def create_model_2():
inputs = Input((32, 32, 32, 1))
#noise = GaussianNoise(sigma=0.1)(x)
conv1 = Convolution3D(32, 3, 3, 3, activation='relu', border_mode='same')(inputs)
conv1 = SpatialDropout3D(0.1)(conv1)
conv1 = Convolution3D(64, 3, 3, 3, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2,2, 2))(conv1)
x = Flatten()(pool1)
x = Dense(64, init='normal')(x)
x = Dropout(0.5)(x)
predictions = Dense(1, init='normal', activation='sigmoid')(x)
model = Model(input=inputs, output=predictions)
model.summary()
optimizer = Adam(lr=1e-5)
model.compile(optimizer=optimizer, loss='binary_crossentropy', metrics=['binary_accuracy','precision','recall','mean_squared_error','accuracy'])
return model
python类MaxPooling3D()的实例源码
def create_model_1():
inputs = Input((32, 32, 32, 1))
#noise = GaussianNoise(sigma=0.1)(x)
conv1 = Convolution3D(32, 3, 3, 3, activation='relu', border_mode='same')(inputs)
conv1 = SpatialDropout3D(0.1)(conv1)
conv1 = Convolution3D(64, 3, 3, 3, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2,2, 2))(conv1)
x = Flatten()(pool1)
x = Dense(64, init='normal')(x)
predictions = Dense(1, init='normal', activation='sigmoid')(x)
model = Model(input=inputs, output=predictions)
model.summary()
optimizer = Adam(lr=1e-5)
model.compile(optimizer=optimizer, loss='binary_crossentropy', metrics=['binary_accuracy','precision','recall','mean_squared_error','accuracy'])
return model
def unet_model_xd3_2_6l_grid(nb_filter=48, dim=5, clen=3 , img_rows=224, img_cols=224 ): # NOTE that this procedure is/should be used with img_rows & img_cols as None
# aiming for architecture similar to the http://cs231n.stanford.edu/reports2016/317_Report.pdf
# Our model is six layers deep, consisting of a series of three CONV-RELU-POOL layyers (with 32, 32, and 64 3x3 filters), a CONV-RELU layer (with 128 3x3 filters), three UPSCALE-CONV-RELU lay- ers (with 64, 32, and 32 3x3 filters), and a final 1x1 CONV- SIGMOID layer to output pixel-level predictions. Its struc- ture resembles Figure 2, though with the number of pixels, filters, and levels as described here
## 3D CNN version of a previously developed unet_model_xd_6j
zconv = clen
inputs = Input((1, dim, img_rows, img_cols))
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(inputs)
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2, 2, 2))(conv1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2, 2, 2))(conv2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv4)
up6 = merge([UpSampling3D(size=(2, 2, 2))(conv4), conv2], mode='concat', concat_axis=1)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up6)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv6)
up7 = merge([UpSampling3D(size=(2, 2, 2))(conv6), conv1], mode='concat', concat_axis=1) # original - only works for even dim
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up7)
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv7)
pool11 = MaxPooling3D(pool_size=(2, 1, 1))(conv7)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool11)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv12)
pool12 = MaxPooling3D(pool_size=(2, 1, 1))(conv12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv13)
pool13 = MaxPooling3D(pool_size=(2, 1, 1))(conv13)
if (dim < 16):
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool13)
else: # need one extra layer to get to 1D x 2D mask ...
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool13)
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv14)
pool14 = MaxPooling3D(pool_size=(2, 1, 1))(conv14)
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool14)
model = Model(input=inputs, output=conv8)
model.compile(optimizer=Adam(lr=1e-4), loss=dice_coef_loss, metrics=[dice_coef])
#model.compile(optimizer=Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-08, decay=0.0), loss=dice_coef_loss, metrics=[dice_coef])
return model
step5_train_nodule_detector.py 文件源码
项目：TC-Lung_nodules_detection
作者: Shicoder
项目源码
文件源码
阅读 31
收藏 0
点赞 0
评论 0
def get_net(input_shape=(CUBE_SIZE, CUBE_SIZE, CUBE_SIZE, 1), load_weight_path=None, features=False, mal=False) -> Model:
inputs = Input(shape=input_shape, name="input_1")
x = inputs
#x = AveragePooling3D(pool_size=(2, 1, 1), strides=(2, 1, 1), border_mode="same")(x)
x = Convolution3D(64, 3, 3, 3, activation='relu', border_mode='same', name='conv1', subsample=(1, 1, 1))(x)
x = MaxPooling3D(pool_size=(1, 2, 2), strides=(1, 2, 2), border_mode='valid', name='pool1')(x)
# 2nd layer group
x = Convolution3D(128, 3, 3, 3, activation='relu', border_mode='same', name='conv2', subsample=(1, 1, 1))(x)
x = MaxPooling3D(pool_size=(2, 2, 2), strides=(2, 2, 2), border_mode='valid', name='pool2')(x)
#if USE_DROPOUT:
# x = Dropout(p=0.3)(x)
# 3rd layer group
x = Convolution3D(256, 3, 3, 3, activation='relu', border_mode='same', name='conv3a', subsample=(1, 1, 1))(x)
x = Convolution3D(256, 3, 3, 3, activation='relu', border_mode='same', name='conv3b', subsample=(1, 1, 1))(x)
x = MaxPooling3D(pool_size=(2, 2, 2), strides=(2, 2, 2), border_mode='valid', name='pool3')(x)
#if USE_DROPOUT:
# x = Dropout(p=0.4)(x)
# 4th layer group
x = Convolution3D(512, 3, 3, 3, activation='relu', border_mode='same', name='conv4a', subsample=(1, 1, 1))(x)
x = Convolution3D(512, 3, 3, 3, activation='relu', border_mode='same', name='conv4b', subsample=(1, 1, 1),)(x)
x = MaxPooling3D(pool_size=(2, 2, 2), strides=(2, 2, 2), border_mode='valid', name='pool4')(x)
#if USE_DROPOUT:
# x = Dropout(p=0.5)(x)
last64 = Convolution3D(64, 2, 2, 2, activation="relu", name="last_64")(x)
out_class = Convolution3D(1, 1, 1, 1, activation="sigmoid", name="out_class_last")(last64)
out_class = Flatten(name="out_class")(out_class)
out_malignancy = Convolution3D(1, 1, 1, 1, activation=None, name="out_malignancy_last")(last64)
out_malignancy = Flatten(name="out_malignancy")(out_malignancy)
model = Model(input=inputs, output=[out_class, out_malignancy])
if load_weight_path is not None:
model.load_weights(load_weight_path, by_name=False)
