Adding site specific __[setup:paths]softwareSrc__ replace pattern to allow for site specific path to software

pythonScripts/runSegmentationDM.py

@@ -201,7 +201,7 @@ def doSegmentation(parameterFile):
     with open(parameterFile) as f:
         pars=json.load(f)
 
-    pars=parseConfig.convert(pars)
+    pars=parseConfig.convert(pars,setup)
     pars=parseConfig.convertValues(pars)
     print(pars)
     

templates/segmentationIRAEMM_ONKO_retro_DM.json

@@ -1,9 +1,9 @@
 {
  "setVariables":["__tempBase__","__segBase__","__segModelPath__","__roiFile__","__petFile__","__ctFile__","__segFile__","__modelName__"],
  "setVariablesComment":"this variables will get updated with local values like home and can be used to set variables further on",
- "__tempBase__":"__home__/temp/iraemm",
- "__segBase__":"/home/studen/software/src/irAEMM/segmentation",
- "__segModelPath__":"/home/studen/software/src/iraemmsegmentationmodels",
+ "__tempBase__":"__[env]home__/temp/iraemm",
+ "__segBase__":"__[setup:paths]softwareSrc__/irAEMM/segmentation",
+ "__segModelPath__":"__[setup:paths]softwareSrc__/iraemmsegmentationmodels",
  "__roiFile__":"testMask.nii.gz",
  "__ctFile__":"testCT.nii.gz",
  "__petFile__":"testPET.nii.gz",
@@ -47,15 +47,6 @@
 	 "__cnnModelPath__":"__segModelPath__",
 	 "__model__":"__modelName__"
  },
- "nnUNet":{
-	 "ModelId":"501",
-	 "configuration":"3d_fullres",
-	 "env":{
-		"nnUNet_raw_data_base":"__tempBase__",
-		"nnUNet_preprocessed":"__tempBase__",
-		"RESULTS_FOLDER":"/home/studen/software/src/iraemmsegmentationmodels"
-	 }
- },
  "deepmedic": {
 	 "config":{
 		 "model":{