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possion_FixPossionModel_siteBYsite_optimal_GCmodify.py
Source:possion_FixPossionModel_siteBYsite_optimal_GCmodify.py 
1#! /usr/bin/env python2# -*- coding: utf-8 -*-3#########################################################################################################4# CNVar: accurate knowledge-based copy number variation prediction using max likelihood method #5# # 6# Copyright (C) 2019 Enming He(emhe@wegene.com) #7# #8# This program is free software: you can redistribute it and/or modify #9# it under the terms of the GNU General Public License as published by #10# the Free Software Foundation, either version 3 of the License, or #11# (at your option) any later version. #12# #13# This program is distributed in the hope that it will be useful, #14# but WITHOUT ANY WARRANTY; without even the implied warranty of #15# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #16# GNU General Public License for more details. #17# #18# You should have received a copy of the GNU General Public License #19# along with this program. If not, see <https://www.gnu.org/licenses/>. #20#########################################################################################################21import os22import sys23import re24import numpy as np25import scipy.stats as stats26import math27import subprocess28import argparse29import read_depth_method_matrix_mem_optimize_GCmodify_GCcorrect30def safe_open(infile):31 if infile.endswith('.gz'):32 import gzip33 return gzip.open(infile)34 else:35 return open(infile)36def read_GCprofile(infile):37 print('reading:GCprofile %s ...' % infile)38 GCprofile = {}39 with open(infile) as f:40 line = f.readline()41 headers = line.strip().split()42 line = f.readline()43 gc_values = line.strip().split()44 45 for i in range(1,len(headers)):46 GCprofile[int(headers[i])] = float(gc_values[i])47 print('finish reading:GCprofile')48 return GCprofile49def possion(cov):50 if cov <= 60:51 rate = 6052 else:53 rate = int(cov)54 Dict = {}55 n = np.arange((rate+1)*2)56 y = stats.poisson.pmf(n,cov)57 for i in n:58 Dict[i] = y[i]59 return Dict60def reverse_possion(cov):61 rate = int(cov)62 Dict = {}63 n = np.arange(rate)64 y = stats.poisson.pmf(n,rate)65 y1 = y.tolist()66 y1.reverse()67 for i in n:68 Dict[i] = y1[i]69 return Dict70def log(Dict,x,logmin):71 if x > max(Dict.keys()) or x < min(Dict.keys()):72 return math.log(logmin)73 else:74 if Dict[x] < logmin:75 return math.log(logmin)76 else:77 return math.log(Dict[x])78def possibility(D,DR,cov,N, CHROM_TEST,START_TEST,END_TEST, MISMATCH, logmin):79 lgP = math.log(1)80 CN_models = {}81 82 def possionCN(CN):83 if (CN!=0):84 CN_model = possion(cov*CN/2)85 else:86 CN_model = possion(MISMATCH * cov)87 return CN_model88 89 for i in range(START_TEST,END_TEST):90 depth = D[(CHROM_TEST,i)]91 CN = round(DR[(CHROM_TEST,i)]/N,2)92 93 if CN not in CN_models:94 CN_models[CN] = possionCN(CN)95 96 y = log(CN_models[CN],depth, logmin)97 98 lgP += y99 return lgP100def read_ref(reffile, CHROM_TEST, START_TEST,END_TEST):101 print('reading ref file: %s ' % reffile)102 depth_sum =0103 count = 0104 D = {}105 with safe_open(reffile) as f:106 for line in f:107 chrom, pos, depth = [int(x) for x in line.strip().split()[0:3]]108 if chrom == CHROM_TEST and pos<= END_TEST and pos>= START_TEST:109 D[(chrom,pos)] = depth110 elif chrom == CHROM_TEST and pos > END_TEST:111 break112 return D113def read_sample(infile,GCprofile, CHROM_TEST, START_TEST,END_TEST ):114 print('reading sample file: %s ...' % infile)115 with safe_open(infile) as f:116 D = {}117 depth_sum = 0118 count = 0119 for line in f:120 chrom, pos, depth_raw = [int(x) for x in line.strip().split()[0:3]]121 