Correct bug in logging

Correct bug in summing images
Treated case of empty source catalog and add source of interest
v 1.3.25

oda_integral_wrapper/wrapper.py

@@ -274,7 +274,7 @@ class INTEGRALwrapper(object):
                                                        summed_mosaic.to_hdu_list()[1:]
                                                        if hh.header['IMATYPE'] != 'NIMAGE']
 
-        self.summed_data.dispatcher_catalog_1.table = INTEGRALwrapper.compute_fluxes(summed_data, detection_threshold)
+        summed_data.dispatcher_catalog_1.table = INTEGRALwrapper.compute_fluxes(summed_data, detection_threshold)
         INTEGRALwrapper.display_sources(summed_data.dispatcher_catalog_1.table, detection_threshold)
         self.summed_data=summed_data
 
@@ -282,6 +282,9 @@ class INTEGRALwrapper(object):
 
     @staticmethod
     def display_sources(stacked_table, min_sigma):
+        if stacked_table is None:
+            INTEGRALwrapper.__log.info("No sources to be displayed")
+            return
         out_str = 'source_name RA DEC Flux Flux_err\n-----------------------------------'
         INTEGRALwrapper.__log.info(out_str)
 
@@ -307,7 +310,7 @@ class INTEGRALwrapper(object):
         #
         stacked_table = summed_data.dispatcher_catalog_1.table
         if len(stacked_table) == 0:
-            self.__log.warning("No sources in the catalog, impossible to compute fluxes")
+            INTEGRALwrapper.__log.warning("No sources in the catalog, impossible to compute fluxes")
             return
 
         #Filter sources by significance
@@ -603,12 +606,23 @@ class INTEGRALwrapper(object):
         #         objects_of_interest=[('Her X-1', Simbad.query )]
         #         objects_of_interest=[('Her X-1', Skycoord )]
         #         objects_of_interest=[ Skycoord(....) ]
+        if image.dispatcher_catalog_1.table is None:
+            INTEGRALwrapper.__log.warning("No sources in the catalog")
+            if objects_of_interest != []:
+                return INTEGRALwrapper.add_objects_of_interest(None, objects_of_interest,
+                                                    flag, isgri_flag)
+            else:
+                return 'none'
 
         sources = image.dispatcher_catalog_1.table[image.dispatcher_catalog_1.table['significance'] >= det_sigma]
 
         if len(sources) == 0:
             INTEGRALwrapper.__log.warning('No sources in the catalog with det_sigma > %.1f' % det_sigma)
-            return 'none'
+            if objects_of_interest != []:
+                return INTEGRALwrapper.add_objects_of_interest(None, objects_of_interest,
+                                                    flag, isgri_flag)
+            else:
+                return 'none'
 
         if not include_new_sources:
             ind = [not 'NEW' in ss for ss in sources['src_names']]
@@ -630,6 +644,11 @@ class INTEGRALwrapper(object):
 
         return copied_image.dispatcher_catalog_1.get_api_dictionary()
 
+    @staticmethod
+    def make_one_source_catalog_string(name, ra, dec, isgri_flag, flag):
+        out_str_templ ='{"cat_frame": "fk5", "cat_coord_units": "deg", "cat_column_list": [[1], ["%s"], [0.0], [%f], [%f], [-32768], [%d], [%d], [0.001]], "cat_column_names": ["meta_ID", "src_names", "significance", "ra", "dec", "NEW_SOURCE", "ISGRI_FLAG", "FLAG", "ERR_RAD"], "cat_column_descr": [["meta_ID", "<i8"], ["src_names", "<U7"], ["significance", "<f8"], ["ra", "<f8"], ["dec", "<f8"], ["NEW_SOURCE", "<i8"], ["ISGRI_FLAG", "<i8"], ["FLAG", "<i8"], ["ERR_RAD", "<f8"]], "cat_lat_name": "dec", "cat_lon_name": "ra"}'
+        return out_str_templ % (name, ra, dec, isgri_flag, flag)
+
     @staticmethod
     def add_objects_of_interest(clean_sources, objects_of_interest, flag=1, isgri_flag=2, tolerance = 1./60.):
         for ooi in objects_of_interest:
@@ -653,37 +672,40 @@ class INTEGRALwrapper(object):
             dec = source_coord.dec.deg
             INTEGRALwrapper.__log.info("RA=%g Dec=%g" % (ra, dec))
 
