CIAO 4.6 Release Notes

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Notable changes and improvements in CIAO 4.6.1:

• Two new tools have been added to help automate the detection of the 0th order location in grating observations: tg_choose_method and tgdetect2
• Sherpa template models have been enhanced to include interpolation between the individual table models. Users can now use templates with all the fit methods (previously only gridsearch was valid).
• The new srcflux script automates the steps necessary to get net counts, rates, and fluxes, with confidence intervals.
• The ACIS parameter-block filename parameter, pbkfile, in mkarf, mkgarf, mkwarf, eff2evt, and mean_energy_map is no longer used. The information is now encoded in the archived data products created with ASCDSVER 8.4.2 and later or reprocessed with chandra_repro. Users with older data who choose not to reprocess their data, can use the new r4_header_update script.
• The suite of hotpixel tools: acis_run_hotpix, acis_find_hotpix, and acis_classify_hotpix has been withdrawn from CIAO. The acis_find_afterglow tool is now the best tool available to identify cosmic ray afterglows without losing a large fraction of events from bright sources.
• A problem affecting the area calculation when complex regions are selected, has been corrected. This problem affected regions which include multiple overlapping shapes. Simple regions were not affected (for more details see the Region section under Libraries).

Sherpa was patched in CIAO 4.6.1 to correct problems when working in units of wavelength (Å)

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• How CALDB 4.6.3 Affects Your Analysis
• How CALDB 4.6.2 Affects Your Analysis
• How CALDB 4.6.1.1 Affects Your Analysis
• How CALDB 4.6.1 Affects Your Analysis
• How CALDB 4.5.9 Affects Your Analysis
• Installation
• Tools
• Parameter Files
• ChIPS
• Sherpa
• Graphical User Interfaces
• Analysis Scripts
• Python Modules
• Libraries
• Environment
• Documentation

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How CALDB 4.6.3 Affects Your Analysis

ACIS Imaging and Grating Data

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

  The new, time-dependent ACIS Gain (T_GAIN) files for May-July 2014 (Epoch 58) are introduced and updated for Epoch 57 in this release, and therefore, affects observations taken since 2014 Feb 01. Other observations are unaffected by these new calibration files.

  Users working with ACIS data taken since 2014 Feb 01 may wish to run chandra_repro and reprocess the data to improve the T_GAIN calibration. The DATE-OBS header keyword records the observation start date.

  See the time-dependent ACIS T_GAIN why page for more information.

  The gain corrections are at the nominal and expected levels of less than 2% of the energy value and users interested in CCD spectroscopy may benefit in applying the new gain adjustment. Grating spectroscopy benefits as well, in the form of improved order sorting. It is unnecessary to apply this adjustment for only doing timing or imaging analysis, although doing so will not have a negative effect.

  Note that only spectra with several hundreds of counts and/or prominent features (in emission or absorption) will show changes from the T-gain refinement that exceed the uncertainties from the gain calibration.

HRC-S Gratings Data

• HRC-S QEU Files for 2014-2020

  Predictive HRC-S QEU files covering the years 2014-2020 have been introduced to account for a consistent ~0.5% per year drop in the QE across the first-order LETG spectrum since the mission launch. A somewhat steeper reduction has been observed in the zeroth-order over time.

  In particular, an error in the CalDB that selects the incorrect QEU file for all 2014 HRC-S observations has been fixed in CalDB 4.6.3 with the 2014 QEU file.

• Old HRC-S QEUs Retired

  Outdated HRC-S QEU files have been removed, and subsequently fixes problems where the incorrect QEU file is selected for all HRC-S observations from 1999.

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How CALDB 4.6.2 Affects Your Analysis

ACIS Imaging and Grating Data

• ACIS QE Contamination Model vN0009

  The ACIS QE contamination model has been upgraded to N0009:

  acisD1999-08-13contamN0009.fits 
  

  This version of the file is necessary due to recent, rapid changes in the optical depth of the contaminant on the optical blocking filter since 2013.3 (roughly 20 April 2013), resulting in an updated ACIS contamination model.

  These changes only affect observations taken since early-mid 2013; the model is otherwise unchanged from the N0008 model introduced in CALDB 4.5.9, with more details about the N0008 model in the ACIS QE contamination model Why document.

  

  ACIS-S3 high CHIPY position

  For sources with a high CHIPY location on ACIS-S3 (CHIPY≥750), there is some uncertainty in the model on the depth of the contaminant layer, which may compromise fitting results at this location when doing imaging spectroscopy.

  These CIAO response tools automatically apply the contamination file when creating ACIS response files:

  • mkarf
  • mkgarf
  • mkwarf
  • mkinstmap

  As well as the scripts which use them:

  • specextract (calls mkwarf and mkarf)
  • fullgarf (calls mkgarf)
  • fluximage (calls mkinstmap)
  • merge_obs (calls mkinstmap)

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

  The new, time-dependent ACIS Gain (T_GAIN) files for February - April 2014 (Epoch 57) are introduced and updated for Epoch 56 in this release, and therefore, affects observations taken since 2013 Nov 01. Other observations are unaffected by these new calibration files.

