MCCD cleanup + MCCD plot package: Adding rejection of objects with zero size that are not flagged

shapepipe/modules/mccd_fit_runner.py

@@ -9,20 +9,32 @@
 """
 
 from shapepipe.modules.module_decorator import module_runner
-from shapepipe.modules.MCCD_package import shapepipe_auxiliary_mccd as aux_mccd
+from shapepipe.modules.mccd_package import shapepipe_auxiliary_mccd\
+    as aux_mccd
 import mccd
 
 
-@module_runner(input_module=['mccd_preprocessing_runner'], version='1.0',
-               file_pattern=['train_star_selection'],
-               file_ext=['.fits'], numbering_scheme='-0000000',
-               depends=['numpy', 'mccd', 'galsim'], run_method='parallel')
-def mccd_fit_runner(input_file_list, run_dirs, file_number_string,
-                    config, w_log):
+@module_runner(
+    input_module=['mccd_preprocessing_runner'],
+    version='1.0',
+    file_pattern=['train_star_selection'],
+    file_ext=['.fits'],
+    numbering_scheme='-0000000',
+    depends=['numpy', 'mccd', 'galsim'],
+    run_method='parallel'
+)
+def mccd_fit_runner(
+    input_file_list,
+    run_dirs,
+    file_number_string,
+    config,
+    module_config_sec,
+    w_log
+):
     # Recover the MCCD config file and its params
-    config_file_path = config.getexpanded('MCCD', 'CONFIG_PATH')
-    mccd_mode = config.get('MCCD', 'MODE')
-    verbose = config.getboolean('MCCD', 'VERBOSE')
+    config_file_path = config.getexpanded(module_config_sec, 'CONFIG_PATH')
+    mccd_mode = config.get(module_config_sec, 'MODE')
+    verbose = config.getboolean(module_config_sec, 'VERBOSE')
 
     # Parse MCCD config file
     mccd_parser = mccd.auxiliary_fun.MCCDParamsParser(config_file_path)
@@ -35,11 +47,18 @@ def mccd_fit_runner(input_file_list, run_dirs, file_number_string,
 
     if mccd_mode == 'FIT':
         aux_mccd.mccd_fit_pipeline(
-            trainstar_path, file_number_string, mccd_parser, output_dir,
-            verbose, saving_name)
+            trainstar_path=trainstar_path,
+            file_number_string=file_number_string,
+            mccd_parser=mccd_parser,
+            output_dir=output_dir,
+            verbose=verbose,
+            saving_name=saving_name,
+            w_log=w_log
+        )
 
     else:
-        raise ValueError('''mccd_fit_runner should be called when the
-        MODE is "FIT".''')
+        raise ValueError(
+            "mccd_fit_runner should be called when the MODE is 'FIT'."
+        )
 
     return None, None

shapepipe/modules/mccd_fit_val_runner.py

@@ -9,20 +9,31 @@
 """
 
 from shapepipe.modules.module_decorator import module_runner
-from shapepipe.modules.MCCD_package import shapepipe_auxiliary_mccd as aux_mccd
+from shapepipe.modules.mccd_package import shapepipe_auxiliary_mccd as aux_mccd
 import mccd
 
 
-@module_runner(input_module=['mccd_preprocessing_runner'], version='1.0',
-               file_pattern=['train_star_selection', 'test_star_selection'],
-               file_ext=['.fits', '.fits'], numbering_scheme='-0000000',
-               depends=['numpy', 'mccd', 'galsim'], run_method='parallel')
-def mccd_fit_val_runner(input_file_list, run_dirs, file_number_string,
-                        config, w_log):
+@module_runner(
+    input_module=['mccd_preprocessing_runner'],
+    version='1.0',
+    file_pattern=['train_star_selection', 'test_star_selection'],
+    file_ext=['.fits', '.fits'],
+    numbering_scheme='-0000000',
+    depends=['numpy', 'mccd', 'galsim'],
+    run_method='parallel'
+)
+def mccd_fit_val_runner(
+    input_file_list,
+    run_dirs,
+    file_number_string,
+    config,
+    module_config_sec,
+    w_log
+):
     # Recover the MCCD config file and its params
-    config_file_path = config.getexpanded('MCCD', 'CONFIG_PATH')
-    mccd_mode = config.get('MCCD', 'MODE')
-    verbose = config.getboolean('MCCD', 'VERBOSE')
+    config_file_path = config.getexpanded(module_config_sec, 'CONFIG_PATH')
+    mccd_mode = config.get(module_config_sec, 'MODE')
+    verbose = config.getboolean(module_config_sec, 'VERBOSE')
 
