def resample_data_or_seg(data,
new_shape,
is_seg,
axis=None,
order=3,
do_separate_z=False,
cval=0,
order_z=0) -> np.ndarray:
"""
Resample data or segmentation
Args:
data: array to resample [C, dims]
new_shape: define new dims (without channels)
is_seg: changes the resampling strategy
axis: anisotropic axis, different resampling order used here
order: order of resampling along the isotropic axis
do_separate_z: Different resampling along z dimensions
cval: //
order_z: if separate z resampling is done then this is the order for resampling in z
Returns:
np.ndarray: resampled array
"""
return nn_preprocessing.resample_data_or_seg(data=data,
new_shape=new_shape,
is_seg=is_seg,
axis=axis,
order=order,
do_separate_z=do_separate_z,
cval=cval,
order_z=order_z)
def resample_and_save(predicted, target_shape, output_file):
predicted_new_shape = resample_data_or_seg(predicted,
target_shape,
False,
order=1,
do_separate_z=False,
cval=0)
seg_new_shape = predicted_new_shape.argmax(0)
np.savez_compressed(output_file, data=seg_new_shape.astype(np.uint8))
def resample_and_save(predicted,
target_shape,
output_file,
force_separate_z=False,
interpolation_order=1,
interpolation_order_z=0):
if isinstance(predicted, str):
assert isfile(predicted), "If isinstance(segmentation_softmax, str) then " \
"isfile(segmentation_softmax) must be True"
del_file = deepcopy(predicted)
predicted = np.load(predicted)
os.remove(del_file)
predicted_new_shape = resample_data_or_seg(predicted,
target_shape,
False,
order=interpolation_order,
do_separate_z=force_separate_z,
order_z=interpolation_order_z)
seg_new_shape = predicted_new_shape.argmax(0)
np.savez_compressed(output_file, data=seg_new_shape.astype(np.uint8))
def save_segmentation_nifti(segmentation,
out_fname,
dct,
order=1,
force_separate_z=None,
order_z=0):
"""
faster and uses less ram than save_segmentation_nifti_from_softmax, but maybe less precise and also does not support
softmax export (which is needed for ensembling). So it's a niche function that may be useful in some cases.
:param segmentation:
:param out_fname:
:param dct:
:param order:
:param force_separate_z:
:return:
"""
# suppress output
print("force_separate_z:", force_separate_z, "interpolation order:", order)
sys.stdout = open(os.devnull, 'w')
if isinstance(segmentation, str):
assert isfile(segmentation), "If isinstance(segmentation_softmax, str) then " \
"isfile(segmentation_softmax) must be True"
del_file = deepcopy(segmentation)
segmentation = np.load(segmentation)
os.remove(del_file)
# first resample, then put result into bbox of cropping, then save
current_shape = segmentation.shape
shape_original_after_cropping = dct.get('size_after_cropping')
shape_original_before_cropping = dct.get('original_size_of_raw_data')
# current_spacing = dct.get('spacing_after_resampling')
# original_spacing = dct.get('original_spacing')
if np.any(
np.array(current_shape) != np.array(shape_original_after_cropping)
):
if order == 0:
seg_old_spacing = resize_segmentation(
segmentation, shape_original_after_cropping, 0)
else:
if force_separate_z is None:
if get_do_separate_z(dct.get('original_spacing')):
do_separate_z = True
lowres_axis = get_lowres_axis(dct.get('original_spacing'))
elif get_do_separate_z(dct.get('spacing_after_resampling')):
do_separate_z = True
lowres_axis = get_lowres_axis(
dct.get('spacing_after_resampling'))
else:
do_separate_z = False
lowres_axis = None
else:
do_separate_z = force_separate_z
if do_separate_z:
lowres_axis = get_lowres_axis(dct.get('original_spacing'))
else:
lowres_axis = None
print("separate z:", do_separate_z, "lowres axis", lowres_axis)
seg_old_spacing = resample_data_or_seg(
segmentation[None],
shape_original_after_cropping,
is_seg=True,
axis=lowres_axis,
order=order,
do_separate_z=do_separate_z,
order_z=order_z)[0]
else:
seg_old_spacing = segmentation