  Users working with ACIS data taken since 2013 Nov 01 may wish to run chandra_repro and reprocess the data to improve the T_GAIN calibration. The DATE-OBS header keyword records the observation start date.

  See the time-dependent ACIS T_GAIN why page for more information.

  The gain corrections are at the nominal and expected levels of less than 2% of the energy value and users interested in CCD spectroscopy may benefit in applying the new gain adjustment. Grating spectroscopy benefits as well, in the form of improved order sorting. It is unnecessary to apply this adjustment for only doing timing or imaging analysis, although doing so will not have a negative effect.

  Note that only spectra with several hundreds of counts and/or prominent features (in emission or absorption) will show changes from the T-gain refinement that exceed the uncertainties from the gain calibration.

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How CALDB 4.6.1.1 Affects Your Analysis

HRC Imaging Data

• Only users who:

  1. analyzed data with CALDB 4.6.1 (released on 26 March 2014) and
  2. analyzed HRC-I observations taken between 01 January 2012 and 01 January 2014 and
  3. run tools such as fluximage and hrc_bkgrnd_lookup to automatically pick the background files

  might notice a difference in results with this update.

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How CALDB 4.6.1 Affects Your Analysis

ACIS Imaging and Grating Data

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

  The new, time-dependent ACIS Gain (T_GAIN) files for November 2013-January 2014 (Epoch 56) are introduced and updated for Epoch 55 in this release, and therefore, affects observations taken since 2013 Aug 01. All other observations are unaffected by these new calibration files.

  Users working with ACIS data taken since 2013 Aug 01 may wish to run chandra_repro and reprocess the data to improve the T_GAIN calibration. The DATE-OBS header keyword records the observation start date.

  See the time-dependent ACIS T_GAIN why page for more information.

  The gain corrections are at the nominal and expected levels of less than 2% of the energy value and users interested in CCD spectroscopy may benefit in applying the new gain adjustment. Grating spectroscopy benefits as well, in the form of improved order sorting. It is unnecessary to apply this adjustment for only doing timing or imaging analysis, although doing so will not have a negative effect.

  Note that only spectra with several hundreds of counts and/or prominent features (in emission or absorption) will show changes from the T-gain refinement that exceed the uncertainties from the gain calibration.

• Secondary Bad Pixel File FP_TEMP Boundary Correction for "Engineering Run" Observations

  Engineering runs (ERs) are observations, primarily used to monitor the ACIS detectors and not of concern to most general users. The error does not affect Standard Processing and more information can be found in the CALDB release notes.

HRC Imaging Data

• HRC-I Background Event Files v2

  New and improved HRC-I background event files are included in this release, being regenerated using the latest level 1 calibration data, including SAMP-based gains (GMAPs) and the latest DEGAP corrections. The newly introduced background files cover the years 2010-2013. All users performing HRC-I imaging or spatial analyses, e.g. when creating a fluxed image, are encouraged to download and use the upgraded files. The new files provide a significant improvement in background estimates for more recent HRC-I observations, since the background increases over time.

  The HRC-I background event files are not included in the main CALDB tarfile. There is a separate HRC background event tarfile available via ciao-install or from the the the CALDB Download page.

  For instructions on using the background event files, follow the The HRC-I Background Event Files thread.

• HRC-I/S RMF EBOUNDS Header Corrections

  The headers of all HRC-I/S files have been updated, removing an errant TLMIN4 keyword in the EBOUNDS block, which has been found to potentially cause problems with some of the CIAO tools. The data contained within the files are not affected by the header keyword.

  Users interested in non-grating spectroscopy with HRC-I and HRC-S should upgrade the CALDB to use the corrected RMF files.

ACIS and HRC PSF Libraries

• PSFLIB is Now Retired

  The hypercube 2D PSF Library is now retired from the CALDB. The mkpsf tool that relied on the PSF libraries was deprecated and removed in CIAO 4.5 (December 2012). No current CIAO tool uses any of these files.

  If disk space is an issue, all the 2d_psf files located in:

  $CALDB/data/chandra/acis/2d_psf/
  
  $CALDB/data/chandra/hrc/2d_psf/
  

  may be deleted from your local system once CALDB 4.6.1 or later is installed.

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How CALDB 4.5.9 Affects Your Analysis

ACIS Imaging and Grating Data

• ACIS QE Contamination Model vN0008

  The ACIS QE contamination model has been upgraded to N0008:

  acisD1999-08-13contamN0008.fits 
  

  This version of the file is necessary due to recent changes in the optical depth and composition of the contaminant deposited on the optical blocking filter over time, resulting in a new ACIS contamination model.

