def test_pad_to_without_data_dict(self):
rand_image = np.random.random([10, 10, 2, 1])
data_dict = {'image': rand_image}
# test without dictionary
tst = PadLayer(('image', ), (0, ), pad_to=(5, 5, 10))
padded = tst.layer_op(data_dict['image'])[0]
self.assertTrue(padded.shape == (10, 10, 10, 1))
depadded = tst.inverse_op(padded)[0]
self.assertTrue(np.all(depadded == rand_image))
def test_pad_to_simple(self):
rand_image = np.random.random([10, 10, 2, 1])
data_dict = {'image': rand_image}
tst = PadLayer(('image', ), (0, ), pad_to=(52, 52, 2))
padded = tst.layer_op(data_dict)
self.assertTrue(padded[0]['image'].shape == (52, 52, 2, 1))
depadded = tst.inverse_op(padded[0])
self.assertTrue(np.all(depadded[0]['image'] == rand_image))
def test_pad_to_odd_numbers(self):
rand_image = np.random.random([10, 10, 2, 1])
data_dict = {'image': rand_image}
tst = PadLayer(('image', ), (0, ), pad_to=(15, 17, 10))
# test straightforward pad_to
padded = tst.layer_op(data_dict)
self.assertTrue(padded[0]['image'].shape == (15, 17, 10, 1))
depadded = tst.inverse_op(padded[0])
self.assertTrue(np.all(depadded[0]['image'] == rand_image))
def run_inverse_test(self, is_array, layer_param, expected_shape):
if is_array:
x = self.get_3d_input()
else:
x = self.get_3d_input_dict()
padding_layer = PadLayer(**layer_param)
out_acti, _ = padding_layer.inverse_op(x)
print(padding_layer)
if is_array:
self.assertAllClose(out_acti.shape, expected_shape)
else:
self.assertAllClose(out_acti['image'].shape, expected_shape)
def run_inverse_test(self, is_array, layer_param, expected_shape):
if is_array:
x = self.get_3d_input()
else:
x = self.get_3d_input_dict()
padding_layer = PadLayer(**layer_param)
out_acti, _ = padding_layer.inverse_op(x)
print(padding_layer)
if is_array:
self.assertAllClose(out_acti.shape, expected_shape)
else:
self.assertAllClose(out_acti['image'].shape, expected_shape)
def get_reader(data_param, image_sets_partitioner, phase):
# Using Nifty Reader
if phase == 'training':
image_reader = ImageReader().initialise(
data_param, file_list=image_sets_partitioner.get_file_list(TRAIN))
elif phase == 'validation':
image_reader = ImageReader().initialise(
data_param, file_list=image_sets_partitioner.get_file_list(VALID))
elif phase == 'inference':
image_reader = ImageReader().initialise(
data_param, file_list=image_sets_partitioner.get_file_list(INFER))
else:
raise Exception('Invalid phase choice: {}'.format(
{'phase': ['train', 'validation', 'inference']}))
# Adding preprocessing layers
mean_variance_norm_layer = MeanVarNormalisationLayer(image_name='image')
pad_layer = PadLayer(image_name=('image', 'label'), border=(8, 8, 8))
image_reader.add_preprocessing_layers([mean_variance_norm_layer])
if phase == 'inference':
image_reader.add_preprocessing_layers([pad_layer])
return image_reader
def initialise_dataset_loader(
self, data_param=None, task_param=None, data_partitioner=None):
self.data_param = data_param
self.segmentation_param = task_param
# read each line of csv files into an instance of Subject
if self.is_training:
file_lists = []
if self.action_param.validation_every_n > 0:
file_lists.append(data_partitioner.train_files)
file_lists.append(data_partitioner.validation_files)
else:
file_lists.append(data_partitioner.train_files)
self.readers = []
for file_list in file_lists:
reader = ImageReader(SUPPORTED_INPUT)
reader.initialise(data_param, task_param, file_list)
self.readers.append(reader)
else: # in the inference process use image input only
inference_reader = ImageReader(['image'])
file_list = data_partitioner.inference_files
inference_reader.initialise(data_param, task_param, file_list)
self.readers = [inference_reader]
foreground_masking_layer = None
if self.net_param.normalise_foreground_only:
foreground_masking_layer = BinaryMaskingLayer(
type_str=self.net_param.foreground_type,
