIN_S BIN_T Apart from the mosaic images the output of the IMA2 level contains a collection of the results from the individual science windows which is contained in the file jmx2_obs_res fits Its content is shown in Fig 14 With the help of cat2ds9 command you can produce a region file found reg to locate these sources at the mosaic image cat2ds9 jmx2_obs_res fits 1 found reg symbol circle color white Note that since the same sources can be found in many ScWs you can have one and the same source repeated several times in the resulting region file You can look at the content of the resulting mosaic images contained in the file jmx2_mosa_ima fits with fu and display them with ds9 exactly as you did with the images from individual ScWs see Fig 15 for the example of image in 7 11 keV energy band In this figure you can see the sources found in single ScW analysis shown with white circles One can see that two additional sources which were not detected in the single ScWs appear in the mosaic image the sources shown by the green crosses If you are interested only in a
63. 65 4 56 4 64 151 13 60 13 76 236 50 24 51 52 66 4 64 4 72 152 13 76 13 92 237 51 52 52 80 67 4 72 4 80 153 13 92 14 08 238 52 80 54 08 68 4 80 4 88 154 14 08 14 24 239 54 08 55 36 69 4 88 4 96 155 14 24 14 40 240 55 36 56 64 70 4 96 5 04 156 14 40 14 56 241 56 64 57 92 71 5 04 5 12 157 14 56 14 72 242 57 92 59 20 72 5 12 5 20 158 14 72 14 88 243 59 20 60 48 73 5 20 5 28 159 14 88 15 04 244 60 48 61 76 74 5 28 5 36 160 15 04 15 30 245 61 76 63 04 75 5 36 5 44 161 15 30 15 56 246 63 04 64 32 76 5 44 5 52 162 15 56 15 82 247 64 32 65 60 77 5 52 5 60 163 15 82 16 08 248 65 60 66 88 78 5 60 5 68 164 16 08 16 34 249 66 88 68 16 79 5 68 5 76 165 16 34 16 60 250 68 16 69 44 80 5 76 5 84 166 16 60 16 86 251 69 44 70 72 81 5 84 5 92 167 16 86 17 12 252 70 72 72 00 82 5 92 6 00 168 17 12 17 38 253 72 00 73 28 83 6 00 6 08 169 17 38 17 64 254 73 28 74 56 84 6 08 6 16 170 17 64 17 90 255 74 56 81 92 85 6 16 6 24 The complete table can also be found in JMXi IMOD GRP structure in extension JMXi FBDS MOD The Xe instrumental background line which is used to verify the gain calibration of the instrument should appear in the channel 209 IS
64. 7 44 185 21 54 21 80 15 0 90 0 96 101 7 44 7 52 186 21 80 22 06 16 0 96 1 02 102 7 52 7 60 187 22 06 22 32 17 1 02 1 08 103 7 60 7 68 188 22 32 22 58 18 1 08 1 14 104 7 68 7 76 189 22 58 22 84 19 1 14 1 20 105 7 76 7 84 190 22 84 23 10 20 1 20 1 26 106 7 84 7 92 191 23 10 23 36 21 1 26 1 32 107 7 92 8 00 192 23 36 23 72 22 1 32 1 38 108 8 00 8 08 193 23 72 24 08 23 1 38 1 44 109 8 08 8 16 194 24 08 24 44 24 1 44 1 50 110 8 16 8 24 195 24 44 24 80 25 1 50 1 56 111 824 8 32 196 24 80 25 16 26 1 56 1 62 112 832 8 42 197 25 16 25 52 27 1 62 1 68 113 842 8 52 198 25 52 25 88 28 1 68 1 74 114 8 52 8 62 199 25 88 26 24 29 1 74 1 80 115 8 62 8 72 200 26 24 26 60 30 1 80 1 86 116 8 72 8 82 201 26 60 26 96 31 1 86 1 92 117 882 8 92 202 26 96 27 32 32 1 92 2 00 118 8 92 9 02 203 27 32 27 68 33 2 00 2 08 119 9 02 9 12 204 27 68 28 04 34 2 08 2 16 120 9 12 9 22 205 28 04 28 40 35 2 16 2 24 121 922 9 32 206 28 40 28 76 36 2 24 2 32 122 932 9 42 207 28 76 29 12 37 2 32 2 40 123 9 42 9 52 208 29 12 29 48 38 2 40 2 48 124 9 52 9 62 209 29 48 29 84 39 2 48 2 56 125 9 62 9 72 210 29 84 30 20 40 2 56 2 64 126 9 72 9 82 211 30 20 30 56 41 2 64 2 72 127 9 82 9 92
65. A is constructed backprojection The information on the found sources and their fluxes is written to the JMXi SRCL RES data structure Table 47 Content of JMXi SRCL RES Data Structure Column Name Description SOURCE_ID ISDC unique source identifier DAY ID Modified Julian Date of source s first identification NAME One commonly used name for the source CLASS source classification code ISDC JEM X Analysis User Manual Issue 10 0 84 RA_OBJ Source right ascension in degrees DEC_OBJ Source declination in degrees ERR_RAD Error radius RELDIST Relative distance of the source d rl r2 where d is a distance to catalog source identified with the source and rn are the respective error radii of the sources SPA_MODL Model for source spatial extension point disk ellipse square gaussian Bspline etc SPA_NPAR Number of parameters for source spatial extension SPA PARS Parameters for source spatial extension SPE MODL Model for source spectrum XSPEC syntax SPE_NPAR Number of parameters for source spectrum SPE_PARS Parameters for source spectrum VAR_MODL Model for source intensity variability const sin burst VAR_NPAR Number of parameters for source intensity variability VAR_PARS Parameters for source intensity variability COMMENTS Comments SPIFLUX_1 SPI flux in the soft SPI energy band SPIFLUX_2 SPI flux in the hard SPI energy band ISGR_FLUX_1 ISGRI flux in the soft ISGRI energy band
66. A_detAccLimit integer Acceptance limit in JMXi DETE MOD data structure Possible values 1 65535 default 16384 IMA_skyImageDim integer Sky image dimension Possible values 1 255 2 511 default 2 15Note that the string will be concatenated to an existing radius selection so that the parameter string must begin with a logical operator such as amp amp ISDC JEM X Analysis User Manual Issue 10 0 55 IMA_useDead Anodes IMA_maxNumSources IMA_edgeEnhanceF actor IMA_loopLimitPeak IMA _detSigSingle IMA_skyRadiusFactor IMA radiusLimit0 IMA _radiusLimit1 IMA_radiusLimit2 IMA _radiusLimit3 IMA_interactionDepth IMA_hotPixelLimit IMA _skyImagesOut IMA_dolBPL boolean integer real real real real real real real real real real string sting Do you want to include dead anodes areas default no Max number of sources in IROS loop default 10 Edge enhancement factor It is used to convert the sky images to significance maps by amplifying the peaks near the edge relative to those near the center default 1 0 Fractional peak power to stop IROS loop default 0 025 Detection significance for source acceptance default 12 0 Sky radius limit factor default 1 0 Detector radius limit E lt 6 keV mm default 120 0 Detector radius limit 6 lt E lt 12 keV mm default 120 0 Detector radius limit 12 lt E lt 20 keV mm
67. D number from the on board software and DEAD8_1 and DEAD16_1 give the time in seconds to do the read in The usual on board CPU speed is 16 MHz Also contains a keyword for the double trigger effect Data Structures used for background handling JMXi DBKG MOD Contains maps giving the spatial distribution of background counts at a number of energy levels including information about detector areas that should nopt be used Data Structure used for imaging and source finding JMXi COLL MOD JMXi MASK MOD JMXi OPNC MOD JMXi VIGN MOD JMXi IROS MOD Contains a collimator description in the form of two lists of the coordinates of the collimator lamellae intersections X and Y coordinates of intersection at the top and at the bottom are given in columns XSECTBOT YSECTBOT XSECTTOP and YSECTTOP Contains the mask description of JEM Xi It is 2D table with axes along Mask X and Y axes Gives the coordinates mm of the centers of the open holes in the mask Contains an array with vignetting factors for the JEM Xi instrument It is a 2D table with axes along X and Y axes This has been used to correct source intensities for collimator shadowing but is now obsolete Contains some basic parameters for the component j_ima_iros Data Structure used for spectral analysis JMXi ENRG MOD Contains the table of ENERG_LO lower limit of channel in keV and EN ERG_HI upper limit of channel in keV to be used in conju
68. DC JEM X Analysis User Manual Issue 10 0 9 4 Performance of the Instrument The properties described in the following have been derived in part from pre flight calibration measurements and modeling and in part from calibration observations in orbit JEM X has had major changes of its configuration since launch the most important being a reduction of the high voltages reducing the gas gain from 1500 down to 500 for JEM X 1 and to 750 for JEM X 2 These changes also affect the instrument performance 4 1 Position Resolution The position determination accuracy depends on the number of source and background counts and on the position in the Field of View FOV Off axis the collimator blocks some of the source photons and beyond the fully coded FOV FCFOV the coding is incomplete Figure 6 shows the position resolution for a source on axis as function of energy The cause of the degradation below 10 keV is the signal to noise ratio of the front end electronics The energy dependence of the position resolution above 10 keV is determined by the increase of the primary photoelectron range with energy The position resolution is slightly degraded compared to the ground calibrations JEM X Position Resolution annan 4 Gas 1 5 atm 5 5 cm Xe 10 CHa JMX1 Gasgain 500 JMX2 Gasgain 750 5 3 S 2 a O 3 x 2 T E 1 am m m am o m m m A AAA AAA AR g 19 20 30 40 Energy kev Fi 6 dd The calculated position re
69. EADTIME Fractional input dead time not including grey filter losses RATE_COR Factor for correcting count rates not including grey filter losses DEAD_EFF Total effective dead time including grey filter C 4 jj cat extract The output catalogue of the selected sources is written to a new source list with the same structure JMXi SRCL CAT Table 45 Content of JMXi SCAL BKG and JMXi SCAL DBG Data Structures Column Name Description DELTAOBT Delta OBT from beginning of Science Window SCALFACT Scaling factor C 5 j image_bin This script creates shadowgrams in several user defined energy bands The result shadowgram can be represented in either skew or standard system and is appended to the index group JMXi EVTS SHD IDX Table 46 Content of JMXi EVTS SHD IDX Column Name Description OBTSTART OBT start of integration OBTEND OBT end of integration TELAPSE Total observation elapsed time in seconds EXPOSURE Mean exposure time over the detector plane CHANMIN Lowest channel of the energy range CHANMAX Highest channel of the energy range SHDIDEN Shadowgram identification number SHDTYPE Shadowgram type 1 standard 2 raw 3 regularized EVNTYPES Code for event types 0 FULL 1 REST 1 both C 6 j_imaging C 6 1 j ima_iros This executable makes a basic image reconstruction for the input shadowgrams in the index group JMXi EVTS SHD IDX The resulting sky image JMXi SKY IM
70. EM X and functional diagram of one unit o 3 Off axis response of JEM X below 50 keV ee 4 Colimator layouts ie sonuca i oe ee A Be A RE 0 5 JEM X coded mask patteri o c end geme sa a ad a g wiae SR Raa SESE Re i ma 6 The position resolution in the detector as a function of energy sooo 7 Empty field backeround spectrum p se ees 64h e p e ae a a a a o a ee ea 8 Predicted 3o source detection limit lt c ecc sa scana seses iara oa iaaa 9 Decomposition of the jema_science_analysis script sec cs cuco ee WO e 1 os oh pe elle OA Oe Ee we A EES PO eed oe ee ES A hme sh bs Me nn kt od bh BA SRD ee Ee eee eee teh hs E Amelie SW Weare os ee a E a Oe RA Woes BS e 13 PiF cleaned image lt a ee a RR EO Ls we A ee ey a i jue obs Tes PIES MS ik koh Po Gee a EGP EAS Siw eee aol de t5 Mossie T 4 aora e HA ed PO e ere A eS 16 Mosaic image in AIToff Hammer projection 2 ooa a a a T_T Tee l i ood ek BA SO Dal te Ge hte A a oe 9 IS CHAD BEDEC 6 ave i o eee A MAb Be ee Rs Ae ARA dh ad 19 Spectr ar AU T2280 5 coa a A eR ae ee eB ES 20 Spectrum of 4U 1722 30 from MasdiC a gt c sack be a de eee eee es 21 Crab lipiteurve first energy band oa s ok he ek eke a a ee ed 22 Detailed decomposition of the jemz_science_analysis script o ooo e ee 23 A shadowgram with a strong on axis source e 24 The distribution of values in an RSTI image e 25 Simplified versi
71. ES SOURCES STRONG ENOUGH TO BE DETECTED IN SINGLE SCIENCE WINDOWS FROM PIF IMAGES OR FROM MOSAICS BASED ON PIF IMAGES THE FITTED FLUXES in src_ls_res SHOULD BE USED TO EXTRACT SPECTRA FOR STRONG SOURCES THESE FLUXES ARE NOT AFFECTED BY THE PIF IMAGING OPTION 6 6 4 The Mosaic Image The IMA2 level produces JEM X mosaic images by combining all the individual j_ima_iros images from the different science windows gathered in the observation group The combined images have longer exposure time As a consequence weaker sources which are not visible in single ScW may appear in the mosaic images In what follows we consider an example of a JEM X mosaic of the Galactic Center region for the revolution 0053 in March 2003 You can browse through the INTEGRAL data archive and check that within this revolution the pointings which have the Galactic Center within the JEM X2 FOV are scw 0053 005300410010 001 swg fits 1 scw 0053 005300420010 001 swg fits 1 ISDC JEM X Analysis User Manual Issue 10 0 24 Fi 13 belis Left Mosaic from conventional images centered on the strong source GRS 1915 105 Right Mosaic from PIF images in the same region of the sky scw 0053 005300490010 001 swg fits 1 scw 0053 005300510010 001 swg fits 1 scw 0053 005300580010 001 swg fits 1 scw 0053 005300590010 001 swg fits 1 scw 0053 005300650010 001 swg fits 1 scw 0053 005300660010 001 swg fits 1 scw 0053 005300670010 001 swg fits 1 scw 0053 005
72. IMA2 This is relatively simple because all the Science Windows belong to the same group so combining the results is trivial But if this is not the case i e if you have run different sets of analysis each one with its own og_create command then you need to make some intermediate steps 14 You basically need to create a file that points to all the Science Windows you want to co add We call this file an index To create an index make a list of the Science Window groups you want to combine and save it as e g dols txt To ensure a proper work of the software give the full path i e your file should look like WORKING DIR obs GROUP1 scw 011901060010 001 swg_jmx2 fits WORKING DIR obs GROUP1 scw 011901070010 001 swg_jmx2 fits WORKING DIR obs GROUP2 scw 012000360010 001 swg_jmx2 fits WORKING DIR obs GROUP2 scw 012000370010 001 swg_jmx2 fits The first 2 files belong to a run with the og_create parameter ogid equal to GROUP1 while the latter two to a run with ogid equal to GROUP2 WORKING DIR has to be the extensive name of REP_BASE_PROD WARNING make sure that obs scw 001 jmx2_sky_ima fits files exist in all the Science Windows you mention otherwise the merging will not work Then give the command that actually builds the fits file from the ASCII file cp dols txt REP_BASE_PROD obs GROUP1 cd REP_BASE_PROD obs GROUP1 txt2idx element dols txt index index_comb fits The file index_comb fits
73. IMA2_srcselect select string CFITSIO selection string applied to input tables default IMA2 srcattach attach boolean Attach resulting table to group default n 8 11 3 j_ima_src_locator jzima_src_locator is a tool to locate point sources in an image It is included in the OSA 7 distribution but is it is not part of the pipeline The primary goal of this tool is to analyze images from JEM X made by j_ima_iros or j_ima_mosaic but it can also be used as a generic tool for a FIT S image file The main condition is that the PSF measured in pixels does not vary significantly over the image Currently j_ima_src_locator operates on a single image but the functionality to get the images from a DAL ISDC JEM X Analysis User Manual Issue 10 0 66 observation group OG a DAL science window group SWG or a DAL index table IDX is being prepared Significance map The starting point for the search for sources is the significance map If the image is accompanied by a significance map this can be given as a parameter with its DOL Detection significance of sources It is assumed that the significance given in the significance map is evaluated pixel by pixel e g based on the number of counts that contribute to each image pixel The significance of an excess in a pixel in the image is evaluated as the number of excess counts divided by the square root of the variance number of sigmas In order to deal with the fact that th
74. ISDC system e Observation Any group of ScW used in the data analysis The observation defined from ISOC in relation with the proposal is only one example of possible ISDC observations Other combinations of Science Windows e of observations are used for example for the Quick Look Analysis or for Off Line Scientific Analysis e Pointing Period during which the spacecraft axis pointing direction remains stable Because of the INTEGRAL dithering strategy the nominal pointing duration is of order of 20 minutes e Slew Period during which the spacecraft is manoeuvred from one stable position to another i e from one pointing to another e Shadowgram The pattern of detected events on the microstrip plate produced when particles and xrays pass through the coded mask and hit the plate e Sky image Image of the sky above the telescope produced when a shadowgram integrated over a given period of time is deconvolved by the image construction software e Mosaic A sky image produced by merging two or more separate sky images so as to cover a greater area of sky or to enhance the signal from a particular area of the sky ISDC JEM X Analysis User Manual Issue 10 0 xii Introduction This document JEM X Analysis User Manual has been written to help you with the JEM X specific part of the INTEGRAL Data Analysis You will find some text in blue along this manual it is used to notify a difference with respect to the previous
75. JMXi B Mod Data Structures Column Name Description CHANNEL Uppermost effective adc channel in a given telemetry bin See also Section 3 2 1 for more details PI Binning During automatic calibration the original PHA values of the events and spectra are converted into keV values based on the fitting of the Fixed Radiation Source System FRSS calibration spectra The upper part of figure 26 shows the FRSS calibration spectra which are used to determine the detector gain on each of the four anode segments of both units at 4 minute intervals The standard FRSS setup has a Cd 109 source with a Nickel window but only one useable doublet is seen the Cadmium 22 1 25 0keV lines This spectrum is shown by the full line Anodes 0 and 2 of unit JEM X each have an Fe 55 source for calibration and the calibration spectrum from these anode segments is shown with the dotted line This spectrum is modelled as an unresolved doublet at 5 9 6 1 keV The FRSS spectrum is sent down as counts in each of 256 PHA channels 0 to 255 that cover logarith mically sized bins of the 4096 ADC channels of the ADC that registers the Pulse Height Amplitude The uppermost ADC channel appearing in each PHA channel is given in the binning table JMXi CALB MOD in the instrument model group The upper channel in the last bin must always be 4095 The logarithmic binning of the ADC channels is chosen to reflect the energy resolution of the detector which is ro
76. LAPSE time interval from beginning to end of data window ONTIME sum of the good time intervals GTI EXPOSURE ONTIME corrected for greyfilter and deadtime DEADC effective fraction surviving when only dead time is considered An example of a shadowgram with a very strong on axis source is shown in Fig 23 The central part of the mask is imaged on the detector and the similarity with the mask pattern Fig 5 can be noticed Figure 23 A shadowgram with a strong on axis source and negligible background Table 14 7_tmage_bin parameters included into the main script Name Name Type Description main script executable nChanBins nChanBins integer Number of energy resolved shadowgrams to create If lt 1 shadowgrams are created in standard bands possible values 7 100 default 4 chanLow chanLow string Lower channel boundaries for shadowgrams default 46 83 129 160 chanHigh chanHigh string Upper channel boundaries for shadowgrams default 82 128 159 223 timeStart timeStart real Start of time interval IJD 1 use swgDOL bounds default 1 timeStop timeStop real End of time interval IJD 1 use swgDOL bounds default 1 BIN_LevtType evtType integer Event type possible values 0 FULL 1 REST 1 both default 1 ISDC JEM X Analysis User Manual Issue 10 0 54 BIN_I_shdType BIN_LshdRes BIN I rowSelect BIN_I_gtiNames BIN_I_chanLo