  Note that these changes do not have any effects at energies above ~1 keV (see changes in effective areas in the ACIS QE contamination model Why document)

  The new model provides significantly lower ACIS effective areas (EAs) compared to the N0007 model for present and future observations; albeit, early- and mid-mission (1999-2009) EAs are not particularly affected by the new model, except for near the carbon, oxygen, and fluorine absorption K-edges. It should be noted that changes near these edges do not significantly affect the fitting results for mid-mission (2004-2009) observations.

  The new contamination model is more realistic than previous models and provides a more accurate representation and prediction of current and future changes of effective ACIS quantum efficiency due to the contamination layer.

  The rate of contaminant build-up has increased significantly since mid-2009, and recently, has presented itself as changing more linearly with time than the previous model estimated (released as CONTAM file model version N0007), which had predicted a leveling-off of the contamination in the future. The concentration of several elemental components in the contamination layer has also been changing, requiring time-varying changes to the optical depths for the C- and F-K absorption edges with respects to the O-K edge, and changes to the spatial-dependent ACIS model, which is also included here.

  Updating the new contamination model for the full mission means that the N0008 CONTAM model is not identically backwards-compatible with the previous N0007 model, but the new model fits the mid-mission contaminant optical depths as the previous model had, indicating that the new model does not significantly affect the early- and mid-mission results.

  

  ACIS-S3 high CHIPY position

  When using a high CHIPY location on ACIS-S3 for imaging spectroscopy, there is some uncertainty in the new model on the depth of the contaminant layer, which may compromise fitting results at this location.

  More information can be found in the CALDB 4.5.9 Release Notes caveat.

  These CIAO response tools automatically apply the contamination file when creating ACIS response files:

  • mkarf
  • mkgarf
  • mkwarf
  • mkinstmap

  As well as the scripts which use them:

  • specextract (calls mkwarf and mkarf)
  • fullgarf (calls mkgarf)
  • fluximage (calls mkinstmap)
  • merge_obs (calls mkinstmap)

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

  There are new, time-dependent ACIS Gain (T_GAIN) files for August 2013 - October 2013 (Epoch 55):

  acisD2013-05-01t_gainN0005.fits
  acisD2013-05-01t_gainN0006.fits
  acisD2013-08-01t_gainN0002.fits
  acisD2013-08-01t_gain_biN0002.fits
  

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

  Users working with ACIS data taken since 2013 May 01 may wish run chandra_repro and reprocess the data to improve the T_GAIN calibration. The DATE-OBS header keyword records the observation start date.

  Note that only spectra with several hundreds of counts and/or prominent features (in emission or absorption) will show changes from the T-gain refinement that exceed the uncertainties from the gain calibration.

HRC-I Imaging Data

• HRC-I Gain Maps

  The latest time-dependent HRC-I Gain Map (GMAP) and the corresponding PI background spectrum—to be applied to observations after 2013 September 16, have been released.

  hrciD2013-09-16sampgainN0001.fits 
  hrciD2013-09-16pibgspecN0001.fits 
  

  Note that HRC-I gain maps are only useful to observers doing hardness ratio or PI spectral analysis studies with HRC-I.

  As the HRC gain continues to slowly decline, the gain maps are updated annually. The change in gain correction is less than 1% on-axis and roughly 5-10% off-axis. Towards the edge of the microchannel plate, the change is up to 15%. Technical details on the gain maps are described in the gain maps section of the HRC calibration website and the in the HRC-I Gain Map Why Document.

  The corresponding background spectrum applicable to the same HRC-I GMAP time period have been generated.

  Users working with HRC-I data may wish run chandra_repro to reprocess the data and improve the gain calibration.

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Installation

Supported Platforms

• CIAO 4.6.1 is supported on:

  • Linux 32 bit and 64 bit (tested on CentOS 6.4 and Red Hat Enterprise 6 )
  • Mac OS X 10.6 & 10.7 Intel 64 bit
  • Mac OS X 10.8 & 10.9 Intel 64 bit

Updates to the ciao-install Installation Script

• ciao-install now reports the version of CIAO it is about to install. Users must download a new version of ciao-install with each CIAO release.

• ciao-install will now prevent users from mistakenly installing different precompiled binary packages into the same directory.

• There is no separate OSX 10.7 (lion) binary package. Lion users will now download the precompiled 10.6 (Snow Leopard) binary package.

• OSX Mavericks users 10.9 will download the Mountain Lion pre-compiled binaries.

• Some OSX users reported problems downloading the CIAO tar files. This was frequently tracked to the ciao-install script using an incompatible version of ftp. The script now uses /usr/bin/ftp to avoid this problem.

Remove old parameter files

• With every new CIAO release, some parameter files are changed: new parameters may be added and occasionally old ones removed or renamed. Deleting or renaming the local parameter directory ensures that the correct parameter files will be accessed the first time a tool is run:

  unix% rm ~/cxcds_param4/*
  

IPython Settings

• Users upgrading from CIAO 4.5 or installing CIAO for the first time need to take no action.