-            #Look for the source of interest in NEW sources by coordinates
-            for ss in clean_sources:
-                if 'NEW' in ss['src_names']:
-                    if np.abs(ra - ss['ra']) <= tolerance and np.abs(dec - ss['dec']) <= tolerance:
-                        INTEGRALwrapper.__log.info('Found ' + ooi + ' in catalog as ' + ss['src_names'])
-                        ind = clean_sources['src_names'] == ss['src_names']
-                        clean_sources['FLAG'][ind] = flag
-                        clean_sources['ISGRI_FLAG'][ind] = isgri_flag
-                        clean_sources['src_names'][ind] = ooi
-
-            #Look for the source of interest in
-            ind = clean_sources['src_names'] == ooi
-            if np.count_nonzero(ind) > 0:
-                INTEGRALwrapper.__log.info('Found ' + ooi + ' in catalog')
-                clean_sources['FLAG'][ind] = flag
-                if 'ISGRI_FLAG' in clean_sources.keys():
-                   clean_sources['ISGRI_FLAG'][ind] = isgri_flag
-                if 'JEMX_FLAG' in clean_sources.keys():
-                   clean_sources['JEMX_FLAG'][ind] = isgri_flag
-            else:
-                INTEGRALwrapper.__log.info('Adding ' + ooi + ' to catalog')
-                try:
-                    INTEGRALwrapper.__log.debug('Flux is present')
-                    clean_sources.add_row((0, ooi, 0, ra, dec, 0, isgri_flag, flag, 1e-3, 0, 0))
-                except:
-                    INTEGRALwrapper.__log.debug('Flux is NOT present')
-                    clean_sources.add_row((0, ooi, 0, ra, dec, 0, isgri_flag, flag, 1e-3))
+            if clean_sources is not None:
+                #Look for the source of interest in NEW sources by coordinates
+                for ss in clean_sources:
+                    if 'NEW' in ss['src_names']:
+                        if np.abs(ra - ss['ra']) <= tolerance and np.abs(dec - ss['dec']) <= tolerance:
+                            INTEGRALwrapper.__log.info('Found ' + ooi + ' in catalog as ' + ss['src_names'])
+                            ind = clean_sources['src_names'] == ss['src_names']
+                            clean_sources['FLAG'][ind] = flag
+                            clean_sources['ISGRI_FLAG'][ind] = isgri_flag
+                            clean_sources['src_names'][ind] = ooi
+
+                #Look for the source of interest in
+                ind = clean_sources['src_names'] == ooi
+                if np.count_nonzero(ind) > 0:
+                    INTEGRALwrapper.__log.info('Found ' + ooi + ' in catalog')
+                    clean_sources['FLAG'][ind] = flag
+                    if 'ISGRI_FLAG' in clean_sources.keys():
+                       clean_sources['ISGRI_FLAG'][ind] = isgri_flag
+                    if 'JEMX_FLAG' in clean_sources.keys():
+                       clean_sources['JEMX_FLAG'][ind] = isgri_flag
+                else:
+                    INTEGRALwrapper.__log.info('Adding ' + ooi + ' to catalog')
+                    try:
+                        INTEGRALwrapper.__log.debug('Flux is present')
+                        clean_sources.add_row((0, ooi, 0, ra, dec, 0, isgri_flag, flag, 1e-3, 0, 0))
+                    except:
+                        INTEGRALwrapper.__log.debug('Flux is NOT present')
+                        clean_sources.add_row((0, ooi, 0, ra, dec, 0, isgri_flag, flag, 1e-3))
 
-        unique_sources = table.unique(clean_sources, keys=['src_names'])
+                unique_sources = table.unique(clean_sources, keys=['src_names'])
 
