Merge pull request #129 from casangi/127-generate-holog-obs-and-extra…

…ct-holog-fix

127 generate holog obs and extract holog fix

src/astrohack/_utils/_dio.py

@@ -222,14 +222,16 @@ def _write_fits(header, imagetype, data, filename, unit, origin):
     return
 
 
-def _create_destination_folder(caller, destination):
+def _create_destination_folder(destination):
     """
     Try to create a folder if it already exists raise a warning
     Args:
         caller: Calling function
         destination: the folder to be created
     """
     logger = _get_astrohack_logger()
+    caller=inspect.stack()[CALLING_FUNCTION].function
+
     try:
         os.mkdir(destination)
     except FileExistsError:

src/astrohack/_utils/_tools.py

@@ -60,11 +60,13 @@ def _remove_suffix(input_string, suffix):
 
     return input_string
 
-
+# DEPRECATED
 def _jsonify(holog_obj):
     """ Convert holog_obs_description dictionay to json format. This just means converting numpy.ndarry
         entries to string lists.
 
+    # DEPRECATED
+
     :param holog_obj: holog_obs_description dictionary.
     :type holog_obj: dict
     :param holog_obj: holog_obs_description dictionary.
@@ -153,6 +155,7 @@ def _parm_to_list(caller, parm, data_dict, prefix):
 
     """
     logger = _get_astrohack_logger()
+
     if parm == 'all':
         oulist = list(data_dict.keys())
     elif isinstance(parm, str):

src/astrohack/extract_holog.py

@@ -12,6 +12,8 @@
 
 from casacore import tables as ctables
 
+from astrohack._utils._tools import NumpyEncoder
+
 from astrohack._utils._constants import pol_str
 from astrohack._utils._conversion import _convert_ant_name_to_id
 from astrohack._utils._extract_holog import _create_holog_meta_data
@@ -57,7 +59,7 @@ def extract_holog(
     :param holog_name: Name of *<holog_name>.holog.zarr* file to create. Defaults to measurement set name with *holog.zarr* extension.
     :type holog_name: str, optional
 
-    :param holog_obs_dict: The *holog_obs_dict* describes which scan and antenna data to extract from the measurement set. As detailed below, this compound dictionary also includes important meta data needed for preprocessing and extraction of the holography data from the measurement set. If not specified holog_obs_dict will be generated. For auto generation of the holog_obs_dict the assumtion is made that the same antanna beam is not mapped twice in a row (alternating sets of antennas is fine).
+    :param holog_obs_dict: The *holog_obs_dict* describes which scan and antenna data to extract from the measurement set. As detailed below, this compound dictionary also includes important meta data needed for preprocessing and extraction of the holography data from the measurement set. If not specified holog_obs_dict will be generated. For auto generation of the holog_obs_dict the assumtion is made that the same antanna beam is not mapped twice in a row (alternating sets of antennas is fine). If the holog_obs_dict is specified, the ddi input is ignored.
     :type holog_obs_dict: dict, optional
 
     :param ddi:  DDI(s) that should be extracted from the measurement set. Defaults to all DDI's in the ms.
@@ -214,7 +216,8 @@ def extract_holog(
     # Create holog_obs_dict or modify user supplied holog_obs_dict.
     ddi = extract_holog_params['ddi']
 
-    if holog_obs_dict is None: #Automatically create holog_obs_dict
+    # Create holog_obs_dict if not specified
+    if holog_obs_dict is None: 
         from astrohack._utils._extract_holog import _create_holog_obs_dict
         holog_obs_dict = _create_holog_obs_dict(
             pnt_dict, 
@@ -234,27 +237,15 @@ def extract_holog(
                     if ddi_id not in ddi:
                         del holog_obs_dict[ddi_key]
 
-    else:
-        #If a user defines a holog_obs_dict it needs to be duplicated for each ddi.
-        holog_obs_dict_with_ddi = {}
-        if ddi == 'all':
-            for ddi_id in ms_ddi:
-                holog_obs_dict_with_ddi['ddi_' + str(ddi_id)] = holog_obs_dict
-        else:
-            for ddi_id in ddi:
-                holog_obs_dict_with_ddi['ddi_' + str(ddi_id)] = holog_obs_dict
-
-        holog_obs_dict = holog_obs_dict_with_ddi
 
     logger.info(f"[{function_name}]: holog_obs_dict: \n%s", pformat(list(holog_obs_dict.values())[0], indent=2, width=2))
 
 
-    outfile_obj = copy.deepcopy(holog_obs_dict)
-
-    _jsonify(outfile_obj)
+    encoded_obj = json.dumps(holog_obs_dict, cls=NumpyEncoder)
 
     with open(".holog_obs_dict.json", "w") as outfile:
-        json.dump(outfile_obj, outfile)
+        json.dump(encoded_obj, outfile)
+
 
