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Code Issues 14 Pull requests 2 Packages Activity Actions

[BUG]: compute_brain_mask fails to find Warp object #394

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synchon wants to merge 3 commits from fix/compute-brain-mask into main
pull from: fix/compute-brain-mask
merge into: juaml:main
Conversation 9 Commits 3 Files changed 3 +9 -20
3 changed files with 9 additions and 20 deletions
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1
docs/changes/newsfragments/394.bugfix Normal file
View file

@ -0,0 +1 @@
Refactor ``compute_brain_mask``'s interface and internals to not fail during native space warping by `Synchon Mandal`_

25
junifer/data/masks/_masks.py
View file

@ -47,7 +47,6 @@ _masks_path = Path(__file__).parent
def compute_brain_mask( def compute_brain_mask(
target_data: Dict[str, Any], target_data: Dict[str, Any],
extra_input: Optional[Dict[str, Any]] = None,
mask_type: str = "brain", mask_type: str = "brain",
threshold: float = 0.5, threshold: float = 0.5,
) -> "Nifti1Image": ) -> "Nifti1Image":
@ -61,9 +60,6 @@ def compute_brain_mask(
target_data : dict target_data : dict
The corresponding item of the data object for which mask will be The corresponding item of the data object for which mask will be
loaded. loaded.
extra_input : dict, optional
The other fields in the data object. Useful for accessing other data
types (default None).
mask_type : {"brain", "gm", "wm"}, optional mask_type : {"brain", "gm", "wm"}, optional
Type of mask to be computed: Type of mask to be computed:
@ -94,26 +90,19 @@ def compute_brain_mask(
# Check pre-requirements for space manipulation # Check pre-requirements for space manipulation
target_space = target_data["space"] target_space = target_data["space"]
# Set target standard space to target space # Conditional for native space-warped target data
target_std_space = target_space
# Extra data type requirement check if target space is native
if target_space == "native": if target_space == "native":
# Check for extra inputs # prewarp_space is added in SpaceWarper and should be there
if extra_input is None: target_std_space = target_data["prewarp_space"]
raise_error( else:
"No extra input provided, requires `Warp` " # Set target standard space to target space
"data type to infer target template space." target_std_space = target_space
)
# Set target standard space to warp file space source
for entry in extra_input["Warp"]:
if entry["dst"] == "native":
target_std_space = entry["src"]
# Fetch template in closest resolution # Fetch template in closest resolution
template = get_template( template = get_template(
space=target_std_space, space=target_std_space,
target_data=target_data, target_data=target_data,
extra_input=extra_input, extra_input=None,
template_type=mask_type, template_type=mask_type,
) )
# Resample template to target image # Resample template to target image

3
junifer/data/masks/tests/test_masks.py
View file

@ -64,8 +64,8 @@ def test_compute_brain_mask(mask_type: str, threshold: float) -> None:
element_data = DefaultDataReader().fit_transform(dg["sub-01"]) element_data = DefaultDataReader().fit_transform(dg["sub-01"])
mask = compute_brain_mask( mask = compute_brain_mask(
target_data=element_data["BOLD"], target_data=element_data["BOLD"],
extra_input=None,
mask_type=mask_type, mask_type=mask_type,
threshold=threshold,
) )
assert isinstance(mask, nib.nifti1.Nifti1Image) assert isinstance(mask, nib.nifti1.Nifti1Image)
@ -104,7 +104,6 @@ def test_compute_brain_mask_for_native(mask_type: str) -> None:
) )
mask = compute_brain_mask( mask = compute_brain_mask(
target_data=element_data["BOLD"], target_data=element_data["BOLD"],
extra_input=None,
mask_type=mask_type, mask_type=mask_type,
) )
assert isinstance(mask, nib.nifti1.Nifti1Image) assert isinstance(mask, nib.nifti1.Nifti1Image)