Merge in code

Jürgen Knödlseder
1 parent 86ba546b
Showing 4 changed files with 24 additions and 24 deletions
cscripts/csspec.par
cscripts/csspec.py
doc/source/users/reference_manual/csspec.rst
examples/show_spectrum.py
@@ -31,19 +31,19 @@ outfile,   f, a, spectrum.fits,,, &quot;Output spectrum file&quot;
 #
 # Script parameters
 #==================
-method,    s, a, AUTO,SLICE|NODES|AUTO,, "Spectrum generation method"
-ebinalg,   s, a, LOG,FILE|LIN|LOG,, "Algorithm for defining energy bins"
-emin,      r, a, 0.1,,, "Start value for first energy bin in TeV"
-emax,      r, a, 100.0,,, "Stop value for last energy bin in TeV"
-enumbins,  i, a, 20,1,200, "Number of energy bins"
-ebinfile,  f, a, NONE,,, "Name of the file containing the energy bin definition"
-statistic, s, h, DEFAULT,DEFAULT|CSTAT|WSTAT|CHI2,, "Optimization statistic"
-calc_ts,   b, h, yes,,, "Compute TS value in each bin"
-calc_ulim, b, h, yes,,, "Compute upper limit in each bin"
-fix_srcs,  b, h, yes,,, "Fix other skymodel parameters"
-fix_bkg,   b, h, no,,, "Fix background parameters"
-dll_sigstep, r, h, 0,0,100, "Step size in standard deviations for log-like profiles"
-dll_sigmax,  r, h, 5,1,100, "Maximum number of standard deviations for log-like profiles"
+method,        s, a, AUTO,SLICE|NODES|AUTO,, "Spectrum generation method"
+ebinalg,       s, a, LOG,FILE|LIN|LOG,, "Algorithm for defining energy bins"
+emin,          r, a, 0.1,,, "Start value for first energy bin in TeV"
+emax,          r, a, 100.0,,, "Stop value for last energy bin in TeV"
+enumbins,      i, a, 20,1,200, "Number of energy bins"
+ebinfile,      f, a, NONE,,, "Name of the file containing the energy bin definition"
+statistic,     s, h, DEFAULT,DEFAULT|CSTAT|WSTAT|CHI2,, "Optimization statistic"
+calc_ts,       b, h, yes,,, "Compute TS value in each bin"
+calc_ulim,     b, h, yes,,, "Compute upper limit in each bin"
+fix_srcs,      b, h, yes,,, "Fix other skymodel parameters"
+fix_bkg,       b, h, no,,, "Fix background parameters"
+dll_sigstep,   r, h, 0.0,0.0,100.0, "Step size in standard deviations for log-like profiles"
+dll_sigmax,    r, h, 5.0,1.0,100.0, "Maximum number of standard deviations for log-like profiles"
 dll_freenodes, b, h, no,,, "Free nodes not being fit when computing log-like profiles"
 #
@@ -2,7 +2,7 @@
 # ==========================================================================
 # Generates a spectrum.
 #
-# Copyright (C) 2014-2019 Michael Mayer
+# Copyright (C) 2014-2020 Michael Mayer
 #
 # 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
@@ -1031,7 +1031,6 @@ class csspec(ctools.csobservation):
             # from [10^-24, 10^-14] or [norm, 10^-14] whichever is broader
             log_start = -24 if (log_norm > -24) else log_norm
             log_step = (-14 - log_start) / (sigsteps-1)
-        
         norm_vals = [10 ** (log_start + i*log_step) for i in range(sigsteps)]
         # Loop through normalizations
@@ -1042,14 +1041,15 @@ class csspec(ctools.csobservation):
             # Re-run the fit
             like.run()
-            
+
             # Store dlikelihood & norm
             dloglike.append(loglike - like.obs().logL())
             if self._method == 'SLICE':
                 norm_scan.append(spectral.eval(elogmean))
             else:
                 norm_scan.append(new_norm)
-            
+
+        # Return
         return (norm_scan, dloglike, -loglike)
     def _create_fits(self, results):
@@ -145,17 +145,17 @@ General parameters
 ``(fix_bkg = no) [boolean]``
     Fix background model parameters?
-``(dll_sigstep) [real]``
+``(dll_sigstep = 0) [real]``
     Step size in standard deviations for log-like profiles. Note this value 
     determines the number of steps to use.
-``(dll_sigmax) [real]``
+``(dll_sigmax = 5.0) [real]``
     Maximum number of standard deviations for log-like profiles. The final number
     of bins generated in the likelihood profile will be:
        2*(dll_sigmax/dll_sigstep) + 1
     ensuring that the central flux will always be evaluated.
-``(dll_freenodes) [boolean]``
+``(dll_freenodes = no) [boolean]``
     Free nodes not being fit when computing log-like profiles. This parameter
     only has an effect if 'method=NODES' is set.
@@ -2,7 +2,7 @@
 # ==========================================================================
 # Display spectrum generated by csspec
 #
-# Copyright (C) 2015-2019 Juergen Knoedlseder
+# Copyright (C) 2015-2020 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
@@ -107,13 +107,13 @@ def get_spectrum_fits(fits):
     # Determine if we can load the delta-log-likelihood profiles
     has_sedtype = table.has_card('SED_TYPE')
-    load_dll = False
+    load_dll    = False
     if has_sedtype:
         seds = table.card('SED_TYPE').string().split(',')
         # Load likelhood columns if present
         if seds[0] == 'likelihood':
-            load_dll = True
+            load_dll    = True
             c_loglike   = table['loglike']
             c_norm_scan = table['norm_scan']
             c_dll_scan  = table['dloglike_scan']
@@ -150,7 +150,7 @@ def get_spectrum_fits(fits):
         spec['dll_scan']    = np.zeros((nrows, c_norm_scan.elements(0)))
         for row in range(nrows):
-            loglike   = c_loglike.real(row)
+            loglike = c_loglike.real(row)
             spec['loglike'].append(loglike)
             spec['engs_scan'].append(c_energy.real(row) - c_ed.real(row))
             for col in range(c_norm_scan.elements(row)):