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Last modified: 28 September 2015

URL: http://cxc.harvard.edu/ciao/releasenotes/ciao_4.0beta1_release.html

CIAO 4.0 Beta 1 Release Notes


The most notable change in CIAO 4.0 Beta 1 is that the ACIS dead area correction is turned on by default; refer to the How CIAO 4.0 Beta 1 and CALDB 3.4.0 Affect Your Analysis section for details. There is a new version of tgextract - named tgextract2 - which provides similar functionality, but allows large and asymmetric regions for better determination of background counts. Significant work has been done on the tool wavdetect, which has two new parameters. The sso_freeze tool has been enhanced so that it can create object-centered aspect solution which, among other uses, allows an object-centered exposure map to be generated. A number of bug fixes to the Data Model library and several CIAO tools are also included.

CIAO 4.0 Beta 1 is the first release of CIAO to be fully GPL compliant. OTS (off-the-shelf) software have been updated to current versions. A set of "smoke test" scripts are included to aid users in verifying installation of the release.

CALDB 3.4.0 is required for the proper operation of CIAO 4.0 Beta 1. CALDB 3.4.0 contains a number of updates, including ACIS time-dependent gain files, updated ACIS blank-sky background files, and HRC-I gain maps.

ChIPS and Sherpa are not included in CIAO 4.0 Beta 1. They will be released in CIAO 4.0 Beta 2 (Summer 2007) and Beta 3 (Fall 2007), respectively.



How CIAO 4.0 Beta 1 and CALDB 3.4.0 Affect Your Analysis

Some tool changes and calibration files released in CIAO 4.0 Beta 1 and CALDB 3.4.0 affect analyses in progress, i.e. a tool or calibration file default has been changed. This section of the release notes describes those changes and which tasks are affected. The changes are arranged by instrument and grating configuration.

ACIS Imaging Data

  • ACIS Dead Area Correction

    The ACIS dead area correction is turned on by default in this release. For complete details on the dead area correction, read the ACIS Dead Area Correction why topic.

    The following CIAO response tools and scripts can apply the dead area correction:

    • mkarf
    • mkinstmap
    • mkgarf
    • mkwarf
    • specextract [New]
    • fullgarf
    • psextract
    • acisspec

    The pbkfile and dafile parameter defaults have been updated to reflect that the correction is applied by default. Refer to the help file for each tool for details, e.g. ahelp mkwarf.

    Turning Off the Correction

    If you are have an analysis in progress and do not want to apply the dead area correction, it is possible to "turn off" the correction. To do so, set the dafile parameter to "NONE" and leave the pbkfile parameter blank. For example:

    unix% pset mkgarf pbkfile="" dafile=NONE
    
  • Time-dependent ACIS Gain (TGAIN) Files

    There are new time-dependent ACIS Gain (TGAIN) files for 01 August 2006 - 31 October 2006 (Epoch 28) and 01 February 2007 - 30 April 2007 (Epoch 29):

    acisD2006-08-01t_gainN0005.fits
    acisD2006-08-01t_gainN0006.fits
    acisD2006-11-01t_gain_biN0002.fits
    acisD2006-11-01t_gainN0002.fits   
    acisD2006-11-01t_gainN0005.fits
    acisD2006-11-01t_gainN0006.fits
    acisD2007-02-01t_gain_biN0002.fits
    acisD2007-02-01t_gainN0002.fits 
    

    The files are applicable to -120 C data only. The acisD2007-02-01t_gain[_bi]N0002.fits files are the new default proccesing files in the CALDB.

    These plots illustrate the degree of change the new files will produce in comparison with the old files.

    Epoch 28

    The changes introduced in these files is very small, nearly negligible.

    The change in these files is 5% or less.

    Epoch 29

    The changes introduced in these files is relatively small (a few percent) at the I3 aimpoint, but not negligible.

    The only significant changes introduced by these updates occur for the CTI-corrected case above 8 keV; even then, the change is 5% or less.

    Users working with ACIS data taken during this period may wish to reprocess to improve the TGAIN calibration in their data. The DATE-OBS header keyword records the observation start date.

    Note that unless you are fitting a spectra with oxygen emission lines, the gain refinement is unlikely to have an effect on the spectrum larger than the uncertainties in determining the gain.

  • ACIS Blank-Sky Background Files

    The newest versions of the ACIS blank-sky background files are now available in the CALDB. These files replace the outdated background files, which have been removed from CALDB 3.4.0.

    There are several improvements in these files:

    • The background data have been divided so that there is one chip per file. A unique background file is returned for each chip that contains data in the event file. Users should no longer see the "WARNING: 2 CALDB files found. Using the first" error when looking up a background file.