77. The characteristics of primary and secondary telemetry formats are listed in Table 2 The default primary format is Full Imaging and the default secondary format is Restricted Imaging Note that in the Spectral Timing format the actual spectral resolution will be slightly lower than that of the Full Imaging mode due to spatial gain variations in the detector It is recommended however that the full imaging format is used both as primary and secondary format Table 2 Characteristics of the JEM X Telemetry Packet Formats Detector Image Timing Spectral Events Format Name Resolution Resolution Resolution per pixels channels packet Full Imaging FULL 256 x 256 1 8192s 122yus 256 lt 105 Restricted Imaging REST 256 x 256 lt 325s 8 lt 320 Countrate None 1 8 s 125 ms 1 n a Spectral Timing SPTT None 1 8192s 122us 256 lt 210 Timing TIME None 1 8192s 122yus None lt 550 Spectrum SPEC None 1 8s 125 ms 64 n a 3 2 Energy Binning 3 2 1 PHA Binning The energy values of the events provided in the telemetry are given as a bin number from 0 to 255 These are non linear groupings of the original 4096 bins of the on board Analog to Digital Converter ADC While the ADC channels are highly linear the PHA bins are designed to be logarithmic so that the energy resolution of the bins parallels that of the detector The actual grouping of the ADC channels into PHA telemetry bins is determ
78. ULL or REST CHANMIN Lowest channel of the energy range CHANMAX Highest channel of the energy range E_MIN Lower bound of the energy range E_MAX Upper bound of the energy range Table 55 Content of JMXi DETE LCR Data Structure Column Name Description TIME Time of measurement for the bin TIMEDEL Integration time for the bin RATE Countrate in the given energy band ERROR Countrate error in the the given energy band BRATE Background countrate in the given energy band BERROR Background countrate error in the given energy band BARYTIME Barycentric time for the bin Table 56 Content of JMXi DETE FLC IDX Data Structure Column Name Description DATAMODE Science format used to create lightcurve FULL or REST CHANMIN Lowest channel of the energy range CHANMAX Highest channel of the energy range E_MIN Lower bound of the energy range E_MAX Upper bound of the energy range PERIOD Period in seconds with which the lightcurve was folded PHASZERO Time of phase zero in IJD Table 57 Content of JMXi DETE FLC IDX Data Structure Column Name Description PHASE ISDC JEM X Analysis User Phase of the center of the bin Manual Issue 10 0 88 PHASEDEL Half width in phase units 0 1 for the bin RATE Countrate in the given energy band ERROR Countrate error in the the given energy band BRATE Background countrate in the given energy band BERROR Background countrate error
79. User Manual Issue 10 0 29 6 6 7 Making images in arbitrary energy bands IMA can use the general energy binning parameters nChanBins chanLow and chanHigh to generate images note however that these parameters always determine the energy binning in the spectral extraction step SPE To use these parameters at the IMA step click on the hidden button and choose the IMA tab Put the IMA_detImagesOut to No and IMA_userImagesOut to Yes If you run the IMA step with such parameter settings jmx isky_ima fits will contain sky images for all bins specified by General Binning Parameters The mosaic image produced at the IMA2 level will also use these energy bins 6 7 Source Spectra Extraction Two spectral extraction algorithms can be used to extract the spectrum of a JEM X source the standard spectral extraction carried out at the SPE level discussed in section 6 7 1 and the spectral extraction from mosaic images discussed in section 6 7 7 Both of them originate from the imaging step WARNING with OSA10 the count rates are scaled to one cm while until OSA9 the count rate was scaled to one dm 6 7 1 Spectral Extraction at SPE level The standard spectral extraction procedure is carried out at the SPE level of the jemaz_science_analysis script by re formatting the source fluxes found at the IMA step The file jmx2_srcl_res fits serves as input for the spectral extraction in each ScW It is important to note h
80. Y axis and source in instrum coordinates Direction cosine between Z axis and source in instrum coordinates ISDC JEM X Analysis User Manual Issue 10 0 90 D jemx_science_analysis parameters description Table 60 jema_science_analysis parameters description Name Type Description ogDOL jemxNum startLevel endLevel skipLevels chatter clobber osimData ignoreScwErrors string integer string string string integer boolean boolean boolean DOL of the Observational Group to be analyzed default JEM X instrument number 1 or 2 default 2 Analysis level at which analysis begins The names of the possible analysis levels are listed in the table 4 default COR Analysis level at which analysis finishes The names of the pos sible analysis levels are listed in the table 4 default IMA2 Analysis levels to be skipped use with caution default BKG LCR BIN_T Verbosity level possible values 0 5 2 normal default 2 Clobber existing output data default y Input data was created by ISDC simulator default n Ignore all SW processing errors default n Parameters copied to several binning data tasks nChanBins chanLow chanHigh timeStart integer string string real Number of energy resolved shadowgrams to create If lt 1 shad owgrams created in standard bands Possibl
81. _CONFIGURATION However you should always be careful while setting this parameter BTIs are set by the JEM X team for specific problematic periods forcing their usage the reliability of the results can not be guaranteed especially for fluxes in BAD_RESPONSE cases 7 3 Rerunning the Analysis Read this if you would like to redo part of your analysis e g if your run has crashed or if you want to change some parameters In case you want to re run the analysis with different parameters run og_create but this time with a different ogid parameter This will create a new tree under obs ogid where all the new results will be stored If the pipeline has crashed in general it is safer to restart your analysis from scratch removing the obs ogid directory and restarting from the og create step In any case we give below a set of recipes that can be useful 131f any executable crashes then it terminates with non zero status The meaning of the status value can be found at http www isdc unige ch integral analysis Errors ISDC JEM X Analysis User Manual Issue 10 0 40 Because of the group concept you cannot just delete the result you do not like and restart the pipeline All results that were produced in the course of the analysis are linked to the group and should be detached before you relaunch the script To do this you can use the og_clean program that will clean an Observation Group up to the level specified with para
82. a on your local system or if you do not have a local archive with the scw and the aux branch available follow the next section instructions to download data from the ISDC WWW site 6 2 Downloading Your Data To retrieve the required analysis data from the archive go to the following URL http www isdc unige ch integral archive You will reach the W3Browse web page which will allow you to build a list of Science Windows ScWs needed to create your observation group for OSA e Type the name of the object Crab in the Object Name Or Coordinates field e Click on the More Options button at the top or at the bottom of the web page e Deselect the All checkbox at the top of the Catalog table and select the SCW Science Window Data one e Press the Specify Additional Parameters button at the bottom of the web page e Deselect the View All checkbox press twice on it at the top of the Query table e Select scw_id and put the value 0102 without the quotes to specify all Scws from Revolution 102 e Select scw_type and put the value pointing without the quotes or simply po to get only pointings e Press the Start Search button at the bottom of the web page At this point you should be at the Query Results page with all the Scws available for revolution 102 e Sort the Scw_id column by clicking on the left arrow below the column name You can then select the
83. aa OR ARE a eR eee 57 8 6 2 E eea de Be hd eae ee bee eH oe ee ee RES 58 8 7 J oe ETE BPC 6 ne ke ee RA we ha a eee BO Po NT a 60 8 7 1 TTC SHEET a aida HA we Bord A A Ye ee ee he hk Z a 60 8 8 GC TEE ll we Od ee A we ek pla eh he we A ee ee ew Goei 60 8 8 1 CERI AU ke ee AAA A A ee he We eG 60 8 9 POU CDOOIG oS ie Se OL ROA A GO Ss SR a Re eo 61 8 9 1 J DEUSE ce ZR ae WR ee ae ee Oe Be A 61 8 9 2 TURIDECAPECA lt a ee a a ee ee 62 8 9 3 E E EN 62 E A A A A ee ERA A A RE 62 BLO JDE A A 63 Ble o AS eB Gs Ss A me a wy Sh on ae a 63 SUS E ere 8 RA dae ee ok ee Bee a A 64 8 11 Observation group level analysis 2 2 ee 64 SILT JAMMIE ed he A AB SL ee a i 64 SL BESOS AAA a eG Be ag 66 SUS E or 0 2 23 eee eR Rad RG e eo ee A ES 66 Known Issues and Limitations 2 s c c oc 5 644 bide he DE a eee ee es 70 A Low Level Processing Data Products eee ee 72 ISDC JEM X Analysis User Manual Issue 10 0 v A SRG coe A A SRR a eR Ee eee oe oe 72 A 1 1 Full Imaging Modes o cden e a og eee eta a ae ee a a 72 A 1 2 Restricted Imaging Mode o e eee eee 73 A 1 3 Spectral Timing mode a peaa yeh ar be ea ek ee he 73 AJA Timing mode 2 44 400 544684 iea dane ae wa be REE Ba N 73 A 1 5 Spectral Mode s c so u 4444 een ewe eee rd Pa ee Darwen G SS 74 A 1 6 Prepared Date ios ce ec Ra BOR Re eee ea SOS da 74 A 1 7 Revolution File Data e RRR ee 74 B Instrument C
84. ad Y position determination 1024 Possibly leaked event from a calibration source 2048 Event detected before SETUP at beginning of Science Window 4096 Event from outside active area of detector 8192 Event coming from known hotspot on detector As you see these STATUS values are the powers of 2 If events are failed in more then one way then STATUS is equal to the sum of the corresponding values the back reconstruction has no problems and rise no ambiguity Events that fail in one or more ways can still be used for some purposes binned spectra don t require ISDC JEM X Analysis User Manual Issue 10 0 82 good position determinations uncertainties in gain determination don t affect sky images etc Therefore each program here after can select all the events that are appropriate for making high quality science data products with the best possible statistics The content of the corrected data structures for the different data modes is given in Table 42 Table 42 Content of JMXi COR Data Structures Column Name Description JMXi FULL COR DETX Corrected X location of the event on the detector DETY Corrected Y location of the event on the detector PI Pulse Invariant energy of the event STATUS Goodness of the corrected events JMXi REST COR DETX Corrected X location of the event on the detector DETY Corrected Y location of the event on the detector REST_PI Pulse Invariant energy of the
85. aic fits moscomb y The moscomb parameter is very important as it tells j_ima_mosaic that we are trying to combine mosaics The user can use either JMX1 or JMX2 j_ ima_mosaic can now produce mosaics either in the default tangential projection or using AIToff Hammer projection useful in particular when mosaicking large parts of the sky such as for the Galactic Plane Scans AIToff Hammer projection can be selected with the parameter IMA2_AITproj yes Table 23 j_ima_mosaic parameters Name Type Description inObsGrp string DOL of observation group default mapSelect string Default for Reconstructed Residual Sources Inten sity maps else RECTI for Rectified Intensity maps or RAWIN for Raw Intensity maps default RECON dolBPL string DOL of the vignetting maps e g ic jmx1 rsp jmx1 bpl grp 0002 fits JMX1 DMAP BPL default radiusSelect real Input images selection radius in deg default 5 eminSelect real Minimum energy keV to select energy interval default o emaxSelect real Maximum energy keV to select energy interval default 80 diameter real Diameter in degrees of the mosaic image 0 allows to fit the size from the angle between input images lt 0 may be used to force larger mosaics default o cdelt real Pixel size in degrees at mosaic center default 0 026 RAcenter real Center of the mosaic image Right Ascension in degrees if lt 0 use the comput
86. aining difference after subtraction of N 255 Number of sky pixels visible from a given detector pixel ISDC JEM X Analysis User Manual Issue 10 0 76 JMXi DAWP BPL Array giving the address of the first sky pixel visible from a given detector pixel JMXi DAST BPL The d_allow_st array contains for each detector pixel the address of the start of the corresponding list in the d_allow array JMXi DMAP BPL 51 arrays giving the number of detector pixels illuminated from each sky pixel vignetting arrays The 51 arrays corresponds to 51 different radius limits covering the range from 75 to 125 mm used in selecting events from the shadowgrams For full description of these and other data structures see the ISDC webpage B 3 Energy Binning ADC to PI PHA Binning The energy values of the events provided in the telemetry are given as a bin number from 0 to 255 These are non linear groupings of the original 4096 bins of the onboard ADC JMXi B MOD data structures Table 35 indicate the ADC bins covered by a given telemetry PHA bin These data structures are part of the instrument model group JMXi IMOD GRP Table 33 Each binning table gives a list of the highest ADC channel within each PHA bin Each of the different data taking modes has its own binning table data structure fitting its telemetry energy resolution Tables with fewer than 256 bins are just subsets of the full 256 bin table Table 35 Content of
87. al FLAG 3 sources will not be neglected data and folded model 4U1722 30_sum_pha fits 4U1722 30_single_pha2 fits 2 T T ayaman 1077 T sit normalized counts s key 1074 T L Energy keV Figure 19 The spectrum of 4U 1722 30 in ScW 0053004200 red and in the whole revolution 0053 black 6 7 7 Spectral Extraction from Mosaic Images Using the mosaic_spec script one can extract the source spectra from mosaic images and from individual ScW images To extract spectra from a mosaic one needs first to produce images in narrow energy bands ISDC JEM X Analysis User Manual Issue 10 0 34 to get a reasonable number of energy bins in the resulting spectrum As an example let us extract the spectrum of 4U 1722 30 from the mosaic images First one needs to create a new observation group using the list of ScWs considered for the mosaic of the Galactic Center region cd REP_BASE_PROD og_create idxSwg mos lst ogid mosspec baseDir instrument JMX2 cd obs mosspec Next one needs to produce the sky images in the 16 chosen energy bins jemx_science_analysis startLevel COR endLevel IMA2 nChanBins 4 IMA_detImagesOut no IMA_userImagesOut yes skipLevels LCR SPE BIN_S BIN_T jemxNum 2 The above command will produce JEM X sky images and the mosaic in the 16 standard energy bands You have to explicitly specify that you want
88. alog to Digital Converter Cosmic Rays Digital Front End Electronics Data Processing Electronics Danish Space Research Institute Diffuse X ray Background Fixed Radiation Source System Fully Coded Field of View Field of View Full Imaging Format Good Time Interval Instrument Characteristics Integral Julian Day Integral Science Operations Centre Integral Science Data Center Instrument Specific Software Joint European Monitor for X rays Hexagonal Uniformly Redundant Array Iterative Removal of Sources MSP OBT OCL OG PCFOV PHA PI RATE REST S C SPTI SPEC SDAST TBW TIME TM ZRFOV SPAG Microstrip Plate On Board Time Off line Calibration Observation Group Partially Coded Field of View Pulse Height Amplitude Pulse Invariant Countrate Format Restricted Imaging Format Spacecraft Spectral Timing Format Spectral Format Science Data Analysis Team To be written Timing Format Telemetry Zero Response Field of View Spatial gain variation of the microstrip plate xi Glossary of Terms e ISDC system the complete ground software system devoted to the processing of the INTEGRAL data and running at the ISDC It includes contributions from the ISDC and from the INTEGRAL instrument teams e Science Window ScW For the operations ISDC defines atomic bits of INTEGRAL operations as either a pointing or a slew and calls them ScWs A set of data produced during a ScW is a basic piece of INTEGRAL data in the
89. as they are specific to a particular grey filter setting Therefore if noticing transient features in the power spectra of very strong sources it should be checked if this is limited to a period of a specific grey filter setting Please check the User Manual for further explanations Since 30 March 2012 there is a new instance of the Instrument Model Group IMOD files version 22 produced by the JEM X Team The usage of these new IMOD files is highly recommended and will be automatic upon update of your copy of the Instrument Characteristics files Note however that the data are fully reliable only above 5 keV For the time being it is not trustable to extract spectra of strong sources with mosaic_spec from images obtained with the PIF option 6 6 3 The flux of a given source can be obtained either with the standard extraction or with mosaic_spec In case the fluxes obtained with the two methods would differ it is suggested to consider the one obtained from the standard extraction SPE level j ima_src_locator might interact wrongly with mosaics obtained in AIToff Hammer projection In case the mosaics are oriented in galactic coordinates j_ima_src_locator stores without converting G_Lon and G_Lat coordinates of the found sources under the columns RA and DEC of the jmxi_sloc_res file ISDC JEM X Analysis User Manual Issue 10 0 71 A Low Level Processing Data Products As it was explained in Section 3 1 JEM X has five
90. ault 1 5 Lower flux limit for alerts of unfound sources Counts s default 0 000 Range of search grid around nominal found source positions default 5 00 Number of grid steps on one side of search grid default 10 Fuzz allowed in relative distances default 0 15 Minimum number of pixels to make a contribution to the sky image default 25 Flag for special re normalization default 0 mm Reduction of collimator height for BPL production default 0 ISDC JEM X Analysis User Manual Issue 10 0 96 IMA_detImagesOut IMA_userImagesOut boolean boolean Should the images used for source detection be in output default yes Do you want the user defined images to be written default no Parameters specific to source spectra extraction SPE SPE_InSourceResult SPE_OutSourceSpectrum SPE_OutSourceARF string string string Input source result JMXi SRCL RES default Output source spectra JMXi SRCL SPE default Output source spectra JMXi SRCL ARF default Parameters specific to source lightcurve extraction LCR LCR_timeStep LCR_vignCorr LCR_evtType LCR_precisionLevel LCR_fluxScaling LCR_skipNearDeadAnode LCR skipHotSpot real boolean integer integer integer boolean boolean Binning time for spectra in seconds negative value means that time bin is equal to the science window exposure