multimod_fusion=self.net_param.multimod_foreground_type,
threshold=0.0)
normalisation_layers = []
if self.net_param.whitening:
mean_var_normaliser = MeanVarNormalisationLayer(
image_name='image',
binary_masking_func=foreground_masking_layer)
normalisation_layers.append(mean_var_normaliser)
if task_param.label_normalisation and \
(self.is_training or not task_param.output_prob):
label_normaliser = DiscreteLabelNormalisationLayer(
image_name='label',
modalities=vars(task_param).get('label'),
model_filename=self.net_param.histogram_ref_file)
normalisation_layers.append(label_normaliser)
volume_padding_layer = []
if self.net_param.volume_padding_size:
volume_padding_layer.append(PadLayer(
image_name=SUPPORTED_INPUT,
border=self.net_param.volume_padding_size))
for reader in self.readers:
reader.add_preprocessing_layers(
normalisation_layers + volume_padding_layer)
def get_label_reader():
reader = ImageReader(['label'])
reader.initialise(MOD_LABEL_DATA, MOD_LABEl_TASK, mod_label_list)
label_normaliser = DiscreteLabelNormalisationLayer(
image_name='label',
modalities=vars(SINGLE_25D_TASK).get('label'),
model_filename=os.path.join('testing_data', 'agg_test.txt'))
reader.add_preprocessing_layers(label_normaliser)
pad_layer = PadLayer(image_name=('label',), border=(5, 6, 7))
reader.add_preprocessing_layers([pad_layer])
return reader
def test_trainable_preprocessing(self):
label_file = os.path.join('testing_data', 'label_reader.txt')
if os.path.exists(label_file):
os.remove(label_file)
label_normaliser = DiscreteLabelNormalisationLayer(
image_name='label',
modalities=vars(LABEL_TASK).get('label'),
model_filename=os.path.join('testing_data', 'label_reader.txt'))
reader = ImageReader(['label'])
with self.assertRaisesRegexp(AssertionError, ''):
reader.add_preprocessing_layers(label_normaliser)
reader.initialise(LABEL_DATA, LABEL_TASK, label_list)
reader.add_preprocessing_layers(label_normaliser)
reader.add_preprocessing_layers(
[PadLayer(image_name=['label'], border=(10, 5, 5))])
idx, data, interp_order = reader(idx=0)
unique_data = np.unique(data['label'])
expected_v1 = np.array([
0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14.,
15., 16., 17., 18., 19., 20., 21., 22., 23., 24., 25., 26., 27.,
28., 29., 30., 31., 32., 33., 34., 35., 36., 37., 38., 39., 40.,
41., 42., 43., 44., 45., 46., 47., 48., 49., 50., 51., 52., 53.,
54., 55., 56., 57., 58., 59., 60., 61., 62., 63., 64., 65., 66.,
67., 68., 69., 70., 71., 72., 73., 74., 75., 76., 77., 78., 79.,
80., 81., 82., 83., 84., 85., 86., 87., 88., 89., 90., 91., 92.,
93., 94., 95., 96., 97., 98., 99., 100., 101., 102., 103., 104.,
105., 106., 107., 108., 109., 110., 111., 112., 113., 114., 115.,
116., 117., 118., 119., 120., 121., 122., 123., 124., 125., 126.,
127., 128., 129., 130., 131., 132., 133., 134., 135., 136., 137.,
138., 139., 140., 141., 142., 143., 144., 145., 146., 147., 148.,
149., 150., 151., 152., 153., 154., 155., 156., 157.
],
dtype=np.float32)
expected_v2 = np.array([
0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 10., 11., 12., 13., 14.,
15., 16., 17., 18., 20., 21., 22., 23., 24., 25., 26., 27., 28.,
29., 30., 31., 32., 33., 34., 35., 36., 37., 38., 39., 40., 41.,
42., 43., 44., 45., 46., 47., 48., 49., 50., 51., 52., 53., 54.,
55., 56., 57., 58., 59., 60., 61., 62., 63., 64., 65., 66., 67.,
68., 69., 70., 71., 72., 73., 74., 75., 76., 77., 78., 79., 80.,
81., 82., 83., 84., 85., 86., 87., 88., 89., 90., 91., 92., 93.,
94., 95., 96., 97., 98., 99., 100., 101., 102., 103., 104., 105.,
106., 107., 108., 109., 110., 111., 112., 113., 114., 115., 116.,
117., 118., 119., 120., 121., 122., 123., 124., 125., 126., 127.,
128., 129., 130., 131., 132., 133., 134., 135., 136., 137., 138.,
139., 140., 141., 142., 143., 144., 145., 146., 147., 148., 149.,
150., 151., 152., 153., 154., 155., 156., 157.
