def test_seg_em():
# Create a reg_aladin object
test_node = FitDwi()
# Check if the command is properly defined
yield assert_equal, test_node.cmd, get_custom_path('fit_dwi')
# Assign some input data
in_file = example_data('diffusion.nii')
bval_file = example_data('bvals')
bvec_file = example_data('bvecs')
test_node.inputs.source_file = in_file
test_node.inputs.bval_file = bval_file
test_node.inputs.bvec_file = bvec_file
cmd_tmp = '{cmd} -bval {bval} -bvec {bvec} -famap dwifit__famap -mcmap \
dwifit__mcmap -mdmap dwifit__mdmap -res dwifit__resmap -rgbmap dwifit__rgbmap \
-source {in_file} -syn dwifit__syn -tenmap2 dwifit__tenmap2 -v1map \
dwifit__v1map'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_dwi'),
in_file=in_file,
bval=bval_file,
bvec=bvec_file)
yield assert_equal, test_node.cmdline, expected_cmd
def test_fit_asl():
""" Testing FitAsl interface."""
# Create the test node
fit_asl = FitAsl()
# Check if the command is properly defined
assert fit_asl.cmd == get_custom_path('fit_asl')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
fit_asl.run()
# Tests on the interface:
# Runs cbf fitting assuming all tissue is GM!
in_file = example_data('asl.nii.gz')
fit_asl.inputs.source_file = in_file
cmd_tmp = '{cmd} -source {in_file} -cbf {cbf} -error {error} -syn {syn}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_asl'),
in_file=in_file,
cbf='asl_cbf.nii.gz',
error='asl_error.nii.gz',
syn='asl_syn.nii.gz',
)
assert fit_asl.cmdline == expected_cmd
# Runs cbf fitting using IR/SR T1 data to estimate the local T1 and uses
# the segmentation data to fit tissue specific blood flow parameters
# (lambda,transit times,T1)
fit_asl2 = FitAsl(sig=True)
in_file = example_data('asl.nii.gz')
t1map = example_data('T1map.nii.gz')
seg = example_data('segmentation0.nii.gz')
fit_asl2.inputs.source_file = in_file
fit_asl2.inputs.t1map = t1map
fit_asl2.inputs.seg = seg
cmd_tmp = '{cmd} -source {in_file} -cbf {cbf} -error {error} \
-seg {seg} -sig -syn {syn} -t1map {t1map}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_asl'),
in_file=in_file,
t1map=t1map,
seg=seg,
cbf='asl_cbf.nii.gz',
error='asl_error.nii.gz',
syn='asl_syn.nii.gz',
)
assert fit_asl2.cmdline == expected_cmd
def test_fit_asl():
""" Testing FitAsl interface."""
# Create the test node
fit_asl = FitAsl()
# Check if the command is properly defined
assert fit_asl.cmd == get_custom_path('fit_asl')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
fit_asl.run()
# Tests on the interface:
# Runs cbf fitting assuming all tissue is GM!
in_file = example_data('asl.nii.gz')
fit_asl.inputs.source_file = in_file
cmd_tmp = '{cmd} -source {in_file} -cbf {cbf} -error {error} -syn {syn}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_asl'),
in_file=in_file,
cbf='asl_cbf.nii.gz',
error='asl_error.nii.gz',
syn='asl_syn.nii.gz',
)
assert fit_asl.cmdline == expected_cmd
# Runs cbf fitting using IR/SR T1 data to estimate the local T1 and uses
# the segmentation data to fit tissue specific blood flow parameters
# (lambda,transit times,T1)
fit_asl2 = FitAsl(sig=True)
in_file = example_data('asl.nii.gz')
t1map = example_data('T1map.nii.gz')
seg = example_data('segmentation0.nii.gz')
fit_asl2.inputs.source_file = in_file
fit_asl2.inputs.t1map = t1map
fit_asl2.inputs.seg = seg
cmd_tmp = '{cmd} -source {in_file} -cbf {cbf} -error {error} \
-seg {seg} -sig -syn {syn} -t1map {t1map}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_asl'),
