From 8f54fadacfa63b31d9760ae69f7bac0988192afd Mon Sep 17 00:00:00 2001
From: Taylor Salo <salot@pennmedicine.upenn.edu>
Date: Thu, 12 Dec 2024 14:17:02 -0500
Subject: [PATCH] Draft medic workflow test.

---
 sdcflows/interfaces/fmap.py                |  2 +-
 sdcflows/workflows/fit/medic.py            |  6 +-
 sdcflows/workflows/fit/tests/test_medic.py | 82 ++++++++++++++++++++++
 3 files changed, 86 insertions(+), 4 deletions(-)
 create mode 100644 sdcflows/workflows/fit/tests/test_medic.py

diff --git a/sdcflows/interfaces/fmap.py b/sdcflows/interfaces/fmap.py
index d86bb112b4..255c4fa3e8 100644
--- a/sdcflows/interfaces/fmap.py
+++ b/sdcflows/interfaces/fmap.py
@@ -475,7 +475,7 @@ class _MEDICInputSpec(CommandLineInputSpec):
 class _MEDICOutputSpec(TraitedSpec):
     native_field_map = File(
         exists=True,
-        desc="4D ative (distorted) space field map in Hertz",
+        desc="4D native (distorted) space field map in Hertz",
     )
     displacement_map = File(
         exists=True,
diff --git a/sdcflows/workflows/fit/medic.py b/sdcflows/workflows/fit/medic.py
index 343d282d30..7d6c5ecfab 100644
--- a/sdcflows/workflows/fit/medic.py
+++ b/sdcflows/workflows/fit/medic.py
@@ -59,7 +59,7 @@ def init_medic_wf(name="medic_wf"):
 
     Outputs
     -------
-    fieldmap : :obj:`str`
+    fmap : :obj:`str`
         The path of the estimated fieldmap time series file. Units are Hertz.
     displacement : :obj:`list` of :obj:`str`
         Path to the displacement time series files. Units are mm.
@@ -85,7 +85,7 @@ def init_medic_wf(name="medic_wf"):
 
     inputnode = pe.Node(niu.IdentityInterface(fields=INPUT_FIELDS), name="inputnode")
     outputnode = pe.Node(
-        niu.IdentityInterface(fields=["fieldmap", "displacement", "method"]),
+        niu.IdentityInterface(fields=["fmap", "displacement", "method"]),
         name="outputnode",
     )
     outputnode.inputs.method = "MEDIC"
@@ -119,7 +119,7 @@ def init_medic_wf(name="medic_wf"):
         (write_metadata, medic, [("out_file", "metadata")]),
         (phase2rad, medic, [("out_file", "phase_files")]),
         (medic, outputnode, [
-            ("native_field_map", "fieldmap"),
+            ("native_field_map", "fmap"),
             ("displacement_map", "displacement"),
         ]),
     ])  # fmt:skip
diff --git a/sdcflows/workflows/fit/tests/test_medic.py b/sdcflows/workflows/fit/tests/test_medic.py
new file mode 100644
index 0000000000..6cf546af7d
--- /dev/null
+++ b/sdcflows/workflows/fit/tests/test_medic.py
@@ -0,0 +1,82 @@
+# 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 <nipreps@gmail.com>
+#
+# 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 phase-difference type of fieldmaps."""
+from pathlib import Path
+from json import loads
+
+import pytest
+
+from ..medic import init_medic_wf, Workflow
+
+
+@pytest.mark.slow
+def test_medic(tmpdir, datadir, workdir, outdir):
+    """Test creation of the workflow."""
+    tmpdir.chdir()
+
+    pattern = 'ds005250/sub-04/ses-2/func/*_part-mag_bold.nii.gz'
+    magnitude_files = sorted(datadir.glob(pattern))
+    phase_files = [f.with_name(f.name.replace("part-mag", "part-phase")) for f in magnitude_files]
+    metadata_dicts = [
+        loads(Path(f.name.replace('.nii.gz', '.json')).read_text()) for f in magnitude_files
+    ]
+
+    wf = Workflow(name=f"medic_{magnitude_files[0].name.replace('.nii.gz', '').replace('-', '_')}")
+    medic_wf = init_medic_wf()
+    medic_wf.inputs.inputnode.magnitude = magnitude_files
+    medic_wf.inputs.inputnode.phase = phase_files
+    medic_wf.inputs.inputnode.metadata = metadata_dicts
+
+    if outdir:
+        from ...outputs import init_fmap_derivatives_wf, init_fmap_reports_wf
+
+        outdir = outdir / "unittests" / magnitude_files[0].split("/")[0]
+        fmap_derivatives_wf = init_fmap_derivatives_wf(
+            output_dir=str(outdir),
+            write_coeff=True,
+            bids_fmap_id="phasediff_id",
+        )
+        fmap_derivatives_wf.inputs.inputnode.source_files = [str(f) for f in magnitude_files]
+        fmap_derivatives_wf.inputs.inputnode.fmap_meta = metadata_dicts
+
+        fmap_reports_wf = init_fmap_reports_wf(
+            output_dir=str(outdir),
+            fmap_type='medic',
+        )
+        fmap_reports_wf.inputs.inputnode.source_files = [str(f) for f in magnitude_files]
+
+        wf.connect([
+            (medic_wf, fmap_reports_wf, [
+                ("outputnode.fmap", "inputnode.fieldmap"),
+            ]),
+            (medic_wf, fmap_derivatives_wf, [
+                ("outputnode.fmap", "inputnode.fieldmap"),
+            ]),
+        ])  # fmt:skip
+    else:
+        wf.add_nodes([medic_wf])
+
+    if workdir:
+        wf.base_dir = str(workdir)
+
+    wf.run(plugin="Linear")