From 636452107d6d3aa83973220f2637d2600631ebf4 Mon Sep 17 00:00:00 2001 From: sulantha2006 Date: Fri, 20 Mar 2020 17:37:21 -0700 Subject: [PATCH 1/3] Adding reverse_forward_transforms and reverse_forward_invert_flags to ANTS Registration outputs. --- nipype/interfaces/ants/registration.py | 10 ++++++++++ nipype/interfaces/ants/tests/test_auto_Registration.py | 2 ++ 2 files changed, 12 insertions(+) diff --git a/nipype/interfaces/ants/registration.py b/nipype/interfaces/ants/registration.py index cb8e363c04..0f6e602591 100644 --- a/nipype/interfaces/ants/registration.py +++ b/nipype/interfaces/ants/registration.py @@ -591,12 +591,18 @@ class RegistrationOutputSpec(TraitedSpec): forward_transforms = traits.List( File(exists=True), desc="List of output transforms for forward registration" ) + reverse_forward_transforms = traits.List( + File(exists=True), desc="List of output transforms for forward registration reversed for antsApplyTransform" + ) reverse_transforms = traits.List( File(exists=True), desc="List of output transforms for reverse registration" ) forward_invert_flags = traits.List( traits.Bool(), desc="List of flags corresponding to the forward transforms" ) + reverse_forward_invert_flags = traits.List( + traits.Bool(), desc="List of flags corresponding to the forward transforms reversed for antsApplyTransform" + ) reverse_invert_flags = traits.List( traits.Bool(), desc="List of flags corresponding to the reverse transforms" ) @@ -1472,6 +1478,10 @@ def _list_outputs(self): outputs["metric_value"] = self._metric_value if self._elapsed_time: outputs["elapsed_time"] = self._elapsed_time + + outputs["reverse_forward_transforms"] = outputs["forward_transforms"][::-1] + outputs["reverse_forward_invert_flags"] = outputs["forward_invert_flags"][::-1] + return outputs diff --git a/nipype/interfaces/ants/tests/test_auto_Registration.py b/nipype/interfaces/ants/tests/test_auto_Registration.py index 33921e8638..dd49cf1eaf 100644 --- a/nipype/interfaces/ants/tests/test_auto_Registration.py +++ b/nipype/interfaces/ants/tests/test_auto_Registration.py @@ -94,6 +94,8 @@ def test_Registration_outputs(): elapsed_time=dict(), forward_invert_flags=dict(), forward_transforms=dict(), + reverse_forward_invert_flags=dict(), + reverse_forward_transforms=dict(), inverse_composite_transform=dict(extensions=None,), inverse_warped_image=dict(extensions=None,), metric_value=dict(), From f8a2e53e79f3eab173693c82b45f43a07299d27b Mon Sep 17 00:00:00 2001 From: sulantha2006 Date: Mon, 23 Mar 2020 16:57:34 -0700 Subject: [PATCH 2/3] doctest: +ELLIPSIS fix --- nipype/interfaces/ants/registration.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/nipype/interfaces/ants/registration.py b/nipype/interfaces/ants/registration.py index 0f6e602591..b9b6700dcd 100644 --- a/nipype/interfaces/ants/registration.py +++ b/nipype/interfaces/ants/registration.py @@ -803,6 +803,8 @@ class Registration(ANTSCommand): 'inverse_composite_transform': '...data/output_InverseComposite.h5', 'inverse_warped_image': , 'metric_value': , + 'reverse_forward_invert_flags': [], + 'reverse_forward_transforms': [], 'reverse_invert_flags': [], 'reverse_transforms': [], 'save_state': '...data/trans.mat', @@ -832,6 +834,9 @@ class Registration(ANTSCommand): 'inverse_composite_transform': , 'inverse_warped_image': , 'metric_value': , + 'reverse_forward_invert_flags': [False, False], + 'reverse_forward_transforms': ['...data/output_1Warp.nii.gz', + '...data/output_0GenericAffine.mat'], 'reverse_invert_flags': [True, False], 'reverse_transforms': ['...data/output_0GenericAffine.mat', \ '...data/output_1InverseWarp.nii.gz'], From f6ba8094427fbcb928a2049b0a24f4624fa79214 Mon Sep 17 00:00:00 2001 From: sulantha2006 Date: Mon, 23 Mar 2020 17:31:24 -0700 Subject: [PATCH 3/3] Fix test_auto_Registration.py --- nipype/interfaces/ants/tests/test_auto_Registration.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nipype/interfaces/ants/tests/test_auto_Registration.py b/nipype/interfaces/ants/tests/test_auto_Registration.py index dd49cf1eaf..151a852820 100644 --- a/nipype/interfaces/ants/tests/test_auto_Registration.py +++ b/nipype/interfaces/ants/tests/test_auto_Registration.py @@ -94,11 +94,11 @@ def test_Registration_outputs(): elapsed_time=dict(), forward_invert_flags=dict(), forward_transforms=dict(), - reverse_forward_invert_flags=dict(), - reverse_forward_transforms=dict(), inverse_composite_transform=dict(extensions=None,), inverse_warped_image=dict(extensions=None,), metric_value=dict(), + reverse_forward_invert_flags=dict(), + reverse_forward_transforms=dict(), reverse_invert_flags=dict(), reverse_transforms=dict(), save_state=dict(extensions=None,),