Merge pull request #3 from dvm-shlee/main

quick patch

plugin/bids/manifest.yaml

@@ -1,23 +1,20 @@
 name: bids
-
+type: plugin
+subtype: tonifti
 version: 0.0.1
+source: bids.py::Bids
 
 authors:
 - Sung-Ho Lee ([email protected])
-
 license: MIT
 description: "BIDS plugin for tonifti app"
 documentation: "README.md"
 citation: CITATION.cff
 
-app:
-  target: tonifti
-  src: bids.py::Bids
-
 dependencies:
 - numpy>=1.18
 
-script:
+argparser:
   name: bids
   help: plugin function for converting file based on various BIDS specification
   arguments:

plugin/myplugin/manifest.yaml

@@ -1,28 +1,25 @@
 name: myplugin
-
+type: plugin
+subtype: tonifti
 version: 0.0.1
+source: myplugin.py::MyPlugIn
 
 authors:
-- Sung-Ho Lee ([email protected])
-
-license: YourLicense
+- MyName ([email protected])
+license: MyLicense
 description: "My plugin."
 documentation: "README.md"
 citation: CITATION.cff
 
-app:
-  target: tonifti
-  src: myplugin.py::MyPlugIn
-
 dependencies:
 - numpy>=1.18
 
-script:
+argparser:
   name: myplugin
-  help: plugin function for SORDINO-MRI reconstruction
+  help: plugin function to multiply dataobj by 2
   arguments:
     - name: "--option"
-      help: "Option for command line integration."
+      help: "Option to activate multiplying dataobj by 2."
       action: "store_true"
       default: false
 

plugin/myplugin/myplugin.py

@@ -108,9 +108,9 @@ def get_dataobj(self, reco_id: Optional[int] = None) -> NDArray:
             dataobj *= 2
         return dataobj
 
-    def get_affine(self, reco_id:Optional[int]=None, 
-                   subj_type:Optional[str]=None, 
-                   subj_position:Optional[str]=None) -> NDArray:
+    def get_affine(self, reco_id: Optional[int] = None, 
+                   subj_type: Optional[str] = None, 
+                   subj_position: Optional[str] = None) -> NDArray:
         """Retrieve the affine transformation matrix.
 
         Args:
@@ -121,10 +121,10 @@ def get_affine(self, reco_id:Optional[int]=None,
         Returns:
             NDArray: Affine transformation matrix.
         """
-        return super().get_affine(scanobj=self, 
-                                  reco_id=reco_id, 
-                                  subj_type=subj_type, 
-                                  subj_position=subj_position)
+        return super().get_affine(scanobj = self, 
+                                  reco_id = reco_id, 
+                                  subj_type = subj_type, 
+                                  subj_position = subj_position)
 
     def get_nifti1header(self) -> Nifti1Header:
         """Retrieve the NIfTI header updated as necessary for this plugin.

plugin/sordino/manifest.yaml

@@ -1,7 +1,8 @@
 name: sordino
 type: plugin
-
+subtype: tonifti
 version: 24.4.27
+source: sordino.py::Sordino
 
 authors:
 - Sung-Ho Lee ([email protected])
@@ -13,17 +14,12 @@ license: MIT
 description: "This plugin converts SORDINO-MRI (acquired in radial trajectory) to NIfTI format."
 documentation: "README.md"
 citation: CITATION.cff
-
-app:
-  target: tonifti
-  src: sordino.py::Sordino
-
 dependencies:
 - numpy>=1.18
 - scipy>=1.11.1
 - sigpy>=0.1.26
 
-script:
+argparser:
   name: sordino
   help: plugin function for SORDINO-MRI reconstruction
   arguments:

bids-recipes/bids-recipes_v1.2.2_brkraw.yaml → recipe/recipe_bids_v1.2.2_brkraw.yaml

@@ -1,3 +1,6 @@
+name: bids_v1.2.2_brkraw
+type: recipe
+subtype: bids-file_metadata
 startup:
   - 'import numpy as np'
 

recipe/recipe_studyinfo_v0.0.1_brkraw.yaml

@@ -0,0 +1,50 @@
+name: studyinfo_v0.0.1_brkraw
+type: recipe
+subtype: studyinfo
+startup: 
+- 
+
+study:
+  date:
+  - header.study_date
+  - header.date
+  dob: header.dbirth
+  id: header.id
+  name: header.name_string
+  operator: study_operator
+  position:
+  - header.study_instrument_position
+  - entry: header.entry
+    position: header.position
+    script: entry.split("_").pop(-1) + "_" + position.split("_").pop(-1)
+  sex:
+  - header.gender
+  - header.sex
+  study_name: header.study_name
+  study_nr: header.study_nr
+  sw_version: header.sw_version
+  type: header.type
+  weight:
+  - header.study_weight
+  - header.weight
+
+scan:
+  dim: image.dim
+  in_plane_shape: image.shape
+  in_plann_resolution: image.resolution
+  method: protocol.scan_method
+  num_cycles: cycle.num_cycles
+  num_slice_packs: slicepack.num_slice_packs
+  num_slices_each_pack: slicepack.num_slices_each_pack
+  ppg: protocol.pulse_program
+  protocol: protocol.protocol_name
+  slice_distances_each_pack: slicepack.slice_distances_each_pack
+  slice_order_scheme: slicepack.slice_order_scheme
+  time_step: cycle.time_step
+
+reco:
+  dim_description:
+    dim_desc: image.dim_desc
+    fg_desc: frame_group.id
+    script: dim_desc + [f.split("_")[-1].lower() for f in fg_desc]
+  type: frame_group.type

bids-spec/bids-spec_v1.2.2_brkraw.yaml → spec/spec_bids_v1.2.2_brkraw.yaml

@@ -1,3 +1,6 @@
+name: bids_v1.2.2_brkraw
+type: bids-spec
+subtype: converter
 brkraw:
   path:
     type: string