91. channels within each subset for the energy bin MATRIX Response values for each channel subset for the energy bin JMXi AXIS ARF contains ancillary response information for an on axis source in the JEM X field of view see Table 40 for details Table 40 Content of JMXi AXIS ARF Data Structure Column Description ENERG_LO Lower energy boundaries of bins ENERG_HI Upper energy boundaries of bins SPECRESP Effective area in cm of the detector for a given source taking all effects into account JMXi FBDS MOD holds the electronic channels of the detector in Full Imaging Mode This data structure is a copy of the data structure with the same name in JMXi IMOD GRP fits See Tables 33 and 38 It is simply repeated for completeness ISDC JEM X Analysis User Manual Issue 10 0 81 C Science Data Products C 1 j correction This script corrects all data available within the Science Window Group for a given JEM X detector C 1 1 _cor_gain The executable j_cor_gain corrects all science data received for the condition of the individual pixels in the detector temporal and spatial changes in the detector gain The PHA channels of every event are converted to PI energies Event energies randomized within their bin and given as floating point keV values are given in column ENERGY of JMXi COR For science events the output consists of energy values given in PI channels For spectra taken in SPEC
92. d to steps already 48 the trigger rate dependency is taken into account while for COR_gainModel 3 the algorithm will not include this dependency in the gain smoothing process For some cases this modeling fails and a Warning with an error code of 321126 is reported The gain correction program continues using linear interpolation values of the gain correction parameters This is an ad hoc solution to ensure pipelines continue to run but implies that the energy determinations of the events will be somewhat off The corresponding events are flagged as having bad gain determination and may be ignored by subsequent steps or lead to distorted results In many cases where linear interpolation is used gain correction of events will be fine The user should look at the full detector spectrum produced by level BIN_S to see whether the Xe line peaks at PI channel 209 The default gain smoothing model is now COR _gainModel 4 If the smoothing goes wrong with model four and you dont like the look of the linear interpolation results try using model 3 All of the foregoing considerations about choice of model number can be ignored if there is an IC table with all the gain corrections already determined The log file will show whether a gain history table JMXi GAIN OCL has been used to correct the data See below spatial gain variations across the entire detector area These are initially determined by pre flight calibration but have been updated using
93. default 117 0 Detector radius limit E gt 20 keV mm default 110 0 Mean depth of interaction in the detector mm default 3 0 Hot pixel limit factor above average default 4 0 Type of output sky images There are the following types RECTIFIED Rectified cleaned intensity maps in counts cm s VARIANCE Variance maps RECONSTRUCTED Reconstructed Residual Sources maps in counts cm s which only differ from the RECTIFIED maps if sources have been found RAWINTENSITY Raw intensity strength maps in counts for which the vignetting correction is not applied RESIDUAL Intensity map in counts cm s after all found source contributions have been subtracted EXPOSURE The exposure map PIF activate the PIF weighted image generation algorithm not to be used with mosaic_spec Only the first five letters are required default RECONSTRUCTED VARIANCE DOL of backprojection file list default ISDC JEM X Analysis User Manual Issue 10 0 56 IMA_bkgShdDOL string DOL of background shadowgrams default IMA signifLim integer Minimum number of pixels to make a contribution to a sky image default 25 IMA _illumNorm integer Flag for special re normalization default 0 IMA_colHreduc real mm Reduction of collimator height for BPL production default 0 IMA_detImagesOut boolean Should the images used for source detection be in output default yes
94. different telemetry formats Full Imaging Restricted Imaging Spectral Timing Spectral and Timing The information sent to ground in Restricted Imaging mode is enhanced with the count rate of the events The time resolution of these Count Rate data is 125 ms while the rate of the image transfer in this mode depends on the brightness of the source and may be up to 32 seconds for the faintest ones see Table 2 for an overview During data taking JEM X instruments can switch autonomously between two preplanned modes according to the fill status of an on board buffer thus avoiding data loss due to the buffer overflow if the secondary mode allows higher transmission rate In addition to the mode switching there is also a grey filter mechanism which can reduce the telemetry load by rejecting a given number up to and including 31 out of 32 hardware triggers The value of the grey filter setting can vary from G 31 all events are accepted to G 0 only one event from each 32 is accepted In general value G of grey filter means that 31 G events from 32 are rejected Table 26 summarizes all scientific data structures created in these modes The data structures for JEM X 1 and JEM X 2 have the similar names so to avoid the unnecessary repetition we write JMXi where it should be replaced by 1 or 2 depending on the instrument Table 26 List of JEM X RAW PRP and COR Data Structures Telemetry Format Raw Prepared Corrected Data Structure
95. duction to the INTEGRAL Data Analysis 1 it is possible to combine the spectra from the different Science Windows To define the source for which you want to combine the spectra you should either input its Source ID or the source coordinates In our case to combine all the spectra belonging to the given Observation Group of the Crab give the following command spe_pick group 0g_jmx2 fits 1 instrument JMX2 source J053432 0 220052 rootname crab The rootname argument allows to choose the name of the resulting spectral data files For example the above command produces the files crab_single_pha2 fits with all individual spectra of the source crab_single_arf2 fits with corresponding individual ARFs crab_sum pha fits with the combined spectrum crab_sum_arf fits with the ARF for the combined spectrum The resulting spectrum crab_sum_pha fits can be analysed with XSPEC exactly in the same way as in the case of the individual ScW spectra see above The result of such analysis is shown in the right panel of Fig 18 You can check that combining the spectra obtained with without fixing the source positions results in slightly different spectral fits in XSPEC It is also possible to combine the spectra of the Science Windows which belong to different observation groups This is explained in section 7 4 2 6 7 6 Extracting Spectra from a given Position in the Sky It can happen that after the IMA level is done you find that there is one m
96. e situation changes Due to the presence of the 25 open mask the counts from a source will affect strongly at most a quarter of the detector pixels but in those it may strongly dominate the pixel counts Consequently it could be advantageous to reduce the weight of pixels illuminated by a bright source when generating images intended for detection of weak sources Since we are always operating with very few counts in the individual detector pixels the pixel counts cannot be used to determine the relevant weights instead the weights are derived from the pixel illumination functions PIF used in the source fitting procedure A new PIF weighted image generation algorithm based on the above considerations have been implemented and is available in the new JEM X Scientific Analysis package PIF imaging can be activated by including the string PIF in the IMA_skyImagesOut string accessible from the jemx_science_analysis GUI as one of the hidden parameters Example IMA_skyImagesOut PIF RECONSTRUCTED VARIANCE Abbreviations as e g PIF RECON VARIA can also be used The PIF imaging technique improves the visibility of weak sources in crowded fields like the Galactic Centre or in the neighborhood of strong sources like the Crab or GRS 1915 105 Figure 13 NOTE HOWEVER THAT PIF IMAGES SHOULD NOT BE USED WITH mosaic spec FOR THE TIME BEING IT IS NOT RELIABLE TO EXTRACT SPECTRA WITH mosaic_spec 6 7 7 FOR STRONG SOURC
97. e REP_BASE_PROD variable to the location where you perform your analysis e g the directory jmx_data_rep Thus type setenv REP_BASE_PROD PWD Then if not already set by default by your system administrator you should set some environment variables and type setenv ISDC_ENV directory_of_OSA_sw_installation setenv ISDC_REF_CAT REP_BASE_PROD cat hec gnrl_refr_cat_0031 fits 1 source ISDC_ENV bin isdc_init_env csh The idea is to e set ISDC_ENV to the location where OSA is installed e set ISDC_REF_CAT to the DOL of the ISDC Reference Catalog e run the OSA set up script isdc_init_env csh which initializes further environment variables relative to ISDC_ENV Besides these mandatory settings there are two optional environment variables COMMONLOGFILE and COMMONSCRIPT which are useful e By default the software logs messages to the screen STDOUT To have also these messages in a file i e common_log txt and make the output chattier use the command setenv COMMONLOGFILE common_log txt e When you launch the analysis the Graphical User Interface GUI is launched As your level of expertise with the software increases you may wish to not have the GUIs pop up when you launch your analysis In this case the variable COMMONSCRIPT must be defined setenv COMMONSCRIPT 1 3If the setenv command fails with a message like setenv command not found or setenv not found then you are probably using the sh family I
98. e input observation group or selected by the user The input intensity IMATYPE RECONSTRUCTED or RECTIFIED or RAWINTENSITY is selected by use of the parameter mapSelect Note that if the user wants to extract fluxes from the image only RECONSTRUCTED recommended or RECTIFIED make sense There are four parameters defining the mosaic skymaps produced in the output file so it can have for each energy band up to four image extensions depending on the chosen options showing in the following respective order 1 RECONSTRUCTED default or RECTIFIED or RAWINTENSITY depending on the input inten sity IMATYPE see above it is the weighted intensity map counts cm s produced by use of the parameter viewIntens 2 VARIANCE the weighted variance map use viewVar 3 SIGNIFICANCE the significance map use viewSig defined as the intensity divided by the square root of the variance at each pixel 4 EXPOSURE the effective exposure times use viewTime expressed in seconds taking account of the dead time grey filter effects and vignetting of the JEM X instruments Notice the vignetting used is normalised to 1 at the center of JEM X FoV so as this corresponds to an effective detector aera of about 70 cm2 in average depending on the actual energy range With the latter option an additional map is also produced in the last extension OBS_TIME of the output file that shows the accumulated raw observati
99. e is named JMX1 SLOC RES and is similar to JMXi SRCL RES which makes it possible to run e g q_identify_srcs and cat2ds9 There are some extra columns with additional information such as SIGMA result of fitting PEAKSIZE volume of peak as fitted Table 25 _ ma_src_locator parameters Name Type Description inDOL string DOL of an image or of a DAL group default jmos fits 1 varDOL string DOL of corresponding variance map default sigDOL string DOL of corresponding significance map If inDOL is a group the two parameters above are ignored If inDOL is an image then sigDOL is used as signif icance map if not empty then varDOL is used as variance map if not empty default ISDC JEM X Analysis User Manual Issue 10 0 67 slocRes outFile catDOL sigmaPSF sigmaFlat erode maxNumsSrcs maxNumCatSrcs boxwidth detsigMin imaTypes savel saveF saveM saveK saveC string string string real real integer integer integer real string boolean boolean boolean boolean boolean File for SLOC RES override Currently not active jemx_science_analysis script default jmx1_sloc_res fits JMX1 SLOC RES Name of output FITS file with source results Name of output file that will be placed where DAL_CURRENT_DIR points default jmx1_sloc_res DOL of user defined X ray catalog FITS tabl
100. e signal from a source is distributed over several adjacent pixels the number is given by the PSF a better source significance evaluation is done by combining several pixels around the source The distribution of significance values in the map is analyzed and a suggested value for the parameter detsigMin is given in the log file search for the string Suggest Variance map If the search for a significance map has failed the alternative is to use a variance map For an individual image it can be given by parameter as a DOL The significance map is constructed by dividing the input image with the local RMS or the square root of the variance map Bootstrap variance In the case of a missing variance map then the local RMS map square root of the variance is built by finding the RMS value by a sliding box excluding the pixels that are the highest contributors to the RMS This method will reduce the effect of the extraordinarily high values of the RMS if there is a source inside the sliding square box Source fitting Once a source candidate has been spotted a gaussian fit with both position sigma and amplitude as free parameters is done around the initial position in the intensity image and both the derived sigma and the peaksize are reported The best source position is given as the fitted peak position Currently there is no way to e g freeze the width of the PSF Output data structure The output data structur
101. e values 7 100 default 4 Lower channel boundaries for shadowgrams and lightcurves default 46 83 129 160 Upper channel boundaries for shadowgrams and lightcurves default 82 128 159 223 Start of time interval IJD 1 use Science Window bounds default 1 ISDC JEM X Analysis User Manual Issue 10 0 91 timeStop nPhaseBins phaseBins radiusLimit real integer string real End of time interval IJD 1 use Science Window bounds default 1 Number of phase bins N lt 0 abs N equally spaced bins default 0 Phase bin sizes separated by space default Use events within this detector radius mm possible values 0 0 130 0 default 122 0 Parameters required for Instrument Characteristics selection IC_Group IC_Alias instMod response string string string string DOL of the Instrument Characteristics master group This group is accessed by the script to find the calibration data relevant for the current Science Window default idx ic ic_master_file fits GROUPING 1 Selection alias for Instrument Characteristics By changing this alias different instances of IC data can be selected default OSA DOL of JEM X Instrument Model Group empty find in IC default Filename of standard RMF and ARF empty find in IC default Parameters specific to corrections COR COR_gainHist
102. e with columns RA OBJ DEC_OBJ FLAG for the positions where a source fit is requested irre spective of the existence of a source default Defines the gaussian PSF width in pixels Start point for the fitting default 1 5 avoid use If set to a positive number then the input image will be flatfielded with a gaussian of this sigma before further analysis default 0 0 Determines how much of the edge of the image where the noise often is overwhelming should be excluded from source finding A high value implies a wide edge to be removed and vice versa default 5 0 Maximum number of sources to search for A limit to the number of sources prevents the output file to expand to an unreasonable size default 14 Maximum number of catalog sources to include used to define the amount of memory to allocate to the internal data arrays default 14 Edge dimension of sliding box The edge size of the box used for finding the local RMS Should be about five times larger than the FWHM of the PSF default 11 Detection significance lower limit With the current scheme put to 14 If you get too many spurious sources then choose a higher value default 0 3 Image types to search for sources Only applicable if the input is a group A good choice is RECON STRUCTED default RECONSTRUCTED Flag for saving input image default n Flag for saving flat fielded image default
103. each ScW cd REP_BASE_PROD og_create idxSwg mos lst ogid ima_lc baseDir instrument JMX2 cd obs ima_lc jemx_science_analysis startLevel COR endLevel IMA jemxNum 2 nChanBins 2 chanLow 46 129 chanHigh 128 223 For each source IMA step output contains fluxes in 3 standard IMA energy bands plus the fluxes in the energy bins specified by nChanBins chanMin and chanMax parameters To extract the ScW by ScW lightcurve from the images one has to run the script src_collect group og_jmx2 fitst 1 results GX354_scw_lc fits instName JMX2 select NAME GX 354 0 As a result the file GX354_scw_lc fits will contain the source lightcurves in the 3 standard and the user defined energy bands To display the lightcurve e g in the 1st user defined energy band 3 10 keV in our example you can use the fv program to plot the FLUX 4 FLUXERR 4 vs TSTART The 4 in the square brackets signifies that one wants to plot the 4 th energy band remember that the first three bins always contains the fluxes in the detection images so the first user bin is the 4th one One can extract the light curve in a single energy bin usuing the following command fcopy GX354_scw_lc fits col TIME TSTART TSTOP 2 RATE FLUX 4 ERROR FLUX_ERR 4 light_curve fits This file can be visualized with lcurve as explained above Note that the source GX 354 0 is a bright X ray binary which is detected in each ScW so that information about
104. ecause the source extraction does not take into account the presence of the other sources 7 If you mix FULL and REST data then be sure to give chanMin Max that match REST channel limits for example chanMin 64 128 160 192 chanMax 127 159 191 223 8 In OSA v 7 0 and later the source position reported in columns RA _OBJ and DEC_OBJ of JMX SRCL RES will always be the one found by j_ima_iros Columns R A CAT and DEC_CAT reflect the catalog position if a user catalog has been defined The SPE and LCR levels will read the RA_OBJ and DEC_OBJ columns and do the extraction using those In order to force the use of the catalog positions which is recommended the JMXi SRCL RES table must be manipulated e g by an ftool to update columns RA_OBJ and DEC_OBJ 9 Light curve extraction is unchanged in OSA 10 compared to previous versions in order to allow the easy generation of short bin light curves However long term stability is not assured in this case the user interested in long term light curves or who doesn t need time bins shorter than the length of a science window is advised to generate light curves from the imaging step as explained in the cook book 10 It has been noticed that in mosaics of JEM X images a plus like depression in the background around certain sources can occur This can happen for sources that are too weak to be noticed in the search for sources in the individual science windows The cleaning process excludes known