if chrom == CHROM_TEST and pos<= END_TEST and pos>= START_TEST:122 depth = int(depth_raw * GCprofile[pos - pos % 50])123 D[(chrom,pos)] = depth124 elif chrom == CHROM_TEST and pos > END_TEST: # if assume background region behinds testing region125 break126 return D127def calculator(LIST,sample,reflist, binsize, slide, gc_config,CHROM_TEST, START_TEST, END_TEST, AVERAGE_DEPTH, MISMATCH, logmin):128 min_start = START_TEST129 max_end = END_TEST130 131 read_depth_method_matrix_mem_optimize_GCmodify_GCcorrect.readDepthMethodMatrixMemOptimizeGCmodifyGCcorrect(sample, binsize, sample, slide, '%s:%s-%s' % (CHROM_TEST, START_TEST-150, END_TEST+150), gc_config) # 150 , end should be wilder132 GCprofile = read_GCprofile('%s.GCprofile.txt' % sample)133 D = read_sample(sample,GCprofile, CHROM_TEST, START_TEST, END_TEST)134 cov = AVERAGE_DEPTH135 for ref_info in reflist:136 ref, Depth_Ref = ref_info.strip().split()137 N = float(Depth_Ref)/2138 DR = read_ref(ref,CHROM_TEST, START_TEST,END_TEST)139 lgP = possibility(D, DR, cov, N, CHROM_TEST,START_TEST,END_TEST, MISMATCH,logmin)140 LIST.append((ref,lgP))141def possionFixPossionModelSiteBYSiteOptionGCmodify(reference_list, sample_list, outfile, threads, detect_region, average_depth, gc_config, binsize, slide_window, logmin, mismatch ):142 143 logmin = float(logmin)144 m1 = re.search('(\d+):(\d+)-(\d+)',detect_region)145 CHROM_TEST = int(m1.group(1))146 START_TEST = int(m1.group(2))147 END_TEST = int(m1.group(3))148 AVERAGE_DEPTH = float(average_depth)149 MISMATCH = float(mismatch)150 151 print('''152 CHROM_TEST = %s153 START_TEST = %s154 END_TEST = %s155 ''' % (CHROM_TEST, START_TEST , END_TEST)156 )157 158 reflist=[]159 samplelist=[]160 161 with open(reference_list) as f:162 for line in f:163 reflist.append(line.strip())164 with open(sample_list) as f:165 for line in f:166 samplelist.append(line.strip())167 168 sample_Dict = {}169 170 for sample in samplelist:171 sample_Dict[sample] = []172 calculator(sample_Dict[sample],sample,reflist, binsize, slide_window,173 gc_config,CHROM_TEST, START_TEST, END_TEST, AVERAGE_DEPTH, MISMATCH, logmin)174 with open(outfile,'w') as w:175 for sample in sample_Dict:176 mylist = sorted(sample_Dict[sample],key=lambda x: x[1],reverse=True)177 rank = 1178 for i in mylist:179 w.write('%s\t%s\t%s\t%s\n' % (sample,i[0], i[1],rank))180 rank += 1181 return 0182if __name__ == '__main__':183 184 parser = argparse.ArgumentParser()185 parser.add_argument('-rl', '--reference_list', help='reference list',required=True)186 parser.add_argument('-sl', '--sample_list', help='sample list',required=True)187 parser.add_argument('-o', '--outfile', help='outfile',required=True)188 parser.add_argument('-t', '--threads', help='threads',default=16)189 parser.add_argument('-r', '--detect_region', help='detect region, chr:start-end ',required=True)190 parser.add_argument('-d', '--average_depth', help='average depth',required=True)191 parser.add_argument('-c', '--gc_config', help='GC config',required=True)192 parser.add_argument('-bz', '--binsize', help='binsize',required=True)193 parser.add_argument('-sw', '--slide_window', help='slide_window',required=True)194 parser.add_argument('-l', '--logmin', help='logmin', default=1e-7)195 parser.add_argument('-m', '--mismatch', help='assume mismatch', default=1e-4)196 args = parser.parse_args()197 198 reference_list = args.reference_list199 sample_list = args.sample_list200 outfile = args.outfile201 threads = args.threads202 detect_region = args.args.detect_region203 average_depth = args.average_depth204 gc_config = args.gc_config205 binsize = args.binsize206 slide_window = args.slide_window207 logmin = args.logmin208 mismatch = args.mismatch209 ...
