def main(hdf_file, plot_dir):
os.makedirs(plot_dir, exist_ok=True)
# setup the datasource
extractor = extr.DataExtractor(categories=(defs.KEY_IMAGES, defs.KEY_LABELS))
indexing_strategy = extr.SliceIndexing()
dataset = extr.PymiaDatasource(hdf_file, indexing_strategy, extractor)
seed = 1
np.random.seed(seed)
sample_idx = 55
# set up transformations without augmentation
transforms_augmentation = []
transforms_before_augmentation = [tfm.Permute(permutation=(2, 0, 1)), ] # to have the channel-dimension first
transforms_after_augmentation = [tfm.Squeeze(entries=(defs.KEY_LABELS,)), ] # get rid of the channel-dimension for the labels
train_transforms = tfm.ComposeTransform(transforms_before_augmentation + transforms_augmentation + transforms_after_augmentation)
dataset.set_transform(train_transforms)
sample = dataset[sample_idx]
plot_sample(plot_dir, 'none', sample)
# augmentation with pymia
transforms_augmentation = [augm.RandomRotation90(axes=(-2, -1)), augm.RandomMirror()]
train_transforms = tfm.ComposeTransform(
transforms_before_augmentation + transforms_augmentation + transforms_after_augmentation)
dataset.set_transform(train_transforms)
sample = dataset[sample_idx]
plot_sample(plot_dir, 'pymia', sample)
# augmentation with batchgenerators
transforms_augmentation = [BatchgeneratorsTransform([
bg_tfm.spatial_transforms.MirrorTransform(axes=(0, 1), data_key=defs.KEY_IMAGES, label_key=defs.KEY_LABELS),
bg_tfm.noise_transforms.GaussianBlurTransform(blur_sigma=(0.2, 1.0), data_key=defs.KEY_IMAGES, label_key=defs.KEY_LABELS),
])]
train_transforms = tfm.ComposeTransform(
transforms_before_augmentation + transforms_augmentation + transforms_after_augmentation)
dataset.set_transform(train_transforms)
sample = dataset[sample_idx]
plot_sample(plot_dir, 'batchgenerators', sample)
# augmentation with TorchIO
transforms_augmentation = [TorchIOTransform(
[tio.RandomFlip(axes=('LR'), flip_probability=1.0, keys=(defs.KEY_IMAGES, defs.KEY_LABELS), seed=seed),
tio.RandomAffine(scales=(0.9, 1.2), degrees=(10), isotropic=False, default_pad_value='otsu',
image_interpolation='NEAREST', keys=(defs.KEY_IMAGES, defs.KEY_LABELS), seed=seed),
])]
train_transforms = tfm.ComposeTransform(
transforms_before_augmentation + transforms_augmentation + transforms_after_augmentation)
dataset.set_transform(train_transforms)
sample = dataset[sample_idx]
plot_sample(plot_dir, 'torchio', sample)
def main(hdf_file: str, data_dir: str):
keys = [
FileTypes.T1, FileTypes.T2, FileTypes.GT, FileTypes.MASK,
FileTypes.AGE, FileTypes.GPA, FileTypes.SEX
]
crawler = pymia_load.FileSystemDataCrawler(data_dir, keys,
DataSetFilePathGenerator(),
DirectoryFilter(), '.mha')
subjects = [
Subject(id_, file_dict) for id_, file_dict in crawler.data.items()
]
if os.path.exists(hdf_file):
os.remove(hdf_file)
with pymia_crt.get_writer(hdf_file) as writer:
callbacks = pymia_crt.get_default_callbacks(writer)
