[WIP] Revise terminal_output

This PR revises the terminal_output feature, making it a class attribute and deprecating the old InputSpec trait.

It also implements new ways of storing the output of a CommandLine, as discussed in #1407. Thus, closes #1407.

Author: oesteban

examples/fmri_ants_openfmri.py

@@ -218,7 +218,7 @@ def create_reg_workflow(name='registration'):
     warpmean.inputs.input_image_type = 0
     warpmean.inputs.interpolation = 'Linear'
     warpmean.inputs.invert_transform_flags = [False, False]
-    warpmean.inputs.terminal_output = 'file'
+    warpmean.terminal_output = 'file'
 
     register.connect(inputnode, 'target_image_brain', warpmean, 'reference_image')
     register.connect(inputnode, 'mean_image', warpmean, 'input_image')
@@ -234,7 +234,7 @@ def create_reg_workflow(name='registration'):
     warpall.inputs.input_image_type = 0
     warpall.inputs.interpolation = 'Linear'
     warpall.inputs.invert_transform_flags = [False, False]
-    warpall.inputs.terminal_output = 'file'
+    warpall.terminal_output = 'file'
 
     register.connect(inputnode, 'target_image_brain', warpall, 'reference_image')
     register.connect(inputnode, 'source_files', warpall, 'input_image')
@@ -428,7 +428,7 @@ def create_fs_reg_workflow(name='registration'):
     warpmean.inputs.input_image_type = 0
     warpmean.inputs.interpolation = 'Linear'
     warpmean.inputs.invert_transform_flags = [False, False]
-    warpmean.inputs.terminal_output = 'file'
+    warpmean.terminal_output = 'file'
     warpmean.inputs.args = '--float'
     # warpmean.inputs.num_threads = 4
     # warpmean.plugin_args = {'sbatch_args': '--mem=4G -c 4'}
@@ -443,7 +443,7 @@ def create_fs_reg_workflow(name='registration'):
     warpall.inputs.input_image_type = 0
     warpall.inputs.interpolation = 'Linear'
     warpall.inputs.invert_transform_flags = [False, False]
-    warpall.inputs.terminal_output = 'file'
+    warpall.terminal_output = 'file'
     warpall.inputs.args = '--float'
     warpall.inputs.num_threads = 2
     warpall.plugin_args = {'sbatch_args': '--mem=6G -c 2'}

examples/rsfmri_vol_surface_preprocessing.py

@@ -547,7 +547,7 @@ def create_reg_workflow(name='registration'):
     warpmean.inputs.input_image_type = 3
     warpmean.inputs.interpolation = 'Linear'
     warpmean.inputs.invert_transform_flags = [False, False]
-    warpmean.inputs.terminal_output = 'file'
+    warpmean.terminal_output = 'file'
     warpmean.inputs.args = '--float'
     warpmean.inputs.num_threads = 4
 
@@ -767,7 +767,7 @@ def merge_files(in1, in2):
     warpall.inputs.input_image_type = 3
     warpall.inputs.interpolation = 'Linear'
     warpall.inputs.invert_transform_flags = [False, False]
-    warpall.inputs.terminal_output = 'file'
+    warpall.terminal_output = 'file'
     warpall.inputs.reference_image = target_file
     warpall.inputs.args = '--float'
     warpall.inputs.num_threads = 1

examples/rsfmri_vol_surface_preprocessing_nipy.py

@@ -482,7 +482,7 @@ def create_reg_workflow(name='registration'):
     warpmean.inputs.input_image_type = 3
     warpmean.inputs.interpolation = 'Linear'
     warpmean.inputs.invert_transform_flags = [False, False]
-    warpmean.inputs.terminal_output = 'file'
+    warpmean.terminal_output = 'file'
     warpmean.inputs.args = '--float'
     warpmean.inputs.num_threads = 4
     warpmean.plugin_args = {'sbatch_args': '-c%d' % 4}
@@ -704,7 +704,7 @@ def merge_files(in1, in2):
     warpall.inputs.input_image_type = 3
     warpall.inputs.interpolation = 'Linear'
     warpall.inputs.invert_transform_flags = [False, False]
-    warpall.inputs.terminal_output = 'file'
+    warpall.terminal_output = 'file'
     warpall.inputs.reference_image = target_file
     warpall.inputs.args = '--float'
     warpall.inputs.num_threads = 2

nipype/interfaces/afni/preprocess.py

@@ -1872,13 +1872,10 @@ class ROIStatsInputSpec(CommandLineInputSpec):
         desc='execute quietly',
         argstr='-quiet',
         position=1)
-    terminal_output = traits.Enum(
-        'allatonce',
+    terminal_output = traits.Enum('allatonce', deprecated='1.0.0',
         desc='Control terminal output:`allatonce` - waits till command is '
              'finished to display output',
-        nohash=True,
-        mandatory=True,
-        usedefault=True)
+        nohash=True)
 
 
 class ROIStatsOutputSpec(TraitedSpec):
@@ -1907,6 +1904,7 @@ class ROIStats(AFNICommandBase):
 
     """
     _cmd = '3dROIstats'
+    _terminal_output = 'allatonce'
     input_spec = ROIStatsInputSpec
     output_spec = ROIStatsOutputSpec