Fixed tests/settings for IBSI2 phase-2

aditiiyer · Apr 9, 2024 · a844bc3 · a844bc3
1 parent 47c82b1
commit a844bc3
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Showing 16 changed files with 296 additions and 210 deletions.
diff --git a/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID1a.json b/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID1a.json
@@ -17,7 +17,10 @@
                        },
                    "firstOrder" :{ 
 				            "offsetForEnergy": 0,
-                            		    "binWidthEntropy":0 }
+                            		    "binWidthEntropy":0 },
+
+                   "mapFeaturenamesToIBSI": "yes"
+
                  },
 
 "featureClass": { 

diff --git a/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID1b.json b/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID1b.json
@@ -8,11 +8,10 @@
 
 "settings": {		   
                 "resample": {
-                     "resolutionXCm": 0.1,
+                     		     "resolutionXCm": 0.1,
 				     "resolutionYCm": 0.1,
 				     "resolutionZCm": 0.1,
-				     "interpMethod": "bspline",
-                     "intensityRounding": "On"
+				     "interpMethod": "bspline"
 			        },
 
                    "padding": {
@@ -27,7 +26,10 @@
                    "firstOrder" :{ 
 				            "offsetForEnergy": 0,
                             "binWidthEntropy":0
-                   }
+                   },
+
+                  "mapFeaturenamesToIBSI": "yes"
+
  },
 
  "featureClass": { 

diff --git a/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID2a.json b/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID2a.json
@@ -21,8 +21,11 @@
                        },
                    "firstOrder" :{ 
 				            "offsetForEnergy": 0,
-                            "binWidthEntropy":0
-                   }
+                            		    "binWidthEntropy":0
+                   },
+
+                  "mapFeaturenamesToIBSI": "yes"
+
 	},
 
 	"featureClass": { 

diff --git a/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID2b.json b/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID2b.json
@@ -10,11 +10,11 @@
 
 "settings": {		   
                 "resample": {
-                     "resolutionXCm": 0.1,
+                     		     "resolutionXCm": 0.1,
 				     "resolutionYCm": 0.1,
 				     "resolutionZCm": 0.1,
 				     "interpMethod": "bspline",
-                     "intensityRounding": "On"
+		                     "intensityRounding": "On"
 			        },
 
                    "padding": {
@@ -30,8 +30,11 @@
 
                    "firstOrder" :{ 
 				            "offsetForEnergy": 0,
-                            "binWidthEntropy":0
-                   }
+                            		    "binWidthEntropy":0
+                   },
+
+                  "mapFeaturenamesToIBSI": "yes"
+
 },
 
 "featureClass": { 

diff --git a/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID3a.json b/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID3a.json
@@ -24,8 +24,11 @@
 
                    "firstOrder" :{ 
 				            "offsetForEnergy": 0,
-                            "binWidthEntropy":0
-                   }
+                            		    "binWidthEntropy":0
+                   },
+
+                  "mapFeaturenamesToIBSI": "yes"
+
 
     },
     "featureClass": { 

diff --git a/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID3b.json b/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID3b.json
@@ -11,11 +11,11 @@
 
 "settings": {		   
                 "resample": {
-                     "resolutionXCm": 0.1,
+                     		     "resolutionXCm": 0.1,
 				     "resolutionYCm": 0.1,
 				     "resolutionZCm": 0.1,
 				     "interpMethod": "bspline",
-                     "intensityRounding": "On"
+                     		     "intensityRounding": "On"
 			        },
 
                    "padding": {
@@ -30,7 +30,10 @@
                    "firstOrder" :{ 
 				            "offsetForEnergy": 0,
                             "binWidthEntropy":0
-                   }
+                   },
+
+                  "mapFeaturenamesToIBSI": "yes"
+
     },
     "featureClass": { 
     			   	    "firstOrder": {"featureList": ["all"]}

diff --git a/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID4a.json b/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID4a.json
@@ -3,18 +3,18 @@
 "structures": ["ROI"],
 
 "imageType": {
-  		  "rotationInvariantLawsEnergy": {
-                "Direction": "2d",
-                "Type": "L5E5",
-	        "Normalize": "yes",
-                "RotationInvariance": {
-				       			"Dim": "2D",
-				       			"AggregationMethod": "max"
+  		"RotationInvariantLawsEnergy": {
+                			"Direction": "2d",
+                			"Type": "L5E5",
+	        			"Normalize": "yes",
+                			"RotationInvariance": {
+				       						"Dim": "2D",
+				       						"AggregationMethod": "max"
                 				  },
-                "EnergyKernelSize": [15,15],
-                "EnergyPadMethod": "mirror",
-                "EnergyPadSize" : [7,7,0]
-			  }
+                			"EnergyKernelSize": [15,15],
+                			"EnergyPadMethod": "mirror",
+                			"EnergyPadSize" : [7,7,0]
+			 	}
 	    },
 
 "settings": {		   
@@ -31,7 +31,9 @@
                    "firstOrder" :{ 
 				            "offsetForEnergy": 0,
                             		   "binWidthEntropy":0
-                   }
+                   },
+
+                   "mapFeaturenamesToIBSI": "yes"
 
     },
 

diff --git a/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID4b.json b/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID4b.json
@@ -3,27 +3,27 @@
 "structures": ["ROI"],
 
