Remove code duplication is cslightcrv and csphasecrv

Jürgen Knödlseder
1 parent 72aad6b0
Showing 4 changed files with 116 additions and 72 deletions
cscripts/cslightcrv.py
cscripts/csphasecrv.py
cscripts/ioutils.py
sonar-project.properties
@@ -22,6 +22,7 @@ import sys
 import gammalib
 import ctools
 from cscripts import obsutils
+from cscripts import ioutils
  
  
 # ================ #
@@ -281,52 +282,24 @@ class cslightcrv(ctools.cscript):
         table = gammalib.GFitsBinTable(nrows)
         table.extname('LIGHTCURVE')
  
-        # Append time columns "MJD" and "e_MJD"
-        mjd   = gammalib.GFitsTableDoubleCol('MJD', nrows)
-        e_mjd = gammalib.GFitsTableDoubleCol('e_MJD', nrows)
-        mjd.unit('days')
-        e_mjd.unit('days')
-        for i, result in enumerate(results):
-            mjd[i]   = result['mjd']
-            e_mjd[i] = result['e_mjd']
-        table.append(mjd)
-        table.append(e_mjd)
-
-        # Create parameter columns
-        for par in self._obs.models()[self._srcname]:
-            if par.is_free():
-                name   = par.name()
-                e_name = 'e_'+par.name()
-                col    = gammalib.GFitsTableDoubleCol(name, nrows)
-                e_col  = gammalib.GFitsTableDoubleCol(e_name, nrows)
-                col.unit(par.unit())
-                e_col.unit(par.unit())
-                for i, result in enumerate(results):
-                    col[i]   = result['values'][name]
-                    e_col[i] = result['values'][e_name]
-                table.append(col)
-                table.append(e_col)
+        # Append time columns
+        ioutils.append_result_column(table, results, 'MJD',   'days', 'mjd')
+        ioutils.append_result_column(table, results, 'e_MJD', 'days', 'e_mjd')
+
+        # Append parameter columns
+        ioutils.append_model_par_column(table, self._obs.models()[self._srcname],
+                                        results)
  
         # Append Test Statistic column "TS"
-        ts = gammalib.GFitsTableDoubleCol('TS', nrows)
-        for i, result in enumerate(results):
-            ts[i] = result['ts']
-        table.append(ts)
-
-        # Append upper limit column "UpperLimit"
-        ul_diff  = gammalib.GFitsTableDoubleCol('DiffUpperLimit', nrows)
-        ul_flux  = gammalib.GFitsTableDoubleCol('FluxUpperLimit', nrows)
-        ul_eflux = gammalib.GFitsTableDoubleCol('EFluxUpperLimit', nrows)
-        ul_diff.unit('ph/cm2/s/MeV')
-        ul_flux.unit('ph/cm2/s')
-        ul_eflux.unit('erg/cm2/s')
-        for i, result in enumerate(results):
-            ul_diff[i]  = result['ul_diff']
-            ul_flux[i]  = result['ul_flux']
-            ul_eflux[i] = result['ul_eflux']
-        table.append(ul_diff)
-        table.append(ul_flux)
-        table.append(ul_eflux)
+        ioutils.append_result_column(table, results, 'TS', '', 'ts')
+
+        # Append upper limit columns
+        ioutils.append_result_column(table, results, 'DiffUpperLimit',
+                                     'ph/cm2/s/MeV', 'ul_diff')
+        ioutils.append_result_column(table, results, 'FluxUpperLimit',
+                                     'ph/cm2/s', 'ul_flux')
+        ioutils.append_result_column(table, results, 'EFluxUpperLimit',
+                                     'erg/cm2/s', 'ul_eflux')
  
         # Return table
         return table
@@ -22,6 +22,7 @@ import sys
 import gammalib
 import ctools
 from cscripts import obsutils
+from cscripts import ioutils
  
  
 # ================ #
@@ -183,7 +184,7 @@ class csphasecrv(ctools.cscript):
  
     def _create_fits_table(self, results):
         """
-        Creates FITS binary table containing light curve results
+        Creates FITS binary table containing phase curve results
  
         Parameters
         ----------
@@ -193,7 +194,7 @@ class csphasecrv(ctools.cscript):
         Returns
         -------
         table : `~gammalib.GFitsBinTable`
-            FITS binary table containing light curve
+            FITS binary table containing phase curve
         """
         # Determine number of rows in FITS table
         nrows = len(results)
@@ -202,29 +203,13 @@ class csphasecrv(ctools.cscript):
         table = gammalib.GFitsBinTable(nrows)
         table.extname('PHASECURVE')
  