],
dtype=np.float32)
compatible_assert = \
np.all(unique_data == expected_v1) or \
np.all(unique_data == expected_v2)
self.assertTrue(compatible_assert)
self.assertAllClose(data['label'].shape, (103, 74, 93, 1, 1))
def initialise_dataset_loader(self, data_param=None, task_param=None):
self.data_param = data_param
self.regression_param = task_param
# read each line of csv files into an instance of Subject
if self.is_training:
self.reader = ImageReader(SUPPORTED_INPUT)
else: # in the inference process use image input only
self.reader = ImageReader(['image'])
self.reader.initialise_reader(data_param, task_param)
mean_var_normaliser = MeanVarNormalisationLayer(image_name='image')
if self.net_param.histogram_ref_file:
histogram_normaliser = HistogramNormalisationLayer(
image_name='image',
modalities=vars(task_param).get('image'),
model_filename=self.net_param.histogram_ref_file,
norm_type=self.net_param.norm_type,
cutoff=self.net_param.cutoff,
name='hist_norm_layer')
else:
histogram_normaliser = None
normalisation_layers = []
if self.net_param.normalisation:
normalisation_layers.append(histogram_normaliser)
if self.net_param.whitening:
normalisation_layers.append(mean_var_normaliser)
augmentation_layers = []
if self.is_training:
if self.action_param.random_flipping_axes != -1:
augmentation_layers.append(
RandomFlipLayer(
flip_axes=self.action_param.random_flipping_axes))
if self.action_param.scaling_percentage:
augmentation_layers.append(
RandomSpatialScalingLayer(
min_percentage=self.action_param.scaling_percentage[0],
max_percentage=self.action_param.scaling_percentage[1])
)
if self.action_param.rotation_angle:
augmentation_layers.append(RandomRotationLayer())
augmentation_layers[-1].init_uniform_angle(
self.action_param.rotation_angle)
volume_padding_layer = []
if self.net_param.volume_padding_size:
volume_padding_layer.append(
PadLayer(image_name=SUPPORTED_INPUT,
border=self.net_param.volume_padding_size))
self.reader.add_preprocessing_layers(volume_padding_layer +
normalisation_layers +
augmentation_layers)
def test_preprocessing_zero_padding(self):
reader = ImageReader(['image'])
reader.initialise(SINGLE_MOD_DATA, SINGLE_MOD_TASK, single_mod_list)
idx, data, interp_order = reader()
self.assertEqual(SINGLE_MOD_DATA['lesion'].interp_order,
interp_order['image'][0])
self.assertAllClose(data['image'].shape, (256, 168, 256, 1, 1))
reader.add_preprocessing_layers(
[PadLayer(image_name=['image'], border=(0, 0, 0))])
idx, data, interp_order = reader(idx=2)
self.assertEqual(idx, 2)
self.assertAllClose(data['image'].shape, (256, 168, 256, 1, 1))
def initialise_dataset_loader(self,
data_param=None,
task_param=None,
data_partitioner=None):
RegressionApplication.initialise_dataset_loader(
self, data_param, task_param, data_partitioner)
if self.is_training:
return
if not task_param.error_map:
# use the regression application implementation
return
try:
reader_phase = self.action_param.dataset_to_infer
except AttributeError:
reader_phase = None
file_lists = data_partitioner.get_file_lists_by(phase=reader_phase,
action=self.action)
# modifying the original readers in regression application
# as we need ground truth labels to generate error maps
self.readers = [
ImageReader(['image',
'output']).initialise(data_param, task_param,
file_list)
for file_list in file_lists
]
mean_var_normaliser = MeanVarNormalisationLayer(image_name='image')
histogram_normaliser = None
if self.net_param.histogram_ref_file:
histogram_normaliser = HistogramNormalisationLayer(
image_name='image',
modalities=vars(task_param).get('image'),
model_filename=self.net_param.histogram_ref_file,
norm_type=self.net_param.norm_type,
cutoff=self.net_param.cutoff,
name='hist_norm_layer')
preprocessors = []
if self.net_param.normalisation:
preprocessors.append(histogram_normaliser)
if self.net_param.whitening:
preprocessors.append(mean_var_normaliser)
if self.net_param.volume_padding_size:
preprocessors.append(
PadLayer(image_name=SUPPORTED_INPUT,
border=self.net_param.volume_padding_size))
self.readers[0].add_preprocessing_layers(preprocessors)
def test_trainable_preprocessing(self):
label_file = os.path.join('testing_data', 'label_reader.txt')
if os.path.exists(label_file):
os.remove(label_file)
label_normaliser = DiscreteLabelNormalisationLayer(
image_name='label',
modalities=vars(LABEL_TASK).get('label'),
model_filename=os.path.join('testing_data', 'label_reader.txt'))
reader = ImageReader(['label'])
with self.assertRaisesRegexp(AssertionError, ''):
reader.add_preprocessing_layers(label_normaliser)
reader.initialise_reader(LABEL_DATA, LABEL_TASK)
reader.add_preprocessing_layers(label_normaliser)
reader.add_preprocessing_layers(
[PadLayer(image_name=['label'], border=(10, 5, 5))])
idx, data, interp_order = reader(idx=0)
unique_data = np.unique(data['label'])
expected = np.array(range(156), dtype=np.float32)
self.assertAllClose(unique_data, expected)
self.assertAllClose(data['label'].shape, (83, 73, 73, 1, 1))
def add_preprocessing(image_reader,
phase,
window_border=None,
data_augmentation=False):
rotation_layer = Rotate()
rotation_layer.init_uniform_angle([-25.0, 25.0])
if phase == 'training':
if data_augmentation:
image_reader.add_preprocessing_layers([rotation_layer])
elif phase == 'inference':
if window_border:
pad_layer = PadLayer(image_name=('image', 'label'),
border=window_border,
mode='constant')
image_reader.add_preprocessing_layers([pad_layer])
else:
raise Exception('Invalid window border!')