# normalize the images and unsqueeze the labels and mask.
# Unsqueeze is needed due to the convention to have the number of channels as last dimension.
# I.e., here we have the shape 10 x 256 x 256 before the unsqueeze operation and after 10 x 256 x 256 x 1
transform = pymia_tfm.ComposeTransform([
pymia_tfm.IntensityNormalization(loop_axis=3,
entries=('images', )),
pymia_tfm.UnSqueeze(entries=('labels', 'mask'))
])
traverser = pymia_crt.SubjectFileTraverser()
traverser.traverse(subjects,
callback=callbacks,
load=LoadData(),
transform=transform)
def main(hdf_file: str, data_dir: str):
if os.path.exists(hdf_file):
raise RuntimeError(
'Dataset file "{}" does already exist'.format(hdf_file))
# let's create some sample data
np.random.seed(42) # to have same sample data
create_sample_data(data_dir, no_subjects=8)
# collect the data
collector = Collector(data_dir)
subjects = collector.get_subject_files()
for subject in subjects:
print(subject.subject)
# get the values for parametric map normalization
min_, max_ = get_normalization_values(subjects, LoadData())
with pymia_crt.Hdf5Writer(hdf_file) as writer:
callbacks = pymia_crt.get_default_callbacks(writer)
callbacks.callbacks.append(
WriteNormalizationCallback(writer, min_, max_))
transform = pymia_tfm.ComposeTransform([
tfm.MRFMaskedLabelNormalization(min_, max_, data.ID_MASK_FG),
pymia_tfm.IntensityNormalization(loop_axis=4,
entries=(pymia_def.KEY_IMAGES, )),
])
traverser = pymia_crt.SubjectFileTraverser()
traverser.traverse(subjects,
callback=callbacks,
load=LoadData(),
transform=transform,
concat_fn=concat)
def get_transform(transform_params: typing.Union[cfg.DictableParameterExt, list, tuple]) -> tfm.Transform:
if isinstance(transform_params, (list, tuple)):
transforms = []
for transform_param in transform_params:
transforms.append(get_transform(transform_param))
return tfm.ComposeTransform(transforms)
if transform_params.type not in transform_registry:
raise ValueError('transform type "{}" unknown'.format(transform_params.type))
return transform_registry[transform_params.type](**transform_params.params)
def occlude(tester, result_dir: str, temporal_dim: int):
for temporal_idx in range(temporal_dim):
print('Occlude temporal dimension {}...'.format(temporal_idx))
# modify extraction transform for occlusion experiment
tester.data_handler.extraction_transform_valid = pymia_tfm.ComposeTransform(
[
pymia_tfm.Squeeze(
entries=(pymia_def.KEY_IMAGES, pymia_def.KEY_LABELS,
data.ID_MASK_FG, data.ID_MASK_T1H2O),
squeeze_axis=0),
tfm.MRFTemporalOcclusion(temporal_idx=temporal_idx,
entries=(pymia_def.KEY_IMAGES, ))
])
tester.result_dir = os.path.join(result_dir,
'occlusion{}'.format(temporal_idx))
tester.predict()
def build_brats_dataset(params: BuildParameters):
collector = collect.Brats17Collector(
params.in_dir) # 17 is same dataset as 18
subject_files = collector.get_subject_files()
if params.split_file is not None:
if params.is_train_data:
train_subjects, valid_subjects, _ = split.load_split(
params.split_file)
selection = train_subjects + valid_subjects
else:
_, _, selection = split.load_split(params.split_file)
subject_files = [sf for sf in subject_files if sf.subject in selection]
assert len(subject_files) == len(selection)
# sort the subject files according to the subject name (identifier)
subject_files.sort(key=lambda sf: sf.subject)
if params.prediction_path is not None:
subject_files = params.add_prediction_fn(subject_files,
params.prediction_path)
fh.create_dir_if_not_exists(params.out_file, is_file=True)
fh.remove_if_exists(params.out_file)
with crt.get_writer(params.out_file) as writer:
callbacks = [
crt.MonitoringCallback(),
crt.WriteNamesCallback(writer),
crt.WriteFilesCallback(writer),
crt.WriteDataCallback(writer),
crt.WriteSubjectCallback(writer),
