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Merge pull request #349 from cindeem/nonbatch-spm-coreg
Nonbatch spm coreg
2 parents bc203b9 + 10bf980 commit 6d253a2

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‎doc/devel/matlab_interface_devel.rst

Lines changed: 87 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -7,6 +7,10 @@ How to wrap a MATLAB script
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This is minimal script for wrapping MATLAB code. You should replace the MATLAB
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code template, and define approriate inputs and outputs.
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Example 1
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+++++++++
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.. testcode::
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from nipype.interfaces.matlab import MatlabCommand
@@ -35,17 +39,95 @@ code template, and define approriate inputs and outputs.
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exit;
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""").substitute(d)
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# mfile = True will create an .m file with your script and executed. Alternatively
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# mfile can be set to False which will cause the matlab code to be passed
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# as a commandline argument to the matlab executable (without creating any files).
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# This, however, is less reliable and harder to debug (code will be reduced to
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# mfile = True will create an .m file with your script and executed.
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# Alternatively
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# mfile can be set to False which will cause the matlab code to be
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# passed
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# as a commandline argument to the matlab executable
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# (without creating any files).
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# This, however, is less reliable and harder to debug
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# (code will be reduced to
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# a single line and stripped of any comments).
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mlab = MatlabCommand(script=script, mfile=True)
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result = mlab.run()
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result = mlab.run()
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return result.runtime
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def _list_outputs(self):
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outputs = self._outputs().get()
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outputs['out_file'] = os.path.abspath(self.inputs.out_file)
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return outputs
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Example 2
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+++++++++
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By subclassing **MatlabCommand** for your main class, and **MatlabInputSpec** for your input and output spec, you gain access to some useful MATLAB hooks
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.. testcode::
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import os
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from nipype.interfaces.base import File, traits
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from nipype.interfaces.matlab import MatlabCommand, MatlabInputSpec
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class HelloWorldInputSpec( MatlabInputSpec):
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name = traits.Str( mandatory = True,
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desc = 'Name of person to say hello to')
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class HelloWorldOutputSpec( MatlabInputSpec):
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matlab_output = traits.Str( )
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class HelloWorld( MatlabCommand):
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""" Basic Hello World that displays Hello <name> in MATLAB
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Returns
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-------
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matlab_output : capture of matlab output which may be
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parsed by user to get computation results
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Examples
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--------
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>>> hello = HelloWorld(matlab_cmd = 'mymatlab')
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>>> hello.inputs.name = 'Monty'
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>>> hello.inputs.mfile = True #creates mfile
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>>> hello.inputs.paths = '/path/to/matlab/toolbox'
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>>> hello.inputs.script_file = 'helloworld_pyscript.m'
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>>> out = hello.run()
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>>> out.outputs['matlab_output']
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"""
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input_spec = HelloWorldInputSpec
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output_spec = HelloWorldOutputSpec
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def _my_script(self):
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"""This is where you implement your script"""
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script = """
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disp('Hello %s Python')
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two = 1 + 1
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"""%(self.inputs.name)
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return script
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def run(self, **inputs):
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## inject your script
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self.inputs.script = self._my_script()
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results = super(MatlabCommand, self).run( **inputs)
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stdout = results.runtime.stdout
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# attach stdout to outputs to access matlab results
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results.outputs.matlab_output = stdout
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return results
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def _list_outputs(self):
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outputs = self._outputs().get()
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return outputs
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‎nipype/interfaces/spm/tests/test_utils.py