105. ectral analysis a response redistribution function RMF should be generated according to the spectral binning specified by the user The j_rebin_rmf script allows to do this very easily There are several ways to 11To force the use of the catalogue positions the JMXiSRCL RES table must be manipulated by e g an ftool to update columns RA_OBJ DEC_OBJ For more details see section 9 ISDC JEM X Analysis User Manual Issue 10 0 30 nChanBins chanLow chanHigh 0 46 223 1 46 130 129 223 2 46 77 130 175 76 129 174 223 3 46 59 77 102 130 153 175 199 58 76 101 129 152 174 198 223 4 46 52 59 68 77 89 102 117 130 51 58 67 76 88 101 116 129 141 153 165 175 187 199 211 140 152 164 174 186 198 210 223 Table 5 Standard energy binning run this script The user can specify the bins individually generate a bin list in a text file see FTOOLS rbnrmf explanations For example j_rebin_rmf chanMin 46 77 130 175 chanMax 76 129 174 233 jemx_num 2 or j_rebin_rmf binlist mybins txt outfile jmx1_rmf_mybins fits Otherwise it is possible to use pre defined standard binnings matching those set with nChanBins lt 1 j_rebin_rmf binlist STD_016 matches nChanBins 4 As a result a file jemx_rebinned_rmf fits unless a different file name has been specified through outfile which contains the rebinned RMF will be produced Note that jemz_num 1 is the default value The output file name default jemx rebinned_rmf fits can
106. ed middle position of the mo saic default 1 ISDC JEM X Analysis User Manual Issue 10 0 65 DECcenter real Center of the mosaic image Declination in degrees not used if RAcenter lt 0 default o outfile string Mosaic FITS file prefix name optional default viewTime boolean Create total exposure Time map if Y produce both raw exposure time map and energy dependent effective exposure maps default Y viewIntens boolean Create raw Intensity map default Y viewVar boolean Create Variance map default Y viewSig boolean Create Significance map default Y view_nb boolean Create a map that shows the number of input images contributing to each pixel default N AITproj boolean Produce map in galactic coordinates using AIToff Hammer projection default N print_ScWs boolean List input Science Windows in mosaic headers default N chatter integer Level of test output default 2 8 11 2 src_collect This executable combines source data obtained by the imaging analysis for individual Science Windows into a single table covering an Observation Group It is possible to retrieve only selected results Table 24 src_collect parameters specific to the IMA2 level Name Name Type Description main script executable IMA2 srcFileDOL results string DOL of the output source list mosaic default
107. el 0 a linear interpolation between gain corrections is used for each event or spectrum at a given time For gainModel 2 a time decay model is used to smooth out statistical noise and discharge glitches at the calibration points It is recommended that gainModel 2 is used for all processing gainModel 1 is obsolete and should not be used it is only included for backward compatibility The JEM X detector gain varies significantly at the beginning of each revolution for a few hours after the instrument has been switched on The pattern is very similar each time and modeled in the gain correction step if the parameter COR_gainModel is not 0 Due to aging of the instruments the JEM X units in particular JEM X1 have become sensitive to not only temperature but also the total hardware trigger rate of the detector For COR_gainModel 4 ISDC JEM X Analysis User Manual Issue 10 0 47 Jjemx_science_analyis jemx_scw_analyis jemx_obs_analyis jemx_obs_analyis j_ima_mosaic src_collect Figure 22 Detailed decomposition of the jemx_science_analysis script performed for revision 2 data ISDC JEM X Analysis User Manual Issue 10 0 jemx_scw_analyis j_correction j cat extract cat extract j image bin j_ima_shadowgram j_imaging j_ima_iros q_identify_sres j_src_extract_spectra j_reform_spectra j_src_extract_le j_bin_evts_spectra j_bin_spec_spectra j_bin_bkg_spectra Grey boxes correspon
108. ension will be correctly interpreted in the file fits 1 case On the command line though the normal CFITSIO and FTOOLS rules apply i e you have to specify it as one of the following file fitsl 1 file fits 1 file fits 1 Note that if no extension is specified explicitly then the first one 1 will be used by default e What are the general functionalities of the GUI When you launch the analysis by default the GUI is launched providing an opportunity to set the values of all desired parameters see Figure 10 On the right side of the panel you see the following buttons Save as With the Save As button a file is created This file stores all parameters as they are currently defined in the GUI as a command line script This file is an executable one and calling it from the command line will launch the instrument analysis program with the parameters as they were defined in the GUI Load With the Load button a previously saved file see Save As can be read and the GUI will update all parameters with the values as they are defined in the loaded file Reset With the Reset button the parameters in the GUI will be reset to the default values as they are defined in the parameter file of the instrument analysis program and stored in the ISDC_ENV pfiles directory Run With Run button the analysis is launched Quit With Quit button you quit the program without analysi
109. event STATUS Goodness of the corrected events JMXi RATE COR RATE_CORR Corrected count rate STATUS Goodness of the data JMXi SPTI COR PI Pulse Invariant energy of the event STATUS Goodness of the corrected events JMXi SPEC COR SPEC_CORR Corrected Counts in the 64 PI channels STATUS Goodness of the corrected spectra The TIME data do not have a COR data structure as the on board time is calculated at ISDC during the Data Preparation so the corrected TIME events are in JMXi TIME PRP C 2 jogti This script builds Good Time Interval information from housekeeping data information about satellite stabil ity and data gaps As a result the program writes the merged GTI into the output GTI table JMXi GNRL GTI Table 43 Table 43 Content of JMXi GNRL GTI Data Structure Column Name Description OBT_START On board time of start of the GTI OBT_END On board time of end of the GTI START IJD time of start of the GTI STOP IJD time of stop of the GTI UTC START UTC time of start of the GTI UTC_STOP UTC time of stop of the GTI C 3 j_ dead time At this step dead time is calculated It is saved to JMXi DEAD SCP Table 44 which is stored once for each science window ISDC JEM X Analysis User Manual Issue 10 0 83 Table 44 Content of JMXi DEAD SCP Data Structure Column Name Description OB_TIME OBT of the dead time calculation D
110. gle JEM X detector by rebinning data in pure spectrum format to spectra The output is written to JMXi SPEC DSP which has the same structure as the data structures described in Table 52 Table 19 j_bin_evts_spectra specific to the BIN_S level Name Name Type Description main script executable nPhaseBins nPhaseBins integer Number of phase bins N lt 0 abs N equally spaced bins default 0 phaseBins phaseBins string Phase bin sizes separated by space default BIN_S _rowSelectSpec rowSelect string CFITSIO selection string on spectrum mode data default gt 8 9 3 j_bin_bkg_spectra This executable generates time resolved spectra for a single JEM X detector by rebinning background model data to spectra Table 20 j_bin_bkg_spectra specific to the BIN_S level Name Name Type Description main script executable BIN_S_evt Type evtType integer Data format to bin possible values 1 all O FULL 1 REST 2 SPTI 4 SPEC default 1 8 10 j_bin_Ic The j_bin_lc script bins event data into lightcurves in different energy bands The binning format is deter mined by input parameters to the executables Empty fields are also binned for use in the background model catalogue This script deals with background issues in a different fashion than the image reconstruction processes There is no attempt at subtracting the background during
111. gle_arf2 fits files The names of the response and ancrfile are inserted in the keyword of the final files so that they are automatically recognised by XSPEC 7 5 Create your own user catalog Read this if you are familiar with the sources in your field of view and you want to build your own catalog for the Imaging step spectral and light curve extraction As already discussed in section 6 6 it can be very useful to use your own input catalog for the imaging and in particular spectral and light curve extraction The easiest way to build it is to modify the general catalog ISDC JEM X Analysis User Manual Issue 10 0 43 with the help of the fcopy program of FTOOLS For example if you want to create a catalog usrcat fits with only three sources Crab 3C111 and XPer do the following cd REP_BASE_PROD fcopy ISDC_REF_CAT NAME Crab NAME 3C 111 NAME X Per usrcat fits chmod w usrcat fits If you want to add a new source not specified in the general reference catalog add a line to usrcat fits with the help of the fv tool and fill in the Source ID NAME RA_OBJ and DEC_OBJ columns As Source_ID you can choose whatever you like provided that this identifier is unique This catalog can be used in JEM X analysis by means of the CAT_I_usrCat parameter see an example in section 6 7 4 The FLAG column in usrcat fits should be set to 1 e g with the program fv to have the cata log source positi
112. haracteristics Data used in Scientific Analysis o 74 Bl The MOTE group o r ee ia Be ee A AAA A aS 74 ES e EHH AI 76 B3 Energy Bionime ADO to Pl ee nR K tarea NE o eee ee 77 BA Detector positions sc se si k smor be ERA aa A e 81 B 5 Detector Response Matrix 1 a a 81 C Selence Data Products o cte ee ee dR R e a a ee Oe ee i be 82 Cel lt lt c 1 o ee aS ke AA A ee Ee a we a 82 CA1 ILOG a RE a s a AR BYE E a OY e Se al a Ge a 82 CL Z T sia E aa a aui a we KOR a Gogs 82 C2 PAU eera ERR GR eee Pee we ee ee ee Oe ee a 83 G3 PUUE a 5 ey Gy By RL T Sh he eR O ee ls SR ds A T N 83 C 4 LE fee ee eRe ee A Rw Rea ow eke a he ee Ree ed 84 Co E oe Oe es De Bee ee EO ee a 84 Go EA 84 C 6 1 TANTOS fe a ee ee RR ER ow eee ke ok ee Ee Ble 24 84 C 6 2 GRENE 0 te Ph AE AAA ee ee a 85 GE Jore enr SDE os oie ce BOS AA Ge S A oe A amp a 85 Ce IN IAN 86 C 8 1 PRONE DAA O ady EE RR REE Ta a ee AA R e 87 CO JD SPEC E 87 C 9 1 TO eVa AE 87 E E Z SPECTO ce ee A eae we a 87 OLIVO ADMG e RA BAG ee A EDR AA Dae ee ae ek A 88 C 11 Observation group level analysis o o eee eee eee 89 ISDC JEM X Analysis User Manual Issue 10 0 vi C 11 1 jimamosaic CVU we T c ek i rosea D jemzscience analysis parameters description ISDC JEM X Analysis User Manual Issue 10 0 vil List of Figures 1 JEM X effective area with the mask taken into account oo o 2 Overall design of J
113. he case of telemetry saturation due to a solar flare or when PICsIT is in non standard mode you can obtain spurious results A typical case is finding an 8 sec period in your data due to the fact that the telemetry restart is synchronized with an 8 sec frame When possible compare your results with IBIS ISGRI ii_light that is immune to this problem and can reach about 0 1 sec binning ISDC JEM X Analysis User Manual Issue 10 0 45 Table 6 JEM X imod files instance number to use indicative To have the exact validity range check the FITS file header in your IC tree JEM X 2 JEM X 1 Revolution interval IMOD instance XXX jmx1_imod_grp_0XXX fits Revolution interval IMOD instance XXX jmx2_imod_grp_0XXX fits 1 8 9 14 15 19 20 37 38 44 45 93 94 163 164 197 198 221 222 244 245 310 311 406 407 458 459 532 533 622 623 659 660 713 714 781 782 869 870 934 935 999 1000 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 ISDC JEM X Analysis User Manual Issue 10 0 1 5 6 9 10 14 15 37 38 44 45 71 72 93 94 135 136 172 173 197 198 244 245 310 311 389 390 499 500 579 580 659 660 713 714 799 800 855 856 857 869 870 934 935 999 1000 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309
114. he first source detection phase of j_ima_iros a catalog match will be searched If found the catalog coordinates will be used during the IROS process The user may want to force j_ima_iros to analyze a source which is not detected with sufficient strength to be included in the basic source set This can be done by assigning specific values to the FLAG column of the user catalog A value of one will force j_ima_iros to derive flux values for the source The flux will be derived from a fit including the basic source set plus the desired source If several sources are marked in this way a separate fit is performed for each source together with the basic source set A value of three for the FLAG will force j_ima_iros to include this source in the basic source set It can be useful for very strong sources near the edge of the FOV that are not detected because they are too close to the edge or the exposure time is too short But beware Forcing irrelevant sources into the IROS process will normally deteriorate the fit The pixel size in the sky image is 1 5 arcmin and the dimensions are 511x511 pixels The distribution of pixel values in the reconstructed and cleaned image RECONSTRUCTED is not Gaus sian see Fig 24 which implies that the detection significance limit should be set somewhat higher e g to 12 than a number of sigma s The presence of the collimator introduces a vignetting of off axis sources Also at off axis angles greate
115. he parameter Intensity specifies which of the possible intensity images will be used for the spectral extraction only RECONSTRUCTED or RECTIFIED can be meaningfully used RECONSTRUCTED is recommended For JEM X the use of the size parameter that in the past was set to size 7 is now obsolete To extract the spectrum from the mosaic image go to the directory which contains jmx2_mosa_ima fits and run mosaic_spec in the following way cd esl mosaic_spec DOL_idx jmx2_mosa_ima fits DOL_spec spectrum_mosa fits JMX2 PHA1 SPE tpl EXTNAME JMX2 MOSA IMA ximg 0 yimg 0 ra 261 89 dec 30 80 posmode 0 widthmode 1 psf 2 0 Intensity RECONSTRUCTED As a result a spectrum spectrum_mosa fits will be extracted from the sky position of 4U 1722 30 In this second case we used the combination of parameters widthmode 1 psf 2 0 as the PSF of mosaic images is slightly larger than the PSF of single pointing images ISDC JEM X Analysis User Manual Issue 10 0 35 To analyse the spectra you need to rebin the response matrix with the help of ftool j_rebin_rmf as it is explained above The ancillary response function ARF for JEM X2 spectra can be automatically extracted from the IC tree using the script j_image_arf j_image_arf jemx_num 2 outfile jmx2_image_arf fits Note that this ARF can only be used with spectra extracted with mosaic_spec either for ScW images or from mosaics The ARFs to be used when running the SPE step and spe_p
116. his can be changed by the user this should not be modified in normal analyses To generate images in arbitrary energy bands see section 6 6 7 In the upper frame of the front panel called General you can choose at which level you want to start and stop the script execution In the Overview chapter you have seen that there are different processing levels of the analysis You can choose to run only some of them The default settings of the jema_science_analysis script are startLevel COR start the script at COR level endLevel IMA2 stop the script at IMA2 level It is advisable always to start with level COR This will allow the processing of the data using the latest knowledge of the calibration of the instrument ISDC JEM X Analysis User Manual Issue 10 0 21 If you want to skip some levels click on the hidden button on the right of the GUI panel to access the whole set of jemx_science_analysis parameters In the frame General you find the skipLevels parameter However be always careful while setting this parameter levels often depend on the previous ones so make sure that your selection makes sense Another useful hidden parameter IMA_skyImagesOut in the IMA section enables you to choose the types of images which you want to output The checkbox IMA_detImagesOut enables you to output also the images in the pre defined energy bands used by the j_ima_iros for the source search This option is not recommended if
117. ible values TJD UTC OBT default OBT ISDC JEM X Analysis User Manual Issue 10 0 51 GTI_Accuracy Accuracy string Accuracy used for OBT to IJD conversion and vice versa possible values any inaccurate accurate default any 55 8 2 5 gti merge This program merges zero one or more GTIs to a new GTI It is an AND operation time in the result GTI is defined to be good if this time is in every input GTI defined as good It also filters times flagged as Bad Time Intervals see Section 7 2 Table 12 gti merge parameters included into the main script Name Name Type Description main script executable GTI_gtiJemxNames JMX1_Mode string Names of JEM X GTIs to be merged JMX2_Mode default GTI BTI Dol BTLDol string DOL of a bad time interval table default gt GTI_BTL Names BTI Names string Periods marked by a type of BTI listed in BTI_Names are excluded from the analysis Possible values are BAD_RESPONSE and BAD_CONFIGURATION which are both excluded by default The user wishing to analyse data from a period affected by some BTI can remove the BTI type from B TI_ Names However in general the result will be scientifically invalid and this functionality must be used with extreme caution default BAD_RESPONSE BAD_CONFIGURATION 8 3 j_dead_time This script derives a history of dead
118. ick are different and are automatically found and attached to the spectra by the jemz_science_analysis script Now you can enter the spectra extracted from the images in the individual ScWs and from the mosaic image into XSPEC and analyse them in a way similar to the one described in the previous sections xspec data spectrum_mosa fits resp jemx_rebinned_rmf fits arf jmx2_image_arf fits cpd xw setplot energy plot ldata The resulting spectrum is shown in Fig 20 data and folded model jmx2_mosa_ima fits A l gt 2 Ta a E 3 i aL E E 1074 L p a E P g 2 1 L J pare Ee x la T EH 4 E 4 2 A A A 1 A 10 20 Energy kev Figure 20 The spectrum of 4U 1722 30 extracted from mosaic image ISDC JEM X Analysis User Manual Issue 10 0 36 6 8 Source Lightcurve Extraction 6 8 1 Lightcurve extraction at LCR level The lightcurves of sources found at the IMA step are created at the LCR level of the jemx_science_analysis script However this step is omitted by default LCR step should be used only for the cases where time bins shorter than the duration of one ScW are necessary If the ScW time scales are sufficient better fluxes are obtained from the IMA step see section 6 8 5 The file jmx2_srcl_res fits serves as an input catalog for the lightcurves extraction in each ScW It is im