crt.WriteImageInformationCallback(writer),
]
has_grade = params.in_dir.endswith('Training')
if has_grade:
callbacks.append(WriteGradeCallback(writer))
callback = crt.ComposeCallback(callbacks)
traverser = crt.SubjectFileTraverser()
traverser.traverse(subject_files,
callback=callback,
load=LoadSubject(),
transform=tfm.ComposeTransform(params.transforms))
def main(hdf_file: str, data_dir: str):
if os.path.exists(hdf_file):
raise RuntimeError('Dataset file "{}" does exist already'.format(hdf_file))
# we threshold I_Q at probability 0.1
probability_threshold = 0.1
# we use image information extracted from 5^3 neighborhood around each point
spatial_size = 5
# let's create some sample data
np.random.seed(42) # to have same sample data
create_sample_data(data_dir, no_subjects=8)
# collect the data
collector = Collector(data_dir)
subjects = collector.get_subject_files()
for subject in subjects:
print(subject.subject)
print('Total of {} subjects'.format(len(subjects)))
os.makedirs(os.path.dirname(hdf_file), exist_ok=True)
with pymia_crt.get_writer(hdf_file) as writer:
callbacks = pymia_crt.get_default_callbacks(writer)
transform = pymia_tfm.ComposeTransform([
pymia_tfm.LambdaTransform(lambda_fn=lambda np_data: np_data.astype(np.float32),
entries=('images',
data.KEY_IMAGE_INFORMATION,
)),
pymia_tfm.LambdaTransform(loop_axis=1, entries=('images', ), lambda_fn=normalize_unit_cube),
pymia_tfm.IntensityNormalization(loop_axis=-1, entries=(data.KEY_IMAGE_INFORMATION,))
])
traverser = pymia_crt.SubjectFileTraverser()
traverser.traverse(subjects, callback=callbacks, load=LoadData(probability_threshold, spatial_size),
transform=transform, concat_fn=concat)
def main(hdf_file, log_dir):
# initialize the evaluator with the metrics and the labels to evaluate
metrics = [metric.DiceCoefficient()]
labels = {1: 'WHITEMATTER',
2: 'GREYMATTER',
3: 'HIPPOCAMPUS',
4: 'AMYGDALA',
5: 'THALAMUS'}
evaluator = eval_.SegmentationEvaluator(metrics, labels)
# we want to log the mean and standard deviation of the metrics among all subjects of the dataset
functions = {'MEAN': np.mean, 'STD': np.std}
statistics_aggregator = writer.StatisticsAggregator(functions=functions)
console_writer = writer.ConsoleStatisticsWriter(functions=functions)
# initialize TensorBoard writer
tb = tensorboard.SummaryWriter(os.path.join(log_dir, 'logging-example-torch'))
# setup the training datasource
train_subjects, valid_subjects = ['Subject_1', 'Subject_2', 'Subject_3'], ['Subject_4']
extractor = extr.DataExtractor(categories=(defs.KEY_IMAGES, defs.KEY_LABELS))
indexing_strategy = extr.SliceIndexing()
augmentation_transforms = [augm.RandomElasticDeformation(), augm.RandomMirror()]
transforms = [tfm.Permute(permutation=(2, 0, 1)), tfm.Squeeze(entries=(defs.KEY_LABELS,))]
train_transforms = tfm.ComposeTransform(augmentation_transforms + transforms)
train_dataset = extr.PymiaDatasource(hdf_file, indexing_strategy, extractor, train_transforms,
subject_subset=train_subjects)
# setup the validation datasource
valid_transforms = tfm.ComposeTransform([tfm.Permute(permutation=(2, 0, 1))])
valid_dataset = extr.PymiaDatasource(hdf_file, indexing_strategy, extractor, valid_transforms,
subject_subset=valid_subjects)
direct_extractor = extr.ComposeExtractor(
[extr.SubjectExtractor(),
extr.ImagePropertiesExtractor(),
extr.DataExtractor(categories=(defs.KEY_LABELS,))]
)
assembler = assm.SubjectAssembler(valid_dataset)
# torch specific handling
pytorch_train_dataset = pymia_torch.PytorchDatasetAdapter(train_dataset)
train_loader = torch_data.dataloader.DataLoader(pytorch_train_dataset, batch_size=16, shuffle=True)
pytorch_valid_dataset = pymia_torch.PytorchDatasetAdapter(valid_dataset)
valid_loader = torch_data.dataloader.DataLoader(pytorch_valid_dataset, batch_size=16, shuffle=False)