WeatherClassifier.py
Source:WeatherClassifier.py
1import numpy as np2import pandas3import argparse4import matplotlib.pyplot as plt5import datetime6from keras.models import Sequential7from keras.layers import Dense, Dropout, advanced_activations8def main():9 # Get input args10 args = parse_arguments()11 # Init random seed for reproducibility12 np.random.seed(0)13 # load the dataset14 dataframe = pandas.read_csv(args["data_path"], engine='python', parse_dates=['DATE'],15 date_parser=lambda x: pandas.to_datetime(x, infer_datetime_format=True))16 # Define the training set using the input begin and end dates17 train_df= dataframe[(dataframe['DATE'] >= datetime.datetime(args["begin_train"],1,1)) &18 (dataframe['DATE'] <= datetime.datetime(args["end_train"],12,31))]19 # Define the testing set using the input begin and end dates20 test_df = dataframe[(dataframe['DATE'] >= datetime.datetime(args["begin_test"],1,1)) &21 (dataframe['DATE'] <= datetime.datetime(args["end_test"],12,31))]22 # Remove null and other invalid entries in the data23 train_data = np.nan_to_num(train_df['TAVG'].values.astype('float32'))24 test_data = np.nan_to_num(test_df['TAVG'].values.astype('float32'))25 # Combine the data to one array26 combined_data = np.append(train_data, test_data)27 # reshape dataset to window matrix28 look_back = 12 # This is the size of the window29 trainX, trainY = create_dataset(train_data, look_back)30 testX, testY = create_dataset(test_data, look_back)31 # Define and fit the model32 model = create_model(look_back=look_back)33 model.fit(trainX, trainY, epochs=500, batch_size=12, verbose=2)34 # Estimate model performance35 trainScore = model.evaluate(trainX, trainY, verbose=0)36 print('Train Score: %.2f MAE' % (trainScore))37 testScore = model.evaluate(testX, testY, verbose=0)38 print('Test Score: %.2f MAE' % (testScore))39 # generate predictions for training40 trainPredict = model.predict(trainX)41 testPredict = model.predict(testX)42 # shift train predictions for plotting43 trainPredictPlot = np.empty((len(combined_data), 1))44 trainPredictPlot[:] = np.nan45 trainPredictPlot[look_back:len(trainPredict) + look_back] = trainPredict46 # shift test predictions for plotting47 testPredictPlot = np.empty((len(combined_data), 1))48 testPredictPlot[:] = np.nan49 testPredictPlot[len(trainPredict) + (look_back * 2) + 1:len(combined_data) - 1] = testPredict50 # Combine the results51 combined_df = train_df.append(test_df)52 combined_dates = combined_df['DATE']53 # plot baseline and predictions54 plt.plot(combined_dates, combined_data, )55 plt.plot(combined_dates, trainPredictPlot)56 plt.plot(combined_dates, testPredictPlot)57 plt.minorticks_on()58 plt.show()59# Standard Model Creation60def create_model(look_back):61 # create and fit Multilayer Perceptron model62 model = Sequential()63 model.add(Dense(100, input_dim=look_back, activation='relu'))64 # model.add(Dense(50, activation='relu'))65 # model.add(Dense(25, activation='relu'))66 # model.add(Dense(10, activation='relu'))67 # model.add(Dense(5, activation='relu'))68 model.add(Dense(1))69 model.compile(loss='mean_absolute_error', optimizer='nadam')70 return model71# convert an array of values into a dataset matrix72def create_dataset(dataset, look_back=1):73 dataX, dataY = [], []74 for i in range(len(dataset) - look_back - 1):75 a = dataset[i:(i + look_back)]76 dataX.append(a)77 dataY.append(dataset[i + look_back])78 return np.array(dataX), np.array(dataY)79# Command Line Arguments are parsed here80def parse_arguments():81 parser = argparse.ArgumentParser()82 parser.add_argument("-dp", "--data_path", help="Data File Path")83 parser.add_argument("-ad", "--adverse", help="Turns on Adversarial Learning")84 parser.add_argument("-m", "--mode", help="Choose mode: full, grid")85 parser.add_argument("-e", "--epochs", help="Number of Epochs", type=int, nargs="*")86 parser.add_argument("-tr", "--train_ratio", nargs="*", type=int,87 help="Set Train Ratios. Enter as a percent (20,40,60,80). Can be a list space delimited")88 parser.add_argument("-bs", "--batch_size", nargs="*", type=int,89 help="Batch size. Can be a list