SSB-42: preliminary implementation of the datacontainers objects

.gitattributes

@@ -11,7 +11,7 @@ CAL/CalibrationCommon/lib/__init__.py -text
 CAL/CalibrationCommon/lib/coordinates.py -text
 CAL/CalibrationCommon/lib/datacontainers/__init__.py -text
 CAL/CalibrationCommon/lib/datacontainers/holography_dataset.py -text
-CAL/CalibrationCommon/lib/datacontainers/holography_observation_specification.py -text
+CAL/CalibrationCommon/lib/datacontainers/holography_observation.py -text
 CAL/CalibrationCommon/lib/datacontainers/holography_specification.py -text
 CAL/CalibrationCommon/lib/datacontainers/measurementset.py -text
 CAL/CalibrationCommon/lib/mshologextract.py -text

CAL/CalibrationCommon/lib/datacontainers/__init__.py

 
 from .holography_dataset import HolographyDataset
 from .holography_specification import HolographySpecification
-from .holography_observation_specification import HolographyObservationSpecification
+from .holography_observation import HolographyObservation
 from .measurementset import MeasurementSet
 
 
-__all__ = [HolographyDataset, HolographyObservationSpecification, HolographySpecification, MeasurementSet]
\ No newline at end of file
+__all__ = [HolographyDataset, HolographyObservation, HolographySpecification, MeasurementSet]
\ No newline at end of file

CAL/CalibrationCommon/lib/datacontainers/holography_dataset.py

+from .holography_specification import HolographySpecification
+from .holography_observation import HolographyObservation
+
+
 class HolographyDataset():
     def __init__(self):
-        self.rcu_list = ()  # array of ints
+        self.rcu_list = set()  # array of ints
         self.mode = None  # integer
-        self.sas_ids = ()  # array of strings
+        self.sas_ids = set()  # array of strings
         self.target_station_name = None  # string
         self.target_station_position = None  # list of 3 floats
         self.source_name = None  # string
         self.source_position = None  # list of 3 floats
-        self.start_time = None  # date time when the observation started in MJD (float)
-        self.end_time = None  # date time when the observation started in MJD (float)
+        self.start_time = None  # date time when the observation started in MJD in seconds (float)
+        self.end_time = None  # date time when the observation started in MJD in seconds (float)
         self.rotation_matrix = None  # array(3,3), translation matrix for
         # (RA, DEC) <-> (l, m) conversion
-        self.antenna_field_position = ()  # coordinates of the antenna position in the target
+        self.antenna_field_position = []  # coordinates of the antenna position in the target
         # station
-        self.reference_stations = ()  # list of reference station names
-        self.frequencies = ()  # list of frequencies
-        self.ra_dec = () # array(Nfrequency, Nbeamlets, 2) contains the ra_dec of which a beam
+        self.reference_stations = set()  # set of reference station names
+        self.frequencies = set()  # set of frequencies
+        self.ra_dec = None # array(Nfrequency, Nbeamlets, 2) contains the ra_dec of which a beam
         # points at given a frequency and a beamlet number
-        self.data = () # array(NreferenceStations, Nfrequencies, Nbeamlets) that contains the
+        self.data = None # array(NreferenceStations, Nfrequencies, Nbeamlets) that contains the
         # 4 polarization crosscorrelation for the 4 polarizations, the l and m coordinates, and
         # the timestamp in mjd of the sample
 
@@ -27,21 +31,65 @@ class HolographyDataset():
         name
         :param station_name: target station name
         :param hb_specifications: a list containing (hbs, ms) per frequency
+
         """
+        self.__collect_preliminary_information(station_name, list_of_hbs_ms_tuples)
 
-    def __collect_preliminary_information(self, list_of_hbs_ms_tuples):
+    def __collect_preliminary_information(self, station_name, list_of_hbs_ho_tuples):
         """
         This routines reads both the holography beam specifications files and the holography
-        measurement sets to gather the list of rcus, the mode, the target station name and position,
+        observation to gather the list of rcus, the mode, the target station name and position,
         the source name and position, the start and the end time, the rotation matrix to convert
         from ra and dec to l and m, the antenna field positions, the list of the reference
         stations, the frequencies, the ra and dec at which the beams point at.
 
