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

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
Jürgen Knödlseder
2 parents 48ad3334 26605dea
Showing 10 changed files with 106 additions and 23 deletions
ChangeLog
Makefile.am
cscripts/csinfo.py
cscripts/csspec.py
dev/00-ctools-deactivate.csh
dev/01-ctools-activate.csh
doc/source/admin/release_history/1.7.4.rst
doc/source/admin/release_history/index.rst
doc/source/develop/releasing/index.rst
doc/source/users/reference_manual/csspec.rst
@@ -16,6 +16,16 @@
         Add support of rectangular On/Off regions (#3248)
+2021-04-28
+
+        * Bug fix version 1.7.4 released
+        ================================
+
+        Add conda activation and deactivation scripts for csh (#3628)
+        Replace spectral model by file function in csspec (#3624)
+        Update csinfo script (#3623)
+
+
 2020-12-02
         * Bug fix version 1.7.3 released
@@ -33,9 +33,11 @@ pkgconfig_DATA = ctools.pc
 # Conda activate directory
 condaactivatedir = $(sysconfdir)/conda/activate.d
-condaactivate_DATA = dev/01-ctools-activate.sh
+condaactivate_DATA = dev/01-ctools-activate.sh \
+                     dev/01-ctools-activate.csh
 condadeactivatedir = $(sysconfdir)/conda/deactivate.d
-condadeactivate_DATA = dev/00-ctools-deactivate.sh
+condadeactivate_DATA = dev/00-ctools-deactivate.sh \
+                       dev/00-ctools-deactivate.csh
 # Manual pages to install
 man_MANS = 
@@ -55,6 +57,7 @@ EXTRA_DIST = README.md \
              doc/Doxyfile doc/source \
              dev/testreport.py \
              dev/01-ctools-activate.sh dev/00-ctools-deactivate.sh \
+             dev/01-ctools-activate.csh dev/00-ctools-deactivate.csh \
              dev/conda.recipe/build.sh \
              dev/conda.recipe/conda_build_config.yaml \
              dev/conda.recipe/meta.yaml.in
@@ -2,7 +2,7 @@
 # ==========================================================================
 # Print info about Gammalib / ctools to the console
 #
-# Copyright (C) 2015-2016 Christoph Deil
+# Copyright (C) 2015-2021 Christoph Deil
 #
 # This program is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
@@ -32,10 +32,13 @@ CTOOL_LIST = &quot;&quot;&quot;
    ctedispcube   Generates energy dispersion cube
    cterror       Calculates likelihood profile errors
    ctexpcube     Generates exposure cube
+   ctfindvar     Search for source variability
    ctlike        Performs maximum likelihood fitting
    ctmapcube     Generates a map cube
    ctmodel       Computes model counts cube
    ctobssim      Simulate CTA observations
+   ctphase       Computes the phase of each event
+   ctprob        Computes event probability for a given model
    ctpsfcube     Generates point spread function cube
    ctselect      Selects event data
    ctskymap      Generates sky map
@@ -47,20 +50,31 @@ CTOOL_LIST = &quot;&quot;&quot;
 # `doc/source/users/reference_manual/index.rst`
 # and needs to be manually updated and kept in sync
 CSCRIPT_LIST = """
+   csbkgmodel    Generates background model for 3D analysis
    cscaldb       Lists available instrument response functions
+   csebins       Generates energy boundaries for stacked analysis
    cslightcrv    Computes lightcurve
    csinfo        Checks ctools and GammaLib installations
    csmodelinfo   Shows model container content
    csmodelmerge  Merges several model containers into one file
+   csmodelselect Select models from model definition file
+   csmodelsois   Generate map cube from subset of models
    csobsdef      Generates observation definition file
    csobsinfo     Shows observation container content
+   csobsselect   Select observations from observation definition file
+   csphagen      Generates PHA, ARF, RMF files based on source/background regions
+   csphasecrv    Computes phase curve
    cspull        Generates pull distribution
    csresmap      Generates residual map
+   csresspec     Generates residual spectrum
+   csscs         Performs spectral component separation
    cssens        Computes CTA sensitivity
    csspec        Computes spectral points
+   cssrcdetect   Detects sources in sky map
    cstsdist      Generates TS distribution
+   cstsmapmerge  Merges slices from Test Statistic map computations
    cstsmapsplit  Creates commands to split the Test Statistic map computations
-   cstsmapmerge  Merges slices from Test Statistic map computations\n
+   csviscube     Computes visibility cube\n
    csobs2caldb   Creates a caldb entry from an input observation
    csroot2caldb  Creates a caldb entry from a ROOT performance file
    csiactdata    Shows information about IACT data available on the user machine
@@ -20,6 +20,7 @@
 # ==========================================================================
 import sys
 import math
+import tempfile    # Kludge for file function generation
 import gammalib
 import ctools
 from cscripts import mputils
@@ -367,6 +368,24 @@ class csspec(ctools.csobservation):
                                          ' Fixing "'+par.name()+'"')
                     par.fix()
+                # Kludge: convert spectral model into a file function
+                nbins       = self._ebounds.size()
+                num         = nbins * 20
+                energies    = gammalib.GEnergies(num, self._ebounds.emin(0),
+                                                      self._ebounds.emax(nbins-1))
+                _, filename = tempfile.mkstemp()
+                f = open(filename, 'w')
+                spectral    = model.spectral()
+                for energy in energies:
+                    value = spectral.eval(energy)
+                    f.write('%20.6f  %20e\n' % (energy.MeV(), value))
