def get_pair_metadata(self, slice_index=0, coord=None):
"""Return dictionary containing input and gt metadata.
Args:
slice_index (int): Index of 2D slice if 2D model is used, else 0.
coord (tuple or list): Coordinates of subvolume in volume if 3D model is used, else None.
Returns:
dict: Input and gt metadata.
"""
gt_meta_dict = []
for gt in self.gt_handle:
if gt is not None:
gt_meta_dict.append(
imed_loader_utils.SampleMetadata({
"zooms":
imed_loader_utils.orient_shapes_hwd(
gt.header.get_zooms(), self.slice_axis),
"data_shape":
imed_loader_utils.orient_shapes_hwd(
gt.header.get_data_shape(), self.slice_axis),
"gt_filenames":
self.metadata[0]["gt_filenames"],
"bounding_box":
self.metadata[0]["bounding_box"]
if 'bounding_box' in self.metadata[0] else None,
"data_type":
'gt',
"crop_params": {}
}))
else:
# Temporarily append null metadata to null gt
gt_meta_dict.append(None)
# Replace null metadata with metadata from other existing classes of the same subject
for idx, gt_metadata in enumerate(gt_meta_dict):
if gt_metadata is None:
gt_meta_dict[idx] = list(filter(None, gt_meta_dict))[0]
input_meta_dict = []
for handle in self.input_handle:
input_meta_dict.append(
imed_loader_utils.SampleMetadata({
"zooms":
imed_loader_utils.orient_shapes_hwd(
handle.header.get_zooms(), self.slice_axis),
"data_shape":
imed_loader_utils.orient_shapes_hwd(
handle.header.get_data_shape(), self.slice_axis),
"data_type":
'im',
"crop_params": {}
}))
dreturn = {
"input_metadata": input_meta_dict,
"gt_metadata": gt_meta_dict,
}
for idx, metadata in enumerate(self.metadata): # loop across channels
metadata["slice_index"] = slice_index
metadata["coord"] = coord
self.metadata[idx] = metadata
for metadata_key in metadata.keys(): # loop across input metadata
dreturn["input_metadata"][idx][metadata_key] = metadata[
metadata_key]
return dreturn
def __getitem__(self, index):
"""Get samples.
Warning: For now, this method only supports one gt / roi.
Args:
index (int): Sample index.
Returns:
dict: Dictionary containing image and label tensors as well as metadata.
"""
line = self.dataframe.iloc[index]
# For HeMIS strategy. Otherwise the values of the matrix dont change anything.
missing_modalities = self.cst_matrix[index]
input_metadata = []
input_tensors = []
# Inputs
with h5py.File(self.path_hdf5, "r") as f:
for i, ct in enumerate(self.cst_lst):
if self.status[ct]:
input_tensor = line[ct] * missing_modalities[i]
else:
input_tensor = f[line[ct]][
line['Slices']] * missing_modalities[i]
input_tensors.append(input_tensor)
# input Metadata
metadata = imed_loader_utils.SampleMetadata({
key: value
for key, value in f['{}/inputs/{}'.format(
line['Subjects'], ct)].attrs.items()
})
metadata['slice_index'] = line["Slices"]
metadata['missing_mod'] = missing_modalities
metadata['crop_params'] = {}
input_metadata.append(metadata)
# GT
gt_img = []
gt_metadata = []
for idx, gt in enumerate(self.gt_lst):
if self.status['gt/' + gt]:
gt_data = line['gt/' + gt]
else:
gt_data = f[line['gt/' + gt]][line['Slices']]
gt_data = gt_data.astype(np.uint8)
gt_img.append(gt_data)
gt_metadata.append(
imed_loader_utils.SampleMetadata({
key: value
for key, value in f[line['gt/' + gt]].attrs.items()
}))
gt_metadata[idx]['crop_params'] = {}
# ROI
roi_img = []
roi_metadata = []
if self.roi_lst:
if self.status['roi/' + self.roi_lst[0]]:
roi_data = line['roi/' + self.roi_lst[0]]
else:
roi_data = f[line['roi/' +
self.roi_lst[0]]][line['Slices']]
roi_data = roi_data.astype(np.uint8)
roi_img.append(roi_data)
roi_metadata.append(
imed_loader_utils.SampleMetadata({
key: value
for key, value in f[line[
'roi/' + self.roi_lst[0]]].attrs.items()
}))
roi_metadata[0]['crop_params'] = {}
# Run transforms on ROI
# ROI goes first because params of ROICrop are needed for the followings
stack_roi, metadata_roi = self.transform(sample=roi_img,
metadata=roi_metadata,
data_type="roi")
# Update metadata_input with metadata_roi
metadata_input = imed_loader_utils.update_metadata(
metadata_roi, input_metadata)
# Run transforms on images
stack_input, metadata_input = self.transform(
sample=input_tensors, metadata=metadata_input, data_type="im")
# Update metadata_input with metadata_roi
metadata_gt = imed_loader_utils.update_metadata(
metadata_input, gt_metadata)
# Run transforms on images
stack_gt, metadata_gt = self.transform(sample=gt_img,
metadata=metadata_gt,
data_type="gt")
data_dict = {
'input': stack_input,
'gt': stack_gt,
'roi': stack_roi,
'input_metadata': metadata_input,
'gt_metadata': metadata_gt,
'roi_metadata': metadata_roi
}
return data_dict
def run_visualization(input, config, number, output, roi):
"""Utility function to visualize Data Augmentation transformations.