119. identify_srcs srcl_cat_dol ISDC_REF_CAT srcl_res_dol jmx2_sloc_res fits instrument 5 use instrument 4 for JEMX 1 and instrument 5 for JEMX 2 As a result the list of sources in the file jmx2_sloc_res fits looks like it is shown in Fig 17 When inspecting the result the user might want to get rid of too many spurious sources or include more sources that seem to be present To achieve the latter the parameter maxNumSrcs must have an adequate value and the detsigMin parameter might be lowered Analogously detsigMin can be increased to avoid false sources and there is some help in the log file to find a reasonable value Giving a negative detsigMin will cause j_ima_src_locator to apply a limit of the first found histogram value exceeding one plus the absolute value of the given detsigMin The JEM X coded mask has an almost non cyclic pattern which ensures imaging artifacts ghost sources are particularly rare Nevertheless in some peculiar cases a bright source inside the FOV might cause the presence of ghosts in the mosaic These artifacts appear at 8 32 degrees from the bright source To verify that a New Source in the sloc_res file is not instead a ghost a simple test consists in checking whether there are bright sources at 8 3 deg from it in the FOV 101f you encounter a doubtful case you can contact the help desk at http www isdc unige ch integral support helpdesk ISDC JEM X Analysis
120. inal 4096 energy channels into 256 calibration telemetry channels This table is used to bin the calibration data only since this is binned in the DFEE and transmitted as housekeeping The bin boundaries have been corrected for any ADC non linearity that might arise during flight Lists the corrected upper limits of the bins used to convert the original 4096 energy channels into 256 full imaging and spectral timing energy telemetry channels The bin boundaries are corrected for ADC non linearity Lists the corrected upper limits of the bins used to convert the original 4096 energy channels into 8 restricted imaging telemetry channels The bin boundaries are corrected for ADC non linearity Lists the corrected upper limits of the bins used to convert the original 4096 energy channels into 64 spectral mode telemetry channels The bin boundaries are corrected for ADC non linearity Contains the fractional corrections in percent to the raw event energy gain coefficients for all event modes from the JEM Xi instrument as determined by pre flight calibrations and in flight data For each pixel the difference is determined compared to the average gain of the entire detector area The second slice of this table contains the percent corrections to be applied for each anode due to anode deaths and instabilities See also Section B 3 Lists the nominal energy boundaries of the PI channels for energy measure ments obtained with full and spectral timing modes
121. ined by a lookup table used by the Data Processing Electronics DPE to pack the telemetry After the high voltage reductions this table has been updated to match the changed ADC signal strengths See also Appendix B 3 for more details ISDC JEM X Analysis User Manual Issue 10 0 7 3 2 2 PI Binning The PI bin limits in keV have been defined so that the entire energy range nominally 3 100 keV is covered and the binsize is a more or less constant fraction of the detector resolution The PI binning table for the Full Imaging mode with the highest number of bins 256 is shown in Table 3 See Appendix B 3 for more details Table 3 Energy boundaries of the PI channels PI Emin Emax PI Emin Emax PI Emin Emax 0 0 00 0 06 86 6 24 6 32 171 17 90 18 16 1 0 06 0 12 87 6 32 6 40 172 18 16 18 42 2 0 12 0 18 88 6 40 6 48 173 18 42 18 68 3 0 18 0 24 89 6 48 6 56 174 18 68 18 94 4 0 24 0 30 90 6 56 6 64 175 18 94 19 20 5 0 30 0 36 91 6 64 6 72 176 19 20 19 46 6 0 36 0 42 92 6 72 6 80 177 19 46 19 72 7 0 42 0 48 93 6 80 6 88 178 19 72 19 98 8 0 48 0 54 94 6 88 6 96 179 19 98 20 24 9 0 54 0 60 95 6 96 7 04 180 20 24 20 50 10 0 60 0 66 96 7 04 7 12 181 20 50 20 76 11 0 66 0 72 97 7 12 7 20 182 20 76 21 02 12 0 72 0 78 98 7 20 7 28 183 21 02 21 28 13 0 78 0 84 99 7 28 7 36 184 21 28 21 54 14 0 84 0 90 100 7 36
122. ing applied to input tables default IMA2 srcattach boolean Attach resulting table to group default y ISDC JEM X Analysis User Manual Issue 10 0 100 References 1 ISDC OSA INTRO Introduction to the INTEGRAL Data Analysis http www isdc unige ch integral download osa doc current osa um intro pdf 1 13 17 20 33 37 39 44 50 51 53 2 JEM X observer s manual http integral esac esa int AO10 AO10_JEMX_ObsMan pdf 1 3 JEM X Analysis Scientific Validation Report http www isdc unige ch integral download osa doc current osa sci_val_jemx pdf 1 4 ISDC OSA INST GUIDE Installation Guide for the INTEGRAL Data Analysis System http www isdc unige ch integral download osa doc current osa_inst_guide pdf 16 5 IASW for JEM X DPE Software Specification Document Space Research Center PAS Warsaw Ver sion 1 11 16 06 00 6 Fenimore amp Cannon 1978 Appl Opt 17 337 7 Instrument Specific Software for JEM X Architectural Design Document http www spacecenter dk oxborrow sdast ISSW ADD10 0 ps 8 Walter R Favre P Dubath P et al 2003 A amp A 411 L25 45 ISDC JEM X Analysis User Manual Issue 10 0 101
123. ivity isolated source on axis 1 6 x 10 4 ph cm 2s 6 keV 1 3 x 1074 ph cm s7 20 keV for a 30 line detection in 10 s Timing resolution 122 us relative timing 1 ms absolute timing T The energy resolution is slowly changing degrading over time t At the half response angle the sensitivity is reduced by a factor 2 relative to the on axis sensitivity ISDC JEM X Analysis User Manual Issue 10 0 ner JEM X Effective Area eiii 19 100 Energy kev Fi 1 ee JEM X effective area with the mask taken into account The dashed line shows the effective area before the high voltage reduction and the full curve shows efficiency when taking into account the effect of the electronic low signal cutoff approximately 2 Instrument Description 2 1 The Overall Design JEM X consists of two identical coded aperture mask telescopes co aligned with the other instruments on INTEGRAL The photon detection system consists of high pressure imaging Microstrip Gas Chambers MSGC located at a distance of 3 4 m from each coded mask Figure 2 shows a schematic diagram of one JEM X unit A single JEM X unit comprises 3 major subsystems the detector the associated electronics and the coded mask The two JEM X units have been used alternatively in the past and are currently operated simultaneously The decision to use only one instrument at a time was made about three months after launch when a gradual loss in
124. jmx2_obs_res fits jmx2_obs_res_original fits With the fdelrow command you detach from the first extension of og_jmx2 fits row number 2 the first row to be deleted number of rows to be deleted 1 you were shown no keyword values N and you agreed to proceed Y At this point you can run again the mosaic step through jemz_science_analysis with Start and End levels both set to IMA2 7 4 Combining results from different observation groups Read this if you have a set of science windows belonging to different runs for which you have already built images spectra or lightcurves and want to combine the results Section 7 4 1 explains how to combine all the existing images in a final mosaic while section 7 4 2 shows how to merge different lightcurves and spectra 7 4 1 Creating a mosaic from different observation groups Suppose you want to analyse 5 Science Windows and are not interested in the final mosaic You create the group with og_create and then you launch the analysis till the imaging step but without the mosaic step i e from COR till IMA see 6 6 An image is created per Science Window but you do not have the overall final mosaic If you then change your mind and decide that you want the mosaic all you have to do is to move in the working directory REP_ BASE_ PROD obs xxx and relaunch the jemx_science_analysis ISDC JEM X Analysis User Manual Issue 10 0 41 command with startLevel IMA2 endLevel
125. l pointings the Science Window Groups can be arbitrarily grouped into bigger groups the Observation Group to select data very efficiently according to the user s needs Indices are a special kind of groups which differ only in the fact that all the the data sets they contain are similar and that the indices know the properties of the data sets they contain Indices are a kind of poor man s database For example an imaging program creates several images of different types flux map significance map in different energy bands These images are stored in an index in which the image type and energy band information is replicated ISDC software is then able to select very efficiently the needed images The user can also make use of the indices just by looking at the index for instance using fv the user can identify immediately the content of each image e Why do I need 1 after a FITS file name A FITS file can have many extensions and sometimes it is necessary to specify as input to a given pa rameter not the file name alone file fits but the extension too file fits 1 or file fits 21 5The IBIS Cookbook is available at the URL http www isdc unige ch integral analysis ISDC JEM X Analysis User Manual Issue 10 0 19 etc The file name with a specified data structure extension is called DOL Data Object Loca tor When you modify the parameter file itself see above or use the GUI the ext
126. lter values have a single event resolution that allows for somewhat better determination of the instantaneous ISDC JEM X Analysis User Manual Issue 10 0 52 deadtime This procedure does not however replace the need for an offline deadtime analysis for very rapidly varying sources 8 4 3 cat extract This script extracts from the ISDC catalogue list of sources relevant to the Science Window in question with the help of cat_extract executable It selects all the sources with fluxes known to be in the selected range and lying in the hollow cone layer defined by user Tf fluxes are not specified then all sources are selected It is possible to specify different flux criteria for different layers Several layers can be mentioned in one call More information on the ISDC catalogue you find in the Introduction to the INTEGRAL Data Analysis 1 In Table 13 you find the description of the parameters specific to the CAT_I level Table 13 j_cat_extract parameters included into the main script Name Type Description CAT _L refCat string DOL of Reference Catalog default ISDC_REF_CAT CAT LusrCat string DOL of User Catalog default CAT LradiusMin string Low limit for the position selection default 0 2 4 CAT LI radiusMax string High limit for the position selection default 2 4 5 8 CAT_LfluxDef string Column used for flux selection possible values 0 No flux selection 1
127. meter endLevel All data structures with a level equal or prior to endLevel will be kept while the data structure with a later level will be erased For example to run the image extraction IMA level you should clean from the group whatever comes after the BIN_I level as this is the level immediately preceding the IMA one og_clean ogDOL 0g_jmx2 fits endLevel BIN_I If og_clean fails it could be due to the fact that the group was corrupted You should try to fix it with dal_clean program dal_clean inDOL og_jmx2 fits checkExt 1 backPtrs 1 checkSum 1 and launch og_clean only afterwards 7 3 1 Creating a second mosaic in the Observation Group If you already extracted a mosaic from the Science Windows in your Observation Group as explained in section 6 6 4 and now you would like to extract a second mosaic on the same Science Windows changing e g the IMA2 diameter parameter you will see that og_jmx2 fits points to the initial mosaic output row 2 of the first extension is jmx2_obs_res fits This will interfere with the new mosaic you are about to launch You will need to detach the previous results from the og_group and rename or delete them To do so you can either clean the og_group with the task og_clean as explained in section 6 6 4 or you can directly detach the former mosaic results from the group cd REP_BASE_PROD obs og_group fdelrow 0g_jmx2 fits 1 2 1 N Y mv jmx2_mosa_ima fits jmx2_mosa_ima_original fits mv
128. mode the output are spectra rebinned into PI channels Table 42 Whenever poor gain determination occurs the relevant events or spectra are flagged in the STATUS column of JMXi COR see the possible STATUS values in Table 41 C 1 2 j cor_position j_cor_position converts detector positions corrected for microstrip plate irregularities into absolute values mm from centre of detector Event positions are randomized within the pixel designated by the two event telemetry values RAWX and RAWY and given as floating point values in columns DETX and DETY of JMXi _COR If an event falls in an area where the position determination is known to be bad then a flag is raised in the STATUS column of the relevant COR extension Bad areas of the detector are signaled in the correction table extensions by having one or both position values equal to 1000 0 plus the corrected position value The possible values of STATUS are given in the Table 41 Table 41 Possible corrected event STATUS values Value Meaning 0 Event good for all analysis purposes 4 Events fall on anode segment with a dead anode in the calibration area currently 4th anode on JEM X 2 8 Event has uncertain time correlation 16 Event comes from an anode regarded as bad 32 Event comes from position next to a bad anode 64 Bad energy due to poor detector gain history determination 128 Bad energy determination due to event position 256 Bad X position determination 512 B
129. n that case please replace the command setenv my_variable my_value by the following command sequence my variable my_value export my_variable In the same manner replace the command source my script by the following command my script the is not a typo 4For example the exit status of the program will now appear ISDC JEM X Analysis User Manual Issue 10 0 18 When the GUI is disabled parameters can be specified on the command line typing name value after the script name To revert and have the GUI again unset the variable unsetenv COMMONSCRIPT 6 4 Useful to know In this section we report some general information that might be useful when running OSA software Most of these information can be found also in the IBIS Cookbook e How do I get some help with the executables All the available help files are stored under ISDC_ENV help To visualize a help file interactively type tool_name h once your environment is set i e the command which tool_name should return the path to it e Where are the parameter files and how can I modify them All the available executables for the analysis of INTEGRAL data are under ISDC_ENV bin The corresponding parameter files are stored under ISDC_ENV pfiles par The first time you launch a script the system will copy the specific tool par from ISDC_ENV pfiles to a local directory user_name pfiles The parameter file in the local directo
130. nction with E_MIN and E MAX as found in JMXi FBDS MOD JMXi RBDS MOD or JMXi SBDS MOD for the spectral response matrix For full description of these and other data structures see the ISDC webpage B 2 The BPL group The abbreviation BPL stands for backprojection lists Essentially this is the Aperture Response Function describing the visible sky elements from a given detector pixel The group JMXi BPL GRP contains a compressed table together with three auxiliary arrays plus vignetting arrays Table 34 describes those Data Structures Table 34 Content of JMXi BPL GRP Group Group Member Description JMXi DALL BPL JMXi DAWL BPL The d_allow array contains for each detector pixel a list of sky directions which have access to this pixel access here means that more half the pixel area is visible from above the mask along the direction in question The number of sky bins in the list corresponding to a given detector pixel is given as an entry in the d_allow_l array the full 16 bit address of the first direction having access to the pixel is given in the d_allow_p array The list itself is organized as a difference list each direction defined by an 8 bit unsigned number giving the difference between in addresses of the previous direction and the current direction Should two directions differ by more than 254 units the difference will be written by N bytes with the value 255 and finally a byte with the rem
131. ng background model data to spectra The output data structures are listed in Table 53 and has structure similar to one described in Table 52 but without BACKFILE and BACKSCAL columns ISDC JEM X Analysis User Manual Issue 10 0 Table 53 List of the j_bin_bkg_spectra output Data Structures Name Description JMXi FULL BSP Contains time resolved background spectra for Full Imaging data JMXi REST BSP Contains time resolved background spectra for Restricted Imaging data JMXi SPEC BSP Contains time resolved background spectra for Spectrum Format data JMXi SPTI BSP Contains time resolved background spectra for Spectral Timing data C 10 7_bin_Ic The j_bin_lc script bins event data into lightcurves in different energy bands There are two possible outputs of this program normal lightcurves and period folded lightcurves In the case of nPhaseBins 0 Data Structures JMXi DETE LCR IDX and JMXi DETE LCR are filled JMXi DETE LCR contains a countrate lightcurve for the whole JEM Xi detector binned from event or countrate data In the case nPhaseBins gt 0 Data Structures JMXi DETE FLC IDX and JMXi DETE FLC are filled JMXi DETE FLC contains a countrate lightcurve folded with a given period for the whole JEM Xi2 detector binned from event or countrate data Table 54 Content of JMXi DETE LCR IDX Data Structure Column Name Description DATAMODE Science format used to create lightcurve F
132. nless a delivered IC gain history table exists for the revolution being processed B Instrument Characteristics Data used in Scientific Analysis B 1 The IMOD group The group JMXi IMOD GRP contains the instrument model description data structures for JEM Xi Table 33 describes those Data Structures from that group that are used in the Scientific Analysis A specific version of these IC files consists of a number of instances each covering a time period during which the instrument setting and response can be considered constant The parameter name for all components and the jemx_science_analysis script is instMod When given as an empty string the script itself will define an appropriate DOL from the general IC tree masterfile Table 33 Content of JMXi IMOD GRP Group Group Member Description Data Structures used at COR level ISDC JEM X Analysis User Manual Issue 10 0 74 JMXi DETE MOD Contains the description of the JEM Xi detector plane Values indicate ac tive and inactive pixels bad anodes and their neighbours calibration spectra overflow areas and permanent hotspots if there are any Data Structures needed for Energy Correction See more details in Section B 3 and Tables 35 38 JMXi CALB MOD JMXi FULB MOD JMXi RESB MOD JMXi SPCB MOD JMXi SPAG MOD JMXi FBDS MOD JMXi RBDS MOD JMXi SBDS MOD Lists the corrected upper limits of the bins used to convert the orig
133. normalized counts s keV normalized counts s7 keV i Energy keV Energy keV Fi 18 ere Left panel Crab spectrum in ScW 010200210010 Right panel Combined Crab spectrum of ScW 010200210010 and ScW 010200220010 The JEM X systematics are of the order of a few percents typically 3 We add this explicitly to jmx2_srcl_spe fits file with the command below fparkey 0 03 jmx2_srcl_spe fits SYS_ERR add yes The obtained spectrum can be analysed e g within XSPEC program xspec XSPEC gt cpd xw XSPEC gt data jmx2_srcl_spe fits 1 XSPEC gt ign 5 0 XSPEC gt setplot energy XSPEC gt model po XSPEC gt fit XSPEC gt plot ldat del The above set of XSPEC commands reads the data file and fits the data with power law model The result is shown in the left panel of Fig 18 The fit results in a photon index of IT 2 08 0 11 and a normalisation at 1 keV of 9 1 To understand the importance of the user catalog let us extract the Crab spectrum using the catalog position of the source not the one found at the IMA level For this you have to re run the analysis starting from the very beginning but specifying that you want to use your own catalog for the spectral and lightcurve extraction Create a new observation group crab_usrcat cd REP_BASE_PROD og_create idxSwg jmx
