<s> """<STR_LIT>""" <EOL> import os <EOL> import csv <EOL> import numpy as np <EOL> import pandas as pd <EOL> import pdb <EOL> from . . features . worm_features import WormFeaturesDos <EOL> from . . import utils <EOL> class Specs ( object ) : <EOL> """<STR_LIT>""" <EOL> def __init__ ( self ) : <EOL> """<STR_LIT>""" <EOL> self . fields_needed = [ <EOL> '<STR_LIT>' , <EOL> '<STR_LIT>' , <EOL> '<STR_LIT>' , <EOL> '<STR_LIT>' , <EOL> '<STR_LIT>' , <EOL> '<STR_LIT:name>' , <EOL> '<STR_LIT>' , <EOL> '<STR_LIT>' , <EOL> '<STR_LIT>' , <EOL> '<STR_LIT>' , <EOL> '<STR_LIT>' , <EOL> '<STR_LIT>' , <EOL> '<STR_LIT>' , <EOL> '<STR_LIT>' ] <EOL> def __repr__ ( self ) : <EOL> return utils . print_object ( self ) <EOL> @ property <EOL> def long_field ( self ) : <EOL> """<STR_LIT>""" <EOL> value = self . feature_field <EOL> if hasattr ( self , '<STR_LIT>' ) and not self . sub_field is not None and self . sub_field != '<STR_LIT>' : <EOL> value += '<STR_LIT:.>' + self . sub_field <EOL> return value <EOL> def get_data ( self , worm_features ) : <EOL> """<STR_LIT>""" <EOL> import pdb <EOL> pdb . set_trace ( ) <EOL> data_object = worm_features . get_feature ( self . feature_field ) <EOL> if data_object is None : <EOL> raise Exception ( "<STR_LIT>" + <EOL> "<STR_LIT>" + self . long_field ) <EOL> else : <EOL> data_array = data_object . value <EOL> return data_array <EOL> data = worm_features <EOL> import pdb <EOL> pdb . set_trace ( ) <EOL> for cur_feature_field in self . feature_field . split ( '<STR_LIT:.>' ) : <EOL> if not hasattr ( data , cur_feature_field ) : <EOL> import pdb <EOL> pdb . set_trace ( ) <EOL> raise Exception ( "<STR_LIT>" + <EOL> "<STR_LIT>" + cur_feature_field + <EOL> "<STR_LIT>" + self . long_field ) <EOL> data = getattr ( data , cur_feature_field ) <EOL> return data <EOL> @ classmethod <EOL> def specs_factory ( cls , csv_path , class_function_handle ) : <EOL> """<STR_LIT>""" <EOL> data_types = { <NUM_LIT:1> : str , <NUM_LIT:2> : float , <NUM_LIT:3> : int , <NUM_LIT:4> : bool } <EOL> feature_type = '<STR_LIT>' <EOL> fs = WormFeaturesDos . get_feature_spec ( extended = False ) <EOL> fs = fs [ fs [ '<STR_LIT>' ] == feature_type ] <EOL> stats_instances = [ ] <EOL> for featureID , feature_details in fs . iterrows ( ) : <EOL> feature_details = feature_details . to_dict ( ) <EOL> stats_instance = class_function_handle ( ) <EOL> import pdb <EOL> pdb . set_trace ( ) <EOL> for feature_detail_key in fields_needed : <EOL> value = feature_details [ feature_detail_key ] <EOL> setattr ( stats_instance , feature_detail_key , value ) <EOL> stats_instances . append ( stats_instance ) <EOL> pdb . set_trace ( ) <EOL> return stats_instances <EOL> with open ( csv_path ) as feature_metadata_file : <EOL> feature_metadata = csv . DictReader ( feature_metadata_file ) <EOL> field_data_types = next ( feature_metadata ) <EOL> for row in feature_metadata : <EOL> stats_instance = class_function_handle ( ) <EOL> for field in row : <EOL> value = None <EOL> if ( row [ field ] != '<STR_LIT>' ) : <EOL> data_type = data_types [ int ( field_data_types [ field ] ) ] <EOL> if data_type == bool : <EOL> value = bool ( int ( row [ field ] ) ) <EOL> else : <EOL> value = data_type ( row [ field ] ) <EOL> setattr ( stats_instance , field , value ) <EOL> if stats_instance . feature_field : <EOL> stats_instances . append ( stats_instance ) <EOL> return stats_instances <EOL> class SimpleSpecs ( Specs ) : <EOL> """<STR_LIT>""" <EOL> def __init__ ( self ) : <EOL> pass <EOL> @ classmethod <EOL> def specs_factory ( cls ) : <EOL> """<STR_LIT>""" <EOL> csv_path = os . path . join ( os . path . dirname ( os . path . realpath ( __file__ ) ) , <EOL> '<STR_LIT>' , <EOL> '<STR_LIT>' ) <EOL> return super ( SimpleSpecs , cls ) . specs_factory ( csv_path , SimpleSpecs ) <EOL> class MovementSpecs ( Specs ) : <EOL> """<STR_LIT>""" <EOL> def __init__ ( self ) : <EOL> pass <EOL> @ classmethod <EOL> def specs_factory ( cls ) : <EOL> """<STR_LIT>""" <EOL> csv_path = os . path . join ( os . path . dirname ( os . path . realpath ( __file__ ) ) , <EOL> '<STR_LIT>' , <EOL> '<STR_LIT>' ) <EOL> return super ( MovementSpecs , cls ) . specs_factory ( csv_path , MovementSpecs ) <EOL> def get_data ( self , worm_features ) : <EOL> """<STR_LIT>""" <EOL> data = super ( MovementSpecs , self ) . get_data ( worm_features ) <EOL> if self . index is not None and data is not None : <EOL> data = data [ self . index , : ] <EOL> return data <EOL> class EventSpecs ( Specs ) : <EOL> """<STR_LIT>""" <EOL> def __init__ ( self ) : <EOL> pass <EOL> @ classmethod <EOL> def specs_factory ( cls ) : <EOL> """<STR_LIT>""" <EOL> csv_path = os . path . join ( os . path . dirname ( os . path . realpath ( __file__ ) ) , <EOL> '<STR_LIT>' , <EOL> '<STR_LIT>' ) <EOL> return super ( EventSpecs , cls ) . specs_factory ( csv_path , EventSpecs ) <EOL> def get_data ( self , worm_features , num_samples = - <NUM_LIT:1> ) : <EOL> """<STR_LIT>""" <EOL> if num_samples == <NUM_LIT:0> : <EOL> num_samples = worm_features . nw . length . size <EOL> parent_data = super ( EventSpecs , self ) . get_data ( worm_features ) <EOL> if num_samples <= <NUM_LIT:0> : <EOL> num_samples = len ( worm_features . morphology . length ) <EOL> parent_data = super ( EventSpecs , self ) . getData ( worm_features ) <EOL> if parent_data is None or parent_data . is_null : <EOL> return None <EOL> if self . sub_field is not None : <EOL> data = getattr ( parent_data , self . sub_field ) <EOL> if self . is_signed : <EOL> negate_mask = getattr ( parent_data , self . signed_field ) <EOL> if len ( negate_mask ) == <NUM_LIT:1> and negate_mask : <EOL> data *= - <NUM_LIT:1> <EOL> elif len ( negate_mask ) == len ( data ) : <EOL> data [ negate_mask ] *= - <NUM_LIT:1> <EOL> elif len ( negate_mask ) == len ( data ) + <NUM_LIT:1> : <EOL> data [ negate_mask [ <NUM_LIT:1> : ] ] *= - <NUM_LIT:1> <EOL> else : <EOL> raise Exception ( "<STR_LIT>" + <EOL> self . signed_field + "<STR_LIT>" + <EOL> self . long_field + "<STR_LIT:U+002CU+0020>" + <EOL> "<STR_LIT>" + <EOL> "<STR_LIT>" + <EOL> "<STR_LIT>" ) <EOL> if self . remove_partial_events : <EOL> start_frames = parent_data . start_frames <EOL> end_frames = parent_data . end_frames <EOL> remove_mask = np . empty ( len ( data ) , dtype = bool ) * False <EOL> if start_frames [ <NUM_LIT:0> ] == <NUM_LIT:0> : <EOL> remove_mask [ : end_frames [ <NUM_LIT:0> ] + <NUM_LIT:1> ] = True <EOL> if end_frames [ - <NUM_LIT:1> ] == num_samples : <EOL> remove_mask [ start_frames [ - <NUM_LIT:1> ] : ] = True <EOL> try : <EOL> data = data [ ~ remove_mask ] <EOL> except : <EOL> pdb . set_trace ( ) <EOL> else : <EOL> pdb . set_trace ( ) <EOL> raise Exception ( "<STR_LIT>" + <EOL> self . long_field ) <EOL> if ( not isinstance ( data , ( float , int ) ) and <EOL> data . size == <NUM_LIT:0> and <EOL> self . make_zero_if_empty ) : <EOL> data = <NUM_LIT:0> <EOL> return data </s>