-        return unique_sources
+                return unique_sources
+            else:
+                return INTEGRALwrapper.make_one_source_catalog_string(ooi, ra, dec, isgri_flag, flag)
 
     @staticmethod
     def sum_spectral_products(spectrum_results, source_name):
@@ -1066,46 +1088,46 @@ class INTEGRALwrapper(object):
         # plt.ylim([dec[np.transpose(m_on)].min(), dec[np.transpose(m_on)].max()])
         plt.xlim([ra.max(), ra.min()])
         plt.ylim([dec.min(), dec.max()])
+        if sources is not None:
+            if len(sources) > 0:
+                ras = np.array([x for x in sources['ra']])
+                decs = np.array([x for x in sources['dec']])
+                names = np.array([x for x in sources['src_names']])
+                sigmas = np.array([x for x in sources['significance']])
+                # Defines relevant indexes for plotting regions
 
-        if len(sources) > 0:
-            ras = np.array([x for x in sources['ra']])
-            decs = np.array([x for x in sources['dec']])
-            names = np.array([x for x in sources['src_names']])
-            sigmas = np.array([x for x in sources['significance']])
-            # Defines relevant indexes for plotting regions
-
-            m_new = np.array(['NEW' in name for name in names])
+                m_new = np.array(['NEW' in name for name in names])
 
-            # m_offaxis = self.source_results.MEAN_VAR > 5
-            # m_noisy = self.source_results.DETSIG_CORR < 5
-            m_noisy = sigmas < 5
+                # m_offaxis = self.source_results.MEAN_VAR > 5
+                # m_noisy = self.source_results.DETSIG_CORR < 5
+                m_noisy = sigmas < 5
 
-            # plot new sources as pink circles
+                # plot new sources as pink circles
 
-            try:
-                m = m_new & (sigmas > det_sigma)
-                ra_coord = ras[m]
-                dec_coord = decs[m]
-                new_names = names[m]
-                if zero_crossing:
-                    ind_ra = ra_coord > 180.
-                    try:
-                        ra_coord[ind_ra] -= 360.
-                    except:
-                        pass
-            except:
-                ra_coord = []
-                dec_coord = []
-                new_names = []
-
-            plt.scatter(ra_coord, dec_coord, s=100, marker="o", facecolors='none',
-                        edgecolors='pink',
-                        lw=3, label="NEW any", zorder=5)
-            for i in range(len(ra_coord)):
-                # print("%f %f %s\n"%(ra_coord[i], dec_coord[i], names[i]))
-                plt.text(ra_coord[i],
-                         dec_coord[i] + 0.5,
-                         new_names[i], color="pink", size=15)
+                try:
+                    m = m_new & (sigmas > det_sigma)
+                    ra_coord = ras[m]
+                    dec_coord = decs[m]
+                    new_names = names[m]
+                    if zero_crossing:
+                        ind_ra = ra_coord > 180.
+                        try:
+                            ra_coord[ind_ra] -= 360.
+                        except:
+                            pass
+                except:
+                    ra_coord = []
+                    dec_coord = []
+                    new_names = []
+
+                plt.scatter(ra_coord, dec_coord, s=100, marker="o", facecolors='none',
+                            edgecolors='pink',
+                            lw=3, label="NEW any", zorder=5)
+                for i in range(len(ra_coord)):
+                    # print("%f %f %s\n"%(ra_coord[i], dec_coord[i], names[i]))
+                    plt.text(ra_coord[i],
+                             dec_coord[i] + 0.5,
+                             new_names[i], color="pink", size=15)
 
         # CF Plots object of interest as green
         for ooi in objects_of_interest:

setup.py

@@ -15,7 +15,7 @@ include_package_data=True
 
 scripts_list = glob.glob('./bin/*')
 setup(name='oda_integral_wrapper',
-      version="1.3.24",
+      version="1.3.25",
       description='wrapper for INTEGRAL analysis using the API plugin for CDCI online data analysis',
       author='Carlo Ferrigno',
       author_email='carlo.ferrigno@unige.ch',