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ChangeLog
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2016-06-23 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/libExtractStar.py (ExposurePSF.comp): error in normalization
[#1558, thanks to K. Boone].
2016-05-10 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/libExtractStar.py (Hyper_PSF3D_PL): set position prior
accuracy to 0.2 spx.
* apps/extract_star/extract_star.py: option '--positionPrior
cubefit' now uses priors from cubefit.
2016-04-29 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: finalize "step" background option.
2016-04-26 Yannick Copin <ycopin@lyonovae03.in2p3.fr>
* apps/extract_star/extract_star.py: new "step" background with
'--skyDeg=-2' (WORK IN PROGRESS).
2016-04-14 Yannick Copin <ycopin@lyonovae03.in2p3.fr>
* apps/extract_star/extract_star.py: expose accountant warning
cuts in global constants.
2016-01-11 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: make libRecord.Accountant
optional.
2015-06-09 Yannick Copin <ycopin@lyonovae03.in2p3.fr>
* apps/extract_star/extract_star.py: add prior warnings to plots,
by a systematic use of (un-finalized) accountant.
2015-06-03 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py (flag_nans): detect suspicious
variance values more than 1e6x median (non-null) variance
[test-case: 12_290_052_003_2_260_720_02-02_000.fits]
* lib/pySNIFS.py (SNIFS_cube.slice2d): do not downcast input
dtype. Has an impact on `SNIFS_cube.WR_3D_fits` and therefore on
`e3dto3d.py`.
2015-06-01 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: new option '--accountant' to
store quality warnings in accountant file.
2015-03-25 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: new option '--positionPrior'
replaces deprecated option '--useDDTprior'; more flexible prior
management updated.
2015-03-16 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/libExtractStar.py (fit_metaslices): use converged metaslice
fit position as initial guess for next metaslice.
2015-03-02 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: previous "1 + |mean_slice|"
is not homogeneous; switch to "|mean| + |mean_slice|"
normalization.
2014-12-01 Yannick Copin <ycopin@lyonovae03.in2p3.fr>
* apps/extract_star/extract_star.py: auto-PEP8.
* lib/libExtractStar.py (__init__): use
ToolBox.Atmosphere.ADR.get_scale(); auto-PEP8.
2014-10-22 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: convert exceptions from tests
against priors into warnings only, since these tests can
eventually be performed a posteriori.
2014-10-21 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/libExtractStar.py (read_psf_param): make function compatible
with previsous keyword name 'ES_PA'.
(fit_metaslices): relax boundaries on alpha parameters (needed for
seeing above 3 arcsec).
2014-10-02 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: switch to 1+|mean|
normalization (rather than max) to help convergence.
* lib/libExtractStar.py (extract_specs): do not force sky
positivity.
2014-10-01 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: new expert option
'--ignorePertinenceTests'.
2014-09-16 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: use standard minimizer
interface 'minimize' for final 3D-fit and relax convergence
tolerance.
2014-09-11 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/libExtractStar.py (read_DDTpos): add sanity check (SN ought
to be located in FoV).
* apps/extract_star/extract_star.py: switch back to
`errorbar(fmt=None)` (deprecated in recent version of matplotlib).
2014-09-09 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: boolean option '--supernova'
replaced by option '--usePriors' setting the hyper-term scaling
factor (default 0: no priors, 1: standard priors); new option
'--useDDTPriors' to use priors on position from DDT[X|Y]P keywords
in 2D- and 3D-fits; pertinence of final fit parameters is tested
against priors if any.
2014-07-22 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: default PSF model is now
'classic-powerlaw'; test on position of SN.
2014-07-21 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py (flag_nans): flag-out
non-finite data or variance values in cubes.
* lib/libExtractStar.py (fit_metaslices): use central spaxels only
to roughly guess point-source position (some DDT-cubes have nasty
NaN's in the external parts).
2014-07-15 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/plot_slices.py: option '-s/--spec l1,l2,...'
can now plot individual spectra.