else:
raise Exception('Invalid phase choice: {}'.format(
{'phase': ['training', 'validation', 'inference']}))
return image_reader
def initialise_dataset_loader(self,
data_param=None,
task_param=None,
data_partitioner=None):
self.data_param = data_param
self.regression_param = task_param
file_lists = self.get_file_lists(data_partitioner)
# read each line of csv files into an instance of Subject
if self.is_training:
self.readers = []
for file_list in file_lists:
reader = ImageReader({'image', 'output', 'weight', 'sampler'})
reader.initialise(data_param, task_param, file_list)
self.readers.append(reader)
elif self.is_inference:
inference_reader = ImageReader(['image'])
file_list = data_partitioner.inference_files
inference_reader.initialise(data_param, task_param, file_lists[0])
self.readers = [inference_reader]
elif self.is_evaluation:
file_list = data_partitioner.inference_files
reader = ImageReader({'image', 'output', 'inferred'})
reader.initialise(data_param, task_param, file_lists[0])
self.readers = [reader]
else:
raise ValueError(
'Action `{}` not supported. Expected one of {}'.format(
self.action, self.SUPPORTED_ACTIONS))
mean_var_normaliser = MeanVarNormalisationLayer(image_name='image')
histogram_normaliser = None
if self.net_param.histogram_ref_file:
histogram_normaliser = HistogramNormalisationLayer(
image_name='image',
modalities=vars(task_param).get('image'),
model_filename=self.net_param.histogram_ref_file,
norm_type=self.net_param.norm_type,
cutoff=self.net_param.cutoff,
name='hist_norm_layer')
normalisation_layers = []
if self.net_param.normalisation:
normalisation_layers.append(histogram_normaliser)
if self.net_param.whitening:
normalisation_layers.append(mean_var_normaliser)
augmentation_layers = []
if self.is_training:
if self.action_param.random_flipping_axes != -1:
augmentation_layers.append(
RandomFlipLayer(
flip_axes=self.action_param.random_flipping_axes))
if self.action_param.scaling_percentage:
augmentation_layers.append(
RandomSpatialScalingLayer(
min_percentage=self.action_param.scaling_percentage[0],
max_percentage=self.action_param.scaling_percentage[1])
)
if self.action_param.rotation_angle:
augmentation_layers.append(RandomRotationLayer())
augmentation_layers[-1].init_uniform_angle(
self.action_param.rotation_angle)
volume_padding_layer = []
if self.net_param.volume_padding_size:
volume_padding_layer.append(
PadLayer(image_name=SUPPORTED_INPUT,
border=self.net_param.volume_padding_size,
mode=self.net_param.volume_padding_mode))
for reader in self.readers:
reader.add_preprocessing_layers(volume_padding_layer +
normalisation_layers +
augmentation_layers)
def initialise_dataset_loader(self, data_param=None, task_param=None, data_partitioner=None):
self.data_param = data_param
self.segmentation_param = task_param
# read each line of csv files into an instance of Subject
if self.is_training:
file_lists = []
if self.action_param.validation_every_n > 0:
file_lists.append(data_partitioner.train_files)
file_lists.append(data_partitioner.validation_files)
else:
file_lists.append(data_partitioner.all_files)
self.readers = []
for file_list in file_lists:
reader = ImageReader(SUPPORTED_INPUT)
reader.initialise(data_param, task_param, file_list)
self.readers.append(reader)
else: # in the inference process use image input only
inference_reader = ImageReader(['image'])
file_list = data_partitioner.inference_files
inference_reader.initialise(data_param, task_param, file_list)
self.readers = [inference_reader]
foreground_masking_layer = None
if self.net_param.normalise_foreground_only:
foreground_masking_layer = BinaryMaskingLayer(
type_str=self.net_param.foreground_type,
multimod_fusion=self.net_param.multimod_foreground_type,
threshold=0.0)
mean_var_normaliser = MeanVarNormalisationLayer(
image_name='image', binary_masking_func=foreground_masking_layer)
histogram_normaliser = None
if self.net_param.histogram_ref_file:
histogram_normaliser = HistogramNormalisationLayer(
image_name='image',
modalities=vars(task_param).get('image'),
model_filename=self.net_param.histogram_ref_file,
binary_masking_func=foreground_masking_layer,
norm_type=self.net_param.norm_type,
cutoff=self.net_param.cutoff,
name='hist_norm_layer')
label_normaliser = None
if self.net_param.histogram_ref_file:
label_normaliser = DiscreteLabelNormalisationLayer(
image_name='label',
modalities=vars(task_param).get('label'),
model_filename=self.net_param.histogram_ref_file)
normalisation_layers = []
if self.net_param.normalisation:
normalisation_layers.append(histogram_normaliser)
if self.net_param.whitening:
normalisation_layers.append(mean_var_normaliser)
if task_param.label_normalisation:
normalisation_layers.append(label_normaliser)
augmentation_layers = []
if self.is_training:
if self.action_param.random_flipping_axes != -1:
augmentation_layers.append(RandomFlipLayer(
flip_axes=self.action_param.random_flipping_axes))
if self.action_param.scaling_percentage:
augmentation_layers.append(RandomSpatialScalingLayer(
