Skip to content

enh: allow uses_qform in FLIRT, ApplyXFM interfaces #1875

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 17 commits into from
Mar 18, 2017
Merged

enh: allow uses_qform in FLIRT, ApplyXFM interfaces #1875

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
17 commits
Select commit Hold shift + click to select a range
67b9d73
fix: auto test
mgxd Feb 24, 2017
a320cc5
fix: allow uses_qform for apply_xfm matrix
mgxd Mar 9, 2017
1156e3c
tst: updated flirt test
mgxd Mar 9, 2017
50e1dfc
tst: updated autotests
mgxd Mar 9, 2017
8e65903
Merge branch 'master' of https://github.com/nipy/nipype
mgxd Mar 10, 2017
35a9b0b
Merge branch 'fix/flirt_xfm' of github.com:mgxd/nipype into fix/flirt…
mgxd Mar 10, 2017
0de0296
fix: incorrect check
mgxd Mar 10, 2017
2be737d
fix: missing args in test cmdline
mgxd Mar 10, 2017
9d1b661
fix: string joining
mgxd Mar 10, 2017
0ee9b72
fix: remove deprecated auto test
mgxd Mar 13, 2017
ba15d5f
fix: autotest conflict
mgxd Mar 13, 2017
2537030
fix: use deepcopy
mgxd Mar 13, 2017
7d5a161
Merge branch 'master' of https://github.com/nipy/nipype into fix/flir…
mgxd Mar 13, 2017
b639ef5
Merge branch 'master' of https://github.com/nipy/nipype into fix/flir…
mgxd Mar 14, 2017
877f64e
Merge branch 'master' of https://github.com/nipy/nipype into fix/flir…
mgxd Mar 15, 2017
4bfea53
fix: autotest causing fail
mgxd Mar 15, 2017
f266c83
Merge branch 'fix/flirt_xfm' of github.com:mgxd/nipype into fix/flirt…
mgxd Mar 15, 2017
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
14 changes: 10 additions & 4 deletions nipype/interfaces/fsl/preprocess.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -400,8 +400,9 @@ class FLIRTInputSpec(FSLCommandInputSpec):
name_template='%s_flirt.log', desc='output log')
in_matrix_file = File(argstr='-init %s', desc='input 4x4 affine matrix')
apply_xfm = traits.Bool(
argstr='-applyxfm', requires=['in_matrix_file'],
desc='apply transformation supplied by in_matrix_file')
argstr='-applyxfm',
desc=('apply transformation supplied by in_matrix_file or uses_qform to'
' use the affine matrix stored in the reference header'))
apply_isoxfm = traits.Float(
argstr='-applyisoxfm %f', xor=['apply_xfm'],
desc='as applyxfm but forces isotropic resampling')
Expand Down Expand Up @@ -561,13 +562,18 @@ def _parse_inputs(self, skip=None):
if isdefined(self.inputs.save_log) and self.inputs.save_log:
if not isdefined(self.inputs.verbose) or self.inputs.verbose == 0:
self.inputs.verbose = 1
if isdefined(self.inputs.apply_xfm) and self.inputs.apply_xfm:
if not self.inputs.in_matrix_file and not self.inputs.uses_qform:
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

shouldn't this be if not isdefined(self.inputs.in_matrix_file) and not (isdefined(self.inputs.uses_qform) and not self.inputs.uses_qform)

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

is isdefined necessary in this case? I added a test for both cases of using apply_xfm

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

what if someone sets them to Undefined

In [1]: from traits.api import Undefined

In [2]: not Undefined
Out[2]: False

Copy link
Member

@satra satra Mar 17, 2017 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

however the check with not appears to work now

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more. 

In [20]: foo.inputs.wmnorms = Undefined

In [21]: not foo.inputs.wmnorms
Out[21]: True

haven't figured out why yet

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@satra should this be changed?

raise RuntimeError('Argument apply_xfm requires in_matrix_file '
'or uses_qform arguments to run')
skip.append('save_log')
return super(FLIRT, self)._parse_inputs(skip=skip)

class ApplyXFMInputSpec(FLIRTInputSpec):
apply_xfm = traits.Bool(
True, argstr='-applyxfm', requires=['in_matrix_file'],
desc='apply transformation supplied by in_matrix_file',
True, argstr='-applyxfm',
desc=('apply transformation supplied by in_matrix_file or uses_qform to'
' use the affine matrix stored in the reference header'),
usedefault=True)


Expand Down
1 change: 0 additions & 1 deletion nipype/interfaces/fsl/tests/test_auto_ApplyXFM.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@ def test_ApplyXFM_inputs():
xor=['apply_xfm'],
),
apply_xfm=dict(argstr='-applyxfm',
requires=['in_matrix_file'],
usedefault=True,
),
args=dict(argstr='%s',
Expand Down
164 changes: 0 additions & 164 deletions nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py
View file
Open in desktop

This file was deleted.

1 change: 0 additions & 1 deletion nipype/interfaces/fsl/tests/test_auto_FLIRT.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@ def test_FLIRT_inputs():
xor=['apply_xfm'],
),
apply_xfm=dict(argstr='-applyxfm',
requires=['in_matrix_file'],
),
args=dict(argstr='%s',
),
Expand Down
20 changes: 18 additions & 2 deletions nipype/interfaces/fsl/tests/test_preprocess.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@

import os
import tempfile
from copy import deepcopy

import pytest
from nipype.utils.filemanip import split_filename, filename_to_list
Expand Down Expand Up @@ -220,12 +221,13 @@ def test_flirt(setup_flirt):
flirter = fsl.FLIRT()
# infile not specified
with pytest.raises(ValueError):
flirter.run()
flirter.cmdline
flirter.inputs.in_file = infile
# reference not specified
with pytest.raises(ValueError):
flirter.run()
flirter.cmdline
flirter.inputs.reference = reffile

# Generate outfile and outmatrix
pth, fname, ext = split_filename(infile)
outfile = fsl_name(flirter, '%s_flirt' % fname)
Expand All @@ -234,6 +236,20 @@ def test_flirt(setup_flirt):
outfile, outmat)
assert flirter.cmdline == realcmd

# test apply_xfm option
axfm = deepcopy(flirter)
axfm.inputs.apply_xfm = True
# in_matrix_file or uses_qform must be defined
with pytest.raises(RuntimeError): axfm.cmdline
axfm2 = deepcopy(axfm)
# test uses_qform
axfm.inputs.uses_qform = True
assert axfm.cmdline == (realcmd + ' -applyxfm -usesqform')
# test in_matrix_file
axfm2.inputs.in_matrix_file = reffile
assert axfm2.cmdline == (realcmd + ' -applyxfm -init %s' % reffile)


_, tmpfile = tempfile.mkstemp(suffix='.nii', dir=tmpdir)
# Loop over all inputs, set a reasonable value and make sure the
# cmdline is updated correctly.
Expand Down