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fhd.py
"""Class for reading FHD save files."""
from astropy import constants as const
from scipy.io.idl import readsav
from itertools import islice
import numpy as np
import warnings
from uvdata import UVData


class FHD(UVData):
    """
    Defines a FHD-specific subclass of UVData for reading FHD save files.
    This class should not be interacted with directly, instead use the read_fhd
    method on the UVData class.
    """

    def read_fhd(self, filelist, use_model=False, run_check=True, run_check_acceptability=True):
        """
        Read in data from a list of FHD files.

        Args:
            filelist: The list of FHD save files to read from. Must include at
                least one polarization file, a params file and a flag file.
            use_model: Option to read in the model visibilities rather than the
                dirty visibilities. Default is False.
            run_check: Option to check for the existence and proper shapes of
                required parameters after reading in the file. Default is True.
            run_check_acceptability: Option to check acceptable range of the values of
                required parameters after reading in the file. Default is True.
        """
        datafiles = {}
        params_file = None
        flags_file = None
        settings_file = None
        if use_model:
            data_name = '_vis_model_'
        else:
            data_name = '_vis_'
        for file in filelist:
            if file.lower().endswith(data_name + 'xx.sav'):
                datafiles['xx'] = xx_datafile = file
            elif file.lower().endswith(data_name + 'yy.sav'):
                datafiles['yy'] = yy_datafile = file
            elif file.lower().endswith(data_name + 'xy.sav'):
                datafiles['xy'] = xy_datafile = file
            elif file.lower().endswith(data_name + 'yx.sav'):
                datafiles['yx'] = yx_datafile = file
            elif file.lower().endswith('_params.sav'):
                params_file = file
            elif file.lower().endswith('_flags.sav'):
                flags_file = file
            elif file.lower().endswith('_settings.txt'):
                settings_file = file
            else:
                continue

        if len(datafiles) < 1:
            raise StandardError('No data files included in file list')
        if params_file is None:
            raise StandardError('No params file included in file list')
        if flags_file is None:
            raise StandardError('No flags file included in file list')
        if settings_file is None:
            warnings.warn('No settings file included in file list')

        # TODO: add checking to make sure params, flags and datafiles are
        # consistent with each other

        vis_data = {}
        for pol, file in datafiles.iteritems():
            this_dict = readsav(file, python_dict=True)
            if use_model:
                vis_data[pol] = this_dict['vis_model_ptr']
            else:
                vis_data[pol] = this_dict['vis_ptr']
            this_obs = this_dict['obs']
            data_shape = vis_data[pol].shape

        obs = this_obs
        bl_info = obs['BASELINE_INFO'][0]
        meta_data = obs['META_DATA'][0]
        astrometry = obs['ASTR'][0]
        fhd_pol_list = []
        for pol in obs['POL_NAMES'][0]:
            fhd_pol_list.append(pol.decode("utf-8").lower())

        params_dict = readsav(params_file, python_dict=True)
        params = params_dict['params']

        flag_file_dict = readsav(flags_file, python_dict=True)
        # The name for this variable changed recently (July 2016). Test for both.
        vis_weights_data = {}
        if 'flag_arr' in flag_file_dict:
            weights_key = 'flag_arr'
        elif 'vis_weights' in flag_file_dict:
            weights_key = 'vis_weights'
        else:
            raise ValueError('No recognized key for visibility weights in flags_file.')
        for index, w in enumerate(flag_file_dict[weights_key]):
            vis_weights_data[fhd_pol_list[index]] = w

        self.Ntimes = int(obs['N_TIME'][0])
        self.Nbls = int(obs['NBASELINES'][0])
        self.Nblts = data_shape[0]
        self.Nfreqs = int(obs['N_FREQ'][0])
        self.Npols = len(vis_data.keys())
        self.Nspws = 1
        self.spw_array = np.array([0])
        self.vis_units = 'JY'

        lin_pol_order = ['xx', 'yy', 'xy', 'yx']
        linear_pol_dict = dict(zip(lin_pol_order, np.arange(5, 9) * -1))
        pol_list = []
        for pol in lin_pol_order:
            if pol in vis_data:
                pol_list.append(linear_pol_dict[pol])
        self.polarization_array = np.asarray(pol_list)

        self.data_array = np.zeros((self.Nblts, self.Nspws, self.Nfreqs,
                                    self.Npols), dtype=np.complex_)
        self.nsample_array = np.zeros((self.Nblts, self.Nspws, self.Nfreqs,
                                       self.Npols), dtype=np.float_)
        self.flag_array = np.zeros((self.Nblts, self.Nspws, self.Nfreqs,
                                    self.Npols), dtype=np.bool_)
        for pol, vis in vis_data.iteritems():
            pol_i = pol_list.index(linear_pol_dict[pol])
            self.data_array[:, 0, :, pol_i] = vis
            self.flag_array[:, 0, :, pol_i] = vis_weights_data[pol] <= 0
            self.nsample_array[:, 0, :, pol_i] = np.abs(vis_weights_data[pol])

        # In FHD, uvws are in seconds not meters!
        self.uvw_array = np.zeros((self.Nblts, 3))
        self.uvw_array[:, 0] = params['UU'][0] * const.c.to('m/s').value
        self.uvw_array[:, 1] = params['VV'][0] * const.c.to('m/s').value
        self.uvw_array[:, 2] = params['WW'][0] * const.c.to('m/s').value