    • The CTI-corrected files also have the time-dependent gain (TGAIN) correction applied.

    • The background files have reasonable TSTART and TSTOP values in the header. This eliminates a CALDB lookup problem that was primarily seen when using CIAO response tools, e.g. via running specextract.

    • There is no TIME column. The TIME column was previously removed before reprojecting the background file, and so was never used in analysis.

    • The FILTER header keyword has been removed. Previous versions of the file had an incorrect filter value, which caused some CALDB lookups to fail.

    The Using the ACIS "Blank-Sky" Background Files thread contains instructions on how to select a file and match it to a specific observation.

    The acis_bkgrnd_lookup script has been updated to use a more accurate method of choosing the background file to match an observation. Users must upgrade to v1.12 of acis_bkgrnd_lookup in order to use the new background files. The script is available as part of the CIAO scripts package, CIAO_4.0_scripts.tar; see the script installation instructions for details.

ACIS Grating Data

  • ACIS Dead Area Correction

    The ACIS dead area correction is turned on by default in this release. For complete details on the dead area correction, read the ACIS Dead Area Correction why topic.

    The following CIAO response tools and scripts can apply the dead area correction:

    • mkarf
    • mkinstmap
    • mkgarf
    • mkwarf
    • specextract [New]
    • fullgarf
    • psextract
    • acisspec

    The pbkfile and dafile parameter defaults have been updated to reflect that the correction is applied by default. Refer to the help file for each tool for details, e.g. ahelp mkwarf.

    Turning Off the Correction

    If you are have an analysis in progress and do not want to apply the dead area correction, it is possible to "turn off" the correction. To do so, set the dafile parameter to "NONE" and leave the pbkfile parameter blank. For example:

    unix% pset mkgarf pbkfile="" dafile=NONE
    
  • Time-dependent ACIS Gain (TGAIN) Files

    There are new time-dependent ACIS Gain (TGAIN) files for 01 August 2006 - 31 October 2006 (Epoch 28) and 01 February 2007 - 30 April 2007 (Epoch 29):

    acisD2006-08-01t_gainN0005.fits
    acisD2006-08-01t_gainN0006.fits
    acisD2006-11-01t_gain_biN0002.fits
    acisD2006-11-01t_gainN0002.fits   
    acisD2006-11-01t_gainN0005.fits
    acisD2006-11-01t_gainN0006.fits
    acisD2007-02-01t_gain_biN0002.fits
    acisD2007-02-01t_gainN0002.fits 
    

    The files are applicable to -120 C data only. The acisD2007-02-01t_gain[_bi]N0002.fits files are the new default proccesing files in the CALDB.

    These plots illustrate the degree of change the new files will produce in comparison with the old files.

    Epoch 28

    The changes introduced in these files is very small, nearly negligible.

    The change in these files is 5% or less.

    Epoch 29

    The changes introduced in these files is relatively small (a few percent) at the I3 aimpoint, but not negligible.

    The only significant changes introduced by these updates occur for the CTI-corrected case above 8 keV; even then, the change is 5% or less.

    Users working with ACIS data taken during this period may wish to reprocess to improve the TGAIN calibration in their data. The DATE-OBS header keyword records the observation start date.

    Note that unless you are fitting a spectra with oxygen emission lines, the gain refinement is unlikely to have an effect on the spectrum larger than the uncertainties in determining the gain.

  • MEG LSFPARM Files

    There are new +/- 1 MEG LSFPARM files for use in creating ACIS/HETG grating RMFs (gRMFs). A very small error was identified in the derivation and calculation of the MEG LSF. The effect of the error was a broadening of the MEG LSF model by approximately 0.007 A.

    These calibration files may only be used with data that have been processed with chip pixel coordinate randomization turned off (check the RAND_TG header keyword). This has been the default in processing and recommendation for data analysis since CIAO 3.1/DS 7.3.0.

    Refer to the Create Grating RMFs for ACIS-S Observations thread for instructions on making gRMFs.

  • ACIS Blank-Sky Background Files

    The newest versions of the ACIS blank-sky background files are now available in the CALDB. These files replace the outdated background files, which have been removed from CALDB 3.4.0.

    There are several improvements in these files:

    • The background data have been divided so that there is one chip per file. A unique background file is returned for each chip that contains data in the event file. Users should no longer see the "WARNING: 2 CALDB files found. Using the first" error when looking up a background file.

    • The CTI-corrected files also have the time-dependent gain (TGAIN) correction applied.

    • The background files have reasonable TSTART and TSTOP values in the header. This eliminates a CALDB lookup problem that was primarily seen when using CIAO response tools, e.g. via running specextract.

