def test_set_augmentation(self):
img_path = os.path.join(base_path, '../test_data/tiffconnector_1/im/')
label_path = os.path.join(base_path,
'../test_data/tiffconnector_1/labels/')
c = TiffConnector(img_path, label_path)
d = Dataset(c)
size = (1, 3, 4)
pad = (1, 2, 2)
m = TrainingBatch(d,
size,
padding_zxy=pad,
batch_size=len(d.label_values()))
self.assertEqual(m.augmentation, {'flip'})
m.augment_by_rotation(True)
self.assertEqual(m.augmentation, {'flip', 'rotate'})
self.assertEqual(m.rotation_range, (-45, 45))
m.augment_by_shear(True)
self.assertEqual(m.augmentation, {'flip', 'rotate', 'shear'})
self.assertEqual(m.shear_range, (-5, 5))
m.augment_by_flipping(False)
self.assertEqual(m.augmentation, {'rotate', 'shear'})
def test_get_pixels_dimension_order(self):
img_path = os.path.join(base_path, '../test_data/tiffconnector_1/im/')
label_path = os.path.join(base_path,
'../test_data/tiffconnector_1/labels/')
c = TiffConnector(img_path, label_path)
d = Dataset(c)
size = (2, 5, 4)
pad = (0, 0, 0)
m = TrainingBatch(d,
size,
padding_zxy=pad,
batch_size=len(d.label_values()))
next(m)
p = m.pixels()
w = m.weights()
self.assertEqual(p.shape, (3, 3, 2, 5, 4))
self.assertEqual(w.shape, (3, 3, 2, 5, 4))
m.set_pixel_dimension_order('bczxy')
p = m.pixels()
w = m.weights()
self.assertEqual(p.shape, (3, 3, 2, 5, 4))
self.assertEqual(w.shape, (3, 3, 2, 5, 4))
m.set_pixel_dimension_order('bzxyc')
p = m.pixels()
w = m.weights()
self.assertEqual(p.shape, (3, 2, 5, 4, 3))
self.assertEqual(w.shape, (3, 2, 5, 4, 3))
def test_normalize_zscore(self):
img_path = os.path.join(base_path, '../test_data/tiffconnector_1/im/')
label_path = os.path.join(base_path,
'../test_data/tiffconnector_1/labels/')
c = TiffConnector(img_path, label_path)
d = Dataset(c)
size = (1, 2, 2)
pad = (0, 0, 0)
batchsize = 2
nr_channels = 3
nz = 1
nx = 4
ny = 5
m = TrainingBatch(d,
size,
padding_zxy=pad,
batch_size=len(d.label_values()))
m.set_normalize_mode('local_z_score')
pixels = np.zeros((batchsize, nr_channels, nz, nx, ny))
pixels[:, 0, :, :, :] = 1
pixels[:, 1, :, :, :] = 2
pixels[:, 2, :, :, :] = 3
p_norm = m._normalize(pixels)
self.assertTrue((p_norm == 0).all())
# add variation
pixels[:, 0, 0, 0, 0] = 2
pixels[:, 0, 0, 0, 1] = 0
pixels[:, 1, 0, 0, 0] = 3
pixels[:, 1, 0, 0, 1] = 1
pixels[:, 2, 0, 0, 0] = 4
pixels[:, 2, 0, 0, 1] = 2
p_norm = m._normalize(pixels)
assert_array_equal(p_norm[:, 0, :, :, :], p_norm[:, 1, :, :, :])
assert_array_equal(p_norm[:, 0, :, :, :], p_norm[:, 2, :, :, :])
val = np.array([[[3.16227766, -3.16227766, 0., 0., 0.],
[0., 0., 0., 0., 0.], [0., 0., 0., 0., 0.],
[0., 0., 0., 0., 0.]]])