134. nual Issue 10 0 20 cd obs crab jemx_science_analysis startLevel COR endLevel IMA nChanBins 4 jemxNum 2 The above command launches the analysis which will run from the Correction step startLevel COR up to the image creation level endLevel IMA It is important to specify that we are interested in the second of JEM X instruments jemxNum 2 nChanBins parameter specifies the energy binning see section 6 7 2 for details At the beginning the script launches the GUI Fig 10 and you can check the parameter settings the full OGA X jemx_science_analysis 46 63129 160 82 126 159 223 Figure 10 GUI for JEM X science analysis list of the parameters is given in Table 60 Only the most important parameters shown in bold in Table 60 appear within the main panel of GUI To access the other hidden parameters click on the button hidden on the right side of the panel The behaviour of the IMA step has changed between OSA 7 and OSA 8 This is because fluxes have now to be extracted using the IMA step in order to profit from the vast improvement in the modelling of the JEM X instruments in OSA 8 Therefore the normal behaviour is that IMA does not produce images for the binning specified under General Binning Tasks By default jemx_science_analysis creates images in the 3 energy ranges 3 7 keV 7 11 keV and 11 20 keV which corresponds to the images used for optimal source detection While t
135. on information copied after the IMA step into the columns RA CAT and DEC CAT of jmxz_srcl_res fits See the Known Issues description in section 9 to force the usage of these coordinates at SPE and LCR levels 7 6 Barycentrisation The tool making such a correction is called barycent Note that it re writes the input file so it may be worth to copy the original file first Below we show an example for 4U 1700 377 Science Window number 011800900010 and observation group identification ogid parameter of og_create equal to OGID cd REP_BASE_PROD obs OGID cp scw 011800900010 001 jmx2_src_lc fits jmx2_src_lc_011800900010_bar fits barycent inCOL TIME outCOL TIME outDOL jmx2_src_1c_011800900010_bar fits 2 inDOL auxDOL aux adp 0118 001 orbit_historic fits ra0BJ 255 9865 decOBJ 37 84414 In the example we have applied barycentrisation to the first energy range of 4U 1700 377 that happens to be in the extension number 2 2 Thus the extension you give as outDOL depends on the source and energy range you need to correct The overview of the content of each extension is in the input file jmx2_src lc fits i e the first extension GROUPING Note that barycent tool does not use group concept and is used directly with the lightcurve but for it successful work the REP_BASE_PROD variable should be set and point to the place in which there is an IC directory e g directory_of_ic_files_installation__ ic
136. on of the vignetting array 26 PRSS calibration Specta 5 424405 cd mr ada HEA EE eee Ee ISDC JEM X Analysis User Manual Issue 10 0 10 11 12 14 21 23 23 25 26 27 28 29 32 34 36 38 48 54 59 61 78 viii List of Tables 10 Ti 12 13 14 15 16 TT 18 19 20 Pil 22 23 24 25 26 27 28 29 30 31 32 ISDC JEM X parameters and performance Characteristics of the JEM X Telemetry Packet Formats Energy boundaries of the PI channels Overview of the JEM X Scientific Analysis Levels Standard energy binning JEM X imod files instance number j_cor_gain parameters included into the main script gti_create parameters included into the main script gti_attitude parameters included into the main script gti_data_gaps parameters included into the main script gti_import parameters included into the main script gti_merge parameters included into the main script j_cat_extract parameters included into the main script j image_bin parameters included into the main script Parameters specific to the IMA level q_identify_srcs parameters included into the main script j_src_lc parameters included into the main script j_bin_evts_spectra specific to the BIN_S level jzbin_evts_spectra specific to the BIN_S level jzbin_bkg_spectra specific to the BIN_S level j_bin_e
137. on times in seconds Tf sky coordinates RAcenter DECcenter are given as parameters to define the center of the mosaic map an ordered list of the input images as a function of their respective weights at the given coordinates is displayed for each energy band in the log file ISDC JEM X Analysis User Manual Issue 10 0 64 Starting from OSA10 it is possible switching the new parameter view_nb to yes to output in a separate extension the number of SCWs contributing to each pixel of the mosaic This new image will be of type NB SING and will be the last extension of the mosaic fits file j ima_mosaic can combine any set of JEM X mosaics even if they have been obtained with different units It is however mandatory that the user must attach all the requested mosaics to a group For instance if the user wants combine mosaics from the three OSA analyses mysrc_1_jmx1 mysrc_2_jmx1 mysrce_3_jmx2 the user shall type dal_create mos_group fits dal_attach mos_group fits obs mysrc_1_jmx1 jmx1_mosa_ima fits obs mysrc_2_jmx1 jmx1_mosa_ima fits obs mysrc_3_jmx2 jmx2_mosa_ima fits 1 27 Vp in the first line indicates that we use the default template which is a group the fina represents two empty child parameters of dal_attach indeed dal_attach can attach up to five children in a single invocation Now the group is ready and one can call 7_ima_mosaic j_ima_mosaic inObsGrp mos_group fits outfile combined_mos
138. onger integration time Fig 19 Sources marked with FLAG 1 in the user catalog will be included in the flux fitting procedure and their derived fluxes will appear in the srcl_res file You can introduce many FLAG 1 sources simultaneously and you will get fluxes estimates for all of them in srcl_res The flux values for the FLAG 1 sources are not derived from a fit including all these sources simultaneously Such a fit might easily be highly unstable Instead the flux estimate for each of the FLAG 1 sources will be extracted from a separate fit for this specific source together with the basic source set i e the strong sources found by j_ima_iros The maximum number of FLAG 1 sources which will be accepted by j_ima_iros in the analysis of a specific science window is 75 However this does not mean that you cannot work with a user catalog with 200 FLAG 1 sources What counts for j_ima_iros is the number of FLAG 1 sources which falls inside the 10 degree diameter field of view for the current science window The program will not fall over if there are more than 75 FLAG 1 sources visible it will simply only accept the first 75 visible FLAG 1 sources in the user catalog Under special circumstances you may want to force a specific source into all the fits for all the FLAG 1 sources This can be done but is not recommended for general use by setting FLAG 3 A maximum of three FLAG 3 sources will be extracted from your user catalog addition
139. ore source from which you would like to extract a spectrum e g you find a weak source which appears only in the mosaic image or you want to fix the position of a strong source with user catalog In this case you can force the script to extract the spectrum from a given position on the sky For this you need to redo the analysis from the CAT_I step after inserting your source in the user catalog with FLAG 1 As an example let us extract the spectrum of the source 4U 1722 30 which is clearly visible in the mosaic image of the Galactic Center region Fig 15 but which was not detected the imaging step you can check that this source does not appear in any of the jmx2_srcl_res fits files in the observation group obs mos For this case the SOURCE_ID NAME RA_OBJ DEC_OBJ are J172733 2 304807 4U 1722 30 261 8883 ISDC JEM X Analysis User Manual Issue 10 0 33 and 30 80194 respectively Fill the corresponding line in the file user_cat fits update column FLAG FLAG 1 and run the jemz_science_analysis with the user defined catalog as explained above The resulting files scw RRRRPPPPSSSF 001 jmx2_srcl_spe fits will contain a row with the spectrum of 4U 1722 30 The quality of the single ScW spectra is not very high because of the short integration time see Fig 19 However with the help of the spe_pick command see previous sub section you can sum up the spectra of individual ScWs and obtain a better spectrum based on l
140. ov OSA8 obs crab scw 01020021001 Fie Edit Tools Heip Index Extension Type Dimension View BL Primary Image o Header 0 GROUPING Binary 32 IMX2 SKY IMA Image R JMX2 SKY IMA Image J4 JMX2 SKY IMA Image 36 JMX2 SKY IMA J6 JMX2 SKY IMA ima 511 X51 z O O N fv Binary Table of jmx2_sky_ima fits 1 in unsaved_data neronov OSA8 obs crab scw 010200210010 001 Fle Edit Tools Help Fa JMX2 SKY IMA _3 IMADESCR _ IMACASE CHANMIN CHANMAX Select 32A JA Invert Figure 11 The content of jmx2_sky_ima fits file UG 2EG JO520 2626 RX J0525 3 2413 3EG J0516 2320 Crab 2EG J0521 2206 Fi 12 ea The image of Crab region Catalog sources in the FOV are shown with white circles The only found source Crab is shown with a red box With the help of ds9 viewer you can display the sky images in any of the three energy bands For example to look at the 7 11 keV image which is contained in the 5th extension of the jmx2_sky_ima fits file you can type ds9 jmx2_sky_ima fits 5 You can load the region files cat reg and found reg created with cat2ds9 by using the Region menu of ds9 or directly from the command line ds9 jmx2_sky_ima fits 5 region cat reg In Fig 12 the left panel shows the Crab region in the second energy band 7 11 keV with the catalog sources and the right one the same region with the found sources Science Wind
141. ow 010200210010 ISDC JEM X Analysis User Manual Issue 10 0 23 6 6 2 Weak Sources and Sources at the Edge of the FOV The source acceptance is based on a positive detection in at least two energy bands However a strong source that only appears in a single energy band may also be accepted Such an acceptance is based on the parameter IMA_detSigSingle Note however that it is NOT a statistical sigma The default value is 12 which prevents most of the spurious detections to be accepted However if the aim is to find the weak sources the value can be reduced to e g 10 Still lower values will probably cause too many spurious sources The number of detector pixels that contribute to the sky image decreases towards the edge of the FOV That implies on one hand that spurious sources are more likely to occur at the edge and on the other hand that sources located there will be less reliable as is reflected in the relative error of the flux determination 6 6 3 PIF cleaning of images around strong sources The image generating algorithm used by default in the JEM X Scientific Analysis assigns equal weights to all active detector pixels This allows to assign errors to the source fluxes with reasonable accuracy For observations where the diffuse background is dominating the count rate this imaging technique appear as the best approach However when bright sources are in the field of view and significantly increases the global count rate th
142. owever that 7 ima_iros will always find a little bit different source positions in different ScWs The deviation of the found source position from the true one may lead to an error in determination of the source spectrum To avoid this difficulty it is recommended to create a user catalog with the names and positions of the sources for which you want to extract the spectra For example in the considered case the source of interest is the Crab and one can just copy the corresponding line from the general reference catalog fcopy ISDC_REF_CAT NAME Crab user_cat fits In the new user_cat fits file you have to change the FLAG column to 1 in this case jema_science_analysis would directly copy the source position information to the jmx2_srcl_res fits after IMA step see Sections 6 7 6 and 8 6 1 for an explanation on the possible FLAG values 6 7 2 Energy binning definition The user must now specify all the bins s he wants in the spectra using nChanBins chanMin and chanMax parameters As this can be tedious standard binnings are provided by setting nChanBins to be lt 1 In this case IMA extracts fluxes in 2 hanBins bins i e a value nChanBins 0 results in a single wide energy bin while a value of 4 results in production of 16 channel spectra The smallest allowed value is 6 corresponding to the 64 channel spectra Table 5 shows the standard energy bins up to 16 channels 6 7 3 Spectral response generation For sp
143. portant to note however that source positions found by j ima_tros will differ slightly from ScW to ScW The deviation of the found source position from the true one will lead to an error in the determination of the source lightcurve To avoid this difficulty it is recommended to create a user catalog in the same way as you did for the spectral extraction with the names and positions of the sources for which you want to extract the lightcurves see section 9 to force usage of the catalogue coordinates 6 8 2 Individual Science Windows Lightcurves To produce the Crab lightcurve we have to run the lightcurve analysis in directory REP_BASE_PROD obs crab_usrcat The LCR level of the jemx_science_analysis script produces the lightcurves of the sources from the catalog of sources found in the imaging analysis jmx2_srcl_res fits To obtain the lightcurve of the only found source Crab you can give the command jemx_science_analysis startLevel LCR endLevel LCR skipLevels nChanBins 2 chanLow 46 129 chanHigh 128 223 CAT_1_usrCat user_cat fits jemxNum 2 LCR_timeStep 100 0 The parameter LCR_timeStep sets the binning time of the light curve in seconds Selecting nChanBins 2 chanLow 46 129 chanHigh 128 223 we choose to produce the lightcurve in two energy bins 3 10 keV and 10 35 keV Notice that the hidden parameter LCR fluxScaling controls the unity in which the count rate is displayed Until OSA9 the count rate was scaled to
144. preting the results We assume that you have already successfully installed the ISDC Off line Scientific Analysis OSA Software version 10 0 The directory in which OSA is installed is referred later as the ISDC_ENV directory If this is not the case look at the Installation Guide for the INTEGRAL Off line Scientific Analysis 4 for detailed help 6 1 Setting Up the Analysis Data In order to set up a proper environment you first have to create an analysis directory e g jmx_data_rep and cd into it mkdir jmx_data_rep cd jmx_data_rep setenv REP_BASE_PROD PWD This working directory will be referred to as the REP BASE PROD directory in the following All the data required in your analysis should then be available from this top directory and they should be organized as follows e scw data produced by the instruments e g event tables cut and stored by ScWs e aux auxiliary data provided by the ground segment e g time correlations e cat ISDC reference catalogue e ic Instrument Characteristics IC such as calibration data and instrument responses e idx set of indices used by the software to select appropriate IC data The JEM X example presented below is based on observations of the Crab from Revolution 102 Part of the required data may already be available on your system In that case you can either copy these data to the relevant working directory or better create soft links as follows
145. r that 2 4 degrees a source is not visible through the mask from the entire detector surface These two effects together form the vignetting The vignetting or throughput factor as a function of angle in two direction is shown in Fig 25 The quadratic cell shape of the collimator introduces the deviation from circular symmetry With OSA5 1 images it was realized that the flux determined from the images was a decreasing function of the off axis angle This effect is corrected in OSA6 by applying a correction map placed in the BPL IC files to the images before they are written to disk Therefore the offline tool mosaic_spec can be used to extract source spectra from j_ima_iros images as well as from mosaic images 8 6 2 qidentify_srcs q identify_src calculates the distance d between each pair consisting of an expected catalogue source and a source found in the FOV by the ISSW This distance and the error radii of the sources ri Ya are used to calculate the relative distance q d y ri 73 It is therefore essential that the quoted position error has a meaningful value The relative distances are then stored in an array Two new arrays are then created one ranking each catalogue source with q lt relDist the largest value of relative distance considered when matching sources for its proximity to each found source and the other ranking each found source with q lt relDist for its proximity to each catalogue source These two arrays are compared
146. r JEM X1 two RFG and two Cd sources were used For JEM X2 all four radioactive sources are Cd Each source illuminates a well defined spot on the microstrip plate Y Cd emits 22 keV and 88 keV photons Fe produces one unresolved doublet at 6 keV The gain of the detector gas is monitored continuously with the help of these sources Figure 4 shows the collimator layout and the locations of the calibration sources There is one calibration source for each anode segment on the MSP The 29 6 keV photons produced by Xe fluorescence can be detected all over the MSP and are used for offline monitoring of the gain correction by the software and also to produce instrument model tables of the spatial gain SPAG variation across the detector plate For the complete archive of these offline analyses see http www spacecenter dk oxborrow sdast GAINresults html ISDC JEM X Analysis User Manual Issue 10 0 4 Relative Transmission 0 1 2 3 4 5 6 7 Off axis angle degrees Fi 3 eee Off axis response of JEM X below 50 keV where the collimator walls are opaque The thick line shows the average transmission through the collimator considering all azimuth angles The square pattern of the collimator introduces an azimuthal dependence of the throughput with a minimum and a maximum as indicated by the two thin curves no response at ZRFOV indicated by dash dot line Calibration sources HH BU SU A ee e
147. r Manual Issue 10 0 95 IMA_radiusLimit3 IMA interactionDepth IMA_hotPixelLimit IMA _skyImagesOut IMA dolBPL IMA_bkgShdDOL IMA_relDist IMA fluxLimit IMA_searchRad IMA gridNum IMA_distFuzz IMA signifLim IMA_illumNorm IMA_collHreduc real real real string string string real real real integer real integer integer real Detector radius limit E gt 20 keV mm default 110 0 Mean depth of interaction in the detector mm default 3 0 Hot pixel limit factor above average default 4 0 Type of output sky images There are the following types RECTIFIED Rectified cleaned intensity maps in counts cm s VARIANCE Variance maps RECONSTRUCTED Reconstructed Residual Sources maps in counts cm s which only differ from the RECTIFIED maps if sources have been found RAWINTENSITY Raw intensity strength maps in counts for which the vignetting correction is not applied RESIDUAL Intensity map in counts cm s after all found source contributions have been subtracted PIF activate the PIF weighted image generation algorithm not to be used with mosaic_spec Only the first five letters are required default RECONSTRUCTED VARIANCE DOL of backprojection file list default empty DOL of background shadowgrams default empty Limit of relative distance mm to catalog position used for iden tifying sources def
