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Merged
merged 13 commits into from
Feb 23, 2018
Merged

antsRegistrationSyNQuick (continuation of #1392 and #2347) #2453

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83e0aa9
wip: added wrapper for antsRegistrationSyNQuick.sh
Mar 3, 2016
26aa5d5
removed wrongly commited file
Mar 3, 2016
ce5ba21
Merge branch 'dev_syn' of https://github.com/fliem/nipype into fliem-…
djarecka Dec 21, 2017
7af657a
applying suggestions from Oscar
djarecka Dec 21, 2017
d256a59
running check-before-commit
djarecka Dec 22, 2017
cc72fbe
small pep8 changes
djarecka Dec 22, 2017
66b28df
Merge remote-tracking branch 'upstream/master' into fliem-dev_syn
effigies Feb 20, 2018
fbf24fa
adding an example to RegistrationSynQuick; using LOCAL_DEFAULT_NUMBER…
djarecka Feb 20, 2018
16ed327
Merge branch 'master' into ants_regsynquick
djarecka Feb 22, 2018
b1ea744
typo
djarecka Feb 23, 2018
3403b0a
after Chris suggestions
djarecka Feb 23, 2018
dbb84a3
fixing doctest with multiple images
djarecka Feb 23, 2018
5cd952f
update auto test
djarecka Feb 23, 2018
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3 changes: 2 additions & 1 deletion nipype/interfaces/ants/__init__.py
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Expand Up @@ -4,7 +4,8 @@
"""Top-level namespace for ants."""

# Registraiton programs
from .registration import ANTS, Registration, MeasureImageSimilarity
from .registration import (ANTS, Registration, RegistrationSynQuick,
MeasureImageSimilarity)

# Resampling Programs
from .resampling import (ApplyTransforms, ApplyTransformsToPoints,
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95 changes: 95 additions & 0 deletions nipype/interfaces/ants/registration.py
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Expand Up @@ -17,6 +17,11 @@
from ..base import TraitedSpec, File, Str, traits, InputMultiPath, isdefined
from .base import ANTSCommand, ANTSCommandInputSpec

try:
LOCAL_DEFAULT_NUMBER_OF_THREADS = int(os.getenv("LOCAL_DEFAULT_NUMBER_OF_THREADS"))
except TypeError:
LOCAL_DEFAULT_NUMBER_OF_THREADS = 1
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Let's just import from .base import LOCAL_DEFAULT_NUMBER_OF_THREADS.

Also, I think in general this variable is kind of pointless, unless somebody's using a fork of nipype where it's defined as something other than 1. This isn't something that needs to be fixed in this PR, but just to flag it for others' attention.



class ANTSInputSpec(ANTSCommandInputSpec):
dimension = traits.Enum(
Expand Down Expand Up @@ -1505,3 +1510,93 @@ def aggregate_outputs(self, runtime=None, needed_outputs=None):
stdout = runtime.stdout.split('\n')
outputs.similarity = float(stdout[0])
return outputs


class RegistrationSynQuickInputSpec(ANTSCommandInputSpec):
dimension = traits.Enum(3, 2, argstr='-d %d',
usedefault=True, desc='image dimension (2 or 3)')
fixed_image = InputMultiPath(File(exists=True), mandatory=True, argstr='-f %s',
desc='Fixed image or source image or reference image')
moving_image = InputMultiPath(File(exists=True), mandatory=True, argstr='-m %s',
desc='Moving image or target image')
output_prefix = Str("transform", usedefault=True, argstr='-o %s',
desc="A prefix that is prepended to all output files")
num_threads = traits.Int(default_value=LOCAL_DEFAULT_NUMBER_OF_THREADS, usedefault=True,
desc='Number of threads (default = 1)', argstr='-n %d')

transform_type = traits.Enum('s', 't', 'r', 'a', 'sr', 'b', 'br', argstr='-t %s',
desc="""
transform type
t: translation
r: rigid
a: rigid + affine
s: rigid + affine + deformable syn (default)
sr: rigid + deformable syn
b: rigid + affine + deformable b-spline syn
br: rigid + deformable b-spline syn""",
usedefault=True)

use_histogram_matching = traits.Bool(False, argstr='-j %d',
desc='use histogram matching')
histogram_bins = traits.Int(default_value=32, argstr='-r %d',
desc='histogram bins for mutual information in SyN stage \
(default = 32)')
spline_distance = traits.Int(default_value=26, argstr='-s %d',
desc='spline distance for deformable B-spline SyN transform \
(default = 26)')
precision_type = traits.Enum('double', 'float', argstr='-p %s',
desc='precision type (default = double)', usedefault=True)


class RegistrationSynQuickOutputSpec(TraitedSpec):
warped_image = File(exists=True, desc="Warped image")
inverse_warped_image = File(exists=True, desc="Inverse warped image")
out_matrix = File(exists=True, desc='Affine matrix')
forward_warp_field = File(exists=True, desc='Forward warp field')
inverse_warp_field = File(exists=True, desc='Inverse warp field')


class RegistrationSynQuick(ANTSCommand):
"""
Reistration using a symmetric image normalization method (SyN).
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"Registration" (you're missing a "g").

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thanks :)

You can read more in Avants et al.; Med Image Anal., 2008
(https://www.ncbi.nlm.nih.gov/pubmed/17659998).

