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3D_DenseNet_UP.py
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# -*- coding: utf-8 -*-
import numpy as np
import matplotlib.pyplot as plt
import scipy.io as sio
from keras.models import Sequential, Model
from keras.layers import Convolution2D, MaxPooling2D, Conv3D, MaxPooling3D, ZeroPadding3D
from keras.layers import Activation, Dropout, Flatten, Dense, BatchNormalization, Input
from keras.utils.np_utils import to_categorical
from sklearn.decomposition import PCA
from keras.optimizers import Adam, SGD, Adadelta, RMSprop, Nadam
import keras.callbacks as kcallbacks
from keras.regularizers import l2
import time
from Utils import zeroPadding, normalization, doPCA, modelStatsRecord, averageAccuracy, \
densenet_UP,cnn_3D_UP
import collections
from sklearn import metrics, preprocessing
import os
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '2'
def indexToAssignment(index_, Row, Col, pad_length):
new_assign = {}
for counter, value in enumerate(index_):
assign_0 = value // Col + pad_length
assign_1 = value % Col + pad_length
new_assign[counter] = [assign_0, assign_1]
return new_assign
def assignmentToIndex(assign_0, assign_1, Row, Col):
new_index = assign_0 * Col + assign_1
return new_index
def selectNeighboringPatch(matrix, pos_row, pos_col, ex_len):
selected_rows = matrix[range(pos_row - ex_len, pos_row + ex_len + 1), :]
selected_patch = selected_rows[:, range(pos_col - ex_len, pos_col + ex_len + 1)]
return selected_patch
def sampling(proptionVal, groundTruth): # divide dataset into train and test datasets
labels_loc = {}
train = {}
test = {}
m = max(groundTruth)
for i in range(m):
indices = [j for j, x in enumerate(groundTruth.ravel().tolist()) if x == i + 1]
np.random.shuffle(indices)
labels_loc[i] = indices
nb_val = int(proptionVal * len(indices))
train[i] = indices[:-nb_val]
test[i] = indices[-nb_val:]
# whole_indices = []
train_indices = []
test_indices = []
for i in range(m):
# whole_indices += labels_loc[i]
train_indices += train[i]
test_indices += test[i]
np.random.shuffle(train_indices)
np.random.shuffle(test_indices)
return train_indices, test_indices
def model_DenseNet():
model_dense = cnn_3D_UP.ResnetBuilder.build_resnet_8((1, img_rows, img_cols, img_channels), nb_classes)
RMS = RMSprop(lr=0.0003)
# Let's train the model using RMSprop
model_dense.compile(loss='categorical_crossentropy', optimizer=RMS, metrics=['accuracy'])
return model_dense
uPavia = sio.loadmat('D:/Tensorflow Learning/3D-DenseNet-Hyperspectral/datasets/UP/PaviaU.mat')
gt_uPavia = sio.loadmat('D:/Tensorflow Learning/3D-DenseNet-Hyperspectral/datasets/UP/PaviaU_gt.mat')
data_UP = uPavia['paviaU']
gt_UP = gt_uPavia['paviaU_gt']
print(data_UP.shape)
# new_gt_UP = set_zeros(gt_UP, [1,4,7,9,13,15,16])
new_gt_UP = gt_UP
batch_size = 16
nb_classes = 9
nb_epoch = 200 # 400
img_rows, img_cols = 11, 11 # 27, 27
patience = 200
INPUT_DIMENSION_CONV = 103
INPUT_DIMENSION = 103
# 10%:10%:80% data for training, validation and testing
TOTAL_SIZE = 42776
VAL_SIZE = 4281
TRAIN_SIZE = 4281
TEST_SIZE = TOTAL_SIZE - TRAIN_SIZE
img_channels = 103
VALIDATION_SPLIT = 0.90 # 10% for training and %90 for validation and testing
img_channels = 103
PATCH_LENGTH = 5 # Patch_size (13*2+1)*(13*2+1)
data = data_UP.reshape(np.prod(data_UP.shape[:2]), np.prod(data_UP.shape[2:]))
gt = new_gt_UP.reshape(np.prod(new_gt_UP.shape[:2]), )
data = preprocessing.scale(data)
# scaler = preprocessing.MaxAbsScaler()
# data = scaler.fit_transform(data)
data_ = data.reshape(data_UP.shape[0], data_UP.shape[1], data_UP.shape[2])
whole_data = data_
padded_data = zeroPadding.zeroPadding_3D(whole_data, PATCH_LENGTH)
ITER = 3
CATEGORY = 9
train_data = np.zeros((TRAIN_SIZE, 2 * PATCH_LENGTH + 1, 2 * PATCH_LENGTH + 1, INPUT_DIMENSION_CONV))
test_data = np.zeros((TEST_SIZE, 2 * PATCH_LENGTH + 1, 2 * PATCH_LENGTH + 1, INPUT_DIMENSION_CONV))
KAPPA_3D_DenseNet = []
OA_3D_DenseNet = []
AA_3D_DenseNet = []
TRAINING_TIME_3D_DenseNet = []
