def test_changedt(create_files_in_directory_plus_output_type):
files, testdir, out_ext = create_files_in_directory_plus_output_type
# Get some fslmaths
cdt = fsl.ChangeDataType()
# Test that we got what we wanted
assert cdt.cmd == "fslmaths"
# Test that it needs a mandatory argument
with pytest.raises(ValueError):
cdt.run()
# Set an in file and out file
cdt.inputs.in_file = "a.nii"
cdt.inputs.out_file = "b.nii"
# But it still shouldn't work
with pytest.raises(ValueError):
cdt.run()
# Now test that we can set the various data types
dtypes = ["float", "char", "int", "short", "double", "input"]
cmdline = "fslmaths a.nii b.nii -odt {}"
for dtype in dtypes:
foo = fsl.MathsCommand(in_file="a.nii",
out_file="b.nii",
output_datatype=dtype)
assert foo.cmdline == cmdline.format(dtype)
def test_changedt(fsl_output_type=None):
prev_type = set_output_type(fsl_output_type)
files, testdir, origdir, out_ext = create_files_in_directory()
# Get some fslmaths
cdt = fsl.ChangeDataType()
# Test that we got what we wanted
yield assert_equal, cdt.cmd, "fslmaths"
# Test that it needs a mandatory argument
yield assert_raises, ValueError, cdt.run
# Set an in file and out file
cdt.inputs.in_file = "a.nii"
cdt.inputs.out_file = "b.nii"
# But it still shouldn't work
yield assert_raises, ValueError, cdt.run
# Now test that we can set the various data types
dtypes = ["float", "char", "int", "short", "double", "input"]
cmdline = "fslmaths a.nii b.nii -odt %s"
for dtype in dtypes:
foo = fsl.MathsCommand(in_file="a.nii", out_file="b.nii", output_datatype=dtype)
yield assert_equal, foo.cmdline, cmdline % dtype
# Clean up our mess
clean_directory(testdir, origdir)
set_output_type(prev_type)
def test_maths_base(fsl_output_type=None):
prev_type = set_output_type(fsl_output_type)
files, testdir, origdir, out_ext = create_files_in_directory()
# Get some fslmaths
maths = fsl.MathsCommand()
# Test that we got what we wanted
yield assert_equal, maths.cmd, "fslmaths"
# Test that it needs a mandatory argument
yield assert_raises, ValueError, maths.run
# Set an in file
maths.inputs.in_file = "a.nii"
out_file = "a_maths%s" % out_ext
# Now test the most basic command line
yield assert_equal, maths.cmdline, "fslmaths a.nii %s" % os.path.join(
testdir, out_file)
# Now test that we can set the various data types
dtypes = ["float", "char", "int", "short", "double", "input"]
int_cmdline = "fslmaths -dt %s a.nii " + os.path.join(testdir, out_file)
out_cmdline = "fslmaths a.nii " + os.path.join(testdir,
out_file) + " -odt %s"
duo_cmdline = "fslmaths -dt %s a.nii " + os.path.join(
testdir, out_file) + " -odt %s"
for dtype in dtypes:
foo = fsl.MathsCommand(in_file="a.nii", internal_datatype=dtype)
yield assert_equal, foo.cmdline, int_cmdline % dtype
bar = fsl.MathsCommand(in_file="a.nii", output_datatype=dtype)
yield assert_equal, bar.cmdline, out_cmdline % dtype
foobar = fsl.MathsCommand(in_file="a.nii",
internal_datatype=dtype,
output_datatype=dtype)
yield assert_equal, foobar.cmdline, duo_cmdline % (dtype, dtype)
# Test that we can ask for an outfile name
maths.inputs.out_file = "b.nii"
yield assert_equal, maths.cmdline, "fslmaths a.nii b.nii"
# Clean up our mess
clean_directory(testdir, origdir)
set_output_type(prev_type)
def test_maths_base(create_files_in_directory_plus_output_type):
files, testdir, out_ext = create_files_in_directory_plus_output_type
# Get some fslmaths
maths = fsl.MathsCommand()
# Test that we got what we wanted
assert maths.cmd == "fslmaths"
# Test that it needs a mandatory argument
with pytest.raises(ValueError):
maths.run()
# Set an in file
maths.inputs.in_file = "a.nii"
out_file = "a_maths{}".format(out_ext)
# Now test the most basic command line
assert maths.cmdline == "fslmaths a.nii {}".format(
os.path.join(testdir, out_file))
# Now test that we can set the various data types
dtypes = ["float", "char", "int", "short", "double", "input"]
int_cmdline = "fslmaths -dt {} a.nii " + os.path.join(testdir, out_file)