#model.compile(optimizer=SGD(lr=LEARN_RATE, momentum=0.9, nesterov=True), loss={"out_class": "binary_crossentropy", "out_malignancy": mean_absolute_error}, metrics={"out_class": [binary_accuracy, binary_crossentropy], "out_malignancy": mean_absolute_error})
model.compile(optimizer=SGD(lr=LEARN_RATE, momentum=0.9, nesterov=True), loss={"out_class": "binary_crossentropy"}, metrics={"out_class": [binary_accuracy, binary_crossentropy]})
if features:
model = Model(input=inputs, output=[last64])
model.summary(line_length=140)
return model
def test_keras_import(self):
# Global Pooling 1D
model = Sequential()
model.add(GlobalMaxPooling1D(input_shape=(1, 16)))
model.build()
self.keras_param_test(model, 0, 5)
# Global Pooling 2D
model = Sequential()
model.add(GlobalMaxPooling2D(input_shape=(1, 16, 16)))
model.build()
self.keras_param_test(model, 0, 8)
# Pooling 1D
model = Sequential()
model.add(MaxPooling1D(pool_size=2, strides=2, padding='same', input_shape=(1, 16)))
model.build()
self.keras_param_test(model, 0, 5)
# Pooling 2D
model = Sequential()
model.add(MaxPooling2D(pool_size=(2, 2), strides=(2, 2), padding='same', input_shape=(1, 16, 16)))
model.build()
self.keras_param_test(model, 0, 8)
# Pooling 3D
model = Sequential()
model.add(MaxPooling3D(pool_size=(2, 2, 2), strides=(2, 2, 2), padding='same',
input_shape=(1, 16, 16, 16)))
model.build()
self.keras_param_test(model, 0, 11)
# ********** Locally-connected Layers **********
def test_keras_export(self):
tests = open(os.path.join(settings.BASE_DIR, 'tests', 'unit', 'keras_app',
'keras_export_test.json'), 'r')
response = json.load(tests)
tests.close()
net = yaml.safe_load(json.dumps(response['net']))
net = {'l0': net['Input'], 'l1': net['Input2'], 'l2': net['Input4'], 'l3': net['Pooling']}
# Pool 1D
net['l1']['connection']['output'].append('l3')
net['l3']['connection']['input'] = ['l1']
net['l3']['params']['layer_type'] = '1D'
net['l3']['shape']['input'] = net['l1']['shape']['output']
net['l3']['shape']['output'] = [12, 12]
inp = data(net['l1'], '', 'l1')['l1']
temp = pooling(net['l3'], [inp], 'l3')
model = Model(inp, temp['l3'])
self.assertEqual(model.layers[2].__class__.__name__, 'MaxPooling1D')
# Pool 2D
net['l0']['connection']['output'].append('l0')
net['l3']['connection']['input'] = ['l0']
net['l3']['params']['layer_type'] = '2D'
net['l3']['shape']['input'] = net['l0']['shape']['output']
net['l3']['shape']['output'] = [3, 226, 226]
inp = data(net['l0'], '', 'l0')['l0']
temp = pooling(net['l3'], [inp], 'l3')
model = Model(inp, temp['l3'])
self.assertEqual(model.layers[2].__class__.__name__, 'MaxPooling2D')
# Pool 3D
net['l2']['connection']['output'].append('l3')
net['l3']['connection']['input'] = ['l2']
net['l3']['params']['layer_type'] = '3D'
net['l3']['shape']['input'] = net['l2']['shape']['output']
net['l3']['shape']['output'] = [3, 226, 226, 18]
inp = data(net['l2'], '', 'l2')['l2']
temp = pooling(net['l3'], [inp], 'l3')
model = Model(inp, temp['l3'])
self.assertEqual(model.layers[2].__class__.__name__, 'MaxPooling3D')
# ********** Locally-connected Layers **********
def create_model_3_noise2():
inputs = Input((32, 32, 32, 1))
noise = GaussianNoise(sigma=0.02)(inputs)
conv1 = Convolution3D(32, 3, 3, 3, activation='relu', border_mode='same')(noise)
conv1 = SpatialDropout3D(0.4)(conv1)
conv1 = Convolution3D(64, 3, 3, 3, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2,2, 2))(conv1)
conv2 = Convolution3D(128, 3, 3, 3, activation='relu', border_mode='same')(pool1)
conv2 = SpatialDropout3D(0.4)(conv2)
conv2 = Convolution3D(128, 3, 3, 3, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2,2, 2))(conv2)
x = Flatten()(pool2)
x = Dense(128, init='normal')(x)
x = Dropout(0.5)(x)
x = Dense(64, init='normal')(x)
predictions = Dense(1, init='normal', activation='sigmoid')(x)
model = Model(input=inputs, output=predictions)
model.summary()
optimizer = Adam(lr=0.00001)
model.compile(optimizer=optimizer, loss='binary_crossentropy', metrics=['binary_accuracy','precision','recall','mean_squared_error','accuracy'])
return model
def create_model_3_noise():
inputs = Input((32, 32, 32, 1))
noise = GaussianNoise(sigma=0.05)(inputs)
conv1 = Convolution3D(32, 3, 3, 3, activation='relu', border_mode='same')(noise)
conv1 = SpatialDropout3D(0.1)(conv1)
conv1 = Convolution3D(64, 3, 3, 3, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2,2, 2))(conv1)
conv2 = Convolution3D(128, 3, 3, 3, activation='relu', border_mode='same')(pool1)
conv2 = SpatialDropout3D(0.1)(conv2)
conv2 = Convolution3D(128, 3, 3, 3, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2,2, 2))(conv2)
x = Flatten()(pool2)
x = Dense(64, init='normal')(x)
x = Dropout(0.5)(x)
predictions = Dense(1, init='normal', activation='sigmoid')(x)
model = Model(input=inputs, output=predictions)
model.summary()
optimizer = Adam(lr=0.000001)
model.compile(optimizer=optimizer, loss='binary_crossentropy', metrics=['binary_accuracy','precision','recall','mean_squared_error','accuracy'])
return model
def create_model_8():
inputs = Input((32, 32, 32, 1))
#noise = GaussianNoise(sigma=0.1)(x)
conv1 = Convolution3D(32, 3, 3, 3, activation='relu', border_mode='same')(inputs)
conv1 = SpatialDropout3D(0.2)(conv1)
conv1 = Convolution3D(64, 3, 3, 3, activation='relu', border_mode='same')(conv1)
conv1 = SpatialDropout3D(0.2)(conv1)
conv1 = Convolution3D(128, 3, 3, 3, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2,2, 2))(conv1)
conv2 = Convolution3D(256, 3, 3, 3, activation='relu', border_mode='same')(pool1)
conv2 = SpatialDropout3D(0.2)(conv2)
conv2 = Convolution3D(512, 3, 3, 3, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2,2, 2))(conv2)
x = Flatten()(pool2)
x = Dense(64, init='normal')(x)
x = Dropout(0.5)(x)
predictions = Dense(1, init='normal', activation='sigmoid')(x)
model = Model(input=inputs, output=predictions)
model.summary()
optimizer = Adam(lr=0.00001)
model.compile(optimizer=optimizer, loss='binary_crossentropy', metrics=['binary_accuracy','precision','recall','mean_squared_error','accuracy'])
return model
def create_model_7():
inputs = Input((32, 32, 32, 1))
#noise = GaussianNoise(sigma=0.1)(x)