148. r Spectral Analysis BIN_T Event binning for Timing Analysis IMA2 Creation of mosaic images and summary on sources found Figure 9 shows the Scientific Analysis overview The details of each step are briefly discussed below COR Data Correction j_correction GTI Corrects science data for instrumental fingerprints such as energy and position corrections as well as flagging events of dubious quality Look up tables of pre flight corrections are used as well as tables of in flight calibrations determined by offline analysis of science data calibration spectra and instrumental background lines Dynamic determination of known transient problems e g hotspots on the detector is also done in this level The majority of calibration tables are stored in the Instrument Model group JMXi IMOD GRP with i 1 and 2 for JEM X1 and JEM X2 respectively but the offline gain history Instrument Characteristics tables are stored separately in JMXi GAIN OCL data structures The latter are also located automatically by the OSA software just like the IMOD group Good Time Handling j_gti Good Time Intervals GTIs are used in the analysis to select only those data taken while the detector was considered to work correctly The corresponding data structures consist simply of a list of start and stop times of those intervals considered good Usually these intervals are generated based on the following data 1 Housekeeping pa
149. ral files named jmxi_imod_grp_ fits Each of them refers to a different period To identify the file to be used together with your data you can check the indicative validity interval reported in table 6 for each imod file In our example based on scw 010200210010 we will use file jmx2_imod_grp_0299 fits At this point you are ready to create the lists of photons cd REP_BASE_PROD obs crab evts_extract group 0g_jmx2 fits events evts_j2 fits instrument JMX2 sources crab_cat fits gtiname MERGED instmod REP_BASE_PROD ic jmx2 mod jmx2_imod_grp_0299 fits pif yes deadc yes attach no barycenter 1 timeformat 0 evttype 0 For JEM X it is currently not possible to save the PIF of a given source The parameter pif can be therefore put equally to yes or no as it adds no information to the output file Now you can produce the Crab power spectrum powspec Ser 1 filename options or file of filenames options evts_j2 fits Name of the window file for default window Newbin Time or negative rebinning 0 001 Number of Newbins Interval INDEF Number of Intervals Frame INDEF Rebin results gt 1 const rebin lt 1 geom rebin 0 none 0 Name of output file default Do you want to plot your results yes Enter PGPLOT device XW hardcopy crab_powerspec ps PS For the details on INTEGRAL absolute timing see Walter et al 2003 8 If your data have many short GTIs e g in t
150. rameters which are compared with pre set limits ISDC JEM X Analysis User Manual Issue 10 0 13 Data Correction Good Time Handling Dead Time Calculation Catalog Source Selection Event Binning for Image Image Reconstruction Source Spectra Extraction Source Lightcurve Creation Detector Spectra Extraction Detector Lightcurve Creation Mosaic Image Creation Grouping the results Corrected data Good Time Intervals Dead Time List of Sources in FOY Binned Events Sky Images and Source List Source Spectra Source Lightcurve Detector Spectra Detector Lightcurve Mosaic Image Found Sources Summary Figure 9 Decomposition of the jemz_science_analysis script ISDC JEM X Analysis User Manual Issue 10 0 14 2 The satellite stability as recorded in the attitude data 3 Gaps lost packets in the telemetry flow In addition this step excludes by default periods when the instrument configuration is not adapted to the production of scientific works either because of hardware problems or because of intentional modifications of the instrument configurations for the purpose of testing and calibrations These periods are marked as bad time intervals in the Instrument Characteristics data DEAD Dead and Live Times j dead_time For each 8 second onboard polling cycle this level calculates the dead time during which photons are lost due to finite read in time of registers e
151. re the Aperture Response Function is calculated off line by a separate set of subroutines For every detector pixel shadowgram pixel a list is generated containing all sky image pixels potentially illuminating this detector pixel Even when stored in compressed format these backprojection lists are of substantial size about 375 Mbyte for each JEM X unit for sky images with 511x511 pixels of 1 5 arcmin The advantage is that the backprojection process which must be repeated many times during the IROS process is quite fast and very important the duration of the backprojection step is independent of the steadily increasing complexity of the raytracing model required by our improved understanding of the intricacies of JEM X ISDC JEM X Analysis User Manual Issue 10 0 57 The backprojection lists are stored as separate IC files JMXi BPL GRP under the general IC tree The search for sources is conducted in three predefined energy bands irrespective of the user selection of energy bands Source results will be reported for all energy bands Sources found in two or three of the search bands will define a basic source set for this observation Optionally the user may specify a user catalog parameter usrCat to enhance and control the performance of j_ ima_iros A subset of the sources in the catalog will automatically be selected corresponding to the current field of view For strong source candidates found during t
152. ritten to the JMXi SPEC RAW data structure Table 32 Content of JMXi SPEC RAW Data Structure Column Name Description GREY_FILTER Grey filter for first event in the spectrum SPECTRUM Counts in 64 channels A 1 6 Prepared Data The main task of the Science Window Pipeline is to prepare raw data for the following Scientific Analysis It converts the housekeeping parameters into the physical units and makes some corrections and transformations of the raw data that are not included in Pre Processing The Summary of all the prepared data structures with scientific information can be found in Table 26 All these data structures have the only column OB_TIME with the full on board time of the relevant data FULL SPTI and TIME OBTs refer to the individual events SPEC OBTs give the time of each spectrum and REST OBTs give only the time of each image so that the OBTs of the events within a single integration period are identical A 1 7 Revolution File Data The gain history table JMXi GAIN CAL IDX and the calibration spectral fitting table JMXi GAIN CAL are both created in the Revolution File Pipeline RFP which runs automatically at ISDC before after parallel with the Data Preparation step The spectral fitting file is created every 256 seconds by j_calib_gain_fitting and the RFP then indexes the results into a single gain history table for each revolution It is this gain history table that gets used automatically in j_cor_gain u
153. ry is the one used for the analysis and is the one you can modify If this parameter file is missing e g you have deleted it the system will just re copy it from ISDC_ENV pfiles as soon as you launch the script again The system knows what to copy from where thanks to the PFILES environment variable that is also used in FTOOLS http heasarc gsfc nasa gov ftools Each parameter is characterized with a letter that specifies the parameter type i e q query parameters are always asked to the user h hidden parameters are not asked to the user and the indicated value is used learned parameters are updated with the user s value during the use of the program The GUI is a fast and easy way to change the parameters see also the explanation at the end of this section e What are groups and indices The ISDC software makes extensive use of groups and indices While it is not necessary to grasp all the details of these concepts a basic understanding is certainly quite useful As implied by their names groups make possible the grouping of data that are logically connected Groups can be seen as a kind of data container not completely unlike standard directories At ISDC we create separate groups for each pointing in which we store the many different data types produced by INTEGRAL and its instruments The user then only has to care about one file the group many tens of files being silently included Severa
154. s included into the main script Name Name Type Description main script executable GTI attStability AttStability real Accepted attitude variability arc min possible values 0 10800 default 3 0 8 2 3 gti_data_gaps This program generates GTIs depending on the presence of the science data A time is defined as bad if there are missing science packets The final GTI is written into the JEMX 1 or JEMX 2 index group and has the name DATA_GAPS Table 10 gtt_data_gaps parameters included into the main script Name Name Type Description main script executable GTI _gtiJemxNames JMX1_Mode string Names of JEM X GTIs to be merged JMX2_Mode string default 8 2 4 gti_import The gti_import reads user GTI table and converts it to a table in ISDC format The user GTI can be defined either in units of OBT IJD or UTC The output is always in OBT The user table can define either bad or good time intervals The output time intervals are always good ones For the definition of the ISDC Julian Date IJD and details of user GTIs creation see Introduction to the INTEGRAL Data Analysis 1 Table 11 gti_import parameters included into the main script Name Name Type Description main script executable GTI gtiUser InGTI string DOL of the input user GTI default gt GTI_TimeFormat TimeFormat string Time format to be used poss
155. s launch Help With Help button the help file of the main script is opened in a separate window hidden With the hidden button you have an access to the hidden parameters with values defined by the instrumental teams Change them with care The environment variable COMMONSCRIPT is used to disable enable the GUI see section 6 3 6 5 A Walk Through the JEM X Analysis After setting up the data and the environment you are ready to call the analysis script on the Crab region observations defined above and stored in the jmx Ist file Firstly create an Observation Group see the description of the executable og_create in the Toolbox and Data Analysis sections of the Introduction to the INTEGRAL Data Analysis 1 og_create idxSwg jmx l1st ogid crab baseDir instrument JMX2 As a result the directory REP_BASE_PROD obs crab will be created It contains the files og_jmx2 fits and swg_idx_jmx2 fits as well as the subdirectory scw necessary for the analysis In the latest version of og_create the file indicated in idxSwg is automatically interpreted as a fits file when the name includes a corey or ve sign 6 6 Examples of Image Creation Now you can go to the directory created with og_create and start the analysis 6To create the structure for both JemX units at the same time it is possible to call og_create only once with the parameter instrument JMX1 JMX2 ISDC JEM X Analysis User Ma
156. s rule is broken we give both names in the description of the executable The detailed description of the results produced at each step can be found in the Appendix section In the Appendix you also find the description of raw and prepared data with which you start the analysis 8 1 3_correction This script corrects all data available within the Science Window Group for a given JEM X detector It calls two executables that do the actual corrections e j_cor_gain e j_cor_position 8 1 1 j_cor_gatn The executable j_cor_gain corrects all science data received at Full Restricted Spectral Timing and Spectral modes for the condition of the individual pixels in the detector temporal and spatial changes in the detector gain The telemetry energy bins PHA channels of each event are converted to PI energies using gain determined by e Temporal gain variations across the detector are determined by the energy channel positions of the fluorescence lines of Cd 109 and Fe 55 sources placed above certain points on each detector The peak positions are determined every four minutes 256 sec to give current time variation of the detector gain and compared to the Cd Fe positions at a reference time when the Xe fluorescence lines of the gas over the entire detector are known The values of the found Cd Fe calibration line positions are kept in the gain history table and are used for gain conversion from PHA to PI channels in two possible ways For gainMod
157. scomb y radiusSelect 1 Combined JEMX 1 and JEMX 2 mosaics have the same structure as JEMX 1 ones with EXTNAME JMX1 MOSA IMA 6 6 6 Finding Sources in the Mosaic Image jzima_src_locator is a tool to locate point sources in an image Since OSA 7 it is included in the OSA distribution but is not part of the pipeline This tool can be used to search for the gaussian excesses in the mosaic image but not to identify the detected sources at the moment 9For details on j ima_mosaic parameters see sections 8 11 1 and Appendix D ISDC JEM X Analysis User Manual Issue 10 0 28 000 IX fv Binary Table of jmx2_sloc_res fits 1 in unsaved_data neronov OSA obs mos1 Figure 17 The content of the jmx2_sloc_res fits file As an example let us find all the significant excesses in the 7 11 keV mosaic image of the Galactic Center region We assume that in the mosaic image jmx2_mosa_ima fits the intensity map is in the extension 2 and the significance is in the extension 4 which is the case if the default value of IMA_skyImages0ut parameter is used The command j_ima_src_locator inDOL jmx2_mosa_ima fits 2 sigDOL jmx2_mosa_ima fits 4 outFile jmx2_sloc_res produces the list of the detected sources jmx2_sloc_res fits In this file all the significant sources in the mosaic image are listed However they are not identified with the known sources To do the source identification you can use the q_identify_srcs script q_
158. solution in the JEM X 1 and JEM X 2 detectors as a function of energy valid after 2002 11 09 JEM X 1 and after 2002 11 12 JEM X 2 ISDC JEM X Analysis User Manual Issue 10 0 10 4 2 Energy Resolution The energy resolution has been determined in the laboratory as AE E FWHM 0 40 y1 El keV 1 120 keV This value has not been significantly affected by the gain change and the corresponding slight rise in impor tance of the electronic noise 4 3 Background The local radiation environment is mainly produced by two components the diffuse X ray background DXB and cosmic rays CR Most of the latter are rejected on board with a combination of pulse height pulse shape anti coincidence and footprint evaluation techniques These techniques allow a particle rejection efficiency of gt 99 9 with carefully tuned selection parameters This high rate of background rejection has ensured that there has been no significant increase in background events in the telemetry despite the steady increase in the CR rate at Solar minimum Figure 7 shows an actual background spectrum which is composed of the diffuse X ray background instru mental background due to the interactions with cosmic rays and three strong instrumental lines due to the cooper and molybdenum in the collimator 8 04 keV and 17 4 keV and Xe fluorescence from the detector gas at 29 6 keV FM1_HIGH_GAIN FM1_LOW_GAIN 1 0 1 0 0 5 0 85 s 0 6 N 0
159. t the IMA and SPE steps is at the moment much better than this 6 8 4 Displaying the Results of the Lightcurve Extraction To see the source lightcurve you should plot the column RATE with error ERROR versus column TIME whereas to see the background lightcurve you should plot column BACKV with error BACKE versus TIME To display the resulting lightcurve it is convenient to use the lcurve program from the FTOOLS package lcurve Number of time series for this task 1 Ser 1 filename options or file of filenames options crab_1c fits 2 Name of the window file for default window U Newbin Time or negative rebinning 100 Number of Newbins Interval 46 take this number from the line above Maximum Newbin No 46 Name of output file default Do you want to plot your results yes Enter PGPLOT device XW hardcopy crab_lc ps PS quit As a result the crab_lc ps file was produced and is shown in Figure 21 ISDC JEM X Analysis User Manual Issue 10 0 38 6 8 5 Lightcurve extraction from the IMA step IMA step of jemz_science_analysis script outputs the fluxes of all detected sources in mxi_srcl_res fits files A Scw by Scw lightcurve of all these sources could be obtained with the help of src_collect script As an example let us produce the Scw by Scw lightcurve of GX 354 0 in two energy bands 3 10 keV and 10 35 keV For this we will need first to extract fluxes from the images in these energy band in
160. t to bin possible values 1 all O FULL 1 REST 2 SPTI 4 SPEC default 1 Parameters specific to detector lightcurve binning BIN_T BIN_T_rowSelect BIN_T_evtType string integer CFITSIO selection string on events default Data format to bin possible values 1 all 0 FULL 1 REST 2 SPTI 4 SPEC default 1 Parameters specific to jemx_obs_analysis IMA_2 ISDC JEM X Analysis User Manual Issue 10 0 98 IMA2_mapSelect IMA2_radiusSelect IMA2_eminSelect IMA2_emaxSelect IMA2_ diameter IMA2_cdelt IMA2_RAcenter IMA2_DECcenter IMA2_outfile IMA2_viewTime IMA2_viewIntens IMA2_viewVar IMA2_viewSig IMA2_view_nb string real real real real real string boolean boolean boolean boolean boolean Types of images to be selected Possible values RAW_RECT Rectified cleaned intensity maps in counts cm s RAW_INT raw intensity strength maps in counts for which the vignetting correction should not have been applied at the IMA level by use of NOVIGN in the IMA_skyImagesOut parameter line but is applied at the mosaicking level RES SRC reconstructed Residual Sources maps in counts cm s which only differ from the RAW_RECT maps if sources have been found at the IROS imaging level default RAW_RECT Input images selection radius in degrees defa
161. terpolation of the gain history table or the decay model smoothing makes an unbroken gain history in these cases Pre launch testing of the flight models and experiments with the flight spare indicate that the strength of the FRSS sources illuminating small spots on the detector causes charging phenomena on the microstrip plate such that the gain at these points is not characteristic of the entire anode segment it represents and may also show sudden drops where small discharges occur This problem is resolved by normalising the gain at each calibration point with the gain determined from the Xe line seen over the entire detector at a particular reference time for which we have plenty of blank field data Temporal changes in these normalised gains are then a direct reflection of the gain variation over the entire detector Reference values of the Xe line and calibration source positions are stored in keywords in the header of JMXi SPAG MOD datastructure in the IMOD group IC data Discharge glitches in the calibration spectra are smoothed out of the time variation correction by using a time smoothing model across an entire revolution of data in j_cor_gain All data including the FRSS spectra are expected to show the 30 33keV Xenon fluorescence doublet to some extent These lines are too weak to act as temporal gain variation markers but at can determined from summing blank field data how well gain determination functions over the entire detector area
