Source code for openquake.hmtk.parsers.catalogue.csv_catalogue_parser

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"""
Module :mod:`openquake.hmtk.parsers.catalogue.csv_catalogue_parser`
implements :class:`CsvCatalogueParser`.
"""
import csv
import numpy as np
from copy import deepcopy
from openquake.hmtk.seismicity.catalogue import Catalogue
from openquake.hmtk.seismicity.gcmt_catalogue import GCMTCatalogue
from openquake.hmtk.parsers.catalogue.base import (
    BaseCatalogueParser, BaseCatalogueWriter)


[docs]class CsvCatalogueParser(BaseCatalogueParser): """CSV Catalogue Parser Class """
[docs] def read_file(self, start_year=None, end_year=None): """ """ filedata = open(self.input_file, 'rU') catalogue = self._setup_catalogue() # Reading the data file data = csv.DictReader(filedata) # Parsing the data content for irow, row in enumerate(data): if irow == 0: valid_key_list = self._header_check( row.keys(), catalogue.TOTAL_ATTRIBUTE_LIST) for key in valid_key_list: if key in catalogue.FLOAT_ATTRIBUTE_LIST: catalogue.data[key] = self._float_check( catalogue.data[key], row[key], irow, key) elif key in catalogue.INT_ATTRIBUTE_LIST: catalogue.data[key] = self._int_check( catalogue.data[key], row[key], irow, key) else: catalogue.data[key].append(row[key]) if start_year: catalogue.start_year = start_year else: catalogue.update_start_year() if end_year: catalogue.end_year = end_year else: catalogue.update_end_year() return catalogue
def _setup_catalogue(self): """ Returns a blank catalogue instance """ return Catalogue() def _header_check(self, input_keys, catalogue_keys): valid_key_list = [] for element in input_keys: if element in catalogue_keys: valid_key_list.append(element) else: print('Catalogue Attribute %s is not ' 'a recognised catalogue key' % element) return valid_key_list def _float_check(self, attribute_array, value, irow, key): '''Checks if value is valid float, appends to array if valid, appends nan if not''' value = value.strip(' ') try: if value: attribute_array = np.hstack([attribute_array, float(value)]) else: attribute_array = np.hstack([attribute_array, np.nan]) except: print(irow, key) msg = 'Input file format error at line: %d' % (irow+2) msg += ' key: %s' % (key) raise ValueError(msg) return attribute_array def _int_check(self, attribute_array, value, irow, key): '''Checks if value is valid integer, appends to array if valid, appends nan if not''' value = value.strip(' ') try: if value: attribute_array = np.hstack([attribute_array, int(value)]) else: attribute_array = np.hstack([attribute_array, np.nan]) except: msg = 'Input file format error at line: %d' % (irow+2) msg += ' key: %s' % (key) raise ValueError(msg) return attribute_array
[docs]class GCMTCsvCatalogueParser(CsvCatalogueParser): """ """ def _setup_catalogue(self): """ """ return GCMTCatalogue()
[docs]class CsvCatalogueWriter(BaseCatalogueWriter): ''' Writes catalogue to csv file ''' # Because the catalogues TOTAL_ATTRIBUTE_LIST is randomly ordered, # the preferred output order is given as a list here OUTPUT_LIST = ['eventID', 'Agency', 'year', 'month', 'day', 'hour', 'minute', 'second', 'timeError', 'longitude', 'latitude', 'SemiMajor90', 'SemiMinor90', 'ErrorStrike', 'depth', 'depthError', 'magnitude', 'sigmaMagnitude', 'magnitudeType']
[docs] def write_file(self, catalogue, flag_vector=None, magnitude_table=None): ''' Writes the catalogue to file, purging events if necessary. :param catalogue: Earthquake catalogue as instance of :class: openquake.hmtk.seismicity.catalogue.Catalogue :param numpy.array flag_vector: Boolean vector specifying whether each event is valid (therefore written) or otherwise :param numpy.ndarray magnitude_table: Magnitude-time table specifying the year and magnitudes of completeness ''' # First apply purging conditions output_catalogue = self.apply_purging(catalogue, flag_vector, magnitude_table) outfile = open(self.output_file, 'wt') writer = csv.DictWriter(outfile, fieldnames=self.OUTPUT_LIST) writer.writeheader() # Quick check to remove nan arrays for key in self.OUTPUT_LIST: cond = (isinstance(output_catalogue.data[key], np.ndarray) and np.all(np.isnan(output_catalogue.data[key]))) if cond: output_catalogue.data[key] = [] # Write the catalogue for iloc in range(0, output_catalogue.get_number_events()): row_dict = {} for key in self.OUTPUT_LIST: if len(output_catalogue.data[key]) > 0: row_dict[key] = output_catalogue.data[key][iloc] else: row_dict[key] = '' writer.writerow(row_dict) outfile.close()