conv1 = Convolution3D(32, 5, 5, 5, activation='relu', border_mode='same')(inputs)
conv1 = SpatialDropout3D(0.1)(conv1)
conv1 = Convolution3D(64, 5, 5, 5, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2,2, 2))(conv1)
conv2 = Convolution3D(128, 5, 5, 5, activation='relu', border_mode='same')(pool1)
conv2 = SpatialDropout3D(0.1)(conv2)
conv2 = Convolution3D(128, 5, 5, 5, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2,2, 2))(conv2)
x = Flatten()(pool2)
x = Dense(64, init='normal')(x)
x = Dropout(0.5)(x)
predictions = Dense(1, init='normal', activation='sigmoid')(x)
model = Model(input=inputs, output=predictions)
model.summary()
optimizer = Adam(lr=0.00001)
model.compile(optimizer=optimizer, loss='binary_crossentropy', metrics=['binary_accuracy','precision','recall','mean_squared_error','accuracy'])
return model
def create_model_6():
inputs = Input((32, 32, 32, 1))
#noise = GaussianNoise(sigma=0.1)(x)
conv1 = Convolution3D(32, 3, 3, 3, activation='relu', border_mode='same')(inputs)
conv1 = SpatialDropout3D(0.1)(conv1)
conv1 = Convolution3D(64, 3, 3, 3, activation='relu', border_mode='same')(conv1)
conv1 = SpatialDropout3D(0.1)(conv1)
conv1 = Convolution3D(64, 3, 3, 3, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2,2, 2))(conv1)
conv2 = Convolution3D(128, 3, 3, 3, activation='relu', border_mode='same')(pool1)
conv2 = SpatialDropout3D(0.1)(conv2)
conv2 = Convolution3D(128, 3, 3, 3, activation='relu', border_mode='same')(conv2)
conv2 = SpatialDropout3D(0.1)(conv2)
conv2 = Convolution3D(128, 3, 3, 3, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2,2, 2))(conv2)
x = Flatten()(pool2)
x = Dense(64, init='normal')(x)
x = Dropout(0.5)(x)
predictions = Dense(1, init='normal', activation='sigmoid')(x)
model = Model(input=inputs, output=predictions)
model.summary()
optimizer = Adam(lr=0.00001)
model.compile(optimizer=optimizer, loss='binary_crossentropy', metrics=['binary_accuracy','precision','recall','mean_squared_error','accuracy'])
return model
def create_model_4():
inputs1 = Input((32, 32, 32, 1))
inputs2 = Input((6,))
#noise = GaussianNoise(sigma=0.1)(x)
conv1 = Convolution3D(32, 3, 3, 3, activation='relu', border_mode='same')(inputs1)
conv1 = SpatialDropout3D(0.1)(conv1)
conv1 = Convolution3D(64, 3, 3, 3, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2,2, 2))(conv1)
conv2 = Convolution3D(128, 3, 3, 3, activation='relu', border_mode='same')(pool1)
conv2 = SpatialDropout3D(0.1)(conv2)
conv2 = Convolution3D(128, 3, 3, 3, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2,2, 2))(conv2)
x = Flatten()(pool2)
x = merge([x, inputs2], mode='concat')
x = Dense(64, init='normal')(x)
x = Dropout(0.5)(x)
predictions = Dense(1, init='normal', activation='sigmoid')(x)
model = Model(input=[inputs1,inputs2], output=predictions)
model.summary()
optimizer = Adam()
model.compile(optimizer=optimizer, loss='binary_crossentropy', metrics=['binary_accuracy','precision','recall','mean_squared_error','accuracy'])
return model
def create_model_3():
inputs = Input((32, 32, 32, 1))
#noise = GaussianNoise(sigma=0.1)(x)
conv1 = Convolution3D(32, 3, 3, 3, activation='relu', border_mode='same')(inputs)
conv1 = SpatialDropout3D(0.1)(conv1)
conv1 = Convolution3D(64, 3, 3, 3, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2,2, 2))(conv1)
conv2 = Convolution3D(128, 3, 3, 3, activation='relu', border_mode='same')(pool1)
conv2 = SpatialDropout3D(0.1)(conv2)
conv2 = Convolution3D(128, 3, 3, 3, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2,2, 2))(conv2)
x = Flatten()(pool2)
x = Dense(64, init='normal')(x)
x = Dropout(0.5)(x)
predictions = Dense(1, init='normal', activation='sigmoid')(x)
model = Model(input=inputs, output=predictions)
model.summary()
optimizer = Adam(lr=0.00001)
model.compile(optimizer=optimizer, loss='binary_crossentropy', metrics=['binary_accuracy','precision','recall','mean_squared_error','accuracy'])
return model
step2_train_nodule_detector.py 文件源码
项目：kaggle_ndsb2017
作者: juliandewit
项目源码
文件源码
阅读 19
收藏 0
点赞 0
评论 0
def get_net(input_shape=(CUBE_SIZE, CUBE_SIZE, CUBE_SIZE, 1), load_weight_path=None, features=False, mal=False) -> Model:
inputs = Input(shape=input_shape, name="input_1")
x = inputs
x = AveragePooling3D(pool_size=(2, 1, 1), strides=(2, 1, 1), border_mode="same")(x)
x = Convolution3D(64, 3, 3, 3, activation='relu', border_mode='same', name='conv1', subsample=(1, 1, 1))(x)
x = MaxPooling3D(pool_size=(1, 2, 2), strides=(1, 2, 2), border_mode='valid', name='pool1')(x)
# 2nd layer group
x = Convolution3D(128, 3, 3, 3, activation='relu', border_mode='same', name='conv2', subsample=(1, 1, 1))(x)
x = MaxPooling3D(pool_size=(2, 2, 2), strides=(2, 2, 2), border_mode='valid', name='pool2')(x)
if USE_DROPOUT:
x = Dropout(p=0.3)(x)
# 3rd layer group
x = Convolution3D(256, 3, 3, 3, activation='relu', border_mode='same', name='conv3a', subsample=(1, 1, 1))(x)
x = Convolution3D(256, 3, 3, 3, activation='relu', border_mode='same', name='conv3b', subsample=(1, 1, 1))(x)
x = MaxPooling3D(pool_size=(2, 2, 2), strides=(2, 2, 2), border_mode='valid', name='pool3')(x)
if USE_DROPOUT:
x = Dropout(p=0.4)(x)
# 4th layer group
x = Convolution3D(512, 3, 3, 3, activation='relu', border_mode='same', name='conv4a', subsample=(1, 1, 1))(x)
x = Convolution3D(512, 3, 3, 3, activation='relu', border_mode='same', name='conv4b', subsample=(1, 1, 1),)(x)
x = MaxPooling3D(pool_size=(2, 2, 2), strides=(2, 2, 2), border_mode='valid', name='pool4')(x)
if USE_DROPOUT:
x = Dropout(p=0.5)(x)
last64 = Convolution3D(64, 2, 2, 2, activation="relu", name="last_64")(x)
out_class = Convolution3D(1, 1, 1, 1, activation="sigmoid", name="out_class_last")(last64)
out_class = Flatten(name="out_class")(out_class)
out_malignancy = Convolution3D(1, 1, 1, 1, activation=None, name="out_malignancy_last")(last64)
out_malignancy = Flatten(name="out_malignancy")(out_malignancy)
model = Model(input=inputs, output=[out_class, out_malignancy])
if load_weight_path is not None:
model.load_weights(load_weight_path, by_name=False)
