Skip to content

Fix/tests #446

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 2 commits into from
Aug 14, 2012
Merged

Fix/tests #446

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
1a387a8
fix: nohash test
satra Aug 14, 2012
e596ad1
fix: tbss workflow doctests
satra Aug 14, 2012
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions nipype/interfaces/base.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1017,11 +1017,11 @@ class must be instantiated with a command argument
>>> cli.cmdline
'ls -al'

>>> cli.inputs.trait_get() #doctest: +SKIP
>>> cli.inputs.trait_get()
{'ignore_exception': False, 'args': '-al', 'environ': {'DISPLAY': ':1'}}

>>> cli.inputs.get_hashval()
({'ignore_exception': False, 'args': '-al', 'environ': {'DISPLAY': ':1'}}, 'b1faf85652295456a906f053d48daef6')
({'args': '-al'}, 'a2f45e04a34630c5f33a75ea2a533cdd')

"""

Expand Down
34 changes: 24 additions & 10 deletions nipype/workflows/dmri/fsl/tbss.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@
# vi: set ft=python sts=4 ts=4 sw=4 et:

import os
from warnings import warn

import nipype.pipeline.engine as pe
import nipype.interfaces.utility as util
import nipype.interfaces.fsl as fsl
Expand Down Expand Up @@ -99,7 +101,7 @@ def create_tbss_2_reg(name="tbss_2_reg"):

>>> from nipype.workflows.dmri.fsl import tbss
>>> tbss2 = create_tbss_2_reg(name="tbss2")
>>> tbss2.inputs.inputnode.target = fsl.Info.standard_image("FMRIB58_FA_1mm.nii.gz")
>>> tbss2.inputs.inputnode.target = fsl.Info.standard_image("FMRIB58_FA_1mm.nii.gz") # doctest: +SKIP
>>> tbss2.inputs.inputnode.fa_list = ['s1_FA.nii', 's2_FA.nii', 's3_FA.nii']
>>> tbss2.inputs.inputnode.mask_list = ['s1_mask.nii', 's2_mask.nii', 's3_mask.nii']

Expand All @@ -126,13 +128,16 @@ def create_tbss_2_reg(name="tbss_2_reg"):
iterfield=['in_file', 'in_weight'],
name="flirt")

fnirt = pe.MapNode(interface=fsl.FNIRT(fieldcoeff_file=True),
iterfield=['in_file', 'inmask_file', 'affine_file'],
name="fnirt")
# Fnirt the FA image to the target
config_file = os.path.join(os.environ["FSLDIR"],
"etc/flirtsch/FA_2_FMRIB58_1mm.cnf")
fnirt = pe.MapNode(interface=fsl.FNIRT(config_file=config_file,
fieldcoeff_file=True),
iterfield=['in_file', 'inmask_file', 'affine_file'],
name="fnirt")
if fsl.no_fsl():
warn('NO FSL found')
else:
config_file = os.path.join(os.environ["FSLDIR"],
"etc/flirtsch/FA_2_FMRIB58_1mm.cnf")
fnirt.inputs.config_file=config_file

# Define the registration workflow
tbss2 = pe.Workflow(name=name)
Expand Down Expand Up @@ -195,7 +200,10 @@ def create_tbss_3_postreg(name='tbss_3_postreg', estimate_skeleton=True):
applywarp = pe.MapNode(interface=fsl.ApplyWarp(),
iterfield=['in_file', 'field_file'],
name="applywarp")
applywarp.inputs.ref_file = fsl.Info.standard_image("FMRIB58_FA_1mm.nii.gz")
if fsl.no_fsl():
warn('NO FSL found')
else:
applywarp.inputs.ref_file = fsl.Info.standard_image("FMRIB58_FA_1mm.nii.gz")

# Merge the FA files into a 4D file
mergefa = pe.Node(fsl.Merge(dimension="t"),
Expand Down Expand Up @@ -402,7 +410,10 @@ def create_tbss_all(name='tbss_all', estimate_skeleton=True):

tbss1 = create_tbss_1_preproc(name='tbss1')
tbss2 = create_tbss_2_reg(name='tbss2')
tbss2.inputs.inputnode.target = fsl.Info.standard_image("FMRIB58_FA_1mm.nii.gz")
if fsl.no_fsl():
warn('NO FSL found')
else:
tbss2.inputs.inputnode.target = fsl.Info.standard_image("FMRIB58_FA_1mm.nii.gz")
tbss3 = create_tbss_3_postreg(name='tbss3', estimate_skeleton=estimate_skeleton)
tbss4 = create_tbss_4_prestats(name='tbss4')

Expand Down Expand Up @@ -522,7 +533,10 @@ def create_tbss_non_FA(name='tbss_non_FA'):
applywarp = pe.MapNode(interface=fsl.ApplyWarp(),
iterfield=['in_file', 'field_file'],
name="applywarp")
applywarp.inputs.ref_file = fsl.Info.standard_image("FMRIB58_FA_1mm.nii.gz")
if fsl.no_fsl():
warn('NO FSL found')
else:
applywarp.inputs.ref_file = fsl.Info.standard_image("FMRIB58_FA_1mm.nii.gz")
# Merge the non FA files into a 4D file
merge = pe.Node(fsl.Merge(dimension="t"), name="merge")
#merged_file="all_FA.nii.gz"
Expand Down