2014-07-11 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/libExtractStar.py (Hyper_PSF3D_PL, Hyper_PSF2D_PL): add
priors on shape parameters (xy and y2).
2014-07-08 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/plot_slices.py: option '-R/--rangePerSlice'
replaced by '-R/--rangePerCube'.
2014-07-07 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/libExtractStar.py (get_slices_lrange): function removed.
2014-07-03 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: new option '--subsampling' to
sub-sample the PSF (default to x3).
2014-07-02 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/libExtractStar.py (Hyper_PSF2D_PL): prior on seeing for
meta-slice.
2014-07-01 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/libExtractStar.py (fit_metaslices): on the way to implement
seeing prior in meta-slice 2D-fit, WORK IN PROGRESS.
2014-06-27 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: option '--supernova'
now (more or less) implemented and functional; works down to
'--nmeta=1'. Prior on seeing in meta-slice fit not yet
implemented; not yet tested in production, WORK STILL IN PROGRESS.
2014-06-25 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/libExtractStar.py (Hyper_PSF3D_PL): hyper-term including
predictions for ADR parameters and power-law expansion
coefficients. WORK IN PROGRESS.
2014-05-30 Yannick Copin <ycopin@lyonovae03.in2p3.fr>
* apps/extract_star/extract_star.py: still work in progress.
2014-05-16 Yannick Copin <ycopin@lyonovae03.in2p3.fr>
* apps/extract_star/extract_star.py: supernova-mode now use
hyper-term to constrain ADR. WORK IN PROGRESS!
2014-05-14 Yannick Copin <ycopin@lyonovae03.in2p3.fr>
* lib/libExtractStar.py (HyperPSF): evolution toward the use of
PSF-related hyper-terms in the chi2.
* lib/pySNIFS_fit.py: slight code refactoring (e.g. use numpy
rather than scipy).
(model.eval_hyper, grad_hyper, objfun, objgrad): add support for
hyper terms in the chi2, STILL EXPERIMENTAL.
(Hyper): example class for an hyper terms.
(model.minimize): wrapper to generic minimizer
scipy.optimize.minimize.
(model.facts): print-out of model parameters.
2014-05-02 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: debugging of power-law
chromaticity (inconsistent ref. wavelength).
2014-04-30 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/pySNIFS_fit.py (model.fit): Help convergence by setting
realistic objective fmin=dof, use auto-offset and auto-scale.
2014-04-08 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: the power-law chromatic
parametrization is now "a(l) = p[-1] * (l/l0)**(p[-2] +
p[-3]*(l/l0 - 1) + ...)", so that a(l0) = p[-1].
2014-01-22 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: ignore "Overwriting existing
file" warnings.
2013-11-19 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: ready for production.
2013-11-15 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: figure tweaks, add some
documentation about ES-keywords in 'fill_header' (still in
progress).
2013-11-14 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/libExtractStar.py: try to make the meta-slice 2D-fit more
robust.
2013-11-12 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py (guessAlphaCoeffs): initial
guess from power-law fit to meta-slice alpha's. This should
complete the implementation of 'power-law' chromatic seeing
dependency.
2013-11-07 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/libExtractStar.py (ExposurePSF.deriv): fix error in jacobian
of classic-powerlaw PSF. WORK STILL IN PROGRESS!
2013-11-06 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: option '-c/--correlation'
replaced by '--psf' (and different PSF model names). Implement new
PSF model 'classic-powerlaw' with a curved power-law chromatic
behavior (rather than a polynomial one). WORK STILL IN PROGRESS!
2013-06-06 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: figure updates, estimate
parallactic angle on the fly if needed.
2012-11-16 Clément BUTON <cbuton@ipnl.in2p3.fr>
* lib/libExtractStar.py (fit_metaslices): Change initial guess
from (0,0) to light weighted centroid.
2012-10-30 Rui Pereira <rui.pereira@in2p3.fr>
* lib/pySNIFS.py: a few python cosmetic fixes and updated
header.update() calls to work with new pyFITS.
2012-10-29 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/subtract_psf.py (and others): pyfits
header.has_key function is deprecated, use `key in header` syntax
instead.