model.compile(optimizer=SGD(lr=LEARN_RATE, momentum=0.9, nesterov=True), loss={"out_class": "binary_crossentropy", "out_malignancy": mean_absolute_error}, metrics={"out_class": [binary_accuracy, binary_crossentropy], "out_malignancy": mean_absolute_error})
if features:
model = Model(input=inputs, output=[last64])
model.summary(line_length=140)
return model
def load_model():
# use simple CNN structure
in_shape = (SequenceLength, IMSIZE[0], IMSIZE[1], 3)
model = Sequential()
model.add(ConvLSTM2D(32, kernel_size=(7, 7), padding='valid', return_sequences=True, input_shape=in_shape))
model.add(Activation('relu'))
model.add(MaxPooling3D(pool_size=(1, 2, 2)))
model.add(ConvLSTM2D(64, kernel_size=(5, 5), padding='valid', return_sequences=True))
model.add(MaxPooling3D(pool_size=(1, 2, 2)))
model.add(ConvLSTM2D(96, kernel_size=(3, 3), padding='valid', return_sequences=True))
model.add(Activation('relu'))
model.add(ConvLSTM2D(96, kernel_size=(3, 3), padding='valid', return_sequences=True))
model.add(Activation('relu'))
model.add(ConvLSTM2D(96, kernel_size=(3, 3), padding='valid', return_sequences=True))
model.add(MaxPooling3D(pool_size=(1, 2, 2)))
model.add(Dense(320))
model.add(Activation('relu'))
model.add(Dropout(0.5))
out_shape = model.output_shape
# print('====Model shape: ', out_shape)
model.add(Reshape((SequenceLength, out_shape[2] * out_shape[3] * out_shape[4])))
model.add(LSTM(64, return_sequences=False))
model.add(Dropout(0.5))
model.add(Dense(N_CLASSES, activation='softmax'))
model.compile(loss='categorical_crossentropy', optimizer='sgd', metrics=['accuracy'])
# model structure summary
print(model.summary())
return model
def unet_model_xd3_2_6l_grid(nb_filter=48, dim=5, clen=3 , img_rows=224, img_cols=224 ): # NOTE that this procedure is/should be used with img_rows & img_cols as None
# aiming for architecture similar to the http://cs231n.stanford.edu/reports2016/317_Report.pdf
# Our model is six layers deep, consisting of a series of three CONV-RELU-POOL layyers (with 32, 32, and 64 3x3 filters), a CONV-RELU layer (with 128 3x3 filters), three UPSCALE-CONV-RELU lay- ers (with 64, 32, and 32 3x3 filters), and a final 1x1 CONV- SIGMOID layer to output pixel-level predictions. Its struc- ture resembles Figure 2, though with the number of pixels, filters, and levels as described here
## 3D CNN version of a previously developed unet_model_xd_6j
zconv = clen
inputs = Input((1, dim, img_rows, img_cols))
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(inputs)
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2, 2, 2))(conv1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2, 2, 2))(conv2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv4)
up6 = merge([UpSampling3D(size=(2, 2, 2))(conv4), conv2], mode='concat', concat_axis=1)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up6)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv6)
up7 = merge([UpSampling3D(size=(2, 2, 2))(conv6), conv1], mode='concat', concat_axis=1) # original - only works for even dim
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up7)
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv7)
pool11 = MaxPooling3D(pool_size=(2, 1, 1))(conv7)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool11)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv12)
pool12 = MaxPooling3D(pool_size=(2, 1, 1))(conv12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv13)
pool13 = MaxPooling3D(pool_size=(2, 1, 1))(conv13)
if (dim < 16):
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool13)
else: # need one extra layer to get to 1D x 2D mask ...
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool13)
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv14)
pool14 = MaxPooling3D(pool_size=(2, 1, 1))(conv14)
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool14)
model = Model(input=inputs, output=conv8)
model.compile(optimizer=Adam(lr=1e-4), loss=dice_coef_loss, metrics=[dice_coef])
#model.compile(optimizer=Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-08, decay=0.0), loss=dice_coef_loss, metrics=[dice_coef])
return model
def unet_model_xd3_2_6l_grid(nb_filter=48, dim=5, clen=3 , img_rows=224, img_cols=224 ): # NOTE that this procedure is/should be used with img_rows & img_cols as None
# aiming for architecture similar to the http://cs231n.stanford.edu/reports2016/317_Report.pdf
# Our model is six layers deep, consisting of a series of three CONV-RELU-POOL layyers (with 32, 32, and 64 3x3 filters), a CONV-RELU layer (with 128 3x3 filters), three UPSCALE-CONV-RELU lay- ers (with 64, 32, and 32 3x3 filters), and a final 1x1 CONV- SIGMOID layer to output pixel-level predictions. Its struc- ture resembles Figure 2, though with the number of pixels, filters, and levels as described here
## 3D CNN version of a previously developed unet_model_xd_6j
zconv = clen
inputs = Input((1, dim, img_rows, img_cols))
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(inputs)
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2, 2, 2))(conv1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2, 2, 2))(conv2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv4)
up6 = merge([UpSampling3D(size=(2, 2, 2))(conv4), conv2], mode='concat', concat_axis=1)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up6)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv6)
up7 = merge([UpSampling3D(size=(2, 2, 2))(conv6), conv1], mode='concat', concat_axis=1) # original - only works for even dim
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up7)
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv7)
pool11 = MaxPooling3D(pool_size=(2, 1, 1))(conv7)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool11)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv12)
pool12 = MaxPooling3D(pool_size=(2, 1, 1))(conv12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv13)
pool13 = MaxPooling3D(pool_size=(2, 1, 1))(conv13)
if (dim < 16):
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool13)
else: # need one extra layer to get to 1D x 2D mask ...