  If upgrading from CIAO 4.4 or earlier, the ipython configuration files stored in the users home directory are incompatible with the new version; a new copy will be installed in a new directory: $HOME/.ipython-ciao4.5. (Note: the file is still called .ipython-ciao4.5!). If you have made customizations with earlier version of CIAO, you will need to manually migrate those changes to work with CIAO 4.6.1.

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Tools

acis_build_badpix

• Adjustments to handling of bias parity errors to only include valid errors when triggering the FEP0 anomaly.

• The minimum maxerr parameter has been changed from zero to one.

• Fix crash if obsfile parameter is left blank.

• Various checks on the input files to ensure the proper files were provided for each input.

• Removed the obsolete pbkext, berrext, and evtsext parameters.

acis_detect_afterglow

• No longer creates empty blocks in cases where the DETNAM keyword in the event file does not match the blocks found in the input badpixel file.

acis_process_events

• Corrected bug that could set time-varying gain file to NONE if the event splithreshold file could not be located in the CALDB.

• The pixadj=CENTROID sub-pixel event position algorithm has been upgraded. Amoung other things, it now correctly ignores bad pixels.

• The spthresh parameter has been removed. The correct split threshold values are specific to each chip and are suppiled via the threshfile input.

acis_classify_hotpix

• Withdrawn. Users should be using acis_find_afterglow

acis_find_hotpix

• Withdrawn. Users should be using acis_find_afterglow

acis_run_hotpix

• Withdrawn. Users should be using acis_find_afterglow

acis_streak_map

• The rotation angle to rotate sky coordinates so they are aligned with respect to cartesian X & Y axes is now computed from a chip coordinate vector parallel, not perpendicular, to the streak direction. This may introduce a small, subtle change in the streaks detected.

• Tool will now error out if there is no data on a chip

dmhedit

• Correct problem where setting the units string could possibly cause memory corruption.

destreak

• When running with ACIS CC-mode data, an error is now produced if a timefile is requested but the exposure time was not set (or set to a value less than zero).

dmmerge

• Update subspace as part of the expanded mosaic support

• No longer crashes when header merging lookupTab points to an empty file.

eff2evt

• The ACIS dead area correction factor is now output as a separate DACORR column. For HRC the value is always 1.0.

• Updated code to read ACIS clocking configuration from input infile instead of separate pbkfile. Updated code to print warning when pbkfile param is specified.

mkacisrmf

• Tool will now use the DY_AVG, DZ_AVG, DTH_AVG keywords to properly setup the coordinate transforms when using WMAP in DET coordinates. The asolfile parameter is no longer required. Note: most WMAPs are now in TDET coordinates so this change has minimal effect.

mkarf

• Updated code to read ACIS clocking configuration from input obsfile instead of separate pbkfile. Updated code to print warning when pbkfile param is specified.

mkarf

• Updated code to read ACIS clocking configuration from input obsfile instead of separate pbkfile. Updated code to print warning when pbkfile param is specified.

mkinstmap

• Updated code to read ACIS clocking configuration from input obsfile instead of separate pbkfile. Updated code to print warning when pbkfile param is specified.

mkgarf

• Updated code to read ACIS clocking configuration from input obsfile instead of separate pbkfile. Updated code to print warning when pbkfile param is specified.

mkwarf

• Updated code to read ACIS clocking configuration from input infile (WMAP) instead of separate pbkfile. Updated code to print warning when pbkfile param is specified.

• Tool will now use the DY_AVG, DZ_AVG, DTH_AVG keywords to properly setup the coordinate transforms when using WMAP in DET coordinates. The asolfile parameter is no longer required. Note: most WMAPs are now in TDET coordinates so this change has minimal effect.

mkpsfmap

• Clarify warning when _PNT keywords are missing.

pget

• Correct error message that incorrectly reported the tool as pset.

modelflux

• Can now run multiple instances of tool using a local copy of the parameter file via the

  unix% modelflux @@local_copy.par ...etc...
  

  parameter syntax

reproject_aspect

• Fixed problem when the infile contained certain types of filters.

roi

• An error is now produced if clobber is not set and roi tries to produce a source file (any source file) with the same name as an existing file.

• An error is now produced if the output file cannot be created.

• no longer drops sources when group=group and 3 or more sources are chained together instead of all intersecting.
• the exclusion regions parameters (defined by the bkgfactor) are now applied to all sources in the background region, no just the current, central source.

skyfov

• Corrected error message when mask file for wrong ObsID is supplied.

srcextent

• Can now run multiple instances of tool using a local copy of the parameter file via the

  unix% srcextent @@local_copy.par ...etc...
  

  parameter syntax

tgdetect

• Replaced all redirected parameters from subtools (celldetect, tgidselectsrc, tgmatchsrc) with the default values found in those tools.

tgdetect2

• New tool to detect the zeroth order centroid. Based on the information provided by tg_choose_method the tool will run either tgdetect or tg_findzo to create the best zeroth order location.

tg_choose_method

• New tool used to determine the best tool for determining the zeroth order centroid (tgdetect or tg_findzo), based on values found in the tg_findzo output.

tg_findzo

• Output postion column is now a SKY vector column. Additional meta-data cleanup.

tgdetect

• Changed parameter defaults to no longer point to various sub-tools (celldetect, tgidselectsrc, and tgmatchsrc).

tgextract2

• Now supports FITS polygons with arrays padded with NaN as well as zero.

tg_findzo

• Internal cleanup to make linear fitting more simples

• The output FITS file now has the NULL Primary header populated.

