GEMINI (March2012)    Gemini IRAF package v1.11.1    GEMINI (March2012)

Release date: March 28, 2012

This document describes the revisions relative to the Gemini IRAF package v1.10

The Gemini IRAF package v1.11.1 is compatible with IRAF v2.14
(gemini_v1111_for_iraf_2.14.tar.gz) and the 32-bit version of IRAF v2.15
(gemini_v1111_for_iraf_2.15.tar.gz). This release will run under both IRAF and
PyRAF environments. Please note that PyRAF users who choose to upgrade to IRAF
v2.15 will need to use PyRAF v1.11. Please refer to
http://www.gemini.edu/sciops/data-and-results/processing-software/requirements 
for other requirements on your IRAF installation including other required
external packages.

WARNING!! The Gemini IRAF package v1.11.1 is NOT compatible with the 64-bit
version of IRAF v2.15.

The binaries distributed with the package were built on Red Hat 9 and 
Mac OS X 10.5 Intel.


PRIMARY REVISIONS
=================

1) GNIRS: a) Added support for the re-built GNIRS that is now installed at
             Gemini North
          b) Improved the data quality calculations for nsextract

2) GEMINI: a) Added a new task (install_check.cl) that enables the user to
              check their Gemini IRAF installation (details provided below)
           b) Removed the dependency on the external package nmisc

3) GEMTOOLS: a) Removed compatibility constraints on fitsutil; the Gemini IRAF
                package is now compatible with any recent version of fitsutil

4) GMOS: a) Improved the data quality calculations for gsextract
         b) Updated the look-up tables for the gratings and filters
         c) Improved the determination of the upper wavelength limit when
            cutting spectroscopic data

5) NIRI: a) Updated the look-up table to include the missing f32 configurations

6) PATCH: a) Enabled support for the new GMOS North e2v Deep Depletion CCDs

DETAILS OF THE REVISIONS
========================

A multitude of minor bug fixes are included in this release. They will not be
listed here. Rather, only the most notable changes or those more likely to be
of interest to the user will be highlighted.

1) GNIRS
------------------
Instruments: GNIRS (parameter changes also affects NIFS, NIRI, Michelle, 
                    T-ReCS)

    a) The majority of the changes needed to support the re-built GNIRS now
       installed at Gemini North are contained in the look-up tables in
       gnirs$data/. Some modifications to the code and the task parameters
       were also necessary to ensure support for GNIRS at Gemini North and
       backward compatibility with old data from GNIRS at Gemini South.

       The software will automatically detect whether the data comes from GNIRS
       at Gemini South or GNIRS at Gemini North. However, the user will, in
       some cases, have to select the correct look-up tables for the input task
       parameters. This applies in particular to the pinhole list and to the
       bad pixel mask (BPM). Please refer to the file gnirs$data/README for a
       list and short description of the look-up tables found in gnirs$data/. 

       Examples of how to reduce GNIRS data can be obtained by running the task
       gnirsexamples. In addition, information on how to reduce GNIRS
       cross-dispersed data can be found at http://www.gemini.edu/sciops/instruments/gnirs/data-format-and-reduction/reducing-xd-spectra

       All users of the GNIRS package (GNIRS users of course, but also users of
       near-IR and mid-IR spectroscopy instruments) should initialize their
       uparm directory to avoid conflicts with old parameter files. To do
       this, either type "unlearn gnirs" at the IRAF or PyRAF prompt, or at the
       shell prompt type "rm uparm/*" from the iraf home directory (where the
       login.cl is located). 

    b) The marking of bad pixels in the data quality (DQ) plane by the task 
       nsextract has been modified. Specifically, pixels are marked as bad in
       the output DQ plane if more than 50% of the pixels in the input aperture
       are bad. 

Notable bug fixes: 
  nsflat: With cross-dispersed data, the intermediate file used to calculate
          the fit to the flat did not have the bad areas masked out correctly.
          The effect was mostly to create noisier flats than ideal. The new
          fix should improve the quality of the processed cross-dispersed 
          flats.

  nsoffset: When running nscombine interactively, the keystroke commands typed
            by the user were not registered. The new fix now registers the
            keystroke commands and enables nscombine to be run interactively.

  nsextract: Correctly implemented the use of fl_project=yes (this section of
             the code contained many bugs).