    • There is no TIME column. The TIME column was previously removed before reprojecting the background file, and so was never used in analysis.

    • The FILTER header keyword has been removed. Previous versions of the file had an incorrect filter value, which caused some CALDB lookups to fail.

    The Using the ACIS "Blank-Sky" Background Files thread contains instructions on how to select a file and match it to a specific observation.

    The acis_bkgrnd_lookup script has been updated to use a more accurate method of choosing the background file to match an observation. Users must upgrade to v1.12 of acis_bkgrnd_lookup in order to use the new background files. The script is available as part of the CIAO scripts package, CIAO_4.0_scripts.tar; see the script installation instructions for details.

  • Grating Dispersion Region Files

    The ACIS grating dispersion region files specify regions in diffraction coordinates that limit the lateral, or cross-dispersion extent of the grating spectral patterns on the ACIS-S detector, to allow for better background characterization.

    unix% ls -1 $CALDB/data/chandra/acis/bcf/disp_reg/
    hetgD1999-07-22disp_regN0001.fits
    letgD1999-07-22disp_regN0001.fits
    letgD1999-07-22disp_regN0002.fits
    

    These calibration files are used by the new tgextract2 tool.

HRC-I Imaging and Grating Data

  • HRC-I Gain Maps

    New gain correction maps are available for HRC-I data. The most important change in determining the new gain map values is including a careful background subtraction when comparing the offset to aimpoint in the calibration data, in addition to excluding background-dominated channels from the comparison.

    Users must reprocess the data with hrc_process_events to apply the new calibration, e.g. by following the Create a New Level=2 Event File thread. The correct file will automatically be chosen by the tool.

    The details of the refinements are presented in the memorandum HRC-I Gain Correction (PS), by J. Posson-Brown and V. Kashyap. For more information, refer to the Gain Response of the HRC webpage.

HRC-S Grating Data

  • HRC-S Quantum Efficiency (QE) File

    HRC-S QE version 9 (hrcsD1999-07-22qeN0009.fits) has been added to the CALDB. The LETGS calibration team has released refinements to the HRC-S QE in the region of the Oxygen K-edge which resolve certain instrumental structures at that point, enabling more accurate characterization of source spectra when using the LETG/HRC-S configuration.

    Create a gARF by following the Compute LETG/HRC-S Grating ARFs thread and the new file will automatically be applied.


Tools

acis_build_badpix

  • Bug fix: the tool would fail crash when doing CALDB lookup if the user supplied a bad obsfile value.

acis_process_events

  • The algorithm used to set STATUS bit 23 for TIMED VFAINT mode events that may be potential background events was changed to ignore pixels that are known to be bad. Previously set VFAINT status bits are unset before the check is done again.

    There is also a warning message if check_vf_pha is set for data that wasn't taken in VFAINT mode.

  • Bug fix: STATUS bit 4, which is used to identify events on bad pixels, was being set for events on bad pixels and events adjacent to bad pixels. Now the bit is set only for events on bad pixels. The number of events for which any bad-pixel STATUS bit is set should remain the same because STATUS bit 5, which is used to identify events adjacent to bad pixels, was (and still is) set properly.

acis_run_hotpix

  • Bug fix: the dmkeypar commands used by this script now have echo="no" set to quiet screen output.

aconvolve

  • Bug fix: the "edges" treatment parameters for double precision sliding cell convolution were being ignored. Also fixed problems with convolutions of 3D images.

  • The kernel parameter has been removed.

acrosscorr

  • The kernel parameter has been removed.

apowerspectrum

  • The kernel parameter has been removed.

arestore

  • The kernel parameter has been removed.

ascii2fits

  • The ascii2fits script has been removed from CIAO. This simple script relied on the VARMM (Variable, Math and Macro S-Lang) library, which is not available in CIAO 4.0 Beta 1. In the future, its functionality will be replaced by the Data Model ASCII kernel.

asphist

  • The tool only prompts for the dtffile parameter if the input file contains HRC data.

axbary

  • The tool prompts for parameters in the same order as they appear in the parameter file.

  • Supporting functions for barycenter operations have been updated.

celldetect

  • The kernel parameter has been removed.

csmooth

  • The kernel parameter has been removed.

destreak

  • The tool has been updated to better handle cases when the streak rate is unusually high; see the description of the max_rowloss_fraction parameter in the help file. The change is relatively minor and should affect only those observations that have a high streak row-loss fraction on ACIS-S4.

dmappend

  • Bug fix: the tool no longer crashes when appending to a file that contains only an image extension.

dmarfadd

  • Bug fix: tool would fail if the input stack file does not exist. It now prints an error message.