2012-09-07 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/libExtractStar.py:
* apps/extract_star/extract_star.py (param_covariance): use
scipy.linalg.pinv2 in place of numpy.linalg.pinv (see
http://goo.gl/n0jFD).
2012-09-07 Yannick Copin <ycopin@lyopc469>
* apps/extract_star/plot_slices.py: new options '-s/--spec' (to
specify plotted spectra at bottom) and '-L/--label' (to label
spaxels).
2012-06-12 Yannick Copin <ycopin@lyopc469>
* lib/libExtractStar_numexpr.py: experimental version of
libExtractStar. using numexpr. Do not use!
2012-04-27 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: new option '-V/--covariance'
to compute and store spectral (lower-triangle) covariance matrix
as extension 'COVAR' in point-source spectrum. It overrides
deprecated option '-V/--variance' (which was on by default) to
store variance as extension of spectrum. WARNING: no support yet
for lossless compression of the covariance matrix; it is therefore
stored uncompressed (which makes a simple spectrum from 5 to 19 MB
for B/R...)
2012-04-26 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: on the way to compute
point-source spectrum covariance matrix from PSF parameter
covariance.
2012-04-23 Rui Pereira <rui.pereira@in2p3.fr>
* lib/libExtractStar.py (get_slices_lrange): remove libES reference.
2012-03-12 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/plot_slices.py: support cubes without
variance (e.g. LFFF). New option '-T/--title'.
2012-02-03 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/libExtractStar.py (metaslice): sanity checks.
* apps/extract_star/plot_slices.py: should now handle meta-slice
cubes.
2012-02-02 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/libExtractStar.py (metaslice): new routine to produce
centered metaslices.
* apps/extract_star/extract_star.py: remove obfuscated and mostly
useless function build_sky_cube.
2012-02-02 Rui Pereira <rui.pereira@in2p3.fr>
* apps/extract_star/subtract_psf.py: added '--sky' option.
* apps/extract_star/extract_fixed_psf.py: added '--skyDeg' option.
2012-02-01 Rui Pereira <rui.pereira@in2p3.fr>
* apps/extract_star/extract_star.py: moved extract_spec into
libExtractStar.py. Added subaperture extraction method. Added
ES_LMIN and ES_LMAX keys to spectrum header and fixed ES_PSF.
* apps/extract_star/subtract_psf.py: moved read_psf_name(),
read_psf_ctes() and read_psf_param into
libExtractStar.py. Recompute lrange from sliced cube if ES_LMIN
and ES_LMAX are not found in the spectrum header.
* apps/extract_star/extract_fixed_star.py: new script to extract a
PSF constrained with a spectrum header values from a (residuals)
cube.
* lib/libExtractStar.py: added a print_msg() similar to the one on
extract_star.py for compatibility with the moved functions:
extract_spec(), read_psf_name(), read_psf_ctes(),
read_psf_param(). Force S.misc.comb in polyConvMatrix().
* lib/pySNIFS_fit.py (model.fit): assume we now always use
scipy>0.6.
2011-12-01 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_z.py: option '-e/--emissionLine' now
accepts arbitrary emission line 'name,l0', to be used with option
'-O/--obsFrame'. New option '-M/--map' to produce spatial map from
input cube.
2011-12-01 Yannick Copin <ycopin@lyopc469>
* apps/extract_star/extract_z.py: on the way to generalize the
code to allow arbitrary night sky line studies.
2011-10-31 Yannick Copin <yannick@lyopc469>
* apps/extract_star/extract_z.py: add [OI] night-sky line
analysis, revive velocity map.
2011-07-19 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py:
* lib/libExtractStar.py: atmospheric routines are now in
ToolBox.Atmosphere.
2011-07-04 Yannick Copin <yannick@lyopc469>
* apps/extract_star/subtract_psf.py: new option '--psfname' to
specify output point-source cube name (requested by SZB).
2011-05-19 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/plot_slices.py: now handle multiple arguments,
display efftime and airmass.
