reorganize configs

models/fmcib_radiomics/config/default.yml

@@ -1,21 +1,22 @@
 general:
   data_base_dir: /app/data
   version: 1.0
-  description: "FMCIB pipeline"
+  description: FMCIB pipeline starting from DICOM files and centroids in json files or slicer exports named by their SeriesInstanceUID
 
 execute:
-- FileStructureImporter
-- CentroidExtractor
+- DicomImporter
+- FileImporter
+- NiftiConverter
 - FMCIBRunner
 - DataOrganizer
 
 modules:
-  FileStructureImporter:
-    structures:
-      - $patientID/CT.nrrd@instance@nrrd:mod=ct
-      - $patientID/masks/GTV-1.nrrd@nrrd:mod=seg
-    import_id: patientID
+
+  FileImporter:
+    instance_id: sid
+    meta: type=fmcibcoordinates
+    type: json
 
   DataOrganizer:
     targets:
-      - json:type=fmcibfeatures-->[i:patientID]/features.json
+      - json:type=fmcibfeatures-->[i:sid]/features.json

models/fmcib_radiomics/config/from_nrrd_mask.yml

@@ -0,0 +1,21 @@
+general:
+  data_base_dir: /app/data
+  version: 1.0
+  description: "FMCIB pipeline starting from a nrrd file image and a nnrd binary mask of the GTV."
+
+execute:
+- FileStructureImporter
+- CentroidExtractor
+- FMCIBRunner
+- DataOrganizer
+
+modules:
+  FileStructureImporter:
+    structures:
+      - $patientID/CT.nrrd@instance@nrrd:mod=ct
+      - $patientID/masks/GTV-1.nrrd@nrrd:mod=seg
+    import_id: patientID
+
+  DataOrganizer:
+    targets:
+      - json:type=fmcibfeatures-->[i:patientID]/features.json