v 1.3.6 : ploting of lightcurves improved. Patched a bug of ddosa (possibly)

that uses names of sources in light curves with spaces at the place of + and -

oda_integral_wrapper/wrapper.py

@@ -55,7 +55,7 @@ class INTEGRALwrapper(object):
             except:
                 raise ConnectionError
 
-    def long_scw_list_call(self, in_total_scw_list, s_max=50, wait=True, **arguments):
+    def long_scw_list_call(self, in_total_scw_list, s_max=50, wait=True, sleep_time=10, **arguments):
         import time
         total_scw_list = sorted(in_total_scw_list)
 
@@ -93,7 +93,7 @@ class INTEGRALwrapper(object):
                     disp_by_call[ys] = oda_api.api.DispatcherAPI(url=self.disp.url, wait=False)
 
                 _disp = disp_by_call[ys]
-
+                #print(type(_disp))
                 data = data_by_call.get(ys, None)
 
                 if data is None or not _disp.is_failed():
@@ -120,7 +120,7 @@ class INTEGRALwrapper(object):
             n_poll += 1
             if not wait:
                 return None
-            time.sleep(5)
+            time.sleep(sleep_time)
 
         loc_keys = data_by_call.keys()
 
@@ -330,18 +330,21 @@ class INTEGRALwrapper(object):
     @staticmethod
     def plot_lc(combined_lc, source_name, systematic_fraction=0, ng_sig_limit=3):
 
+        # In LC name has no "-" nor "+" ??????
+        patched_source_name = source_name.replace('-', ' ').replace('+', ' ')
+
         from scipy import stats
+        hdu = None
         for j, dd in enumerate(combined_lc._p_list):
-            if dd.meta_data['src_name'] == source_name:
-                IND_src_combined = j
+            INTEGRALwrapper.__log.debug(dd.meta_data['src_name'])
+            if dd.meta_data['src_name'] == source_name or dd.meta_data['src_name'] == patched_source_name:
                 for ii, du in enumerate(dd.data_unit):
                     if 'LC' in du.name:
-                        IND_lc_combined = ii
+                        hdu = du.to_fits_hdu()
 
-        for dd in combined_lc._p_list:
-            if dd.meta_data['src_name'] == source_name:
-                INTEGRALwrapper.__log.info('Source ' + source_name)
-                hdu = combined_lc._p_list[IND_src_combined].data_unit[IND_lc_combined].to_fits_hdu()
+        if hdu is None:
+            INTEGRALwrapper.__log.info('Source ' + source_name + ' not found in lc, not plotting')
+            return None
 
         x = hdu.data['TIME']
         y = hdu.data['RATE']
@@ -357,8 +360,10 @@ class INTEGRALwrapper(object):
         meany = np.sum(y / dy ** 2) / np.sum(1. / dy ** 2)
         err_mean = np.sum(1 / dy ** 2)
 
+        std_dev = np.std(y)
+
         fig = plt.figure()
-        _ = plt.errorbar(x, y, yerr=dy, marker='o', capsize=0)
+        _ = plt.errorbar(x, y, yerr=dy, marker='o', capsize=0, linestyle='', label='Lightcurve')
         _ = plt.axhline(meany, color='green', linewidth=3)
         _ = plt.xlabel('Time [IJD]')
         _ = plt.ylabel('Rate')
@@ -367,9 +372,35 @@ class INTEGRALwrapper(object):
         prob_limit = stats.norm().sf(ng_sig_limit)
         chi2_limit = stats.chi2(ndof).isf(prob_limit)
         band_width = np.sqrt(chi2_limit / err_mean)
-
+        INTEGRALwrapper.__log.debug('%g %g %g %g %g %g %g' %(
+            meany, err_mean, std_dev, prob_limit, chi2_limit, band_width, ng_sig_limit))
         _ = plt.axhspan(meany - band_width, meany + band_width, color='green', alpha=0.3,
-                        label=f'{ng_sig_limit} $\sigma$, {100 * systematic_fraction}% syst')
+                        label=f'{ng_sig_limit} $\sigma_m$, {100 * systematic_fraction}% syst')
+
+        _ = plt.axhspan(meany - std_dev*ng_sig_limit, meany + std_dev*ng_sig_limit,
+                        color='cyan', alpha=0.3,
+                        label=f'{ng_sig_limit} $\sigma_d$, {100 * systematic_fraction}% syst')
+
+        _ = plt.legend()
+        ind = (y - band_width)/dy > ng_sig_limit
+        if np.sum(ind) > 0:
+            _ = plt.plot(x[ind], y[ind], marker='x', color='red', linestyle='', markersize=10)
+            INTEGRALwrapper.__log.info('We found positive excesses on the lightcurve at times')
+            good_ind = np.where(ind)
+            #print(good_ind[0][0:-1], good_ind[0][1:])
+            old_time = -1
+            for i,j in zip(good_ind[0][0:-1], good_ind[0][1:]):
+                #print(i,j)
+
+                if j-i > 2:
+                    if x[i] != old_time :
+                        INTEGRALwrapper.__log.info('%f' % x[i])
+                    INTEGRALwrapper.__log.info('%f' % (x[j]))
+                # else:
+                #     INTEGRALwrapper.__log.info('%f' % ((x[i]+x[j])/2))
+
+                old_time = x[j]
+
 