2011-05-03 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: the "chi2" quantities
computed in the least-square case (for 2D/3D logs and residual
plots) are now proper residual sum of squares.
2011-05-03 Clement BUTON <cbuton@pi-intra-143.physik.uni-bonn.de>
* apps/extract_star/extract_star.py: Propagate the changes related
to the previously introduced option '-L/--leastSquares' in
create_3Dlog definition and in the 'residuals' plots.
2011-05-02 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: new option
'-L/--leastSquares' to perform least-square fits (previously
introduced option '--no_var' was buggy and has been removed).
2011-04-28 Clement BUTON <cbuton@pi-intra-143.physik.uni-bonn.de>
* apps/extract_star/extract_star.py: Add the option '--no_var'
which fix the variance of the cube to 1.0 (or to NaN if the value
was a NaN and to -1 if the value was <0).
2011-04-01 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/plot_slices.py: minor update.
2011-03-07 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/pySNIFS.py (spectrum.__init__): add ignore_missing_end=True
to please latest pyfits.
2011-01-31 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/plot_slices.py: new option '-s/--stack' to
display stacked spectra instead of mean spectrum.
2011-01-06 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py: minor refactoring.
2011-01-05 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/subtract_psf.py: now supports 3D
cubes (request from S.Bailey).
* apps/extract_star/plot_slices.py: new option '-V/--variance' to
plot variance rather than signal.
2011-01-04 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/subtract_psf.py: should be functional now.
* apps/extract_star/plot_slices.py: minor updates.
* lib/pySNIFS.py (SNIFS_cube.__init__): initialize self.data =
self.var = None beforehand.
2011-01-03 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/subtract_psf.py: reconstruct and subtract
extract_star PSF from extracted cube and spectrum (WORK IN
PROGRESS).
* lib/pySNIFS.py (SNIFS_cube.__init__): initialize self.lend in
any case.
2011-01-02 Yannick Copin <yannick@lyopc469>
* apps/extract_star/PSF_analysis.py:
* apps/extract_star/extract_star.py: cast ncol and nrow to int, to
please matplotlib 1.0, and other minor tweaks.
2010-12-17 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/plot_slices.py: cast ncol and nrow to int, to
please matplotlib 1.0.
2010-11-15 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py (extract_spec): direct use of
N.linalg instead of scipy.linalg; use pseudo-inverse for linear
least-square fit.
2010-10-27 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* lib/libExtractStar.py: switch from scipy to numpy, scipy-0.8.0
optimize.fsolve returns a 1D-array instead of a scalar.
* apps/extract_star/extract_star.py (fit_slices): further contrain
adjusted parameters, debug print-outs.
* lib/pySNIFS_fit.py (model.fit): fmin_tnc status=[0,1,2] mean fit
convergence.
2010-10-26 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py (main): normalize input
meta-slice cube to max(axis=-1)=1 (per-slice normalization).
2010-10-25 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_star.py (fit_slices): use
pseudo-inverse of hessian matrix;
(main): normalize input meta-slice cube to max(axis=None)=1.
2010-10-18 Yannick Copin <yannick@lyopc469>
* apps/extract_star/extract_z.py: add barycentric correction to
get heliocentric redshift.
2010-10-15 Yannick Copin <ycopin@lyopc548.in2p3.fr>
* apps/extract_star/extract_z.py:
* apps/extract_star/extract_host.py: minor updates.
* apps/extract_star/extract_star.py: switch from scipy to numpy.
2010-06-17 Stephen Bailey <stephen.bailey@in2p3.fr>
* lib/pySNIFS.py : fixed bug with generating fits tables with
variable length columns which was causing adjust_dichroic crashes.
2010-05-14 Clément BUTON <cbuton@lyoma81.in2p3.fr>
* lib/libExtractStar.py: Update PSF correlation chromaticity
parameters.
2010-05-03 Clément BUTON <cbuton@lyoma81.in2p3.fr>
* apps/extract_star/extract_star.py: Decrease figures size of
plots (from [12,10] to [8,6]) to resolve disk space problem (see
Stephen email 'extract_star pngs and web png directory' from
05/03/2010).