u_net = unet.UNetModel(ch_in=2, ch_out=6, n_channels=16, n_pooling=3).to(device)
print(u_net)
optimizer = optim.Adam(u_net.parameters(), lr=1e-3)
train_batches = len(train_loader)
# looping over the data in the dataset
epochs = 100
for epoch in range(epochs):
u_net.train()
print(f'Epoch {epoch + 1}/{epochs}')
# training
print('training')
for i, batch in enumerate(train_loader):
x, y = batch[defs.KEY_IMAGES].to(device), batch[defs.KEY_LABELS].to(device).long()
logits = u_net(x)
optimizer.zero_grad()
loss = F.cross_entropy(logits, y)
loss.backward()
optimizer.step()
tb.add_scalar('train/loss', loss.item(), epoch*train_batches + i)
print(f'[{i + 1}/{train_batches}]\tloss: {loss.item()}')
# validation
print('validation')
with torch.no_grad():
u_net.eval()
valid_batches = len(valid_loader)
for i, batch in enumerate(valid_loader):
x, sample_indices = batch[defs.KEY_IMAGES].to(device), batch[defs.KEY_SAMPLE_INDEX]
logits = u_net(x)
prediction = logits.argmax(dim=1, keepdim=True)
numpy_prediction = prediction.cpu().numpy().transpose((0, 2, 3, 1))
is_last = i == valid_batches - 1
assembler.add_batch(numpy_prediction, sample_indices.numpy(), is_last)
for subject_index in assembler.subjects_ready:
subject_prediction = assembler.get_assembled_subject(subject_index)
direct_sample = train_dataset.direct_extract(direct_extractor, subject_index)
target, image_properties = direct_sample[defs.KEY_LABELS], direct_sample[defs.KEY_PROPERTIES]
# evaluate the prediction against the reference
evaluator.evaluate(subject_prediction[..., 0], target[..., 0], direct_sample[defs.KEY_SUBJECT])
# calculate mean and standard deviation of each metric
results = statistics_aggregator.calculate(evaluator.results)
# log to TensorBoard into category train
for result in results:
tb.add_scalar(f'valid/{result.metric}-{result.id_}', result.value, epoch)
console_writer.write(evaluator.results)
# clear results such that the evaluator is ready for the next evaluation
evaluator.clear()
def __init__(self,
config: cfg.Configuration,
subjects_train,
subjects_valid,
subjects_test,
collate_fn=pymia_cnv.TensorFlowCollate()):
super().__init__()
indexing_strategy = PointCloudIndexing(config.no_points)
self.dataset = pymia_extr.ParameterizableDataset(
config.database_file,
indexing_strategy,
pymia_extr.SubjectExtractor(), # for the usual select_indices
None)
self.no_subjects_train = len(subjects_train)
self.no_subjects_valid = len(subjects_valid)
self.no_subjects_test = len(
subjects_valid
) # same as validation for this kind of cross validation
# get sampler ids by subjects
sampler_ids_train = pymia_extr.select_indices(
self.dataset, pymia_extr.SubjectSelection(subjects_train))
sampler_ids_valid = pymia_extr.select_indices(
self.dataset, pymia_extr.SubjectSelection(subjects_valid))
categories = ('images', 'labels')
categories_tfm = ('images', 'labels')
if config.use_image_information:
image_information_categories = (data.KEY_IMAGE_INFORMATION, )
categories += image_information_categories
categories_tfm += image_information_categories
collate_fn.entries += image_information_categories
# define point cloud shuffler for augmentation
sizes = {}
for idx in range(len(self.dataset.get_subjects())):
sample = self.dataset.direct_extract(PointCloudSizeExtractor(),
idx)
sizes[idx] = sample['size']
self.point_cloud_shuffler = aug.PointCloudShuffler(sizes)
self.point_cloud_shuffler_valid = aug.PointCloudShuffler(
sizes
) # will only shuffle once at instantiation because shuffle() is not called during training (see set_seed)
data_extractor_train = aug.ShuffledDataExtractor(
self.point_cloud_shuffler, categories)
data_extractor_valid = aug.ShuffledDataExtractor(
self.point_cloud_shuffler_valid, categories)
data_extractor_test = aug.ShuffledDataExtractor(