assert_array_almost_equal(val, p_norm[0, 0, :, :, :])
def test_normalize_global(self):
img_path = os.path.join(base_path, '../test_data/tiffconnector_1/im/')
label_path = os.path.join(base_path,
'../test_data/tiffconnector_1/labels/')
c = TiffConnector(img_path, label_path)
d = Dataset(c)
size = (1, 2, 2)
pad = (0, 0, 0)
batchsize = 2
nr_channels = 3
nz = 1
nx = 4
ny = 5
val = np.array(
[[[0.33333333, 0.33333333, 0.33333333, 0.33333333, 0.33333333],
[0.33333333, 0.33333333, 0.33333333, 0.33333333, 0.33333333],
[0.33333333, 0.33333333, 0.33333333, 0.33333333, 0.33333333],
[0.33333333, 0.33333333, 0.33333333, 0.33333333, 0.33333333]],
[[0.66666667, 0.66666667, 0.66666667, 0.66666667, 0.66666667],
[0.66666667, 0.66666667, 0.66666667, 0.66666667, 0.66666667],
[0.66666667, 0.66666667, 0.66666667, 0.66666667, 0.66666667],
[0.66666667, 0.66666667, 0.66666667, 0.66666667, 0.66666667]],
[[1., 1., 1., 1., 1.], [1., 1., 1., 1., 1.], [1., 1., 1., 1., 1.],
[1., 1., 1., 1., 1.]]])
m = TrainingBatch(d,
size,
padding_zxy=pad,
batch_size=len(d.label_values()))
m.set_normalize_mode('global', minmax=[0, 3])
pixels = np.zeros((batchsize, nr_channels, nz, nx, ny))
pixels[:, 0, :, :, :] = 1
pixels[:, 1, :, :, :] = 2
pixels[:, 2, :, :, :] = 3
p_norm = m._normalize(pixels)
pprint(p_norm)
print(pixels.shape)
print(p_norm.shape)
assert_array_almost_equal(val, p_norm[0, :, 0, :, :])
def test_random_tile(self):
img_path = os.path.join(base_path, '../test_data/tiffconnector_1/im/')
label_path = os.path.join(base_path,
'../test_data/tiffconnector_1/labels/')
c = TiffConnector(img_path, label_path)
d = Dataset(c)
size = (1, 3, 4)
pad = (1, 2, 2)
m = TrainingBatch(d,
size,
padding_zxy=pad,
batch_size=len(d.label_values()))
m._random_tile(for_label=1)
def test_normalize_global_auto(self):
img_path = os.path.join(base_path, '../test_data/tiffconnector_1/im/')
label_path = os.path.join(base_path,
'../test_data/tiffconnector_1/labels/')
c = TiffConnector(img_path, label_path)
d = Dataset(c)
size = (1, 5, 4)
pad = (0, 0, 0)
m = TrainingBatch(d,
size,
padding_zxy=pad,
batch_size=len(d.label_values()))
assert m.global_norm_minmax is None
m.set_normalize_mode('global')
assert len(m.global_norm_minmax) == 3
def test_set_pixel_dimension_order(self):
img_path = os.path.join(base_path, '../test_data/tiffconnector_1/im/')
label_path = os.path.join(base_path,
'../test_data/tiffconnector_1/labels/')
c = TiffConnector(img_path, label_path)
d = Dataset(c)
size = (1, 3, 4)
pad = (1, 2, 2)
m = TrainingBatch(d,
size,
padding_zxy=pad,
batch_size=len(d.label_values()))
m.set_pixel_dimension_order('bczxy')
self.assertEqual([0, 1, 2, 3, 4], m.pixel_dimension_order)
m.set_pixel_dimension_order('bzxyc')
self.assertEqual([0, 4, 1, 2, 3], m.pixel_dimension_order)
def test_getitem_multichannel_labels(self):
# define data loacations
pixel_image_dir = os.path.join(base_path,
'../test_data/tiffconnector_1/im/')
label_image_dir = os.path.join(
base_path, '../test_data/tiffconnector_1/labels_multichannel/')
tile_size = (1, 5, 4) # size of network output layer in zxy
# padding of network input layer in zxy, in respect to output layer
padding = (0, 2, 2)
# make training_batch mb and prediction interface p with
# TiffConnector binding
c = TiffConnector(pixel_image_dir,
label_image_dir,
savepath=self.tmpdir)
d = Dataset(c)
m = TrainingBatch(d,
tile_size,
padding_zxy=padding,
batch_size=len(d.label_values()))
for counter, mini in enumerate(m):
# shape is (6, 6, 1, 5, 4):
# batchsize 6 , 6 label-classes, 1 z, 5 x, 4 y
weights = mini.weights()
# shape is (6, 3, 1, 9, 8):
# batchsize 6, 6 channels, 1 z, 9 x, 4 y (more xy due to padding)
pixels = mini.pixels()
self.assertEqual(weights.shape, (6, 6, 1, 5, 4))
self.assertEqual(pixels.shape, (6, 3, 1, 9, 8))
# apply training on mini.pixels and mini.weights goes here
if counter > 10: # m is infinite
break
class Session(object):
'''
A session is used for training a model with a connected dataset (pixels
and labels) or for predicting connected data (pixels) with an already
trained model.
