From 7072042e955269c3e3da27a47b2b2bdf1a857265 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Tue, 14 Mar 2017 15:16:50 -0400 Subject: [PATCH 1/2] Improve readability of modelgen examples. The single-line examples in the documentation are rendering oddly, so I just made them multiline to make them easier to read. --- nipype/algorithms/modelgen.py | 44 +++++++++++++++++++++-------------- 1 file changed, 27 insertions(+), 17 deletions(-) diff --git a/nipype/algorithms/modelgen.py b/nipype/algorithms/modelgen.py index 3a0b2ef8b0..c58e330816 100644 --- a/nipype/algorithms/modelgen.py +++ b/nipype/algorithms/modelgen.py @@ -261,22 +261,28 @@ class SpecifyModel(BaseInterface): >>> s.inputs.functional_runs = ['functional2.nii', 'functional3.nii'] >>> s.inputs.time_repetition = 6 >>> s.inputs.high_pass_filter_cutoff = 128. - >>> info = [Bunch(conditions=['cond1'], onsets=[[2, 50, 100, 180]],\ - durations=[[1]]), \ - Bunch(conditions=['cond1'], onsets=[[30, 40, 100, 150]], \ + >>> info = [Bunch(conditions=['cond1'], + onsets=[[2, 50, 100, 180]], + durations=[[1]]), + Bunch(conditions=['cond1'], + onsets=[[30, 40, 100, 150]], durations=[[1]])] >>> s.inputs.subject_info = info Using pmod: - >>> info = [Bunch(conditions=['cond1', 'cond2'], \ - onsets=[[2, 50],[100, 180]], durations=[[0],[0]], \ - pmod=[Bunch(name=['amp'], poly=[2], param=[[1, 2]]),\ - None]), \ - Bunch(conditions=['cond1', 'cond2'], \ - onsets=[[20, 120],[80, 160]], durations=[[0],[0]], \ - pmod=[Bunch(name=['amp'], poly=[2], param=[[1, 2]]), \ - None])] + >>> info = [Bunch(conditions=['cond1', 'cond2'], + onsets=[[2, 50],[100, 180]], + durations=[[0],[0]], + pmod=[Bunch(name=['amp'], poly=[2], + param=[[1, 2]]), + None]), + Bunch(conditions=['cond1', 'cond2'], + onsets=[[20, 120],[80, 160]], + durations=[[0],[0]], + pmod=[Bunch(name=['amp'], poly=[2], + param=[[1, 2]]), + None])] >>> s.inputs.subject_info = info """ @@ -442,9 +448,11 @@ class SpecifySPMModel(SpecifyModel): >>> s.inputs.functional_runs = ['functional2.nii', 'functional3.nii'] >>> s.inputs.time_repetition = 6 >>> s.inputs.concatenate_runs = True - >>> info = [Bunch(conditions=['cond1'], onsets=[[2, 50, 100, 180]], \ - durations=[[1]]), \ - Bunch(conditions=['cond1'], onsets=[[30, 40, 100, 150]], \ + >>> info = [Bunch(conditions=['cond1'], + onsets=[[2, 50, 100, 180]], + durations=[[1]]), + Bunch(conditions=['cond1'], + onsets=[[30, 40, 100, 150]], durations=[[1]])] >>> s.inputs.subject_info = info @@ -608,9 +616,11 @@ class SpecifySparseModel(SpecifyModel): >>> s.inputs.time_acquisition = 2 >>> s.inputs.high_pass_filter_cutoff = 128. >>> s.inputs.model_hrf = True - >>> info = [Bunch(conditions=['cond1'], onsets=[[2, 50, 100, 180]], \ - durations=[[1]]), \ - Bunch(conditions=['cond1'], onsets=[[30, 40, 100, 150]], \ + >>> info = [Bunch(conditions=['cond1'], + onsets=[[2, 50, 100, 180]], + durations=[[1]]), + Bunch(conditions=['cond1'], + onsets=[[30, 40, 100, 150]], durations=[[1]])] >>> s.inputs.subject_info = info From 1e50c126d7b7c66162e95efcdd52978f26ef0fc0 