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CHANGELOG
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CHANGELOG
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# ========================================================================================
# M O D I F I C A T I O N H I S T O R Y
# ========================================================================================
------------------------------------------------------------------------------------------
VERSION DATE DESCRIPTION
------------------------------------------------------------------------------------------
V7.3.0 2024-11-12 CHANGED Major: 1) Changed name of routine to ngistPipeline
2) Optimized Voronoi Binning: Improved speed and reduced
RAM usage by using scipy's spatial.cKDTree for nearest-neighbor
searches. 3) Switched Parallelization to Joblib: Enhanced performance
and memory management by switching from multiprocess to joblib for
parallel computing. 4) Transitioned to HDF5 for Pipeline Data Tables:
Improved memory management and support for large data operations by
transitioning from FITS to HDF5 tables.
CHANGED Minor: A) Rename Scripts: Renamed scripts that duplicate module
names, e.g., ppxf.py. B) FITS File Branding: Removed FITS file branding
from skipped galaxies. C) MapViewer Read HDF5: MapViewer can read the
HDF5 pipeline files AND FITS files to maintain backward compatibility
with older results directories. D) General Tidying: General tidy-ups
and added docstrings. E) GAS Spaxel mode: Fixed previous bug in GAS
module related to incorrect nbin definition in Spaxel mode. F) CONT
module: Reverted back to default MUSE header keywords in generated
cubes. Fixed bug that called KIN module config setting instead of CONT.
V7.2.1 2024-07-28 ADDED: Ability to create BPT maps in the GAS module if all required
emission lines are present. Note: there is currently no AoN
threshold applied to these lines.
V7.2.0 2024-07-21 ADDED: Implemented MC realizations to estimate
uncertainties of template weights and mean stellar population properties
for the SFH module using the method in Pessa et al. 2023-AA.
V7.1.0 2024-07-20 ADDED: Added a new option for an SNR-dependent bias setting similar
to what was adopted for SAMI in van de Sande et al. 2017-ApJ
The new option can be called as "muse" which uses the SNR from the best-fit
solution or "muse_snr_prefit" that uses the snr from the pre-scaled variance
V7.0.0 2024-07-08 CHANGED: New user module added called UMOD. This currently only
accepts a twocomp_ppxf fitting function.
FIXED:
Minor fixes and code cleanup.
V6.1.1 2024-07-03 FIXED:
Multiple bugs in multiple modules. Please use commit history for all changes.
CHANGED:
Turned saving AllSpectra.fits module back on if GAS is fitted in SPAXEL mode,
but AllSpectra.fits is removed once GAS routine has finished running.
V6.1.0 2024-06-24 FIXED:
Multiple bugs in multiple modules. Please use commit history for all changes.
CHANGED:
Turned off saving AllSpectra.fits module.
ADDED:
Two component stellar kinematic fitting module in pPXF. Calling sequence
"TWOCOMP_KIN" with "twocomp_ppxf.py". Only works with MOM = 2 and MILES SSP
library.
V6.0.1 2024-04-24 FIXED:
Minor fixes and code cleanup
V6.0.0 2024-04-18 FIXED:
Parallel = False in SFH module
REMOVED:
Template reshape immediately after creation in SFH module
ADDED:
Template reshape before creation of optimal_template in run_ppxf
ADDED:
Continuum normalisation step before running pPXF in KIN, CONT, and
SFH modules.
V5.4.5 2024-04-18 ADDED:
The ability to return an E(B-V) dust map in the SFH module.
V5.4.4 2024-03-25 CHANGED:
Name from gist-geckos to nGIST!
ADDED:
The ability to define the BIAS value in the KIN module. If not set by the
user, the default value in the MasterConfig file is 'Auto', which uses the
default implementation provided with pPXF from Cappellari & Emsellem 2004.
CHANGED:
_initialise.py ascii text art to reflect code name change.
V5.4.3 2024-01-29 CHANGED:
addGISTHeaderComment so that it doesn't need to open the every fits file
and so that only the ext[0] has the gist-geckos branding added. This
saves a lot of time.
ADDED:
XBIN and YBIN pixel Voronoi bin centres to the SPATIAL_BINNING maps files.
V5.4.2 2024-01-12 FIXED:
Bug that was introduced into the CONT module in V5.4.1 that caused it
to run, even when results were already in the results directory and
OW_OUTPUT = False.
V5.4.1 2024-01-11 REMOVED:
'KIN' from the continuum cube file names, as this is now a separate module
Superfluous Fits header updates that occured even when OW_OUTPUT was set
to False. These updates now only occur if OW_OUTPUT = True or the files are
being created for the first time.
V5.4.0 2024-01-10 FIXED:
Bug in GAS module that prevented the _BIN and _SPAXEL maps files from saving
when run in 'BOTH' mode.
OW_OUTPUT = False still overwriting results in the GAS module.
ADDED:
Hardcoded ADEG=-1 into the continuum module to be in line with the procedure for
the GAS and SFH modules. The configFile keyword ['CONT']['ADEG'] is no longer
required and should be removed from your MasterConfig.yaml file.
