Change Logs

3.2.3

Dependency Updates

gempy.library

  • Ensure compatibility with SciPy v1.15 (matching.py)

Improvements

gempy

  • Improve interrupt handling and allow additional loggers to enhance the operation of GOATS.

3.2.2

Bug Fixes

geminidr.ghost

  • Fix an issue where the GHOST reduction would fail if specific header values were not in the expected format.

Improvements

  • Reduce memory usage in flagCosmicRays and QECorrect primitives.

3.2.1

Improvements

geminidr & gempy

  • Improved speed and success rate of wavelength calibration.

geminidr.ghost

  • Added makeIRAFCompatible primitive to write order-combined GHOST spectra in a non-FITS-standard format that is compatible with IRAF.

Bug fixes

geminidr.ghost

  • Cause data validation to fail for echellograms without exactly 4 extensions.

  • Fixed an occasional issue with bad pixels causing traceFibers to fail.

geminidr.interactive

  • Fixed issues where certain values were not initialized correctly.

  • Fixed stylesheet issues

New Features

gemini_instruments.gnirs

  • Preemptively added support for handling GNIRS data produced with the new detector controller software that will be installed in coming months. An additional patch release will be issued once the gain, read noise, and other detector properties are known.

Documentation

  • Several updates to the GHOST tutorials to fix errors and improve clarity.

Interface Modifications

gemini_instruments.gnirs

  • New prims_motor_steps descriptor to support flat association with HR-IFU

and SciOps prism mechanism reproducibility workarounds adopted in Apr-2024.

gemini_instruments.ghost

  • Change GHOST fast/low read mode from “fast” to “rapid”.

3.2.0

This release includes support for GHOST data reduction and the new CCDs installed in GMOS-S in late 2023.

New Features

Full support for the reduction of GHOST data.

This is based on the external GHOSTDR package, with important improvements. Includes changes to the names and scope of primitives to better align with the other instrument recipes.

Support for new GMOS-S CCDs installed in late 2023.

Improvements

astrodata.wcs

  • Support for reading and writing log-linear wavelength axes to/from FITS.

  • Support for reading and writing tabular wavelength information to/from FITS.

astrodata.provenance

  • Renamed the PROVHISTORY table to HISTORY, and changed wording in the code from “provenance history” to simply “history”.

astrodata.fits

  • Support reading ASCII tables when opening FITS files with astrodata

geminidr.core

  • Creation of new skip_primitive parameter, e.g., reduce -p skyCorrectFromSlit:skip_primitive=True which allows any primitive in a recipe to be skipped. Note that inconsiderate use of this may cause a recipe to crash because the inputs to the subsequent primitive in the recipe may be inappropriate.

  • Creation of new write_outputs parameter, e.g., reduce -p ADUToElectrons:write_outputs=True which will write to disk the outputs of the primitive.

  • Allow input files to shiftImages to recognize tabs or multiple whitespaces as the delimiter

geminidr.gsaoi

  • Modification to the nostack science recipe to not “store” the image but rather continue and detect sources in the images in anticipation of the likely stacking that will follow later. The output images will have the _sourcesDetected suffix rather than the _image suffix.

recipe_system.cal_service

  • Whitespace now allowed in directory paths (if quoted), e.g., databases = "~/.my dragons/dragons.db"

Bug fixes

geminidr.core

  • Set default calculateSensitivity.bandpass parameter to 0.001 nm to better handle pure spectra in flux density units.

  • Allow display to handle non-standard extension names, which did not work as intended.

geminidr.gmos

  • Fix the QE model selection for the GMOS-S EEV CDDs.

recipe_system

  • Set the engineering flag to False for all data stored in the local calibration database, to ensure that it can be retrieved.

Compatibility

geminidr.interactive

  • The interactive tools are now compatible with and require bokeh v3 and above.

3.1.0

This release includes new science-approved support for GMOS longslit data, along with new interactive tools to optimize the spectroscopic reduction. The calibration service has also been refactored with significant changes that the user need to be aware of. Please read on.

New Features

Science quality support for GMOS longslit spectroscopy, including nod-and-shuffle.

Please refer to the tutorial, GMOS Longslit Data Reduction Tutorial. DRAGONS is now the official software for reducing GMOS longslit data in normal and nod-and-shuffle mode.

New browser-base interactive tools to support spectroscopy.

The following primitives have an interactive mode that can be activated with the -p interactive=True flag:

  • normalizeFlat

  • determineWavelengthSolution

  • skyCorrectFromSlit

  • findApertures

  • traceApertures

  • calculateSensitivity

The GSAOI alignment and stacking is now done in DRAGONS.

