def setup_infile(tmpdir):
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = str(tmpdir)
tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
open(tmp_infile, 'w')
return (tmp_infile, tmp_dir)
def setup_infile():
global tmp_infile, tmp_dir
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = tempfile.mkdtemp()
tmp_infile = os.path.join(tmp_dir, "foo" + ext)
open(tmp_infile, "w")
return tmp_infile, tmp_dir
def setup_flirt(tmpdir):
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = str(tmpdir)
_, infile = tempfile.mkstemp(suffix=ext, dir=tmp_dir)
_, reffile = tempfile.mkstemp(suffix=ext, dir=tmp_dir)
return (tmp_dir, infile, reffile)
def setup_flirt(tmpdir):
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = str(tmpdir)
_, infile = tempfile.mkstemp(suffix=ext, dir=tmp_dir)
_, reffile = tempfile.mkstemp(suffix=ext, dir=tmp_dir)
return (tmp_dir, infile, reffile)
def create_files_in_directory(request):
func_prev_type = set_output_type(request.param)
testdir = os.path.realpath(mkdtemp())
origdir = os.getcwd()
os.chdir(testdir)
filelist = ['a.nii', 'b.nii']
for f in filelist:
hdr = nb.Nifti1Header()
shape = (3, 3, 3, 4)
hdr.set_data_shape(shape)
img = np.random.random(shape)
nb.save(nb.Nifti1Image(img, np.eye(4), hdr),
os.path.join(testdir, f))
out_ext = Info.output_type_to_ext(Info.output_type())
def fin():
if os.path.exists(testdir):
rmtree(testdir)
set_output_type(func_prev_type)
os.chdir(origdir)
request.addfinalizer(fin)
return (filelist, testdir, out_ext)
def setup_infile():
global tmp_infile, tmp_dir
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = tempfile.mkdtemp()
tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
file(tmp_infile, 'w')
return tmp_infile, tmp_dir
def setup_infile():
global tmp_infile, tmp_dir
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = tempfile.mkdtemp()
tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
open(tmp_infile, 'w')
return tmp_infile, tmp_dir
def setup_infile(tmpdir):
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = str(tmpdir)
tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
open(tmp_infile, 'w')
return (tmp_infile, tmp_dir)
def setup_flirt(tmpdir):
ext = Info.output_type_to_ext(Info.output_type())
infile = tmpdir.join("infile"+ext)
infile.open("w")
reffile = tmpdir.join("reffile"+ext)
reffile.open("w")
return (tmpdir, infile.strpath, reffile.strpath)
def setup_flirt(tmpdir):
ext = Info.output_type_to_ext(Info.output_type())
infile = tmpdir.join("infile" + ext)
infile.open("w")
reffile = tmpdir.join("reffile" + ext)
reffile.open("w")
return (tmpdir, infile.strpath, reffile.strpath)
def setup_infile():
global tmp_infile, tmp_dir, cwd
cwd = os.getcwd()
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = tempfile.mkdtemp()
tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
open(tmp_infile, 'w')
os.chdir(tmp_dir)
return tmp_infile, tmp_dir
def setup_infile():
global tmp_infile, tmp_dir, cwd
cwd = os.getcwd()
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = tempfile.mkdtemp()
tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
file(tmp_infile, 'w')
os.chdir(tmp_dir)
return tmp_infile, tmp_dir
def set_output_type(fsl_output_type):
prev_output_type = os.environ.get('FSLOUTPUTTYPE', None)
if fsl_output_type is not None:
os.environ['FSLOUTPUTTYPE'] = fsl_output_type
elif 'FSLOUTPUTTYPE' in os.environ:
del os.environ['FSLOUTPUTTYPE']
FSLCommand.set_default_output_type(Info.output_type())
return prev_output_type
def set_output_type(fsl_output_type):