V5.3.2 2023-12-13 FIXED:
Fixed bug in WriteFits LS module where it wasn't using the idx_inside selection
V5.3.1 2023-12-11 CHANGED:
Removed the subtraction of the median Velocity in the MapViewer velocity maps.
V5.3.0 2023-12-10 ADDED:
Added keyword to config file SPEC_EMICLEAN (True/False) to enable/disable the
use of emission line cleaned spectra from the Emission Line Fitting Module.
Minor changes to 'ppxf.py' scripts for printing status during fitting.
V5.2.3 2023-12-09 FIXED:
Changed the velscale_ratio from 1 to 2 to match the KIN and SFH
module.
V5.2.2 2023-12-08 FIXED:
Galaxy spectra our now normalised before being fitted in the
StellarKinematics and SFH modules. Output best-fit model is scaled
back to match original flux of galaxy spectrum.
V5.2.1 2023-11-23 ADDED:
SPATIAL_BINNING module now outputs maps for table.fits. StellarKinematics
and SFH modules now calculates the postfit signal-to-noise ratio from the
residuals and output these in the saved fits files
V5.2.0 2023-11-8 ADDED:
A new continuum module was created based on the StellarKinematics module.
V5.1.5 2023-10-11 FIXED:
SFH module ppxf.py so that it now recognises whether the emission
line module has already been run. If so, it will take the emission-
subtracted 'cleaned' spectrum as input to the SFH module.
V5.1.4 2023-09-12 ADDED:
Ability to turn the pPXF CLEAN function on or off using the keywords:
config['KIN']['DOCLEAN'] = True/False
config['SFH']['DOCLEAN'] = True/False
FIXED:
Cleaned the ppxf.py SFH module code to match the format of Kinematic module
V5.1.3 2023-08-10 ADDED:
Ability to use the stellar templates from Walcher et al. 2009
in the stellar kinematics module.
To use this option, the keywords have to be :
config['KIN']['LSF_TEMP'] = 'lsf_WALCHER'
config['KIN']['TEMPLATE_SET'] = 'walcher'
config['KIN']['LIBRARY'] = '/Walcher/'
V5.1.2 2023-08-07 FIXED:
Ability to run spaxel-based emission line fits using the pPXF module.
if config['GAS']['METHOD'] = 'ppxf', 'MAGPIGandalf', or 'Gandalf',
config['GAS']['LEVEL'] can be 'BIN' or 'SPAXEL' ('BOTH not yet implemented
for ppxf module.
ADDED:
config['GENERAL']['OUTPUT']_KIN_ORIGcube.fits, a file containing the
original spectra cut to the wavelength range at which the continuum
cube was made, for use with config['GENERAL']['OUTPUT']_KIN_CONTcube.fits
and config['GENERAL']['OUTPUT']_KIN_LINEcube.fits for work with the
continuum cubes.
V5.1.1 2023-07-28 ADDED:
Ability to implement a foreground Galactic dust extinction using the
config['READ_DATA']['EBmV'] keyword.
V5.1.0 2023-07-26 ADDED:
A new ppxf-based emission line fitting module based on the PHANGS DAP
V5.0.5 2023-07-18 ADDED:
SFH module has been updated to use a 3-step noise estimation and
sigma clipping method, in line with the stellar kinematics module.
V5.0.4. 2023-05-26 ADDED:
MAGPI gandalf implementation sub-module. There are now two options
for GAS METHOD: 'gandalf' and 'MAGPI_gandalf'. Recommend adopting
'MAGPI_gandalf' from now on.
V5.0.3. 2023-05-24 ADDED:
Code to subtract the bestfit stellar continuum and construct a
continuum subtracted cube.
V5.0.2 2023-05-17 FIXED:
* Identified origin of LSF module crash which was due to a bug in
ppxf_util.gaussian_filter1d(). This bug will be fixed in version
8.2.5 of pPXF. In older pPXF version replace line 665 in
ppxf_util.py with p = int(1.0 + 4*np.max(sig))
V5.0.1 2023-05-05 FIXED:
* Fixed bugs in mapviewer/createFigure.py and mapviewer/helperFunctions.py
by changing all references of PyQT to PyQT5,
* Fixed bug in mapviewer/plotData.py by changing np.int to np.int32
V5.0 2023-04-06 CHANGED:
* Created the ability to use multiple stellar template libraries in the one GIST
call. This will be useful is you for e.g. want to use one template set for
the stellar kinematics, and another for the emission lines and stellar populations.
* MasterConfig.yaml now has a slightly different format, where you define the
template set used for each module individually.
V4.0.1 2023-03-27 FIXED:
* Fixed bug in MUSE_WFM.py to accept cubes with more than 2
extensions.
* Fixed calculation of SNR, which was done as median(flux)/median(error)
but should be defined as median(flux/error)
* Updated spatialMasking default.py script to allow for using actual
SNR cutoff of spaxels instead of isophote based SNR. Two choices are
the default threshold_method = 'isophote' and threshold_method =
'actual'. Two choices are NOT available within yaml file just yet.