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Parameter Files

acis_build_badpix

• Several parameter have been removed from acis_build_badpix. They identified the block name in the FITS file to use which is unnecessary given how the tools work. The parameters removed are:

  • pbkext
  • berrext
  • evtsext

• The maxberr parameter min value has changed from 0 to 1.

acis_process_events

• The spthresh parameter has been removed. The splithreshold values should only come in from the threshfile file.

eff2evt

• The pbkfile parameter is now deprecated

mean_energy_map

• The pbkfile parameter is now deprecated

mkacisrmf

• The asolfile parameter is now deprecated

mkarf

• The pbkfile parameter is now deprecated

mkgarf

• The pbkfile parameter is now deprecated

mkinstmap

• The pbkfile parameter is now deprecated

mkwarf

• The pbkfile parameter is now deprecated

• The asolfile parameter is now deprecated

tgdetect

• The default values for tgdetect parameter are now provided explicitly in the .par file rather than being redirected to various sub-tools. This makes the tool more robust when multiple tools are being run at the same time. The list of parameters that changed is

  • bkgerrvalue
  • bkgvalue
  • celldetect_log
  • convolve
  • eband
  • eenergy
  • max_separation
  • psftable
  • setsrcid
  • snr_ratio_limit
  • thresh

fluximage

• The pbkfile parameter has been removed.

specextract

• The pbkfile parameter has been removed.
• New dtffile parameter has been added to support HRC
• New refcoord parameter has been added to allow ARF and RMFs to be created when there are 0 counts (for upper limits).
• New weight_rmf parameter added to create RMFs, only used when weight=yes.
• The ptype parameter has been removed. All spectrum should be PI.

merge_obs

• The pbkfile parameter has been removed.

flux_obs

• The pbkfile parameter has been removed.

fullgarf

• The pbkfile parameter has been removed.

mktgresp

• The pbkfile parameter has been removed.

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ChIPS

load_colormap

• Now accepts either a two-dimensional array or sets of one-dimensional arrays to define the colormap. Values are not normalized and expected to be between 0 and 1. Values outside of that range are ignored.

• Verify that the specified slot is on of chips_usercmap1, chips_usercmap2, or chips_usercmap3

make_script

• Fixed make_script" when input file contained spaces and/or quotes.

set_preference

• Modified the behavior of 'default' foreground and background color property values. The new behavior causes all objects to update when a default color preference is modified. For instance,

  set_preference("foreground.display","goldenrod") 
  

  will cause all objects in the window with a 'default' foreground color to appear in gold on the display.

• Fixed problems with the error message to not appearing when an invalid grid scale value was specified

• Fixed the attribute name being lost from the error message when the attribute has three levels of depth (e.g. curve.symbol.style)
• Fixed an issue when when changing the value of default color, the color would revert back to the preloaded preference after doing an print_window

GUI

• The color widget was updated so that the color name or hex value is always displayed in the label and the label is highlighted when 'default' is the selected color.

• Fixed axis the combobox / text entry tickformat widget in the chips GUI to treat %ra as equivalent to %ra4 in terms of what is displayed in the pulldown option box.

• Addressed issued deleting values in positional widgets on OSX. This includes the range widgets and positional widgets for annotation in the main window.

• GUI events were not being registered when the window is resized to be larger. This prevented activities like picks, panning, zooming, popup menu, etc. Also removed restriction on resizing the window smaller

• Removed issue with bounding box of label if user uses "add annotation" from the menu while creating a label

• Fixed an issue where using the tilde key when interactively placing labels was being treated as a backspace/delete instead of adding the tilde. A similar problem could be observed with circumflex characters (such as \~o).

• Fixed a bug where changing window grid properties through the GUI causes a crash if the grid color was something other than default.

