Merge pull request #457 from effigies/fix/one-layer-syn

fix: Only fit high-frequency spline for SyN-SDC

Author: effigies

.circleci/config.yml

@@ -341,7 +341,7 @@ jobs:
                 nipreps/sdcflows:latest \
                 pytest -v --junit-xml=/out/pytest.xml \
                        --cov sdcflows --cov-report xml:/out/unittests.xml \
-                       sdcflows/
+                       -n auto sdcflows/
       - save_cache:
           key: workdir-v3-{{ .Branch }}-{{ .BuildNum }}
           paths:

.github/workflows/unittests.yml

@@ -175,7 +175,7 @@ jobs:
       run: |
         export LD_LIBRARY_PATH=/usr/lib/fsl/5.0:$LD_LIBRARY_PATH
         export PATH=$ANTSPATH:${AFNI_HOME}:/usr/lib/fsl/5.0:$PATH
-        pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules sdcflows
+        pytest -v --cov sdcflows --cov-report xml:cov.xml --doctest-modules -n auto sdcflows
 
     - uses: codecov/codecov-action@v4
       with:

sdcflows/utils/epimanip.py

@@ -23,13 +23,6 @@
 """
 Manipulation of EPI data.
 
-.. testsetup::
-
-    >>> tmpdir = getfixture('tmpdir')
-    >>> tmp = tmpdir.chdir() # changing to a temporary directory
-    >>> nb.Nifti1Image(np.zeros((90, 90, 60)), None, None).to_filename(
-    ...     tmpdir.join('epi.nii.gz').strpath)
-
 """
 
 
@@ -42,6 +35,15 @@ def get_trt(in_meta, in_file=None):
     The first option is that a ``TotalReadoutTime`` field is found
     in the JSON sidecar:
 
+    .. testsetup::
+
+        >>> cwd = os.getcwd()
+        >>> tmpdir = getfixture('tmpdir')
+        >>> tmp = tmpdir.chdir() # changing to a temporary directory
+        >>> nb.Nifti1Image(np.zeros((90, 90, 60)), None, None).to_filename(
+        ...     tmpdir.join('epi.nii.gz').strpath)
+
+
     >>> meta = {'TotalReadoutTime': 0.05251}
     >>> get_trt(meta)
     0.05251
@@ -157,6 +159,10 @@ def get_trt(in_meta, in_file=None):
     Traceback (most recent call last):
     ValueError:
 
+    .. testcleanup::
+
+        >>> os.chdir(cwd)
+
     .. admonition:: Thanks
 
         With thanks to Dr. Rorden for his thorough

sdcflows/workflows/fit/syn.py

@@ -22,17 +22,6 @@
 #
 """
 Estimating the susceptibility distortions without fieldmaps.
-
-.. testsetup::
-
-    >>> tmpdir = getfixture('tmpdir')
-    >>> tmp = tmpdir.chdir() # changing to a temporary directory
-    >>> data = np.zeros((10, 10, 10, 1, 3))
-    >>> data[..., 1] = 1
-    >>> nb.Nifti1Image(data, None, None).to_filename(
-    ...     tmpdir.join('field.nii.gz').strpath)
-
-
 """
 from nipype.pipeline import engine as pe
 from nipype.interfaces import utility as niu
@@ -138,9 +127,7 @@ def init_syn_sdc_wf(
     from ...interfaces.bspline import (
         ApplyCoeffsField,
         BSplineApprox,
-        DEFAULT_LF_ZOOMS_MM,
         DEFAULT_HF_ZOOMS_MM,
-        DEFAULT_ZOOMS_MM,
     )
     from ...interfaces.brainmask import BinaryDilation, Union
 
@@ -272,9 +259,10 @@ def init_syn_sdc_wf(
         name="bs_filter",
     )
     bs_filter.interface._always_run = debug
-    bs_filter.inputs.bs_spacing = (
-        [DEFAULT_LF_ZOOMS_MM, DEFAULT_HF_ZOOMS_MM] if not sloppy else [DEFAULT_ZOOMS_MM]
-    )
+    bs_filter.inputs.bs_spacing = [DEFAULT_HF_ZOOMS_MM]
+
+    if sloppy:
+        bs_filter.inputs.zooms_min = 4.0
 
     workflow.connect([
         (inputnode, readout_time, [(("epi_ref", _pop), "in_file"),