prev_output_type = os.environ.get('FSLOUTPUTTYPE', None)
if fsl_output_type is not None:
os.environ['FSLOUTPUTTYPE'] = fsl_output_type
elif 'FSLOUTPUTTYPE' in os.environ:
del os.environ['FSLOUTPUTTYPE']
FSLCommand.set_default_output_type(Info.output_type())
return prev_output_type
def setup_infile(request):
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = tempfile.mkdtemp()
tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
open(tmp_infile, 'w')
def fin():
shutil.rmtree(tmp_dir)
request.addfinalizer(fin)
return (tmp_infile, tmp_dir)
def setup_infile(request):
ext = Info.output_type_to_ext(Info.output_type())
tmp_dir = tempfile.mkdtemp()
tmp_infile = os.path.join(tmp_dir, 'foo' + ext)
open(tmp_infile, 'w')
def fin():
shutil.rmtree(tmp_dir)
request.addfinalizer(fin)
return (tmp_infile, tmp_dir)
def setup_flirt(request):
ext = Info.output_type_to_ext(Info.output_type())
tmpdir = tempfile.mkdtemp()
_, infile = tempfile.mkstemp(suffix=ext, dir=tmpdir)
_, reffile = tempfile.mkstemp(suffix=ext, dir=tmpdir)
def teardown_flirt():
shutil.rmtree(tmpdir)
request.addfinalizer(teardown_flirt)
return (tmpdir, infile, reffile)
def setup_flirt(request):
ext = Info.output_type_to_ext(Info.output_type())
tmpdir = tempfile.mkdtemp()
_, infile = tempfile.mkstemp(suffix=ext, dir=tmpdir)
_, reffile = tempfile.mkstemp(suffix=ext, dir=tmpdir)
def teardown_flirt():
shutil.rmtree(tmpdir)
request.addfinalizer(teardown_flirt)
return (tmpdir, infile, reffile)
def create_files_in_directory_plus_output_type(request, tmpdir):
func_prev_type = set_output_type(request.param)
origdir = tmpdir.chdir()
filelist = ['a.nii', 'b.nii']
nifti_image_files(tmpdir.strpath, filelist, shape=(3,3,3,4))
out_ext = Info.output_type_to_ext(Info.output_type())
def fin():
set_output_type(func_prev_type)
origdir.chdir()
request.addfinalizer(fin)
return (filelist, tmpdir.strpath, out_ext)
def create_files_in_directory_plus_output_type(request, tmpdir):
func_prev_type = set_output_type(request.param)
origdir = tmpdir.chdir()
filelist = ['a.nii', 'b.nii']
nifti_image_files(tmpdir.strpath, filelist, shape=(3, 3, 3, 4))
out_ext = Info.output_type_to_ext(Info.output_type())
def fin():
set_output_type(func_prev_type)
origdir.chdir()
request.addfinalizer(fin)
return (filelist, tmpdir.strpath, out_ext)
def create_files_in_directory():
testdir = os.path.realpath(mkdtemp())
origdir = os.getcwd()
os.chdir(testdir)
filelist = ['a.nii', 'b.nii']
for f in filelist:
hdr = nb.Nifti1Header()
shape = (3, 3, 3, 4)
hdr.set_data_shape(shape)
img = np.random.random(shape)
nb.save(nb.Nifti1Image(img, np.eye(4), hdr), os.path.join(testdir, f))
out_ext = Info.output_type_to_ext(Info.output_type())
return filelist, testdir, origdir, out_ext
def create_files_in_directory():
testdir = os.path.realpath(mkdtemp())
origdir = os.getcwd()
os.chdir(testdir)
filelist = ['a.nii', 'b.nii']
for f in filelist:
hdr = nb.Nifti1Header()
shape = (3, 3, 3, 4)
hdr.set_data_shape(shape)
img = np.random.random(shape)
nb.save(nb.Nifti1Image(img, np.eye(4), hdr),
os.path.join(testdir, f))
out_ext = Info.output_type_to_ext(Info.output_type())
return filelist, testdir, origdir, out_ext
def setup_infile(tmpdir):
ext = Info.output_type_to_ext(Info.output_type())
tmp_infile = tmpdir.join('foo' + ext)
tmp_infile.open("w")
return (tmp_infile.strpath, tmpdir.strpath)
def setup_infile(tmpdir):
ext = Info.output_type_to_ext(Info.output_type())
tmp_infile = tmpdir.join('foo' + ext)
tmp_infile.open("w")
return (tmp_infile.strpath, tmpdir.strpath)