Data augmentation is a key part of the Deep Learning training scheme. This script aims at facilitating the
fine-tuning of data augmentation parameters. To do so, this script provides a step-by-step visualization of the
transformations that are applied on data.
This function applies a series of transformations (defined in a configuration file
``-c``) to ``-n`` 2D slices randomly extracted from an input image (``-i``), and save as png the resulting sample
after each transform.
For example::
ivadomed_visualize_transforms -i t2s.nii.gz -n 1 -c config.json -r t2s_seg.nii.gz
Provides a visualization of a series of three transformation on a randomly selected slice:
.. image:: ../../images/transforms_im.png
:width: 600px
:align: center
And on a binary mask::
ivadomed_visualize_transforms -i t2s_gmseg.nii.gz -n 1 -c config.json -r t2s_seg.nii.gz
Gives:
.. image:: ../../images/transforms_gt.png
:width: 600px
:align: center
Args:
input (string): Image filename. Flag: ``--input``, ``-i``
config (string): Configuration file filename. Flag: ``--config``, ``-c``
number (int): Number of slices randomly extracted. Flag: ``--number``, ``-n``
output (string): Folder path where the results are saved. Flag: ``--ofolder``, ``-o``
roi (string): Filename of the region of interest. Only needed if ROICrop is part of the transformations.
Flag: ``--roi``, ``-r``
"""
# Load context
with open(config, "r") as fhandle:
context = json.load(fhandle)
# Create output folder
if not os.path.isdir(output):
os.makedirs(output)
# Slice extracted according to below axis
axis = imed_utils.AXIS_DCT[context["loader_parameters"]["slice_axis"]]
# Get data
input_img, input_data = get_data(input, axis)
# Image or Mask
is_mask = np.array_equal(input_data, input_data.astype(bool))
# Get zooms
zooms = imed_loader_utils.orient_shapes_hwd(input_img.header.get_zooms(),
slice_axis=axis)
# Get indexes
indexes = random.sample(range(0, input_data.shape[2]), number)
# Get training transforms
training_transforms, _, _ = imed_transforms.get_subdatasets_transforms(
context["transformation"])
if "ROICrop" in training_transforms:
if roi and os.path.isfile(roi):
roi_img, roi_data = get_data(roi, axis)
else:
print(
"\nPlease provide ROI image (-r) in order to apply ROICrop transformation."
)
exit()
# Compose transforms
dict_transforms = {}
stg_transforms = ""
for transform_name in training_transforms:
# We skip NumpyToTensor transform since that s only a change of data type
if transform_name == "NumpyToTensor":
continue
# Update stg_transforms
stg_transforms += transform_name + "_"
# Add new transform to Compose
dict_transforms.update(
{transform_name: training_transforms[transform_name]})
composed_transforms = imed_transforms.Compose(dict_transforms)
# Loop across slices
for i in indexes:
data = [input_data[:, :, i]]
# Init metadata
metadata = imed_loader_utils.SampleMetadata({
"zooms":
zooms,
"data_type":
"gt" if is_mask else "im"
})
# Apply transformations to ROI
if "CenterCrop" in training_transforms or (
"ROICrop" in training_transforms and os.path.isfile(roi)):
metadata.__setitem__('crop_params', {})
# Apply transformations to image
stack_im, _ = composed_transforms(
sample=data,
metadata=[metadata for _ in range(number)],
data_type="im")
# Plot before / after transformation
fname_out = os.path.join(
output, stg_transforms + "slice" + str(i) + ".png")
print("Fname out: {}.".format(fname_out))
print("\t{}".format(dict(metadata)))
# rescale intensities
if len(stg_transforms[:-1].split("_")) == 1:
before = np.rot90(
imed_maths.rescale_values_array(data[0], 0.0, 1.0))
else:
before = after
after = np.rot90(
imed_maths.rescale_values_array(stack_im[0], 0.0, 1.0))
# Plot
imed_utils.plot_transformed_sample(
before,
after,
list_title=[
"\n".join(stg_transforms[:-1].split("_")[:-1]),
"\n".join(stg_transforms[:-1].split("_"))
],
fname_out=fname_out,
cmap="jet" if is_mask else "gray")