space delimited")90 parser.add_argument("-n", "--neurons", nargs="*", type=int,91 help="Number of Neurons. Can be a list space delimited")92 parser.add_argument("-o", "--optimizer", nargs="*",93 help="Optimizers. Can be a list space delimited")94 parser.add_argument("-w", "--weight_constraint", nargs="*", type=int,95 help="Weight Constraint. Can be a list space delimited")96 parser.add_argument("-d", "--dropout", nargs="*", type=int,97 help="Dropout. Enter as percent (10,20,30,40...). Can be a list space delimited.")98 parser.add_argument("-model", "--model", help="Select which model to run: all, one_layer, four_decr, four_same")99 parser.add_argument("-s", "--splits", help="Number of Splits for SSS", type=int)100 parser.add_argument("-btr", "--begin_train", help="Year to begin training (1940-2016)", type=int)101 parser.add_argument("-etr", "--end_train", help="Year to end training. Should be higher than begin & <=2017", type=int)102 parser.add_argument("-bts", "--begin_test", help="Year to begin testing (1940-2017)", type=int)103 parser.add_argument("-ets", "--end_test", help="Year to end testing. Should be higher than begin test.", type=int)104 args = parser.parse_args()105 arguments = {}106 if args.data_path:107 arguments["data_path"] = args.data_path108 else:109 print("Default Data Path: ../Data/BWIMonthly1939.csv")110 arguments["data_path"] = "../Data/BWIMonthly1939.csv"111 if args.adverse:112 adverse = True113 else:114 adverse = False115 arguments["adverse"] = adverse116 if args.mode == "grid":117 mode = "grid"118 print("Mode is %s" % mode)119 else:120 mode = "full"121 print("Mode is %s" % mode)122 arguments["mode"] = mode123 if args.model == "all":124 model = ["oneLayer", "fourDecr", "fourSame"]125 elif args.model in ["oneLayer", "fourDecr", "fourSame"]:126 model = [args.model]127 else:128 print("Defaulting to All models")129 model = ["oneLayer", "fourDecr", "fourSame"]130 arguments["model"] = model131 if args.epochs:132 epochs = args.epochs133 else:134 print("Defaulting to 16 epochs")135 epochs = 16136 arguments["epochs"] = epochs137 if args.train_ratio:138 train_ratio = args.train_ratio139 else:140 print("Defaulting to testing all ratios")141 train_ratio = [20, 40, 60, 80]142 arguments["train_ratio"] = train_ratio143 if args.batch_size:144 batch_size = args.batch_size145 else:146 print("Defaulting to Batch Size 10")147 batch_size = 10148 arguments["batch_size"] = batch_size149 if args.neurons:150 neurons = args.neurons151 else:152 print("Defaulting to 45 Neurons")153 neurons = 45154 arguments["neurons"] = neurons155 if args.optimizer:156 optimizer = args.optimizer157 else:158 print("Defaulting to NADAM Optimizer")159 optimizer = "Nadam"160 arguments["optimizer"] = optimizer161 if args.weight_constraint:162 weight_constraint = args.weight_constraint163 else:164 print("Defaulting to weight constraint 5")165 weight_constraint = 5166 arguments["weight_constraint"] = weight_constraint167 if args.dropout:168 dropout = args.dropout169 else:170 print("Defaulting to dropout of 10%")171 dropout = 10172 arguments["dropout"] = dropout173 if args.splits:174 splits = args.splits175 else:176 print("Defaulting to 1 SSS Split")177 splits = 1178 arguments["splits"] = splits179 if args.begin_train:180 begin_train = args.begin_train181 else:182 print("Default begin training is 1940")183 begin_train = 1940184 arguments["begin_train"] = begin_train185 if args.end_train:186 end_train = args.end_train187 else:188 print("Defult end training is 1980")189 end_train = 1980190 if end_train < begin_train:191 print("End_Train should be bigger than Begin_Train")192 exit(1)193 arguments["end_train"] = end_train194 if args.begin_test:195 begin_test = args.begin_test196 else:197 print("Default begin test is 1981")198 begin_test = 1981199 arguments["begin_test"] = begin_test200 if args.end_test:201 end_test = args.end_test202 else:203 print("Default end test is 2017")204 end_test = 2017205 if end_test < begin_test:206 print("End_Test should be bigger than Begin_Test")207 exit(1)208 arguments["end_test"] = end_test209 return arguments210if __name__ == "__main__":...