Lines changed: 61 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,61 @@
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# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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# vi: set ft=python sts=4 ts=4 sw=4 et:
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import os
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from nipype.testing import (assert_equal, assert_false,assert_raises,
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assert_true, skipif, example_data)
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from nipype.interfaces.spm import no_spm
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import nipype.interfaces.spm.utils as spmu
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from nipype.interfaces.base import isdefined
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from nipype.utils.filemanip import split_filename, fname_presuffix
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from nipype.interfaces.base import TraitError
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def test_coreg():
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moving = example_data(infile = 'functional.nii')
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target = example_data(infile = 'T1.nii')
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mat = example_data(infile = 'trans.mat')
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coreg = spmu.CalcCoregAffine(matlab_cmd = 'mymatlab')
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coreg.inputs.target = target
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assert_equal(coreg.inputs.matlab_cmd, 'mymatlab')
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coreg.inputs.moving = moving
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assert_equal( isdefined(coreg.inputs.mat),False)
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pth, mov, _ = split_filename(moving)
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_, tgt, _ = split_filename(target)
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mat = os.path.join(pth, '%s_to_%s.mat'%(mov,tgt))
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invmat = fname_presuffix(mat, prefix = 'inverse_')
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scrpt = coreg._make_matlab_command(None)
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assert_equal(coreg.inputs.mat, mat)
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assert_equal( coreg.inputs.invmat, invmat)
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def test_apply_transform():
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moving = example_data(infile = 'functional.nii')
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mat = example_data(infile = 'trans.mat')
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applymat = spmu.ApplyTransform(matlab_cmd = 'mymatlab')
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assert_equal( applymat.inputs.matlab_cmd, 'mymatlab' )
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applymat.inputs.in_file = moving
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applymat.inputs.mat = mat
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scrpt = applymat._make_matlab_command(None)
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expected = 'img_space = spm_get_space(infile);'
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assert_equal( expected in scrpt, True)
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expected = 'spm_get_space(infile, transform.M * img_space);'
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assert_equal(expected in scrpt, True)
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def test_reslice():
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moving = example_data(infile = 'functional.nii')
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space_defining = example_data(infile = 'T1.nii')
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reslice = spmu.Reslice(matlab_cmd = 'mymatlab_version')
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assert_equal( reslice.inputs.matlab_cmd, 'mymatlab_version')
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reslice.inputs.in_file = moving
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reslice.inputs.space_defining = space_defining
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assert_equal( reslice.inputs.interp, 0)
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assert_raises(TraitError,reslice.inputs.trait_set,interp = 'nearest')
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assert_raises(TraitError, reslice.inputs.trait_set, interp = 10)
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reslice.inputs.interp = 1
54+
script = reslice._make_matlab_command(None)
55+
outfile = fname_presuffix(moving, prefix='r')
56+
assert_equal(reslice.inputs.out_file, outfile)
57+
expected = '\nflags.mean=0;\nflags.which=1;\nflags.mask=0;'
58+
assert_equal(expected in script.replace(' ',''), True)
59+
expected_interp = 'flags.interp = 1;\n'
60+
assert_equal(expected_interp in script, True)
61+
assert_equal('spm_reslice(invols, flags);' in script, True)

‎nipype/interfaces/spm/utils.py

Lines changed: 181 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,11 @@
1-
from nipype.interfaces.spm.base import SPMCommandInputSpec, SPMCommand
2-
from nipype.interfaces.base import File
3-
from nipype.utils.filemanip import split_filename
1+
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
2+
# vi: set ft=python sts=4 ts=4 sw=4 et:
3+
from nipype.interfaces.spm.base import SPMCommandInputSpec, SPMCommand, Info
4+
from nipype.interfaces.matlab import MatlabCommand
5+
from nipype.interfaces.base import (TraitedSpec, BaseInterface,
6+
BaseInterfaceInputSpec, isdefined)
7+
from nipype.interfaces.base import File, traits
8+
from nipype.utils.filemanip import split_filename, fname_presuffix
49
import os
510