+                f.close()
+                spectral = gammalib.GModelSpectralFunc(filename, 1.0)
+                model.spectral(spectral)
+                self._log_string(gammalib.EXPLICIT, ' Converting spectral model '
+                                 'into file function via temporary file "%s"' %
+                                 filename)
+
                 # Free the normalisation parameter which is assumed to be
                 # the first spectral parameter
                 normpar = model.spectral()[0]
@@ -956,7 +975,7 @@ class csspec(ctools.csobservation):
                 result['dloglike']  = dlogL
                 result['logL']      = loglike
-            # Compute upper limit
+            # Compute upper flux limit
             if self['calc_ulim'].boolean():
                 # Logging information
@@ -1072,7 +1091,7 @@ class csspec(ctools.csobservation):
            (not self['dll_freenodes'].boolean()):
             for par in spectral:
                 par.fix()
-        
+
         # Re-compute the log-likelihood
         like.run()
         loglike = like.obs().logL()
@@ -1200,7 +1219,7 @@ class csspec(ctools.csobservation):
         table.append(dnde)
         table.append(TSvalues)
         table.append(Npred_values)
-        
+
         # Define the SED type
         table.card('SED_TYPE', 'norm,e2dnde,dnde,npred', 'SED type')
+#!/bin/csh
+
+unsetenv CTOOLS
+unsetenv CALDB
+#!/bin/csh
+
+setenv CTOOLS ${CONDA_PREFIX}
+source ${CTOOLS}/bin/ctools-init.csh
+unsetenv PYTHONPATH
+unsetenv LD_LIBRARY_PATH
+unsetenv DYLD_LIBRARY_PATH
+.. _1.7.4:
+
+ctools 1.7.4 release (28 April 2021)
+====================================
+
+Overview
+--------
+
+ctools 1.7.4 is a bug fix release for ctools release 1.7.
+
+The following bugs were fixed:
+
+* [`3628 <https://cta-redmine.irap.omp.eu/issues/3628>`_] -
+  Add conda activation and deactivation scripts for csh
+* [`3624 <https://cta-redmine.irap.omp.eu/issues/3624>`_] -
+  Replace spectral model by file function in :ref:`csspec`
+* [`3623 <https://cta-redmine.irap.omp.eu/issues/3623>`_] -
+  Update csinfo script
@@ -7,6 +7,7 @@ Release History
    :maxdepth: 1
    ctools 2.0 <2.0>
+   ctools 1.7.4 <1.7.4>
    ctools 1.7.3 <1.7.3>
    ctools 1.7.2 <1.7.2>
    ctools 1.7.1 <1.7.1>
@@ -21,4 +21,5 @@ To create a new ctools release you have to go through the following steps:
    * added unit tests for all new code
    * added a page about the software changes to the release history
    * updated the User documentation if necessary
+   * updated the csinfo script if necessary
@@ -20,19 +20,28 @@ flux limit that is particularly useful in case that the source is not
 significantly detected within a spectral bin (hidden parameter ``calc_ulim``).
 There are three fundamental methods to run the script depending on the value of
-the ``method`` parameter. If ``method=SLICE`` the energy interval defined by the
-``emin`` and ``emax`` parameters is divided into a number of energy bins and an
-independent maximum likelihood fit is performed in each of the energy bins. If
-``method=NODES`` the spectral model will be replaced by a node function that will
-be fit to all data. Alternatively, if ``method=BINS`` the spectral model will be
-replaced by a bin function that will be fit to all data. While with the ``NODES``
-method the spectral points are in general not statistically independent, the
-``BINS`` method assures that the spectral points are statistically independent.
-The ``NODES`` and ``BINS`` methods are particularly useful if data from instruments
-other than CTA should be analyses, such as data from Fermi/LAT, COMPTEL or
-INTEGRAL/SPI. By default, ``method`` is set to ``AUTO`` which will automatically
-select the method based on the input data. For CTA-only observations ``SLICE`` will
-be used, otherwise ``NODES`` will be used.
+the ``method`` parameter, ``SLICE``, ``BINS`` and ``NODES``.
+
+If ``method=SLICE`` the energy interval defined by the ``emin`` and ``emax``
+parameters is divided into a number of energy bins and an independent maximum
+likelihood fit is performed in each of the energy bins. In order to cope with
+all kinds of spectral models, including composite spectra, input spectrum will
+be converted into a file function, with the normalisation of the file function
+being the fit parameter for each energy bin. This implies that spectral
+components are merged into a single function using the model parameters that
+are specified in the input model.
+
+If ``method=BINS`` the spectral model will be replaced by a bin function that
+will be fit to all data, with ``method=NODES`` the spectral model will be replaced
+by a node function. The advantage of ``BINS`` over ``NODES`` is that with ``BINS``
+the spectral flux points are statistically independent, while with ``NODES`` the
+underlying spectral model connects spectral flux points using a piecewise power
+law. Both methods are particularly useful if non-CTA data should be fitted such
+as data from Fermi/LAT, CGRO/COMPTEL or INTEGRAL/SPI.
+
+By default, ``method`` is set to ``AUTO`` which will automatically select the
+method based on the input data. For CTA-only observations ``SLICE`` will be used,
+otherwise ``NODES`` will be used.
 The spectral binning is either defined by a FITS file containing the energy
 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
 ``calc_ts=yes``), the upper flux limit (option ``calc_ulim=yes``) and the
 predicted number of events (only for unbinned data).
-.. warning::
-   The upper limit computation is not yet implemented for the ``NODES`` method.
-
 General parameters
 ------------------