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Aug 5, 2015
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20150804 an ts float test #1159

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ff2f983
ENH: Adding new ants command line feature.
hjmjohnson Oct 22, 2014
9acb53e
ENH: Adding --float to antsReg and BFit cmdlines
hjmjohnson Aug 4, 2015
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178 changes: 98 additions & 80 deletions nipype/interfaces/ants/registration.py
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Original file line number Diff line number Diff line change
Expand Up @@ -291,6 +291,11 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
'each stage directly updates the estimated linear transform from the previous '
'stage. (e.g. Translation -> Rigid -> Affine). '
))
# NOTE: Even though only 0=False and 1=True are allowed, ants uses integer
# values instead of booleans
float = traits.Bool(
argstr='--float %d', default=False,
desc=('Use float instead of double for computations.'))

transforms = traits.List(traits.Enum('Rigid', 'Affine', 'CompositeAffine',
'Similarity', 'Translation', 'BSpline',
Expand Down Expand Up @@ -405,6 +410,16 @@ class Registration(ANTSCommand):
>>> reg3.cmdline
'antsRegistration --collapse-output-transforms 0 --dimensionality 3 --initial-moving-transform [ trans.mat, 1 ] --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] --convergence [ 1500x200, 1e-08, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] --convergence [ 100x50x30, 1e-09, 20 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.025, 0.975 ] --write-composite-transform 1'

>>> reg3a = copy.deepcopy(reg)
>>> reg3a.inputs.float = True
>>> reg3a.cmdline
'antsRegistration --collapse-output-transforms 0 --dimensionality 3 --float 1 --initial-moving-transform [ trans.mat, 1 ] --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] --convergence [ 1500x200, 1e-08, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] --convergence [ 100x50x30, 1e-09, 20 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ] --write-composite-transform 1'

>>> reg3b = copy.deepcopy(reg)
>>> reg3b.inputs.float = False
>>> reg3b.cmdline
'antsRegistration --collapse-output-transforms 0 --dimensionality 3 --float 0 --initial-moving-transform [ trans.mat, 1 ] --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] --convergence [ 1500x200, 1e-08, 20 ] --smoothing-sigmas 1.0x0.0vox --shrink-factors 2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform SyN[ 0.25, 3.0, 0.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32 ] --convergence [ 100x50x30, 1e-09, 20 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 3x2x1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.0, 1.0 ] --write-composite-transform 1'

>>> # Test collapse transforms flag
>>> reg4 = copy.deepcopy(reg)
>>> reg.inputs.save_state = 'trans.mat'
Expand Down Expand Up @@ -647,8 +662,9 @@ def _format_arg(self, opt, spec, val):
if not self._quantilesDone:
return self._formatWinsorizeImageIntensities()
return '' # Must return something for argstr!
elif opt == 'collapse_linear_transforms_to_fixed_image_header':
return '' # Command no longer exist, so return empty string for backwards compatibility
# This feature was removed from recent versions of antsRegistration due to corrupt outputs.
#elif opt == 'collapse_linear_transforms_to_fixed_image_header':
# return self._formatCollapseLinearTransformsToFixedImageHeader()
return super(Registration, self)._format_arg(opt, spec, val)

def _outputFileNames(self, prefix, count, transform, inverse=False):
Expand Down Expand Up @@ -684,91 +700,93 @@ def _list_outputs(self):
if isdefined(self.inputs.invert_initial_moving_transform):
invert_initial_moving_transform = self.inputs.invert_initial_moving_transform

if not self.inputs.collapse_output_transforms:
transformCount = 0
if isdefined(self.inputs.initial_moving_transform):
outputs['forward_transforms'].append(
self.inputs.initial_moving_transform)
outputs['forward_invert_flags'].append(
invert_initial_moving_transform)
outputs['reverse_transforms'].insert(
0, self.inputs.initial_moving_transform)
outputs['reverse_invert_flags'].insert(
0, not invert_initial_moving_transform) # Prepend
transformCount += 1
elif isdefined(self.inputs.initial_moving_transform_com):
forwardFileName, forwardInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix,
transformCount,
'Initial')
reverseFileName, reverseInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix,
transformCount,
'Initial',
True)
outputs['forward_transforms'].append(os.path.abspath(forwardFileName))
outputs['forward_invert_flags'].append(False)
outputs['reverse_transforms'].insert(0,
os.path.abspath(reverseFileName))
outputs['reverse_invert_flags'].insert(0, True)
transformCount += 1

for count in range(len(self.inputs.transforms)):
forwardFileName, forwardInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
self.inputs.transforms[count])
reverseFileName, reverseInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
self.inputs.transforms[count], True)
outputs['forward_transforms'].append(
os.path.abspath(forwardFileName))
outputs['forward_invert_flags'].append(forwardInverseMode)
outputs['reverse_transforms'].insert(
0, os.path.abspath(reverseFileName))
outputs[
'reverse_invert_flags'].insert(0, reverseInverseMode)
transformCount += 1
elif not self.inputs.write_composite_transform:
transformCount = 0
isLinear = [any(self._linear_transform_names == t)
for t in self.inputs.transforms]
collapse_list = []

if isdefined(self.inputs.initial_moving_transform) or \
isdefined(self.inputs.initial_moving_transform_com):
isLinear.insert(0, True)