162. the source flux in each ScW is always available in the jmx2_srcl_res fits files For a weaker source like 1E 1740 7 2942 which is not always detected in single ScWs one has to force jemz_science_analysis to output information about the flux or an upper limit on the flux of the source into jmx2_srcl_res fits files in each ScW by running the analysis with the user defined input source catalog as it is explained in section 7 5 7 Useful recipes for JEM X data analysis This section collects some recipes that can be useful in the analysis of JEM X data in analogy to the recipes described in the IBIS cookbook available at URL http www isdc unige ch integral analysis 7 1 User GTIs The way of creating User Good Time Intervals is described in the Introduction to the INTEGRAL Data Analysis 1 a convenient tool gti_user exists for this purpose To use your own GTI within the JEM X analysis you should set two parameters GTI_gtiUser defining the location of your file and GTI _TimeFormat defining the time format of the user GTI table The possible values of the GTI_TimeFormat are IJD for the Integral Julian Date see Introduction to the INTEGRAL Data Analysis 1 UTC and OBT Below you find ISDC JEM X Analysis User Manual Issue 10 0 39 an example of the command to launch the JEM X analysis with the default values and the user GTI table user_gti fits jemx_science_analysis startLevel COR endLevel IMA COR_outputExists y
163. tml Table 7 j cor_gain parameters included into the main script Name Type Description COR_gainHist string DOL of the Index Group with gain variation history JMXi GAIN CAL IDX Empty string automatically takes the value of any IC Gain History DOL default ISDC JEM X Analysis User Manual Issue 10 0 49 COR_gainModel integer With this parameter you choose the smoothing model to be ap plied possible values 1 default Let the algorithm choose between the optimal model to be used 0 Linear interpolation between gain history values 1 Fixed gain parameters obsolete This value will automatically default to model 2 2 Exponential gain decay with linear segment immediately af ter switch Models the normal time variation of gain slope in a revolution 3 Non trigger dependent model 4 Hardware trigger dependency in the smoothing If there is no significant trigger variation during the revolution then the program defaults back to model 3 default 1 8 1 2 j_cor_position The program works with the data received in Full amp Restricted Imaging modes With the use of the position mapping tables see Appendix B 4 j_cor_position converts detector positions corrected for microstrip plate irregularities into absolute values This component also determines whether there are hotspots on the microstrip plate and flags all the events orginating in hotspot areas so that these e
164. tra is made through j_ima_iros j_reform_spectra simply reformats the fluxes in the user defined energy bins Please see j_ima_iros Sect 8 6 1 for more detail 8 8 7 src_extract_Ic This application extracts energy binned light curves for each found point source in the FOV Background subtraction is an integral part of the data extraction The only used executable is j_src_lc 8 8 1 jsrc_lc Creates binned lightcurves for each found source in FOV The output data structure contains a countrate light curve for a given source and a given energy range of the JEM Xi instrument Table 17 j_src_lc parameters included into the main script Name Type Description LCR_timeStep LCR_evtType LCR_precisionLevel LCR tAccuracy LCR_useRaDec LCR_rowSelect real integer integer integer boolean string Binning time s for lightcurves default 10 Event type possible values O FULL 1 REST 1 both default 1 Speed precision level see more details in Section 8 7 1 possible values O basic approach 20 more detailed approach default 20 Time Correlation accuracy possible values 0 high 1 low 3 any default 3 default y CFITSIO selection string on events default Use sky coordinates Ra Dec instead of instrument coordinates ISDC JEM X Analysis User Manual Issue 10 0 60 Y direction cosine 0 10 0 05 0
165. ts for the interpretation of the gamma ray data In addition JEM X has a higher spatial resolution than the gamma ray instruments This aids with the identification of sources in crowded fields JEM X operates simultaneously with the main gamma ray instruments IBIS and SPI It is based on the same principle as the two gamma ray instruments on INTEGRAL sky imaging using a coded aperture During the recurrent scans along the galactic plane JEM X provides rapid alerts for the emergence of new transients or unusual activity in known sources These sources may be unobservable by the other instruments on INTEGRAL Finally JEM X may deliver independent scientific results concerning sources with soft spectra serendip itously detected in the field of view FOV during the normal observations mask The performance of JEM X is summarized in Table 1 Table 1 JEM X parameters and performance Energy range 3 35 keV Energy resolution AE E 0 40 x 1 E keV 1 120 keV Field of view diameter 4 8 Fully illuminated 7 5 Half response 13 2 Zero response Angular resolution FWHM 3 Relative point source location error 1 90 confidence radius for a 50 isolated source Continuum sensitivity for a single JEM X unit isolated source on axis 1 2 x 10 7 ph cm s tkeV 1 6 keV 1 0 x 10 4 ph cm s keV A 30 keV for a 3 cont detection in 10 s AE 0 5E Narrow line sensit
166. ughly AE 0 47 E inkeV Many things are expected to affect the pulse size the ADC will register for a given event energy detector temperature gas pressure micro strip plate charging the age of the gas and maybe some as yet unknown influences This is why FRSS spectrum are sent in the housekeeping every 256 seconds to correct the gain ISDC JEM X Analysis User Manual Issue 10 0 77 counts Xe 30 33KeV Od E Sheet 163 165 196 198 255 PHA channel Energy KeV E AH 22 RN l ha ADC Channel X Cd 1 4 Cd l 4 lt Xe gt at T at TO at TO Gain Offset GO 0 Figure 26 FRSS calibration spectra ISDC JEM X Analysis User Manual Issue 10 0 78 continuously Since the ADC is known to be linear to better than the accuracy used by the telemetry we can assume a relationship between event energy and ADC channel n E Go 6 n 1 The PHA binned spectra are fitted by gaussian line models and the resulting peak positions at 22 1KeV and 6 KeV are used to find the raw gain conversion factor G1 in KeV per ADC channel for the four minute interval Both this value of G1 and the peak ADC channels are saved to JMXi GAIN CAL as keywords The contents of JMXi GAIN CAL is tabulated over an entire revolution and over the entire mission in a gain history table JMXi GAIN CAL IDX which is read by j cor gain to perform the gain conversion In the gain correction program j_cor_gain the peak positions are
167. ult 4 8 Minimum energy keV to select energy interval default 0 0 Maximum energy keV to select energy interval default 80 0 Diameter in degrees of the mosaic image 0 allows to fit the mosaic size from the inputs lt 0 can be used for larger mosaics default 0 0 Pixel size in degrees at mosaic center default 0 026 Center of the mosaic image Right Ascension in degrees If lt 0 use the computed middle position of the mosaic default 1 Center of the mosaic image Declination in degrees not used if RAcenter lt 0 default 0 0 Prefix of the mosaic FITS file for each energy band default Create total exposure time map if Y gt OBS_TIME_n fits where n is the number of combined input skymaps default y Create raw Intensity map default y Create Variance map default y Create Significance map default y Create a map that shows the number of input images contributing to each pixel default n ISDC JEM X Analysis User Manual Issue 10 0 99 IMA2_dolBPL string DOL of the vignetting maps e 8 ice jmx1 rsp jmx1_bpl_grp_0002 fits JMX1 DMAP BPL default IMA2_print_ScWs boolean List input Science Windows in mosaic headers default n IMA2_AITproj boolean Project map in galactic coordinates using AIToff Hammer pro jection default n IMA2_srcFileDOL string DOL of the output source list mosaic default IMA2 srcselect string CFITSIO selection str
168. uous categories Multiple and Confused the program makes no attempt to separate sources further or resolve conflicts between various possible matches this should be done by a human More details on the format of the output result is given in Appendix C 6 2 Table 16 q_identify_srcs parameters included into the main script Name Type Description IMA_relDist IMA fluxLimit IMA_searchRad IMA_gridNum real real real integer This is a parameter that sets the allowed separation between CAT sources and RES sources that are to be considered as the same relDist is calculated from relDist d yri r5 Here d is a dis tance between the sources and r and rg are the error radii default 1 5 Lower flux limit for alerts of unfound sources Counts cm s default 0 0 Range of search grid in degrees around nominal found source positions default 0 25 Number of grid steps on one side of search grid default 25 ISDC JEM X Analysis User Manual Issue 10 0 59 IMA_distFuzz real Fractional difference in the relative distance of two found sources that allows them still to be considered equally good fits for a catalogue source default 0 15 8 7 j_src_extract_spectra This script derives JEM X countrate spectra for all sources found in the current Science Window It calls a single executable 7_reform_spectra 8 7 1 reform_spectra Since OSA v 8 0 extraction of source spec
169. ven period can be produced BIN_T Creates Detector Light Curves j_bin_lc Creates binned lightcurves for entire detector area IMA2 Mosaic Image Creation j_ima_mosaic src_collect Generates mosaic sky images and creates the list of all found sources Works only on FULL and REST data see Table 2 Since October 18 2004 all public INTEGRAL data are available including already the correction step and also the instrumental GTI and deadtime handling have been already performed at the science window level This allows to speed up the scientific analysis of JEM X data as there is no need to redo the COR GTI and DEAD levels but you can directly start JEM X analysis from the CAT_I level It is however recommended that users run the science analysis from the COR level onwards especially after downloading new software and IMOD IC files This will undoubtedly give better results than the archived data Archived data necessarily fossilize our understanding of the instruments as it was at the time of the archival processing and can therefore be several years out of date since our knowledge of the instruments and the software to process the data is still improving ISDC JEM X Analysis User Manual Issue 10 0 15 6 Cookbook for JEM X analysis The Cookbook describes how to use the OSA JEM X software It covers the following steps e Setting up the analysis data e Setting the environment e Launching the analysis e Inter
170. vent processing time grey filter losses buffer losses and double event triggers CAT I Catalogue Source Selection j_cat_extract Selects a list of known sources from the given catalogue Creates a source data structure containing source location and expected flux values BIN_I Event Binning for Imaging j_image_binning Defines the energy bins to be used for imaging selects good events within the GTI and creates shadowgrams Works only on FULL and REST data see Table 2 IMA Image Reconstruction j_imaging Generates sky images and performs search for significant sources If sources are detected a new source data structure is created including part of the information from the input catalogue concerning the identified sources Works only on FULL and REST data see Table 2 SPE Spectra Extraction j_src_extract_spectra Extracts spectra for individual sources found at IMA step and produces the specific response files ARFs needed for spectral fitting with the XSPEC package Works only on FULL data see Table 2 LCR Extract Source Light Curves j_src_extract_lc Produces light curves for individual sources Works only on FULL data see Table 2 BIN_S Event Binning for Spectral Analysis j_bin_spectra Creates detector spectra i e spectra of all events recorded within the GTI are corrected for greyfilter ontime and deadtime A series of spectra resolved in time or phase over a gi
171. vents can be ignored by the rest of the science analysis It also flags dubious events coming from dead anodes inactive areas around the detector and areas around the calibration areas See Appendix C 1 for the description of j_correction output 8 2 gti This script builds Good Time Interval information from housekeeping data information about satellite stability and data gaps It calls the following executables to obtain the GTIs e gti_create e gti_attitude gti_data_gaps gti_import e gti_merge More information concerning the definition of the Good Time Intervals and the creation of user defined GTIs is given in the Introduction to the INTEGRAL Data Analysis 1 8 2 1 gti_create This program generates Good Time Intervals see section 7 1 page 39 depending on housekeeping data and other parameters defining by a limit in a limit table the time is bad if the value of any parameter was out of limit ISDC JEM X Analysis User Manual Issue 10 0 50 Table 8 gti_create parameters included into the main script Name Type Description GTI _limitTable string DOL of table with parameter limits default 8 2 2 gti_attitude A GTI is defined for each period of time where the pointing stability is better than the accepted tolerance The spacecraft GTI is named ATTITUDE For slews this GTI is always set to be good independent of any input data Table 9 gti_attitude parameter
172. vts_lc specific to the BIN_T level j bin_rate_lc parameters specific to the BIN_T level JAMGOINOSGLC DATAMELELS o soea d pea ai piet src_collect parameters specific to the IMA2 level j ima_src_locator parameters o List of JEM X RAW PRP and COR Data Structures Content of JMXi FULL RAW Data Structure 0 00 0000 ce eee eee eee eee Content of JMXi REST RAW Data Structure Content of JMXi RATE RAW Data Structure Content of JMXi SPTI RAW Data Structure 0 0 000 0c eee eee ee eee Content of JMXi TIME RAW Data Structure Content of JMXi SPEC RAW Data Structure JEM X Analysis User Manual Issue 10 0 49 33 Content of JMXi IMOD GRP Group 2 hee ea g manea sa m e R ee 34 Content of JMX1 BPL GRP Group gt sce oca a hee Bee ee ae a ee a 35 Content of JMXi B Mod Data Structures 0 2 000002 ee 36 Content of JMXi GAIN CAL IDX Index 2 0 eee eee ee eens 37 Content of JMXi GAIN CAL Index e nea s aa Di 38 Content of JEMXi BDS MOD Data Structures e 39 Content of JMXi RMF RSP Data Structure oe a oc acra sameaa reti 40 Content of JMXi AXIS ARF Data Structure c sas noe samoa e 41 Possible corrected event STATUS values o e 42 Content of JMXi COR Data Structures 0 e e e o 43 Content of JMXi GNRL GTI Data Structure e
173. wDet BIN_LchanHighDet shd Type shdRes rowSelect gtiNames chanLowDet chanHighDet integer Type of shadowgram possible values 1 standard 2 raw standard 3 regular default 2 string DOL of the output shadowgrams default string CFITSIO selection string on events default amp amp STATUS lt 256 15 string Names of GTI tables to be used default string Three lower channel boundaries for shadowgrams for source detection default 46 96 135 string Three upper channel boundaries for shadowgrams for source detection default 95 134 178 8 6 imaging This component deconvolves the shadowgrams to make sky images performs a search for sources and derives flux estimates Before OSA5 these tasks were divided into three components j_ima_basic_recon j ima_src_find and jima _cor_intensity but the new component j_ima_iros does it all The advantages are e g more reliable flux estimates better images and better vignetting correction This script calls the following executables e j_ima_tros e q_identify_srcs Parameters specific to the IMA level are given in Table 15 Table 15 Parameters specific to the IMA level Name Type Description IMA_makeNewBPL boolean Do you want to create a new backprojection file default no IMA _newBackProjFile string Base name of new backprojection file default IM
174. y for this channel in keV E_MAX Maximum energy for this channel in keV ISDC JEM X Analysis User Manual Issue 10 0 80 B 4 Detector positions Initially the position of an event is given as raw detector pixel numbers 0 255 where value 0 0 lies outside the active detector area RAWX and RAWY are integers During COR processing level these detector values are corrected for known errors in the position determination across the detector area with the the help of JEMXi CORX MOD and JEMXi CORY MOD The position correction models provide detector coordinates of each pixel in millimeters from the center of the detector columns DETX and DETY The center most intersection of the collimator defines the detector center Each shadowgram pixel is 1mm and the origin of the detector coordinates is at 127 5 127 5 expressed as corrected pixels B 5 Detector Response Matrix The IC file JMXi RMF GRP fits is a grouping table with three children JMXi RMF RSP JMXi FBDS MOD and JMXi AXIS ARF JMXi RMF RSP is the standard detector response normalized to the sum of 1 0 over the detector channels see Table 39 for more details Table 39 Content of JMXi RMF RSP Data Structure Column Description ENERG_LO Low energy bound of the energy bin keV ENERG_HI High energy bound of the energy bin keV N_GRP Number of channel subsets for the energy bin F_CHAN First channel in each subset for the energy bin N_CHAN Number of
175. you want to extract a spectrum from the mosaic image later In the middle of the GUI front panel you have a possibility to choose a user input catalog the parameter CAT_I_usrCat At the moment you can leave it empty the software will use the general INTEGRAL source catalog for the analysis However for the correct extraction of spectra and lightcurves of the sources it is recommended to create a user catalog with the positions of the sources for which you plan to extract the spectra and or the lightcurves We will come back to this in the following sections and sect 7 5 Once you are satisfied with the settings save them by pressing the Save As button at the front panel of GUI and then press Run to start the data reduction 6 6 1 Results from the Image Step After jemz_science_analysis finishes its operation the results are stored separately for each ScW of the obser vation group They are located in the subdirectories named scw RRRRPPPPSSSF 001 where RRRRPPPPSSSF is the number of the ScW Go to one of these directories and have a look at the files cd scw 010200210010 001 ls This is the output from all the processing steps done by the script The output image is jmx2_sky_ima fits You can check it using e g fu fv jmx2_sky_ima fits You will find that this file contains 7 extensions the index of all images 3 cleaned sky images RECONSTRUCTED type and 3 variance maps one for each of the 3 selected

INTEGRAL Science Data Centre JEM-X Analysis User Manual

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