Update zenodo sample testing for FMCIB and add file annotations (#107)

Co-authored-by: Leonard Nürnberg <[email protected]>

Author: surajpaib

models/fmcib_radiomics/config/default.yml

@@ -31,4 +31,13 @@ modules:
     targets:
     - csv-->[i:sid]/features.csv
   # - nifit:mod=seg:origin=dicomseg-->[i:sid]/masks/[basename]
-  # - nifti-->[i:sid]/nifti/[d:mod]/[basename]
+  # - nifti-->[i:sid]/nifti/[d:mod]/[basename]
+
+sample:
+  input:
+    dicom/: Dicom files of the CT scan and the DICOMSEG file containing the segmentations.
+    dicom/1.3.6.1.4.1.14519.5.2.1.4334.1501.312037286778380630549945195741/1-1.dcm: DICOMSEG file (arbitrary file name)
+    dicom/1.3.6.1.4.1.14519.5.2.1.4334.1501.312037286778380630549945195741/0.dcm: CT slice (arbitrary file name)
+    dicom/1.3.6.1.4.1.14519.5.2.1.4334.1501.312037286778380630549945195741/1.dcm: CT slice (arbitrary file name)
+  output:
+    1.3.6.1.4.1.14519.5.2.1.4334.1501.312037286778380630549945195741/features.csv: The CSV file containing a set of features extracted from the input CT image

models/fmcib_radiomics/config/from_centroids.yml

@@ -18,3 +18,11 @@ modules:
   DataOrganizer:
     targets:
     - csv-->[i:patientID]/features.csv
+
+sample:
+  input:
+    LUNG1-001/: A folder named after a instance identifier LUNG1-001
+    LUNG1-001/centroids.json: A file named centroids.json containing the centroids of the ROIs per instance
+    LUNG1-001/CT.nrrd: A nrrd file named CT.nrrd containing the CT image per instance
+  output:
+    LUNG1-001/features.csv: The CSV file containing a set of features extracted from the input CT image per instance

models/fmcib_radiomics/config/from_json.yml

@@ -20,3 +20,11 @@ modules:
   DataOrganizer:
     targets:
       - csv-->[i:sid]/features.csv
+
+sample:
+  input:
+    1.3.6.1.4.1.32722.99.99.298991776521342375010861296712563382046.json: Json file with centroids named by the SeriesInstanceUID of the related CT image
+    CT_1.3.6.1.4.1.32722.99.99.298991776521342375010861296712563382046/: Input directory
+      containing the CT image
+  output:
+    1.3.6.1.4.1.32722.99.99.298991776521342375010861296712563382046/features.csv: The CSV file containing a set of features extracted from the input CT image

models/fmcib_radiomics/config/from_nifti_mask.yml

@@ -19,3 +19,10 @@ modules:
   DataOrganizer:
     targets:
       - csv-->[i:patientID]/features.csv
+
+sample:
+  input:
+    lung_001/CT.nii.gz: A nifti file named containing the CT image per instance
+    lung_001/masks/GTV.nii.gz: A nifti file with a binary gtv label map which center is used as seed point
+  output:
+    lung_001/features.csv: The CSV file containing a set of features extracted from the input CT image

models/fmcib_radiomics/config/from_rtstruct.yml

@@ -30,4 +30,13 @@ modules:
   DataOrganizer:
     targets:
       - csv-->[i:sid]/features.csv
-        # - nifti-->[i:sid]/nifti/[d:mod]/[basename]
+        # - nifti-->[i:sid]/nifti/[d:mod]/[basename]
+
+sample:
+  input:
+    RTSTRUCT_1.2.246.352.71.2.494841863751.4253616.20190218155318/: Arbitrary input directory
+      containing the RTStruct dicom file 
+    CT_1.3.6.1.4.1.9590.100.1.2.170217758912108379426621313680109428629/: Arbitrary input directory
+      containing the CT image
+  output:
+    1.3.6.1.4.1.9590.100.1.2.170217758912108379426621313680109428629/features.csv: The CSV file containing a set of features extracted from the input CT image

models/fmcib_radiomics/config/from_slicer.yml

@@ -18,3 +18,10 @@ modules:
   DataOrganizer:
     targets:
       - csv-->[i:patientID]/features.csv
+
+sample:
+  input:
+    1.3.6.1.4.1.32722.99.99.239341353911714368772597187099978969331/0 Unnamed Series.nrrd: A nrrd file named containing the CT image per instance
+    1.3.6.1.4.1.32722.99.99.239341353911714368772597187099978969331/F.mrk.json: A slicer markup file named containing seed point for the ROI
+  output:
+    1.3.6.1.4.1.32722.99.99.239341353911714368772597187099978969331/features.csv: The CSV file containing a set of features extracted from the input CT image

models/fmcib_radiomics/mhub.toml

@@ -1,2 +1,2 @@
 [model.deployment]
-test = "https://zenodo.org/records/14205464/files/test.zip"
+test = "https://zenodo.org/records/14947770/files/test_fmcib_latest.zip"