bbox = dct.get('crop_bbox')
if bbox is not None:
seg_old_size = np.zeros(shape_original_before_cropping)
for c in range(3):
bbox[c][1] = np.min((bbox[c][0] + seg_old_spacing.shape[c],
shape_original_before_cropping[c]))
seg_old_size[bbox[0][0]:bbox[0][1], bbox[1][0]:bbox[1][1],
bbox[2][0]:bbox[2][1]] = seg_old_spacing
else:
seg_old_size = seg_old_spacing
seg_resized_itk = sitk.GetImageFromArray(seg_old_size.astype(np.uint8))
seg_resized_itk.SetSpacing(dct['itk_spacing'])
seg_resized_itk.SetOrigin(dct['itk_origin'])
seg_resized_itk.SetDirection(dct['itk_direction'])
sitk.WriteImage(seg_resized_itk, out_fname)
sys.stdout = sys.__stdout__
def save_segmentation_nifti_from_softmax(
segmentation_softmax: Union[str, np.ndarray],
out_fname: str,
properties_dict: dict,
order: int = 1,
region_class_order: Tuple[Tuple[int]] = None,
seg_postprogess_fn: callable = None,
seg_postprocess_args: tuple = None,
resampled_npz_fname: str = None,
non_postprocessed_fname: str = None,
force_separate_z: bool = None,
interpolation_order_z: int = 0,
verbose: bool = True):
"""
This is a utility for writing segmentations to nifto and npz. It requires the data to have been preprocessed by
GenericPreprocessor because it depends on the property dictionary output (dct) to know the geometry of the original
data. segmentation_softmax does not have to have the same size in pixels as the original data, it will be
resampled to match that. This is generally useful because the spacings our networks operate on are most of the time
not the native spacings of the image data.
If seg_postprogess_fn is not None then seg_postprogess_fnseg_postprogess_fn(segmentation, *seg_postprocess_args)
will be called before nifto export
There is a problem with python process communication that prevents us from communicating obejcts
larger than 2 GB between processes (basically when the length of the pickle string that will be sent is
communicated by the multiprocessing.Pipe object then the placeholder (\%i I think) does not allow for long
enough strings (lol). This could be fixed by changing i to l (for long) but that would require manually
patching system python code.) We circumvent that problem here by saving softmax_pred to a npy file that will
then be read (and finally deleted) by the Process. save_segmentation_nifti_from_softmax can take either
filename or np.ndarray for segmentation_softmax and will handle this automatically
:param segmentation_softmax:
:param out_fname:
:param properties_dict:
:param order:
:param region_class_order:
:param seg_postprogess_fn:
:param seg_postprocess_args:
:param resampled_npz_fname:
:param non_postprocessed_fname:
:param force_separate_z: if None then we dynamically decide how to resample along z, if True/False then always
/never resample along z separately. Do not touch unless you know what you are doing
:param interpolation_order_z: if separate z resampling is done then this is the order for resampling in z
:param verbose:
:return:
"""
if verbose:
print("force_separate_z:", force_separate_z, "interpolation order:",
order)
if isinstance(segmentation_softmax, str):
assert isfile(segmentation_softmax), "If isinstance(segmentation_softmax, str) then " \
"isfile(segmentation_softmax) must be True"
del_file = deepcopy(segmentation_softmax)
segmentation_softmax = np.load(segmentation_softmax)
os.remove(del_file)
# first resample, then put result into bbox of cropping, then save
current_shape = segmentation_softmax.shape
shape_original_after_cropping = properties_dict.get('size_after_cropping')
shape_original_before_cropping = properties_dict.get(
'original_size_of_raw_data')
# current_spacing = dct.get('spacing_after_resampling')
# original_spacing = dct.get('original_spacing')
if np.any([
i != j for i, j in zip(np.array(current_shape[1:]),
np.array(shape_original_after_cropping))
