GEMINI (December2011) Gemini IRAF package v1.11 GEMINI (December2011) Release date: December 30, 2011 This document describes the revisions relative to the Gemini IRAF package v1.10 The Gemini IRAF package v1.11 is compatible with IRAF v2.14 (gemini_v111_for_iraf_2.14.tar.gz) and the 32-bit version of IRAF v2.15 (gemini_v111_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 is NOT compatible with the 64-bit version of IRAF v2.15. WARNING!! The Gemini IRAF package v1.11 does NOT support the new GMOS North e2v CCDs. However, this release is the foundation for the upcoming patch that will provide full support for the new GMOS North e2v CCDs. PIs with new GMOS North e2v data should install v1.11 of the Gemini IRAF package in preparation for the upcoming patch. Due to the unexpected use of 6-amp mode, the gmos package has undergone many changes to ensure compatibility with 6-amp data. Characterization of the new CCDs (e.g., accurately measuring the gain) is still to be completed, along with the scientific verification of the code for the new GMOS North e2v CCDs. 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 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. 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.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.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.gnsdark: - New default values: fl_over = yes sat = "default" (from 65000) nbiascontam = "default" (from 4) 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.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_2010oct12_bpm.fits" gnirs.nswedit: - New parameter: arrayid