• Cleaned up window grids behavior to allow property settings to be immediately displayed in the window. Also changed buttons from "Ok" and "Cancel" to "Close" and "Reset"
• Fixed coordinates not being reported in the gui when the axis tickformat is %z or %Z

split

• Fixed precisions issues when doing a split that can result in different values describing the plot borders from info command

load_state

• Fixed problem trying to load_state when a plot object was deleted.

set_data_aspect_ratio

• Updated the error message for set_data_aspect_ratio when an invalid data aspect ratio is supplied

annotations

• Fixed a bug where adding annotations to a plot when multiple plots existed would cause multiple annotation to be created in the same location.

redo

• Fixed memory issue that could cause potential segv's redoing a single undo command

axes

• Fixed the binding of axes with different scaling (linear vs log) so that the slave axis updates to reflect the limits and scale of the master axis (first axis in the bind parameters)

• Modified the behavior of axis labels and colorbar labels so they no longer rotate by 180 degrees when an axis or label is moved from one side of a plot to the other. In addition, the initial coordinates of each are now specified in absolute coordinates with 0 being horizontal left to right and 90 being vertical bottom to top.

• Setting the axis majorgrid visible property was always returning true if the minor grid of the same axis was visible.

• Updated get_preference("axis") to retrieve axis.(x|y).label.(text|angle)

add_image

• will no longer display an image in physical or logical transform when the associated transform is an unknown WCS. Instead a warning will be given for these cases.

• Dictionary style attribute structures now support lists. e.g.

  chips-1> add_image (img, {threshold:[1,2]})
  

• Fixed add_image so that it no longer fails when the last argument is an empty attribute structure. e.g.

  chip-1> add_image (img, ChipsImage ())
  

undo

• Fix for a crash that occurs when undoing lots of commands in a plot that contains a colorbar.

• Fixed issue where clear-ing all windows and then executing an undo() would cause a crash.

add_region

• Modified the generic region failure message "chips ERROR: Region creation attempt failed" to be more descriptive when a user provides a degenerate polygon.

print_window

• Added the ability to specify the renderer used when printing to file. This addresses issues with ATI Gallium drivers flipping plots. A new preference was added called export.printmethod that takes the following parameters

  • framebuffer (default)
  • xoffscreen
  • none

  ATI users with Gallium drivers should use xoffscreen. A none option was added for the worst case scenario and to help with debugging. However, it is not recommended in general use.

• Fixed problems producing vector format outputs (ps, eps, pdf) of large datasets. Previously the output produced was blank.

• Update print methods so that vector formats (eps, ps and pdf) will use LC_NUMERIC en_US.UTF-8 for coordinates even if the user's LANG is set to something else.

grid_objects

• Fixed issues with window grids not properly displaying based off on the values set in the user's preferences.

• Grid preferences are now written to the $HOME/.chips.rc and can be accessed / set via set_preference and get_preference commands.

General

• Fixed add and set object calls so that they handle spaces in text attribute

set_colorbar

• Allow setting label.text to be a blank/empty string; in CIAO 4.5 this would cause problems with the undo command.

---

Sherpa

Template Models

• The ability to interpolate between templates loaded with load_template_model(), so that intermediate parameter values may be found during a fit;
• The ability to use templates with fitting methods other than "gridsearch";
• The ability to combine templates with other Sherpa models and fit on all parameters (from both the template and continuous models).

XSPEC models

• The XSPEC module cosmology defaults are now set to:

  H0 = 70 q0 = 0 Lambda0 = 0.73
  

  This matches the settings now documented at http://heasarc.nasa.gov/docs/xanadu/xspec/manual/XScosmo.html

I/O

• OSX 10.8 and 10.9 users can now restore their save files.

• The default format for all the save_* routines have been changed to write ASCII files, except for save_pha, save_image, and save_table.

• Usage message updated to be consistent with chips.

• A problem reading grating Type-II HRC pha files has been corrected.

• The precision of values returned by get_pvalue_results has been increased.

• The output format of model min/max values now use %g to provide nicely formatted values (e.g. 100 instead of 1e+02)

statistics

• When user-supplied errors are used with any of the chi^2 minimization statistics, the value will now simply be reported as

  Statistics = chi2
  

• For data with user-supplied errors, users can now select the chi2 statistic

  sherpa-1> set_stat("chi2")
  

• Bug with user-defined scales fixed

• Corrected the output of calc_stat_info when multiple datasets are defined.

filter

• ignore_bad() now ignores NaN values in non-PHA datasets.

models

• The range of the theta parameter of all 2D models has changed from 0:2*PI to -2*PI:2*PI.

• Two new 2D models have been added disk2d and shell2d. These were contributed by Christoph Deil of the HESS project.

• Trying to guess model parameters before the data have been loaded now results in a better error message.

• load_psf models are all now frozen by default.

• The default minium value for const1d and scale1d are set to allow negative values.

• absorptionvoigt is no longer allowed to go beyond full absorption (i.e. negative values are disallowed)

• A bug in how filtering is done in the Seaton extinction model has been corrected.

Exception handling

• Allow unregistered ModelErr exceptions to be thrown from user models.

• set_coord now reports the available options when given a bad value

• set_full_model provides better feedback when trying to mix model objects and model strings.

• reg_proj clarify error message when incorrect limits are supplied.

• When using set_full_model the various *_source commands, eg get_source do not work. The error message they report however is confusing. This has been reworded.