in_file=in_file,
t1map=t1map,
seg=seg,
cbf='asl_cbf.nii.gz',
error='asl_error.nii.gz',
syn='asl_syn.nii.gz',
)
assert fit_asl2.cmdline == expected_cmd
def test_dwi_tool():
# Create a node object
test_node = DwiTool()
# Check if the command is properly defined
assert test_node.cmd == get_custom_path('dwi_tool')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
test_node.run()
# Assign some input data
in_file = example_data('diffusion.nii')
bval_file = example_data('bvals')
bvec_file = example_data('bvecs')
b0_file = example_data('b0.nii')
mask_file = example_data('mask.nii')
test_node.inputs.source_file = in_file
test_node.inputs.mask_file = mask_file
test_node.inputs.bval_file = bval_file
test_node.inputs.bvec_file = bvec_file
test_node.inputs.b0_file = b0_file
test_node.inputs.dti_flag = True
cmd_tmp = '{cmd} -source {in_file} -bval {bval} -bvec {bvec} -b0 {b0} \
-mask {mask} -dti -famap {fa} -logdti2 {log} -mcmap {mc} -mdmap {md} \
-rgbmap {rgb} -syn {syn} -v1map {v1}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('dwi_tool'),
in_file=in_file,
bval=bval_file,
bvec=bvec_file,
b0=b0_file,
mask=mask_file,
fa=os.path.join(os.getcwd(),
'diffusion_famap.nii.gz'),
log=os.path.join(os.getcwd(),
'diffusion_logdti2.nii.gz'),
mc=os.path.join(os.getcwd(),
'diffusion_mcmap.nii.gz'),
md=os.path.join(os.getcwd(),
'diffusion_mdmap.nii.gz'),
rgb=os.path.join(os.getcwd(),
'diffusion_rgbmap.nii.gz'),
syn=os.path.join(os.getcwd(),
'diffusion_syn.nii.gz'),
v1=os.path.join(os.getcwd(),
'diffusion_v1map.nii.gz'))
assert test_node.cmdline == expected_cmd
def test_seg_em():
# Create a reg_aladin object
test_node = DwiTool()
# Check if the command is properly defined
yield assert_equal, test_node.cmd, get_custom_path("dwi_tool")
# Assign some input data
in_file = example_data("diffusion.nii")
test_node.inputs.source_file = in_file
cmd_tmp = "{cmd} -famap dwifit__famap -logdti2 dwifit__logdti2 -mdmap \
dwifit__mdmap -rgbmap dwifit__rgbmap -source {in_file} -v1map dwifit__v1map"
expected_cmd = cmd_tmp.format(cmd=get_custom_path("dwi_tool"), in_file=in_file)
yield assert_equal, test_node.cmdline, expected_cmd
def test_dwi_tool():
""" Testing DwiTool interface."""
# Create a node object
dwi_tool = DwiTool()
# Check if the command is properly defined
assert dwi_tool.cmd == get_custom_path('dwi_tool')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
dwi_tool.run()
# Assign some input data
in_file = example_data('dwi.nii.gz')
bval_file = example_data('bvals')
bvec_file = example_data('bvecs')
b0_file = example_data('b0.nii')
mask_file = example_data('mask.nii.gz')
dwi_tool.inputs.source_file = in_file
dwi_tool.inputs.mask_file = mask_file
dwi_tool.inputs.bval_file = bval_file
dwi_tool.inputs.bvec_file = bvec_file
dwi_tool.inputs.b0_file = b0_file
dwi_tool.inputs.dti_flag = True
cmd_tmp = '{cmd} -source {in_file} -bval {bval} -bvec {bvec} -b0 {b0} \
-mask {mask} -dti -famap {fa} -logdti2 {log} -mcmap {mc} -mdmap {md} \
-rgbmap {rgb} -syn {syn} -v1map {v1}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('dwi_tool'),
in_file=in_file,
bval=bval_file,
bvec=bvec_file,
b0=b0_file,
mask=mask_file,
fa='dwi_famap.nii.gz',
log='dwi_logdti2.nii.gz',
mc='dwi_mcmap.nii.gz',
md='dwi_mdmap.nii.gz',
rgb='dwi_rgbmap.nii.gz',
syn='dwi_syn.nii.gz',
v1='dwi_v1map.nii.gz')
assert dwi_tool.cmdline == expected_cmd
def test_dwi_tool():
""" Testing DwiTool interface."""
