🐛 Patch NetCorr._list_outputs

CPAC/utils/interfaces/netcorr.py

@@ -19,6 +19,61 @@
 class NetCorr(NipypeNetCorr):  # noqa: D101
     input_spec = NetCorrInputSpec
 
+    def _list_outputs(self):
+        """``nipype.interfaces.afni.preprocess.NetCorr._list_outputs`` with a bugfix.
+
+        Notes
+        -----
+        This method can be removed once nipy/nipype#3697 is merged and a release
+        including that PR is included in the C-PAC image.
+        """
+        # STATEMENT OF CHANGES:
+        #     This function is derived from sources licensed under the Apache-2.0 terms,
+        #     and this function has been changed.
+
+        # CHANGES:
+        #     * Includes changes from https://github.com/nipy/nipype/pull/3697 prior to all commits between https://github.com/nipy/nipype/tree/1.8.6 and that PR being merged and released.
+
+        # ORIGINAL WORK'S ATTRIBUTION NOTICE:
+        #    Copyright (c) 2009-2016, Nipype developers
+
+        #    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.
+
+        #    Prior to release 0.12, Nipype was licensed under a BSD license.
+
+        # Modifications copyright (C) 2024  C-PAC Developers
+        import glob
+        import os
+
+        from nipype.interfaces.base.traits_extension import isdefined
+
+        outputs = self.output_spec().get()
+
+        if not isdefined(self.inputs.out_file):
+            prefix = self._gen_fname(self.inputs.in_file, suffix="_netcorr")
+        else:
+            prefix = self.inputs.out_file
+
+        # All outputs should be in the same directory as the prefix
+        odir = os.path.dirname(os.path.abspath(prefix))
+        outputs["out_corr_matrix"] = glob.glob(os.path.join(odir, "*.netcc"))[0]
+
+        if self.inputs.ts_wb_corr or self.inputs.ts_wb_Z:
+            corrdir = os.path.join(odir, prefix + "_000_INDIV")
+            outputs["out_corr_maps"] = glob.glob(os.path.join(corrdir, "*.nii.gz"))
+
+        return outputs
+
 
 NetCorr.__doc__ = f"""{NipypeNetCorr.__doc__}
 `CPAC.utils.interfaces.netcorr.NetCorr` adds an additional optional input, `automask_off`