sarimax_script.py
Source:sarimax_script.py
1import matplotlib.pyplot as plt2import pandas as pd3import numpy as np4import itertools5import statsmodels.api as sm6from statsmodels.tsa.stattools import adfuller7from datetime import datetime, timedelta8from dateutil.relativedelta import *9import statsmodels.tsa.api as smt10import seaborn as sns11from sklearn.metrics import mean_squared_error12import pickle13from script import *14#function to create training and testing set15def create_train_test(data, start_train, end_train, start_test, end_test, test_length=24):16 df_train = data.loc[start_train:end_train, :]17 df_test = data.loc[start_test:end_test, :]18 start = datetime.strptime(start_test, '%Y-%m-%d %H:%M:%S')19 date_list = [start + relativedelta(hours=x) for x in range(0,test_length)] #test set will always have 24 hours20 future = pd.DataFrame(index=date_list, columns= df_train.columns)21 df_train = pd.concat([df_train, future])22 return df_train, df_test23#function to add all exogenous variables24def add_exog(data, weather, start_time, end_time):25 #add dummy variables for precipitation26 precip = pd.get_dummies(weather.precip_type)27 data = data.join(precip)28 data['Day_of_Week'] = data.index.dayofweek29 data['Weekend'] = data.apply(is_weekend, axis=1)30 data['Temperature'] = weather.loc[start_time:end_time, 'temperature']31 data['Humidity'] = weather.loc[start_time:end_time, 'humidity']32 data['Precip_Intensity'] = weather.loc[start_time:end_time, 'precip_intensity']33 data.rename(columns={'rain':'Rain', 'sleet':'Sleet', 'snow':'Snow'}, inplace=True)34 #fill missing values with mean35 data['Temperature'] = data.Temperature.fillna(np.mean(data['Temperature']))36 data['Humidity'] = data.Humidity.fillna(np.mean(data['Humidity']))37 data['Precip_Intensity'] = data.Precip_Intensity.fillna(np.mean(data['Precip_Intensity']))38 return data39#function to start/end dates for train and test40def find_dates(building_id, length=1, total_length=30, final_date=None):41 start_train, end_test = find_egauge_dates(building_id, total_length)42 time_delta_1 = timedelta(days=length)43 time_delta_2 = timedelta(hours=1)44 end_train = end_test - time_delta_145 start_test = end_train + time_delta_246 start_train = str(start_train)47 end_train = str(end_train)48 start_test = str(start_test)49 end_test = str(end_test)50 return start_train, end_train, start_test, end_test51def fit_exog_arima(data, weather, building_id, length=1, total_length=30, test_length=24):52 start_train, end_train, start_test, end_test = find_dates(building_id, length=length, total_length=total_length)53 df_train, df_test = create_train_test(data, start_train, end_train, start_test, end_test, test_length)54 df_exog = add_exog(df_train, weather, start_train, end_test)55 exogenous = df_exog.loc[start_train:,['Weekend','Temperature','Humidity','car1']].astype(float)56 endogenous = df_exog.loc[:,'Hourly_Usage'].astype(float)57# low_aic = gridsearch_arima(endogenous,exogenous)58# arima_model = sm.tsa.statespace.SARIMAX(endog=endogenous,59# exog = exogenous,60# trend=None,61# order=low_aic[0],62# seasonal_order=low_aic[1],63# enforce_stationarity=False,64# enforce_invertibility=False)65 arima_model = sm.tsa.statespace.SARIMAX(endog=endogenous,66 exog = exogenous,67 trend=None,68 order=(1, 0, 1),69 seasonal_order=(0, 1, 1, 24),70 enforce_stationarity=False,71 enforce_invertibility=False)72 results = arima_model.fit()73 return df_exog, results74def plot_exog_arima(data, data_exog, model, building_id, length=1, total_length=30, test_length=24):75 start_train, end_train, start_test, end_test = find_dates(building_id, length=length, total_length=total_length)76 df_train, df_test = create_train_test(data, start_train, end_train, start_test, end_test, test_length=test_length)77 df_exog_train, df_exog_test = create_train_test(data_exog, start_train, end_train, start_test, end_test, test_length=test_length)78 mse, rmse = add_forecast(model, df_test, df_exog_train, start_test, end_test)79 plot_forecast(df_exog_train, 500)80 return mse, rmse, df_exog_train81#function to find optimal parameters and resulting AIC score82def gridsearch_arima(y, exog=None):83 p = d = q = range(0, 2)84 pdq = list(itertools.product(p, d, q))85 seasonal_pdq = [(x[0], x[1], x[2], 24) for x in list(itertools.product(p, d, q))]86 low_aic = [0,0,50000]87 for param in pdq:88 for param_seasonal in seasonal_pdq:89 try:90 model = sm.tsa.statespace.SARIMAX(y,91 exog=exog,92 order=param,93 seasonal_order=param_seasonal,94 enforce_stationarity=False,95 enforce_invertibility=False)96 results = model.fit()97 if results.aic < low_aic[2]:98 low_aic = [param, param_seasonal, results.aic]99# print('ARIMA{}x{}24 - AIC:{}'.format(param, param_seasonal, results.aic))100 except:101 continue102 return low_aic103#function to forecast with fitted model, returns MSE and RMSE104def add_forecast(model, test, train, start_time, end_time):105 train['forecast'] = model.predict(start=start_time, end=end_time)106 y_true = test.loc[start_time:end_time, 'Hourly_Usage']107 y_pred = train.loc[start_time:end_time, 'forecast']108 train.loc[start_time:end_time, 'Hourly_Usage'] = test.loc[start_time:end_time, 'Hourly_Usage']109 mse = mean_squared_error(y_true, y_pred)110 rmse = np.sqrt(mse)111 return mse, rmse112def plot_forecast(data, datapoints):113 fig = plt.figure(figsize=(16,8))114 plt.plot(data['Hourly_Usage'][datapoints:])115 plt.plot(data['forecast'])116 plt.legend()117#function to find mean car charge118def mean_car_charge(data, start, end):119 car_charge = {}120 for index in data.Time_Index.unique():121 car_charge[index] = np.mean(data[data.Time_Index==index].car1)122 return car_charge123#function to add all exogenous variables124def create_exog_endo(data, weather, building_id, length=1, total_length=30):125 start_train, end_train, start_test, end_test = find_dates(building_id, length, total_length)126 df_train, df_test = create_train_test(data, start_train, end_train, start_test, end_test, 24*length)127 car_charge = mean_car_charge(data, start_train,end_train)128 df_train['Time_Index'] = df_train.index.weekday_name+ df_train.index.hour.astype(str)129 df_train['Temperature'] = weather.loc[start_train:end_test, 'temperature']130 df_train['Humidity'] = weather.loc[start_train:end_test, 'humidity']131 for time in df_train.loc[start_test:end_test,:].index:132 df_train.loc[time,'car1'] = car_charge[df_train.loc[time,'Time_Index']]133 #fill missing values with mean134 df_train['Temperature'] = df_train.Temperature.fillna(np.mean(df_train['Temperature']))135 df_train['Humidity'] = df_train.Humidity.fillna(np.mean(df_train['Humidity']))136 exogenous = df_train.loc[start_train:,['Temperature','Humidity','car1']].astype(float)137 endogenous = df_train.loc[:,'Hourly_Usage'].astype(float)138 return df_train, exogenous, endogenous139#function to fit SARIMAX model with create_exog_endo140def fit_exog_arima_new(exogenous, endogenous):141 low_aic = gridsearch_arima(endogenous,exogenous)142 arima_model = sm.tsa.statespace.SARIMAX(endog=endogenous,143 exog = exogenous,144 trend=None,145 order=low_aic[0],146 seasonal_order=low_aic[1],147 enforce_stationarity=False,148 enforce_invertibility=False)149 arima_exog_results = arima_model.fit()...