2) GEMINI
------------------
Instruments: All

    a) A task called install_check.cl has been added to the top level of the
       Gemini IRAF package. To use this task to check a Gemini IRAF
       installation, define and execute the task by typing the following at the
       IRAF or PyRAF prompt:

           ecl> task $install_check=/iraf/extern/gemini/install_check.cl
           ecl> install_check

       If the Gemini IRAF package is installed in a non-standard location
       (i.e., somewhere other than /iraf/extern/gemini/), be sure to update the
       path to the task in the task definition above.

    b) All occurrences of nmisc.psfmeasure, nmisc.xregister and nmisc.fixpix
       were replaced with calls to noao.obsutil.psfmeasure,
       images.immatch.xregister and imexpr respectively. The Gemini IRAF
       package v1.11 is no longer dependent on the external package nmisc. 

3) GEMTOOLS
------------------
Instruments: All

    a) For IRAF v2.15, the nhedit task was moved from fitsutil to the main IRAF
       package imutil. The Gemini IRAF package was updated so that it is now
       compatible with any recent version of fitsutil. In addition, the
       gemhedit task now automatically uses whichever version of nhedit is
       available, depending on the user's specific installation. Users can
       benefit from this automatic selection by using gemhedit in their own
       code.

4) GMOS
------------------
Instruments: GMOS North and South

    a) The marking of bad pixels in the data quality (DQ) plane by the task 
       gsextract has been modified. Specifically, pixels are marked as bad in
       the output DQ plane if more than 50% of the pixels in the input aperture
       are bad. 
       
    b) New filters have been added to the gmos$data/GMOSfilters.dat look-up 
       table. The new filters are Z_G0322 and Y_G0323.
       
       Also the Y offset value for the B600 grating has been improved. 
       Manual adjustment of that value should no longer be needed.

    c) The upper wavelength limit when cutting spectroscopic data is now
       determined using the grating  wavelength interval, the upper limit of
       the filter band-pass, the 2% quantum efficiency cut-off of the detector
       in the red or the edge of the detector, whichever has the shortest
       wavelength. In addition, the user can override this default behaviour.

Notable bug fixes:
  gsflat: Features in long slit flats were spatially offset in y from the
          correct row by a grating-dependent number of rows. The new fix
          creates more appropriate flats, which will improve the accuracy of
          the correction of the pixel-to-pixel variations.

5) NIRI
------------------
Instruments: NIRI

    a) There were missing configurations for the f32 camera in the look-up 
       table, which has now been updated to include the missing information.

6) PATCH
------------------
Instruments: All

    a) Support for the new GMOS North e2v Deep Depletion CCDs is now available.
       The gmos package has undergone many changes to ensure compatibility with
       6-amp data from the new CCDs, including improved gain values and the
       addition of new BPMs, while maintaining complete backward compatibility
       with all data taken using the old GMOS CCDs. Please note that for the
       new CCDs, only data taken in slow read, low gain mode is supported. For
       other modes, please contact the GMOS team. Full support for the other
       modes will be included in a future release.

Notable bug fixes:
  - Improved variance and data quality propagation in gmos.gftransform

  - Addition of variance and data quality propagation gmos.gnsskysub and
    gmos.gnscombine 

  - Improved log message in gmos.gstransform to describe how to proceed when
    using arcs with a different ROI to the science spectrum

  - Upgrades to a number of tasks in the GEMTOOLS and GNIRS packages that allow
    the database parameter to be defined with a trailing slash

  - Corrected gnirs.nsreduce so that nsappwave actually gets called if the data
    had been previously cut

  - Inclusion of an improved BPM for GNIRS North

  - Fixed typos in gmos.gmosexamples, gnirs.gnirsexamples and niri.niriexamples

SUMMARY OF ALL CHANGED PARAMETERS
=================================

If a task listed below is causing problems, it is very likely that the task is
accessing an old parameter file that does not contain the updated parameters
and/or values. To resolve the problem, the old parameter files for the Gemini
IRAF package must be removed from the uparm directory. To do this, at the IRAF
or PyRAF prompt, load gemini, then type "unlearn gemini". If it is not
desirable to remove all the old parameter files for the Gemini IRAF tasks, it
is possible to "unlearn" the individual task. 

