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| import os | |
| import warnings | |
| warnings.filterwarnings("ignore", category=DeprecationWarning) | |
| import pandas as pd | |
| import difflib | |
| import json | |
| import pickle as pkl | |
| import csv | |
| import numpy as np | |
| # ----------------------------------------------------------------------------------------------------------------- # | |
| class DogBreed(object): | |
| def __init__(self, abbrev, name_akc=None, name_stanext=None, name_xlsx=None, path_akc=None, path_stanext=None, ind_in_xlsx=None, ind_in_xlsx_matrix=None, ind_in_stanext=None, clade=None): | |
| self._abbrev = abbrev | |
| self._name_xlsx = name_xlsx | |
| self._name_akc = name_akc | |
| self._name_stanext = name_stanext | |
| self._path_stanext = path_stanext | |
| self._additional_names = set() | |
| if self._name_akc is not None: | |
| self.add_akc_info(name_akc, path_akc) | |
| if self._name_stanext is not None: | |
| self.add_stanext_info(name_stanext, path_stanext, ind_in_stanext) | |
| if self._name_xlsx is not None: | |
| self.add_xlsx_info(name_xlsx, ind_in_xlsx, ind_in_xlsx_matrix, clade) | |
| def add_xlsx_info(self, name_xlsx, ind_in_xlsx, ind_in_xlsx_matrix, clade): | |
| assert (name_xlsx is not None) and (ind_in_xlsx is not None) and (ind_in_xlsx_matrix is not None) and (clade is not None) | |
| self._name_xlsx = name_xlsx | |
| self._ind_in_xlsx = ind_in_xlsx | |
| self._ind_in_xlsx_matrix = ind_in_xlsx_matrix | |
| self._clade = clade | |
| def add_stanext_info(self, name_stanext, path_stanext, ind_in_stanext): | |
| assert (name_stanext is not None) and (path_stanext is not None) and (ind_in_stanext is not None) | |
| self._name_stanext = name_stanext | |
| self._path_stanext = path_stanext | |
| self._ind_in_stanext = ind_in_stanext | |
| def add_akc_info(self, name_akc, path_akc): | |
| assert (name_akc is not None) and (path_akc is not None) | |
| self._name_akc = name_akc | |
| self._path_akc = path_akc | |
| def add_additional_names(self, name_list): | |
| self._additional_names = self._additional_names.union(set(name_list)) | |
| def add_text_info(self, text_height, text_weight, text_life_exp): | |
| self._text_height = text_height | |
| self._text_weight = text_weight | |
| self._text_life_exp = text_life_exp | |
| def get_datasets(self): | |
| # all datasets in which this breed is found | |
| datasets = set() | |
| if self._name_akc is not None: | |
| datasets.add('akc') | |
| if self._name_stanext is not None: | |
| datasets.add('stanext') | |
| if self._name_xlsx is not None: | |
| datasets.add('xlsx') | |
| return datasets | |
| def get_names(self): | |
| # set of names for this breed | |
| names = {self._abbrev, self._name_akc, self._name_stanext, self._name_xlsx, self._path_stanext}.union(self._additional_names) | |
| names.discard(None) | |
| return names | |
| def get_names_as_pointing_dict(self): | |
| # each name points to the abbreviation | |
| names = self.get_names() | |
| my_dict = {} | |
| for name in names: | |
| my_dict[name] = self._abbrev | |
| return my_dict | |
| def print_overview(self): | |
| # print important information to get an overview of the class instance | |
| if self._name_akc is not None: | |
| name = self._name_akc | |
| elif self._name_xlsx is not None: | |
| name = self._name_xlsx | |
| else: | |
| name = self._name_stanext | |
| print('----------------------------------------------------') | |
| print('----- dog breed: ' + name ) | |
| print('----------------------------------------------------') | |
| print('[names]') | |
| print(self.get_names()) | |
| print('[datasets]') | |
| print(self.get_datasets()) | |
| # see https://stackoverflow.com/questions/9058305/getting-attributes-of-a-class | |
| print('[instance attributes]') | |
| for attribute, value in self.__dict__.items(): | |
| print(attribute, '=', value) | |
| def use_dict_to_save_class_instance(self): | |
| my_dict = {} | |
| for attribute, value in self.__dict__.items(): | |
| my_dict[attribute] = value | |
| return my_dict | |