         plot_title = source_name
         _ = plt.title(plot_title)
@@ -611,7 +642,10 @@ class INTEGRALwrapper(object):
 
     @staticmethod
     def write_lc_fits_files(lc, source_name, subcases_pattern, output_dir='.'):
-        lcprod = [l for l in lc._p_list if l.meta_data['src_name'] == source_name]
+        # In LC name has no "-" nor "+" ??????
+        patched_source_name = source_name.replace('-', ' ').replace('+', ' ')
+        lcprod = [l for l in lc._p_list if l.meta_data['src_name'] == source_name or \
+                  l.meta_data['src_name'] == patched_source_name]
         if (len(lcprod) < 1):
             INTEGRALwrapper.__log.warning("source %s not found in light curve products" % source_name)
             return "none", 0, 0, 0
@@ -621,16 +655,20 @@ class INTEGRALwrapper(object):
                 "source %s is found more than once light curve products, writing only the first one" % source_name)
 
         instrument = lcprod[0].data_unit[1].header['INSTRUME']
+        if instrument == 'IBIS':
+            ind_extension = 1
+        else:
+            ind_extension = 2
 
         lc_fn = output_dir + "/%s_lc_%s_%s.fits" % (instrument, source_name.replace(' ', '_'), subcases_pattern)
         lcprod[0].write_fits_file(lc_fn)
 
         ff = fits.open(lc_fn)  # , mode='update'
-        mjdref = float(ff[1].header['MJDREF'])
-        tstart = float(ff[1].header['TSTART']) + mjdref
-        tstop = float(ff[1].header['TSTOP']) + mjdref
+        mjdref = float(ff[ind_extension].header['MJDREF'])
+        tstart = float(ff[ind_extension].header['TSTART']) + mjdref
+        tstop = float(ff[ind_extension].header['TSTOP']) + mjdref
         try:
-            exposure = ff[1].header['EXPOSURE']
+            exposure = float(ff[ind_extension].header['EXPOSURE'])
         except:
             exposure = -1
 
@@ -721,36 +759,6 @@ class INTEGRALwrapper(object):
 
         return spec_fn, tstart, tstop, exposure
 
-    @staticmethod
-    def write_lc_fits_files(lc, source_name, subcases_pattern, output_dir='.'):
-
-        lcprod = [l for l in lc._p_list if l.meta_data['src_name'] == source_name]
-        if (len(lcprod) < 1):
-            INTEGRALwrapper.__log.warning("source %s not found in light curve products" % source_name)
-            return "none", 0, 0, 0
-
-        if (len(lcprod) > 1):
-            INTEGRALwrapper.__log.warning(
-                "source %s is found more than once light curve products, writing only the first one" % source_name)
-
-        instrument = lcprod[0].data_unit[1].header['INSTRUME']
-
-        lc_fn = output_dir + "/%s_lc_%s_%s.fits" % (instrument, source_name.replace(' ', '_'), subcases_pattern)
-        lcprod[0].write_fits_file(lc_fn)
-
-        ff = fits.open(lc_fn)  # , mode='update'
-        mjdref = ff[1].header['MJDREF']
-        tstart = float(ff[1].header['TSTART']) + mjdref
-        tstop = float(ff[1].header['TSTOP']) + mjdref
-        try:
-            exposure = ff[1].header['EXPOSURE']
-        except:
-            exposure = -1
-
-        ff.close()
-
-        return lc_fn, tstart, tstop, exposure
-
     @staticmethod
     def show_spectral_products(summed_data):
         for dd, nn in zip(summed_data._p_list, summed_data._n_list):

setup.py

@@ -19,7 +19,7 @@ include_package_data=True
 
 scripts_list = glob.glob('./bin/*')
 setup(name='oda_integral_wrapper',
-      version="1.3.5",
+      version="1.3.6",
       description='wrapper for INTEGRAL analysis using the API plugin for CDCI online data analysis',
       author='Carlo Ferrigno',
       author_email='carlo.ferrigno@unige.ch',