        # bl_info.JDATE (a vector of length Ntimes) is the only safe date/time
        # to use in FHD files.
        # (obs.JD0 (float) and params.TIME (vector of length Nblts) are
        #   context dependent and are not safe
        #   because they depend on the phasing of the visibilities)
        # the values in bl_info.JDATE are the JD for each integration.
        # We need to expand up to Nblts.
        int_times = bl_info['JDATE'][0]
        bin_offset = bl_info['BIN_OFFSET'][0]
        if self.Ntimes != len(int_times):
            warnings.warn('Ntimes does not match the number of unique times in the data')
        self.time_array = np.zeros(self.Nblts)
        if self.Ntimes == 1:
            self.time_array.fill(int_times)
        else:
            for ii in range(0, len(int_times)):
                if ii < (len(int_times) - 1):
                    self.time_array[bin_offset[ii]:bin_offset[ii + 1]] = int_times[ii]
                else:
                    self.time_array[bin_offset[ii]:] = int_times[ii]

        # Note that FHD antenna arrays are 1-indexed so we subtract 1
        # to get 0-indexed arrays
        self.ant_1_array = bl_info['TILE_A'][0] - 1
        self.ant_2_array = bl_info['TILE_B'][0] - 1

        self.Nants_data = int(len(np.unique(self.ant_1_array.tolist() + self.ant_2_array.tolist())))

        self.antenna_names = bl_info['TILE_NAMES'][0].tolist()
        self.Nants_telescope = len(self.antenna_names)
        self.antenna_numbers = np.arange(self.Nants_telescope)

        self.baseline_array = \
            self.antnums_to_baseline(self.ant_1_array,
                                     self.ant_2_array)
        if self.Nbls != len(np.unique(self.baseline_array)):
            warnings.warn('Nbls does not match the number of unique baselines in the data')

        if len(bl_info['FREQ'][0]) != self.Nfreqs:
            warnings.warn('Nfreqs does not match the number of frequencies in the data')
        self.freq_array = np.zeros((self.Nspws, len(bl_info['FREQ'][0])), dtype=np.float_)
        self.freq_array[0, :] = bl_info['FREQ'][0]

        if not np.isclose(obs['OBSRA'][0], obs['PHASERA'][0]) or \
                not np.isclose(obs['OBSDEC'][0], obs['PHASEDEC'][0]):
            warnings.warn('These visibilities may have been phased '
                          'improperly -- without changing the uvw locations')

        self.set_phased()
        self.phase_center_ra_degrees = np.float(obs['OBSRA'][0])
        self.phase_center_dec_degrees = np.float(obs['OBSDEC'][0])

        # this is generated in FHD by subtracting the JD of neighboring
        # integrations. This can have limited accuracy, so it can be slightly
        # off the actual value.
        # (e.g. 1.999426... rather than 2)
        self.integration_time = float(obs['TIME_RES'][0])
        self.channel_width = float(obs['FREQ_RES'][0])

        # # --- observation information ---
        self.telescope_name = str(obs['INSTRUMENT'][0].decode())

        # This is a bit of a kludge because nothing like object_name exists
        # in FHD files.
        # At least for the MWA, obs.ORIG_PHASERA and obs.ORIG_PHASEDEC specify
        # the field the telescope was nominally pointing at
        # (May need to be revisited, but probably isn't too important)
        self.object_name = 'Field RA(deg): ' + str(obs['ORIG_PHASERA'][0]) + \
                           ', Dec:' + str(obs['ORIG_PHASEDEC'][0])
        # For the MWA, this can sometimes be converted to EoR fields
        if self.telescope_name.lower() == 'mwa':
            if np.isclose(obs['ORIG_PHASERA'][0], 0) and \
                    np.isclose(obs['ORIG_PHASEDEC'][0], -27):
                object_name = 'EoR 0 Field'

        self.instrument = self.telescope_name
        self.telescope_location_lat_lon_alt_degrees = (float(obs['LAT'][0]),
                                                       float(obs['LON'][0]),
                                                       float(obs['ALT'][0]))

        self.set_lsts_from_time_array()

        # history: add the first few lines from the settings file
        if settings_file is not None:
            history_list = ['fhd settings info']
            with open(settings_file) as f:
                # TODO Make this reading more robust.
                head = list(islice(f, 11))
            for line in head:
                newline = ' '.join(str.split(line))
                if not line.startswith('##'):
                    history_list.append(newline)
            self.history = '    '.join(history_list)
        else:
            self.history = ''
        if self.pyuvdata_version_str not in self.history.replace('\n', ''):
            self.history += self.pyuvdata_version_str

        self.phase_center_epoch = astrometry['EQUINOX'][0]

        # TODO Once FHD starts reading and saving the antenna table info from
        #    uvfits, that information should be read into the following optional
        #    parameters:
        # 'xyz_telescope_frame'
        # 'x_telescope'
        # 'y_telescope'
        # 'z_telescope'
        # 'antenna_positions'
        # 'GST0'
        # 'RDate'
        # 'earth_omega'
        # 'DUT1'
        # 'TIMESYS'

        try:
            self.set_telescope_params()
        except ValueError, ve:
            warnings.warn(str(ve))

        # check if object has all required uv_properties set
        if run_check:
            self.check(run_check_acceptability=run_check_acceptability)
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