min_percentage=self.action_param.scaling_percentage[0],
max_percentage=self.action_param.scaling_percentage[1]))
if self.action_param.rotation_angle or \
self.action_param.rotation_angle_x or \
self.action_param.rotation_angle_y or \
self.action_param.rotation_angle_z:
rotation_layer = RandomRotationLayer()
if self.action_param.rotation_angle:
rotation_layer.init_uniform_angle(
self.action_param.rotation_angle)
else:
rotation_layer.init_non_uniform_angle(
self.action_param.rotation_angle_x,
self.action_param.rotation_angle_y,
self.action_param.rotation_angle_z)
augmentation_layers.append(rotation_layer)
volume_padding_layer = []
if self.net_param.volume_padding_size:
volume_padding_layer.append(PadLayer(
image_name=SUPPORTED_INPUT,
border=self.net_param.volume_padding_size))
for reader in self.readers:
reader.add_preprocessing_layers(
volume_padding_layer +
normalisation_layers +
augmentation_layers)
def initialise_dataset_loader(
self, data_param=None, task_param=None, data_partitioner=None):
self.data_param = data_param
self.segmentation_param = task_param
# initialise input image readers
if self.is_training:
reader_names = ('image', 'label', 'weight_map', 'sampler')
elif self.is_inference:
# in the inference process use `image` input only
reader_names = ('image',)
elif self.is_evaluation:
reader_names = ('image', 'label', 'inferred')
else:
tf.logging.fatal(
'Action `%s` not supported. Expected one of %s',
self.action, self.SUPPORTED_PHASES)
raise ValueError
try:
reader_phase = self.action_param.dataset_to_infer
except AttributeError:
reader_phase = None
file_lists = data_partitioner.get_file_lists_by(
phase=reader_phase, action=self.action)
self.readers = [
ImageReader(reader_names).initialise(
data_param, task_param, file_list) for file_list in file_lists]
# initialise input preprocessing layers
foreground_masking_layer = BinaryMaskingLayer(
type_str=self.net_param.foreground_type,
multimod_fusion=self.net_param.multimod_foreground_type,
threshold=0.0) \
if self.net_param.normalise_foreground_only else None
mean_var_normaliser = MeanVarNormalisationLayer(
image_name='image', binary_masking_func=foreground_masking_layer) \
if self.net_param.whitening else None
percentile_normaliser = PercentileNormalisationLayer(
image_name='image', binary_masking_func=foreground_masking_layer, cutoff=self.net_param.cutoff) \
if self.net_param.percentile_normalisation else None
histogram_normaliser = HistogramNormalisationLayer(
image_name='image',
modalities=vars(task_param).get('image'),
model_filename=self.net_param.histogram_ref_file,
binary_masking_func=foreground_masking_layer,
norm_type=self.net_param.norm_type,
cutoff=self.net_param.cutoff,
name='hist_norm_layer') \
if (self.net_param.histogram_ref_file and
self.net_param.normalisation) else None
label_normalisers = None
if self.net_param.histogram_ref_file and \
task_param.label_normalisation:
label_normalisers = [DiscreteLabelNormalisationLayer(
image_name='label',
modalities=vars(task_param).get('label'),
model_filename=self.net_param.histogram_ref_file)]
if self.is_evaluation:
label_normalisers.append(
DiscreteLabelNormalisationLayer(
image_name='inferred',
modalities=vars(task_param).get('inferred'),
model_filename=self.net_param.histogram_ref_file))
label_normalisers[-1].key = label_normalisers[0].key
normalisation_layers = []
if histogram_normaliser is not None:
normalisation_layers.append(histogram_normaliser)
if mean_var_normaliser is not None:
normalisation_layers.append(mean_var_normaliser)
if percentile_normaliser is not None:
normalisation_layers.append(percentile_normaliser)
if task_param.label_normalisation and \
(self.is_training or not task_param.output_prob):
normalisation_layers.extend(label_normalisers)
volume_padding_layer = []
if self.net_param.volume_padding_size:
volume_padding_layer.append(PadLayer(
image_name=SUPPORTED_INPUT,
border=self.net_param.volume_padding_size,
mode=self.net_param.volume_padding_mode))
# initialise training data augmentation layers
augmentation_layers = []
if self.is_training:
train_param = self.action_param
if train_param.random_flipping_axes != -1:
augmentation_layers.append(RandomFlipLayer(
flip_axes=train_param.random_flipping_axes))
if train_param.scaling_percentage:
augmentation_layers.append(RandomSpatialScalingLayer(
min_percentage=train_param.scaling_percentage[0],
max_percentage=train_param.scaling_percentage[1],
antialiasing=train_param.antialiasing))
if train_param.rotation_angle or \
train_param.rotation_angle_x or \
train_param.rotation_angle_y or \
train_param.rotation_angle_z:
rotation_layer = RandomRotationLayer()
if train_param.rotation_angle:
rotation_layer.init_uniform_angle(
train_param.rotation_angle)
else:
rotation_layer.init_non_uniform_angle(
train_param.rotation_angle_x,
train_param.rotation_angle_y,
train_param.rotation_angle_z)
augmentation_layers.append(rotation_layer)
if train_param.do_elastic_deformation:
spatial_rank = list(self.readers[0].spatial_ranks.values())[0]