  • Fixed crash that could happen when more than 12 files were input.

  • Cleaned up warnings when grating keywords are missing (not required to create valid output).

  • The kernel parameter has been removed.

dmcontour

  • The kernel parameter has been removed.

dmcoords

  • When running the tool in parameter mode, the "sim" and "displace" values get added to the values obtained from the aspect solution file. If "Set SIM/DISPLACE [x y z ax ay az]" is used in interactive mode, however, those values are taken as absolute, even if an aspect solution file was specified.

  • Bug fix: if you feed dmcoords a chip coordinate which is outside the valid range of 0.5:1024.5, it now prints a warning about "Bad chip coordinates: Negative or zero value(s)".

dmdiff

  • Bug fix: the tool no longer truncates the tolerance range on a header key with a real value to an integer. This was effectively making the tolerance more restrictive.

  • Bug fix: the error printed when trying to compare two columns that have different datatypes and/or different cases in the column name has been improved.

  • The limit of 300 columns per file has been removed.

dmextract

  • Bug fix: a parse error would occur when the grid syntax was used in the input file filter, e.g. "[bin col=grid(file[filter]);weight]", and a background file was specified. (Even though the grid syntax was part of the input file filter, it was the parsing of the background file that causes the failure.)

dmfilth

  • The calculation of the POISSON distribution has been updated to be more numerically stable. Previously, the tool would fail if pixels had more than ~100 counts/pixel and this distribution was used.

  • The DIST, POISSON, and GLOBAL distribution arrays have all been updated from static to dynamic allocation.

  • A normalized Gaussian distribution is substituted for the Poisson distribution when average background is greater than 500 counts/pixel to avoid numerical problems.

dmimg2jpg

  • The log and powerlaw scaling routines were rewritten to give better results for normalized (fluxed) images. Changes to the powerlaw routine are subtle, but users should see marked improvement in the log scaling routine.

  • The scalefunction options now include "asinh".

dmimgpick

  • Bug fix: if the input image was not square, dmimgpick would have a problem related to how the tool checks if the pixel being "picked" is outside the image and the tool would fail with a segmentation fault. This bug was seen on Linux and Mac OS X platforms.

dmjoin

  • The joinfile parameter can take a stack of input files. The tool checks the consistency of the number and type of columns in the stack.

dmmakereg

  • Bug fix: using region="bounds(...)" and kernel=ascii produces a region file formatted for use into ds9, e.g. box(xmid,ymid,width,height,angle).

dmmerge

  • Bug fix: the tool checks the length of text columns before merging the files and exits if they do not match.

dmpaste

  • The kernel parameter has been removed.

dmsort

  • The kernel parameter has been removed.

dmtcalc

  • The kernel parameter has been removed.

dmtype2split

  • dmtype2split no longer assumes an output block name of "SPECTRUM". It is necessary to specify the output block name, e.g.

    dmtype2split infile="pha2.fits[#row=4:4]" outfile="HEG_p1.pha[SPECTRUM]" 
    

    If no block name is given, the input filename is used to name it.

  • Bug fix: when writing out vector columns, only the first component was copied to the output file. Now both components of the vector are written to the output as scalar columns.

  • Bug fix: the tool no longer writes incorrect CHANTYPE and BACKSCAL header keyword values. The values are copied from the input file.

get_src_region

  • There are a number of bug fixes for the case where all the values in a floating-point image were between 0 and 1, such as the "threshold" value getting cast to an integer and Null/NaN/DSS-region checking not working correctly.

  • The tool would fail on Linux when there were no "bright" pixels in the image.

  • The kernel parameter has been removed.

hrc_dtfstats

  • The infile parameter can take a stack of input files. The stack is combined into a single output file. All the records from all the DTF files in the stack (which pass the GTI filter in the gtifiles parameter) are used to compute average quantities for the output file.

  • The lookupTab parameter was added to provide header merging rules.

lightcurve

  • The lightcurve tool has been removed from CIAO. The dmextract should be used for creating lightcurves; this has been the recommendation since CIAO 3.0 (August 2003).

mkacisrmf

  • Two new parameters have been added to mkacisrmf: asolfile and obsfile.

    If the aspect solution file(s) for the observation are provided in the asolfile parameter, the average dither values are used to derive the correct instrument coordinates for an input WMAP in DETX,DETY coordinates.

    The obsfile value serves only for CALDB lookup. The value defaults to the wmap parameter value, so users don't have to specify both.

  • Bug fix: if the WMAP file is empty (i.e. all values are zero), the tool issues a warning.

