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cross_validation_bagging_classifier_ridge_regression.py
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cross_validation_bagging_classifier_ridge_regression.py
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import numpy as np
import pandas as pd
import datetime
import matplotlib.pyplot as plt
from sklearn.cross_validation import train_test_split
import sklearn.preprocessing as preprocessing
from sklearn import linear_model
from sklearn.metrics import mean_squared_error
from sklearn import svm
from sklearn import ensemble
import write_submission
import read_dataset
import Binary_Classification
def split_and_build_class(X, y):
# X_train = X[: 4061]
# X_test = X[4061:]
# y_train = y[: 4061]
# y_test = y[4061:]
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.3)
print X_train.shape
print X_test.shape
# X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.3)
# Normalize the input data.
imp = preprocessing.Imputer(missing_values='NaN', strategy='mean', axis=0)
fixed_X_train = X_train[:, 1:]
imp.fit(fixed_X_train)
fixed_X_train = imp.transform(fixed_X_train)
preprocessing.normalize(fixed_X_train, copy=False)
X_train[:, 1:] = fixed_X_train
fixed_X_test = X_test[:, 1:]
imp.fit(fixed_X_test)
fixed_X_test = imp.transform(fixed_X_test)
preprocessing.normalize(fixed_X_test, copy=False)
X_test[:, 1:] = fixed_X_test
train_data = read_dataset.microData()
train_data.get_data(X_train)
y_train = train_data.set_output(y_train)
test_data = read_dataset.microData()
test_data.get_data(X_test)
y_test = test_data.set_output(y_test)
return [X_train, X_test, y_train, y_test, train_data, test_data]
def run_regression(X, y):
clf = ensemble.BaggingClassifier(n_estimators=1000)
clf.fit(X, y)
return clf
def main():
# Read the dataset.
dataset_path = './dataset/'
dataset_file_path = './dataset_file_path.csv'
df_path = pd.read_csv(dataset_file_path)
all_file_param = read_dataset.read_all_dataset(df_path)
file_amount = len(all_file_param)
plot_files = ['Training set Microclimate (2 hour intervals)']
yield_file = 'Target Variable Water Yield'
# plot_files = ['Training set Microclimate (2 hour intervals)',
# 'Training set Microclimate (5 minute intervals)']
# Set up features for micro files.
micro_features = read_dataset.set_features(dataset_path, plot_files)
# Read yield file for micro training file.
yield_df = None
for k in xrange(file_amount):
file = all_file_param[k]
if file.data_name == yield_file:
yield_path = dataset_path + file.file_path
yield_df = pd.read_csv(yield_path)
break
# Traverse all the dataset.
for k in xrange(file_amount):
file = all_file_param[k]
if file.data_name not in plot_files:
continue
print '==========' + file.data_name + '=========='
path = dataset_path + file.file_path
df = pd.read_csv(path)
# Split the micro training file into training dataset and test dataset.
X_train, X_test, y_train, y_test, train_data, test_data = split_and_build_class(df.values, yield_df.values)
# [train_data, test_data] = split_and_build_class(df.values, yield_df.values)
y_train_binary = Binary_Classification.transform_to_binary(y_train)
# Run SVM.
clf = run_regression(X_train[:, 1:], y_train_binary)
y_hat_test_binary = clf.predict(X_test[:, 1:])
print 'Number of Class 1 in Training Data:', np.count_nonzero(y_train_binary)
print 'Number of Class 1 in Test Data:', np.count_nonzero(y_test)
print 'Number of Class 1 in Predicted Data:', np.count_nonzero(y_hat_test_binary)
# Run Ridge Regression.
X_train_regression = []
y_train_regression = []
X_test_regression = []
y_hat_test_regression = []
for i in xrange(len(y_train_binary)):
if y_train_binary[i] != 0:
X_train_regression.append(X_train[i])
y_train_regression.append(y_train[i])
X_train_regression = np.array(X_train_regression)
'''
=====Regression=====
'''
clf_regression = linear_model.Ridge(normalize=True)
# clf_regression.fit(X_train_regression[:, 1:], y_train_regression)
clf_regression.fit(X_train[:, 1:], y_train)
'''
====================
'''
for i in xrange(len(y_hat_test_binary)):
if y_hat_test_binary[i] != 0:
X_test_regression.append(X_test[i])
X_test_regression = np.array(X_test_regression)
if len(X_test_regression):
y_hat_test_regression = clf_regression.predict(X_test_regression[:, 1:])
j = 0
y_hat_test = []
if len(X_test_regression):
for i in xrange(len(y_hat_test_binary)):
if y_hat_test_binary[i] == 0:
y_hat_test.append(y_hat_test_binary[i])
else:
y_hat_test.append(y_hat_test_regression[j])
j += 1
y_hat_test = np.array(y_hat_test)
else:
y_hat_test = y_hat_test_binary
cmap = plt.get_cmap('jet_r')
plt.figure(figsize=(10, 10))
interval = file.interval
intervel_minute = read_dataset.get_interval_minute(interval)
test_size = y_hat_test.shape[0]
plt.plot([i for i in xrange(test_size)], y_hat_test)
plt.plot([i for i in xrange(test_size)], y_test)
plt.legend(['Prediction', 'Real'])
plt.suptitle('Cross Validation + Bagging Classifier + Ridge Regression')
plt.savefig('Cross Validation + Bagging Classifier + Ridge Regression.png', bbox_inches='tight')
loss = np.sqrt(mean_squared_error(y_test, y_hat_test))
print 'Cross Validation + Bagging Classifier + Ridge Regression loss =', loss
'''
=======================================================================
'''
# Predict test and write submission
submission_file_name = 'Submission format'
submission_file = None
test_file_name = 'Test set Microclimate (2 hour intervals)'
test_file = None
for k in xrange(file_amount):
file = all_file_param[k]
if file.data_name == submission_file_name:
submission_file = file
break
submission_path = dataset_path + submission_file.file_path
df_submission = pd.read_csv(submission_path, index_col=0, parse_dates=[0])
for k in xrange(file_amount):
file = all_file_param[k]
if file.data_name == test_file_name:
test_file = file
break
test_path = dataset_path + test_file.file_path
df_test = pd.read_csv(test_path, index_col=0, parse_dates=[0])
X_combined = write_submission.combine_table(df_submission, df_test)
imp = preprocessing.Imputer(missing_values='NaN', strategy='mean', axis=0)
fixed_X = X_combined.values[:, 0:]
imp.fit(fixed_X)
X_combined.values[:, 0:] = imp.transform(fixed_X)
preprocessing.normalize(X_combined.values, copy=False)
y_submission = write_submission.write_submission_binary_classifier_and_regression(
X_combined, clf, clf_regression, df_submission,
'Cross Validation + Bagging Classifier + Ridge Regression Submission')
main()