augmentation_layers.append(RandomElasticDeformationLayer(
spatial_rank=spatial_rank,
num_controlpoints=train_param.num_ctrl_points,
std_deformation_sigma=train_param.deformation_sigma,
proportion_to_augment=train_param.proportion_to_deform))
# only add augmentation to first reader (not validation reader)
self.readers[0].add_preprocessing_layers(
volume_padding_layer + normalisation_layers + augmentation_layers)
for reader in self.readers[1:]:
reader.add_preprocessing_layers(
volume_padding_layer + normalisation_layers)
def initialise_dataset_loader(self,
data_param=None,
task_param=None,
data_partitioner=None):
self.data_param = data_param
self.segmentation_param = task_param
# initialise input image readers
if self.is_training:
reader_names = ('image', 'label', 'weight', 'sampler')
elif self.is_inference:
# in the inference process use `image` input only
reader_names = ('image', )
elif self.is_evaluation:
reader_names = ('image', 'label', 'inferred')
else:
tf.logging.fatal('Action `%s` not supported. Expected one of %s',
self.action, self.SUPPORTED_PHASES)
raise ValueError
try:
reader_phase = self.action_param.dataset_to_infer
except AttributeError:
reader_phase = None
file_lists = data_partitioner.get_file_lists_by(phase=reader_phase,
action=self.action)
self.readers = [
ImageReader(reader_names).initialise(data_param, task_param,
file_list)
for file_list in file_lists
]
foreground_masking_layer = None
if self.net_param.normalise_foreground_only:
foreground_masking_layer = BinaryMaskingLayer(
type_str=self.net_param.foreground_type,
multimod_fusion=self.net_param.multimod_foreground_type,
threshold=0.0)
mean_var_normaliser = MeanVarNormalisationLayer(
image_name='image', binary_masking_func=foreground_masking_layer)
histogram_normaliser = None
if self.net_param.histogram_ref_file:
histogram_normaliser = HistogramNormalisationLayer(
image_name='image',
modalities=vars(task_param).get('image'),
model_filename=self.net_param.histogram_ref_file,
binary_masking_func=foreground_masking_layer,
norm_type=self.net_param.norm_type,
cutoff=self.net_param.cutoff,
name='hist_norm_layer')
label_normaliser = None
if self.net_param.histogram_ref_file:
label_normaliser = DiscreteLabelNormalisationLayer(
image_name='label',
modalities=vars(task_param).get('label'),
model_filename=self.net_param.histogram_ref_file)
normalisation_layers = []
if self.net_param.normalisation:
normalisation_layers.append(histogram_normaliser)
if self.net_param.whitening:
normalisation_layers.append(mean_var_normaliser)
if task_param.label_normalisation and \
(self.is_training or not task_param.output_prob):
normalisation_layers.append(label_normaliser)
augmentation_layers = []
if self.is_training:
if self.action_param.random_flipping_axes != -1:
augmentation_layers.append(
RandomFlipLayer(
flip_axes=self.action_param.random_flipping_axes))
if self.action_param.scaling_percentage:
augmentation_layers.append(
RandomSpatialScalingLayer(
min_percentage=self.action_param.scaling_percentage[0],
max_percentage=self.action_param.scaling_percentage[1])
)
if self.action_param.rotation_angle or \
self.action_param.rotation_angle_x or \
self.action_param.rotation_angle_y or \
self.action_param.rotation_angle_z:
rotation_layer = RandomRotationLayer()
if self.action_param.rotation_angle:
rotation_layer.init_uniform_angle(
self.action_param.rotation_angle)
else:
rotation_layer.init_non_uniform_angle(
self.action_param.rotation_angle_x,
self.action_param.rotation_angle_y,
self.action_param.rotation_angle_z)
augmentation_layers.append(rotation_layer)
if self.action_param.bias_field_range:
bias_field_layer = RandomBiasFieldLayer()
bias_field_layer.init_order(self.action_param.bf_order)
bias_field_layer.init_uniform_coeff(
self.action_param.bias_field_range)
augmentation_layers.append(bias_field_layer)
volume_padding_layer = [
PadLayer(image_name=SUPPORTED_INPUT,
border=self.net_param.volume_padding_size,
mode=self.net_param.volume_padding_mode,
pad_to=self.net_param.volume_padding_to_size)
]
self.readers[0].add_preprocessing_layers(volume_padding_layer +
normalisation_layers +
augmentation_layers)
for reader in self.readers[1:]:
reader.add_preprocessing_layers(volume_padding_layer +
normalisation_layers)
'interp_order': 0
},
}
#This option is to read 2D slices
# data_param = {'MR': {'path_to_search': './sample_images','spatial_window_size': (48,48,41),
# 'filename_contains': ['middleSlice','mhd'], 'pixdim': (1,1), 'axcodes': ['L','P','S'],'interp_order': 3},
# 'sampler': {'path_to_search': './sample_images', 'spatial_window_size': (48,48,1),
# 'filename_contains': ['middleLabels','mhd'],'pixdim': (1,1), 'axcodes': ['L','P','S'],'interp_order': 0},
# }
#Create image reader and add padding layer with 'constant' value 0
#This will ensure that samples are taken even at the beginning and ending slice
reader = ImageReader().initialise(data_param)
reader.add_preprocessing_layers(
PadLayer(image_name=['MR', 'sampler'],
border=(20, 20, 20),