  • Bug fix: the tool will generate the correct RMF for a non-standard channel grid, e.g. channel="69:128:1".

mkarf

  • The ACIS dead area correction is "on" by default in CIAO 4.0 Beta 1. The pbkfile and dafile parameter defaults have been updated to reflect this. The pbkfile parameter is now automatic (i.e. not hidden) and there is no default value. The default value of the dafile parameter has been changed to "CALDB".

    Users who wish to continue analysis without the dead area correction should set both of these parameter values to "NONE".

mkgarf

  • The obsfile parameter is no longer redirected to the value of the asphistfile by default. The recommended input to this parameter is now a level 2 event file or similar FITS file.

  • The ACIS dead area correction is "on" by default in CIAO 4.0 Beta 1. The pbkfile and dafile parameter defaults have been updated to reflect this. The pbkfile parameter is now automatic (i.e. not hidden) and there is no default value. The default value of the dafile parameter has been changed to "CALDB".

    Users who wish to continue analysis without the dead area correction should set both of these parameter values to "NONE".

mkinstmap

  • The ACIS dead area correction is "on" by default in CIAO 4.0 Beta 1. The pbkfile and dafile parameter defaults have been updated to reflect this. The pbkfile parameter is now automatic (i.e. not hidden) and there is no default value. The default value of the dafile parameter has been changed to "CALDB".

    Users who wish to continue analysis without the dead area correction should set both of these parameter values to "NONE".

mkoif

  • The mkoif tool has been removed from CIAO.

mkwarf

  • The ACIS dead area correction is "on" by default in CIAO 4.0 Beta 1. The pbkfile and dafile parameter defaults have been updated to reflect this. The pbkfile parameter is now automatic (i.e. not hidden) and there is no default value. The default value of the dafile parameter has been changed to "CALDB".

    Users who wish to continue analysis without the dead area correction should set both of these parameter values to "NONE".

  • Bug fix: a check for invalid chip coordinates has been added to mkwarf. The edge of the WMAP (in detector coordinates) could get mapped to chip coordinates at 1024.5 which was rounded to 1025. The tool then tried to find the FEF region to convert chipy=1025 (for which there is none) and thus failed.

  • Added support for WMAPs in TDET coordinates in addition to DET coordinates.

psf_project_ray

  • Bug fix: when the evtfile parameter was used, only the first 10 characters of the DETNAM header keyword value were copied to the output.

specextract

  • Two new parameters have been added to specextract to allow the ACIS dead area correction to be taken into account: pbkfile and dafile.

    The ACIS dead area correction is "on" by default in CIAO 4.0 Beta 1. The pbkfile parameter has no default value, and the dafile parameter default is "CALDB". If a stack of input filenames is given to specextract, there must be the same number of parameter block files specified.

    Users who wish to continue analysis without the dead area correction should set both of these parameter values to "NONE".

sso_freeze

  • Two new parameters have been added to sso_freeze: asolfile and ocsolfile. They can be used to create an object-centered aspect solution file, which may then be used to generate an exposure map or response file (ARF) for the data.

tg_create_mask

  • In order to use the parameter sX_width_heg/meg/leg to set the output width, sX_zero_rad must be set. If sX_zero_rad is not set, a warning will be displayed to tell the users that the radius and the width are computed by using input_psf_tab.

tg_resolve_events

  • tg_resolve_events cannot accept a stack of files for the input, output, or regionfile parameters. The tool now checks that only one filename is supplied for each.

tgdetect

  • Bug fix: a problem would occur when running this tool with snr_thresh=3 because that is the default value of the celldetect thresh parameter. celldetect is called by tgdetect, and a logic bug was causing a section of code not to execute when the values are equal. The bug has been fixed.

tgextract

  • Bug fix: the tool now writes the DETCHANS header keyword in the output PHA2 file. This will eliminate an error seen by XSpec users.

tgextract2

  • New Tool!

    tgextract2 is an alternative to tgextract, providing the same functionality with a different parameter interface and slightly different output format. It allows large and asymmetric regions for better determination of background counts.

    • The tool will optionally compute the BACKSCALE (BG_AREA column) from the region and events, enabling support of large regions which extend off detector or non-uniform regions.
    • The BG_AREA and BACKSCAL are output as arrays.

      Note that Sherpa 3.4 cannot use the BACKSCAL array properly; it will read in only the first value in the array. ISIS [http://space.mit.edu/CXC/ISIS/] reads in the whole array correctly.

    • Tool parameters and output columns are consistent with the dmextract tool, where applicable.

    This tool is not back-compatible with tgextract.

vtpdetect

  • Bug fix: when vtpdetect is given an image which has been blocked by a factor other than 1, it no longer double-corrects the radii.

  • The kernel parameter has been removed.

wavdetect

  • (wavdetect calls wtransform, hence the identical release notes for these two tools.)

  • An alternative algorithm for specifying the allowed number of false sources detected has been added to this tool. Based on extensive new simulations to determine the dependence of the number of pixels per false source on source significance and background (expressed in the new sigcalfile parameter), the tool can now determine the significance threshold for source detection itself, if the user inputs directly the desired false source rate (e.g., desired number of false sources per field per scale). Both threshold algorithms are fully supported, and users need make no changes if they still wish to use the current algorithm. The new algorithm is restricted to symmetric wavelets but can be applied to non-Chandra data.

  • An alternative algorithm for specifying the allowed number of false sources detected has been added to this tool. There are two new parameters related to the new algorithm: falsesrc and sigcalfile.

    falsesrc sets the number of false sources allowed per scale in the image. That number is combined with image size and scale information, using additional simulation results contained in the file defined by the sigcalfile parameter, to determine the threshold significance for each pixel; consequently the value given for the parameter sigthresh is ignored. If falsesrc is set to a negative number, the code uses sigthresh instead to determine thresholds.

    The data file for the false-source algorithm is set in the sigcalfile parameter. The file contains simulation results that are used with the false-source algorithm. This file is included with with the release and may be used for both Chandra and non-Chandra data. The user may not specify "CALDB" for this parameter.

  • The kernel parameter has been removed.

wtransform

  • (wavdetect calls wtransform, hence the identical release notes for these two tools.)

  • An alternative algorithm for specifying the allowed number of false sources detected has been added to this tool. Based on extensive new simulations to determine the dependence of the number of pixels per false source on source significance and background (expressed in the new sigcalfile parameter), the tool can now determine the significance threshold for source detection itself, if the user inputs directly the desired false source rate (e.g., desired number of false sources per field per scale). Both threshold algorithms are fully supported, and users need make no changes if they still wish to use the current algorithm. The new algorithm is restricted to symmetric wavelets but can be applied to non-Chandra data.

  • An alternative algorithm for specifying the allowed number of false sources detected has been added to this tool. There are two new parameters related to this addition: falsesrc and sigcalfile.

    falsesrc sets the number of false sources allowed per scale in the image. That number is combined with image size and scale information, using additional simulation results contained in the file defined by the sigcalfile parameter, to determine the threshold significance for each pixel; consequently the value given for the parameter sigthresh is ignored. If falsesrc is set to a negative number, the code uses sigthresh instead to determine thresholds.

    The data file for the false-source algorithm is set in the sigcalfile parameter. The file contains simulation results that are used with the false-source algorithm. This file is included with with the release and may be used for both Chandra and non-Chandra data. The user may not specify "CALDB" for this parameter.

  • The kernel parameter has been removed.


Parameter Files

The CIAO 4.0 Beta 1 software establishes a separate local parameter file directory, ~/cxcds_param_beta. This allows users to run both CIAO 3.4 and CIAO 4.0 Beta 1 without having to worry about parameter file conflicts.

A summary of parameter files changes is provided in this section. Refer to the Tools section of these release notes for complete details.

hrc_dtfstats

  • New lookupTab parameter provides header merging rules.

mkacisrmf

  • Two new parameters: asolfile (aspect solution file) and obsfile (observation file for CALDB lookup).

mkarf

  • The pbkfile and dafile parameter defaults have been updated to reflect that the ACIS dead area correction is "on" by default in CIAO 4.0 Beta 1.

mkgarf

  • The obsfile parameter is no longer redirected to the value of the asphistfile.

  • The pbkfile and dafile parameter defaults have been updated to reflect that the ACIS dead area correction is "on" by default in CIAO 4.0 Beta 1.

mkinstmap

  • The pbkfile and dafile parameter defaults have been updated to reflect that the ACIS dead area correction is "on" by default in CIAO 4.0 Beta 1.

mkwarf

  • The pbkfile and dafile parameter defaults have been updated to reflect that the ACIS dead area correction is "on" by default in CIAO 4.0 Beta 1.

specextract

  • Two new parameters to allow the ACIS dead area correction to be taken into account: pbkfile and dafile.

sso_freeze

  • Two new parameters for use in creating an object-centered aspect solution file: asolfile and ocsolfile.

wavdetect

  • Two new parameters related to detecting false sources: falsesrc and sigcalfile.

wtransform

  • Two new parameters related to detecting false sources: falsesrc and sigcalfile.

kernel parameter

  • The kernel parameter has been removed from the following tools:

    • aconvolve
    • acrosscorr
    • apowerspectrum
    • arestore
    • celldetect
    • csmooth
    • dmarfadd
    • dmcontour
    • dmpaste
    • dmsort
    • dmtcalc
    • get_src_region
    • vtpdetect
    • wavdetect
    • wtransform

Data Model

Bug Fixes

  • The DM would not complain when given a component in a FITS region file that did not exist (e.g. "file.fits[component=99]" when there was no component numbered 99).