# Create a node object
dwi_tool = DwiTool()
# Check if the command is properly defined
assert dwi_tool.cmd == get_custom_path('dwi_tool')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
dwi_tool.run()
# Assign some input data
in_file = example_data('dwi.nii.gz')
bval_file = example_data('bvals')
bvec_file = example_data('bvecs')
b0_file = example_data('b0.nii')
mask_file = example_data('mask.nii.gz')
dwi_tool.inputs.source_file = in_file
dwi_tool.inputs.mask_file = mask_file
dwi_tool.inputs.bval_file = bval_file
dwi_tool.inputs.bvec_file = bvec_file
dwi_tool.inputs.b0_file = b0_file
dwi_tool.inputs.dti_flag = True
cmd_tmp = '{cmd} -source {in_file} -bval {bval} -bvec {bvec} -b0 {b0} \
-mask {mask} -dti -famap {fa} -logdti2 {log} -mcmap {mc} -mdmap {md} \
-rgbmap {rgb} -syn {syn} -v1map {v1}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('dwi_tool'),
in_file=in_file,
bval=bval_file,
bvec=bvec_file,
b0=b0_file,
mask=mask_file,
fa='dwi_famap.nii.gz',
log='dwi_logdti2.nii.gz',
mc='dwi_mcmap.nii.gz',
md='dwi_mdmap.nii.gz',
rgb='dwi_rgbmap.nii.gz',
syn='dwi_syn.nii.gz',
v1='dwi_v1map.nii.gz')
assert dwi_tool.cmdline == expected_cmd
def test_seg_em():
# Create a reg_aladin object
test_node = FitQt1()
# Check if the command is properly defined
yield assert_equal, test_node.cmd, get_custom_path('fit_qt1')
# Assign some input data
in_file = example_data('im1.nii')
test_node.inputs.source_file = in_file
cmd_tmp = '{cmd} -source {in_file} -error im1_error -m0map im1_m0map \
-mcmap im1_mcmap -res im1_res -syn im1_syn -t1map im1_t1map'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_qt1'),
in_file=in_file)
yield assert_equal, test_node.cmdline, expected_cmd
def test_seg_em():
# Create a reg_aladin object
test_node = FitAsl()
# Check if the command is properly defined
yield assert_equal, test_node.cmd, get_custom_path('fit_asl')
# Assign some input data
in_file = example_data('im1.nii')
test_node.inputs.source_file = in_file
cmd_tmp = '{cmd} -cbf im1_cbf -error im1_error -source {in_file} \
-syn im1_syn'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_asl'),
in_file=in_file)
yield assert_equal, test_node.cmdline, expected_cmd
def test_dwi_tool():
# Create a node object
test_node = DwiTool()
# Check if the command is properly defined
assert test_node.cmd == get_custom_path('dwi_tool')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
test_node.run()
# Assign some input data
in_file = example_data('diffusion.nii')
bval_file = example_data('bvals')
bvec_file = example_data('bvecs')
b0_file = example_data('b0.nii')
mask_file = example_data('mask.nii')
test_node.inputs.source_file = in_file
test_node.inputs.mask_file = mask_file
test_node.inputs.bval_file = bval_file
test_node.inputs.bvec_file = bvec_file
test_node.inputs.b0_file = b0_file
test_node.inputs.dti_flag = True
cmd_tmp = '{cmd} -source {in_file} -bval {bval} -bvec {bvec} -b0 {b0} \
-mask {mask} -dti -famap {fa} -logdti2 {log} -mcmap {mc} -mdmap {md} \
-rgbmap {rgb} -syn {syn} -v1map {v1}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('dwi_tool'),
in_file=in_file,
bval=bval_file,
bvec=bvec_file,
b0=b0_file,
mask=mask_file,
fa=os.path.join(os.getcwd(), 'diffusion_famap.nii.gz'),
log=os.path.join(os.getcwd(), 'diffusion_logdti2.nii.gz'),
mc=os.path.join(os.getcwd(), 'diffusion_mcmap.nii.gz'),
md=os.path.join(os.getcwd(), 'diffusion_mdmap.nii.gz'),
rgb=os.path.join(os.getcwd(), 'diffusion_rgbmap.nii.gz'),
syn=os.path.join(os.getcwd(), 'diffusion_syn.nii.gz'),
v1=os.path.join(os.getcwd(), 'diffusion_v1map.nii.gz'))
assert test_node.cmdline == expected_cmd
def test_fit_dwi():
""" Testing FitDwi interface."""