]):
if force_separate_z is None:
if get_do_separate_z(properties_dict.get('original_spacing')):
do_separate_z = True
lowres_axis = get_lowres_axis(
properties_dict.get('original_spacing'))
elif get_do_separate_z(
properties_dict.get('spacing_after_resampling')):
do_separate_z = True
lowres_axis = get_lowres_axis(
properties_dict.get('spacing_after_resampling'))
else:
do_separate_z = False
lowres_axis = None
else:
do_separate_z = force_separate_z
if do_separate_z:
lowres_axis = get_lowres_axis(
properties_dict.get('original_spacing'))
else:
lowres_axis = None
if verbose:
print("separate z:", do_separate_z, "lowres axis", lowres_axis)
seg_old_spacing = resample_data_or_seg(segmentation_softmax,
shape_original_after_cropping,
is_seg=False,
axis=lowres_axis,
order=order,
do_separate_z=do_separate_z,
cval=0,
order_z=interpolation_order_z)
# seg_old_spacing = resize_softmax_output(segmentation_softmax, shape_original_after_cropping, order=order)
else:
if verbose: print("no resampling necessary")
seg_old_spacing = segmentation_softmax
if resampled_npz_fname is not None:
seg_old_size = np.zeros(shape_original_before_cropping)
bbox = properties_dict.get('crop_bbox')
seg_old_size[bbox[0][0]:bbox[0][1], bbox[1][0]:bbox[1][1],
bbox[2][0]:bbox[2][1]] = seg_old_spacing[1]
np.savez_compressed(resampled_npz_fname,
softmax=seg_old_size.astype(np.float16))
# this is needed for ensembling if the nonlinearity is sigmoid
if region_class_order is not None:
properties_dict['regions_class_order'] = region_class_order
save_pickle(properties_dict, resampled_npz_fname[:-4] + ".pkl")
if region_class_order is None:
seg_old_spacing = seg_old_spacing.argmax(0)
else:
seg_old_spacing_final = np.zeros(seg_old_spacing.shape[1:])
for i, c in enumerate(region_class_order):
seg_old_spacing_final[seg_old_spacing[i] > 0.5] = c
seg_old_spacing = seg_old_spacing_final
bbox = properties_dict.get('crop_bbox')
if bbox is not None:
seg_old_size = np.zeros(shape_original_before_cropping)
for c in range(3):
bbox[c][1] = np.min((bbox[c][0] + seg_old_spacing.shape[c],
shape_original_before_cropping[c]))
seg_old_size[bbox[0][0]:bbox[0][1], bbox[1][0]:bbox[1][1],
bbox[2][0]:bbox[2][1]] = seg_old_spacing
else:
seg_old_size = seg_old_spacing
if seg_postprogess_fn is not None:
seg_old_size_postprocessed = seg_postprogess_fn(
np.copy(seg_old_size), *seg_postprocess_args)
else:
seg_old_size_postprocessed = seg_old_size
seg_resized_itk = sitk.GetImageFromArray(
seg_old_size_postprocessed.astype(np.uint8))
seg_resized_itk.SetSpacing(properties_dict['itk_spacing'])
seg_resized_itk.SetOrigin(properties_dict['itk_origin'])
seg_resized_itk.SetDirection(properties_dict['itk_direction'])
sitk.WriteImage(seg_resized_itk, out_fname)
if (non_postprocessed_fname is not None) and (seg_postprogess_fn
is not None):
seg_resized_itk = sitk.GetImageFromArray(seg_old_size.astype(np.uint8))
seg_resized_itk.SetSpacing(properties_dict['itk_spacing'])
seg_resized_itk.SetOrigin(properties_dict['itk_origin'])
seg_resized_itk.SetDirection(properties_dict['itk_direction'])
sitk.WriteImage(seg_resized_itk, non_postprocessed_fname)
def save_segmentation_nifti_from_softmax(segmentation_softmax, out_fname, dct, order=1, region_class_order=None,
seg_postprogess_fn=None, seg_postprocess_args=None, resampled_npz_fname=None,
non_postprocessed_fname=None):
"""
This is a utility for writing segmentations to nifto and npz. It requires the data to have been preprocessed by
GenericPreprocessor because it depends on the property dictionary output (dct) to know the geometry of the original
data. segmentation_softmax does not have to have the same size in pixels as the original data, it will be
resampled to match that. This is generally useful because the spacings our networks operate on are most of the time
not the native spacings of the image data.