Examples
--------

>>> import copy, pprint
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You're not using these imports

>>> from nipype.interfaces.ants import Registration
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RegistrationSynQuick

>>> reg = RegistrationSynQuick()
>>> reg.inputs.fixed_image = 'fixed1.nii'
>>> reg.inputs.moving_image = 'moving1.nii'
>>> reg.inputs.num_threads = 2
>>> reg.cmdline
'antsRegistrationSynQuick.sh -d 3 -f fixed1.nii -m moving1.nii -n 2 -o transform -p d -t s'
>>> reg.run() # doctest: +SKIP
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From the help:

     NB:  Multiple image pairs can be specified for registration during the SyN stage.
          Specify additional images using the '-m' and '-f' options.  Note that image
          pair correspondence is given by the order specified on the command line.
          Only the first fixed and moving image pair is used for the linear resgitration
          stages.

We should add a doctest to make sure that if fixed_image and moving_image are lists, that we see -f fixed1.nii -f fixed2.nii -m moving1.nii -m moving2.nii (or similar).

It may be more trouble than it's worth to verify that the lists are of the same length.

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it gives -f fixed1.nii fixed2.nii -m moving1.nii moving2.nii, but i haven't checked if it is properly propagated to the main Registration (couldn't find also examples that confirms that this is a proper command)

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Okay, then I think we want to change the argstrs for fixed_image and moving_image to -f %s... and -m %s..., respectively. (The ... will change -f A B to -f A -f B.)

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I pushed before reading this comment.

But do you know this is correct syntax of command line? If yes, I can change it, but just wasn't sure what is the correct syntax

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Yes. -f A B will fail, while -f A -f B will succeed.

"""


_cmd = 'antsRegistrationSynQuick.sh'
input_spec = RegistrationSynQuickInputSpec
output_spec = RegistrationSynQuickOutputSpec

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Just to avoid being affected by upstream changes, we should override _num_threads_update() to do nothing.

def _num_threads_update(self):
    """antsRegistrationSynQuick.sh ignores environment variables, so override environment update"""

def _format_arg(self, name, spec, value):
if name == 'precision_type':
return spec.argstr % value[0]
return super(RegistrationSynQuick, self)._format_arg(name, spec, value)

def _list_outputs(self):
outputs = self.output_spec().get()
outputs['warped_image'] = os.path.abspath(self.inputs.output_prefix + 'Warped.nii.gz')
outputs['inverse_warped_image'] = os.path.abspath(
self.inputs.output_prefix + 'InverseWarped.nii.gz')
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Just to be a little more concise, maybe we can do the following:

out_base = os.path.abspath(self.inputs.output_prefix)
outputs['warped_image'] = out_base + 'Warped.nii.gz'
outputs['inverse_warped_image'] = out_base + 'InverseWarped.nii.gz'

and so on...

outputs['out_matrix'] = os.path.abspath(self.inputs.output_prefix + '0GenericAffine.mat')

# todo in the case of linear transformation-only there won't be fields. is there a more elegant way to specify that?
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What you have seems like a reasonable approach to me.

if self.inputs.transform_type not in ('t', 'r', 'a'):
outputs['forward_warp_field'] = os.path.abspath(
self.inputs.output_prefix + '1Warp.nii.gz')
outputs['inverse_warp_field'] = os.path.abspath(
self.inputs.output_prefix + '1InverseWarp.nii.gz')
return outputs
68 changes: 68 additions & 0 deletions nipype/interfaces/ants/tests/test_auto_RegistrationSynQuick.py
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@@ -0,0 +1,68 @@
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
from __future__ import unicode_literals
from ..registration import RegistrationSynQuick


def test_RegistrationSynQuick_inputs():
input_map = dict(
args=dict(argstr='%s', ),
dimension=dict(
argstr='-d %d',
usedefault=True,
),
environ=dict(
nohash=True,
usedefault=True,
),
fixed_image=dict(
argstr='-f %s',
mandatory=True,
),
histogram_bins=dict(argstr='-r %d', ),
ignore_exception=dict(
deprecated='1.0.0',
nohash=True,
usedefault=True,
),
moving_image=dict(
argstr='-m %s',
mandatory=True,
),
num_threads=dict(argstr='-n %d', ),
output_prefix=dict(
argstr='-o %s',
usedefault=True,
),
precision_type=dict(
argstr='-p %s',
usedefault=True,
),
spline_distance=dict(argstr='-s %d', ),
terminal_output=dict(
deprecated='1.0.0',
nohash=True,
),
transform_type=dict(
argstr='-t %s',
usedefault=True,
),
use_histogram_matching=dict(argstr='-j %d', ),
)
inputs = RegistrationSynQuick.input_spec()

for key, metadata in list(input_map.items()):
for metakey, value in list(metadata.items()):
assert getattr(inputs.traits()[key], metakey) == value
def test_RegistrationSynQuick_outputs():
output_map = dict(
forward_warp_field=dict(),
inverse_warp_field=dict(),
inverse_warped_image=dict(),
out_matrix=dict(),
warped_image=dict(),
)
outputs = RegistrationSynQuick.output_spec()

for key, metadata in list(output_map.items()):
for metakey, value in list(metadata.items()):
assert getattr(outputs.traits()[key], metakey) == value