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Tue, 14 Mar 2017 16:21:31 -0400 Subject: [PATCH 2/2] Fix whitespace in a way that actually works. Apparently multiline examples are not allowed, but this at least gets rid of the whitespace between arguments in the documentation. --- nipype/algorithms/modelgen.py | 44 +++++++++++------------------------ 1 file changed, 14 insertions(+), 30 deletions(-) diff --git a/nipype/algorithms/modelgen.py b/nipype/algorithms/modelgen.py index c58e330816..349e7557fd 100644 --- a/nipype/algorithms/modelgen.py +++ b/nipype/algorithms/modelgen.py @@ -261,28 +261,18 @@ class SpecifyModel(BaseInterface): >>> s.inputs.functional_runs = ['functional2.nii', 'functional3.nii'] >>> s.inputs.time_repetition = 6 >>> s.inputs.high_pass_filter_cutoff = 128. - >>> info = [Bunch(conditions=['cond1'], - onsets=[[2, 50, 100, 180]], - durations=[[1]]), - Bunch(conditions=['cond1'], - onsets=[[30, 40, 100, 150]], - durations=[[1]])] + >>> info = [Bunch(conditions=['cond1'], onsets=[[2, 50, 100, 180]], \ +durations=[[1]]), Bunch(conditions=['cond1'], onsets=[[30, 40, 100, 150]], \ +durations=[[1]])] >>> s.inputs.subject_info = info Using pmod: - >>> info = [Bunch(conditions=['cond1', 'cond2'], - onsets=[[2, 50],[100, 180]], - durations=[[0],[0]], - pmod=[Bunch(name=['amp'], poly=[2], - param=[[1, 2]]), - None]), - Bunch(conditions=['cond1', 'cond2'], - onsets=[[20, 120],[80, 160]], - durations=[[0],[0]], - pmod=[Bunch(name=['amp'], poly=[2], - param=[[1, 2]]), - None])] + >>> info = [Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 50],[100, 180]], \ +durations=[[0],[0]], pmod=[Bunch(name=['amp'], poly=[2], param=[[1, 2]]), \ +None]), Bunch(conditions=['cond1', 'cond2'], onsets=[[20, 120],[80, 160]], \ +durations=[[0],[0]], pmod=[Bunch(name=['amp'], poly=[2], param=[[1, 2]]), \ +None])] >>> s.inputs.subject_info = info """ @@ -448,12 +438,9 @@ class SpecifySPMModel(SpecifyModel): >>> s.inputs.functional_runs = ['functional2.nii', 'functional3.nii'] >>> s.inputs.time_repetition = 6 >>> s.inputs.concatenate_runs = True - >>> info = [Bunch(conditions=['cond1'], - onsets=[[2, 50, 100, 180]], - durations=[[1]]), - Bunch(conditions=['cond1'], - onsets=[[30, 40, 100, 150]], - durations=[[1]])] + >>> info = [Bunch(conditions=['cond1'], onsets=[[2, 50, 100, 180]], \ +durations=[[1]]), Bunch(conditions=['cond1'], onsets=[[30, 40, 100, 150]], \ +durations=[[1]])] >>> s.inputs.subject_info = info """ @@ -616,12 +603,9 @@ class SpecifySparseModel(SpecifyModel): >>> s.inputs.time_acquisition = 2 >>> s.inputs.high_pass_filter_cutoff = 128. >>> s.inputs.model_hrf = True - >>> info = [Bunch(conditions=['cond1'], - onsets=[[2, 50, 100, 180]], - durations=[[1]]), - Bunch(conditions=['cond1'], - onsets=[[30, 40, 100, 150]], - durations=[[1]])] + >>> info = [Bunch(conditions=['cond1'], onsets=[[2, 50, 100, 180]], \ +durations=[[1]]), Bunch(conditions=['cond1'], onsets=[[30, 40, 100, 150]], \ +durations=[[1]])] >>> s.inputs.subject_info = info """