Other

• A problem with using set_analysis('wavelength') or ('wave') that affected equivalent width calculations has been corrected.

• sample_flux has been upgraded to remove a restriction that could lead to an exception being raised that prevented the routine from running.

• get_draws has been upgrade remove an unnecessary matrix inversion check that could prevent the algorithm from running.

• Fix to stand-alone sherpa to no longer require WCS library when trying to

  >>> import sherpa.astro.ui as ui 
  

• Various upgrades to support newer version of GCC and OSX's clang compilers.

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Graphical User Interfaces

peg

• Added the following tools to the analysis menu: tg_findzo, tgdetect2, and tg_choose_method. The following tools were removed: acis_find_hotpix, acis_run_hotpix, and acis_classify_hotpix.

• Modified code to force display of icons on buttons

prism

• Added the follow tools to the analysis menu: tg_findzo, tgdetect2, and tg_choose_method. The following tools were removed: acis_find_hotpix, acis_run_hotpix, and acis_classify_hotpix.

• Modified code to force display icons on buttons

• New option to enable/disable filtering of raw keywords. Previously was only an option in .prismrc

• Suppress XPA warnings when ds9 launced from GUI is closed by user.

• Current directory is now in the short-cuts pane when opening new files.

• Multiple files can now be specified on the command line

  unix% prism *.fits
  

  will open all FITS files, each in a separate tab.

• Change to edit mode whenever a column or keyword value has been is changed.

• Provide warning when specified input file does not exist.

• Updated the text displayed in the prism tabs to include any filters.

obsvis

• Fixed issues with obsvis hanging when a user used ds9's "select all" regions to select all FoV's. Due to the the fix the 3 markers describing position and SIM offsets will no longer be brought to the front when they are selected interactively. They will still be brought forward when going through the menu.

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Analysis Scripts

specextract

• The pbkfile parameter has been removed. The script will now check the input event file for the necessary parameter block related keywords and error out if they are not found.

• The ptype parameter has been removed. Users should only make pulse-height invarianant, PI, spectrum.

• Support has been added to create HRC spectrum and response files. This includes the additon of the dtffile parameter. Usually the script will locate the correct file automatically; however, in some circumstances users may be required to set the file name explicitly.

• New refcoord parameters allows the script to create an empty spectrum but with valid ARF and RMF files for a specific location on the sky even when there are 0 events in the source region. This is needed to compute upper limits for non-detections.

• New weight_rmf parameter introduced, since the behavior of the weight=yes parameter has changed to only create a weighted ARF. By default, an unweighted RMF is produced if weight=yes unless otherwise specified by by weight_rmf, since the improvement in the RMF is only a few percent in most cases, while being significantly more computationally expensive.
• The output ARF and RMF are now always named .arf and .rmf; regardless if they are weighted or not.
• Several intermediate output files are now automatically cleaned up.

srcflux

• Given an event file and a location, this script will compute various estimates of the net source flux.

  unix% srcflux acisf13459_repro_evt2.fits "0:55:51.013 +26:22:43.95" myout
  ...
  Summary of source fluxes
  
  Position                               0.5 - 7.0 keV                           
                                         Value        90% Conf Interval          
  0 55 51.01 +26 22 43.9  Rate           0.00191 c/s (0.00168,0.00214)           
                          Flux           2.27E-14 erg/cm2/s (2E-14,2.55E-14)     
                          Mod.Flux       2.43E-14 erg/cm2/s (2.14E-14,2.73E-14)  
  

  This script automates the steps needed to run aprates and several other tools.

  The outputs are saved in a *.flux file. The script also creates the spectrum and associated response files needed to do details spectral fitting with sherpa.

chandra_repro

• Now uses tgdetect2 when recreate_tg_mask=1

• Will check the event 1 file header and update with the new set of keywords using the r4_header_update script.

• Added pix_adj=centroid as an option for acis_process_events

r4_header_update

• This script will check the header of the input file and add the new keywords parameter block and/or SIM related keywords -- those discussed in the Watch Out page.

psfsize_srcs

• This tool will create a circular region that encloses the specified fraction of the PSF (default is 90%) at the specified energy (CSC broad band: 2.3keV).

src_psffrac

• This script will determine the PSF fraction a circular region encloses at a specified energy. It only works with circular regions.

dax

• The ds9 analysis scripts have been repackaged to be included in the contributed source package.

• There is a new Sherpa menu that allow users to automatically fit some simple spectral models. From the same menu users can also perform simple 2D fits to the data.

• Users can now get flux values by drawing a source and background region on a Chandra event file and selecting Regions → Aperture Photometry

• There is a new Period Fold option in the Histogram menu that will run the pfold tool.

• There is a new Convex Hull option in the Regions menu that will run the dmimghull tool.

• There are two new options in the Regions menu to look up the PSF size at a location and one to look up the psf fraction for a given source region.