         All this data is essential to interpret the recorded holography beams cross correlations
-        :param list_of_hbs_ms_tuples: a list containing (hbs, ms) per frequency
+        :param list_of_hbs_ho_tuples: a list containing (hbs, ho) per frequency
+        :type list_of_hbs_ho_tuples: list[(HolographySpecification, HolographyObservation)]
         """
-        for hbs, ms in list_of_hbs_ms_tuples:
-            pass
+        mode = set()
+        source_name = set()
+        source_position = set()
+
+        for hbs, ho in list_of_hbs_ho_tuples:
+            if station_name in hbs.target_station_names:
+
+                beam_specifications = hbs.get_beam_specifications_per_station_name(station_name)
+                for beam_specification in beam_specifications:
+                    self.rcu_list.update(beam_specification.rcus_involved)
+                    mode.update(beam_specification.rcus_mode)
+                    source_name.update(ho.source_name)
+                    source_position.update(
+                        (beam_specification.station_pointing['ra'],
+                         beam_specification.station_pointing['dec'],
+                         beam_specification.station_pointing['coordinate_system']
+                        ))
+
+                    self.start_time = ho.start_mjd
+                    self.end_time = ho.end_mjd
+                    self.frequencies = ho.frequency
+                    self.sas_ids.update(ho.sas_id)
+
+                    self.target_station_name = station_name
+                    self.reference_stations.update(hbs.reference_station_names)
+
+            else:
+                continue
+
+        if len(mode) > 1:
+            raise ValueError('Multiple RCUs mode are not supported')
+        else:
+            self.mode = self.mode.pop()
+
+        if len(source_position) > 1:
+            raise ValueError('Multiple source positions are not supported')
+        else:
+            self.source_position = source_position
+
+        if len(source_name) > 1:
+            raise ValueError('Multiple source name are not supported')
+        else:
+            self.source_name = source_name
 
     @staticmethod
     def load_from_file(path):

CAL/CalibrationCommon/lib/datacontainers/holography_observation_specification.py → CAL/CalibrationCommon/lib/datacontainers/holography_observation.py

 import re
 import os
-
+import astropy.time as astrotime
+from datetime import datetime
 from .measurementset import MeasurementSet
 
-class HolographyObservationSpecification():
-    def __init__(self, path, sas_id, ms_for_a_given_beamlet, observation_start_datetime,
-                 observation_end_datetime):
+class HolographyObservation():
+    def __init__(self, path, sas_id, ms_for_a_given_beamlet_number, start_mjd_in_seconds,
+                 end_mjd_in_seconds, frequency, source_name):
+        """
+        :param path:
+        :type path: str
+        :param sas_id:
+        :type sas_id: int
+        :param ms_for_a_given_beamlet_number:
+        :param start_mjd_in_seconds:
+        :type start_mjd_in_seconds: float
+        :param end_mjd_in_seconds:
+        :type end_mjd_in_seconds: float
+        :param frequency:
+        :type frequency: float
+        :param source_name:
+        :type source_name: str
+        """
         self.path = path
         self.sas_id = sas_id
-        self.ms_for_a_given_beamlet = ms_for_a_given_beamlet
-        self.start_datetime = observation_start_datetime
-        self.end_datetime = observation_end_datetime
+        self.ms_for_a_given_beamlet_number = ms_for_a_given_beamlet_number
+        self.start_datetime = HolographyObservation.__mjd_to_datetime(start_mjd_in_seconds)
+        self.end_datetime = HolographyObservation.__mjd_to_datetime(end_mjd_in_seconds)
+        self.start_mjd = start_mjd_in_seconds
+        self.end_mjd = end_mjd_in_seconds
+        self.frequency = frequency
+        self.source_name = source_name
+
+    @staticmethod
+    def __mjd_to_datetime(mjd_time_seconds):
+        """
+        Convert the modified julian date in seconds in a datetime object
+        :param mjd_time_seconds: modified julian data in seconds
+        :return: the date time of the given julian date
+        :rtype: datetime
+        """
+        hour_in_seconds = 60 * 60
+        day_in_seconds = hour_in_seconds * 24
+        return astrotime.Time(mjd_time_seconds / day_in_seconds, format='mjd',
+                              scale='utc').to_datetime()
 
     @staticmethod
     def __compute_time_range_from_ms_list(ms_list):
@@ -23,6 +56,17 @@ class HolographyObservationSpecification():
                 observation_end = ms_end_time
         return observation_start, observation_end
 
+    @staticmethod
+    def extract_unique_source_names_from_ms_list(ms_list):
+        """
+        Returns a set of unique source names given a list of measurement sets
+        :param ms_list: a list of measurement set where to extract the reference frequencies
+        :type ms_list: list[MeasurementSet]
+        :return: a set of frequencies
+        :rtype: set[str]
+        """
+        return {ms.get_source_name() for ms in ms_list}
+
     @staticmethod
     def list_observations_in_path(path):
         ms_dir_name_pattern = 'L(?P<sas_id>\d{6})'
@@ -33,19 +77,51 @@ class HolographyObservationSpecification():
             if match:
                 sas_id = int(match.group('sas_id'))
 
-                ms_indexed_per_beamlet_number = HolographyObservationSpecification.\
+                ms_indexed_per_beamlet_number = HolographyObservation. \
                     create_ms_dict_from_ms_name_list_and_path(dirnames, root)
 