     ######## Get Scan and Subscan IDs ########
     # SDM Tables Short Description (https://drive.google.com/file/d/16a3g0GQxgcO7N_ZabfdtexQ8r2jRbYIS/view)
@@ -651,12 +642,9 @@ def generate_holog_obs_dict(
                 if ddi_id not in ddi:
                     del holog_obs_dict[ddi_key]
 
-
-    outfile_obj = copy.deepcopy(holog_obs_dict)
-
-    _jsonify(outfile_obj)
+    encoded_obj = json.dumps(holog_obs_dict, cls=NumpyEncoder)
 
     with open(".holog_obs_dict.json", "w") as outfile:
-        json.dump(outfile_obj, outfile)
+        json.dump(encoded_obj, outfile)
 
-    return outfile_obj
+    return json.loads(encoded_obj)

src/astrohack/mds.py

@@ -217,7 +217,7 @@ def export_to_fits(self, destination, complex_split='cartesian', ant_id=None, dd
         parms_passed = parms_passed and _check_parms(fname, parm_dict, 'parallel', [bool], default=True)
 
         _parm_check_passed(fname, parms_passed)
-        _create_destination_folder(fname, parm_dict['destination'])
+        _create_destination_folder(parm_dict['destination'])
         parm_dict['metadata'] = self._meta_data
         _dask_general_compute(fname, self, _export_to_fits_holog_chunk, parm_dict, ['ant', 'ddi'], parallel=parallel)
 
@@ -280,7 +280,7 @@ def plot_apertures(self, destination, ant_id=None, ddi=None, plot_screws=False,
         parms_passed = parms_passed and _check_parms(fname, parm_dict, 'dpi', [int], default=300)
 
         _parm_check_passed(fname, parms_passed)
-        _create_destination_folder(fname, parm_dict['destination'])
+        _create_destination_folder(parm_dict['destination'])
         _dask_general_compute(fname, self, _plot_aperture_chunk, parm_dict, ['ant', 'ddi'], parallel=parallel)
 
     def plot_beams(self, destination, ant_id=None, ddi=None, complex_split='polar', display=True, colormap='viridis',
@@ -338,7 +338,7 @@ def plot_beams(self, destination, ant_id=None, ddi=None, complex_split='polar',
         parms_passed = parms_passed and _check_parms(fname, parm_dict, 'dpi', [int], default=300)
 
         _parm_check_passed(fname, parms_passed)
-        _create_destination_folder(fname, parm_dict['destination'])
+        _create_destination_folder(parm_dict['destination'])
         _dask_general_compute(fname, self, _plot_beam_chunk, parm_dict, ['ant', 'ddi'], parallel=parallel)
 
 
@@ -533,7 +533,7 @@ def plot_diagnostics(self, destination, delta=0.01, ant_id=None, ddi=None, map_i
         parms_passed = parms_passed and _check_parms(fname, parm_dict, 'parallel', [bool], default=False)
 
         _parm_check_passed(fname, parms_passed)
-        _create_destination_folder(fname, parm_dict['destination'])
+        _create_destination_folder(parm_dict['destination'])
         key_order = ["ddi", "map", "ant"]
         _dask_general_compute(fname, self, _calibration_plot_chunk, parm_dict, key_order, parallel)
 
@@ -678,7 +678,7 @@ def export_screws(self, destination, ant_id=None, ddi=None, unit='mm', threshold
         parms_passed = parms_passed and _check_parms(fname, parm_dict, 'dpi', [int], default=300)
 
         _parm_check_passed(fname, parms_passed)
-        _create_destination_folder(fname, parm_dict['destination'])
+        _create_destination_folder(parm_dict['destination'])
         _dask_general_compute(fname, self, _export_screws_chunk, parm_dict, ['ant', 'ddi'], parallel=False)
 
     def plot_antennae(self, destination, ant_id=None, ddi=None, plot_type='deviation', plot_screws=False, unit=None,
@@ -769,7 +769,7 @@ def plot_antennae(self, destination, ant_id=None, ddi=None, plot_type='deviation
         parms_passed = parms_passed and _check_parms(fname, parm_dict, 'dpi', [int], default=300)
 
         _parm_check_passed(fname, parms_passed)
-        _create_destination_folder(fname, parm_dict['destination'])
+        _create_destination_folder(parm_dict['destination'])
         _dask_general_compute(fname, self, _plot_antenna_chunk, parm_dict, ['ant', 'ddi'], parallel=parallel)
 
     def export_to_fits(self, destination, ant_id=None, ddi=None, parallel=False):
@@ -806,7 +806,7 @@ def export_to_fits(self, destination, ant_id=None, ddi=None, parallel=False):
         parms_passed = parms_passed and _check_parms(fname, parm_dict, 'parallel', [bool], default=True)
 
         _parm_check_passed(fname, parms_passed)
-        _create_destination_folder(fname, parm_dict['destination'])
+        _create_destination_folder(parm_dict['destination'])
         _dask_general_compute(fname, self, _export_to_fits_panel_chunk, parm_dict, ['ant', 'ddi'], parallel=parallel)