Parameters
----------
data : yapic_io.TrainingBatch
Connector object for binding pixel and label data
'''
def __init__(self):
self.dataset = None
self.model = None
self.data = None
self.data_val = None
self.history = None
self.data_predict = None
self.log_filename = None
self.output_tile_size_zxy = None
self.padding_zxy = None
def load_training_data(self, image_path, label_path):
'''
Connect to a training dataset.
Parameters
----------
image_path : string
Path to folder with tiff images.
label_path : string
Path to folder with label tiff images or path to ilastik project
file (.ilp file).
'''
print(image_path)
print(label_path)
self.dataset = Dataset(io_connector(image_path, label_path))
def load_prediction_data(self, image_path, save_path):
'''
Connect to a prediction dataset.
Parameters
----------
image_path : string
Path to folder with tiff images to predict.
save_path : string
Path to folder for saving prediction images.
'''
self.dataset = Dataset(
io_connector(image_path,
'/tmp/this_should_not_exist',
savepath=save_path))
def make_model(self, model_name, input_tile_size_zxy):
'''
Initialzes a neural network and sets tile sizes of the data connector
accordingly to model input/output shapes.
Parameters
----------
model_name : string
Either 'unet_2d' or 'unet_2p5d'
input_tile_size_zxy: (nr_zslices, nr_x, nr_y)
Input shape of the model. Large input shapes require large memory
for used GPU hardware. For 'unet_2d', nr_zslices has to be 1.
'''
print('tile size zxy: {}'.format(input_tile_size_zxy))
assert len(input_tile_size_zxy) == 3
nr_channels = self.dataset.image_dimensions(0)[0]
print('nr_channels: {}'.format(nr_channels))
input_size_czxy = [nr_channels] + list(input_tile_size_zxy)
n_classes = len(self.dataset.label_values())
self.model = make_model(model_name, n_classes, input_size_czxy)
output_tile_size_zxy = self.model.output_shape[-4:-1]
self._configure_minibatch_data(input_tile_size_zxy,
output_tile_size_zxy)
def load_model(self, model_filepath):
'''
Import a Keras model in hfd5 format.