self.point_cloud_shuffler_valid, categories=('indices', 'labels'))
# define extractors
self.extractor_train = pymia_extr.ComposeExtractor([
pymia_extr.NamesExtractor(), # required for SelectiveDataExtractor
pymia_extr.SubjectExtractor(), # required for plotting
PointCloudSizeExtractor(), # to init_shape in SubjectAssembler
data_extractor_train,
pymia_extr.IndexingExtractor(
), # for SubjectAssembler (assembling)
pymia_extr.ImageShapeExtractor() # for SubjectAssembler (shape)
])
self.extractor_valid = pymia_extr.ComposeExtractor([
pymia_extr.NamesExtractor(), # required for SelectiveDataExtractor
pymia_extr.SubjectExtractor(), # required for plotting
PointCloudSizeExtractor(), # to init_shape in SubjectAssembler
data_extractor_valid,
pymia_extr.IndexingExtractor(),
pymia_extr.ImageShapeExtractor()
])
self.extractor_test = pymia_extr.ComposeExtractor([
pymia_extr.NamesExtractor(), # required for SelectiveDataExtractor
pymia_extr.SubjectExtractor(),
data_extractor_test, # we need the indices, i.e. the point's coordinates,
# to convert the point cloud back to an image
pymia_extr.DataExtractor(
categories=('gt', ),
ignore_indexing=True), # the ground truth is used for the
# validation at config.save_validation_nth_epoch
pymia_extr.ImagePropertiesExtractor(),
pymia_extr.ImageShapeExtractor()
])
# define transforms for extraction
self.extraction_transform_train = pymia_tfm.ComposeTransform([
pymia_tfm.Squeeze(entries=('labels', ),
squeeze_axis=-1), # for PyTorch loss functions
pymia_tfm.LambdaTransform(
lambda_fn=lambda np_data: np_data.astype(np.int64),
entries=('labels', )),
# for PyTorch loss functions
])
self.extraction_transform_valid = pymia_tfm.ComposeTransform([
pymia_tfm.Squeeze(entries=('labels', ),
squeeze_axis=-1), # for PyTorch loss functions
pymia_tfm.LambdaTransform(
lambda_fn=lambda np_data: np_data.astype(np.int64),
entries=('labels', ))
# for PyTorch loss functions
])
if config.use_jitter:
self.extraction_transform_train.transforms.append(
aug.PointCloudJitter())
self.extraction_transform_valid.transforms.append(
aug.PointCloudJitter())
if config.use_rotation:
self.extraction_transform_train.transforms.append(
aug.PointCloudRotate())
self.extraction_transform_valid.transforms.append(
aug.PointCloudRotate())
# need to add probability concatenation after augmentation!
if config.use_point_feature:
self.extraction_transform_train.transforms.append(
ConcatenateCoordinatesAndPointFeatures())
self.extraction_transform_valid.transforms.append(
ConcatenateCoordinatesAndPointFeatures())
if config.use_image_information:
spatial_size = config.image_information_config.spatial_size
def slice_patches(np_data):
z = (np_data.shape[1] - spatial_size) // 2
y = (np_data.shape[2] - spatial_size) // 2
x = (np_data.shape[3] - spatial_size) // 2
np_data = np_data[:, z:(z + spatial_size),
y:(y + spatial_size),
x:(x + spatial_size), :]
return np_data
self.extraction_transform_train.transforms.append(
pymia_tfm.LambdaTransform(
lambda_fn=slice_patches,
entries=image_information_categories))
self.extraction_transform_valid.transforms.append(
pymia_tfm.LambdaTransform(
lambda_fn=slice_patches,
entries=image_information_categories))
# define loaders
training_sampler = pymia_extr.SubsetRandomSampler(sampler_ids_train)
self.loader_train = pymia_extr.DataLoader(self.dataset,
config.batch_size_training,
sampler=training_sampler,
collate_fn=collate_fn,
num_workers=1)
validation_sampler = pymia_extr.SubsetSequentialSampler(
sampler_ids_valid)
self.loader_valid = pymia_extr.DataLoader(self.dataset,
config.batch_size_testing,
sampler=validation_sampler,
collate_fn=collate_fn,
num_workers=1)
self.loader_test = pymia_extr.DataLoader(self.dataset,
config.batch_size_testing,
sampler=validation_sampler,
