Skip to content

ants composite transform is a single file not a list #1183

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 3 commits into from
Aug 16, 2015
Merged

ants composite transform is a single file not a list #1183

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
31581aa
there is always only one composite transform - a list is not appropriate
chrisgorgo Aug 13, 2015
543cb16
fixed syntax
chrisgorgo Aug 13, 2015
851454c
fixed doctests
chrisgorgo Aug 13, 2015
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
31 changes: 14 additions & 17 deletions nipype/interfaces/ants/registration.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -189,8 +189,8 @@ def _list_outputs(self):
self.inputs.output_transform_prefix + 'Warp.nii.gz')
outputs['inverse_warp_transform'] = os.path.abspath(
self.inputs.output_transform_prefix + 'InverseWarp.nii.gz')
#outputs['metaheader'] = os.path.abspath(self.inputs.output_transform_prefix + 'velocity.mhd')
#outputs['metaheader_raw'] = os.path.abspath(self.inputs.output_transform_prefix + 'velocity.raw')
# outputs['metaheader'] = os.path.abspath(self.inputs.output_transform_prefix + 'velocity.mhd')
# outputs['metaheader_raw'] = os.path.abspath(self.inputs.output_transform_prefix + 'velocity.raw')
return outputs


Expand Down Expand Up @@ -351,10 +351,8 @@ class RegistrationOutputSpec(TraitedSpec):
), desc='List of flags corresponding to the forward transforms')
reverse_invert_flags = traits.List(traits.Bool(
), desc='List of flags corresponding to the reverse transforms')
composite_transform = traits.List(
File(exists=True), desc='Composite transform file')
inverse_composite_transform = traits.List(
File(exists=True), desc='Inverse composite transform file')
composite_transform = File(exists=True, desc='Composite transform file')
inverse_composite_transform = File(exists=True, desc='Inverse composite transform file')
warped_image = File(desc="Outputs warped image")
inverse_warped_image = File(desc="Outputs the inverse of the warped image")
save_state = File(desc="The saved registration state to be restored")
Expand Down Expand Up @@ -428,7 +426,7 @@ class Registration(ANTSCommand):
>>> reg4.inputs.collapse_output_transforms = True
>>> outputs = reg4._list_outputs()
>>> print outputs #doctest: +ELLIPSIS
{'reverse_invert_flags': [], 'inverse_composite_transform': ['.../nipype/testing/data/output_InverseComposite.h5'], 'warped_image': '.../nipype/testing/data/output_warped_image.nii.gz', 'inverse_warped_image': <undefined>, 'forward_invert_flags': [], 'reverse_transforms': [], 'save_state': <undefined>, 'composite_transform': ['.../nipype/testing/data/output_Composite.h5'], 'forward_transforms': []}
{'reverse_invert_flags': [], 'inverse_composite_transform': '.../nipype/testing/data/output_InverseComposite.h5', 'warped_image': '.../nipype/testing/data/output_warped_image.nii.gz', 'inverse_warped_image': <undefined>, 'forward_invert_flags': [], 'reverse_transforms': [], 'save_state': <undefined>, 'composite_transform': '.../nipype/testing/data/output_Composite.h5', 'forward_transforms': []}

>>> # Test collapse transforms flag
>>> reg4b = copy.deepcopy(reg4)
Expand Down Expand Up @@ -500,7 +498,7 @@ def _formatMetric(self, index):
items = stage_inputs.items()
indexes = range(0, len(name_input))
# dict-comprehension only works with python 2.7 and up
#specs = [{k: v[i] for k, v in items} for i in indexes]
# specs = [{k: v[i] for k, v in items} for i in indexes]
specs = [dict([(k, v[i]) for k, v in items]) for i in indexes]
else:
specs = [stage_inputs]
Expand Down Expand Up @@ -550,17 +548,17 @@ def _formatRegistration(self):
retval.append('--metric %s' % metric)
retval.append('--convergence %s' % self._formatConvergence(ii))
if isdefined(self.inputs.sigma_units):
retval.append('--smoothing-sigmas %s%s' %
retval.append('--smoothing-sigmas %s%s' %
(self._antsJoinList(self.inputs.smoothing_sigmas[
ii]),
self.inputs.sigma_units[ii]))
else:
retval.append('--smoothing-sigmas %s' %
retval.append('--smoothing-sigmas %s' %
self._antsJoinList(self.inputs.smoothing_sigmas[ii]))
retval.append('--shrink-factors %s' %
retval.append('--shrink-factors %s' %
self._antsJoinList(self.inputs.shrink_factors[ii]))
if isdefined(self.inputs.use_estimate_learning_rate_once):
retval.append('--use-estimate-learning-rate-once %d' %
retval.append('--use-estimate-learning-rate-once %d' %
self.inputs.use_estimate_learning_rate_once[ii])
if isdefined(self.inputs.use_histogram_matching):
# use_histogram_matching is either a common flag for all transforms
Expand Down Expand Up @@ -663,7 +661,7 @@ def _format_arg(self, opt, spec, val):
return self._formatWinsorizeImageIntensities()
return '' # Must return something for argstr!
# This feature was removed from recent versions of antsRegistration due to corrupt outputs.
#elif opt == 'collapse_linear_transforms_to_fixed_image_header':
# elif opt == 'collapse_linear_transforms_to_fixed_image_header':
# return self._formatCollapseLinearTransformsToFixedImageHeader()
return super(Registration, self)._format_arg(opt, spec, val)

Expand Down Expand Up @@ -702,12 +700,11 @@ def _list_outputs(self):

if self.inputs.write_composite_transform:
fileName = self.inputs.output_transform_prefix + 'Composite.h5'
outputs['composite_transform'] = [os.path.abspath(fileName)]
outputs['composite_transform'] = os.path.abspath(fileName)
fileName = self.inputs.output_transform_prefix + \
'InverseComposite.h5'
outputs['inverse_composite_transform'] = [
os.path.abspath(fileName)]
else: # If composite transforms are written, then individuals are not written (as of 2014-10-26
outputs['inverse_composite_transform'] = os.path.abspath(fileName)
else: # If composite transforms are written, then individuals are not written (as of 2014-10-26
if not self.inputs.collapse_output_transforms:
transformCount = 0
if isdefined(self.inputs.initial_moving_transform):
Expand Down