mode='constant'))
_, img, _ = reader(idx=0)
#Create samplers with window_size
weighted_sampler = WeightedSampler(reader, window_sizes=(48, 48, 48))
balanced_sampler = BalancedSampler(reader, window_sizes=(48, 48, 48))
uniform_sampler = UniformSampler(reader, window_sizes=(48, 48, 48))
#Generate N samples for each type
N = 30
import tensorflow as tf
# adding the tensorflow tensors
next_window = weighted_sampler.pop_batch_op()
def initialise_dataset_loader(self,
data_param=None,
task_param=None,
data_partitioner=None):
self.data_param = data_param
self.regression_param = task_param
# initialise input image readers
if self.is_training:
reader_names = ('image', 'output', 'weight', 'sampler')
elif self.is_inference:
# in the inference process use `image` input only
reader_names = ('image', )
elif self.is_evaluation:
reader_names = ('image', 'output', 'inferred')
else:
tf.logging.fatal('Action `%s` not supported. Expected one of %s',
self.action, self.SUPPORTED_PHASES)
raise ValueError
try:
reader_phase = self.action_param.dataset_to_infer
except AttributeError:
reader_phase = None
file_lists = data_partitioner.get_file_lists_by(phase=reader_phase,
action=self.action)
self.readers = [
ImageReader(reader_names).initialise(data_param, task_param,
file_list)
for file_list in file_lists
]
# initialise input preprocessing layers
mean_var_normaliser = MeanVarNormalisationLayer(image_name='image') \
if self.net_param.whitening else None
histogram_normaliser = HistogramNormalisationLayer(
image_name='image',
modalities=vars(task_param).get('image'),
model_filename=self.net_param.histogram_ref_file,
norm_type=self.net_param.norm_type,
cutoff=self.net_param.cutoff,
name='hist_norm_layer') \
if (self.net_param.histogram_ref_file and
self.net_param.normalisation) else None
normalisation_layers = []
if histogram_normaliser is not None:
normalisation_layers.append(histogram_normaliser)
if mean_var_normaliser is not None:
normalisation_layers.append(mean_var_normaliser)
volume_padding_layer = []
if self.net_param.volume_padding_size:
volume_padding_layer.append(
PadLayer(image_name=SUPPORTED_INPUT,
border=self.net_param.volume_padding_size,
mode=self.net_param.volume_padding_mode))
# initialise training data augmentation layers
augmentation_layers = []
if self.is_training:
train_param = self.action_param
if train_param.random_flipping_axes != -1:
augmentation_layers.append(
RandomFlipLayer(
flip_axes=train_param.random_flipping_axes))
if train_param.scaling_percentage:
augmentation_layers.append(
RandomSpatialScalingLayer(
min_percentage=train_param.scaling_percentage[0],
max_percentage=train_param.scaling_percentage[1]))
if train_param.rotation_angle:
rotation_layer = RandomRotationLayer()
if train_param.rotation_angle:
rotation_layer.init_uniform_angle(
train_param.rotation_angle)
augmentation_layers.append(rotation_layer)
if train_param.do_elastic_deformation:
spatial_rank = list(self.readers[0].spatial_ranks.values())[0]
augmentation_layers.append(
RandomElasticDeformationLayer(
spatial_rank=spatial_rank,
num_controlpoints=train_param.num_ctrl_points,
std_deformation_sigma=train_param.deformation_sigma,
proportion_to_augment=train_param.proportion_to_deform)
)
# only add augmentation to first reader (not validation reader)
self.readers[0].add_preprocessing_layers(volume_padding_layer +
normalisation_layers +
augmentation_layers)
for reader in self.readers[1:]:
reader.add_preprocessing_layers(volume_padding_layer +
normalisation_layers)
reader.add_preprocessing_layers(
MeanVarNormalisationLayer(image_name='MR',
binary_masking_func=binary_masking_func))
_, vol, _ = reader(idx=idx)
plot_slices(vol['MR'],
vol['CT'],
vol['LABELS'],
idx,
title='Normalized MR image')
#sitk.WriteImage(sitk.GetImageFromArray(vol['MR'][:,:,:,0,0]),'./whitenned.mhd')
# Use border as half of spatial_window_size, so the NN can learn more from the borders
#Use constant mode padding, I have modified niftynet.layers.pad to use constant_values=np.amin(image)
reader.add_preprocessing_layers(
PadLayer(image_name=['MR', 'CT', 'LABELS'],
border=(24, 24, 48),
mode='constant'))
_, vol, _ = reader(idx=idx)
plot_slices(vol['MR'], vol['CT'], vol['LABELS'], idx, title='Padded images')
#sitk.WriteImage(sitk.GetImageFromArray(vol['CT'][:,:,:,0,0]),'./padded.mhd')
print(vol['MR'].shape)
#Add rotation layer
rotation_layer = Rotate()
rotation_layer.init_uniform_angle(
[-10.0, 10.0]) #randomly rotate between -10 and 10 degrees
reader.add_preprocessing_layers([rotation_layer])
_, vol, _ = reader(idx=idx)
plot_slices(vol['MR'], vol['CT'], vol['LABELS'], idx, title='Rotated images')
#sitk.WriteImage(sitk.GetImageFromArray(vol['CT'][:,:,:,0,0]),'./rotated.mhd')
# config parameters
###
spatial_window_size = (100, 100)
border = (12, 12)
volume_padding_size = (50, 50)
data_param = \
{'MR': {
'path_to_search': '~/Desktop/useful_scripts/visualise_windows',
'filename_contains': 'example.png'}}
###
# create an image reader
###
reader = ImageReader().initialise(data_param)
