From ab4e15a397e42d6b7a023c7b460ed66099534c85 Mon Sep 17 00:00:00 2001 From: Olivia Stanley Date: Mon, 10 Jun 2019 11:20:25 -0400 Subject: [PATCH 1/3] modified afni's cat_matvec to accept empty string opposed to opkey --- nipype/interfaces/afni/utils.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py index 5fe3e199ec..bbb174954f 100644 --- a/nipype/interfaces/afni/utils.py +++ b/nipype/interfaces/afni/utils.py @@ -617,11 +617,15 @@ class CatMatvec(AFNICommand): def _format_arg(self, name, spec, value): if name == 'in_file': - return spec.argstr % (' '.join([i[0] + ' -' + i[1] - for i in value])) + xfm_args='' + for v in value: + if len(v[1])>0: + xfm_args += ' ' + v[0] + ' -' + v[1] + ' ' + else: + xfm_args += ' ' + v[0] + ' ' + return spec.argstr % (xfm_args) return super(CatMatvec, self)._format_arg(name, spec, value) - class CenterMassInputSpec(CommandLineInputSpec): in_file = File( desc='input file to 3dCM', From 67b10fbe0838756027ae50c1d22d55de5f6fa198 Mon Sep 17 00:00:00 2001 From: Olivia Stanley Date: Tue, 17 Sep 2019 10:35:26 -0400 Subject: [PATCH 2/3] made required PR changes to logic and spacing --- nipype/interfaces/afni/utils.py | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py index bbb174954f..742d157c58 100644 --- a/nipype/interfaces/afni/utils.py +++ b/nipype/interfaces/afni/utils.py @@ -617,15 +617,12 @@ class CatMatvec(AFNICommand): def _format_arg(self, name, spec, value): if name == 'in_file': - xfm_args='' - for v in value: - if len(v[1])>0: - xfm_args += ' ' + v[0] + ' -' + v[1] + ' ' - else: - xfm_args += ' ' + v[0] + ' ' - return spec.argstr % (xfm_args) + # Concatenate a series of filenames, with optional opkeys + return ' '.join('%s -%s' % (mfile, opkey) if opkey else mfile + for mfile, opkey in value) return super(CatMatvec, self)._format_arg(name, spec, value) + class CenterMassInputSpec(CommandLineInputSpec): in_file = File( desc='input file to 3dCM', From 845463d516ffaeb9a14b6a44bb2b1465ee86a044 Mon Sep 17 00:00:00 2001 From: ostanley Date: Tue, 17 Sep 2019 11:41:10 -0400 Subject: [PATCH 3/3] added style change Co-Authored-By: Chris Markiewicz --- nipype/interfaces/afni/utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py index 06951056ec..38a9da3efb 100644 --- a/nipype/interfaces/afni/utils.py +++ b/nipype/interfaces/afni/utils.py @@ -621,7 +621,7 @@ def _format_arg(self, name, spec, value): if name == 'in_file': # Concatenate a series of filenames, with optional opkeys return ' '.join('%s -%s' % (mfile, opkey) if opkey else mfile - for mfile, opkey in value) + for mfile, opkey in value) return super(CatMatvec, self)._format_arg(name, spec, value)