# Create a node object
fit_dwi = FitDwi()
# Check if the command is properly defined
assert fit_dwi.cmd == get_custom_path('fit_dwi')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
fit_dwi.run()
# Assign some input data
in_file = example_data('dwi.nii.gz')
bval_file = example_data('bvals')
bvec_file = example_data('bvecs')
fit_dwi.inputs.source_file = in_file
fit_dwi.inputs.bval_file = bval_file
fit_dwi.inputs.bvec_file = bvec_file
fit_dwi.inputs.dti_flag = True
cmd_tmp = '{cmd} -source {in_file} -bval {bval} -bvec {bvec} -dti \
-error {error} -famap {fa} -mcmap {mc} -mcout {mcout} -mdmap {md} -nodiff \
{nodiff} -res {res} -rgbmap {rgb} -syn {syn} -tenmap2 {ten2} -v1map {v1}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_dwi'),
in_file=in_file,
bval=bval_file,
bvec=bvec_file,
error='dwi_error.nii.gz',
fa='dwi_famap.nii.gz',
mc='dwi_mcmap.nii.gz',
md='dwi_mdmap.nii.gz',
nodiff='dwi_no_diff.nii.gz',
res='dwi_resmap.nii.gz',
rgb='dwi_rgbmap.nii.gz',
syn='dwi_syn.nii.gz',
ten2='dwi_tenmap2.nii.gz',
v1='dwi_v1map.nii.gz',
mcout='dwi_mcout.txt')
assert fit_dwi.cmdline == expected_cmd
def test_fit_dwi():
""" Testing FitDwi interface."""
# Create a node object
fit_dwi = FitDwi()
# Check if the command is properly defined
assert fit_dwi.cmd == get_custom_path('fit_dwi')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
fit_dwi.run()
# Assign some input data
in_file = example_data('dwi.nii.gz')
bval_file = example_data('bvals')
bvec_file = example_data('bvecs')
fit_dwi.inputs.source_file = in_file
fit_dwi.inputs.bval_file = bval_file
fit_dwi.inputs.bvec_file = bvec_file
fit_dwi.inputs.dti_flag = True
cmd_tmp = '{cmd} -source {in_file} -bval {bval} -bvec {bvec} -dti \
-error {error} -famap {fa} -mcmap {mc} -mcout {mcout} -mdmap {md} -nodiff \
{nodiff} -res {res} -rgbmap {rgb} -syn {syn} -tenmap2 {ten2} -v1map {v1}'
expected_cmd = cmd_tmp.format(cmd=get_custom_path('fit_dwi'),
in_file=in_file,
bval=bval_file,
bvec=bvec_file,
error='dwi_error.nii.gz',
fa='dwi_famap.nii.gz',
mc='dwi_mcmap.nii.gz',
md='dwi_mdmap.nii.gz',
nodiff='dwi_no_diff.nii.gz',
res='dwi_resmap.nii.gz',
rgb='dwi_rgbmap.nii.gz',
syn='dwi_syn.nii.gz',
ten2='dwi_tenmap2.nii.gz',
v1='dwi_v1map.nii.gz',
mcout='dwi_mcout.txt')
assert fit_dwi.cmdline == expected_cmd
def test_fit_qt1():
""" Testing FitQt1 interface."""
# Create a node object
fit_qt1 = FitQt1()
# Check if the command is properly defined
assert fit_qt1.cmd == get_custom_path('fit_qt1')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
fit_qt1.run()
# Regular test:
in_file = example_data('TI4D.nii.gz')
fit_qt1.inputs.source_file = in_file
cmd_tmp = '{cmd} -source {in_file} -comp {comp} -error {error} -m0map \
{map0} -mcmap {cmap} -res {res} -syn {syn} -t1map {t1map}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_qt1'),
in_file=in_file,
comp='TI4D_comp.nii.gz',
map0='TI4D_m0map.nii.gz',
error='TI4D_error.nii.gz',
cmap='TI4D_mcmap.nii.gz',
res='TI4D_res.nii.gz',
t1map='TI4D_t1map.nii.gz',
syn='TI4D_syn.nii.gz',
)
assert fit_qt1.cmdline == expected_cmd
# Runs T1 fitting to inversion and saturation recovery data (NLSQR)
fit_qt1_2 = FitQt1(tis=[1, 2, 5], ir_flag=True)
in_file = example_data('TI4D.nii.gz')