2010-04-15 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/plot_slices.py: new option
'-R/--rangePerSlice'.
2010-04-14 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/plot_slices.py: Visualize mean slices and mean
spectrum of a cube.
* apps/extract_star/extract_star.py (fit_slices): centroid
estimated from 2D-gaussian fit should be more robust and help on
low S-to-N cubes (Mantis #1455). Extracted variance spectrum is
now stored as an extension by default (option '-V/--variance' set
to True by default); new option '--varianceAside' to force storage
in individual spectrum. New option '--nmeta' to specify number of
meta-slices in 2D-fit; default value (12) is similar to what was
used before. Option '--keepmodel' now saves meta-slices cube
('meta_xxx') in addition to adjusted model ('psf_xxx'). Debug of
'fit1' plot (Mantis #1453) and some other debug plots.
2010-03-10 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py: minor updates.
* lib/libExtractStar.py: hide Chebychev's polynomials in chebEval
instead of a global variable. Minor rewriting.
2010-02-23 Clément BUTON <cbuton@lyoma81.in2p3.fr>
* lib/libExtractStar.py: minor bug correction related to
'scipy.special' importation.
2010-02-16 Clément BUTON <cbuton@lyoma81.in2p3.fr>
* apps/extract_star/extract_star.py: add '--correlations' option
which allow to choose between 'old' and 'new' version of the PSF
shape parameters correlations (default is 'old').
* lib/libExtractStar.py: add '--correlations' option
which allow to choose between 'old' and 'new' version of the PSF
shape parameters correlations (default is 'old').
2010-02-12 Clément BUTON <cbuton@lyoma81.in2p3.fr>
* apps/extract_star/extract_star.py: Major update of the
guassian+moffat PSF description (chromaticity, use of checbychev
polynomials, etc). Update plots.
* lib/libExtractStar.py: Major update of the guassian+moffat PSF
description (chromaticity, use of checbychev polynomials,
etc). Add classes for red and blue exposures.
2009-12-01 Stephen Bailey <stephen.bailey@in2p3.fr>
* apps/cube_explorer/cube_explorer.py,
* apps/extract_star/convert_3DPSF.py: numarray removed.
2009-11-19 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py: update to handle new 3D FITS
file. WARNING: the source extraction proceeds correctly, but some
plots are wrong...
* lib/pySNIFS.py (SNIFS_cube.__init__): update reading SNIFS_cube
from a 3D FITS file using new convention (signal in primary
extension, variance in 'VARIANCE' extension).
2009-11-17 Kerstin Paech <paech@physik.uni-bonn.der>
* lib/pySNIFS.py: removed the numarray/numpy switch. Fixed Mantis
issue #1331: pySNIFS produced corrupt e3d-fits-files for a certain
class of input-fits files due to mismatch between header and data
formats.
2009-11-13 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/e3dto3d.py: convertor from SNIFS Euro3D cubes to
NAXIS=3 FITS cubes.
* lib/pySNIFS.py (SNIFS_cube.WR_3d_fits): data cube is stored in
primary extension, while variance is stored in 1st ('VARIANCE')
extension. Euro3D cube header is propagated in output file.
2009-06-29 Yannick Copin <ycopin@lbl.gov>
* apps/extract_star/extract_star.py: remove call to S.degrees(),
not available for python-2.4.
2009-06-10 Yannick Copin <ycopin@lbl.gov>
* apps/extract_star/extract_star.py: aperture radius (option
'-r/--radius') for aperture-based methods can be specified in
arcsec or in seeing sigmas. Plot updates.
2009-05-20 Yannick Copin <ycopin@lyopc469>
* apps/extract_star/extract_star.py (setPSF3Dconstraints): new
expert option '--psf3Dconstraints' to specify constraints on PSF
parameters during 3D-fit. Each parameter (0=delta, 1=theta,
2,3=position, 4=PA, 5...6+ellDeg=ellipticity coeffs and
7+ellDeg...8+ellDeg+alphaDeg=alpha coeffs) can be constrained
individually strictly (e.g. '0:1' to force delta to 1) or loosely
(e.g. '2:-1,1' to constrain x-position within ±1). Note that
constraints on polynomial coeffs have to be expressed as function
of lr := (2*lambda - (lmin+lmax))/(lmax-lmin), while the coeffs
stored in header keywords are for polynoms of lr := lambda/lref-1.