-        # Append phase columns "PHASE_MIN" and "PHASE_MAX"
-        phmin = gammalib.GFitsTableDoubleCol('PHASE_MIN', nrows)
-        phmax = gammalib.GFitsTableDoubleCol('PHASE_MAX', nrows)
-        for i, result in enumerate(results):
-            phmin[i] = result['phmin']
-            phmax[i] = result['phmax']
-        table.append(phmin)
-        table.append(phmax)
+        # Append phase columns
+        ioutils.append_result_column(table, results, 'PHASE_MIN', '', 'phmin')
+        ioutils.append_result_column(table, results, 'PHASE_MAX', '', 'phmax')
  
-        # Create parameter columns
-        for par in self._obs.models()[self._srcname]:
-            if par.is_free():
-                name   = par.name()
-                e_name = 'e_'+par.name()
-                col    = gammalib.GFitsTableDoubleCol(name, nrows)
-                e_col  = gammalib.GFitsTableDoubleCol(e_name, nrows)
-                col.unit(par.unit())
-                e_col.unit(par.unit())
-                for i, result in enumerate(results):
-                    col[i]   = result['values'][name]
-                    e_col[i] = result['values'][e_name]
-                table.append(col)
-                table.append(e_col)
+        # Append parameter columns
+        ioutils.append_model_par_column(table, self._obs.models()[self._srcname],
+                                        results)
  
         # Return table
         return table
@@ -401,7 +386,7 @@ class csphasecrv(ctools.cscript):
         # Create FITS file
         self._create_fits()
  
-        # Optionally publish light curve
+        # Optionally publish phase curve
         if self['publish'].boolean():
             self.publish()
  
@@ -433,7 +418,7 @@ class csphasecrv(ctools.cscript):
         # Write header
         self._log_header1(gammalib.TERSE, 'Publish phase curve')
  
-        # Continue only if light curve is valid
+        # Continue only if phase curve is valid
         if self._fits.contains('PHASECURVE'):
  
             # Set default name is user name is empty
 # ==========================================================================
 # Utility functions for input and output
 #
-# Copyright (C) 2016 Juergen Knoedlseder
+# Copyright (C) 2016-2017 Juergen Knoedlseder
 #
 # 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
@@ -193,3 +193,89 @@ def get_args_options(options, usage):
  
     # Return arguments and options
     return args, options
+
+
+# =========================================== #
+# Append model parameter column to FITS table #
+# =========================================== #
+def append_result_column(table, results, name, unit, key):
+    """
+    Append result column to FITS table
+
+    Parameters
+    ----------
+    table : `~gammalib.GFitsTable`
+        FITS table
+    results : list of dict
+        Parameter values
+    name : str
+        Column name
+    unit : str
+        Column unit
+    key : str
+        Result key
+    """
+    # Determine number of rows in FITS table
+    nrows = len(results)
+
+    # Allocate double precision column and set units
+    col = gammalib.GFitsTableDoubleCol(name, nrows)
+    col.unit(unit)
+
+    # Fill results in columns
+    for i, result in enumerate(results):
+        col[i] = result[key]
+
+    # Append column to table
+    table.append(col)
+
+    # Return
+    return
+
+
+# =========================================== #
+# Append model parameter column to FITS table #
+# =========================================== #
+def append_model_par_column(table, model, results):
+    """
+    Append model parameter column to FITS table
+
+    Parameters
+    ----------
+    table : `~gammalib.GFitsTable`
+        FITS table
+    model : `~gammalib.GModel`
+        Model
+    results : list of dict
+        Parameter values
+    """
+    # Determine number of rows in FITS table
+    nrows = len(results)
+
+    # Loop over all parameters in model
+    for par in model:
+
+        # Append parameter column only if model parameter is free
+        if par.is_free():
+
+            # Set column names
+            name   = par.name()
+            e_name = 'e_'+par.name()
+
+            # Allocate double precision columns and set units
+            col    = gammalib.GFitsTableDoubleCol(name, nrows)
+            e_col  = gammalib.GFitsTableDoubleCol(e_name, nrows)
+            col.unit(par.unit())
+            e_col.unit(par.unit())
+
+            # Fill results in columns
+            for i, result in enumerate(results):
+                col[i]   = result['values'][name]
+                e_col[i] = result['values'][e_name]
+
+            # Append columns to table
+            table.append(col)
+            table.append(e_col)
+
+    # Return
+    return
@@ -21,7 +21,7 @@ sonar.cxx.missingIncludeWarnings=False
  
 # Exclusions
 sonar.exclusions=cscripts/tests/**,pyext/build/**,pyext/ctools/tools.py,pyext/ctools/*_wrap.cpp,pyext/ctools/tests/**,dev/**,doc/**,test/dev/**
-sonar.coverage.exclusions=test/science_verification.py,test/test_examples.py
+sonar.coverage.exclusions=test/science_verification.py,test/test_examples.py,pyext/setup.py
 sonar.cpd.exclusions=examples/**,test/**,pyext/ctools/tools.py
  
 # C++ configuration