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[BUG]: Fix SpaceWarper to handle native space data conversion in "auto" mode #482

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synchon merged 5 commits from fix/native-data-with-auto-space-warper into main 2026-03-12 13:32:01 +00:00
Conversation 4 Commits 5 Files changed 2 +29 -33
2 changed files with 29 additions and 33 deletions
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1
docs/changes/newsfragments/482.bugfix Normal file
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@ -0,0 +1 @@
Allow :class:`.SpaceWarper` to convert data from native to template space when ``using="auto"`` by `Fede Raimondo`_ and `Synchon Mandal`_

41
junifer/preprocess/warping/space_warper.py
View file

@ -129,20 +129,21 @@ class SpaceWarper(BasePreprocessor):
------
ValueError
If ``extra_input`` is None when transforming to native space
i.e., using ``"T1w"`` as reference.
i.e., using ``"T1w"`` as reference or converting from native to
template space or
if the ``reference`` key is missing from ``input`` when converting
from native to template space.
RuntimeError
If warper could not be found in ``extra_input`` when
``using="auto"`` or converting from native space or
if the data is in the correct space and does not require
warping or
if FSL is used when ``reference="T1w"``.
if FSL or "auto" is used when ``reference!="T1w"``.
"""
logger.info(f"Warping to {self.reference} space using SpaceWarper")
# Transform to native space
if (
self.using in ["fsl", "ants", "auto"] and self.reference == "T1w"
): # pragma: no cover
if self.reference == "T1w": # pragma: no cover
# Check for extra inputs
if extra_input is None:
raise_error(
@ -150,20 +151,8 @@ class SpaceWarper(BasePreprocessor):
f"`{self.reference}` data types in particular."
)
# Conditional preprocessor
if self.using == "fsl":
input = FSLWarper().preprocess(
input=input,
extra_input=extra_input,
reference=self.reference,
)
elif self.using == "ants":
input = ANTsWarper().preprocess(
input=input,
extra_input=extra_input,
reference=self.reference,
)
elif self.using == "auto":
warper = None
if self.using == "auto":
for entry in extra_input["Warp"]:
if entry["dst"] == "native":
warper = entry["warper"]
@ -171,6 +160,8 @@ class SpaceWarper(BasePreprocessor):
raise_error(
klass=RuntimeError, msg="Could not find correct warper"
)
else:
warper = self.using
if warper == "fsl":
input = FSLWarper().preprocess(
input=input,
@ -183,8 +174,7 @@ class SpaceWarper(BasePreprocessor):
extra_input=extra_input,
reference=self.reference,
)
# Transform to template space
if self.using in ["fsl", "ants"] and self.reference != "T1w":
else:
input_space = input["space"]
# Check pre-requirements for space manipulation
if self.using == "ants" and self.reference == input_space:
@ -241,12 +231,12 @@ class SpaceWarper(BasePreprocessor):
)
else:
# Transform from MNI to MNI template space not possible
if self.using == "fsl":
if self.using in ["fsl", "auto"]:
raise_error(
(
f"Warping from {input_space} space to "
f"{self.reference} space not possible with "
"FSL, use ANTs instead."
f"{self.using}, use ANTs instead."
),
klass=RuntimeError,
)
@ -257,5 +247,10 @@ class SpaceWarper(BasePreprocessor):
extra_input={},
reference=self.reference,
)
logger.debug("Completed warping step")
logger.debug("Warped data types: ")
for k, v in input.items():
if k in ["data", "meta"]:
continue
logger.debug(f"\t{k}: {v}")
return input