• dmimgdist is now available in the Image Processing menu under Distance Transform

• Image moments are now availble under the Statistics menu.

reproject_obs

• No-longer updates the PBKFILE header keyword or copies over/links the PBK files.

acis_bkgrnd_lookup

• minor fix when using an image of multiple chips as the infile argument.

search_csc

• Corrected the conversion factor for the search radius, sepn when radunit=deg. The value in the output file was correct, the value printed to the terminal was slightly off.

fullgarf

• Removed the pbkfile parameter.

mktgresp

• Removed the pbkfile parameter.

merge_all

• Withdrawn. Users should be using merge_obs.

mkBgreg.pl and mkSubBgReg.pl

• Withdrawn. Users should use roi and splitroi.

ciao_contrib.runtool

• Updated for the new CIAO tools, scripts, and parameter changes.

chips_contrib.helix

• chips_contrib.helix is a set of routines to create a Cube Helix color lookup table.

crates_contrib.utils.add_keyval

• Withdrawn. Users should use set_key.

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Python Modules

pycrates

• Corrects problem where the size of string columns increases by 1 when read then write.

• corrected problem accessing blocks by number when the file contains multiple blocks with the same name (HDUNAME keyword value.)

• Corrects problem in calculation of checksum for virtual columns which resulted in crash on 32-bit machines, when the file is large.

• Corrects crash resulting from creating unneeded empty subspace components.

• Corrects problem where extending vector column values would result in subsequent incorrect access into the array.

• Initial support to recognize read-only files when asked to open read+write.

• Correct the transform type when retrieving the EQSRC column to be RA---TAN,DEC--TAN

• Update to allow columns with "()"'s. The ()'s and the value inside the ()'s are removed from the column name.

• Corrects a missing import of the Math module

• Corrects bug where String type column size (string length) would shrink if the Crate contains only 1 row.

• Performance upgrades reading in large images.

• Enable read/write of table with empty column(s) (no values). Will now generate a table with 0 rows and properly described columns.

• Partial support for regions being saved as part of the image subspace.

• Corrects problem where 'nrows' (number of rows) value is not updating if columns are deleted.

  Also corrects case where 'ncols' (number of columns) value can go negative.

pycaldb

• Corrects issue on OSX platforms where import order of psflib, pypixlib, pycaldb4 modules can result in import error.

• A new argument has been added to the constructor -- the value is a file name which will be used to seed the query (eg set start/stop times, FP_TEMP, etc)

  >>> import caldb4 as c
  >>> gain = c.Caldb("chandra", "acis", "det_gain", "my_evt.fits")    
  >>> gain.search
  ['/soft/ciao-4.6/CALDB/data/chandra/acis/det_gain/acisD2000-01-29gain_ctiN0006.fits[1]']
  

pypsf

• Corrects issue on OSX platforms where import order of psflib, pypixlib, pycaldb4 modules can result in import error.

pyregion

• Corrects issue on OSX platforms where import order of psflib, pypixlib, pycaldb4 modules can result in import error.

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Libraries

Header

• Prevent a crash when an empty header merging rules file is supplied.

Transform

• Correct Transform::copy() to retain correct Transform object type in python

• Creates a generic WCSTransform class in which various projection types may be used. The WCSTanTransform now is specific for the TAN projection.

Datamodel

• New routine, dmp_descriptor_reset_range, enables a post-facto change to a column descriptor's legal range. In addition to changing the range values themselves, it resets the default subsubspace ranges.

• Update to ASCII kernel to recognize G format in Tab Separated Value (TSV) files.

Region

• When intersecting complex region description with new regions, incorrect elements may have been left behind when the intersection goes null. This would result in an incorrect subspace description and area calculation.

CALDB

• Fixed problem where calibration file name were constructed incorrectly when CAL_DEV column of index file contains a URL.

cxcparam

• Enable pset of enumerations in the min field

  unix% pset dmhedit operation.p_min="add|delete"
  

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Environment

Off-the-Shelf (OTS) Package Versions

• The following OTS packages are included with CIAO 4.6.1. For more information on how the OTS packages are built for use with CIAO, refer to the INSTALL_SOURCE file distributed with the software.

  Executables

  • ds9 7.2

  Python

  • Python 2.7.5
  • NumPy 1.7.1
  • ipython 0.13.2

  Libraries

  • cfitsio v3.35
  • fftw 3.3.3
  • xpa 2.1.14
  • jpeg 9
  • XSPEC v12.8.0.k.1 (models only)
  • VTK 5.10.1
  • CCfits 2.4
  • fontconfig 2.8.0
  • freetype 2.4.4
  • gsl 1.15
  • readline 6.2
  • vte 0.25.1
  • wcssubs 3.8.3
• The ciaover command will now report the version of the Calibration Database as well as the version of the Analysis Scripts package. In addition the full path to the Python executable is shown (even when using the precompiled CIAO version).

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Documentation

Note

• Many pages have been updated to reflect the changes in this release. Several analysis threads are still under review.

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