TESTING_TIME_3D_DenseNet = []
ELEMENT_ACC_3D_DenseNet = np.zeros((ITER, CATEGORY))
# seeds = [1220, 1221, 1222, 1223, 1224, 1225, 1226, 1227, 1228, 1229]
seeds = [1220, 1221, 1222]
for index_iter in range(ITER):
print("# %d Iteration" % (index_iter + 1))
best_weights_DenseNet_path = 'D:/Tensorflow Learning/3D-DenseNet-Hyperspectral/models-up-3dcnn/UP_best_3D_DenseNet_' + str(
index_iter + 1) + '.hdf5'
np.random.seed(seeds[index_iter])
train_indices, test_indices = sampling(VALIDATION_SPLIT, gt)
y_train = gt[train_indices] - 1
y_train = to_categorical(np.asarray(y_train))
y_test = gt[test_indices] - 1
y_test = to_categorical(np.asarray(y_test))
# print ("Validation data:")
# collections.Counter(y_test_raw[-VAL_SIZE:])
# print ("Testing data:")
# collections.Counter(y_test_raw[:-VAL_SIZE])
train_assign = indexToAssignment(train_indices, whole_data.shape[0], whole_data.shape[1], PATCH_LENGTH)
for i in range(len(train_assign)):
train_data[i] = selectNeighboringPatch(padded_data, train_assign[i][0], train_assign[i][1], PATCH_LENGTH)
test_assign = indexToAssignment(test_indices, whole_data.shape[0], whole_data.shape[1], PATCH_LENGTH)
for i in range(len(test_assign)):
test_data[i] = selectNeighboringPatch(padded_data, test_assign[i][0], test_assign[i][1], PATCH_LENGTH)
x_train = train_data.reshape(train_data.shape[0], train_data.shape[1], train_data.shape[2], INPUT_DIMENSION_CONV)
x_test_all = test_data.reshape(test_data.shape[0], test_data.shape[1], test_data.shape[2], INPUT_DIMENSION_CONV)
x_val = x_test_all[-VAL_SIZE:]
y_val = y_test[-VAL_SIZE:]
x_test = x_test_all[:-VAL_SIZE]
y_test = y_test[:-VAL_SIZE]
model_densenet = model_DenseNet()
earlyStopping6 = kcallbacks.EarlyStopping(monitor='val_loss', patience=patience, verbose=1, mode='auto')
saveBestModel6 = kcallbacks.ModelCheckpoint(best_weights_DenseNet_path, monitor='val_loss', verbose=1,
save_best_only=True,
mode='auto')
tic6 = time.clock()
print(x_train.shape, x_test.shape)
history_3d_densenet = model_densenet.fit(
x_train.reshape(x_train.shape[0], x_train.shape[1], x_train.shape[2], x_train.shape[3], 1), y_train,
validation_data=(x_val.reshape(x_val.shape[0], x_val.shape[1], x_val.shape[2], x_val.shape[3], 1), y_val),
batch_size=batch_size,
nb_epoch=nb_epoch, shuffle=True, callbacks=[earlyStopping6, saveBestModel6])
toc6 = time.clock()
tic7 = time.clock()
loss_and_metrics_3d_densenet = model_densenet.evaluate(
x_test.reshape(x_test.shape[0], x_test.shape[1], x_test.shape[2], x_test.shape[3], 1), y_test,
batch_size=batch_size)
toc7 = time.clock()
print('3D DenseNet Time: ', toc6 - tic6)
print('3D DenseNet Test time:', toc7 - tic7)
print('3D DenseNet Test score:', loss_and_metrics_3d_densenet[0])
print('3D DenseNet Test accuracy:', loss_and_metrics_3d_densenet[1])
print(history_3d_densenet.history.keys())
pred_test = model_densenet.predict(
x_test.reshape(x_test.shape[0], x_test.shape[1], x_test.shape[2], x_test.shape[3], 1)).argmax(axis=1)
collections.Counter(pred_test)
gt_test = gt[test_indices] - 1
overall_acc = metrics.accuracy_score(pred_test, gt_test[:-VAL_SIZE])
confusion_matrix = metrics.confusion_matrix(pred_test, gt_test[:-VAL_SIZE])
each_acc, average_acc = averageAccuracy.AA_andEachClassAccuracy(confusion_matrix)
kappa = metrics.cohen_kappa_score(pred_test, gt_test[:-VAL_SIZE])
KAPPA_3D_DenseNet.append(kappa)
OA_3D_DenseNet.append(overall_acc)
AA_3D_DenseNet.append(average_acc)
TRAINING_TIME_3D_DenseNet.append(toc6 - tic6)
TESTING_TIME_3D_DenseNet.append(toc7 - tic7)
ELEMENT_ACC_3D_DenseNet[index_iter, :] = each_acc
print("3D DenseNet finished.")
print("# %d Iteration" % (index_iter + 1))
modelStatsRecord.outputStats(KAPPA_3D_DenseNet, OA_3D_DenseNet, AA_3D_DenseNet, ELEMENT_ACC_3D_DenseNet,
TRAINING_TIME_3D_DenseNet, TESTING_TIME_3D_DenseNet,
history_3d_densenet, loss_and_metrics_3d_densenet, CATEGORY,
'D:/Tensorflow Learning/3D-DenseNet-Hyperspectral/records-up-3dcnn/UP_train_3D_10.txt',
'D:/Tensorflow Learning/3D-DenseNet-Hyperspectral/records-up-3dcnn/UP_train_3D_element_10.txt')