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool13)
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv14)
pool14 = MaxPooling3D(pool_size=(2, 1, 1))(conv14)
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool14)
model = Model(input=inputs, output=conv8)
model.compile(optimizer=Adam(lr=1e-4), loss=dice_coef_loss, metrics=[dice_coef])
#model.compile(optimizer=Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-08, decay=0.0), loss=dice_coef_loss, metrics=[dice_coef])
return model
def unet_model_xd3_2_6l_grid(nb_filter=48, dim=5, clen=3 , img_rows=224, img_cols=224 ): # NOTE that this procedure is/should be used with img_rows & img_cols as None
# aiming for architecture similar to the http://cs231n.stanford.edu/reports2016/317_Report.pdf
# Our model is six layers deep, consisting of a series of three CONV-RELU-POOL layyers (with 32, 32, and 64 3x3 filters), a CONV-RELU layer (with 128 3x3 filters), three UPSCALE-CONV-RELU lay- ers (with 64, 32, and 32 3x3 filters), and a final 1x1 CONV- SIGMOID layer to output pixel-level predictions. Its struc- ture resembles Figure 2, though with the number of pixels, filters, and levels as described here
## 3D CNN version of a previously developed unet_model_xd_6j
zconv = clen
inputs = Input((1, dim, img_rows, img_cols))
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(inputs)
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2, 2, 2))(conv1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2, 2, 2))(conv2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv4)
up6 = merge([UpSampling3D(size=(2, 2, 2))(conv4), conv2], mode='concat', concat_axis=1)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up6)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv6)
up7 = merge([UpSampling3D(size=(2, 2, 2))(conv6), conv1], mode='concat', concat_axis=1) # original - only works for even dim
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up7)
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv7)
pool11 = MaxPooling3D(pool_size=(2, 1, 1))(conv7)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool11)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv12)
pool12 = MaxPooling3D(pool_size=(2, 1, 1))(conv12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv13)
pool13 = MaxPooling3D(pool_size=(2, 1, 1))(conv13)
if (dim < 16):
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool13)
else: # need one extra layer to get to 1D x 2D mask ...
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool13)
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv14)
pool14 = MaxPooling3D(pool_size=(2, 1, 1))(conv14)
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool14)
model = Model(input=inputs, output=conv8)
model.compile(optimizer=Adam(lr=1e-4), loss=dice_coef_loss, metrics=[dice_coef])
#model.compile(optimizer=Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-08, decay=0.0), loss=dice_coef_loss, metrics=[dice_coef])
return model
def unet_model_xd3_2_6l_grid(nb_filter=48, dim=5, clen=3 , img_rows=224, img_cols=224 ): # NOTE that this procedure is/should be used with img_rows & img_cols as None
# aiming for architecture similar to the http://cs231n.stanford.edu/reports2016/317_Report.pdf
# Our model is six layers deep, consisting of a series of three CONV-RELU-POOL layyers (with 32, 32, and 64 3x3 filters), a CONV-RELU layer (with 128 3x3 filters), three UPSCALE-CONV-RELU lay- ers (with 64, 32, and 32 3x3 filters), and a final 1x1 CONV- SIGMOID layer to output pixel-level predictions. Its struc- ture resembles Figure 2, though with the number of pixels, filters, and levels as described here
## 3D CNN version of a previously developed unet_model_xd_6j
zconv = clen
inputs = Input((1, dim, img_rows, img_cols))
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(inputs)
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2, 2, 2))(conv1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2, 2, 2))(conv2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv4)
up6 = merge([UpSampling3D(size=(2, 2, 2))(conv4), conv2], mode='concat', concat_axis=1)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up6)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv6)
up7 = merge([UpSampling3D(size=(2, 2, 2))(conv6), conv1], mode='concat', concat_axis=1) # original - only works for even dim
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up7)
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv7)
pool11 = MaxPooling3D(pool_size=(2, 1, 1))(conv7)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool11)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv12)
pool12 = MaxPooling3D(pool_size=(2, 1, 1))(conv12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv13)
pool13 = MaxPooling3D(pool_size=(2, 1, 1))(conv13)
if (dim < 16):
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool13)
else: # need one extra layer to get to 1D x 2D mask ...
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool13)
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv14)
pool14 = MaxPooling3D(pool_size=(2, 1, 1))(conv14)
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool14)
model = Model(input=inputs, output=conv8)
model.compile(optimizer=Adam(lr=1e-4), loss=dice_coef_loss, metrics=[dice_coef])
#model.compile(optimizer=Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-08, decay=0.0), loss=dice_coef_loss, metrics=[dice_coef])
return model
def unet_model_xd3_2_6l_grid(nb_filter=48, dim=5, clen=3 , img_rows=224, img_cols=224 ): # NOTE that this procedure is/should be used with img_rows & img_cols as None
# aiming for architecture similar to the http://cs231n.stanford.edu/reports2016/317_Report.pdf
# Our model is six layers deep, consisting of a series of three CONV-RELU-POOL layyers (with 32, 32, and 64 3x3 filters), a CONV-RELU layer (with 128 3x3 filters), three UPSCALE-CONV-RELU lay- ers (with 64, 32, and 32 3x3 filters), and a final 1x1 CONV- SIGMOID layer to output pixel-level predictions. Its struc- ture resembles Figure 2, though with the number of pixels, filters, and levels as described here
## 3D CNN version of a previously developed unet_model_xd_6j
zconv = clen
inputs = Input((1, dim, img_rows, img_cols))
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(inputs)
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2, 2, 2))(conv1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2, 2, 2))(conv2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv4)
up6 = merge([UpSampling3D(size=(2, 2, 2))(conv4), conv2], mode='concat', concat_axis=1)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up6)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv6)
up7 = merge([UpSampling3D(size=(2, 2, 2))(conv6), conv1], mode='concat', concat_axis=1) # original - only works for even dim
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up7)
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv7)
pool11 = MaxPooling3D(pool_size=(2, 1, 1))(conv7)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool11)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv12)
pool12 = MaxPooling3D(pool_size=(2, 1, 1))(conv12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv13)
pool13 = MaxPooling3D(pool_size=(2, 1, 1))(conv13)
if (dim < 16):
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool13)
else: # need one extra layer to get to 1D x 2D mask ...
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool13)
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv14)
pool14 = MaxPooling3D(pool_size=(2, 1, 1))(conv14)
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool14)
model = Model(input=inputs, output=conv8)
model.compile(optimizer=Adam(lr=1e-4), loss=dice_coef_loss, metrics=[dice_coef])
#model.compile(optimizer=Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-08, decay=0.0), loss=dice_coef_loss, metrics=[dice_coef])
return model
def unet_model_xd3_2_6l_grid(nb_filter=48, dim=5, clen=3 , img_rows=224, img_cols=224 ): # NOTE that this procedure is/should be used with img_rows & img_cols as None
# aiming for architecture similar to the http://cs231n.stanford.edu/reports2016/317_Report.pdf
# Our model is six layers deep, consisting of a series of three CONV-RELU-POOL layyers (with 32, 32, and 64 3x3 filters), a CONV-RELU layer (with 128 3x3 filters), three UPSCALE-CONV-RELU lay- ers (with 64, 32, and 32 3x3 filters), and a final 1x1 CONV- SIGMOID layer to output pixel-level predictions. Its struc- ture resembles Figure 2, though with the number of pixels, filters, and levels as described here
## 3D CNN version of a previously developed unet_model_xd_6j
zconv = clen
inputs = Input((1, dim, img_rows, img_cols))
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(inputs)
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2, 2, 2))(conv1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2, 2, 2))(conv2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv4)
up6 = merge([UpSampling3D(size=(2, 2, 2))(conv4), conv2], mode='concat', concat_axis=1)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up6)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv6)
up7 = merge([UpSampling3D(size=(2, 2, 2))(conv6), conv1], mode='concat', concat_axis=1) # original - only works for even dim
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up7)
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv7)
pool11 = MaxPooling3D(pool_size=(2, 1, 1))(conv7)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool11)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv12)
pool12 = MaxPooling3D(pool_size=(2, 1, 1))(conv12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv13)
pool13 = MaxPooling3D(pool_size=(2, 1, 1))(conv13)
if (dim < 16):
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool13)
else: # need one extra layer to get to 1D x 2D mask ...
