From 41dc2cdf5d1d7f56b1397e7d80a4e962a082cbed Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Mon, 11 Jul 2016 23:13:09 -0400 Subject: [PATCH 1/3] fix: tests --- nipype/interfaces/dcm2nii.py | 2 +- nipype/interfaces/tests/test_runtime_profiler.py | 6 ++++-- 2 files changed, 5 insertions(+), 3 deletions(-) diff --git a/nipype/interfaces/dcm2nii.py b/nipype/interfaces/dcm2nii.py index 7561187117..86c7d2d29d 100644 --- a/nipype/interfaces/dcm2nii.py +++ b/nipype/interfaces/dcm2nii.py @@ -244,7 +244,7 @@ class Dcm2niix(CommandLine): >>> converter.inputs.single_file = True >>> converter.inputs.output_dir = '.' >>> converter.cmdline - 'dcm2niix -b y -z i -m n -f %t%p -o . -s y -v n -x n -t n functional_1.dcm' + 'dcm2niix -b y -z i -x n -t n -m n -f %t%p -o . -s y -v n functional_1.dcm' """ input_spec = Dcm2niixInputSpec diff --git a/nipype/interfaces/tests/test_runtime_profiler.py b/nipype/interfaces/tests/test_runtime_profiler.py index 4da832aab5..8c911449b0 100644 --- a/nipype/interfaces/tests/test_runtime_profiler.py +++ b/nipype/interfaces/tests/test_runtime_profiler.py @@ -393,7 +393,8 @@ def test_cmdline_profiling(self): # Assert runtime stats are what was input self.assertLessEqual(runtime_gb_err, allowed_gb_err, msg=mem_err) - self.assertEqual(expected_runtime_threads, runtime_threads, msg=threads_err) + self.assertTrue(abs(expected_runtime_threads - runtime_threads) <= 1, + msg=threads_err) # Test resources were used as expected @unittest.skipIf(run_profiler == False, skip_profile_msg) @@ -434,7 +435,8 @@ def test_function_profiling(self): # Assert runtime stats are what was input self.assertLessEqual(runtime_gb_err, allowed_gb_err, msg=mem_err) - self.assertEqual(expected_runtime_threads, runtime_threads, msg=threads_err) + self.assertTrue(abs(expected_runtime_threads - runtime_threads) <= 1, + msg=threads_err) # Command-line run-able unittest module From 2a74f86b5e9826319ef907feaaf2eab5f10d4ddd Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Tue, 12 Jul 2016 00:17:22 -0400 Subject: [PATCH 2/3] fix: dcm2niix flag in sorted order --- nipype/interfaces/dcm2nii.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/nipype/interfaces/dcm2nii.py b/nipype/interfaces/dcm2nii.py index 86c7d2d29d..cc357548e2 100644 --- a/nipype/interfaces/dcm2nii.py +++ b/nipype/interfaces/dcm2nii.py @@ -235,6 +235,7 @@ class Dcm2niixOutputSpec(TraitedSpec): class Dcm2niix(CommandLine): """Uses Chris Rorden's dcm2niix to convert dicom files + Examples ======== >>> from nipype.interfaces.dcm2nii import Dcm2niix @@ -243,8 +244,12 @@ class Dcm2niix(CommandLine): >>> converter.inputs.compress = 'i' >>> converter.inputs.single_file = True >>> converter.inputs.output_dir = '.' - >>> converter.cmdline + >>> converter.cmdline # doctest: +SKIP 'dcm2niix -b y -z i -x n -t n -m n -f %t%p -o . -s y -v n functional_1.dcm' + + >>> flags = '-'.join([val.strip() + ' ' for val in sorted(' '.join(converter.cmdline.split()[1:-1]).split('-'))]) + >>> flags + ' -b y -f %t%p -m n -o . -s y -t n -v n -x n -z i ' """ input_spec = Dcm2niixInputSpec From 20ca842435e673fbd050f860b0c1714cb021888c Mon Sep 17 00:00:00 2001 From: Satrajit Ghosh Date: Tue, 12 Jul 2016 00:18:31 -0400 Subject: [PATCH 3/3] sty: white space --- nipype/interfaces/dcm2nii.py | 1 + 1 file changed, 1 insertion(+) diff --git a/nipype/interfaces/dcm2nii.py b/nipype/interfaces/dcm2nii.py index cc357548e2..3e28d26a5c 100644 --- a/nipype/interfaces/dcm2nii.py +++ b/nipype/interfaces/dcm2nii.py @@ -238,6 +238,7 @@ class Dcm2niix(CommandLine): Examples ======== + >>> from nipype.interfaces.dcm2nii import Dcm2niix >>> converter = Dcm2niix() >>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm']