CIAO 4.1.2 Release Notes

(17 Sep 2009) CALDB 4.1.4 has been released.

(20 Apr 2009) CIAO 4.1 has been patched to CIAO 4.1.2.

CIAO 4.1.2 includes several new CIAO tools, which were initially developed for use with the Chandra Source Catalog (CSC): acis_streak_map, dither_region, evalpos, glvary, and pileup_map. There are also two new tools, also developed for the CSC which are run from the CIAO command line and have a parameter file, but uses Sherpa to do the calculations: srcextent and modelflux.

In addition to a number of improvements to Sherpa in this release, there is a new command - script (S-Lang or Python help) - which saves every command typed in a Sherpa session to a file.

CIAO 4.1.2 includes a full installation of the CIAO software for Solaris 10 (SunOS 5.10, SPARC). There is also a beta version of a new script, ciao-install, which automates the installation of CIAO and CALDB. Another new script, check_ciao_caldb checks that the CALDB is properly installed for use with CIAO.

CIAO 4.1 Release Notes
CIAO 4.1.1 Release Notes

• How CALDB 4.1.4 Affects Your Analysis
• How CALDB 4.1.3 Affects Your Analysis
• Installation
• Tools
• Parameter Files
• Sherpa
• GUIs (Graphical User Interfaces)
• Analysis Scripts and Modules
• Documentation

How CALDB 4.1.4 Affects Your Analysis

ACIS -120 C Imaging and Grating Data

• Time-dependent ACIS Gain (TGAIN) Files for -120 C Data

  There are new time-dependent ACIS Gain (TGAIN) files for 01 May 2009 - 30 July 2009 (Epoch 38):

  acisD2009-02-01t_gainN0005.fits
  acisD2009-02-01t_gainN0006.fits
  acisD2009-05-01t_gainN0002.fits
  acisD2009-05-01t_gain_biN0002.fits
  

  The files are applicable to -120 C focal plane temperature only.

  These plots illustrate the degree of change the new files will produce in comparison with the old files. Note that the corrections at other points across the chip surface may be significantly from these aimpoint plots.

  • ACIS-I3 aimpoint: version N0006 files showing T_GAIN energy shifts

    There is very little change at this location on the chip by this upgrade. Other locations will vary more significantly.

  • ACIS-S3 aimpoint: with CTI correction applied

    For this location and chip, the upgrade is more significant (difference between the solid green and dashed blue curves), primarily at the highest energy points above 6 keV.

  • ACIS-S3 aimpoint: no CTI correction applied

    As is usually the case, the corrections are more scattered over the full range for the non-CTI case. However while these variations are significant relative to the 0.3% gain setting standard for the calibrations, they are not unusually strong.

  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.

How CALDB 4.1.3 Affects Your Analysis

ACIS -120 C Imaging Data

• Time-dependent ACIS Gain (TGAIN) Files for -120 C Data

  There are new time-dependent ACIS Gain (TGAIN) files for 01 February 2009 - 30 April 2009 (Epoch 37):

  acisD2008-11-01t_gainN0005.fits
  acisD2008-11-01t_gainN0006.fits
  acisD2009-02-01t_gain_biN0002.fits
  acisD2009-02-01t_gainN0002.fits
  

  The files are applicable to -120 C focal plane temperature only. The acisD2009-02-01t_gain_biN0002.fits file is the new default processing file in the CALDB.

  These plots illustrate the degree of change the new files will produce in comparison with the old files. Note that the corrections at other points across the chip surface may be significantly from these aimpoint plots.

  • ACIS-I3 aimpoint: version N0006 files showing T_GAIN energy shifts

    There is very little change at this location on the chip by this upgrade. Other locations will vary more significantly.

  • ACIS-S3 aimpoint: with CTI correction applied

    For this location and chip, the upgrade is more significant (difference between the solid green and dashed blue curves), primarily at the highest energy points above 6 keV.

  • ACIS-S3 aimpoint: no CTI correction applied

    As is usually the case, the corrections are more scattered over the full range for the non-CTI case. However while these variations are significant relative to the 0.3% gain setting standard for the calibrations, they are not unusually strong.

  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.

• Corrections to CALDB lookup for CTI calibration

  Prior to CALDB 4.1.3, if acis_process_events was run with apply_cti=no, running the tool again would never apply the CTI correction. This was due to a CALDB lookup problem which is fixed in CALDB 4.1.3.

  This change does not require any analysis to be redone.

• Corrections to CALDB lookup for Blank-sky Background Files

  Prior to CALDB 4.1.3, there was a CALDB lookup problem that affected three of the ACIS blank-sky background files. The acis_bkgrnd_lookup script would fail to return any files in this case. The problem has been fixed in CALDB 4.1.3.

  This change does not require any analysis to be redone.

ACIS -120 C Grating Data

• Time-dependent ACIS Gain (TGAIN) Files for -120 C Data

  There are new time-dependent ACIS Gain (TGAIN) files for 01 February 2009 - 30 April 2009 (Epoch 37):

  acisD2008-11-01t_gainN0005.fits
  acisD2008-11-01t_gainN0006.fits
  acisD2009-02-01t_gain_biN0002.fits
  acisD2009-02-01t_gainN0002.fits
  

  The files are applicable to -120 C focal plane temperature only. The acisD2009-02-01t_gain_biN0002.fits file is the new default processing file in the CALDB.

  These plots illustrate the degree of change the new files will produce in comparison with the old files. Note that the corrections at other points across the chip surface may be significantly from these aimpoint plots.

  • ACIS-I3 aimpoint: version N0006 files showing T_GAIN energy shifts

    There is very little change at this location on the chip by this upgrade. Other locations will vary more significantly.

  • ACIS-S3 aimpoint: with CTI correction applied

    For this location and chip, the upgrade is more significant (difference between the solid green and dashed blue curves), primarily at the highest energy points above 6 keV.

  • ACIS-S3 aimpoint: no CTI correction applied

    As is usually the case, the corrections are more scattered over the full range for the non-CTI case. However while these variations are significant relative to the 0.3% gain setting standard for the calibrations, they are not unusually strong.

  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.

• Corrections to CALDB lookup for CTI calibration

  Prior to CALDB 4.1.3, if acis_process_events was run with apply_cti=no, running the tool again would never apply the CTI correction. This was due to a CALDB lookup problem which is fixed in CALDB 4.1.3.

  This change does not require any analysis to be redone.

Installation

Solaris 10 Release

• CIAO 4.1.2 includes a full installation of the CIAO software for Solaris 10 (SunOS 5.10, SPARC). This is the first time the software has been made available for this platform. Download CIAO for Solaris 10

Installation Script

• There is a new script, ciao-install, which automates the installation and upgrade of CIAO and CALDB. The ciao-install thread and README explain how it is used. CIAO 4.1.2 contains a beta release of ciao-install; user comments on the script may be submitted via Helpdesk.

Clearing out .ipython-ciao

• CIAO 4.1 includes IPython in the CIAO OTS directory which is used by Sherpa and ChIPS to provide command-line user interfaces. These programs create an IPython profile in the directory $HOME/.ipython-ciao.

  In order to access the new Sherpa functions in CIAO 4.1.2, users must delete the files in $HOME/.ipython-ciao.

  If advanced users have made any personal customizations to those files, they will have to be copied again into $HOME/.ipython-ciao after resetting the directory.

Tools

acis_streak_map

• New Tool!

  The acis_streak_map tool generates high frequency background maps for individual ACIS chips. It is specifically designed to identify streaks on a chip caused by bright source photons striking pixels along the readout column during readout.

  This tool was initially developed for use with the Chandra Source Catalog.

arestore

• Bug Fix: The tool checks that the PSF image is smaller than the data and prints an error if it is not. If a PSF larger than the data were used, there would be artifacts in the output file.

dither_region

• New Tool!

  The dither_region tool takes a region on the sky and computes its location on the detector. When part of the region falls onto a bad pixel, goes off the detector, or goes outside the bounds of the mask (optional), the area is decremented.

  This tool was initially developed for use with the Chandra Source Catalog.

dmcoords

• The "asolfile" parameter, which takes the input aspect solution file, has been changed from hidden to required. The SIM drift has become significant over the Chandra mission lifetime and the mean dy and dz from the aspect solution are needed to get accurate coordinate conversions.

• Bug Fix: When dmcoords is run with a missing or incorrect aspect solution, the error message reports the correct filename.

• Bug Fix: The exit status is set to "bad" (1) when the tool can't open a non-existent file.

dmextract

• The error "Could not create keyword 'POISSERR' in file ''." has been downgraded to a warning when opt=generic.

• Improved syntax checking will notice a missing "]" in a filter.

dmfilth

• Bug Fix: Background regions no longer need to be supplied when using the BILINT method. The files weren't actually applied in this case, so the tool output will be unchanged.

dmgti

• Bug fix for the case where N-1 row is is good but the N row is bad. Instead of setting the stop time to the start of the Nth row, the tool would set it to the stop time of the Nth row.

dmimg2jpg

• The default value of the "showaim" (put crosshair at aimpoint) and "showgrid" (show grid on image) parameters is set to "no".

dmimgthresh

• Bug Fix: If given a non-existent exposure map, the tool will exit with an error.

dmregrid

• Bug Fix: The tool will exit with an error if bad binning syntax is provided, e.g. providing column names in the "bin" parameter.

evalpos

• New Tool!

  The evalpos tool looks up the pixel value in an image at the input (RA,DEC) coordinates.

  This tool was initially developed for use with the Chandra Source Catalog.

glvary

• New Tool!

  The glvary tool implements the Gregory-Loredo variability test algorithm. It splits the events into multiple time bins and looks for significant deviations.

  This tool was initially developed for use with the Chandra Source Catalog.

lim_sens

• The tool writes the command history to the header of the output file.

mkpsfmap

• The tool outputs the units of the image pixels: "arcsec", "logical", or "physical".

modelflux

• New Sherpa Tool!

  The modelflux tool calculates the energy flux and photon flux for a given count rate, spectrum response, and a Sherpa source model. Given a flux or photon flux, the tool will also calculate the appropriate count rate.

  This tool is run from the CIAO command line and has a parameter file, but uses Sherpa to do the calculations. It was initially developed for use with the Chandra Source Catalog.

pileup_map

• New Tool!

  The pileup_map tool computes a rough estimate of the amount of pileup. The output image is the number of counts per ACIS frame.

  This tool was initially developed for use with the Chandra Source Catalog.

reproject_events

• Bug Fix: The value of the TELESCOP header keyword is now case-insensitive.

• Bug Fix: The tool exits with an error if the file specified in the "matchfile" parameter is missing.

skyfov

• The tool prints a warning when the aspect file is missing.

srcextent

• New Sherpa Tool!

  The srcextent tool calculates the sizes and associated errors of a photon-count source image or list of source images using the Mexican Hat Optimization (MHO) algorithm. The tool can be used to determine - within a confidence interval - if the source is extended.

  This tool is run from the CIAO command line and has a parameter file, but uses Sherpa to do the calculations. It was initially developed for use with the Chandra Source Catalog.

wavdetect

• There are two new separators allowed in the "scales" parameter value: comma (,) and semicolon (;).

Parameter Files

dmcoords

• The "asolfile" parameter, which takes the input aspect solution file, has been changed from hidden to required. The SIM drift has become significant over the Chandra mission lifetime and the mean dy and dz from the aspect solution are needed to get accurate coordinate conversions.

dmimg2jpg

• The default value of the "showaim" (put crosshair at aimpoint) and "showgrid" (show grid on image) parameters is set to "no".

Sherpa

Wavelength analysis

• Sherpa models assume that model parameters (e.g., line positions) are always in keV, regardless of whether the user is working in energy or wavelength space.

  Data filtering may still be done in wavelength space if that's what the user is choosing.

Log of Sherpa commands

• New Sherpa Function!

  The script (S-Lang or Python help) function saves every command typed in a Sherpa session to a file.

Loading ASCII files

• The load functions for ASCII files have been updated to handle the case where only one column is read from the file better.

  If there is a header in the ASCII file (i.e., the first N lines are comments, indicated by a '#' character), then the last line of the header is taken to be a list of columns that should be read in using the ASCII kernel. For instance, if there are four columns in the ASCII file, but the last line of the header is "# A B", then only the first two columns are read in and named "A" and "B".

  The last comment line may be a single word, e.g. "# A", and is not necessarily meant to indicate column names. In this case, only a single column is read in by the DM ASCII kernel. However, Sherpa expects there to be at least two columns (x- and y-arrays for a data set).

  In the case where only one column name is defined:

  1. Sherpa reads the file again and attempts to load all columns in it.

     sherpa> load_data("simptab.dat")
     WARNING: Only found 1 column in simptab.dat, trying again with
              Data Model syntax : simptab.dat[opt colnames=none]
              Read simptab.dat successfully
     

     In this case there were actually two columns, though the header indicated only one. When Sherpa tried again, appending "[opt colnames=none]" to the file name, both columns were found and the data set was loaded successfully.

  2. If the file really only has one column, an error is printed.

     sherpa> load_table("onetab.dat")
     WARNING: Only found 1 column in onetab.dat, trying again with
              Data Model syntax : onetab.dat[opt colnames=none]
     IOError: Only found 1 column in onetab.dat, need at least 2
     

     The load_table command fails because there really is only one column in the file. Then an error is printed.

XSpec Models

• The following models are new in CIAO 4.1.2:

  • xskerrdisk (S-Lang or Python help): accretion disk line emission with BH spin as free parameter
  • xsnsmax (S-Lang or Python help): neutron star magnetic atmosphere
  • xsnthcomp (S-Lang or Python help): thermally Comptonized continuum
  • xsspexpcut (S-Lang or Python help): super-exponential cut-off absorption

  Sherpa includes the "additive" and "multiplicative" models of XSpec version 12.5.0ab. Please note that the ahelp files for the XSpec models incorrectly list the version as 12.5.0q.

projection and covariance

• The projection command reports to the screen when the search for confidence limits for a parameter has been completed, e.g.

  Confidence limits search for g2.fwhm finished (1 of 3)
  Confidence limits search for g2.pos finished (2 of 3)
  Confidence limits search for g2.ampl finished (3 of 3)
  

• The covariance matrix is now available after covar() (S-Lang or Python help) is run, via the "extra_output" field from get_covar_results() (S-Lang or Python help).

Fitting with a PSF

• The kernel information and default parameter values are included in the model information after calling set_psf (S-Lang or Python help).

• Bug fix: corrected a problem in the reference counting in the PSF model which caused the model to clobber memory it shouldn't have.

Improvements to Plotting

• plot_fit_delchi and plot_fit_resid have a new "clearwindow" option, which allows multiples of those plots to be displayed in the same ChIPS frame. Refer to the the plot_fit ahelp file (S-Lang or Python help) for examples on how to use "clearwindow".

• Source model plots are now plotted as histograms, similar to PHA model plots, and are correctly labeled when working in wavelength space. ARF plots are also plotted as histograms and support wavelength space.

• A bug in plot_bkg_fit() (S-Lang or Python help) has been fixed, to plot the correct background by background ID (bkg_id).

Gamma and Beta functions from the CEPHES library

• The following CEPHES functions are available within Sherpa:

  • gamma (S-Lang or Python help): gamma function
  • lgam (S-Lang or Python help): natural log of the gamma function
  • igamc (S-Lang or Python help): complement of the incomplete gamma (upper) function
  • igam (S-Lang or Python help): the incomplete gamma (lower) function
  • incbet (S-Lang or Python help): the incomplete Beta function

GUIs (Graphical User Interfaces)

ds9 and dax

• The Gregory Loredo lightcurve tool, glvary, has been added to dax.

Analysis Scripts and Modules

check_ciao_caldb

• New Script!

  The check_ciao_caldb script tests the installation of the CIAO Calibration Database (CALDB).

  ciao> check_ciao_caldb
  CALDB environment variable = /soft/ciao-4.1/CALDB
          which is a link to = /soft/caldb41/
               CALDB version = 4.1.2
               relelase date = 2009-03-26T18:00:00
  CALDB query completed successfully.
  

CIAO and Sherpa Modules

• New modules have been added to the contributed tarfile: crates_contrib (S-Lang or Python help), sherpa_contrib (S-Lang or Python help), and ciao_contrib (S-Lang or Python help) (loads both crates_contrib and sherpa_contrib). See the Contributed Sherpa Scripts section of the scripts page and the individual help files for more information.

Documentation

Ahelp

• Ahelp files have been added for all the new tools and Sherpa functions in CIAO 4.1.2. In addition, there are help files which describe the ChIPS and Sherpa configuration files: chipsrc and sherparc.

• There are three deprecated help files which will be removed from the next full CIAO release: get_full_model.xml, psf1d.xml, and psf2d.xml. Users have the option of manually deleting these files from $ASCDS_INSTALL/doc/xml .

New CIAO Threads

• Installing CIAO using the ciao-install Tool

• Measuring Source Extent

• Search for Variability in a Source (S-Lang or Python)

New Sherpa Documentation

• A new "Latest Updates" page documents detailed information about important updates to Sherpa functionality.

• The Download Software section of the Sherpa navigation bar provides easy access to Contributed Sherpa Packages and Contributed Sherpa Scripts .

• New Threads:

  • Radial and elliptical profiles of Image Data Thread (S-Lang or Python)
  • Simulating Chandra ACIS-S LETG Spectra with Sherpa (S-Lang or Python)
  • Measuring Line Parameters with an HETG/ACIS-S Spectrum (S-Lang or Python)
  • Measuring Line Parameters with an LETG/ACIS-S Spectrum (S-Lang or Python)

• A Sherpa Frequently Asked Questions page is now available. The "Command Comparison" FAQ highlights new features of "load" functions.