Please see the appropriate help file for more information about the specific
parameter changes listed below.

    gemtools.ckcal:
      - New default value:  database = "" (from "database/")

    gemtools.gemhedit:
      - New parameter:      delete

    gmos.gbias:
      - New default values: fl_over = yes
                            sat = "default" (from 65000)
                            nbiascontam = "default" (from 4)

    gmos.gbpm:
      - New default value:  sat = "default" (from 65000)

      - New parameters:     fl_qecorr (future support, not yet implemented)
                            qe_data (future support, not yet implemented)
                            qe_datadir (future support, not yet implemented)

    gmos.gdisplay:
      - New default value:  gap = "default" (from 37)

    gmos.gfreduce:
      - New default values: fl_over = yes
                            nbiascontam = "default" (from 4)

      - New parameters:     fl_qecorr (future support, not yet implemented)
                            qe_refim (future support, not yet implemented)
                            fl_keep_qeim (future support, not yet implemented)
                            qe_corrpref (future support, not yet implemented)
                            qe_corrimages (future support, not yet implemented)
                            qe_data (future support, not yet implemented)
                            qe_datadir (future support, not yet implemented)

    gmos.ggdbhelper:
      - New parameter:      logfile

    gmos.giflat:
      - New default values: fl_over = yes
                            sat = "default" (from 65000)
                            nbiascontam = "default" (from 4)

      - New parameters:     fl_qecorr (future support, not yet implemented)
                            qe_data (future support, not yet implemented)
                            qe_datadir (future support, not yet implemented)

    gmos.gireduce:
      - New default values: fl_over = yes
                            sat = "default" (from 65000)
                            nbiascontam = "default" (from 4)

      - New parameters:     fl_qecorr (future support, not yet implemented)
                            qe_refim (future support, not yet implemented)
                            fl_keep_qeim (future support, not yet implemented)
                            qe_corrpref (future support, not yet implemented)
                            qe_corrimages (future support, not yet implemented)
                            qe_data (future support, not yet implemented)
                            qe_datadir (future support, not yet implemented)

    gmos.girmfringe:
      - New default values: statsec="default" (from "[SCI,2][*,*]")

    gmos.gmosaic:
      - New default value:  gap = "default" (from 37)

      - New parameter:      key_ccdsec

    gmos.gnscombine:
      - New parameter:      sci_ext
                            var_ext
                            dq_ext
                            mdf_ext
                            fl_vardq
                            status
    gmos.gnsdark:
      - New default values: fl_over = yes
                            sat = "default" (from 65000)
                            nbiascontam = "default" (from 4)

    gmos.gnsskysub:
      - New parameters:     sci_ext
                            var_ext
                            dq_ext
                            mdf_ext
                            fl_vardq

    gmos.gsextract:
      - New parameter:      database

    gmos.gsflat:
      - New default values: fl_over = yes
                            sat = "default" (from 65000)
                            nbiascontam = "default" (from 4)

      - New parameters:     fl_qecorr (future support, not yet implemented)
                            qe_refim (future support, not yet implemented)
                            fl_keep_qeim (future support, not yet implemented)
                            qe_corrpref (future support, not yet implemented)
                            qe_corrimages (future support, not yet implemented)
                            qe_data (future support, not yet implemented)
                            qe_datadir (future support, not yet implemented)
                            wave_limit
                            minval
                            fl_seprows

    gmos.gsreduce:
      - New default values: fl_over = yes
                            sat = "default" (from 65000)
                            nbiascontam = "default" (from 4)

      - New parameters:     fl_qecorr (future support, not yet implemented)
                            qe_refim (future support, not yet implemented)
                            fl_keep_qeim (future support, not yet implemented)
                            qe_corrpref (future support, not yet implemented)
                            qe_corrimages (future support, not yet implemented)
                            qe_data (future support, not yet implemented)
                            qe_datadir (future support, not yet implemented)
                            wave_limit

    gmos.gtile:
      - New parameters:     fl_pad
                            padvalue
                            chipgap

    gmos.mostools.mdfplot:
      - New parameter:      instrume (future support for F2 MOS)

    gnirs.nsextract:
      - New parameters:     fl_vardq
                            fl_usetabap
                            weights

    gnirs.nsmdfhelper:
      - New parameters:     ixovershoot
                            slitwidth

    gnirs.nsprepare:
      - New default value:  bpm = "gnirs$data/gnirsn_2011apr07_bpm.fits"

    gnirs.nswedit:
      - New parameter:      arrayid