611
class Analyze2niiInputSpec(SPMCommandInputSpec):
@@ -28,3 +33,176 @@ def _list_outputs(self):
2833
outputs = self._outputs().get()
2934
outputs['nifti_file'] = self.output_name
3035
return outputs
36+
37+
class CalcCoregAffineInputSpec(SPMCommandInputSpec):
38+
target = File( exists = True, mandatory = True,
39+
desc = 'target for generating affine transform')
40+
moving = File( exists = True, mandatory = True,
41+
desc = 'volume transform can be applied to register with target')
42+
mat = File( desc = 'Filename used to store affine matrix')
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invmat = File( desc = 'Filename used to store inverse affine matrix')
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46+
class CalcCoregAffineOutputSpec(SPMCommandInputSpec):
47+
mat = File(exists = True, desc = 'Matlab file holding transform')
48+
invmat = File( desc = 'Matlab file holding inverse transform')
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50+
51+
class CalcCoregAffine(SPMCommand):
52+
""" Uses SPM (spm_coreg) to calculate the transform mapping
53+
moving to target. Saves Transform in mat (matlab binary file)
54+
Also saves inverse transform
55+
56+
Examples
57+
--------
58+
59+
>>> import nipype.interfaces.spm.utils as spmu
60+
>>> coreg = spmu.CalcCoregAffine(matlab_cmd='matlab-spm8')
61+
>>> coreg.inputs.target = 'structural.nii'
62+
>>> coreg.inputs.moving = 'functional.nii'
63+
>>> coreg.inputs.mat = 'func_to_struct.mat'
64+
>>> coreg.run() # doctest: +SKIP
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66+
Notes
67+
-----
68+
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* the output file mat is saves as a matlab binary file
70+
* calculating the transforms does NOT change either input image
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it does not **move** the moving image, only calculates the transform
72+
that can be used to move it
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"""
74+
75+
input_spec = CalcCoregAffineInputSpec
76+
output_spec = CalcCoregAffineOutputSpec
77+
78+
def _make_inv_file(self):
79+
""" makes filename to hold inverse transform if not specified"""
80+
invmat = fname_presuffix(self.inputs.mat, prefix = 'inverse_')
81+
return invmat
82+
83+
def _make_mat_file(self):
84+
""" makes name for matfile if doesn exist"""
85+
pth, mv, _ = split_filename(self.inputs.moving)
86+
_, tgt, _ = split_filename(self.inputs.target)
87+
mat = os.path.join(pth, '%s_to_%s.mat'%(mv,tgt))
88+
return mat
89+
90+
def _make_matlab_command(self, _):
91+
"""checks for SPM, generates script"""
92+
if not isdefined(self.inputs.mat):
93+
self.inputs.mat = self._make_mat_file()
94+
if not isdefined(self.inputs.invmat):
95+
self.inputs.invmat = self._make_inv_file()
96+
script = """
97+
target = '%s';
98+
moving = '%s';
99+
targetv = spm_vol(target);
100+
movingv = spm_vol(moving);
101+
x = spm_coreg(movingv, targetv);
102+
M = spm_matrix(x(:)');
103+
save('%s' , 'M' );
104+
M = inv(spm_matrix(x(:)'));
105+
save('%s','M')
106+
"""%(self.inputs.target,
107+
self.inputs.moving,
108+
self.inputs.mat,
109+
self.inputs.invmat)
110+
return script
111+
112+
def _list_outputs(self):
113+
outputs = self._outputs().get()
114+
outputs['mat'] = os.path.abspath(self.inputs.mat)
115+
outputs['invmat'] = os.path.abspath(self.inputs.invmat)
116+
return outputs
117+
118+
class ApplyTransformInputSpec(SPMCommandInputSpec):
119+
in_file = File( exists = True, mandatory = True,
120+
desc='file to apply transform to, (only updates header)')
121+
mat = File( exists = True, mandatory = True,
122+
desc='file holding transform to apply')
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class ApplyTransformOutputSpec(SPMCommandInputSpec):
126+
out_file = File(exists = True, desc = 'File with updated header')
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class ApplyTransform(SPMCommand):
130+
""" Uses spm to apply transform stored in a .mat file to given file
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Examples
133+
--------
134+
135+
>>> import nipype.interfaces.spm.utils as spmu
136+
>>> applymat = spmu.ApplyTransform(matlab_cmd='matlab-spm8')
137+
>>> applymat.inputs.in_file = 'functional.nii'
138+
>>> applymat.inputs.mat = 'func_to_struct.mat'
139+
>>> applymat.run() # doctest: +SKIP
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Notes
142+
-----
143+
CHANGES YOUR INPUT FILE (applies transform by updating the header)
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"""
145+
input_spec = ApplyTransformInputSpec
146+
output_spec = ApplyTransformOutputSpec
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148+
def _make_matlab_command(self, _):
149+
"""checks for SPM, generates script"""
150+
script = """
151+
infile = '%s';
152+
transform = load('%s');
153+
img_space = spm_get_space(infile);
154+
spm_get_space(infile, transform.M * img_space);
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"""%(self.inputs.in_file,
156+
self.inputs.mat)
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return script
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def _list_outputs(self):
160+
outputs = self._outputs().get()
161+
outputs['out_file'] = os.path.abspath(self.inputs.mat)
162+
return outputs
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class ResliceInputSpec(SPMCommandInputSpec):
165+
in_file = File( exists = True, mandatory=True,
166+
desc='file to apply transform to, (only updates header)')
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space_defining = File ( exists = True, mandatory = True,
168+
desc = 'Volume defining space to slice in_file into')
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interp = traits.Range(low = 0, high = 7, usedefault = True,
171+
desc='degree of b-spline used for interpolation'\
172+
'0 is nearest neighbor (default)')
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out_file = File(desc = 'Optional file to save resliced volume')
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class ResliceOutputSpec(SPMCommandInputSpec):
178+
out_file = File( exists = True, desc = 'resliced volume')
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class Reslice(SPMCommand):
181+
""" uses spm_reslice to resample in_file into space of space_defining"""
182+
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input_spec = ResliceInputSpec
184+
output_spec = ResliceOutputSpec
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186+
def _make_matlab_command(self, _):
187+
""" generates script"""
188+
if not isdefined(self.inputs.out_file):
189+
self.inputs.out_file = fname_presuffix(self.inputs.in_file,
190+
prefix = 'r')
191+
script = """
192+
flags.mean = 0;
193+
flags.which = 1;
194+
flags.mask = 0;
195+
flags.interp = %d;
196+
infiles = strvcat(\'%s\', \'%s\');
197+
invols = spm_vol(infiles);
198+
spm_reslice(invols, flags);
199+
"""%(self.inputs.interp,
200+
self.inputs.space_defining,
201+
self.inputs.in_file)
202+
return script
203+
204+
def _list_outputs(self):
205+
outputs = self._outputs().get()
206+
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
207+
return outputs
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