Iftach Sadeh / ctools

Commit 358cc09746a1e3dab4a3f54f314f2dc841f4aa7f

Authored by Jürgen Knödlseder
2 parents 48ad3334 26605dea

Merge branch 'master' into devel 

# Conflicts:
#	ChangeLog
#	NEWS
#	README.md
#	configure.ac
#	cscripts/csspec.py
#	doc/Doxyfile
#	doc/source/admin/download.rst
#	doc/source/admin/release_history/index.rst
#	doc/source/conf.py
#	doc/source/users/reference_manual/csspec.rst
#	sonar-project.properties
Inline Side-by-side
Showing 10 changed files with 106 additions and 23 deletions
ChangeLog
  View file @358cc09
... ... @@ -16,6 +16,16 @@
16 16 Add support of rectangular On/Off regions (#3248)
17 17  
18 18  
  19 +2021-04-28
  20 +
  21 + * Bug fix version 1.7.4 released
  22 + ================================
  23 +
  24 + Add conda activation and deactivation scripts for csh (#3628)
  25 + Replace spectral model by file function in csspec (#3624)
  26 + Update csinfo script (#3623)
  27 +
  28 +
19 29 2020-12-02
20 30  
21 31 * Bug fix version 1.7.3 released
... ...
Makefile.am
  View file @358cc09
... ... @@ -33,9 +33,11 @@ pkgconfig_DATA = ctools.pc
33 33  
34 34 # Conda activate directory
35 35 condaactivatedir = $(sysconfdir)/conda/activate.d
36   -condaactivate_DATA = dev/01-ctools-activate.sh
  36 +condaactivate_DATA = dev/01-ctools-activate.sh \
  37 + dev/01-ctools-activate.csh
37 38 condadeactivatedir = $(sysconfdir)/conda/deactivate.d
38   -condadeactivate_DATA = dev/00-ctools-deactivate.sh
  39 +condadeactivate_DATA = dev/00-ctools-deactivate.sh \
  40 + dev/00-ctools-deactivate.csh
39 41  
40 42 # Manual pages to install
41 43 man_MANS =
... ... @@ -55,6 +57,7 @@ EXTRA_DIST = README.md \
55 57 doc/Doxyfile doc/source \
56 58 dev/testreport.py \
57 59 dev/01-ctools-activate.sh dev/00-ctools-deactivate.sh \
  60 + dev/01-ctools-activate.csh dev/00-ctools-deactivate.csh \
58 61 dev/conda.recipe/build.sh \
59 62 dev/conda.recipe/conda_build_config.yaml \
60 63 dev/conda.recipe/meta.yaml.in
... ...
cscripts/csinfo.py
  View file @358cc09
... ... @@ -2,7 +2,7 @@
2 2 # ==========================================================================
3 3 # Print info about Gammalib / ctools to the console
4 4 #
5   -# Copyright (C) 2015-2016 Christoph Deil
  5 +# Copyright (C) 2015-2021 Christoph Deil
6 6 #
7 7 # This program is free software: you can redistribute it and/or modify
8 8 # it under the terms of the GNU General Public License as published by
... ... @@ -32,10 +32,13 @@ CTOOL_LIST = """
32 32 ctedispcube Generates energy dispersion cube
33 33 cterror Calculates likelihood profile errors
34 34 ctexpcube Generates exposure cube
  35 + ctfindvar Search for source variability
35 36 ctlike Performs maximum likelihood fitting
36 37 ctmapcube Generates a map cube
37 38 ctmodel Computes model counts cube
38 39 ctobssim Simulate CTA observations
  40 + ctphase Computes the phase of each event
  41 + ctprob Computes event probability for a given model
39 42 ctpsfcube Generates point spread function cube
40 43 ctselect Selects event data
41 44 ctskymap Generates sky map
... ... @@ -47,20 +50,31 @@ CTOOL_LIST = """
47 50 # `doc/source/users/reference_manual/index.rst`
48 51 # and needs to be manually updated and kept in sync
49 52 CSCRIPT_LIST = """
  53 + csbkgmodel Generates background model for 3D analysis
50 54 cscaldb Lists available instrument response functions
  55 + csebins Generates energy boundaries for stacked analysis
51 56 cslightcrv Computes lightcurve
52 57 csinfo Checks ctools and GammaLib installations
53 58 csmodelinfo Shows model container content
54 59 csmodelmerge Merges several model containers into one file
  60 + csmodelselect Select models from model definition file
  61 + csmodelsois Generate map cube from subset of models
55 62 csobsdef Generates observation definition file
56 63 csobsinfo Shows observation container content
  64 + csobsselect Select observations from observation definition file
  65 + csphagen Generates PHA, ARF, RMF files based on source/background regions
  66 + csphasecrv Computes phase curve
57 67 cspull Generates pull distribution
58 68 csresmap Generates residual map
  69 + csresspec Generates residual spectrum
  70 + csscs Performs spectral component separation
59 71 cssens Computes CTA sensitivity
60 72 csspec Computes spectral points
  73 + cssrcdetect Detects sources in sky map
61 74 cstsdist Generates TS distribution
  75 + cstsmapmerge Merges slices from Test Statistic map computations
62 76 cstsmapsplit Creates commands to split the Test Statistic map computations
63   - cstsmapmerge Merges slices from Test Statistic map computations\n
  77 + csviscube Computes visibility cube\n
64 78 csobs2caldb Creates a caldb entry from an input observation
65 79 csroot2caldb Creates a caldb entry from a ROOT performance file
66 80 csiactdata Shows information about IACT data available on the user machine
... ...