[docs] def apply_purging(self, catalogue, flag_vector, magnitude_table): ''' Apply all the various purging conditions, if specified. :param catalogue: Earthquake catalogue as instance of :class:`openquake.hmtk.seismicity.catalogue.Catalogue` :param numpy.array flag_vector: Boolean vector specifying whether each event is valid (therefore written) or otherwise :param numpy.ndarray magnitude_table: Magnitude-time table specifying the year and magnitudes of completeness ''' output_catalogue = deepcopy(catalogue) if magnitude_table is not None: if flag_vector is not None: output_catalogue.catalogue_mt_filter( magnitude_table, flag_vector) return output_catalogue else: output_catalogue.catalogue_mt_filter( magnitude_table) return output_catalogue if flag_vector is not None: output_catalogue.purge_catalogue(flag_vector) return output_catalogue
[docs]class CsvGCMTCatalogueWriter(CsvCatalogueWriter): ''' Writes GCMT catalogue to csv file ''' OUTPUT_LIST = ['eventID', 'centroidID', 'Agency', 'year', 'month', 'day', 'hour', 'minute', 'second', 'timeError', 'longitude', 'latitude', 'depth', 'depthError', 'magnitude', 'sigmaMagnitude', 'magnitudeType', 'moment', 'SemiMajor90', 'SemiMinor90', 'ErrorStrike', 'strike1', 'rake1', 'dip1', 'strike2', 'rake2', 'dip2', 'f_clvd', 'e_rel', 'eigenvalue_b', 'azimuth_b', 'plunge_b', 'eigenvalue_p', 'azimuth_p', 'plunge_p', 'eigenvalue_t', 'azimuth_t', 'plunge_t']
[docs] def write_file(self, catalogue, flag_vector=None, magnitude_table=None): ''' Writes the catalogue to file, purging events if necessary. :param catalogue: Earthquake catalogue as instance of :class: openquake.hmtk.seismicity.catalogue.Catalogue :param numpy.array flag_vector: Boolean vector specifying whether each event is valid (therefore written) or otherwise :param numpy.ndarray magnitude_table: Magnitude-time table specifying the year and magnitudes of completeness ''' # First apply purging conditions output_catalogue = self.apply_purging(catalogue, flag_vector, magnitude_table) outfile = open(self.output_file, 'wt') writer = csv.DictWriter(outfile, fieldnames=self.OUTPUT_LIST) writer.writeheader() # Quick check to remove nan arrays for key in self.OUTPUT_LIST: cond = (isinstance(output_catalogue.data[key], np.ndarray) and np.all(np.isnan(output_catalogue.data[key]))) if cond: output_catalogue.data[key] = [] # Write the catalogue for iloc in range(0, output_catalogue.get_number_events()): row_dict = {} for key in self.OUTPUT_LIST: if len(output_catalogue.data[key]) > 0: row_dict[key] = output_catalogue.data[key][iloc] else: row_dict[key] = '' writer.writerow(row_dict) outfile.close()
[docs] def apply_purging(self, catalogue, flag_vector, magnitude_table): ''' Apply all the various purging conditions, if specified. :param catalogue: Earthquake catalogue as instance of :class: openquake.hmtk.seismicity.catalogue.Catalogue: :param numpy.array flag_vector: Boolean vector specifying whether each event is valid (therefore written) or otherwise :param numpy.ndarray magnitude_table: Magnitude-time table specifying the year and magnitudes of completeness ''' output_catalogue = deepcopy(catalogue) if magnitude_table is not None: if flag_vector is not None: output_catalogue.catalogue_mt_filter( magnitude_table, flag_vector) return output_catalogue else: output_catalogue.catalogue_mt_filter( magnitude_table) return output_catalogue if flag_vector is not None: output_catalogue.purge_catalogue(flag_vector) return output_catalogue