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool13)
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv14)
pool14 = MaxPooling3D(pool_size=(2, 1, 1))(conv14)
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool14)
model = Model(input=inputs, output=conv8)
model.compile(optimizer=Adam(lr=1e-4), loss=dice_coef_loss, metrics=[dice_coef])
#model.compile(optimizer=Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-08, decay=0.0), loss=dice_coef_loss, metrics=[dice_coef])
return model
def unet_model_xd3_2_6l_grid(nb_filter=48, dim=5, clen=3 , img_rows=224, img_cols=224 ): # NOTE that this procedure is/should be used with img_rows & img_cols as None
# aiming for architecture similar to the http://cs231n.stanford.edu/reports2016/317_Report.pdf
# Our model is six layers deep, consisting of a series of three CONV-RELU-POOL layyers (with 32, 32, and 64 3x3 filters), a CONV-RELU layer (with 128 3x3 filters), three UPSCALE-CONV-RELU lay- ers (with 64, 32, and 32 3x3 filters), and a final 1x1 CONV- SIGMOID layer to output pixel-level predictions. Its struc- ture resembles Figure 2, though with the number of pixels, filters, and levels as described here
## 3D CNN version of a previously developed unet_model_xd_6j
zconv = clen
inputs = Input((1, dim, img_rows, img_cols))
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(inputs)
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2, 2, 2))(conv1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2, 2, 2))(conv2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv4)
up6 = merge([UpSampling3D(size=(2, 2, 2))(conv4), conv2], mode='concat', concat_axis=1)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up6)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv6)
up7 = merge([UpSampling3D(size=(2, 2, 2))(conv6), conv1], mode='concat', concat_axis=1) # original - only works for even dim
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up7)
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv7)
pool11 = MaxPooling3D(pool_size=(2, 1, 1))(conv7)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool11)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv12)
pool12 = MaxPooling3D(pool_size=(2, 1, 1))(conv12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv13)
pool13 = MaxPooling3D(pool_size=(2, 1, 1))(conv13)
if (dim < 16):
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool13)
else: # need one extra layer to get to 1D x 2D mask ...
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool13)
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv14)
pool14 = MaxPooling3D(pool_size=(2, 1, 1))(conv14)
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool14)
model = Model(input=inputs, output=conv8)
model.compile(optimizer=Adam(lr=1e-4), loss=dice_coef_loss, metrics=[dice_coef])
#model.compile(optimizer=Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-08, decay=0.0), loss=dice_coef_loss, metrics=[dice_coef])
return model
def unet_model_xd3_2_6l_grid(nb_filter=48, dim=5, clen=3 , img_rows=224, img_cols=224 ): # NOTE that this procedure is/should be used with img_rows & img_cols as None
# aiming for architecture similar to the http://cs231n.stanford.edu/reports2016/317_Report.pdf
# Our model is six layers deep, consisting of a series of three CONV-RELU-POOL layyers (with 32, 32, and 64 3x3 filters), a CONV-RELU layer (with 128 3x3 filters), three UPSCALE-CONV-RELU lay- ers (with 64, 32, and 32 3x3 filters), and a final 1x1 CONV- SIGMOID layer to output pixel-level predictions. Its struc- ture resembles Figure 2, though with the number of pixels, filters, and levels as described here
## 3D CNN version of a previously developed unet_model_xd_6j
zconv = clen
inputs = Input((1, dim, img_rows, img_cols))
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(inputs)
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2, 2, 2))(conv1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2, 2, 2))(conv2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv4)
up6 = merge([UpSampling3D(size=(2, 2, 2))(conv4), conv2], mode='concat', concat_axis=1)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up6)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv6)
up7 = merge([UpSampling3D(size=(2, 2, 2))(conv6), conv1], mode='concat', concat_axis=1) # original - only works for even dim
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up7)
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv7)
pool11 = MaxPooling3D(pool_size=(2, 1, 1))(conv7)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool11)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv12)
pool12 = MaxPooling3D(pool_size=(2, 1, 1))(conv12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv13)
pool13 = MaxPooling3D(pool_size=(2, 1, 1))(conv13)
if (dim < 16):
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool13)
else: # need one extra layer to get to 1D x 2D mask ...
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool13)
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv14)
pool14 = MaxPooling3D(pool_size=(2, 1, 1))(conv14)
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool14)
model = Model(input=inputs, output=conv8)
model.compile(optimizer=Adam(lr=1e-4), loss=dice_coef_loss, metrics=[dice_coef])
#model.compile(optimizer=Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-08, decay=0.0), loss=dice_coef_loss, metrics=[dice_coef])
return model
def unet_model_xd3_2_6l_grid(nb_filter=48, dim=5, clen=3 , img_rows=224, img_cols=224 ): # NOTE that this procedure is/should be used with img_rows & img_cols as None
# aiming for architecture similar to the http://cs231n.stanford.edu/reports2016/317_Report.pdf
# Our model is six layers deep, consisting of a series of three CONV-RELU-POOL layyers (with 32, 32, and 64 3x3 filters), a CONV-RELU layer (with 128 3x3 filters), three UPSCALE-CONV-RELU lay- ers (with 64, 32, and 32 3x3 filters), and a final 1x1 CONV- SIGMOID layer to output pixel-level predictions. Its struc- ture resembles Figure 2, though with the number of pixels, filters, and levels as described here
## 3D CNN version of a previously developed unet_model_xd_6j
zconv = clen
inputs = Input((1, dim, img_rows, img_cols))
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(inputs)
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2, 2, 2))(conv1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2, 2, 2))(conv2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv4)
up6 = merge([UpSampling3D(size=(2, 2, 2))(conv4), conv2], mode='concat', concat_axis=1)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up6)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv6)
up7 = merge([UpSampling3D(size=(2, 2, 2))(conv6), conv1], mode='concat', concat_axis=1) # original - only works for even dim
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up7)
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv7)
pool11 = MaxPooling3D(pool_size=(2, 1, 1))(conv7)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool11)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv12)
pool12 = MaxPooling3D(pool_size=(2, 1, 1))(conv12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv13)
pool13 = MaxPooling3D(pool_size=(2, 1, 1))(conv13)
if (dim < 16):
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool13)
else: # need one extra layer to get to 1D x 2D mask ...
