Repair 3dQwarp workflow

.github/workflows/unittests.yml

@@ -107,7 +107,7 @@ jobs:
         pip install datalad datalad-osf
     - name: Install fsl
       run: |
-        conda install fsl-fugue fsl-topup
+        conda install fsl-fugue fsl-topup fsl-bet2
     - uses: actions/checkout@v4
     - name: Install dependencies
       timeout-minutes: 5

Dockerfile

@@ -72,7 +72,8 @@ RUN mkdir -p /opt/afni-latest \
         -name "3dTshift" -or \
         -name "3dUnifize" -or \
         -name "3dAutomask" -or \
-        -name "3dvolreg" \) -delete
+        -name "3dvolreg" -or \
+        -name "3dQwarp" \) -delete
 
 # Convert3d 1.4.0
 FROM downloader as c3d

env.yml

@@ -23,3 +23,4 @@ dependencies:
   # Workflow dependencies: FSL (versions pinned in 6.0.6.2)
   - fsl-fugue=2201.2
   - fsl-topup=2203.1
+  - fsl-bet2=2111.8

sdcflows/utils/epimanip.py

@@ -188,10 +188,14 @@ def get_trt(in_meta, in_file=None):
             raise ValueError(f"'{trt}'")
 
         return trt
+    elif in_file is None:
+        msg = "Unable to find TotalReadoutTime in metadata and in_file \
+               not defined."
+        raise AssertionError(msg)
 
     # npe = N voxels PE direction
     pe_index = "ijk".index(in_meta["PhaseEncodingDirection"][0])
-    npe = nb.load(in_file).shape[pe_index]
+    npe = nb.loadsave.load(in_file).shape[pe_index]
 
     # Use case 2: EES is defined
     ees = in_meta.get("EffectiveEchoSpacing")
@@ -252,7 +256,9 @@ def epi_mask(in_file, out_file=None):
     maxnorm = np.percentile(closed[closed > 0], 90)
     closed = np.clip(closed, a_min=0.0, a_max=maxnorm)
     # Calculate index of center of masses
-    cm = tuple(np.round(ndimage.measurements.center_of_mass(closed)).astype(int))
+    cm = tuple(
+        np.round(ndimage.measurements.center_of_mass(closed)).astype(int)
+    )
     # Erode the picture of the brain by a lot
     eroded = ndimage.grey_erosion(closed, structure=ball(5))
     # Calculate the residual
@@ -268,6 +274,8 @@ def epi_mask(in_file, out_file=None):
     hdr = img.header.copy()
     hdr.set_data_dtype("uint8")
     nb.Nifti1Image(
-        ndimage.binary_dilation(labels == 2, ball(2)).astype("uint8"), img.affine, hdr
+        ndimage.binary_dilation(labels == 2, ball(2)).astype("uint8"),
+        img.affine,
+        hdr,
     ).to_filename(out_file)
     return out_file

sdcflows/utils/tests/test_epimanip.py

@@ -0,0 +1,33 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2021 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Test EPI manipulation routines."""
+import pytest
+from sdcflows.utils.epimanip import get_trt
+
+
+def test_get_trt_err_wo_trt_and_in_file():
+    """Test that calling get_trt with dict that does not have TotalReadoutTime \
+    and no in_file raises AssertionError.
+    """
+    with pytest.raises(AssertionError):
+        get_trt(in_meta={})