MOPEX Change Log

MOPEX release 08/21/08 (v18.1.5)

The following changes were made to MOPEX for the latest release. Updated from the Feb 08 version. See below for previous updates.

1. New IRAC PRFs
   New IRAC PRFs are now available, and are a significant improvement over those previously released by the SSC. For true point sources, we are able to obtain agreement between fitted and aperture flux measurements at better than the 1% level. See IRAC PRF Fitting. Sample IRAC APEX namelists in the ./cdf directory contain an example of the new PRF file names. The PRFs are strictly valid only for IRAC BCDs.


2. APEX QA included in the GUI
   The APEX QA pipeline has been included in the GUI. It is used for subtracting points sources from the input images to check the quality of the PRF fitting.


3. PRF Estimate included in the GUI
   The PRF Estimate pipeline has been included in the GUI. It allows users to create PRFs from their own data. Not for use with IRAC data or any other undersampled data.


4. New SNR option
   A new option for point-source fitted SNR is available ("Photerr"). This uses errors in a fixed box around each source. For most purposes, adopting the data uncertainties as the errors gives acceptable results. Set the following switch in the Apex namelist:
   
   use_data_unc_for_fitted_SNR = 1
   
   and the following parameter in the "sourcestimate" block:
   
   Use_Photerr_for_SNR = 1,
   
   See the file README_new_snr_option_081108.pdf for more information (this file can also be found in <MOPEX_installation_directory>/readme).


5. New Apex User List option (still experimental)
   There is a beta-testing version of modules designed to let the user input a list of source positions to be point-source fitted by APEX. See the file README_apex_user_list_081108 for more information (this file can also be found in <MOPEX_installation_directory>/readme/).


6. Final mosaics use CD matrix
   To keep up with the current FITS standard, the final mosaics produced by mosaic_combine have the "CD matrix" form of the WCS. However, some intermediate products will still have the old "CDELT" style, because that is what the modules are using internally.


7. Different paths now allowed for PRF files
   Other directory paths are now allowed for PRF and MOSAIC_PRF files, in addition to ./cal, which was previously enforced by the command-line Perl scripts. The default backup names "PRF.fits" and "Mosaic_PRF.fits" are no longer searched for.


8. Flux input to prf_estimate turned off
   There is a problem in prf_estimate.pl when the input list of sources has a "flux" column. Use of this flux has been turned off. It will now always estimate fluxes from the cropped images themselves.


9. Mosaic Reinterpolate on a list of different-sized arrays
   There was a problem with memory allocation with different-sized arrays in mosaic_reint. This has been fixed.


10. Linux roundoff errors
    Linux versions are now being compiled with gcc as 32-bit versions with the SSE floating-point rules. The latter is to turn off the default extended precision of gcc, which was giving numerical differences in some pieces of code compared to Solaris 10 and Intel Macs.


11. flatfield.pl problem on Macs
    This was due to unrecognized NaNs and has been fixed.


12. Table column overflows by sourcestimate
    This usually showed up as an error from aperture. This has been fixed.


13. Incorrect WCS in absolute_minimum and median mosaics
    These have been fixed


14. Weight by exposure time option added to the Mosaic Coadder module in the GUI.


15. RMask bug that prevented Bottom Threshold from being larger than Top Threshold has been fixed.


16. Fitting Area parameters in the Source Estimate module now take precedence over the presence of the Fit Radius module.


17. Fixed the bug that prevented the RMasks from being properly reset when the list of input images is changed in the GUI.


18. The module Mosaic Geom can now be run in the GUI without including the FIF module.


19. The GUI will now display a subset of the output files for most modules.


20. A bug preventing the delete_intermediate_files option from working in the GUI has been fixed.


21. A bug affecting the creation of moving object mosaics has been fixed. Users can now choose the input BCD that they wish to set as the stationary reference frame.


22. A glossary of keywords has been included in the GUI help.


23. Some minor fixes have been made to the filenames in namelists exported from the GUI.

Mopex Release 02/21/08 (v16.3.7)

The following changes were made to the modules and scripts used by both the command-line and GUI versions of MOPEX. Updated from the June 2007 version. See below for updates from the previous version.