2009-03-31 Yannick Copin <ycopin@lbl.gov>
* apps/extract_star/extract_star.py: the so-called PA parameter of
the PSF is not the PA of the adjusted ellipse, but half the x*y
coefficient. Similarly, ell is not the ellipticity, but the y**2
coefficient: x2 + ell*y2 + 2*PA*x*y + ... = 0. One should use
quadEllipse for conversion, and use full covariance matrix to
compute and plot associated errors.
2009-03-24 Yannick Copin <ycopin@lbl.gov>
* apps/extract_star/extract_star.py: plot updates.
2009-02-17 Yannick Copin <ycopin@lbl.gov>
* apps/extract_star/extract_star.py: new option '-V/--variance' to
store variance spectrum as extension to signal spectrum.
* lib/pySNIFS.py (spectrum.WR_fits_file): variance extension if
any is named 'VARIANCE'.
* apps/extract_star/extract_star.py: add binned points in radial
plot.
2008-11-10 Yannick Copin <ycopin@lyopc469>
* apps/extract_star/extract_z.py: add detection level.
2008-11-07 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py: use polynoms of (2*lbda -
(lmin+lmax))/(lmax-lmin) internally to decrease covariance between
coefficients. Keyword coeffs are converted to polynom of
lbda/5000A-1 to ease inter-channel comparison.
* lib/libExtractStar.py (polyConvert): polynomial utility to
convert P(x) to P~(x~:=a+b*x).
2008-11-05 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_z.py:
* apps/extract_star/extract_star.py: covariance matrix is *twice*
the invert of hessian for chi2-fit.
2008-11-03 Yannick Copin <ycopin@lyopc469>
* apps/extract_star/extract_z.py: split lines + background, add
correlation matrix plot, store results in keywords.
2008-10-31 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_z.py: extract redshift on galaxy
spectrum from [OII] or Halpha/[NII] (previously included in
extract_host.py).
* apps/extract_star/extract_host.py: remove redshift fitting, now
in extract_z.py.
2008-10-31 Yannick Copin <ycopin@lyopc469>
* apps/extract_star/extract_host.py: extend max. redshift to 0.13
(SNF20070912-000 is at ~0.12).
2008-10-24 Yannick Copin <ycopin@lyopc469>
* apps/extract_star/extract_host.py: adjust mean redshift on
galaxy spectrum from [OII] or [NII]/Halpha lines. Still
experimental: velocity map.
2008-10-23 Yannick Copin <ycopin@lyopc469>
* lib/pySNIFS.py (SNIFS_cube.__init__): generate a
'e3d_data_header' attribute in the fits3d_file case just for
consistency.
* apps/extract_star/extract_host.py: handle reference galaxy FITS
3D-cubes from DDT (after a bit of massage).
2008-10-22 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_host.py: Simple host spectrum
extraction on reference cube. Sky spectrum is estimated from bottom
quartile, and galaxy+sky from top quartile.
2008-09-24 Yannick Copin <ycopin@lyopc469>
* apps/extract_star/extract_star.py (extract_spec): do not apply
Laplacian filter prior to spectrum extraction (was causing Mantis
#1282).
2008-06-23 Yannick Copin <ycopin@lyopc469>
* apps/extract_star/extract_star.py: now calls external
libExtractStar.py.
* lib/libExtractStar.py: ADR and PSF utilities externalized from
extract_star.
2008-06-20 Yannick Copin <ycopin@ipnl.in2p3.fr>
* lib/pySNIFS_fit.py (model.fit_bfgs): similar to model.fit but
using S.optimize.fmin_l_bfgs_b as fit engine instead of
S.optimize.fmin_tnc (for testing purpose, much slower than TNC).
