collated all parcellations to a single directory before returning

Author: tclose

specs/australian-imaging-service/mri/human/neuro/t1w/preprocess.yaml

@@ -108,6 +108,10 @@ commands:
         column_defaults:
           datatype: medimage/nifti-gz # medimage/dicom-series  # the default
     outputs: # List the outputs generated by the pipeline
+      parcellations:
+        field: parcellations
+        datatype: medimage-mrtrix3/image-format+directory-of # MIME-type or "MIME-like" format
+        help: generated parcellation images # description of field presented in UI
       vis_image_fsl:
         field: vis_image_fsl
         datatype: medimage-mrtrix3/image-format-gz # MIME-type or "MIME-like" format
@@ -132,98 +136,6 @@ commands:
         field: ftt_image_hsvs
         datatype: medimage-mrtrix3/image-format-gz # MIME-type or "MIME-like" format
         help: 5tt image HSVS # description of field presented in UI
-      aparca2009s:
-        field: aparca2009s
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: aparca2009s parcellation image
-      aparc:
-        field: aparc
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: aparc parcellation image
-      desikan:
-        field: desikan
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: desikan parcellation image
-      destrieux:
-        field: destrieux
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: destrieux parcellation image
-      economo:
-        field: economo
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: economo parcellation image
-      glasser360:
-        field: glasser360
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: glasser360 parcellation image
-      hcpmmp1:
-        field: hcpmmp1
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: hcpmmp1 parcellation image
-      schaefer100:
-        field: schaefer100
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: schaefer100 parcellation image
-      schaefer1000:
-        field: schaefer1000
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: schaefer1000 parcellation image
-      schaefer200:
-        field: schaefer200
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: schaefer200 parcellation image
-      schaefer300:
-        field: schaefer300
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: schaefer300 parcellation image
-      schaefer400:
-        field: schaefer400
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: schaefer400 parcellation image
-      schaefer500:
-        field: schaefer500
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: schaefer500 parcellation image
-      schaefer600:
-        field: schaefer600
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: schaefer600 parcellation image
-      schaefer700:
-        field: schaefer700
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: schaefer700 parcellation image
-      schaefer800:
-        field: schaefer800
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: schaefer800 parcellation image
-      schaefer900:
-        field: schaefer900
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: schaefer900 parcellation image
-      vosdewael100:
-        field: vosdewael100
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: vosdewael100 parcellation image
-      vosdewael200:
-        field: vosdewael200
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: vosdewael200 parcellation image
-      vosdewael300:
-        field: vosdewael300
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: vosdewael300 parcellation image
-      vosdewael400:
-        field: vosdewael400
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: vosdewael400 parcellation image
-      yeo17:
-        field: Yeo17
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: Yeo17 parcellation image
-      yeo7:
-        field: Yeo7
-        datatype: medimage-mrtrix3/image-format # MIME-type or "MIME-like" format
-        help: Yeo7 parcellation image
     parameters:
       parcellation:
         datatype: field/text # Format of the field

src/australianimagingservice/mri/human/neuro/t1w/preprocess.py

@@ -10,16 +10,19 @@
     FivettGen_Freesurfer,
     FivettGen_Fsl,
 )
-from fileformats.generic import Directory
+from fileformats.generic import Directory, DirectoryOf
 from fileformats.medimage import NiftiGz
+from fileformats.medimage_mrtrix3 import ImageFormat as Mif
 from pydra.tasks.fastsurfer.latest import Fastsurfer
+from pydra.engine.task import FunctionTask
+from pydra.engine.specs import BaseSpec
 from pathlib import Path
 import os
 
 os.environ["SUBJECTS_DIR"] = ""
 
 
-def preprocess(
+def single_parc(
     parcellation: str,
     freesurfer_home: Path,
     mrtrix_lut_dir: Path,
@@ -1033,7 +1036,7 @@ def join_task_catalogue(
 ]  # List of different parcellations
 
 
-def preprocess_all_parcs(
+def all_parcs(
     freesurfer_home: Path,
     mrtrix_lut_dir: Path,
     cache_dir: Path,
@@ -1055,6 +1058,28 @@ def preprocess_all_parcs(
         cache_dir=cache_dir,
     )
 
+    def collate_parcs(out_dir: Path, **parcs: Mif) -> DirectoryOf[Mif]:  # type: ignore[type-arg]
+        for name, parc in parcs.values():
+            parc.copy(out_dir, new_stem=name)
+        return DirectoryOf[Mif](out_dir)  # type: ignore[no-any-return,type-arg,misc]
+
+    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]
+            ),
+        )
+    )
+
     for parcellation in parcellation_list:
 
         wf.add(
@@ -1071,8 +1096,13 @@ def preprocess_all_parcs(
             )
         )
 
-        wf.set_output([(parcellation, getattr(wf, parcellation).lzout.parc_image)])
+        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))

src/australianimagingservice/mri/human/neuro/t1w/tests/test_preprocess.py

@@ -1,5 +1,5 @@
-from australianimagingservice.mri.human.neuro.t1w.preprocess import preprocess
+from australianimagingservice.mri.human.neuro.t1w.preprocess import all_parcs
 
 
 def test_t1w_preprocess():
-    preprocess()
+    all_parcs()