Parameters
----------
model_filepath : string
Path to .h5 model file
'''
model = load_keras_model(model_filepath)
n_classes_model = model.output_shape[-1]
output_tile_size_zxy = model.output_shape[-4:-1]
n_channels_model = model.input_shape[-1]
input_tile_size_zxy = model.input_shape[-4:-1]
n_classes_data = len(self.dataset.label_values())
n_channels_data = self.dataset.image_dimensions(0)[0]
msg = ('nr of model classes ({}) and data classes ({}) '
'is not equal').format(n_classes_model, n_classes_data)
if n_classes_data > 0:
assert n_classes_data == n_classes_model, msg
msg = ('nr of model channels ({}) and iamge channels ({}) '
'is not equal').format(n_channels_model, n_channels_data)
assert n_channels_data == n_channels_model, msg
self._configure_minibatch_data(input_tile_size_zxy,
output_tile_size_zxy)
self.model = model
def _configure_minibatch_data(self, input_tile_size_zxy,
output_tile_size_zxy):
padding_zxy = tuple(
((np.array(input_tile_size_zxy) - np.array(output_tile_size_zxy)) /
2).astype(np.int))
self.data_val = None
self.data = TrainingBatch(self.dataset,
output_tile_size_zxy,
padding_zxy=padding_zxy)
self.data.set_normalize_mode('local')
self.data.set_pixel_dimension_order('bzxyc')
next(self.data)
self.output_tile_size_zxy = output_tile_size_zxy
self.padding_zxy = padding_zxy
def define_validation_data(self, valfraction):
'''
Splits the dataset into a training fraction and a validation fraction.
Parameters
----------
valfraction : float
Approximate fraction of validation data. Has to be between 0 and 1.
'''
if self.data_val is not None:
logger.warning('skipping define_validation_data: already defined')
return None
if self.data is None:
logger.warning('skipping, data not defined yet')
return None
self.data.remove_unlabeled_tiles()
self.data_val = self.data.split(valfraction)
def train(self,
max_epochs=3000,
steps_per_epoch=24,
log_filename=None,
model_filename='model.h5'):
'''
Starts a training run.
Parameters
----------
max_epochs : int
Number of epochs.
steps_per_epoch : int
Number of training steps per epoch.
log_filename : string
Path to the csv file for logging loss and accuracy.
model_filename : string
Path to h5 keras model file
Notes
-----
Validation is executed once each epoch.
Logging to csv file is executed once each epoch.
'''
callbacks = []
if self.data_val:
save_model_callback = keras.callbacks.ModelCheckpoint(
model_filename,
monitor='val_loss',
verbose=0,
save_best_only=True)
else:
save_model_callback = keras.callbacks.ModelCheckpoint(
model_filename, monitor='loss', verbose=0, save_best_only=True)
callbacks.append(save_model_callback)
if log_filename:
callbacks.append(
keras.callbacks.CSVLogger(log_filename,
separator=',',
append=False))
training_data = ((mb.pixels(), mb.weights()) for mb in self.data)
if self.data_val:
validation_data = ((mb.pixels(), mb.weights())
for mb in self.data_val)
else:
validation_data = None
self.history = self.model.fit_generator(
training_data,
validation_data=validation_data,
epochs=max_epochs,
validation_steps=steps_per_epoch,
steps_per_epoch=steps_per_epoch,
callbacks=callbacks,
workers=0)
return self.history
def predict(self):
data_predict = PredictionBatch(self.dataset, 2,
self.output_tile_size_zxy,
self.padding_zxy)
data_predict.set_normalize_mode('local')
data_predict.set_pixel_dimension_order('bzxyc')
for item in data_predict:
result = self.model.predict(item.pixels())
item.put_probmap_data(result)
def set_augmentation(self, augment_string):
'''
Define data augmentation settings for model training.
Parameters
----------
augment_string : string
Choose 'flip' and/or 'rotate' and/or 'shear'.
Use '+' to specify multiple augmentations (e.g. flip+rotate).
'''
if self.data is None:
logger.warning(
'could not set augmentation to {}. Run make_model() first')
return
ut.handle_augmentation_setting(self.data, augment_string)
def set_normalization(self, norm_string):
'''
Set pixel normalization scope.
Parameters
----------
norm_string : string
For minibatch-wise normalization choose 'local_z_score' or 'local'.
For global normalization use global_<min>+<max>
(e.g. 'global_0+255' for 8-bit images and 'global_0+65535' for
16-bit images).
Choose 'off' to deactivate.
'''
if self.data is None:
logger.warning(
'could not set normalizarion to {}. Run make_model() first')
return
ut.handle_normalization_setting(self.data, norm_string)