* lib/pySNIFS_fit.py (model.fit): debugging to accomodate scipy
0.6.0 (reversed output order, buggy auto-offset).
* setup.py (main): old extract_star2.py (2-gaussian PSF) not
installed anymore.
2008-05-26 Emmanuel Pecontal
* lib/pySNIFS.py : Allow to create a SNIFS_cube object from a 3D
fits file
* apps/extract_star : Test if the input datacube is a e3d or a
fits3d file
2008-05-19 Clément BUTON <cbuton@bigbrother.dhcp.lbnl.us>
* lib/pySNIFS_fit.py (model.fit): minor changes
* apps/extract_star/PSF_analysis.py: same point source extractor
than extract_star, except that all the PSF parameters can be
correlated or free. (based on extract_star 1.86)
* lib/pySNIFS_fit.py (model.fit): Fmin_tnc's outputs inversion
in the new version of scipy ('0.6.0').
2008-05-13 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py: long bug fighting session,
lots of leftovers...
* lib/pySNIFS_fit.py: rephrasing and optimizations.
2008-04-23 Yannick Copin <ycopin@ipnl.in2p3.fr>
* lib/pySNIFS.py (SNIFS_cube.WR_3d_fits): debugging.
* apps/extract_star/extract_star.py: new option '--keepmodel' to store
meta-slice model in 3D-cube.
2008-04-09 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py: new radial chi2 plot
(commented out).
* apps/extract_star/convert_3DPSF.py: ad-hoc convertor from PSF
3D-cube simulated by G.Rigaudier to Euro3D cube suitable for
extract_star (requires IFU python wrapper IFU_py_io).
* apps/extract_star/psf_sympy.py: toy script to check PSF model
and derivatives under sympy.
2008-03-11 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py: can now fit the PSF without
any background ('-S -1').
2008-03-07 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py: new cut for 'long exposure'
above 12s.
2008-03-06 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py: option '--supernova' now
discards completely 3D fit.
2008-03-04 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py: add FoV to ADR plot.
2008-03-03 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py (estimate_parangle): estimate
parallactic angle from header if 'PARANG' keyword is missing.
2008-02-19 yannick.copin <yannick.copin@laposte.net>
* apps/extract_star/extract_star.py: test positivity of alpha and
ellipticity after 3D fit.
2008-02-18 Clément Buton <cbuton@lyopc387.in2p3.fr>
* apps/extract_star/extract_star.py : add new option '-F' to
create a log file with adjusted parameters of final 3D fit.
2008-02-13 yannick.copin <yannick.copin@laposte.net>
* apps/extract_star/extract_star.py: new meta-slice selection
process from position at reference wavelength, updated graphics,
new option '--supernova' to fix ADR and position in 3D fit
(EXPERIMENTAL).
2008-02-11 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py (ExposurePSF.__init__): use
'PRESSURE' and 'TEMP' estimates from cube keywords.
* lib/pySNIFS.py (SNIFS_cube.__init__): self.e3d_data_header is
now a plain dictionary (instead of a list of items [(key,value)]).
2008-02-04 Clément Buton <cbuton@lyopc387.in2p3.fr>
* apps/extract_star/extract_star.py: Add new keywords and change
the log file.
2008-01-28 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py: debug initial guess for
polynomial background, use constant ref. lambda (5000 A).
2008-01-23 Yannick Copin <ycopin@ipnl.in2p3.fr>
* lib/pySNIFS.py (SNIFS_cube.__init__): debug i,j spx coords
computed from arcsec coords x,y.
2008-01-09 Clément Buton <cbuton@lyopc387.in2p3.fr>
* apps/extract_star/extract_star.py: Minor changes.
* lib/pySNIFS.py (fit_poly): Add a warning in fit_poly when number
of point is not sufficient to make a fit.
2008-01-07 Clément Buton <cbuton@lyopc387.in2p3.fr>
* apps/extract_star/extract_star.py (fit_slices): Fit a 2D
polynomial of degree skyDeg on the edge pixels of a given cube
slice as guess of the slice by slice fit.
