Merge branch '100-write-unit-test-for-astrohackextract_holog' into 13…

…2-generate_holog_obs_dict-ingnoring-point_name-input

src/astrohack/_utils/_extract_holog.py

@@ -383,7 +383,7 @@ def _create_holog_file(
             )
 
 
-def _create_holog_obs_dict(pnt_dict,baseline_average_distance,baseline_average_nearest,ant_names,ant_pos,ant_names_main):
+def _create_holog_obs_dict(pnt_dict, baseline_average_distance, baseline_average_nearest, ant_names, ant_pos, ant_names_main):
     '''
     Generate holog_obs_dict.
     '''
@@ -524,33 +524,33 @@ def _create_holog_meta_data(holog_file, holog_dict, input_params):
 
     for ddi, map_dict in holog_dict.items():
         if "ddi_" in ddi:
-            for map, ant_dict in map_dict.items():
-                if "map_" in map:
+            for mapping, ant_dict in map_dict.items():
+                if "map_" in mapping:
                     for ant, xds in ant_dict.items():
                         if "ant_" in ant:
                             if ant not in ant_holog_dict:
-                                ant_holog_dict[ant] = {ddi:{map:{}}}
+                                ant_holog_dict[ant] = {ddi:{mapping:{}}}
                             elif ddi not in ant_holog_dict[ant]:
-                                ant_holog_dict[ant][ddi] = {map:{}}
+                                ant_holog_dict[ant][ddi] = {mapping:{}}
 
-                            ant_holog_dict[ant][ddi][map] = xds.to_dict(data=False)
+                            ant_holog_dict[ant][ddi][mapping] = xds.to_dict(data=False)
                             cell_sizes.append(xds.attrs["grid_parms"]["cell_size"])
                             n_pixs.append(xds.attrs["grid_parms"]["n_pix"])
                             telescope_names.append(xds.attrs['telescope_name'])
 
     cell_sizes_sigfigs =  _significant_digits(cell_sizes, digits=3)
 
     if not (len(set(cell_sizes_sigfigs)) == 1):
-        logger.error('Cell size not consistant: ' + str(cell_sizes))
-        raise
+        logger.error('Cell size not consistent: ' + str(cell_sizes))
+        raise Exception('Cell size not consistent: ' + str(cell_sizes))
 
     if not (len(set(n_pixs)) == 1):
-        logger.error('Number of pixels not consistant: ' + str(n_pixs))
-        raise
+        logger.error('Number of pixels not consistent: ' + str(n_pixs))
+        #raise Exception('Number of pixels not consistent: ' + str(n_pixs))
 
     if not (len(set(telescope_names)) == 1):
-        logger.error('Telescope name not consistant: ' + str(telescope_names))
-        raise
+        logger.error('Telescope name not consistent: ' + str(telescope_names))
+        raise Exception('Telescope name not consistent: ' + str(telescope_names))
 
     output_meta_file = "{name}/{ext}".format(name=holog_file, ext=".holog_json")
 

src/astrohack/extract_holog.py

@@ -29,7 +29,10 @@
 from astrohack._utils._tools import _remove_suffix
 from astrohack._utils._tools import _jsonify
 
+from astrohack._utils._extract_holog import _create_holog_obs_dict
+
 from astrohack.mds import AstrohackHologFile
+from astrohack.mds import AstrohackPointFile
 
 from astrohack.extract_pointing import extract_pointing
 
@@ -53,7 +56,7 @@ def extract_holog(
     :param ms_name: Name of input measurement file name.
     :type ms_name: str
 
-    :param point_name: Name of *<point_name>.point.zarr* file to use.
+    :param point_name: Name of *<point_name>.point.zarr* file to use. This is must be provided.
     :type holog_name: str
 
     :param holog_name: Name of *<holog_name>.holog.zarr* file to create. Defaults to measurement set name with *holog.zarr* extension.
@@ -439,7 +442,7 @@ def _check_extract_holog_params(function_name, extract_holog_params):
     if not parm_check:
         logger.error(f'[{function_name}]: Parameter holog_obs_dict must be of type {str(dict)}.')
 
-    parms_passed = parms_passed and _check_parms(function_name, extract_holog_params, 'baseline_average_distance', [float, int, str], default='all')
+    parms_passed = parms_passed and _check_parms(function_name, extract_holog_params, 'baseline_average_distance', [int, float, str], default='all')
 
     parms_passed = parms_passed and _check_parms(function_name, extract_holog_params, 'baseline_average_nearest', [int, str], default='all')
 
@@ -460,15 +463,14 @@ def _check_extract_holog_params(function_name, extract_holog_params):
 
 def generate_holog_obs_dict(
     ms_name,
-    point_name=None,
+    point_name,
     ddi='all',
     baseline_average_distance='all',
     baseline_average_nearest='all',
-    overwrite=False,
     parallel=False
 ):
     """
-    Extract holography and optionally pointing data, from measurement set. Creates holography output file.
+    Generate holography observation dictionary, from measurement set..
 