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool13)
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv14)
pool14 = MaxPooling3D(pool_size=(2, 1, 1))(conv14)
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool14)
model = Model(input=inputs, output=conv8)
model.compile(optimizer=Adam(lr=1e-4), loss=dice_coef_loss, metrics=[dice_coef])
#model.compile(optimizer=Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-08, decay=0.0), loss=dice_coef_loss, metrics=[dice_coef])
return model
def unet_model_xd3_2_6l_grid(nb_filter=48, dim=5, clen=3 , img_rows=224, img_cols=224 ): # NOTE that this procedure is/should be used with img_rows & img_cols as None
# aiming for architecture similar to the http://cs231n.stanford.edu/reports2016/317_Report.pdf
# Our model is six layers deep, consisting of a series of three CONV-RELU-POOL layyers (with 32, 32, and 64 3x3 filters), a CONV-RELU layer (with 128 3x3 filters), three UPSCALE-CONV-RELU lay- ers (with 64, 32, and 32 3x3 filters), and a final 1x1 CONV- SIGMOID layer to output pixel-level predictions. Its struc- ture resembles Figure 2, though with the number of pixels, filters, and levels as described here
## 3D CNN version of a previously developed unet_model_xd_6j
zconv = clen
inputs = Input((1, dim, img_rows, img_cols))
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(inputs)
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2, 2, 2))(conv1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2, 2, 2))(conv2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv4)
up6 = merge([UpSampling3D(size=(2, 2, 2))(conv4), conv2], mode='concat', concat_axis=1)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up6)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv6)
up7 = merge([UpSampling3D(size=(2, 2, 2))(conv6), conv1], mode='concat', concat_axis=1) # original - only works for even dim
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up7)
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv7)
pool11 = MaxPooling3D(pool_size=(2, 1, 1))(conv7)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool11)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv12)
pool12 = MaxPooling3D(pool_size=(2, 1, 1))(conv12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv13)
pool13 = MaxPooling3D(pool_size=(2, 1, 1))(conv13)
if (dim < 16):
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool13)
else: # need one extra layer to get to 1D x 2D mask ...
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool13)
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv14)
pool14 = MaxPooling3D(pool_size=(2, 1, 1))(conv14)
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool14)
model = Model(input=inputs, output=conv8)
model.compile(optimizer=Adam(lr=1e-4), loss=dice_coef_loss, metrics=[dice_coef])
#model.compile(optimizer=Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-08, decay=0.0), loss=dice_coef_loss, metrics=[dice_coef])
return model
def unet_model_xd3_2_6l_grid(nb_filter=48, dim=5, clen=3 , img_rows=224, img_cols=224 ): # NOTE that this procedure is/should be used with img_rows & img_cols as None
# aiming for architecture similar to the http://cs231n.stanford.edu/reports2016/317_Report.pdf
# Our model is six layers deep, consisting of a series of three CONV-RELU-POOL layyers (with 32, 32, and 64 3x3 filters), a CONV-RELU layer (with 128 3x3 filters), three UPSCALE-CONV-RELU lay- ers (with 64, 32, and 32 3x3 filters), and a final 1x1 CONV- SIGMOID layer to output pixel-level predictions. Its struc- ture resembles Figure 2, though with the number of pixels, filters, and levels as described here
## 3D CNN version of a previously developed unet_model_xd_6j
zconv = clen
inputs = Input((1, dim, img_rows, img_cols))
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(inputs)
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2, 2, 2))(conv1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2, 2, 2))(conv2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv4)
up6 = merge([UpSampling3D(size=(2, 2, 2))(conv4), conv2], mode='concat', concat_axis=1)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up6)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv6)
up7 = merge([UpSampling3D(size=(2, 2, 2))(conv6), conv1], mode='concat', concat_axis=1) # original - only works for even dim
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up7)
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv7)
pool11 = MaxPooling3D(pool_size=(2, 1, 1))(conv7)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool11)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv12)
pool12 = MaxPooling3D(pool_size=(2, 1, 1))(conv12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv13)
pool13 = MaxPooling3D(pool_size=(2, 1, 1))(conv13)
if (dim < 16):
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool13)
else: # need one extra layer to get to 1D x 2D mask ...
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool13)
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv14)
pool14 = MaxPooling3D(pool_size=(2, 1, 1))(conv14)
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool14)
model = Model(input=inputs, output=conv8)
model.compile(optimizer=Adam(lr=1e-4), loss=dice_coef_loss, metrics=[dice_coef])
#model.compile(optimizer=Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-08, decay=0.0), loss=dice_coef_loss, metrics=[dice_coef])
return model
def unet_model_xd3_2_6l_grid(nb_filter=48, dim=5, clen=3 , img_rows=224, img_cols=224 ): # NOTE that this procedure is/should be used with img_rows & img_cols as None
# aiming for architecture similar to the http://cs231n.stanford.edu/reports2016/317_Report.pdf
# Our model is six layers deep, consisting of a series of three CONV-RELU-POOL layyers (with 32, 32, and 64 3x3 filters), a CONV-RELU layer (with 128 3x3 filters), three UPSCALE-CONV-RELU lay- ers (with 64, 32, and 32 3x3 filters), and a final 1x1 CONV- SIGMOID layer to output pixel-level predictions. Its struc- ture resembles Figure 2, though with the number of pixels, filters, and levels as described here
## 3D CNN version of a previously developed unet_model_xd_6j
zconv = clen
inputs = Input((1, dim, img_rows, img_cols))
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(inputs)
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2, 2, 2))(conv1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2, 2, 2))(conv2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv4)
up6 = merge([UpSampling3D(size=(2, 2, 2))(conv4), conv2], mode='concat', concat_axis=1)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up6)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv6)
up7 = merge([UpSampling3D(size=(2, 2, 2))(conv6), conv1], mode='concat', concat_axis=1) # original - only works for even dim
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up7)
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv7)
pool11 = MaxPooling3D(pool_size=(2, 1, 1))(conv7)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool11)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv12)
pool12 = MaxPooling3D(pool_size=(2, 1, 1))(conv12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv13)
pool13 = MaxPooling3D(pool_size=(2, 1, 1))(conv13)
if (dim < 16):
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool13)
else: # need one extra layer to get to 1D x 2D mask ...
