from sklearn.cross_validation import train_test_split
from keras.models import model_from_json
import cPickle as pickle
batch_size = 32
nb_classes = 3
nb_epoch = 10
data_augmentation = True
# input image dimensions
img_rows, img_cols = 100,100
# the mitosis images are RGB
img_channels = 1
# the data, shuffled and split between train and test sets
image_list = create_image_list('/data/50_50_100_40', sample_size=[-1,-1,-1,-1,-1], use_mr=True)
with open('image_list.pkl', 'w+') as f:
pickle.dump(image_list, f)
# Create testset data for cross-val
num_images = len(image_list)
test_size = int(0.1 * num_images)
print("Train size: ", num_images-test_size)
print("Test size: ", test_size)
model = Sequential()
model.add(Convolution2D(256, 3, 3, border_mode='same',
input_shape=(img_channels, img_rows, img_cols)))
model.add(Activation('relu'))
from sklearn.cross_validation import train_test_split
from keras.models import model_from_json
import cPickle as pickle
batch_size = 32
nb_classes = 2
nb_epoch = 10
data_augmentation = True
# input image dimensions
img_rows, img_cols = 100,100
# the mitosis images are RGB
img_channels = 3
# the data, shuffled and split between train and test sets
image_list = create_image_list('/data/50_50_100_40', sample_size=[-1,-1,0,-1,-1], use_mr=True)
with open('image_list.pkl', 'w+') as f:
pickle.dump(image_list, f)
# Create testset data for cross-val
num_images = len(image_list)
test_size = int(0.1 * num_images)
print("Train size: ", num_images-test_size)
print("Test size: ", test_size)
print("Training Distribution: ", get_counts(image_list[0:-test_size], nb_classes))
model = Sequential()
model.add(Convolution2D(256, 6, 6, border_mode='same',
input_shape=(img_channels, img_rows, img_cols)))
precision = precision_score(y_true, y_predicted, labels=labels, average=method)
recall = recall_score(y_true, y_predicted, labels=labels, average=method)
accuracy = accuracy_score(y_true, y_predicted)
print "Precision Score {}".format(precision)
print "Recall Score {}".format(recall)
y_0 = y_predicted[y_true==0]
y_1 = y_predicted[y_true==1]
y_2 = y_predicted[y_true==2]
print "Non-mitosis: True = {}, Predicted = {}".format((y_true==0).sum(), (y_0==0).sum())
print "Mitosis: True = {}, Predicted = {}".format((y_true==1).sum(), (y_1==1).sum())
print "Background: True = {}, Predicted = {}".format((y_true==2).sum(), (y_2==2).sum())
print confusion_matrix(y_true, y_predicted)
if __name__ == '__main__':
print "Unpacking the model"
model = unpack_model('../runs/gpu0/cnn1_model_architecture.json', '../runs/gpu0/cnn1_model_weights.h5')
print "Unpickling the image list"
with open ('../runs/gpu1/image_list.pkl') as f:
image_list_train = pickle.load(f)
print "Creating test image list"
image_list_test = create_image_list(path='/data/Test/ScannerA', sample_size=[-1,-1,0,0,0], use_mr=False)
print "Calculating distribution of train"
image_names, count_0, count_1, count_2 = get_names_count(image_list_train)
print "Creating X, y for test {}".format(len(image_list_test))
X, y = get_input(image_list_test)
print "Predicting on test"
y_prob = predict_prob(model, X, y)
y_predicted = np.argmax(y_prob, axis=1)
#y_predicted = thresholding(y_prob, count_0*1./y.size, count_1*1./y.size, count_2*1./y.size)
get_metrics(y, y_predicted, [0,1], "binary")
def get_test(path):
image_list = create_image_list(path=path, use_mr=False)
X, y = get_input(image_list)
return X, y
def get_test(path):
image_list = create_image_list(path=path, use_mr=False)
X, y = get_input(image_list)
return X, y
return model, model.get_weights()
batch_size = 32
nb_classes = 3
nb_epoch = 10
data_augmentation = True
# input image dimensions
img_rows, img_cols = 100, 100
# the mitosis images are RGB
img_channels = 3
# the data, shuffled and split between train and test sets
image_list = create_image_list('/data/50_50_100_40',
sample_size=[-1, -1, -1, -1, -1],
use_mr=True)
image_names, clusters = get_image_clusters(
'/home/ubuntu/capstone/code/clustering/image_names.pkl',
'/home/ubuntu/capstone/code/clustering/clusters.pkl')
with open('image_list.pkl', 'w+') as f:
pickle.dump(image_list, f)
# define two groups of layers: feature (convolutions) and classification (dense)
feature_layers = [
Convolution2D(32,
3,
3,
border_mode='same',
input_shape=(img_channels, img_rows, img_cols)),
y_1 = y_predicted[y_true == 1]
y_2 = y_predicted[y_true == 2]
print "Background: True = {}, Predicted = {}".format((y_true == 0).sum(),
(y_0 == 0).sum())
print "Non_Mitosis: True = {}, Predicted = {}".format((y_true == 1).sum(),
(y_1 == 1).sum())
print "Mitosis: True = {}, Predicted = {}".format((y_true == 2).sum(),
(y_2 == 2).sum())
print confusion_matrix(y_true, y_predicted)
if __name__ == '__main__':
print "Unpacking the model"
model = unpack_model('../runs/gpu1/ccn1_model_architecture.json',
'../runs/gpu1/ccn1_model_weights.h5')
print "Unpickling the image list"
with open('../runs/gpu1/image_list.pkl') as f:
image_list_train = pickle.load(f)