If seg_postprogess_fn is not None then seg_postprogess_fnseg_postprogess_fn(segmentation, *seg_postprocess_args)
will be called before nifto export
There is a problem with python process communication that prevents us from communicating obejcts
larger than 2 GB between processes (basically when the length of the pickle string that will be sent is
communicated by the multiprocessing.Pipe object then the placeholder (\%i I think) does not allow for long
enough strings (lol). This could be fixed by changing i to l (for long) but that would require manually
patching system python code.) We circumvent that problem here by saving softmax_pred to a npy file that will
then be read (and finally deleted) by the Process. save_segmentation_nifti_from_softmax can take either
filename or np.ndarray for segmentation_softmax and will handle this automatically
:param segmentation_softmax:
:param out_fname:
:param dct:
:param order:
:param region_class_order:
:param seg_postprogess_fn:
:param seg_postprocess_args:
:param resampled_npz_fname:
:param non_postprocessed_fname:
:return:
"""
if isinstance(segmentation_softmax, str):
assert isfile(segmentation_softmax), "If isinstance(segmentation_softmax, str) then " \
"isfile(segmentation_softmax) must be True"
del_file = deepcopy(segmentation_softmax)
segmentation_softmax = np.load(segmentation_softmax)
os.remove(del_file)
# first resample, then put result into bbox of cropping, then save
current_shape = segmentation_softmax.shape
shape_original_after_cropping = dct.get('size_after_cropping')
shape_original_before_cropping = dct.get('original_size_of_raw_data')
# current_spacing = dct.get('spacing_after_resampling')
# original_spacing = dct.get('original_spacing')
if np.any(np.array(current_shape) != np.array(shape_original_after_cropping)):
if get_do_separate_z(dct.get('original_spacing')):
do_separate_z = True
lowres_axis = get_lowres_axis(dct.get('original_spacing'))
elif get_do_separate_z(dct.get('spacing_after_resampling')):
do_separate_z = True
lowres_axis = get_lowres_axis(dct.get('spacing_after_resampling'))
else:
do_separate_z = False
lowres_axis = None
print("separate z:",do_separate_z, "lowres axis", lowres_axis)
seg_old_spacing = resample_data_or_seg(segmentation_softmax, shape_original_after_cropping, is_seg=False,
axis=lowres_axis, order=order, do_separate_z=do_separate_z, cval=0)
#seg_old_spacing = resize_softmax_output(segmentation_softmax, shape_original_after_cropping, order=order)
else:
seg_old_spacing = segmentation_softmax
if resampled_npz_fname is not None:
np.savez_compressed(resampled_npz_fname, softmax=seg_old_spacing.astype(np.float16))
save_pickle(dct, resampled_npz_fname[:-4] + ".pkl")
if region_class_order is None:
seg_old_spacing = seg_old_spacing.argmax(0)
else:
seg_old_spacing_final = np.zeros(seg_old_spacing.shape[1:])
for i, c in enumerate(region_class_order):
seg_old_spacing_final[seg_old_spacing[i] > 0.5] = c
seg_old_spacing = seg_old_spacing_final
bbox = dct.get('crop_bbox')
if bbox is not None:
seg_old_size = np.zeros(shape_original_before_cropping)
for c in range(3):
bbox[c][1] = np.min((bbox[c][0] + seg_old_spacing.shape[c], shape_original_before_cropping[c]))
seg_old_size[bbox[0][0]:bbox[0][1],
bbox[1][0]:bbox[1][1],
bbox[2][0]:bbox[2][1]] = seg_old_spacing
else:
seg_old_size = seg_old_spacing
if seg_postprogess_fn is not None:
seg_old_size_postprocessed = seg_postprogess_fn(np.copy(seg_old_size), *seg_postprocess_args)
else:
seg_old_size_postprocessed = seg_old_size
seg_resized_itk = sitk.GetImageFromArray(seg_old_size_postprocessed.astype(np.uint8))
seg_resized_itk.SetSpacing(dct['itk_spacing'])
seg_resized_itk.SetOrigin(dct['itk_origin'])
seg_resized_itk.SetDirection(dct['itk_direction'])
print(out_fname, 'CHUJE!!!')
sitk.WriteImage(seg_resized_itk, out_fname)
sitk.WriteImage(seg_resized_itk, join(dirname(out_fname), 'OutputLabel.nii'))
if (non_postprocessed_fname is not None) and (seg_postprogess_fn is not None):
seg_resized_itk = sitk.GetImageFromArray(seg_old_size.astype(np.uint8))
seg_resized_itk.SetSpacing(dct['itk_spacing'])
seg_resized_itk.SetOrigin(dct['itk_origin'])
seg_resized_itk.SetDirection(dct['itk_direction'])
sitk.WriteImage(seg_resized_itk, non_postprocessed_fname)
sitk.WriteImage(seg_resized_itk, join(dirname(non_postprocessed_fname), 'OutputLabel.nii'))