 
-                start_datetime, end_datetime = HolographyObservationSpecification.\
+                start_mjd_in_seconds, end_mjd_in_seconds = HolographyObservation.\
                     __compute_time_range_from_ms_list(
                     ms_indexed_per_beamlet_number.values())
 
+                unique_frequencies = HolographyObservation. \
+                    extract_unique_reference_frequencies_from_ms_list(
+                    ms_indexed_per_beamlet_number.values())
+
+                if len(unique_frequencies) > 1:
+                    raise ValueError(
+                        'Multiple reference frequencies per observation are not supported')
+                else:
+                    frequency = unique_frequencies.pop()
+
+                unique_source_names = HolographyObservation.\
+                    extract_unique_source_names_from_ms_list(ms_indexed_per_beamlet_number.values())
+
+                if len(unique_source_names) > 1:
+                    raise ValueError(
+                        'Multiple source target per observation are not supported'
+                    )
+                else:
+                    source_name = unique_source_names.pop()
+
                 observations_list.append(
-                    HolographyObservationSpecification(path, sas_id, ms_indexed_per_beamlet_number,
-                                                       start_datetime, end_datetime))
+                    HolographyObservation(path, sas_id, ms_indexed_per_beamlet_number,
+                                          start_mjd_in_seconds, end_mjd_in_seconds, frequency,
+                                          source_name))
         return observations_list
 
+    @staticmethod
+    def extract_unique_reference_frequencies_from_ms_list(ms_list):
+        """
+        Returns a set of reference frequencies given a list of measurement setss
+        :param ms_list: a list of measurement set where to extract the reference frequencies
+        :type ms_list: list[MeasurementSet]
+        :return: returns a set of frequencies
+        :rtype: set[float]
+        """
+        return {ms.get_frequency() for ms in ms_list}
+
     @staticmethod
     def create_ms_dict_from_ms_name_list_and_path(list_of_ms_names, path):
         """

CAL/CalibrationCommon/lib/datacontainers/holography_specification.py

@@ -4,6 +4,18 @@ import re
 import os
 
 
+class HolographyStationBeamSpecification(object):
+    station_name = None
+    rcus_mode = None
+    sub_band_ids = ()
+    mode_description = None
+    rcus_involved = ()
+    beamlets = ()
+    station_pointing = ()
+    virtual_pointing = ()
+    station_type = ()
+
+
 class HolographySpecification(object):
     hs_name_pattern = r'Holog-(?P<date>\d{8})-(?P<comment>.*)-(?P<id>\d{3}).txt'
 
@@ -12,7 +24,8 @@ class HolographySpecification(object):
         self.name = name
         self.id, self.date, self.comment = HolographySpecification.\
             extract_id_date_comment_from_name(name)
-
+        self.reference_station_names = None
+        self.target_station_names = None
         self.station_specification_map = defaultdict(list)
         self.start_datetime = None
         self.end_datetime = None
@@ -86,31 +99,27 @@ class HolographySpecification(object):
 
     @staticmethod
     def _parse_line(splitted_line):
-        rcus_mode = int(splitted_line['rcus_mode'])
-        sub_band_ids = [int(sub_band) for sub_band in splitted_line['sub_band'].split(',')]
-        mode_description = splitted_line['mode_description']
-        rcus_involved = splitted_line['rcus']
-        beamlets = splitted_line['beamlets']
 
-        station_pointing = HolographySpecification._parse_pointing(
+
+        beam_specification = HolographyStationBeamSpecification()
+
+        beam_specification.rcus_mode = int(splitted_line['rcus_mode'])
+        beam_specification.sub_band_ids = [int(sub_band) for sub_band in splitted_line['sub_band'].split(',')]
+        beam_specification.mode_description = splitted_line['mode_description']
+        beam_specification.rcus_involved = splitted_line['rcus']
+        beam_specification.beamlets = splitted_line['beamlets']
+
+        beam_specification.station_pointing = HolographySpecification._parse_pointing(
             splitted_line['station_pointing'])
-        virtual_pointing = HolographySpecification._parse_pointing(
+        beam_specification.virtual_pointing = HolographySpecification._parse_pointing(
             splitted_line['virtual_pointing'])
-        if len(sub_band_ids) == 1:
-            station_type = 'target'
+        if len(beam_specification.sub_band_ids) == 1:
+            beam_specification.station_type = 'target'
         else:
-            station_type = 'reference'
-        station_name = splitted_line['station_name']
-
-        return dict(station_name=station_name,
-                    rcus_mode=rcus_mode,
-                    sub_band_ids=sub_band_ids,
-                    mode_description=mode_description,
-                    rcus_involved=rcus_involved,
-                    beamlets=beamlets,
-                    station_pointing=station_pointing,
-                    virtual_pointing=virtual_pointing,
-                    station_type=station_type)
+            beam_specification.station_type = 'reference'
+        beam_specification.station_name = splitted_line['station_name']
+
+        return beam_specification
 
     def _parse_lines(self, lines):
         splitted_lines = HolographySpecification._split_lines(lines)
@@ -118,7 +127,7 @@ class HolographySpecification(object):
         for line in splitted_lines:
             parsed_line = HolographySpecification._parse_line(line)
 