print "Creating test image list"
image_list_test = create_image_list(path='/data/Test/ScannerA',
use_mr=False)
print "Calculating distribution of train"
image_names, count_0, count_1, count_2 = get_names_count(image_list_train)
print "Creating X, y for test {}".format(len(image_list_test))
X, y = get_input(image_list_test)
print "Predicting on test"
y_prob = predict_prob(model, X, y)
y_predicted = thresholding(y_prob, count_0 * 1. / y.size,
count_1 * 1. / y.size, count_2 * 1. / y.size)
get_metrics(y, y_predicted)
def get_metrics(y_true, y_predicted):
precision = precision_score(y_true, y_predicted, labels=[0,1,2], average="weighted")
recall = recall_score(y_true, y_predicted, labels=[0,1,2], average="weighted")
print "Precision Score {}".format(precision)
print "Recall Score {}".format(recall)
y_0 = y_predicted[y_true==0]
y_1 = y_predicted[y_true==1]
y_2 = y_predicted[y_true==2]
print "Background: True = {}, Predicted = {}".format((y_true==0).sum(), (y_0==0).sum())
print "Non_Mitosis: True = {}, Predicted = {}".format((y_true==1).sum(), (y_1==1).sum())
print "Mitosis: True = {}, Predicted = {}".format((y_true==2).sum(), (y_2==2).sum())
print confusion_matrix(y_true, y_predicted)
if __name__ == '__main__':
print "Unpacking the model"
model = unpack_model('../runs/gpu1/ccn1_model_architecture.json', '../runs/gpu1/ccn1_model_weights.h5')
print "Unpickling the image list"
with open ('../runs/gpu1/image_list.pkl') as f:
image_list_train = pickle.load(f)
print "Creating test image list"
image_list_test = create_image_list(path='/data/Test/ScannerA', use_mr=False)
print "Calculating distribution of train"
image_names, count_0, count_1, count_2 = get_names_count(image_list_train)
print "Creating X, y for test {}".format(len(image_list_test))
X, y = get_input(image_list_test)
print "Predicting on test"
y_prob = predict_prob(model, X, y)
y_predicted = thresholding(y_prob, count_0*1./y.size, count_1*1./y.size, count_2*1./y.size)
get_metrics(y, y_predicted)
from sklearn.cross_validation import train_test_split
from keras.models import model_from_json
import cPickle as pickle
batch_size = 32
nb_classes = 3
nb_epoch = 10
data_augmentation = True
# input image dimensions
img_rows, img_cols = 100,100
# the mitosis images are RGB
img_channels = 3
# the data, shuffled and split between train and test sets
image_list = create_image_list('/data/ScannerA', sample_size=[-1,-1,-1,-1,-1], use_mr=True)
with open('image_list.pkl', 'w+') as f:
pickle.dump(image_list, f)
# Create testset data for cross-val
num_images = len(image_list)
test_size = int(0.2 * num_images)
print("Train size: ", num_images-test_size)
print("Test size: ", test_size)
model = Sequential()
model.add(Convolution2D(32, 3, 3, border_mode='same',
input_shape=(img_channels, img_rows, img_cols)))
model.add(Activation('relu'))
y_2 = y_predicted[y_true == 2]
print "Non-mitosis: True = {}, Predicted = {}".format((y_true == 0).sum(),
(y_0 == 0).sum())
print "Mitosis: True = {}, Predicted = {}".format((y_true == 1).sum(),
(y_1 == 1).sum())
print "Background: True = {}, Predicted = {}".format((y_true == 2).sum(),
(y_2 == 2).sum())
print confusion_matrix(y_true, y_predicted)
if __name__ == '__main__':
print "Unpacking the model"
model = unpack_model('../runs/gpu0/cnn1_model_architecture.json',
'../runs/gpu0/cnn1_model_weights.h5')
print "Unpickling the image list"
with open('../runs/gpu1/image_list.pkl') as f:
image_list_train = pickle.load(f)
print "Creating test image list"
image_list_test = create_image_list(path='/data/Test/ScannerA',
sample_size=[-1, -1, 0, 0, 0],
use_mr=False)
print "Calculating distribution of train"
image_names, count_0, count_1, count_2 = get_names_count(image_list_train)
print "Creating X, y for test {}".format(len(image_list_test))
X, y = get_input(image_list_test)
print "Predicting on test"
y_prob = predict_prob(model, X, y)
y_predicted = np.argmax(y_prob, axis=1)
#y_predicted = thresholding(y_prob, count_0*1./y.size, count_1*1./y.size, count_2*1./y.size)
get_metrics(y, y_predicted, [0, 1], "binary")
batch_size = 32
nb_classes = 3
nb_epoch = 10
data_augmentation = True
# input image dimensions
img_rows, img_cols = 100,100
# the mitosis images are RGB
img_channels = 3
# the data, shuffled and split between train and test sets
image_list = create_image_list('/data/50_50_100_40', sample_size=[-1,-1,-1,-1,-1], use_mr=True)
image_names, clusters = get_image_clusters('/home/ubuntu/capstone/code/clustering/image_names.pkl','/home/ubuntu/capstone/code/clustering/clusters.pkl')
with open('image_list.pkl', 'w+') as f:
pickle.dump(image_list, f)
# define two groups of layers: feature (convolutions) and classification (dense)
feature_layers = [
Convolution2D(32, 3, 3, border_mode='same',
input_shape=(img_channels, img_rows, img_cols)),
Activation('relu'),
Convolution2D(32, 3, 3),
Activation('relu'),
MaxPooling2D(pool_size=(2, 2)),
Dropout(0.1),
Convolution2D(64, 3, 3, border_mode='same'),