     # Parse MCCD config file
     mccd_parser = mccd.auxiliary_fun.MCCDParamsParser(config_file_path)
@@ -45,7 +56,9 @@ def mccd_fit_val_runner(input_file_list, run_dirs, file_number_string,
             mccd_parser=mccd_parser,
             output_dir=output_dir,
             verbose=verbose,
-            saving_name=fit_saving_name)
+            saving_name=fit_saving_name,
+            w_log=w_log
+        )
 
         # Fitted model is found in the output directory
         mccd_model_path = output_dir + fit_saving_name + file_number_string \
@@ -58,10 +71,13 @@ def mccd_fit_val_runner(input_file_list, run_dirs, file_number_string,
             output_dir=output_dir,
             file_number_string=file_number_string,
             w_log=w_log,
-            val_saving_name=val_saving_name)
+            val_saving_name=val_saving_name
+        )
 
     else:
-        raise ValueError('''mccd_fit_val_runner should be called when the
-        MODE is "FIT_VALIDATION".''')
+        raise ValueError(
+            "mccd_fit_val_runner should be called when the MODE"
+            + " is 'FIT_VALIDATION'."
+        )
 
     return None, None

shapepipe/modules/mccd_interp_runner.py

@@ -9,34 +9,49 @@
 """
 
 from shapepipe.modules.module_decorator import module_runner
-from shapepipe.modules.MCCD_package import mccd_interpolation_script\
+from shapepipe.modules.mccd_package import mccd_interpolation_script\
     as mccd_interp
-from shapepipe.modules.MCCD_package import shapepipe_auxiliary_mccd as aux_mccd
+from shapepipe.modules.mccd_package import shapepipe_auxiliary_mccd\
+    as aux_mccd
 import os
 
 
-@module_runner(input_module=['setools_runner'],
-               version='1.0',
-               file_pattern=['galaxy_selection'],
-               file_ext=['.npy'],
-               depends=['numpy', 'astropy', 'galsim', 'sqlitedict', 'mccd'],
-               run_method='parallel')
-def mccd_interp_runner(input_file_list, run_dirs, file_number_string,
-                       config, w_log):
-
-    mode = config.getexpanded('MCCD_INTERP_RUNNER', 'MODE')
-    pos_params = config.getlist('MCCD_INTERP_RUNNER', 'POSITION_PARAMS')
-    get_shapes = config.getboolean('MCCD_INTERP_RUNNER', 'GET_SHAPES')
+@module_runner(
+    input_module=['setools_runner'],
+    version='1.0',
+    file_pattern=['galaxy_selection'],
+    file_ext=['.npy'],
+    depends=['numpy', 'astropy', 'galsim', 'sqlitedict', 'mccd'],
+    run_method='parallel'
+)
+def mccd_interp_runner(
+    input_file_list,
+    run_dirs,
+    file_number_string,
+    config,
+    module_config_sec,
+    w_log
+):
+
+    mode = config.getexpanded(module_config_sec, 'MODE')
+    pos_params = config.getlist(module_config_sec, 'POSITION_PARAMS')
+    get_shapes = config.getboolean(module_config_sec, 'GET_SHAPES')
     mccd_model_extension = '.npy'
     output_dir = run_dirs['output']
 