The package disco_stu is no longer needed. The default GSAOI recipe will align and stack. See the tutorial, GSAOI Imaging Data Reduction Tutorial

The bad pixel masks are now handled as the other calibration files.

They are distributed through the archive instead of with the package. They are also fully integrated into the calibration service. See the various tutorials for details.

The calibration service has been through a large refactor.

It is now possible to have the processed calibrations stored automatically (was a user step before), and it possible to serially search more than one database. See below for details on the new configuration file, Interface Modifications. For usage examples, see the various tutorials.

New imaging recipes.
For Flamingos-2, GSAOI, NIRI:

ultradeep See Flamingos-2 Imaging Data Reduction Tutorial for an example.

GMOS:

reduceSeparateCCDs and reduceSeparateCCDCentral (See GMOS Imaging Data Reduction Tutorial for an example.

Interface Modifications

recipe_system

  • There has been many changes to the calibration service. Most of them are internal but the one big change for the users is the configuration file. The configuration file now ~/.dragons/dragonrc (was ~/.geminidr/rsys.cfg). The syntax inside the file has changed a bit too.

    • New [interactive] section. This is used to set the browser that the interactive tools will use. Valid browsers: “safari”, “chrome”, “firefox”:

      [interactive]
browser = safari

    • New format for the [calib] section. The variable is now named databases, plural, and multiple databases can be defined to be searched serially. One database per line. The name of the database can now be set by the user instead of being hardcoded to cal_manager.db. Two new flags can be set get and store to, respectively, “get” processed calibrations for that database, and “store” them to it.

      [calib]
databases = /Users/someone/data/myprogramcal.db get store
            https://archive.gemini.edu get

geminidr

  • You must now ensure that the bad pixel masks (BPMs) can be found in a database. The BPMs are no longer distributed with the software. They are downloadable from the archive. See the “Tips and Tricks” section of any tutorial (except Flamingos-2).

Improvements

geminidr

  • As mentioned above, the BPMs are now stored in archive. Using the archive to distribute the BPMs will allow us to make new BPMs available rapidly, for example, when new bad columns appear in GMOS CCDs, after a catastrophic event like the amplifier 5 failure in January 2022, or when the CCDs are replaced.

  • Several new or improved algorithms compared to 3.0.x.

Documentation

geminidr

  • There has been some restructuring of the tutorials to better present multiple examples within a tutorial.

  • Several new examples for Flamingos-2 and GMOS imaging tutorials.

  • Several science quality examples for the new GMOS longslit spectroscopy support.

astrodata

  • The three previously separated astrodata manuals, “Cheat Sheet”, “User Manual”, and “Programmer Manual” have been consolidated into one master document. Please fix your link, Astrodata Manual.

Compatibility

  • DRAGONS v3.1 is compatible with Python 3.7 to 3.10. The pre-release tests were done with Python 3.10. Please note that DRAGONS v3.1.x will the last minor version to support Python v3.7.

  • The conda package was built and tested against conda-forge dependencies. STScI has dropped support of the astroconda channel. Make sure that you adjust your conda channels.

    If you already have a ~/.condarc file, make sure that the channels are set as follows:

    channels:
  - http://astroconda.gemini.edu/public
  - https://conda.anaconda.org/conda-forge
  - defaults

    If you are installing conda for the first time, see the installation instructions here: Installation Guide

3.0.4

Bug Fixes

geminidr.gmos

  • Allow maskFaultyAmp to work on astrodata objects with no mask.

  • Fix maskFaultyAmp to work on central stamp ROI.

geminidr.core

  • Adjust minimal dither separation for fringe frame creation.

astrodata

  • Fix AstroData info() method to handle extensions with no pixels. Required for upcoming GHOST data.

Improvements

geminidr.gmos

  • Update to the GMOS-S Hamamatsu 4x4 imaging illumination mask.

geminidr.core

  • Improve behavior of addIllumMaskToDQ to cope with larger shifts due to recent GMOS misalignment.

  • Add provenance for the flux calibration step.

gemini_instruments.f2

  • Switched to using WAVELENG for central_wavelength for F2 to be better aligned with the instrument and observatory software.

gempy

  • In dataselect, make the disperser selection default to the “pretty” mode rather than requiring the full component ID.

Quality Assessment Pipeline

  • Increase robustness of measureIQ for 2D spectra.

  • Interface improvements to the QAP Specviewer.

  • Fix missing maskFaultyAmp in some QAP recipes.

  • Limit the number of aperture/spectra selected in GMOS LS QA recipes for performance reasons.

3.0.2 and 3.0.3

Note that 3.0.2 was found to have one broken recipe, 3.0.3 fixes it.

Bug Fixes

geminidr.core

  • Continue without crashing when traceApertures cannot identify a starting location for a trace.