  • In vector filtering cases where the components are non-adjacent dissimilar type columns, e.g. (tg_lam,pi), the dmcopy tool and the DM table filtering function would produce different results due to a difference in filtering logic.

Enhancements

  • The DM will rename transform descriptors if another descriptor already has the name. Includes changes where default image axis names are redefined after all file descriptors are generated to avoid clashes between default names and those defined in the file.

  • If a file contains vector columns with single range subspace, the subspace is applied to each vector component. The output file contains individual subspaces for each component.


User Interface

Prism

  • The prism file browsing GUI is included, but does not have any plotting capability - i.e. the "Interactive Plot" or "Histogram" options in the "Visualization" menu - since these functions require ChIPS.

firstlook and filtwin

  • The firstlook and filtwin GUIs have been removed from CIAO.


Libraries

cxcparam

  • There are updates to the parser to allow spaces around commas in the parameter file, e.g. "infile, s, a, ...", in order to be compatible with some FTOOLS parameter files.

dslib

  • The WCS routines have been updated to handle images with physical coordinates but no world coordinates.

psflib

  • New routines to access the PSF/ECF info:

      psfGetInit()
      psfGetFree()
      psfGetRadius()
      psfGetECF()
    
  • Updated to use either the old (one table) or new (multiple blocks) style of ECF tables.

regionlib

  • Bug fix: using region="bounds(...)" and kernel=ascii produces a region file formatted for use into ds9, e.g. box(xmid,ymid,width,height,angle).

tcdlib

  • Added new routines for double precision FFT and Slide convolutions.

  • Significant speed up in convolutions.

  • Bug fix: the "edges" treatment parameters for double precision sliding cell convolution were being ignored. Also fixed problems with convolutions of 3D images.


S-Lang Modules

paramio

  • Bug fix: the paccess() function returns a NULL when the parameter file cannot be found.


Analysis Scripts

The CIAO contributed scripts package is available from the Scripts page and is considered a required part of the installation. The script installation instructions explain where the scripts should be unpacked within the CIAO directory tree.

acis_bkgrnd_lookup v2.0

  • The script has been updated to to run under S-Lang v2. Code updates were made to replace the VARMM (Variable, Math and Macro S-Lang) library with the cxcdm (CXC Data Model) module. Otherwise, acis_bkgrnd_lookup functionality is unchanged.

acis_fef_lookup v1.21

  • The script has been updated to to run under S-Lang v2. Otherwise, acis_fef_lookup functionality is unchanged.

acisspec v4.1

  • The ACIS dead area correction is "on" by default in CIAO 4.0 Beta 1. The pbkfile and dafile parameter defaults have been updated to reflect this. The pbkfile parameter is now automatic (i.e. not hidden) and there is no default value. The default value of the dafile parameter has been changed to "CALDB".

  • The kernel parameter was removed from dmtcalc and dmpaste.

add_grating_orders v2.4

  • It is necessary to specify an output block name of "SPECTRUM" in the dmtype2split commands used by the script. Quotation marks were also added to a dmhedit command so that the correct pathname written in the ANCRFILE header keyword in the output PHA file.

  • The kernel parameter was removed from dmtcalc and dmpaste.

add_grating_spectra v3.3

  • The kernel parameter was removed from dmtcalc and dmpaste.

analyze_ltcrv.sl v1.6

  • The plotting routines have been removed from the script, since ChIPS is not available. Otherwise, analyze_ltcrv.sl functionality is unchanged.

  • The script has been updated to use the cxcdm module in place of VARMM (Variable, Math and Macro S-Lang library).

fullgarf v4.1.1

  • The ACIS dead area correction is "on" by default in CIAO 4.0 Beta 1. The pbkfile and dafile parameter defaults have been updated to reflect this. The pbkfile parameter is now automatic (i.e. not hidden) and there is no default value. The default value of the dafile parameter has been changed to "CALDB".

  • An additional parameter change was made in mkgarf. The obsfile value is set explicitly to the name of the event file instead of being redirected to the asphistfile parameter value.

get_sky_limits v1.9

  • The script now uses the cxcdm module to inspect the input file. This uncovered a few bugs for images with no physical or world-coordinate systems. It also means that the case of the axis names, as reported on-screen and saved to the dmfilter parameter, may change.

lc_clean.sl v1.10

  • The plotting routines have been removed from the script, since ChIPS is not available. Otherwise, lc_clean.sl functionality is unchanged.