2008-01-06 yannick.copin <yannick.copin@laposte.net>
* apps/extract_star/extract_star.py (extract_spec): catch
L.LinAlgError about singular matrix.
2007-12-20 Yannick Copin <ycopin@ipnl.in2p3.fr>
* lib/pySNIFS.py:
* lib/pySNIFS_plot.py: pylab-related methods extracted from
pySNIFS.py.
2007-12-05 Yannick Copin <ycopin@ipnl.in2p3.fr>
* lib/pySNIFS_fit.py (model.fit): reduced khi2 is khi2/DoF with
DoF = N - P, N=nb of points, P=nb of parameters.
(model.flat_param()): removed (was not working anyway...).
* apps/extract_star/extract_star.py: ADR angle theta is now
equivalent to parallactic angle.
2007-12-03 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py (polyfit_clip): add a maximum
nb of iterations (could oscillate indefinitely between two
configurations). Definite (hopefully) estimate of ADR angle
theta (= parallactic angle - 90deg).
2007-11-30 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py: extrapolate signal outside
FoV when aperture hits edge (only in 'aperture' method). Some
options renamed ('-d' to '-S', '-a' to '-A', '-e' to '-E').
2007-11-28 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py: handle negative sky, raise an
error when aperture hits FoV edges, optimal summation (using a
variance sigma-clipped linear fit).
2007-11-23 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py (comp_spec): added a
discussion about NNLS.
2007-11-22 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py: new estimate of ADR angle.
2007-11-21 Clément Buton <cbuton@lyopc387.in2p3.fr>
* apps/extract_star/extract_star.py: new option '-e/--ellDeg' to
choose polynomial degree of ellipticity.
2007-11-19 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py (comp_spec): on the way to
optimal extraction.
2007-11-16 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py: implement plain aperture
photometry (new option '-m/--method PSF|aperture'). Debug seeing
estimate.
2007-11-16 Clément Buton <cbuton@lyopc387.in2p3.fr>
* apps/extract_star/extract_star.py: build_sky_cube is now working
normally.
2007-11-15 Clément Buton <cbuton@lyopc387.in2p3.fr>
* apps/extract_star/extract_star.py: Add fwhm estimate.
2007-11-15 yannick.copin <yannick.copin@laposte.net>
* apps/extract_star/extract_star.py: debug of graphical
options. Modifications (mainly in comp_spec) in preparation to
aperture and optimal photometry.
2007-11-14 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py: make both short_ and
long_exposure_psf inherit from a ExposurePSF class. Normalize PSF
from within psf.comp (new keyword normed).
2007-11-14 Clément Buton <cbuton@lyopc387.in2p3.fr>
* lib/pySNIFS_fit.py (fnnls): replace any(x) by x.any().
* apps/extract_star/extract_star.py: Correct a bug related to the
polynomial of the sky. Make the code robust.
2007-11-13 Clément Buton <cbuton@lyopc387.in2p3.fr>
* apps/extract_star/extract_star.py: Correct minor bug.
2007-11-12 Yannick Copin <ycopin@ipnl.in2p3.fr>
* lib/pySNIFS_fit.py (model.check_grad): new keyword param.
* apps/extract_star/extract_star.py: force alpha to >0.
2007-11-09 Clément Buton <cbuton@lyopc387.in2p3.fr>
* apps/extract_star/extract_star.py: Correct determination of
theta_guest for the 3D fit.
2007-11-08 Clément Buton <cbuton@lyopc387.in2p3.fr>
* apps/extract_star/extract_star.py: Change relative lambda in
lambda/lambda_ref - 1.
2007-11-07 Clément Buton <cbuton@lyopc387.in2p3.fr>
* apps/extract_star/extract_star.py: add an option to choose the
polynomial degree of alpha.
2007-11-07 Yannick Copin <ycopin@ipnl.in2p3.fr>
* apps/extract_star/extract_star.py (comp_spec): check for
negative variance.
2007-11-06 Clément Buton <cbuton@lyopc387.in2p3.fr>