def test_binarymaths(create_files_in_directory):
files, testdir, out_ext = create_files_in_directory
# Get the command
maths = fsl.BinaryMaths(in_file="a.nii", out_file="c.nii")
# Test the underlying command
assert maths.cmd == "fslmaths"
# Test that it fails without an operation an
with pytest.raises(ValueError):
maths.run()
# Test the different operations
ops = ["add", "sub", "mul", "div", "rem", "min", "max"]
operands = ["b.nii", -2, -0.5, 0, .123456, np.pi, 500]
for op in ops:
for ent in operands:
maths = fsl.BinaryMaths(in_file="a.nii", out_file="c.nii", operation=op)
if ent == "b.nii":
maths.inputs.operand_file = ent
assert maths.cmdline == "fslmaths a.nii -%s b.nii c.nii" % op
else:
maths.inputs.operand_value = ent
assert maths.cmdline == "fslmaths a.nii -%s %.8f c.nii" % (op, ent)
# Test that we don't need to ask for an out file
for op in ops:
maths = fsl.BinaryMaths(in_file="a.nii", operation=op, operand_file="b.nii")
assert maths.cmdline == "fslmaths a.nii -%s b.nii %s" % (op, os.path.join(testdir, "a_maths%s" % out_ext))
def test_binarymaths(fsl_output_type=None):
prev_type = set_output_type(fsl_output_type)
files, testdir, origdir, out_ext = create_files_in_directory()
# Get the command
maths = fsl.BinaryMaths(in_file="a.nii", out_file="c.nii")
# Test the underlying command
yield assert_equal, maths.cmd, "fslmaths"
# Test that it fails without an operation an
yield assert_raises, ValueError, maths.run
# Test the different operations
ops = ["add", "sub", "mul", "div", "rem", "min", "max"]
operands = ["b.nii", -2, -0.5, 0, .123456, np.pi, 500]
for op in ops:
for ent in operands:
maths = fsl.BinaryMaths(in_file="a.nii", out_file="c.nii", operation=op)
if ent == "b.nii":
maths.inputs.operand_file = ent
yield assert_equal, maths.cmdline, "fslmaths a.nii -%s b.nii c.nii" % op
else:
maths.inputs.operand_value = ent
yield assert_equal, maths.cmdline, "fslmaths a.nii -%s %.8f c.nii" % (op, ent)
# Test that we don't need to ask for an out file
for op in ops:
maths = fsl.BinaryMaths(in_file="a.nii", operation=op, operand_file="b.nii")
yield assert_equal, maths.cmdline, "fslmaths a.nii -%s b.nii %s" % (op, os.path.join(testdir, "a_maths%s" % out_ext))
# Clean up our mess
clean_directory(testdir, origdir)
set_output_type(prev_type)
def convert_2_cbf(savgfl, denom):
jnk, flnm = os.path.split(savgfl)
subn, jnk = flnm.split('_sur')
cbf = os.path.join(output_dir, '%s_cbf' % (subn))
l = 0.9 #blood/tissue water partition coefficient, in g/ml
num = os.path.join(output_dir, 'd_num')
mul = math.BinaryMaths()
mul.inputs.in_file = savgfl
mul.inputs.operand_value = l
mul.inputs.operation = 'mul'
mul.inputs.out_file = num
mul.inputs.output_type = 'NIFTI_GZ'
mul.inputs.ignore_exception = True
mul.run()
num = num + '.nii.gz'
immth = math.BinaryMaths()
immth.inputs.in_file = num
immth.inputs.operand_file = denom
immth.inputs.operation = 'div'
immth.inputs.out_file = cbf
immth.inputs.output_type = 'NIFTI_GZ'
immth.inputs.ignore_exception = True
immth.run()
cbf = cbf + '.nii.gz'
os.system('rm %s' % (os.path.join(output_dir, 'd_*.nii.gz')))
return cbf
def surround_avg(scan1, scan2):
jnk, flnm = os.path.split(scan1)
subn, jnk = flnm.split('_sess')
savgfl = os.path.join(output_dir, '%s_surroundavg' % (subn))
divisor = nib.load(scan1).get_data().shape[3]
immth = math.BinaryMaths()
immth.inputs.in_file = scan1
immth.inputs.operand_file = scan2
immth.inputs.operation = 'sub'
immth.inputs.out_file = savgfl
immth.inputs.output_type = 'NIFTI_GZ'
immth.inputs.ignore_exception = True
immth.run()
savgfl = savgfl + '.nii.gz'
return savgfl
def define_denominator(ctrl_mean):
alpha = 0.85 # assumed inversion efficiency of pCASL
T1b = 1.664 #T1 of blood, in s
w = 0.900 # post labeling delay in s
tau = 1.5 # labeling duration in s
e = 2.71828 # euler's number
term3 = e**((-w) / T1b) - e**((-(tau + w)) / T1b)
factor = (2 * alpha) * T1b * term3
denom = os.path.join(output_dir, 'denom')
mul = math.BinaryMaths()
mul.inputs.in_file = ctrl_mean
mul.inputs.operand_value = factor
mul.inputs.operation = 'mul'
mul.inputs.out_file = denom
mul.inputs.output_type = 'NIFTI_GZ'
mul.inputs.ignore_exception = True
mul.run()
denom = denom + '.nii.gz'
return denom
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