10000 ENH: Update PETsurfer interface by mnoergaard · Pull Request #3602 · nipy/nipype · GitHub
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ENH: Update PETsurfer interface #3602

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Merged
merged 9 commits into from
Mar 20, 2024
Merged

ENH: Update PETsurfer interface #3602

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bd9d406
GTMPVC: add extra outputs to outputspec and GTMPVC class
mnoergaard Sep 8, 2023
ad5e559
FIX: update description of GTMPVC interface
mnoergaard Sep 8, 2023
f66b50f
ENH: update naming of MRTM interface to MRTM1 (more clear definition)
mnoergaard Sep 8, 2023
4df6a4b
ENH: update LoganRef interface to Logan (reference modeling is not us…
mnoergaard Sep 8, 2023
15eb049
ENH: add BP clipping arguments to mri_glmfit
mnoergaard Sep 8, 2023
0df01a7
formatted with black
bendhouseart Mar 19, 2024
ced00b1
Merge pull request #5 from bendhouseart/update_petsurfer
mnoergaard Mar 20, 2024
75f0ba0
TEST: Update tests
effigies Mar 20, 2024
6b7bda4
Merge remote-tracking branch 'upstream/master' into update_petsurfer
effigies Mar 20, 2024
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TEST: Update tests
  • Loading branch information
@effigies
effigies committed Mar 20, 2024
commit 75f0ba0b4ed33c25189eabd7dc77ec4997563847
6 changes: 6 additions & 0 deletions nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,12 @@ def test_GLMFit_inputs():
args=dict(
argstr="%s",
),
bp_clip_max=dict(
argstr="--bp-clip-max %f",
),
bp_clip_neg=dict(
argstr="--bp-clip-neg",
),
calc_AR1=dict(
argstr="--tar1",
),
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15 changes: 15 additions & 0 deletions nipype/interfaces/freesurfer/tests/test_auto_GTMPVC.py
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Expand Up @@ -207,6 +207,9 @@ def test_GTMPVC_inputs():

def test_GTMPVC_outputs():
output_map = dict(
eres=dict(
extensions=None,
),
gtm_file=dict(
extensions=None,
),
Expand Down Expand Up @@ -256,6 +259,18 @@ def test_GTMPVC_outputs():
reg_rbvpet2anat=dict(
extensions=None,
),
seg=dict(
extensions=None,
),
seg_ctab=dict(
extensions=None,
),
tissue_fraction=dict(
extensions=None,
),
tissue_fraction_psf=dict(
extensions=None,
),
yhat=dict(
extensions=None,
),
Expand Down
16 changes: 11 additions & 5 deletions ...es/freesurfer/tests/test_auto_LoganRef.py → ...faces/freesurfer/tests/test_auto_Logan.py
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
from ..petsurfer import LoganRef
from ..petsurfer import Logan


def test_LoganRef_inputs():
def test_Logan_inputs():
input_map = dict(
allow_ill_cond=dict(
argstr="--illcond",
Expand All @@ -13,6 +13,12 @@ def test_LoganRef_inputs():
args=dict(
argstr="%s",
),
bp_clip_max=dict(
argstr="--bp-clip-max %f",
),
bp_clip_neg=dict(
argstr="--bp-clip-neg",
),
calc_AR1=dict(
argstr="--tar1",
),
Expand Down Expand Up @@ -214,14 +220,14 @@ def test_LoganRef_inputs():
xor=("weight_file", "weight_inv", "weight_sqrt"),
),
)
inputs = LoganRef.input_spec()
inputs = Logan.input_spec()

for key, metadata in list(input_map.items()):
for metakey, value in list(metadata.items()):
assert getattr(inputs.traits()[key], metakey) == value


def test_LoganRef_outputs():
def test_Logan_outputs():
output_map = dict(
beta_file=dict(
extensions=None,
Expand Down Expand Up @@ -271,7 +277,7 @@ def test_LoganRef_outputs():
extensions=None,
),
)
outputs = LoganRef.output_spec()
outputs = Logan.output_spec()

for key, metadata in list(output_map.items()):
for metakey, value in list(metadata.items()):
Expand Down
16 changes: 11 additions & 5 deletions ...rfaces/freesurfer/tests/test_auto_MRTM.py → ...faces/freesurfer/tests/test_auto_MRTM1.py
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
from ..petsurfer import MRTM
from ..petsurfer import MRTM1


def test_MRTM_inputs():
def test_MRTM1_inputs():
input_map = dict(
allow_ill_cond=dict(
argstr="--illcond",
Expand All @@ -13,6 +13,12 @@ def test_MRTM_inputs():
args=dict(
argstr="%s",
),
bp_clip_max=dict(
argstr="--bp-clip-max %f",
),
bp_clip_neg=dict(
argstr="--bp-clip-neg",
),
calc_AR1=dict(
argstr="--tar1",
),
Expand Down Expand Up @@ -214,14 +220,14 @@ def test_MRTM_inputs():
xor=("weight_file", "weight_inv", "weight_sqrt"),
),
)
inputs = MRTM.input_spec()
inputs = MRTM1.input_spec()

for key, metadata in list(input_map.items()):
for metakey, value in list(metadata.items()):
assert getattr(inputs.traits()[key], metakey) == value


def test_MRTM_outputs():
def test_MRTM1_outputs():
output_map = dict(
beta_file=dict(
extensions=None,
Expand Down Expand Up @@ -271,7 +277,7 @@ def test_MRTM_outputs():
extensions=None,
),
)
outputs = MRTM.output_spec()
outputs = MRTM1.output_spec()

for key, metadata in list(output_map.items()):
for metakey, value in list(metadata.items()):
Expand Down
6 changes: 6 additions & 0 deletions nipype/interfaces/freesurfer/tests/test_auto_MRTM2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,12 @@ def test_MRTM2_inputs():
args=dict(
argstr="%s",
),
bp_clip_max=dict(
argstr="--bp-clip-max %f",
),
bp_clip_neg=dict(
argstr="--bp-clip-neg",
),
calc_AR1=dict(
argstr="--tar1",
),
Expand Down
6 changes: 6 additions & 0 deletions nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,12 @@ def test_OneSampleTTest_inputs():
args=dict(
argstr="%s",
),
bp_clip_max=dict(
argstr="--bp-clip-max %f",
),
bp_clip_neg=dict(
argstr="--bp-clip-neg",
),
calc_AR1=dict(
argstr="--tar1",
),
Expand Down
0