cscripts/csspec.py
  View file @358cc09
... ... @@ -20,6 +20,7 @@
20 20 # ==========================================================================
21 21 import sys
22 22 import math
  23 +import tempfile # Kludge for file function generation
23 24 import gammalib
24 25 import ctools
25 26 from cscripts import mputils
... ... @@ -367,6 +368,24 @@ class csspec(ctools.csobservation):
367 368 ' Fixing "'+par.name()+'"')
368 369 par.fix()
369 370  
  371 + # Kludge: convert spectral model into a file function
  372 + nbins = self._ebounds.size()
  373 + num = nbins * 20
  374 + energies = gammalib.GEnergies(num, self._ebounds.emin(0),
  375 + self._ebounds.emax(nbins-1))
  376 + _, filename = tempfile.mkstemp()
  377 + f = open(filename, 'w')
  378 + spectral = model.spectral()
  379 + for energy in energies:
  380 + value = spectral.eval(energy)
  381 + f.write('%20.6f %20e\n' % (energy.MeV(), value))
  382 + f.close()
  383 + spectral = gammalib.GModelSpectralFunc(filename, 1.0)
  384 + model.spectral(spectral)
  385 + self._log_string(gammalib.EXPLICIT, ' Converting spectral model '
  386 + 'into file function via temporary file "%s"' %
  387 + filename)
  388 +
370 389 # Free the normalisation parameter which is assumed to be
371 390 # the first spectral parameter
372 391 normpar = model.spectral()[0]
... ... @@ -956,7 +975,7 @@ class csspec(ctools.csobservation):
956 975 result['dloglike'] = dlogL
957 976 result['logL'] = loglike
958 977  
959   - # Compute upper limit
  978 + # Compute upper flux limit
960 979 if self['calc_ulim'].boolean():
961 980  
962 981 # Logging information
... ... @@ -1072,7 +1091,7 @@ class csspec(ctools.csobservation):
1072 1091 (not self['dll_freenodes'].boolean()):
1073 1092 for par in spectral:
1074 1093 par.fix()
1075   -
  1094 +
1076 1095 # Re-compute the log-likelihood
1077 1096 like.run()
1078 1097 loglike = like.obs().logL()
... ... @@ -1200,7 +1219,7 @@ class csspec(ctools.csobservation):
1200 1219 table.append(dnde)
1201 1220 table.append(TSvalues)
1202 1221 table.append(Npred_values)
1203   -
  1222 +
1204 1223 # Define the SED type
1205 1224 table.card('SED_TYPE', 'norm,e2dnde,dnde,npred', 'SED type')
1206 1225  
... ...
dev/00-ctools-deactivate.csh 0 → 100644
  View file @358cc09
  1 +#!/bin/csh
  2 +
  3 +unsetenv CTOOLS
  4 +unsetenv CALDB
... ...
dev/01-ctools-activate.csh 0 → 100644
  View file @358cc09
  1 +#!/bin/csh
  2 +
  3 +setenv CTOOLS ${CONDA_PREFIX}
  4 +source ${CTOOLS}/bin/ctools-init.csh
  5 +unsetenv PYTHONPATH
  6 +unsetenv LD_LIBRARY_PATH
  7 +unsetenv DYLD_LIBRARY_PATH
... ...
doc/source/admin/release_history/1.7.4.rst 0 → 100644
  View file @358cc09
  1 +.. _1.7.4:
  2 +
  3 +ctools 1.7.4 release (28 April 2021)
  4 +====================================
  5 +
  6 +Overview
  7 +--------
  8 +
  9 +ctools 1.7.4 is a bug fix release for ctools release 1.7.
