Document examples regarding the use of reduction configuration files

Progress on #73

examples/ifs_reduction.py

@@ -1,16 +1,16 @@
 import sphere.IFS as IFS
 
-######################################################################
-# Since version 1.4 of the pipeline, the default -1.75° true North   #
-# offset is automatically added to the derotation angles. The offset #
-# value can be modified in the configuration of the reduction:       #
-#                                                                    #
-#   >>> reduction.config[\'cal_true_north\'] = xxx                   #
-#                                                                    #
-# To avoid any issues, make sure to:                                 #
-#   * either reprocess data previously processed with version <1.4   #
-#   * or take into account the offset in your astrometric analysis   #
-######################################################################
+###############################################################################
+# Since version 1.4 of the pipeline, the default -1.75° true North offset is  #
+# automatically added to the derotation angles. The offset value can be       #
+# modified in the configuration of the reduction:                             #
+#                                                                             #
+#   >>> reduction.config[\'cal_true_north\'] = xxx                            #
+#                                                                             #
+# To avoid any issues, make sure to:                                          #
+#   * either reprocess data previously processed with version <1.4            #
+#   * or take into account the offset in your astrometric analysis            #
+###############################################################################
 
 ####################################################@
 # full reduction
@@ -19,6 +19,20 @@
 #%% init reduction
 reduction = IFS.Reduction('/Users/avigan/data/sphere-test-target/IFS/', log_level='info')
 
+###############################################################################
+# It is possible to provide a default JSON configuration file to set some (or #
+# all) of the reduction parameters to a default value different from the ones #
+# hard-coded in the sphere package. This is done with the keyword:            #
+#   user_config='... path to the file ...'                                    #
+# The increasing priority for setting reduction parameters is the following:  #
+#   0- default values hard-coded in the sphere package                        #
+#   1- values contained in the file pointed by the user_config keyword, if a  #
+#      file path is provided and exists                                       #
+#   2- values contained in a reduction_config.json file left in the reduction #
+#      directory by a previous reduction                                      #
+#   3- values manually set by the user (see examples below)                   #
+###############################################################################
+
 #%% configuration
 reduction.config['preproc_collapse_science'] = True
 reduction.config['preproc_collapse_type']    = 'coadd'

examples/irdis_imaging_reduction.py

@@ -1,16 +1,16 @@
 import sphere.IRDIS as IRDIS
 
-######################################################################
-# Since version 1.4 of the pipeline, the default -1.75° true North   #
-# offset is automatically added to the derotation angles. The offset #
-# value can be modified in the configuration of the reduction:       #
-#                                                                    #
-#   >>> reduction.config[\'cal_true_north\'] = xxx                   #
-#                                                                    #
-# To avoid any issues, make sure to:                                 #
-#   * either reprocess data previously processed with version <1.4   #
-#   * or take into account the offset in your astrometric analysis   #
-######################################################################
+###############################################################################
+# Since version 1.4 of the pipeline, the default -1.75° true North offset is  #
+# automatically added to the derotation angles. The offset value can be       #
+# modified in the configuration of the reduction:                             #
+#                                                                             #
+#   >>> reduction.config[\'cal_true_north\'] = xxx                            #
+#                                                                             #
+# To avoid any issues, make sure to:                                          #
+#   * either reprocess data previously processed with version <1.4            #
+#   * or take into account the offset in your astrometric analysis            #
+###############################################################################
 
 ####################################################@
 # full reduction
@@ -19,6 +19,20 @@
 #%% init reduction
 reduction = IRDIS.ImagingReduction('/Users/avigan/data/sphere-test-target/IRD/DBI/', log_level='info')
 
+###############################################################################
+# It is possible to provide a default JSON configuration file to set some (or #
+# all) of the reduction parameters to a default value different from the ones #
+# hard-coded in the sphere package. This is done with the keyword:            #
+#   user_config='... path to the file ...'                                    #
+# The increasing priority for setting reduction parameters is the following:  #
+#   0- default values hard-coded in the sphere package                        #
+#   1- values contained in the file pointed by the user_config keyword, if a  #
+#      file path is provided and exists                                       #
+#   2- values contained in a reduction_config.json file left in the reduction #
+#      directory by a previous reduction                                      #
+#   3- values manually set by the user (see examples below)                   #
+###############################################################################
+
 #%% configuration
 reduction.config['combine_psf_dim']          = 80
 reduction.config['combine_science_dim']      = 400

examples/irdis_spectro_reduction.py

@@ -7,6 +7,20 @@
 #%% init reduction
 reduction = IRDIS.SpectroReduction('/Users/avigan/data/sphere-test-target/IRD/LSS/', log_level='info')
 
+###############################################################################
+# It is possible to provide a default JSON configuration file to set some (or #
+# all) of the reduction parameters to a default value different from the ones #
+# hard-coded in the sphere package. This is done with the keyword:            #
+#   user_config='... path to the file ...'                                    #
+# The increasing priority for setting reduction parameters is the following:  #
+#   0- default values hard-coded in the sphere package                        #
+#   1- values contained in the file pointed by the user_config keyword, if a  #
+#      file path is provided and exists                                       #
+#   2- values contained in a reduction_config.json file left in the reduction #
+#      directory by a previous reduction                                      #
+#   3- values manually set by the user (see examples below)                   #
+###############################################################################
+
 #%% configuration
 reduction.config['combine_science_dim'] = 300
 reduction.config['combine_center_selection'] = 'first'