  • The script checks for the histogram module and defaults to the cxcdm module if histogram is unavailable. This replaces the CIAO 3.4 use of VARMM (Variable, Math and Macro S-Lang library).

merge_all v3.7

  • An outdated ChIPS workaround was replaced by dmtcalc.

  • A few instances of dmlist were replaced by dmkeypar. Users may see tiny changes in the SIM_Z values printed to the screen, but the output files are unchanged.

psextract v4.0.1

  • The ACIS dead area correction is "on" by default in CIAO 4.0 Beta 1. The pbkfile and dafile parameter defaults have been updated to reflect this. The pbkfile parameter is now automatic (i.e. not hidden) and there is no default value. The default value of the dafile parameter has been changed to "CALDB".

    Note that psextract applies the same pbkfile to the source and background datasets. If this is not appropriate for your analysis, you will have to run mkarf independently to create an ARF with the dead area correction. (In this case, make sure to "turn off" the correction during the psextract run, i.e. pbkfile=NONE and dafile=NONE.)

Missing Scripts

  • Due to dependencies on ChIPS or Sherpa, a number of CIAO scripts have been removed temporarily from the contributed scripts package. They will be replaced once the functionality is available or the script has been rewritten.

    CIAO scripts with some ChIPS or Sherpa dependency (e.g. for plotting):

    • monitor_photom
    • regions.sl
    • show_tgain_corr
    • show_wgt.sl
    • spectrum.sl
    • tg_osort_img
    • tg_scale_reg

    Sherpa-specific scripts:

    • chart_spectrum.sl
    • paramest.sl
    • setplot.sl
    • sherpa_paramset.sl
    • sherpa_plotfns.sl
    • sherpa_utils.sl
    • simspec

Obsolete Scripts

  • The following obsolete scripts have been removed from the contributed scripts package:

    • acis_expmap
    • color_image
    • sstats.sl

Documentation

Download pages

  • There are known problems with the CIAO download pages in Internet Explorer on the Mac OS X platform. We recommend that you choose an alternate browser - such as Safari (distributed with Mac OS X) or Mozilla Firefox [http://www.mozilla.org/products/firefox/] - to avoid download problems.

Ahelp

  • HTML versions (e.g. "ahelp -w") of the ahelp pages are no longer packaged with CIAO. Users who wish to have a copy of the page in HTML when they are not online should download the CIAO Web Pages. ("ahelp ahelp" incorrectly still lists this as an option.)

  • Using the "ahelp -i" command to display the HTML ahelp page from the CIAO website will bring up the CIAO 3.4 version of the help file. Users will have to change the URL in the browser to point to http://cxc.harvard.edu/ciaobeta/ahelp/ to get the CIAO 4.0 Beta 1 help file.

  • Documentation on the S-Lang Run-Time Library is no longer packaged as ahelp files. Users can access this info from within slsh via "help", e.g.:

    slsh> help assoc_get_keys;
    assoc_get_keys
    
     SYNOPSIS
      Return all the key names of an Associative Array
    
    ...
    

Analysis Threads

  • The CIAO Science Threads are in the process of being tested and updated for the CIAO 4.0 Beta 1 release. Please check the "Last Update" information at the top of each thread to see if it has been reviewed yet.

Missing Threads

  • Due to dependencies on ChIPS, a number of CIAO threads have been removed temporarily from the website. Users will need to run these threads in CIAO 3.4 if these threads are crucial to the analysis (links go to the CIAO 3.4 version of the thread).

    • Introduction to Plotting Using ChIPS

    • Measure Grating Dispersion Distance

    • Processing ACA Monitor Window Data

    • Create an Order-Sorting Image

    • Displaying the FEF Regions Covered by a Source

    • Calculating Spectral Weights

Obsolete Threads

  • The following obsolete threads have been removed from the website (links go to the CIAO 3.4 version of the thread).

    • Extracting Extended Source Spectra and Responses: use specextract for these analyses

    • Correcting Responses for ACIS Contamination: the information is available from the ACIS QE Degradation why topic

    • Updating dmgroup Syntax for CIAO 3: refer to the dmgroup help file for syntax

    • Calculating Statistics of Images: the obsolete script used in this thread, sstats.sl, was removed from CIAO; refer to the dmstat help file for syntax

    • Creating Accurate RA, Dec Coordinates for src2 Files: the detections in the src2.fits files are not sufficient for direct use in analysis. Users interested in spatial analysis should perform their own detection runs with one of the three Chandra Detect tools: celldetect, wavdetect, and vtpdetect.



Last modified: 28 September 2015
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