fit_qt1_2.inputs.source_file = in_file
cmd_tmp = '{cmd} -source {in_file} -IR -TIs 1.0 2.0 5.0 \
-comp {comp} -error {error} -m0map {map0} -mcmap {cmap} -res {res} \
-syn {syn} -t1map {t1map}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_qt1'),
in_file=in_file,
comp='TI4D_comp.nii.gz',
map0='TI4D_m0map.nii.gz',
error='TI4D_error.nii.gz',
cmap='TI4D_mcmap.nii.gz',
res='TI4D_res.nii.gz',
t1map='TI4D_t1map.nii.gz',
syn='TI4D_syn.nii.gz',
)
assert fit_qt1_2.cmdline == expected_cmd
# Runs T1 fitting to spoiled gradient echo (SPGR) data (NLSQR)
fit_qt1_3 = FitQt1(flips=[2, 4, 8], spgr=True)
in_file = example_data('TI4D.nii.gz')
fit_qt1_3.inputs.source_file = in_file
cmd_tmp = '{cmd} -source {in_file} -comp {comp} -error {error} \
-flips 2.0 4.0 8.0 -m0map {map0} -mcmap {cmap} -res {res} -SPGR -syn {syn} \
-t1map {t1map}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_qt1'),
in_file=in_file,
comp='TI4D_comp.nii.gz',
map0='TI4D_m0map.nii.gz',
error='TI4D_error.nii.gz',
cmap='TI4D_mcmap.nii.gz',
res='TI4D_res.nii.gz',
t1map='TI4D_t1map.nii.gz',
syn='TI4D_syn.nii.gz',
)
assert fit_qt1_3.cmdline == expected_cmd
def test_fit_qt1():
""" Testing FitQt1 interface."""
# Create a node object
fit_qt1 = FitQt1()
# Check if the command is properly defined
assert fit_qt1.cmd == get_custom_path('fit_qt1')
# test raising error with mandatory args absent
with pytest.raises(ValueError):
fit_qt1.run()
# Regular test:
in_file = example_data('TI4D.nii.gz')
fit_qt1.inputs.source_file = in_file
cmd_tmp = '{cmd} -source {in_file} -comp {comp} -error {error} -m0map \
{map0} -mcmap {cmap} -res {res} -syn {syn} -t1map {t1map}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_qt1'),
in_file=in_file,
comp='TI4D_comp.nii.gz',
map0='TI4D_m0map.nii.gz',
error='TI4D_error.nii.gz',
cmap='TI4D_mcmap.nii.gz',
res='TI4D_res.nii.gz',
t1map='TI4D_t1map.nii.gz',
syn='TI4D_syn.nii.gz',
)
assert fit_qt1.cmdline == expected_cmd
# Runs T1 fitting to inversion and saturation recovery data (NLSQR)
fit_qt1_2 = FitQt1(tis=[1, 2, 5], ir_flag=True)
in_file = example_data('TI4D.nii.gz')
fit_qt1_2.inputs.source_file = in_file
cmd_tmp = '{cmd} -source {in_file} -IR -TIs 1.0 2.0 5.0 \
-comp {comp} -error {error} -m0map {map0} -mcmap {cmap} -res {res} \
-syn {syn} -t1map {t1map}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_qt1'),
in_file=in_file,
comp='TI4D_comp.nii.gz',
map0='TI4D_m0map.nii.gz',
error='TI4D_error.nii.gz',
cmap='TI4D_mcmap.nii.gz',
res='TI4D_res.nii.gz',
t1map='TI4D_t1map.nii.gz',
syn='TI4D_syn.nii.gz',
)
assert fit_qt1_2.cmdline == expected_cmd
# Runs T1 fitting to spoiled gradient echo (SPGR) data (NLSQR)
fit_qt1_3 = FitQt1(flips=[2, 4, 8], spgr=True)
in_file = example_data('TI4D.nii.gz')
fit_qt1_3.inputs.source_file = in_file
cmd_tmp = '{cmd} -source {in_file} -comp {comp} -error {error} \
-flips 2.0 4.0 8.0 -m0map {map0} -mcmap {cmap} -res {res} -SPGR -syn {syn} \
-t1map {t1map}'
expected_cmd = cmd_tmp.format(
cmd=get_custom_path('fit_qt1'),
in_file=in_file,
comp='TI4D_comp.nii.gz',
map0='TI4D_m0map.nii.gz',
error='TI4D_error.nii.gz',
cmap='TI4D_mcmap.nii.gz',
res='TI4D_res.nii.gz',
t1map='TI4D_t1map.nii.gz',
syn='TI4D_syn.nii.gz',
)
assert fit_qt1_3.cmdline == expected_cmd