def __init__(self,
name,
volume_config,
slicing_config,
defect_augmentation_config,
master_config=None):
assert isinstance(volume_config, dict)
assert isinstance(slicing_config, dict)
assert isinstance(defect_augmentation_config, dict)
assert 'raw' in volume_config
assert 'segmentation' in volume_config
volume_config = deepcopy(volume_config)
self.scaling_factors = volume_config.pop("scaling_factors")
# Get kwargs for raw volume
raw_volume_kwargs = dict(volume_config.get('raw'))
# check if we have special dict entries for names in the defect augmentation
# slicing config
augmentation_config = deepcopy(defect_augmentation_config)
for slicing_key, slicing_item in augmentation_config[
'artifact_source']['slicing_config'].items():
if isinstance(slicing_item, dict):
new_item = augmentation_config['artifact_source'][
'slicing_config'][slicing_key][name]
augmentation_config['artifact_source']['slicing_config'][
slicing_key] = new_item
raw_volume_kwargs.update(
{'defect_augmentation_config': augmentation_config})
raw_volume_kwargs.update(slicing_config)
# Build raw volume
self.raw_volume = RawVolumeWithDefectAugmentation(name=name,
**raw_volume_kwargs)
# Get kwargs for segmentation volume
segmentation_volume_kwargs = dict(volume_config.get('segmentation'))
segmentation_volume_kwargs.update(slicing_config)
self.affinity_config = segmentation_volume_kwargs.pop(
'affinity_config', None)
# Build segmentation volume
self.segmentation_volume = SegmentationVolume(
name=name, **segmentation_volume_kwargs)
rejection_threshold = volume_config.get('rejection_threshold', 0.92)
super().__init__(self.raw_volume,
self.segmentation_volume,
sync=True,
rejection_dataset_indices=1,
rejection_criterion=RejectSingleLabelVolumes(
1.0, 0.95))
# Set master config (for transforms)
self.master_config = {} if master_config is None else master_config
# Get transforms
self.transforms = self.get_transforms()
def __init__(self,
name,
volume_config,
slicing_config,
defect_augmentation_config,
master_config=None):
assert isinstance(volume_config, dict)
assert isinstance(slicing_config, dict)
assert isinstance(defect_augmentation_config, dict)
assert 'raw' in volume_config
assert 'segmentation' in volume_config
volume_config = deepcopy(volume_config)
# Get kwargs for raw volume
raw_volume_kwargs = dict(volume_config.get('raw'))
# check if we have special dict entries for names in the defect augmentation
# slicing config
augmentation_config = deepcopy(defect_augmentation_config)
for slicing_key, slicing_item in augmentation_config[
'artifact_source']['slicing_config'].items():
if isinstance(slicing_item, dict):
new_item = augmentation_config['artifact_source'][
'slicing_config'][slicing_key][name]
augmentation_config['artifact_source']['slicing_config'][
slicing_key] = new_item
raw_volume_kwargs.update(
{'defect_augmentation_config': augmentation_config})
raw_volume_kwargs.update(slicing_config)
# Build raw volume
ignore_slice_list = deepcopy(
augmentation_config.get("ignore_slice_list", None))
if isinstance(ignore_slice_list, dict):
ignore_slice_list = ignore_slice_list.get(name, [])
self.raw_volume = RawVolumeWithDefectAugmentation(
name=name,
ignore_slice_list=ignore_slice_list,
**raw_volume_kwargs)
# Get kwargs for segmentation volume
segmentation_volume_kwargs = dict(volume_config.get('segmentation'))
segmentation_volume_kwargs.update(slicing_config)
self.affinity_config = segmentation_volume_kwargs.pop(
'affinity_config', None)
# Build segmentation volume
self.segmentation_volume = SegmentationVolume(
name=name, **segmentation_volume_kwargs)
volumes_to_load = [self.raw_volume, self.segmentation_volume]
# Load additional masks:
self.extra_masks_volume = None
if volume_config.get('extra_masks', False):
extra_masks_kwargs = dict(volume_config.get('extra_masks'))
extra_masks_kwargs.update(slicing_config)
self.extra_masks_volume = SegmentationVolume(name=name,
**extra_masks_kwargs)
volumes_to_load.append(self.extra_masks_volume)
rejection_threshold = volume_config.get('rejection_threshold', 0.5)
super().__init__(*volumes_to_load,
sync=True,
rejection_dataset_indices=1,
rejection_criterion=RejectSingleLabelVolumes(
1.0,
rejection_threshold,
defected_label=master_config.get(
'duplicate_GT_defected_slices',
{}).get('defect_label', -1)))
# Set master config (for transforms)
self.master_config = {} if master_config is None else deepcopy(
master_config)
# Get transforms
self.transforms = self.get_transforms()
def __init__(self,
name,
volume_config,
slicing_config,
defect_augmentation_config,
master_config=None):
raise DeprecationWarning("Use newer version in segmfriends")
assert isinstance(volume_config, dict)
assert isinstance(slicing_config, dict)
assert isinstance(defect_augmentation_config, dict)
assert 'raw' in volume_config
assert 'segmentation' in volume_config
assert 'various_masks' in volume_config
volume_config = deepcopy(volume_config)
# Get kwargs for raw volume
raw_volume_kwargs = dict(volume_config.get('raw'))
# check if we have special dict entries for names in the defect augmentation
# slicing config
augmentation_config = deepcopy(defect_augmentation_config)
for slicing_key, slicing_item in augmentation_config[
'artifact_source']['slicing_config'].items():
if isinstance(slicing_item, dict):
new_item = augmentation_config['artifact_source'][
'slicing_config'][slicing_key][name]
augmentation_config['artifact_source']['slicing_config'][
slicing_key] = new_item
raw_volume_kwargs.update(
{'defect_augmentation_config': augmentation_config})
raw_volume_kwargs.update(slicing_config)
# Build raw volume
self.raw_volume = RawVolumeWithDefectAugmentation(name=name,
**raw_volume_kwargs)
# Get kwargs for segmentation volume
segmentation_volume_kwargs = dict(volume_config.get('segmentation'))
segmentation_volume_kwargs.update(slicing_config)
self.affinity_config = segmentation_volume_kwargs.pop(
'affinity_config', None)
# Build segmentation volume
self.segmentation_volume = SegmentationVolume(
name=name, **segmentation_volume_kwargs)
# Load additional masks:
various_masks_kwargs = dict(volume_config.get('various_masks'))
various_masks_kwargs.update(slicing_config)
self.mask_volume = SegmentationVolume(name=name,
**various_masks_kwargs)
rejection_threshold = volume_config.get('rejection_threshold', 0.5)
super().__init__(self.raw_volume,
self.segmentation_volume,
self.mask_volume,
sync=True,
rejection_dataset_indices=1,
rejection_criterion=RejectSingleLabelVolumes(
1.0,
rejection_threshold,
defected_label=master_config.get(
'duplicate_GT_defected_slices',
{}).get('defect_label', -1)))
# Set master config (for transforms)
self.master_config = {} if master_config is None else deepcopy(
master_config)
# Get transforms
self.transforms = self.get_transforms()