reader.add_preprocessing_layers( # add volume padding layer
[PadLayer(image_name=['MR'], border=volume_padding_size, mode='constant')])
###
# show 'volume' -- without window sampling
###
image_2d = ImageWindowDataset(reader)()['MR'][0, :, :, 0, 0, 0]
vis_coordinates(image_2d, saving_name='output/image.png')
###
# create & show uniform random samples
###
uniform_sampler = UniformSampler(reader,
spatial_window_size,
windows_per_image=100)
next_window = uniform_sampler.pop_batch_op()
coords = []
def initialise_dataset_loader(self,
data_param=None,
task_param=None,
data_partitioner=None):
self.data_param = data_param
self.segmentation_param = task_param
file_lists = self.get_file_lists(data_partitioner)
# read each line of csv files into an instance of Subject
if self.is_training:
self.readers = []
for file_list in file_lists:
reader = ImageReader({'image', 'label', 'weight', 'sampler'})
reader.initialise(data_param, task_param, file_list)
self.readers.append(reader)
elif self.is_inference:
# in the inference process use image input only
inference_reader = ImageReader({'image'})
file_list = pd.concat([
data_partitioner.inference_files,
data_partitioner.validation_files
],
axis=0)
file_list.index = range(file_list.shape[0])
inference_reader.initialise(data_param, task_param, file_list)
self.readers = [inference_reader]
elif self.is_evaluation:
file_list = data_partitioner.inference_files
reader = ImageReader({'image', 'label', 'inferred'})
reader.initialise(data_param, task_param, file_list)
self.readers = [reader]
else:
raise ValueError(
'Action `{}` not supported. Expected one of {}'.format(
self.action, self.SUPPORTED_ACTIONS))
foreground_masking_layer = None
if self.net_param.normalise_foreground_only:
foreground_masking_layer = BinaryMaskingLayer(
type_str=self.net_param.foreground_type,
multimod_fusion=self.net_param.multimod_foreground_type,
threshold=0.0)
mean_var_normaliser = MeanVarNormalisationLayer(
image_name='image', binary_masking_func=foreground_masking_layer)
histogram_normaliser = None
if self.net_param.histogram_ref_file:
histogram_normaliser = HistogramNormalisationLayer(
image_name='image',
modalities=vars(task_param).get('image'),
model_filename=self.net_param.histogram_ref_file,
binary_masking_func=foreground_masking_layer,
norm_type=self.net_param.norm_type,
cutoff=self.net_param.cutoff,
name='hist_norm_layer')
label_normalisers = None
if self.net_param.histogram_ref_file and \
task_param.label_normalisation:
label_normalisers = [
DiscreteLabelNormalisationLayer(
image_name='label',
modalities=vars(task_param).get('label'),
model_filename=self.net_param.histogram_ref_file)
]
if self.is_evaluation:
label_normalisers.append(
DiscreteLabelNormalisationLayer(
image_name='inferred',
modalities=vars(task_param).get('inferred'),
model_filename=self.net_param.histogram_ref_file))
label_normalisers[-1].key = label_normalisers[0].key
normalisation_layers = []
if self.net_param.normalisation:
normalisation_layers.append(histogram_normaliser)
if self.net_param.whitening:
normalisation_layers.append(mean_var_normaliser)
if task_param.label_normalisation and \
(self.is_training or not task_param.output_prob):
normalisation_layers.extend(label_normalisers)
augmentation_layers = []
if self.is_training:
if self.action_param.random_flipping_axes != -1:
augmentation_layers.append(
RandomFlipLayer(
flip_axes=self.action_param.random_flipping_axes))
if self.action_param.scaling_percentage:
augmentation_layers.append(
RandomSpatialScalingLayer(
min_percentage=self.action_param.scaling_percentage[0],
max_percentage=self.action_param.scaling_percentage[1])
)
if self.action_param.rotation_angle or \
self.action_param.rotation_angle_x or \
self.action_param.rotation_angle_y or \
self.action_param.rotation_angle_z:
rotation_layer = RandomRotationLayer()
if self.action_param.rotation_angle:
rotation_layer.init_uniform_angle(
self.action_param.rotation_angle)
else:
rotation_layer.init_non_uniform_angle(
self.action_param.rotation_angle_x,
self.action_param.rotation_angle_y,
self.action_param.rotation_angle_z)
augmentation_layers.append(rotation_layer)
# add deformation layer
if self.action_param.do_elastic_deformation:
spatial_rank = list(self.readers[0].spatial_ranks.values())[0]
augmentation_layers.append(
RandomElasticDeformationLayer(
spatial_rank=spatial_rank,
num_controlpoints=self.action_param.num_ctrl_points,
std_deformation_sigma=self.action_param.
deformation_sigma,
proportion_to_augment=self.action_param.
proportion_to_deform))
volume_padding_layer = []
if self.net_param.volume_padding_size:
volume_padding_layer.append(
PadLayer(image_name=SUPPORTED_INPUT,
border=self.net_param.volume_padding_size))
# only add augmentation to first reader (not validation reader)
self.readers[0].add_preprocessing_layers(volume_padding_layer +
normalisation_layers +
augmentation_layers)
for reader in self.readers[1:]:
reader.add_preprocessing_layers(volume_padding_layer +
normalisation_layers)