data_parse.py
Source:data_parse.py
1import re2import os3import csv4import sys5import numpy as np6import pickle as pkl7from random import sample8from DataProcess.config import ConfigParam9class DataParse:10 def random_embedding(self, embedding_dim, word_num):11 """12 éæºççæwordçembeddingï¼è¿éå¦ææè¯æå
足çè¯ï¼å¯ä»¥ç´æ¥ä½¿ç¨word2vecè念åºè¯åéï¼è¿æ ·è¯ä¹é´çåºå«å¯è½æ´å¤§ã13 :param embedding_dim: è¯åéç维度ã14 :return: numpy format array. shape is : (vocab, embedding_dim)15 """16 # æ ¹æ®åå
¸å¤§å°word_numç»åå
¸å
æ¯ä¸ä¸ªåè¯çæä¸ä¸ªembedding_dim维度çåéã17 # éç¨æªææ£å¤ªåå¸çæ¹å¼çæãåææ¯åè®¾ä½ çæ°æ®é满足æ£å¤ªåå¸18 embedding_mat = np.random.uniform(-0.25, 0.25, (word_num, embedding_dim))19 embedding_mat = np.float32(embedding_mat)20 return embedding_mat21class Data_Inter:22 """23 çæè®ç»æ°æ®24 """25 def __init__(self, vocab_au, vocab_key):26 self.config = ConfigParam()27 self.vocab_au = vocab_au # åå
¸è·¯å¾28 self.vocab_key = vocab_key # åå
¸è·¯å¾29 self.index = 030 self.index_test = 031 self.reload_num = 1032 # train set33 self.task_sentence = pkl.load(open('DataProcess/data_manage_key_mapping.pkl', mode='rb'))34 self.au_all, self.ke_all = self.get_author_art()35 print(self.au_all.shape, self.ke_all.shape)36 # TRAIN37 self.get_data_mapping()38 def get_data_mapping(self):39 self.shuffle_all = sample(range(0, self.au_all.shape[0], 1), self.au_all.shape[0])40 self.all_sam = len(self.shuffle_all)41 self.au = self.au_all[self.shuffle_all[: int(self.all_sam * 0.7)]] # 0.842 self.ke = self.ke_all[self.shuffle_all[: int(self.all_sam * 0.7)]]43 self.au_test = self.au_all[self.shuffle_all[int(self.all_sam * 0.7):]]44 self.ke_test = self.ke_all[self.shuffle_all[int(self.all_sam * 0.7):]]45 self.shuffle = sample(range(0, self.au.shape[0], 1), self.au.shape[0])46 self.shuffle_test = sample(range(0, self.au_test.shape[0], 1), self.au_test.shape[0])47 self.end = self.au.shape[0]48 self.end_test = self.au_test.shape[0]49 def get_author_art(self):50 auth = []51 keys = []52 for j in self.task_sentence:53 for k in j:54 auth.append(k[: 2])55 keys.append(k[2][: 7])56 return np.array(auth), np.array(keys)57 def next(self):58 # è·åæ¹59 sentence = []60 task_ = []61 if self.index + self.config.batch_size < self.end: # 没æéåå°æ«å°¾62 it_data = self.shuffle[self.index: self.index + self.config.batch_size]63 self.index += self.config.batch_size # æ è¯è·åæ¹æ¬¡çç´¢å¼å¼éæ¹æ¹å64 elif self.index + self.config.batch_size == self.end: # å好éåå°æ«å°¾65 it_data = self.shuffle[self.index + self.config.batch_size: self.end]66 self.shuffle = sample(range(0, self.end, 1), self.end)67 self.index = 068 else:69 it_data = self.shuffle[self.index: self.end] # éæºéå70 self.shuffle = sample(range(0, self.end, 1), self.end)71 