1. Uncertainties will now be calculated for aperture photometry, using data uncertainties. No additional input required.
   Aperture uncertainties were added to the Mopex aperture module. It uses the data uncertainties (or "gain-estimated" ones, if enabled). The aperture flux uncertainty is simply the sum over the aperture area:
   
   sigma^2 = Sum ( sigma(i)^2 )
   
   The bad value and the value if missing is "-9.99". Any bad uncertainty value in the aperture will lead to a -9.99. Uncertainty in background subtraction is not included.
   
   The columns are called "ap_unc1", "ap_unc2", etc. in the aperture.tbl and extract_raw.tbl. The Apex "select" script can select on them in creating the final extract.tbl.
   
   
2. Option to use data uncertainties in APEX's SNR
   There is a new switch for command-line namelists apex.pl and apex_1frame.pl and in the GUI:
   
   use_data_unc_for_fitted_SNR = 1.
   
   The switch tells MOPEX to use the data uncertainties for calculating the signal-to-noise ratio given in the final extract table. Default is 0, and it will use the current gaussnoise noise estimate (i.e. basically the background RMS). This is also setable on the command line of apex.pl and apex_1frame.pl, as option "w". If set, it will switch to the data uncertainties (or the "gain-estimated" ones if enabled). See the Apex User's Guide for how the Apex SNR is defined.
   
   This step is part of our re-evaluation of Apex's signal-to-noise estimates. Most users will not need this switch at the present time.
   
   
3. Improved mosaics with Drizzle interpolation using RMasks. No additional inout required.
   Users can use the Drizzle interpolation option (INTERP_METHOD = 2) in Mosaic Interpolate and use their choice of outlier rejection. The interpolation is run twice - the first time through runs a linear interpolation scheme, which is then passed to the outlier rejection algorithm to create the RMasks. The interpolation is then re-run with the Drizzle algorithm, masking out the bad pixels flagged in the RMasks. Users should not run Mosaic Reinterpolation when using Drizzle.
   
   
4. Bug Fixes:
   Overlap (bad indexing in determining clusters) - Major.
   The Overlap version of mopex_030106 was not affected. A bug was present in the version released with the GUI which may in some cases lead to improper overlap corrections. It has been fixed in this version.
   
   Sourcestimate (typo in X,Y pixel ratio) - Minor.
   Only important if your pixels were very non-square.
   
   See the MOPEX bug list for a full list of fixes of previously reported bugs

Mopex Release 06/15/07

The following changes were made to the modules and scripts which both the commandline and GUI MOPEX use (updating them from the 1 March 2006 version):

• Environment settings for command-line MOPEX are now in mopex-script-env.csh instead of mopex.csh.

• The module "detect" was modified to provide higher precision in the x,y positions in the output detection table.

• The Perl module "mosaic.pl" was modified to allow use of existing Rmasks.

• The module "sed_fif" was modified to generate SED mosaics for special cases when PA_SLT ~= 0 or 180. The computation of ROT_SLT was also revised for all cases.

• A bug was fixed in the "aperture" module. It gave potentially incorrect aperture fluxes when distortion was present, for example in BCD data.

• Use of the Galactic and Ecliptic coordinate systems was implemented in addition to the Equatorial system Mopex has used so far. Also all of the projections implemented in the WCS library are now available for use in Mopex. The coordinate system and projection type of the mosaic are specified in the following namelist block:

  &FIDUCIALIMAGEFRAMEIN 
  ... 
  Projection_Type = "ARC", 
  Coordinate_System = "Galactic", 
  &END
  

  The default value of the projection type is "TAN" and of the coordinate system "J2000". The possible options for the coordinate system are "J2000", "Galactic", and "Ecliptic". The options for the projecton type are:

  LIN, AZP, TAN, SIN, STG, ARC, ZPN, ZEA, AIR, CYP, CAR, MER, CEA, COP, COD, COE, COO, BON, PCO, GLS, PAR, AIT, MOL, CSC, QSC, TSC, NCP, DSS, PLT

• A new switch "use_extract_table_for_aperture" has been added to control the input of the aperture photometry module. The default value if 1, i.e. the extract table is used as input for the module aperture. If the switch is set to 0, then the detection table is used as input for the module aperture. It is especially useful for extended objects when point source fitting is not applicable and only aperture photometry measurements can be performed.