     :param ms_name: Name of input measurement file name.
     :type ms_name: str
@@ -482,12 +484,9 @@ def generate_holog_obs_dict(
     :param baseline_average_nearest: To increase the signal to noise for a mapping antenna mutiple reference antennas can be used. The baseline_average_nearest is the number of nearest reference antennas to use. The baseline_average_nearest is only used if the holog_obs_dict is not specified.  baseline_average_distance and baseline_average_nearest can not be used together.
     :type holog_obs_dict: int, optional
 
-    :param point_name: Name of *<point_name>.point.zarr* file to create. Defaults to measurement set name with *point.zarr* extension.
+    :param point_name: Name of *<point_name>.point.zarr* file to use. 
     :type point_name: str, optional
 
-    :param overwrite: Boolean for whether to overwrite current holog.zarr and point.zarr files, defaults to False.
-    :type overwrite: bool, optional
-
     :param parallel: Boolean for whether to process in parallel. Defaults to False
     :type parallel: bool, optional
 
@@ -558,26 +557,8 @@ def generate_holog_obs_dict(
 
     function_name = inspect.stack()[CURRENT_FUNCTION].function
 
-    _check_if_file_exists(extract_holog_params['ms_name'])
-
-    if os.path.exists(point_name) is False or point_name==None:
-
-        logger.debug('[{caller}]: File {file} does not exists. Extracting ...'.format(caller=function_name, file=point_name))
-
-        from astrohack._utils._tools import _remove_suffix
-
-        point_name = _remove_suffix(ms_name, '.ms') + '.point.zarr'
-        extract_holog_params['point_name'] = point_name
-
-        logger.debug('[{caller}]: Extracting pointing to {output}'.format(caller=function_name, output=point_name))
-
-
-    pnt_dict = extract_pointing(
-        ms_name=extract_holog_params['ms_name'],
-        point_name=extract_holog_params['point_name'],
-        parallel=extract_holog_params['parallel'],
-        overwrite=extract_holog_params['overwrite']
-    )
+    _check_if_file_exists(ms_name)
+    _check_if_file_exists(point_name)
 
     ######## Get Spectral Windows ########
     ctb = ctables.table(
@@ -586,9 +567,11 @@ def generate_holog_obs_dict(
         lockoptions={"option": "usernoread"},
         ack=False,
     )
+
     ddi_spw = ctb.getcol("SPECTRAL_WINDOW_ID")
     ddpol_indexol = ctb.getcol("POLARIZATION_ID")
     ms_ddi = np.arange(len(ddi_spw))
+
     ctb.close()
 
     ######## Get Antenna IDs and Names ########
@@ -622,19 +605,20 @@ def generate_holog_obs_dict(
 
     # Create holog_obs_dict or modify user supplied holog_obs_dict.
     ddi = extract_holog_params['ddi']
-
 
-    from astrohack._utils._extract_holog import _create_holog_obs_dict
+    pnt_mds = AstrohackPointFile(extract_holog_params['point_name'])
+    pnt_mds._open()
+
     holog_obs_dict = _create_holog_obs_dict(
-            pnt_dict, 
+            pnt_mds, 
             extract_holog_params['baseline_average_distance'],
             extract_holog_params['baseline_average_nearest'], 
             ant_names, 
             ant_pos,
             ant_names_main
     )
 
-        #From the generated holog_obs_dict subselect user supplied ddis.
+    #From the generated holog_obs_dict subselect user supplied ddis.
     if ddi != 'all':
         holog_obs_dict_keys = list(holog_obs_dict.keys())
         for ddi_key in holog_obs_dict_keys:

src/astrohack/extract_pointing.py

@@ -78,14 +78,30 @@ def extract_pointing(
     function_name = inspect.stack()[CURRENT_FUNCTION].function
 
     ######### Parameter Checking #########
-    extract_pointing_params = _check_extract_pointing_params(function_name=function_name, extract_point_params=extract_pointing_params)
+    extract_pointing_params = _check_extract_pointing_params(
+        function_name=function_name, 
+        extract_point_params=extract_pointing_params
+    )
 
     input_params = extract_pointing_params.copy()
 
     try:
         _check_if_file_exists(extract_pointing_params['ms_name'])
         _check_if_file_will_be_overwritten(extract_pointing_params['point_name'], extract_pointing_params['overwrite'])
-
+
+        # Until check params is changed, comment this out.
+        '''
+        if point_name==None:
+        
+            logger.debug('[{caller}]: File {file} does not exists. Extracting ...'.format(caller=function_name, file=point_name))
+            
+            from astrohack._utils._tools import _remove_suffix
+
+            point_name = _remove_suffix(ms_name, '.ms') + '.point.zarr'
+            extract_holog_params['point_name'] = point_name
+            
+            logger.debug('[{caller}]: Extracting pointing to {output}'.format(caller=function_name, output=point_name))
+        '''
 
         pnt_dict = _extract_pointing(
             ms_name=extract_pointing_params['ms_name'], 
@@ -110,7 +126,7 @@ def extract_pointing(
     except Exception as exception:
         logger.error("There was an error, exiting:: Exception: {exception}".format(exception=exception))
 
-        return
+        return None
 
 def _check_extract_pointing_params(function_name, extract_point_params):