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool13)
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv14)
pool14 = MaxPooling3D(pool_size=(2, 1, 1))(conv14)
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool14)
model = Model(input=inputs, output=conv8)
model.compile(optimizer=Adam(lr=1e-4), loss=dice_coef_loss, metrics=[dice_coef])
#model.compile(optimizer=Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-08, decay=0.0), loss=dice_coef_loss, metrics=[dice_coef])
return model
def unet_model_xd3_2_6l_grid(nb_filter=48, dim=5, clen=3 , img_rows=224, img_cols=224 ): # NOTE that this procedure is/should be used with img_rows & img_cols as None
# aiming for architecture similar to the http://cs231n.stanford.edu/reports2016/317_Report.pdf
# Our model is six layers deep, consisting of a series of three CONV-RELU-POOL layyers (with 32, 32, and 64 3x3 filters), a CONV-RELU layer (with 128 3x3 filters), three UPSCALE-CONV-RELU lay- ers (with 64, 32, and 32 3x3 filters), and a final 1x1 CONV- SIGMOID layer to output pixel-level predictions. Its struc- ture resembles Figure 2, though with the number of pixels, filters, and levels as described here
## 3D CNN version of a previously developed unet_model_xd_6j
zconv = clen
inputs = Input((1, dim, img_rows, img_cols))
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(inputs)
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2, 2, 2))(conv1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2, 2, 2))(conv2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv4)
up6 = merge([UpSampling3D(size=(2, 2, 2))(conv4), conv2], mode='concat', concat_axis=1)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up6)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv6)
up7 = merge([UpSampling3D(size=(2, 2, 2))(conv6), conv1], mode='concat', concat_axis=1) # original - only works for even dim
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up7)
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv7)
pool11 = MaxPooling3D(pool_size=(2, 1, 1))(conv7)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool11)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv12)
pool12 = MaxPooling3D(pool_size=(2, 1, 1))(conv12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv13)
pool13 = MaxPooling3D(pool_size=(2, 1, 1))(conv13)
if (dim < 16):
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool13)
else: # need one extra layer to get to 1D x 2D mask ...
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool13)
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv14)
pool14 = MaxPooling3D(pool_size=(2, 1, 1))(conv14)
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool14)
model = Model(input=inputs, output=conv8)
model.compile(optimizer=Adam(lr=1e-4), loss=dice_coef_loss, metrics=[dice_coef])
#model.compile(optimizer=Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-08, decay=0.0), loss=dice_coef_loss, metrics=[dice_coef])
return model
def unet_model_xd3_2_6l_grid(nb_filter=48, dim=5, clen=3 , img_rows=224, img_cols=224 ): # NOTE that this procedure is/should be used with img_rows & img_cols as None
# aiming for architecture similar to the http://cs231n.stanford.edu/reports2016/317_Report.pdf
# Our model is six layers deep, consisting of a series of three CONV-RELU-POOL layyers (with 32, 32, and 64 3x3 filters), a CONV-RELU layer (with 128 3x3 filters), three UPSCALE-CONV-RELU lay- ers (with 64, 32, and 32 3x3 filters), and a final 1x1 CONV- SIGMOID layer to output pixel-level predictions. Its struc- ture resembles Figure 2, though with the number of pixels, filters, and levels as described here
## 3D CNN version of a previously developed unet_model_xd_6j
zconv = clen
inputs = Input((1, dim, img_rows, img_cols))
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(inputs)
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2, 2, 2))(conv1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2, 2, 2))(conv2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv4)
up6 = merge([UpSampling3D(size=(2, 2, 2))(conv4), conv2], mode='concat', concat_axis=1)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up6)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv6)
up7 = merge([UpSampling3D(size=(2, 2, 2))(conv6), conv1], mode='concat', concat_axis=1) # original - only works for even dim
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up7)
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv7)
pool11 = MaxPooling3D(pool_size=(2, 1, 1))(conv7)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool11)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv12)
pool12 = MaxPooling3D(pool_size=(2, 1, 1))(conv12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv13)
pool13 = MaxPooling3D(pool_size=(2, 1, 1))(conv13)
if (dim < 16):
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool13)
else: # need one extra layer to get to 1D x 2D mask ...
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool13)
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv14)
pool14 = MaxPooling3D(pool_size=(2, 1, 1))(conv14)
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool14)
model = Model(input=inputs, output=conv8)
model.compile(optimizer=Adam(lr=1e-4), loss=dice_coef_loss, metrics=[dice_coef])
#model.compile(optimizer=Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-08, decay=0.0), loss=dice_coef_loss, metrics=[dice_coef])
return model
def unet_model_xd3_2_6l_grid(nb_filter=48, dim=5, clen=3 , img_rows=224, img_cols=224 ): # NOTE that this procedure is/should be used with img_rows & img_cols as None
# aiming for architecture similar to the http://cs231n.stanford.edu/reports2016/317_Report.pdf
# Our model is six layers deep, consisting of a series of three CONV-RELU-POOL layyers (with 32, 32, and 64 3x3 filters), a CONV-RELU layer (with 128 3x3 filters), three UPSCALE-CONV-RELU lay- ers (with 64, 32, and 32 3x3 filters), and a final 1x1 CONV- SIGMOID layer to output pixel-level predictions. Its struc- ture resembles Figure 2, though with the number of pixels, filters, and levels as described here
## 3D CNN version of a previously developed unet_model_xd_6j
zconv = clen
inputs = Input((1, dim, img_rows, img_cols))
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(inputs)
conv1 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv1)
pool1 = MaxPooling3D(pool_size=(2, 2, 2))(conv1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool1)
conv2 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv2)
pool2 = MaxPooling3D(pool_size=(2, 2, 2))(conv2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(pool2)
conv4 = Convolution3D(4*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv4)
up6 = merge([UpSampling3D(size=(2, 2, 2))(conv4), conv2], mode='concat', concat_axis=1)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up6)
conv6 = Convolution3D(2*nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv6)
up7 = merge([UpSampling3D(size=(2, 2, 2))(conv6), conv1], mode='concat', concat_axis=1) # original - only works for even dim
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(up7)
conv7 = Convolution3D(nb_filter, zconv, clen, clen, activation='relu', border_mode='same')(conv7)
pool11 = MaxPooling3D(pool_size=(2, 1, 1))(conv7)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool11)
conv12 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv12)
pool12 = MaxPooling3D(pool_size=(2, 1, 1))(conv12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool12)
conv13 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv13)
pool13 = MaxPooling3D(pool_size=(2, 1, 1))(conv13)
if (dim < 16):
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool13)
else: # need one extra layer to get to 1D x 2D mask ...
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(pool13)
conv14 = Convolution3D(2*nb_filter, zconv, 1, 1, activation='relu', border_mode='same')(conv14)
pool14 = MaxPooling3D(pool_size=(2, 1, 1))(conv14)
conv8 = Convolution3D(1, 1, 1, 1, activation='sigmoid')(pool14)
model = Model(input=inputs, output=conv8)
model.compile(optimizer=Adam(lr=1e-4), loss=dice_coef_loss, metrics=[dice_coef])
#model.compile(optimizer=Adam(lr=0.001, beta_1=0.9, beta_2=0.999, epsilon=1e-08, decay=0.0), loss=dice_coef_loss, metrics=[dice_coef])
return model
