Bug correction in multi-components fitting

camel.py

@@ -854,6 +854,7 @@ def buildmaps(conf, cube, hdr, var=None, plot=False, debug=False, free_ratio=Fal
     contind = [i for i in range(len(parinfo), len(parinfo) + conf['DGCTNUM'] + 1)]
     for i in range(conf['DGCTNUM'] + 1):
         parinfo.append(copy.deepcopy(parbase))
+        components = np.append(components, -1)
     params = np.zeros(len(parinfo), dtype='>f4')
     for i in range(len(parinfo)):
         params[i] = parinfo[i]['value']
@@ -901,10 +902,10 @@ def buildmaps(conf, cube, hdr, var=None, plot=False, debug=False, free_ratio=Fal
             #Parameters initialisation
             p = np.copy(params)
             
-            #Line intensity initisalisation
+            #Line intensity initialisation
             for i in intind:
                 if parinfo[i]['fixed'] == 0:
-                    p[i] = 5 * std * 10 ** (- components[i] + 1)
+                    p[i] = 5 * std * 10 ** (- components[i] + 1.)
 
             #for i in range(els.index):
                 #if parinfo[2 * els.index + i]['fixed'] == 0:  p[2 * els.index + i] = 2 * std
@@ -1207,6 +1208,8 @@ def camel(filename, plot=False, debug=False, free_ratio=False, multi_comp=1, mul
     #Reading of configuration file
     logger.info("Reading configuration file " + filename)
     try:
+        if filename == '':
+            filename = None
         conf = readconfig(filename, config)
     except:
         logger.info("Configuration file problem")

create_config.py

@@ -33,7 +33,7 @@ def create_config(path, cubefile, varfile, catfile, lines, suffixeout, commonw=T
     lines: string
         indicates which lines to fit: 'ha' for Halpha, 'hb' for Hbeta, 'hg' for Hgamma, 'hd' for Hdelta, 'n2' for NII6548 and NII6583, 's2' for SII6716 and SII6731, 'o2' for OII, 'o3' for OIII4959 and OIII5007. The concatenation of several lines is possible to fit several lines.
     suffixeout: string
-        suffixe for the output configartion file name
+        suffixe for the output configuration file name
     commonw: bool
         specifies if a common width has to be used for the various lines
     dz: float
@@ -53,13 +53,13 @@ def create_config(path, cubefile, varfile, catfile, lines, suffixeout, commonw=T
     sclip: int
         sigma clipping threshold (sclip * sigma) to clean the cube
     xyclip: int
-        size of the local bos for the sigma-clipping (in pixels)
+        size of the local box for the sigma-clipping (in pixels)
     nclip: int
-        number of pass for the sigma-clipping
+        number of passes for the sigma-clipping
     wsmooth: int
         spectral smooth method
     ssmooth: float
-        gaussian spatial smooth FWHM in pixels
+        Gaussian spatial smooth FWHM in pixels
     '''
     
     #ipdb.set_trace()
@@ -174,6 +174,8 @@ def create_config(path, cubefile, varfile, catfile, lines, suffixeout, commonw=T
             fo.write('REDMIN  = ' + str(line['Z'] - dz) + ' / minimum redshift\n')
             fo.write('REDMAX  = ' + str(line['Z'] + dz) + ' / maximum redshift\n')
         else:
+            fo.write('REDMIN  = ' + str(line['Z'] - 0.1) + ' / minimum redshift\n')
+            fo.write('REDMAX  = ' + str(line['Z'] + 0.1) + ' / maximum redshift\n')
             logger.error('dz must be not None and non-zero')
         
         fo.write('INITW   = ' + str(initw) + ' / initial linewidth in km/s during the line fitting process \n')    

samel.py

@@ -654,7 +654,7 @@ def buildmaps(conf, data, hdr, var=None, plot=False, debug=False, free_ratio=Fal
         linewaves = np.append(linewaves, linewave)
         components = np.append(components, np.ones(len(parinfom), dtype='i') * (comp + 1))
 
-    #Continuum parametres
+    #Continuum parameters
     parbase = {'value': 0., 'fixed': 0, 'limited': [0, 0], 'limits': [0., 0.], 'tied': '', 'mpmaxstep': 0, 'mpminstep': 0, 'parname': ''}
     if conf['DGCTNUM'] == -1:  # case without continuum
         conf['DGCTNUM'] = 0
@@ -665,6 +665,7 @@ def buildmaps(conf, data, hdr, var=None, plot=False, debug=False, free_ratio=Fal
     contind = [i for i in range(len(parinfo), len(parinfo) + conf['DGCTNUM'] + 1)]
     for i in range(conf['DGCTNUM'] + 1):
         parinfo.append(copy.deepcopy(parbase))
+        components = np.append(components, -1)
     params = np.zeros(len(parinfo), dtype='>f4')
     for i in range(len(parinfo)):
         params[i] = parinfo[i]['value']
@@ -699,12 +700,12 @@ def buildmaps(conf, data, hdr, var=None, plot=False, debug=False, free_ratio=Fal
     #Parameters initialisation
     p = np.copy(params)
     
-    #Line intensity initisalisation
+    #Line intensity initialisation
     for i in intind:
         if parinfo[i]['fixed'] == 0:
-            p[i] = 5 * std * 10 ** (- components[i] + 1)
+            p[i] = 5 * std * 10 ** (- components[i] + 1.)
 
-    #Inititalisation of continuum (degree 0)
+    #Initialisation of continuum (degree 0)
     if not contfixed:
         p[contind[0]] = np.median(fa['spectrum'])
     for z in np.arange(zzmin, zzmax, zstep):
@@ -881,8 +882,8 @@ def buildmaps(conf, data, hdr, var=None, plot=False, debug=False, free_ratio=Fal
     for comp in range(multi_comp):
         count = 0
         print('Component %5i' % (comp + 1))
-        print('Redshfit: %5.2f' % (zmap[comp * els.index + comind]))
-        print('Redshfit error: %5.2f' % (ezmap[comp * els.index + comind]))
+        print('Redshift: %5.5f' % (zmap[comp * els.index + comind]))
+        print('Redshift error: %5.5f' % (ezmap[comp * els.index + comind]))
         print('Velocity: %5.2f' % (rvmap[comp * els.index + comind]))
         print('Velocity error: %5.2f' % (ervmap[comp * els.index + comind]))