fixed up location of collate_parcs, i.e. within all_parcs workflow

Australian-Imaging-Service · Nov 18, 2024 · f688029 · f688029
1 parent 79ded64
commit f688029
Showing 1 changed file with 73 additions and 50 deletions.
diff --git a/src/australianimagingservice/mri/human/neuro/t1w/preprocess.py b/src/australianimagingservice/mri/human/neuro/t1w/preprocess.py
@@ -1019,55 +1019,6 @@ def join_task_catalogue(
             ),
         ]
     )
-
-    wf.add(
-        FunctionTask(
-            collate_parcs,
-            name="collate_parcs",
-            input_spec=SpecInfo(
-                name="CollateParcsInputs",
-                bases=(BaseSpec,),
-                fields=[(p, Mif) for p in parcellation_list],
-            ),
-            output_spec=SpecInfo(
-                name="CollateParcsOutputs",
-                bases=(BaseSpec,),
-                fields=[("out_dir", DirectoryOf[Mif])],  # type: ignore[misc]
-            ),
-            out_dir="out_dir",
-        )
-    )
-
-    for parcellation in parcellation_list:
-
-        wf.add(
-            single_parc(
-                t1w=wf.lzin.t1w,
-                parcellation=parcellation,
-                freesurfer_home=freesurfer_home,
-                mrtrix_lut_dir=mrtrix_lut_dir,
-                cache_dir=cache_dir,
-                fs_license=fs_license,
-                fastsurfer_executable=fastsurfer_executable,
-                fastsurfer_python=fastsurfer_python,
-                name=parcellation,
-            )
-        )
-
-        setattr(
-            wf.collate_parcs.inputs,
-            parcellation,
-            getattr(wf, parcellation).lzout.parc_image,
-        )
-
-    wf.set_output(("parcellations", wf.collate_parcs.lzout.out_dir))
-    wf.set_output(("vis_image_fsl", wf.desikan.lzout.vis_image_fsl))
-    wf.set_output(("ftt_image_fsl", wf.desikan.lzout.ftt_image_fsl))
-    wf.set_output(("vis_image_freesurfer", wf.desikan.lzout.vis_image_freesurfer))
-    wf.set_output(("ftt_image_freesurfer", wf.desikan.lzout.ftt_image_freesurfer))
-    wf.set_output(("vis_image_hsvs", wf.desikan.lzout.vis_image_hsvs))
-    wf.set_output(("ftt_image_hsvs", wf.desikan.lzout.ftt_image_hsvs))
-
     return wf
 
 
@@ -1118,11 +1069,59 @@ def all_parcs(
     }
 
     wf = Workflow(
-        name="t1_processing_pipeline",
+        name=name,
         input_spec=input_spec,
         cache_dir=cache_dir,
     )
 
+    wf.add(
+        FunctionTask(
+            collate_parcs,
+            name="collate_parcs",
+            input_spec=SpecInfo(
+                name="CollateParcsInputs",
+                bases=(BaseSpec,),
+                fields=[(p, Mif) for p in parcellation_list],
+            ),
+            output_spec=SpecInfo(
+                name="CollateParcsOutputs",
+                bases=(BaseSpec,),
+                fields=[("out_dir", DirectoryOf[Mif])],  # type: ignore[misc]
+            ),
+            out_dir="out_dir",
+        )
+    )
+
+    for parcellation in parcellation_list:
+
+        wf.add(
+            single_parc(
+                t1w=wf.lzin.t1w,
+                parcellation=parcellation,
+                freesurfer_home=freesurfer_home,
+                mrtrix_lut_dir=mrtrix_lut_dir,
+                cache_dir=cache_dir,
+                fs_license=fs_license,
+                fastsurfer_executable=fastsurfer_executable,
+                fastsurfer_python=fastsurfer_python,
+                name=parcellation,
+            )
+        )
+
+        setattr(
+            wf.collate_parcs.inputs,
+            parcellation,
+            getattr(wf, parcellation).lzout.parc_image,
+        )
+
+    wf.set_output(("parcellations", wf.collate_parcs.lzout.out_dir))
+    wf.set_output(("vis_image_fsl", wf.desikan.lzout.vis_image_fsl))
+    wf.set_output(("ftt_image_fsl", wf.desikan.lzout.ftt_image_fsl))
+    wf.set_output(("vis_image_freesurfer", wf.desikan.lzout.vis_image_freesurfer))
+    wf.set_output(("ftt_image_freesurfer", wf.desikan.lzout.ftt_image_freesurfer))
+    wf.set_output(("vis_image_hsvs", wf.desikan.lzout.vis_image_hsvs))
+    wf.set_output(("ftt_image_hsvs", wf.desikan.lzout.ftt_image_hsvs))
+
     return wf
 
 
@@ -1142,3 +1141,27 @@ def collate_parcs(out_dir: Path = None, **parcs: "Mif") -> "DirectoryOf[Mif]":
 
     wf = all_parcs(*args)  # type: ignore[arg-type]
     wf(t1w=sys.argv[1])
+# if __name__ == "__main__":
+#     import sys
+
+#     # Expecting the first argument to be the T1-weighted image path
+#     t1w_path = sys.argv[1]
+
+#     # Provide sensible default values or pass from command-line arguments
+#     # freesurfer_home = "/Applications/freesurfer/"  # Adjust this path as per your setup
+#     # mrtrix_lut_dir = "/Users/arkievdsouza/mrtrix3/share/mrtrix3/labelconvert/"  # Adjust this path as per your setup
+#     # cache_dir = "/Users/arkievdsouza/git/t1-pipeline/working-dir/"  # Temporary directory for cache
+#     # fs_license = (
+#     #     "/Applications/freesurfer/license.txt "  # Path to the FreeSurfer license file
+#     # )
+
+#     # Pass the arguments explicitly
+#     wf = all_parcs(*sys.argv[1])
+#     #     freesurfer_home=freesurfer_home,
+#     #     mrtrix_lut_dir=mrtrix_lut_dir,
+#     #     cache_dir=cache_dir,
+#     #     fs_license=fs_license,
+#     # )  # type: ignore[arg-type]
+
+#     # # Run the workflow with the T1-weighted image as input
+#     wf(t1w=t1w_path)