  • Fix issues with assignment of on-source/sky frames when the user specifies specific frames.

  • Fix bug where stackFrames crashed if using the statsec parameter when scaling or zero-offsetting.

  • In fringeCorrect, do_cal=force has been reactivated.

  • Better handling of infinites and NaN in the flat normalization.

geminidr.gmos

  • Added new primitive to the recipes to mask amplifier 5 in GMOS-S data obtained since January 28, 2022. GMOS-S amplifier 5 suffered a major failure and it is not usable.

  • Ensure that the masks are used when calculating the statistics in scaleByIntensity.

geminidr.gnirs

  • Added missing support for YPHOT filter.

geminidr.f2*

  • Support of the Flamingos 2 filters.

New Features

** geminidr **

  • Add wave_units and data_units parameters to write1DSpectra to configure the output

  • Under-the-hood modification to distinguish data reduced in quicklook mode versus science mode.

Interface Modifications

  • Internal Gemini catalog server URL updated.

Documentation

  • Various fixes to the documentation affecting formatting, not the content.

3.0.1

Bug Fixes

geminidr.core

  • Fix bug where section start/end comparison was made on string, not numeric, values.

gempy.library.transform

  • Fix bug that caused longslit spectra to have incorrect WCS, offset from true slit location.

Interface Modifications

geminidr.core

  • Expose min_snr parameter in findApertures, make use_snr=False the default, and estimate noise from pixel-to-pixel variations, regardless of its value.

Documentation

  • Various fixes to the documentation.

3.0.0

This release includes new support for GMOS longslit data. Reduction of GMOS longslit data is offered only quicklook mode. It does not produce science quality outputs, yet.

Bug Fixes

geminidr

  • In imaging mode, the science recipes now include a call to scaleByExposureTime before the stacking step. It is now possible to stack frames with different exposure times.

gemini_instruments.gemini

  • Fix the GCALLAMP tag for NIR data to include the QH lamp.

geminidr.core

  • Remove incorrect logging in separateSky when object and/or sky files are specified.

  • Improve algorithm for separating on-source and on-sky frames.

  • Avoid upsampling OBJMASK from uint8 to uint16

  • In near-IR imaging mode, frames that fail to be sky subtracted are removed from the main reduction stream to avoid contamination. The reduction continues with the “good” frames. If all frames fail the sky subtraction, then all frames will be passed to the next step of the reduction.

geminidr.gemini

  • Fix to the calculation of the CC-band used in nighttime sky quality assessment.

  • Fix to the calculation of the BG-band used in nighttime sky quality assessment.

gempy.gemini

  • Ensure NIRI skyflats satisfy calibration association requirements

gempy.numdisplay

  • Fix a Python 3 compatibility issue.

New Features

geminidr

  • Quicklook (--ql mode) reduction support for GMOS longslit data.

geminidr.core

  • Add remove_first parameter to removeFirstFrame primitive.

  • Add match_radius parameter to adjustWCSToReference primitive.

  • Add an IRAF compatibility primitive and recipe for Flamingos 2.

astrodata and recipe_system

  • Provenance history stored with the data in tables named: PROVENANCE and PROVHISTORY.

Interface Modifications

geminidr.core

  • biasCorrect, darkCorrect, flatCorrect. The do_bias, do_dark, and do_flat input parameters have been replaced with do_cal with more options than True or False. Use showpars to inspect the options.

Compatibility

  • Python 2 support has been dropped. Starting with v3.0.0, DRAGONS requires Python 3. All tests were run on Python 3.7, and this version of Python now serves as the minimal required version.

  • Improved the F2 processed products backward compatibility with Gemini IRAF.

Documentation

  • Fix various links in the documentation.

  • Add examples and cross-reference to disco-stu usage documentation.

  • New tutorial for the quicklook reduction of GMOS longslit data.

2.1.1

Bug Fixes

geminidr.core

  • Fix a crash when a section was used when stacking.

gempy scripts

  • Add missing third party adpkg and drpkg support to utility scripts dataselect, showpars, typewalk, and showrecipes.

gempy.library

  • Fix to Jacobian calculation for non-affine transforms

recipe_system.adcc

  • Make adcc more robust to missing connection to fitsstore.

Compatibility

gempy.gemini

  • Add compatibility with sigma_clip for astropy v3.1+

  • Add IRAF compatibility keywords on GMOS mosaiced data.

  • Add compatibility with astroquery 0.4.

geminidr.core

  • Add compatibility with sigma_clip fro astropy v3.1+

geminidr.gmos

  • Add IRAF compatibility recipe.

Documentation

  • Various fixes to documentation and instruction manual following feedback from users.