  10 +
  11 +The following bugs were fixed:
  12 +
  13 +* [`3628 <https://cta-redmine.irap.omp.eu/issues/3628>`_] -
  14 + Add conda activation and deactivation scripts for csh
  15 +* [`3624 <https://cta-redmine.irap.omp.eu/issues/3624>`_] -
  16 + Replace spectral model by file function in :ref:`csspec`
  17 +* [`3623 <https://cta-redmine.irap.omp.eu/issues/3623>`_] -
  18 + Update csinfo script
... ...
doc/source/admin/release_history/index.rst
  View file @358cc09
... ... @@ -7,6 +7,7 @@ Release History
7 7 :maxdepth: 1
8 8  
9 9 ctools 2.0 <2.0>
  10 + ctools 1.7.4 <1.7.4>
10 11 ctools 1.7.3 <1.7.3>
11 12 ctools 1.7.2 <1.7.2>
12 13 ctools 1.7.1 <1.7.1>
... ...
doc/source/develop/releasing/index.rst
  View file @358cc09
... ... @@ -21,4 +21,5 @@ To create a new ctools release you have to go through the following steps:
21 21 * added unit tests for all new code
22 22 * added a page about the software changes to the release history
23 23 * updated the User documentation if necessary
  24 + * updated the csinfo script if necessary
24 25  
... ...
doc/source/users/reference_manual/csspec.rst
  View file @358cc09
... ... @@ -20,19 +20,28 @@ flux limit that is particularly useful in case that the source is not
20 20 significantly detected within a spectral bin (hidden parameter ``calc_ulim``).
21 21  
22 22 There are three fundamental methods to run the script depending on the value of
23   -the ``method`` parameter. If ``method=SLICE`` the energy interval defined by the
24   -``emin`` and ``emax`` parameters is divided into a number of energy bins and an
25   -independent maximum likelihood fit is performed in each of the energy bins. If
26   -``method=NODES`` the spectral model will be replaced by a node function that will
27   -be fit to all data. Alternatively, if ``method=BINS`` the spectral model will be
28   -replaced by a bin function that will be fit to all data. While with the ``NODES``
29   -method the spectral points are in general not statistically independent, the
30   -``BINS`` method assures that the spectral points are statistically independent.
31   -The ``NODES`` and ``BINS`` methods are particularly useful if data from instruments
32   -other than CTA should be analyses, such as data from Fermi/LAT, COMPTEL or
33   -INTEGRAL/SPI. By default, ``method`` is set to ``AUTO`` which will automatically
34   -select the method based on the input data. For CTA-only observations ``SLICE`` will
35   -be used, otherwise ``NODES`` will be used.
  23 +the ``method`` parameter, ``SLICE``, ``BINS`` and ``NODES``.
  24 +
  25 +If ``method=SLICE`` the energy interval defined by the ``emin`` and ``emax``
  26 +parameters is divided into a number of energy bins and an independent maximum
  27 +likelihood fit is performed in each of the energy bins. In order to cope with
  28 +all kinds of spectral models, including composite spectra, input spectrum will
  29 +be converted into a file function, with the normalisation of the file function
  30 +being the fit parameter for each energy bin. This implies that spectral
  31 +components are merged into a single function using the model parameters that
  32 +are specified in the input model.
  33 +
  34 +If ``method=BINS`` the spectral model will be replaced by a bin function that
  35 +will be fit to all data, with ``method=NODES`` the spectral model will be replaced
  36 +by a node function. The advantage of ``BINS`` over ``NODES`` is that with ``BINS``
  37 +the spectral flux points are statistically independent, while with ``NODES`` the
  38 +underlying spectral model connects spectral flux points using a piecewise power
  39 +law. Both methods are particularly useful if non-CTA data should be fitted such
  40 +as data from Fermi/LAT, CGRO/COMPTEL or INTEGRAL/SPI.
  41 +
  42 +By default, ``method`` is set to ``AUTO`` which will automatically select the
  43 +method based on the input data. For CTA-only observations ``SLICE`` will be used,
  44 +otherwise ``NODES`` will be used.
36 45  
37 46 The spectral binning is either defined by a FITS file containing the energy
38 47 boundaries of each bin (option ``ebinalg=FILE``) or as ``enumbins`` bins spread
... ... @@ -59,9 +68,6 @@ the fitted flux and flux error, the Test Statistics value (option
59 68 ``calc_ts=yes``), the upper flux limit (option ``calc_ulim=yes``) and the
60 69 predicted number of events (only for unbinned data).
61 70  
62   -.. warning::
63   - The upper limit computation is not yet implemented for the ``NODES`` method.
64   -
65 71  
66 72 General parameters
67 73 ------------------
... ...