| def use_dict_to_load_class_instance(self, my_dict): | |
| for attribute, value in my_dict.items(): | |
| setattr(self, attribute, value) | |
| return | |
| # ----------------------------------------------------------------------------------------------------------------- # | |
| def get_name_list_from_summary(summary): | |
| name_from_abbrev_dict = {} | |
| for breed in summary.values(): | |
| abbrev = breed._abbrev | |
| all_names = breed.get_names() | |
| name_from_abbrev_dict[abbrev] = list(all_names) | |
| return name_from_abbrev_dict | |
| def get_partial_summary(summary, part): | |
| assert part in ['xlsx', 'akc', 'stanext'] | |
| partial_summary = {} | |
| for key, value in summary.items(): | |
| if (part == 'xlsx' and value._name_xlsx is not None) \ | |
| or (part == 'akc' and value._name_akc is not None) \ | |
| or (part == 'stanext' and value._name_stanext is not None): | |
| partial_summary[key] = value | |
| return partial_summary | |
| def get_akc_but_not_stanext_partial_summary(summary): | |
| partial_summary = {} | |
| for key, value in summary.items(): | |
| if value._name_akc is not None: | |
| if value._name_stanext is None: | |
| partial_summary[key] = value | |
| return partial_summary | |
| # ----------------------------------------------------------------------------------------------------------------- # | |
| def main_load_dog_breed_classes(path_complete_abbrev_dict_v1, path_complete_summary_breeds_v1): | |
| with open(path_complete_abbrev_dict_v1, 'rb') as file: | |
| complete_abbrev_dict = pkl.load(file) | |
| with open(path_complete_summary_breeds_v1, 'rb') as file: | |
| complete_summary_breeds_attributes_only = pkl.load(file) | |
| complete_summary_breeds = {} | |
| for key, value in complete_summary_breeds_attributes_only.items(): | |
| attributes_only = complete_summary_breeds_attributes_only[key] | |
| complete_summary_breeds[key] = DogBreed(abbrev=attributes_only['_abbrev']) | |
| complete_summary_breeds[key].use_dict_to_load_class_instance(attributes_only) | |
| return complete_abbrev_dict, complete_summary_breeds | |
| # ----------------------------------------------------------------------------------------------------------------- # | |
| def load_similarity_matrix_raw(xlsx_path): | |
| # --- LOAD EXCEL FILE FROM DOG BREED PAPER | |
| xlsx = pd.read_excel(xlsx_path) | |
| # create an array | |
| abbrev_indices = {} | |
| matrix_raw = np.zeros((168, 168)) | |
| for ind in range(1, 169): | |
| abbrev = xlsx[xlsx.columns[2]][ind] | |
| abbrev_indices[abbrev] = ind-1 | |
| for ind_col in range(0, 168): | |
| for ind_row in range(0, 168): | |
| matrix_raw[ind_col, ind_row] = float(xlsx[xlsx.columns[3+ind_col]][1+ind_row]) | |
| return matrix_raw, abbrev_indices | |
| # ----------------------------------------------------------------------------------------------------------------- # | |
| # ----------------------------------------------------------------------------------------------------------------- # | |
| # load the (in advance created) final dict of dog breed classes | |
| ROOT_PATH_BREED_DATA = os.path.join(os.path.dirname(os.path.abspath(__file__)), '..', '..', '..', 'data', 'breed_data') | |
| path_complete_abbrev_dict_v1 = os.path.join(ROOT_PATH_BREED_DATA, 'complete_abbrev_dict_v2.pkl') | |
| path_complete_summary_breeds_v1 = os.path.join(ROOT_PATH_BREED_DATA, 'complete_summary_breeds_v2.pkl') | |
| COMPLETE_ABBREV_DICT, COMPLETE_SUMMARY_BREEDS = main_load_dog_breed_classes(path_complete_abbrev_dict_v1, path_complete_summary_breeds_v1) | |
| # load similarity matrix, data from: | |
| # Parker H. G., Dreger D. L., Rimbault M., Davis B. W., Mullen A. B., Carpintero-Ramirez G., and Ostrander E. A. | |
| # Genomic analyses reveal the influence of geographic origin, migration, and hybridization on modern dog breed | |
| # development. Cell Reports, 4(19):697–708, 2017. | |
| xlsx_path = os.path.join(ROOT_PATH_BREED_DATA, 'NIHMS866262-supplement-2.xlsx') | |
| SIM_MATRIX_RAW, SIM_ABBREV_INDICES = load_similarity_matrix_raw(xlsx_path) | |