out_cmdline = "fslmaths a.nii " + os.path.join(testdir,
out_file) + " -odt {}"
duo_cmdline = ("fslmaths -dt {} a.nii " + os.path.join(testdir, out_file) +
" -odt {}")
for dtype in dtypes:
foo = fsl.MathsCommand(in_file="a.nii", internal_datatype=dtype)
assert foo.cmdline == int_cmdline.format(dtype)
bar = fsl.MathsCommand(in_file="a.nii", output_datatype=dtype)
assert bar.cmdline == out_cmdline.format(dtype)
foobar = fsl.MathsCommand(in_file="a.nii",
internal_datatype=dtype,
output_datatype=dtype)
assert foobar.cmdline == duo_cmdline.format(dtype, dtype)
# Test that we can ask for an outfile name
maths.inputs.out_file = "b.nii"
assert maths.cmdline == "fslmaths a.nii b.nii"
def qap_mask_workflow(workflow, resource_pool, config):
import os
import sys
import nipype.interfaces.io as nio
import nipype.pipeline.engine as pe
import nipype.interfaces.utility as niu
import nipype.interfaces.fsl.maths as fsl
from nipype.interfaces.fsl.base import Info
from qap_workflows_utils import select_thresh, \
slice_head_mask
from workflow_utils import check_input_resources, \
check_config_settings
# check_input_resources(resource_pool, 'anatomical_reorient')
# check_input_resources(resource_pool, 'ants_affine_xfm')
if 'template_skull_for_anat' not in config:
config['template_skull_for_anat'] = Info.standard_image(
'MNI152_T1_2mm.nii.gz')
check_config_settings(config, 'template_skull_for_anat')
if 'flirt_affine_xfm' not in resource_pool.keys():
from anatomical_preproc import flirt_anatomical_linear_registration
workflow, resource_pool = \
flirt_anatomical_linear_registration(workflow, resource_pool,
config)
if 'anatomical_reorient' not in resource_pool.keys():
from anatomical_preproc import anatomical_reorient_workflow
workflow, resource_pool = \
anatomical_reorient_workflow(workflow, resource_pool, config)
select_thresh = pe.Node(niu.Function(input_names=['input_skull'],
output_names=['thresh_out'],
function=select_thresh),
name='qap_headmask_select_thresh',
iterfield=['input_skull'])
mask_skull = pe.Node(fsl.Threshold(args='-bin'),
name='qap_headmask_thresh')
dilate_node = pe.Node(
fsl.MathsCommand(args='-dilM -dilM -dilM -dilM -dilM -dilM'),
name='qap_headmask_dilate')
erode_node = pe.Node(
fsl.MathsCommand(args='-eroF -eroF -eroF -eroF -eroF -eroF'),
name='qap_headmask_erode')
slice_head_mask = pe.Node(niu.Function(
input_names=['infile', 'transform', 'standard'],
output_names=['outfile_path'],
function=slice_head_mask),
name='qap_headmask_slice_head_mask')
combine_masks = pe.Node(fsl.BinaryMaths(operation='add', args='-bin'),
name='qap_headmask_combine_masks')
if len(resource_pool['anatomical_reorient']) == 2:
node, out_file = resource_pool['anatomical_reorient']
workflow.connect([(node, select_thresh, [(out_file, 'input_skull')]),
(node, mask_skull, [(out_file, 'in_file')]),
(node, slice_head_mask, [(out_file, 'infile')])])
else:
select_thresh.inputs.input_skull = resource_pool['anatomical_reorient']
mask_skull.inputs.in_file = resource_pool['anatomical_reorient']
# convert_fsl_xfm.inputs.infile =
# resource_pool['anatomical_reorient']
slice_head_mask.inputs.infile = resource_pool['anatomical_reorient']
if len(resource_pool['flirt_affine_xfm']) == 2:
node, out_file = resource_pool['flirt_affine_xfm']
workflow.connect(node, out_file, slice_head_mask, 'transform')
else:
slice_head_mask.inputs.transform = resource_pool['flirt_affine_xfm']
# convert_fsl_xfm.inputs.standard = config['template_skull_for_anat']
slice_head_mask.inputs.standard = config['template_skull_for_anat']
workflow.connect([
(select_thresh, mask_skull, [('thresh_out', 'thresh')]),
# (convert_fsl_xfm, slice_head_mask, [('converted_xfm', 'transform')])
(mask_skull, dilate_node, [('out_file', 'in_file')]),
(dilate_node, erode_node, [('out_file', 'in_file')]),
(erode_node, combine_masks, [('out_file', 'in_file')]),
(slice_head_mask, combine_masks, [('outfile_path', 'operand_file')])
])
resource_pool['qap_head_mask'] = (combine_masks, 'out_file')
return workflow, resource_pool