-            self.station_specification_map[parsed_line['station_name']] += [parsed_line]
+            self.station_specification_map[parsed_line.station_name] += [parsed_line]
 
     def _update_class_attributes(self):
         self.station_names = self.station_specification_map.keys()
@@ -128,7 +137,16 @@ class HolographySpecification(object):
         self.target_station_names = [station_name for station_name in
                                         self.station_specification_map
                                         if len(self.station_specification_map[station_name]) > 1]
-        print(self.target_station_names, self.reference_station_names)
+
+    def get_beam_specifications_per_station_name(self, station_name):
+        """
+        Returns a list of beam specifications for the given station name
+        :param station_name: name of the station
+        :type station_name: str
+        :return: a list of beam specifications
+        :rtype: list[HolographyStationBeamSpecification]
+        """
+        return self.station_specification_map[station_name]
     
     def read_file(self):
         lines = self._read_lines()
@@ -154,5 +172,3 @@ class HolographySpecification(object):
         date = datetime.datetime.strptime(date, '%Y%m%d')
         return hs_id, date, comment
 
-
-

CAL/CalibrationCommon/lib/datacontainers/measurementset.py

@@ -3,6 +3,7 @@ import astropy.time as astrotime
 import os
 import re
 
+
 class MeasurementSet(object):
     ms_name_pattern = r'L(?P<sas_id>\d{6})_SB(?P<sub_band_id>\d{3})_uv\.MS'
 
@@ -29,10 +30,48 @@ class MeasurementSet(object):
         data_table = MS_Table(self.path)
         return data_table
 
+    def get_pointing_table(self):
+        pointing_table = MS_Table(self.path + '/POINTING')
+        return pointing_table
+
     def get_antenna_table(self):
         antenna_table = MS_Table(self.path + '/ANTENNA')
         return antenna_table
 
+    def get_lofar_antenna_field_table(self):
+        antenna_field_table = MS_Table(self.path + '/LOFAR_ANTENNA_FIELD')
+        return antenna_field_table
+
+    def get_station_position_tile_offsets_and_axes_coordinate_for_station_name(self, station_name):
+        antenna_table = self.get_antenna_table()
+        antenna_field_table = self.get_lofar_antenna_field_table()
+        try:
+            station_name_index = antenna_table.index('NAME').rownr(station_name)
+
+            station_position = antenna_field_table.getcell('POSITION', station_name_index)
+            tile_offsets = antenna_field_table.getcell('TILE_ELEMENT_OFFSET', station_name_index)
+            axes_coordinate = antenna_field_table.getcell('COORDINATE_AXES', station_name_index)
+
+        finally:
+            antenna_table.close()
+            antenna_field_table.close()
+        return (station_position, tile_offsets, axes_coordinate)
+
+
+    def __extract_source_name_from_pointing(self):
+        pointing_table = self.get_pointing_table()
+        try:
+            unique_names = {name for name in pointing_table.getcol('NAME')}
+
+            if len(unique_names) > 1:
+                raise ValueError('Expected only a source as a target for the observation')
+            else:
+                source_name = unique_names.pop()
+        finally:
+            pointing_table.close()
+
+        return source_name
+
     def get_spectral_window_table(self):
         spectral_window_table = MS_Table(self.path + '/SPECTRAL_WINDOW')
         return spectral_window_table
@@ -45,15 +84,16 @@ class MeasurementSet(object):
         observation_table = self.get_observation_table()
 
         try:
-            start_time_in_seconds, end_time_in_seconds = observation_table.getcol('TIME_RANGE')
-            hour_in_seconds = 60 * 60
-            day_in_seconds = hour_in_seconds * 24
-            start_time = astrotime.Time(start_time_in_seconds/day_in_seconds, format='mjd', scale='utc')
-            end_time = astrotime.Time(start_time_in_seconds / day_in_seconds, format='mjd', scale='utc')
+            start_time, end_time = observation_table.getcol('TIME_RANGE')
+
         finally:
             observation_table.close()
 
-        return start_time.to_datetime(), end_time.to_datetime()
+        return start_time, end_time
+
+    def get_source_name(self):
+        return self.__extract_source_name_from_pointing()
+
 
     def read_cross_correlation_per_station_names(self, reference, target):
         data_table = self.get_data_table()