# Only files returned by collapse_output_transforms
if any(isLinear):
collapse_list.append('GenericAffine')
if not all(isLinear):
collapse_list.append('SyN')

for transform in collapse_list:
forwardFileName, forwardInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix,
transformCount,
transform,
inverse=False)
reverseFileName, reverseInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix,
transformCount,
transform,
inverse=True)
outputs['forward_transforms'].append(os.path.abspath(
forwardFileName))
outputs['forward_invert_flags'].append(forwardInverseMode)
outputs['reverse_transforms'].append(
os.path.abspath(reverseFileName))
outputs['reverse_invert_flags'].append(reverseInverseMode)
transformCount += 1
if self.inputs.write_composite_transform:
fileName = self.inputs.output_transform_prefix + 'Composite.h5'
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
if not self.inputs.collapse_output_transforms:
transformCount = 0
if isdefined(self.inputs.initial_moving_transform):
outputs['forward_transforms'].append(
self.inputs.initial_moving_transform)
outputs['forward_invert_flags'].append(
invert_initial_moving_transform)
outputs['reverse_transforms'].insert(
0, self.inputs.initial_moving_transform)
outputs['reverse_invert_flags'].insert(
0, not invert_initial_moving_transform) # Prepend
transformCount += 1
elif isdefined(self.inputs.initial_moving_transform_com):
forwardFileName, forwardInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix,
transformCount,
'Initial')
reverseFileName, reverseInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix,
transformCount,
'Initial',
True)
outputs['forward_transforms'].append(os.path.abspath(forwardFileName))
outputs['forward_invert_flags'].append(False)
outputs['reverse_transforms'].insert(0,
os.path.abspath(reverseFileName))
outputs['reverse_invert_flags'].insert(0, True)
transformCount += 1

for count in range(len(self.inputs.transforms)):
forwardFileName, forwardInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
self.inputs.transforms[count])
reverseFileName, reverseInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix, transformCount,
self.inputs.transforms[count], True)
outputs['forward_transforms'].append(
os.path.abspath(forwardFileName))
outputs['forward_invert_flags'].append(forwardInverseMode)
outputs['reverse_transforms'].insert(
0, os.path.abspath(reverseFileName))
outputs[
'reverse_invert_flags'].insert(0, reverseInverseMode)
transformCount += 1
else:
transformCount = 0
isLinear = [any(self._linear_transform_names == t)
for t in self.inputs.transforms]
collapse_list = []

if isdefined(self.inputs.initial_moving_transform) or \
isdefined(self.inputs.initial_moving_transform_com):
isLinear.insert(0, True)

# Only files returned by collapse_output_transforms
if any(isLinear):
collapse_list.append('GenericAffine')
if not all(isLinear):
collapse_list.append('SyN')

for transform in collapse_list:
forwardFileName, forwardInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix,
transformCount,
transform,
inverse=False)
reverseFileName, reverseInverseMode = self._outputFileNames(
self.inputs.output_transform_prefix,
transformCount,
transform,
inverse=True)
outputs['forward_transforms'].append(os.path.abspath(
forwardFileName))
outputs['forward_invert_flags'].append(forwardInverseMode)
outputs['reverse_transforms'].append(
os.path.abspath(reverseFileName))
outputs['reverse_invert_flags'].append(reverseInverseMode)
transformCount += 1

out_filename = self._get_outputfilenames(inverse=False)
inv_out_filename = self._get_outputfilenames(inverse=True)
if out_filename:
Expand Down
1 change: 1 addition & 0 deletions nipype/interfaces/slicer/registration/brainsfit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,7 @@ class BRAINSFitInputSpec(CommandLineInputSpec):
NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02 = traits.Bool(desc="DO NOT USE THIS FLAG", argstr="--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02 ")
permitParameterVariation = InputMultiPath(traits.Int, desc="A bit vector to permit linear transform parameters to vary under optimization. The vector order corresponds with transform parameters, and beyond the end ones fill in as a default. For instance, you can choose to rotate only in x (pitch) with 1,0,0; this is mostly for expert use in turning on and off individual degrees of freedom in rotation, translation or scaling without multiplying the number of transform representations; this trick is probably meaningless when tried with the general affine transform.", sep=",", argstr="--permitParameterVariation %s")
costMetric = traits.Enum("MMI", "MSE", "NC", "MC", desc="The cost metric to be used during fitting. Defaults to MMI. Options are MMI (Mattes Mutual Information), MSE (Mean Square Error), NC (Normalized Correlation), MC (Match Cardinality for binary images)", argstr="--costMetric %s")
writeOutputTransformInFloat = traits.Bool(desc="By default, the output registration transforms (either the output composite transform or each transform component) are written to the disk in double precision. If this flag is ON, the output transforms will be written in single (float) precision. It is especially important if the output transform is a displacement field transform, or it is a composite transform that includes several displacement fields.", argstr="--writeOutputTransformInFloat ")


class BRAINSFitOutputSpec(TraitedSpec):
Expand Down
2 changes: 2 additions & 0 deletions nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -146,6 +146,8 @@ def test_BRAINSFit_inputs():
),
writeTransformOnFailure=dict(argstr='--writeTransformOnFailure ',
),
writeOutputTransformInFloat=dict(argstr='--writeOutputTransformInFloat ',
),
)
inputs = BRAINSFit.input_spec()

Expand Down