collate_fn=collate_fn,
num_workers=1)
self.extraction_transform_test = None
def __init__(self,
config: cfg.Configuration,
subjects_train,
subjects_valid,
subjects_test,
collate_fn=pymia_cnv.TorchCollate(
('images', 'labels', 'mask_fg', 'mask_t1h2o'))):
super().__init__()
indexing_strategy = pymia_extr.SliceIndexing()
self.dataset = pymia_extr.ParameterizableDataset(
config.database_file,
indexing_strategy,
pymia_extr.SubjectExtractor(), # for the usual select_indices
None)
self.no_subjects_train = len(subjects_train)
self.no_subjects_valid = len(subjects_valid)
self.no_subjects_test = 0
# get sampler ids by subjects
sampler_ids_train = pymia_extr.select_indices(
self.dataset, pymia_extr.SubjectSelection(subjects_train))
sampler_ids_valid = pymia_extr.select_indices(
self.dataset, pymia_extr.SubjectSelection(subjects_valid))
# define extractors
self.extractor_train = pymia_extr.ComposeExtractor([
pymia_extr.DataExtractor(categories=('images', 'labels')),
pymia_extr.IndexingExtractor(
), # for SubjectAssembler (assembling)
pymia_extr.ImageShapeExtractor() # for SubjectAssembler (shape)
])
self.extractor_valid = pymia_extr.ComposeExtractor([
pymia_extr.DataExtractor(categories=('images', 'labels')),
pymia_extr.IndexingExtractor(
), # for SubjectAssembler (assembling)
pymia_extr.ImageShapeExtractor() # for SubjectAssembler (shape)
])
self.extractor_test = pymia_extr.ComposeExtractor([
pymia_extr.SubjectExtractor(),
pymia_extr.DataExtractor(categories=('labels', )),
pymia_extr.ImagePropertiesExtractor(),
pymia_extr.ImageShapeExtractor()
])
# define transforms for extraction
self.extraction_transform_train = pymia_tfm.ComposeTransform([
pymia_tfm.SizeCorrection((cfg.TENSOR_WIDTH, cfg.TENSOR_HEIGHT)),
pymia_tfm.Permute((2, 0, 1)),
pymia_tfm.Squeeze(entries=('labels', ),
squeeze_axis=0), # for PyTorch loss functions
pymia_tfm.LambdaTransform(
lambda_fn=lambda np_data: np_data.astype(np.int64),
entries=('labels', )),
# for PyTorch loss functions
pymia_tfm.ToTorchTensor()
])
self.extraction_transform_valid = pymia_tfm.ComposeTransform([
pymia_tfm.SizeCorrection((cfg.TENSOR_WIDTH, cfg.TENSOR_HEIGHT)),
pymia_tfm.Permute((2, 0, 1)),
pymia_tfm.Squeeze(entries=('labels', ),
squeeze_axis=0), # for PyTorch loss functions
pymia_tfm.LambdaTransform(
lambda_fn=lambda np_data: np_data.astype(np.int64),
entries=('labels', )),
# for PyTorch loss functions
pymia_tfm.ToTorchTensor()
])
self.extraction_transform_test = None
# define loaders
training_sampler = pymia_extr.SubsetRandomSampler(sampler_ids_train)
self.loader_train = pymia_extr.DataLoader(self.dataset,
config.batch_size_training,
sampler=training_sampler,
collate_fn=collate_fn,
num_workers=1)
validation_sampler = pymia_extr.SubsetSequentialSampler(
sampler_ids_valid)
self.loader_valid = pymia_extr.DataLoader(self.dataset,
config.batch_size_testing,
sampler=validation_sampler,
collate_fn=collate_fn,
num_workers=1)
self.loader_test = None
def main(hdf_file, log_dir):
# initialize the evaluator with the metrics and the labels to evaluate
metrics = [metric.DiceCoefficient()]
labels = {
1: 'WHITEMATTER',
2: 'GREYMATTER',
3: 'HIPPOCAMPUS',
4: 'AMYGDALA',
5: 'THALAMUS'
}
evaluator = eval_.SegmentationEvaluator(metrics, labels)
# we want to log the mean and standard deviation of the metrics among all subjects of the dataset
functions = {'MEAN': np.mean, 'STD': np.std}
statistics_aggregator = writer.StatisticsAggregator(functions=functions)
console_writer = writer.ConsoleStatisticsWriter(functions=functions)
# initialize TensorBoard writer
summary_writer = tf.summary.create_file_writer(
os.path.join(log_dir, 'logging-example-tensorflow'))
# setup the training datasource
train_subjects, valid_subjects = ['Subject_1', 'Subject_2',
'Subject_3'], ['Subject_4']