remain = self.shuffle[: self.index + self.config.batch_size - self.end] # å©ä½72 it_data = np.concatenate((it_data, remain), axis=0)73 self.index = 074 if self.reload_num > 0:75 self.get_data_mapping()76 self.reload_num -= 177 # print('it_data:', it_data)78 sentences_au = self.au[it_data]79 sentences_key = self.ke[it_data]80 for cur_sentences, cur_task in zip(sentences_au, sentences_key):81 task_.append(self.sentence2index(cur_sentences, self.vocab_au)) # author mapping82 sentence.append(self.sentence2index(cur_task, self.vocab_key)) # keys mapping83 return np.array(sentence), np.array(task_)84 def next_test(self):85 # è·åæ¹86 sentence = []87 task_ = []88 if self.index_test + self.config.batch_size <= self.end_test: # 没æéåå°æ«å°¾89 # ä»task_sentenceéé¢è·åself.config.batch_size大å°çå90 it_data = self.shuffle_test[self.index_test: self.index_test + self.config.batch_size] # è¿ä»£æ°æ®91 self.index_test += self.config.batch_size # æ è¯è·åæ¹æ¬¡çç´¢å¼å¼éæ¹æ¹å92 elif self.index_test + self.config.batch_size == self.end_test: # å好éåå°æ«å°¾93 it_data = self.shuffle_test[self.index_test + self.config.batch_size: self.end_test]94 self.shuffle_test = sample(range(0, self.end_test, 1), self.end_test)95 self.index_test = 0 # éç½®indexãé常ç®åçå°å¦æ°å¦é®é¢ï¼åé¢ä¸å¨æ³¨éäºï¼ä¸ç¼ä¾¿æ96 else:97 it_data = self.shuffle_test[self.index_test: self.end_test] # éæºéå98 self.shuffle_test = sample(range(0, self.end_test, 1), self.end_test)99 remain = self.shuffle_test[: self.index_test + self.config.batch_size - self.end_test] # å©ä½100 it_data = np.concatenate((it_data, remain), axis=0)101 self.index_test = 0102 sentences_au = self.au_test[it_data]103 sentences_key = self.ke_test[it_data]104 for cur_sentences, cur_task in zip(sentences_au, sentences_key):105 task_.append(self.sentence2index(cur_sentences, self.vocab_au)) # author mapping106 sentence.append(self.sentence2index(cur_task, self.vocab_key)) # keys mapping107 return np.array(sentence), np.array(task_)108 def sentence2index(self, sen, vocab):109 sen2id = []110 for cur_sen in sen:111 sen2id.append(vocab.get(cur_sen, 0)) # å¦ææ¾ä¸å°ï¼å°±ç¨0代æ¿ã112 return sen2id113 def task2index(self, cur_tasks, mapping):114 assert isinstance(cur_tasks, list) and len(cur_tasks) > 0 and hasattr(cur_tasks, '__len__')115 assert isinstance(mapping, dict) and len(mapping) > 0116 cur_task2index_mapping = []117 for cur_task in cur_tasks:118 cur_task2index_mapping.append(mapping[cur_task])119 return cur_task2index_mapping120if __name__ == '__main__':121 from DataProcess.dataset_info import info122 au_vocab, key_vocab, au_len, key = info('DataProcess/data_manage_key_mapping.pkl')...
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