Retain only 3D feature calc for config C

aditiiyer · Mar 27, 2024 · 8ca5d83 · 8ca5d83
1 parent 7a585c5
commit 8ca5d83
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Showing 5 changed files with 58 additions and 242 deletions.
diff --git a/cerr/datasets/radiomics_settings/IBSIsettings/IBSI1/IBSI1IDC1.json b/cerr/datasets/radiomics_settings/IBSIsettings/IBSI1/IBSI1IDC1.json
@@ -8,87 +8,76 @@
 
 "settings": {		   
 
-             "resample": {
+            "resample": {
 				 "resolutionXCm": 0.2,
 				 "resolutionYCm": 0.2,
 				 "resolutionZCm": 0.2,
 				 "interpMethod": "linear",
-				 "intensityRounding": "On"
+                                 "intensityRounding": "On"
 			},
-			
-	     "padding": {
-			                         "method": "expand",
-			                         "size": [10,10,10]
+
+           "padding": {
+                         "method": "expand",
+                         "size": [10,10,10]
                       },
-
-	     "perturbation": {
-			           },
+
 
-	     "firstOrder" :{ 
+            "perturbation": {
+			           },
+
+	    "firstOrder" :{ 
 				   "binWidthEntropy": 25,
 				   "offsetForEnergy": 0
-                                 },
-
-	     "texture" :{ 
+                               },
+		           
+            "texture" :{ 
 				"binwidth": 25,
 		                "minSegThreshold": -1000,
 		                "maxSegThreshold": 400,
                 		"minClipIntensity": -1000,
                 		"maxClipIntensity": 400,
-		                "directionality": "2D",
+		                "directionality": "3D",
 				"avgType": "texture",
 				"voxelOffset": 1,
-				"patchRadiusVox": [1, 1, 0],
+				"patchRadiusVox": [1, 1, 1],
 				"imgDiffThresh": 0
                               },
-
-		   "shape" :{ 
-			       "rcs": []
-                            },
-
-		  "ivh" :{ 
-			    "binwidth": 2.5,
-			    "xForIxPct": [10, 20, 30, 40, 50, 60, 70, 80, 90],
-			    "xForIxCc": [],
-			    "xForVxPct": [10, 20, 30, 40, 50, 60, 70, 80, 90],
-			    "xForVxAbs": []		
-                         },
-
-                  "mapFeaturenamesToIBSI": "yes"
+
+            "ivh" :{ 
+	     	    			    "binwidth": 2.5,
+	     	    			    "xForIxPct": [10, 20, 30, 40, 50, 60, 70, 80, 90],
+	     	    			    "xForIxCc": [],
+	     	    			    "xForVxPct": [10, 20, 30, 40, 50, 60, 70, 80, 90],
+	     	    			    "xForVxAbs": []		
+	                              },
+
+            "mapFeaturenamesToIBSI": "yes"
 
 	    },
 
 
  "featureClass":{
 
 
-        "shape": {
-			"featureList": ["all"]
+		"glcm": {
+			    	  "featureList": ["all"]
                  },
 
-        "firstOrder": {
-			 "featureList": ["all"]
-		},
-
-        "glcm": {
-			 "featureList": ["all"]
-                },
-
-	"glrlm": {
-			 "featureList": ["all"]
+		"glrlm": {
+			    	  "featureList": ["all"]
 
 		 },
-
-	"glszm": {
-		        "featureList": ["all"]  
-                 },
-
-	"gldm": {
-			 "featureList": ["all"]
-                },
-
-	"gtdm": {			    	
-                         "featureList": ["all"]               
+		 
+		"glszm": {
+		 		 		        "featureList": ["all"]  
+		},
+		 		 
+		"gldm": {
+		 		 			 "featureList": ["all"]
+		},
+		 		 
+		"gtdm": {			    	
+		 		                          "featureList": ["all"]               
 		}
 
 

diff --git a/cerr/datasets/radiomics_settings/IBSIsettings/IBSI1/IBSI1IDC2.json b/cerr/datasets/radiomics_settings/IBSIsettings/IBSI1/IBSI1IDC2.json
@@ -36,21 +36,21 @@
 		                "maxSegThreshold": 400,
                 		"minClipIntensity": -1000,
                 		"maxClipIntensity": 400,
-		                "directionality": "2D",
+		                "directionality": "3D",
 				"avgType": "feature",
 				"voxelOffset": 1,
-				"patchRadiusVox": [1, 1, 0],
+				"patchRadiusVox": [1, 1, 1],
 				"imgDiffThresh": 0
                               },
 
             "ivh" :{ 
-	    			    "binwidth": 2.5,
-	    			    "xForIxPct": [10, 20, 30, 40, 50, 60, 70, 80, 90],
-	    			    "xForIxCc": [],
-	    			    "xForVxPct": [10, 20, 30, 40, 50, 60, 70, 80, 90],
-	    			    "xForVxAbs": []		
-                         },
-
+	  	    			    "binwidth": 2.5,
+	  	    			    "xForIxPct": [10, 20, 30, 40, 50, 60, 70, 80, 90],
+	  	    			    "xForIxCc": [],
+	  	    			    "xForVxPct": [10, 20, 30, 40, 50, 60, 70, 80, 90],
+	  	    			    "xForVxAbs": []		
+	                           },
+	                                
             "mapFeaturenamesToIBSI": "yes"
 
 	    },
@@ -69,19 +69,18 @@
 		 },
 
 		"glszm": {
-		 		        "featureList": ["all"]  
+		 		 		        "featureList": ["all"]  
 		},
-
+		 		 
 		"gldm": {
-		 			 "featureList": ["all"]
+		 		 			 "featureList": ["all"]
 		},
-
+		 		 
 		"gtdm": {			    	
-		                          "featureList": ["all"]               
+		 		                          "featureList": ["all"]               
 		}
 
 
-
             }
 
 }
diff --git a/cerr/datasets/radiomics_settings/IBSIsettings/IBSI1/IBSI1IDC3.json b/cerr/datasets/radiomics_settings/IBSIsettings/IBSI1/IBSI1IDC3.json
diff --git a/cerr/datasets/radiomics_settings/IBSIsettings/IBSI1/IBSI1IDC4.json b/cerr/datasets/radiomics_settings/IBSIsettings/IBSI1/IBSI1IDC4.json
diff --git a/tests/IBSI1tests.py b/tests/IBSI1tests.py
@@ -59,7 +59,7 @@ def compareVals(cerrFeatS, refFeatNames, refValsV, tolV):
 
         # Find matching reference feature value
         matchName = featName[sepIdx+1:]
-        matchName = matchName.replace('_3D','')
+        #matchName = matchName.replace('_3D','')
         matchIdx = refFeatNames.index(matchName) if matchName in refFeatNames else None
         ibsiFeatList[featIdx] = matchName
 
@@ -82,11 +82,11 @@ def run_tests():
     structNum = 0
 
     # Feature extraction settings
-    configList = ['A1','A2','B1','B2','C1','C2','C3','C4']
+    configList = ['A1','A2','B1','B2','C1','C2']
 
     #A1: 2.5D, texture calc. combine across directions | A2: 2.5D, texture calc. per direction
     #B1: 2.5D, texture calc. combine across directions | B2: 2.5D, texture calc. per direction
-    #C1: 2.5D, texture calc. combine across directions | C2: 2.5D, texture calc. per direction | C3: 3D, texture calc. combine across directions | C4: 3D, texture calc. per direction
+    #C1: 3D, texture calc. combine across directions   | C2: 3D, texture calc. per direction
 
     # Loop over settings
     for idx in range(len(configList)):