extractor = extr.DataExtractor(categories=(defs.KEY_IMAGES,
defs.KEY_LABELS))
indexing_strategy = extr.SliceIndexing()
augmentation_transforms = [
augm.RandomElasticDeformation(),
augm.RandomMirror()
]
transforms = [tfm.Squeeze(entries=(defs.KEY_LABELS, ))]
train_transforms = tfm.ComposeTransform(augmentation_transforms +
transforms)
train_dataset = extr.PymiaDatasource(hdf_file,
indexing_strategy,
extractor,
train_transforms,
subject_subset=train_subjects)
# setup the validation datasource
batch_size = 16
valid_transforms = tfm.ComposeTransform([])
valid_dataset = extr.PymiaDatasource(hdf_file,
indexing_strategy,
extractor,
valid_transforms,
subject_subset=valid_subjects)
direct_extractor = extr.ComposeExtractor([
extr.SubjectExtractor(),
extr.ImagePropertiesExtractor(),
extr.DataExtractor(categories=(defs.KEY_LABELS, ))
])
assembler = assm.SubjectAssembler(valid_dataset)
# tensorflow specific handling
train_gen_fn = pymia_tf.get_tf_generator(train_dataset)
tf_train_dataset = tf.data.Dataset.from_generator(
generator=train_gen_fn,
output_types={
defs.KEY_IMAGES: tf.float32,
defs.KEY_LABELS: tf.int64,
defs.KEY_SAMPLE_INDEX: tf.int64
})
tf_train_dataset = tf_train_dataset.batch(batch_size).shuffle(
len(train_dataset))
valid_gen_fn = pymia_tf.get_tf_generator(valid_dataset)
tf_valid_dataset = tf.data.Dataset.from_generator(
generator=valid_gen_fn,
output_types={
defs.KEY_IMAGES: tf.float32,
defs.KEY_LABELS: tf.int64,
defs.KEY_SAMPLE_INDEX: tf.int64
})
tf_valid_dataset = tf_valid_dataset.batch(batch_size)
u_net = unet.build_model(channels=2,
num_classes=6,
layer_depth=3,
filters_root=16)
optimizer = tf.keras.optimizers.Adam(learning_rate=1e-3)
train_loss = tf.keras.metrics.Mean('train_loss', dtype=tf.float32)
train_batches = len(train_dataset) // batch_size
# looping over the data in the dataset
epochs = 100
for epoch in range(epochs):
print(f'Epoch {epoch + 1}/{epochs}')
# training
print('training')
for i, batch in enumerate(tf_train_dataset):
x, y = batch[defs.KEY_IMAGES], batch[defs.KEY_LABELS]
with tf.GradientTape() as tape:
logits = u_net(x, training=True)
loss = tf.keras.losses.sparse_categorical_crossentropy(
y, logits, from_logits=True)
grads = tape.gradient(loss, u_net.trainable_variables)
optimizer.apply_gradients(zip(grads, u_net.trainable_variables))
train_loss(loss)
with summary_writer.as_default():
tf.summary.scalar('train/loss',
train_loss.result(),
step=epoch * train_batches + i)
print(
f'[{i + 1}/{train_batches}]\tloss: {train_loss.result().numpy()}'
)
# validation
print('validation')
valid_batches = len(valid_dataset) // batch_size
for i, batch in enumerate(tf_valid_dataset):
x, sample_indices = batch[defs.KEY_IMAGES], batch[
defs.KEY_SAMPLE_INDEX]
logits = u_net(x)
prediction = tf.expand_dims(tf.math.argmax(logits, -1), -1)
numpy_prediction = prediction.numpy()
is_last = i == valid_batches - 1
assembler.add_batch(numpy_prediction, sample_indices.numpy(),
is_last)
for subject_index in assembler.subjects_ready:
subject_prediction = assembler.get_assembled_subject(
subject_index)
direct_sample = train_dataset.direct_extract(
direct_extractor, subject_index)
target, image_properties = direct_sample[
defs.KEY_LABELS], direct_sample[defs.KEY_PROPERTIES]
# evaluate the prediction against the reference
evaluator.evaluate(subject_prediction[..., 0], target[..., 0],
direct_sample[defs.KEY_SUBJECT])
# calculate mean and standard deviation of each metric
results = statistics_aggregator.calculate(evaluator.results)
# log to TensorBoard into category train
with summary_writer.as_default():
for result in results:
tf.summary.scalar(f'valid/{result.metric}-{result.id_}',
result.value, epoch)
console_writer.write(evaluator.results)
# clear results such that the evaluator is ready for the next evaluation
evaluator.clear()