     if mode == 'CLASSIC':
-        psf_model_dir = config.getexpanded('MCCD_INTERP_RUNNER',
-                                           'PSF_MODEL_DIR')
-        psf_model_pattern = config.get('MCCD_INTERP_RUNNER',
-                                       'PSF_MODEL_PATTERN')
-        psf_separator = config.get('MCCD_INTERP_RUNNER',
-                                   'PSF_MODEL_SEPARATOR')
+        psf_model_dir = config.getexpanded(
+            module_config_sec,
+            'PSF_MODEL_DIR'
+        )
+        psf_model_pattern = config.get(
+            module_config_sec,
+            'PSF_MODEL_PATTERN'
+        )
+        psf_separator = config.get(
+            module_config_sec,
+            'PSF_MODEL_SEPARATOR'
+        )
         # psfcat_path, galcat_path = input_file_list
         galcat_path = input_file_list[0]
 
@@ -52,8 +67,10 @@ def mccd_interp_runner(input_file_list, run_dirs, file_number_string,
 
         if not os.path.exists(psf_model_path):
             error_msg = "The corresponding PSF model was not not found."
-            w_log.info("Error message: {}.\n On catalog with id: {}.".format(
-                error_msg, file_number_string))
+            w_log.info(
+                f"Error message: {error_msg}.\n On catalog with"
+                + f" id: {file_number_string}."
+            )
 
             return None, None
 
@@ -64,37 +81,50 @@ def mccd_interp_runner(input_file_list, run_dirs, file_number_string,
             pos_params=pos_params,
             ccd_id=int(ccd_id),
             saving_path=saving_path,
-            get_shapes=get_shapes)
+            get_shapes=get_shapes
+        )
 
         if output_msg is not None:
-            w_log.info("Error message: {}.\n On catalog with id: {}.".format(
-                output_msg, file_number_string))
+            w_log.info(
+                f"Error message: {output_msg}.\n On catalog with"
+                + f" id: {file_number_string}."
+            )
 
     elif mode == 'MULTI-EPOCH':
-        psf_model_dir = config.getexpanded('MCCD_INTERP_RUNNER',
-                                           'PSF_MODEL_DIR')
-        psf_model_pattern = config.get('MCCD_INTERP_RUNNER',
-                                       'PSF_MODEL_PATTERN')
-        f_wcs_path = config.getexpanded('MCCD_INTERP_RUNNER',
-                                        'ME_LOG_WCS')
+        psf_model_dir = config.getexpanded(
+            module_config_sec,
+            'PSF_MODEL_DIR'
+        )
+        psf_model_pattern = config.get(
+            module_config_sec,
+            'PSF_MODEL_PATTERN'
+        )
+        f_wcs_path = config.getexpanded(
+            module_config_sec,
+            'ME_LOG_WCS'
+        )
 
         galcat_path = input_file_list[0]
 
-        inst = mccd_interp.MCCDinterpolator(None,
-                                            galcat_path,
-                                            output_dir,
-                                            file_number_string,
-                                            w_log,
-                                            pos_params,
-                                            get_shapes)
+        inst = mccd_interp.MCCDinterpolator(
+            None,
+            galcat_path,
+            output_dir,
+            file_number_string,
+            w_log,
+            pos_params,
+            get_shapes
+        )
 
         inst.process_me(psf_model_dir, psf_model_pattern, f_wcs_path)
 
     elif mode == 'VALIDATION':
-        ValueError('''MODE has to be in MULTI-EPOCH or CLASSIC.
-        For validation use MCCD validation runner''')
+        ValueError(
+            "MODE has to be in MULTI-EPOCH or CLASSIC. For validation"
+            + " use MCCD validation runner."
+        )
 
     else:
-        ValueError('MODE has to be in : [CLASSIC, MULTI-EPOCH]')
+        ValueError("MODE has to be in : [CLASSIC, MULTI-EPOCH]")
 
     return None, None