V4.0 2023-03-09 First version of the gist-geckos pipeline!
CHANGED:
* Updated the MasterConfig file to MasterConfig.yaml to make more
human-readable. This is now the input file to use.
* Updated _initialise.py and main_pipeline.py to accept YAML.
* New GIST call is:
gistPipeline --config configFiles/MasterConfig.yaml --default-dir configFiles/defaultDir
V3.1.0 2021-09-09 Last GIST version maintained by Adrian Bittner as Astronomer.
FIXED:
* Fixed bug in GAS plotting routine related to defunct spaxels
V3.0.5 2021-05-28 FIXED:
* Fixed bug in KIN plotting routine to work with both two and
four kinematic moments. Thanks to Geoff Chih-Fan Chen for
pointing out this issue.
V3.0.4 2021-03-19 FIXED:
* Replaced MUSE_WFMAO read-in routine by MUSE_WFMAON and
MUSE_WFMAOE to account for the distinct wavelength ranges
affected by the LGS facility in the nominal and extended modes
of the MUSE wide-field mode.
Thanks to Aishwarya Girdhar for pointing out this bug.
* Fixed Mapviewer, gandalf.py, and gistPlot_kin.py to work with
only two kinematic moments. Thanks to Sebastien Comeron for
reporting these issues.
* Account for the correct de-redshifting of sky-masks in
pyGandALF. Thanks to Andrew Battisti for the suggestion.
V3.0.3 2020-12-11 FIXED:
* Change MUSE read-in routines to read pixelsize from header
* Correct wavelength range affected by laser guide stars in MUSE
adaptive optics read-in routines. Masking now extends to 6050A
* Fixed Mapviewer to show wavelengths in Angstrom if only a
plain spectrum (without any other analysis) is displayed.
Thanks to Sebastien Comeron for pointing out these bugs.
V3.0.2 2020-10-19 FIXED:
* Fixed typo in log-messages from read-in routines
* Fixed bug in gandalf.py that prevented some output columns to
be written to disk. Thanks to Andrew Battisti for pointing
out these two issues.
V3.0.1 2020-09-03 CHANGED:
* Assure compatibility with pPXF version 7 by adopting the
_bvls_solve and nnls_flags from pPXF version 6 into pyGandALF.
Thanks to Michele Cappellari for his permission to include
these functions.
* Relaxed version dependencies of other packages in setup.py.
* Changed the default value of the ftol parameter in pyGandALF
to 1e-5, in order to improve the reliability of the fit.
V3.0 2020-08-20 Substantial revision and restructuring of the source code. Please
consider the documentation for a detailed description of all
changes.
V2.1 2020-04-06 CHANGED:
* Changed definition of npad variable in Gandalf analogue
to PPXF. Thanks to Alireza Molaeinezhad for the suggestion.
* Check dimensions of templates at read-in to allow the use of
Miles stars. Thanks to Thomas Spriggs for the suggestion.
* Modified CALIFA read-in routines to pass variances in
error spectra.
FIXED:
* Added missing np.sqrt in the calculation of error spectra
of bins consisting of single spaxels. Thanks to Sebastien
Comeron for reporting this bug.
* Neglect negative BIN_IDs in the calculation of the reference
velocity in Mapviewer. Thanks to Isabel Pérez.
* Enable DEBUG-mode in read-in routines by passing shape of cube
Thanks to Adriano Poci for reporting this bug.
* Mapviewer: Plot the spectrum of the nearest valid bin if a bin
outside of the Voronoi-region is selected.
Thanks to Michela Rubino.
V2.0.0 2019-11-13 ADDED:
* Support different wavelength ranges in different modules,
including a separate wavelength range for the SNR calculation.
* Support AO in MUSE wide- and narrow-field mode
Thanks to Sebastien Comeron for the suggestion.
* Support of sky-lines in spectralMasking_*.config
Thanks to Sebastien Comeron for the suggestion.
CHANGED:
* Propagate defunct spaxels through the pipeline
V1.1.1 2019-10-31 FIXED:
* Apply de-redshifting to laser wavelength range in MUSE_NFM.py
* Apply de-redshifting to LSF
Thanks to Sebastien Comeron for reporting these bugs.
V1.1.0 2019-08-16 ADDED:
* Allow different initial guesses for different bins in pPXF
Thanks to Michela Rubino for the suggestion.
* Read-in routine for single spectra in txt-format "PLAINTXT.py"
FIXED:
* spectralMasking_SFH.config to handle one or zero masks
* Orientation of maps in plotting routines
* GandALF taking into account the LSF in doublet lines
CHANGED:
* Use stellar kinematics as initial guess on GandALF fit
* Use np.nansum instead of np.nanmean to co-add spectra into
Voronoi-bins
* Pass ORIGIN in units of pixels
REMOVED:
* *_gandalf-residuals_*.fits output
V1.0.0 2019-06-11 Release of first version