 "imageType": {
-  		  "rotationInvariantLawsEnergy": {
-                "Direction": "3d",
-                "Type": "L5E5E5",
-				"Normalize": "yes",
-                "RotationInvariance": {
+  		  "RotationInvariantLawsEnergy": {
+                			"Direction": "3d",
+                			"Type": "L5E5E5",
+					"Normalize": "yes",
+                			"RotationInvariance": {
 				       						"Dim": "3D",
 				       						"AggregationMethod": "max"
-                },
-                "EnergyKernelSize": [15,15,15],
-                "EnergyPadMethod": "mirror",
-                "EnergyPadSize" : [7,7,7]
-			  }
+               								 },
+                			"EnergyKernelSize": [15,15,15],
+                			"EnergyPadMethod": "mirror",
+                			"EnergyPadSize" : [7,7,7]
+			 	 }
 	    },
 
 "settings": {		   
                    "resample": {
-                     "resolutionXCm": 0.1,
+                     		     "resolutionXCm": 0.1,
 				     "resolutionYCm": 0.1,
 				     "resolutionZCm": 0.1,
 				     "interpMethod": "bspline",
-                     "intensityRounding": "On"
+                     		     "intensityRounding": "On"
 			        },
                    "padding": {
                    		"cropToMaskBounds": "no",
@@ -37,7 +37,9 @@
                    "firstOrder" :{ 
 				            "offsetForEnergy": 0,
                             "binWidthEntropy":0
-                   }
+                   },
+
+                  "mapFeaturenamesToIBSI": "yes"
 
     },
 

diff --git a/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID5a.json b/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID5a.json
@@ -5,11 +5,11 @@
 "imageType": {
   		  "Gabor": {
 			    	   "Sigma_mm": 5,
-				       "Wavlength_mm": 2,
-                       "SpatialAspectRatio": 1.5,
-                       "Orientation":[22.5,45,67.5,90,112.5,135,157.5,180,202.5,225,247.5,270,292.5,315,337.5,360],
-                       "OrientationAggregation": "average",
-                       "ImagePlane": "Axial"
+				   "Wavlength_mm": 2,
+                       		   "SpatialAspectRatio": 1.5,
+                       		   "Orientation":[22.5,45,67.5,90,112.5,135,157.5,180,202.5,225,247.5,270,292.5,315,337.5,360],
+                       		   "OrientationAggregation": "average",
+                       		   "ImagePlane": "Axial"
 			 	     }
 	    },
 
@@ -20,16 +20,19 @@
                                 "method": "mirror",  
                                 "size": [50,50,0]
                               },
+
                    "texture" :{ 
 		                         "minSegThreshold": -1000,
 		                         "maxSegThreshold": 400
 	                          },
+
                    "firstOrder" :{ 
 				            "offsetForEnergy": 0,
-                            "binWidthEntropy":0
-                            }
-
-
+                            		    "binWidthEntropy":0
+                            },
+
+                   "mapFeaturenamesToIBSI": "yes"
+
 	    },
 
 "featureClass": { 

diff --git a/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID5b.json b/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID5b.json
@@ -5,38 +5,42 @@
 "imageType": {
   		  "Gabor": {
 			    	   "Sigma_mm": 5,
-				       "Wavlength_mm": 2,
-                       "SpatialAspectRatio": 1.5,
-                       "Orientation":[22.5,45,67.5,90,112.5,135,157.5,180,202.5,225,247.5,270,292.5,315,337.5,360],
-                       "OrientationAggregation": "average",
-                       "ImagePlane": ["Axial","Sagittal","Coronal"],
-                       "PlaneAggregation": "average"
-			 	     }
+				   "Wavlength_mm": 2,
+                       		   "SpatialAspectRatio": 1.5,
+                       		   "Orientation":[22.5,45,67.5,90,112.5,135,157.5,180,202.5,225,247.5,270,292.5,315,337.5,360],
+                       		   "OrientationAggregation": "average",
+                       		   "ImagePlane": ["Axial","Sagittal","Coronal"],
+                       		   "PlaneAggregation": "average"
+			 	}
 	    },
 
 "settings": {		   
 
                    "resample": {
-                         "resolutionXCm": 0.1,
-				         "resolutionYCm": 0.1,
-				         "resolutionZCm": 0.1,
-				         "interpMethod": "sitkBSpline",
-                         "intensityRounding": "On"
+                         		"resolutionXCm": 0.1,
+				        "resolutionYCm": 0.1,
+				        "resolutionZCm": 0.1,
+				        "interpMethod": "bspline",
+                         		"intensityRounding": "On"
 			        },
+
                    "padding": {
                                 "cropToMaskBounds": "no",
                                 "method": "mirror",  
                                 "size": [49,49,49]
                               },
+
                    "texture" :{ 
 		                         "minSegThreshold": -1000,
 		                         "maxSegThreshold": 400
 	                          },
+
                    "firstOrder" :{ 
 				            "offsetForEnergy": 0,
-                            "binWidthEntropy":0
-                            }
-
+                            		    "binWidthEntropy":0
+                            },
+
+                   "mapFeaturenamesToIBSI": "yes"
 
 	    },
 

diff --git a/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID6a.json b/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID6a.json
@@ -29,9 +29,15 @@
                    "firstOrder" :{ 
 				            "offsetForEnergy": 0,
                             "binWidthEntropy":0
-                            }
-
+                            },
+
+                  "mapFeaturenamesToIBSI": "yes"
 
-	    }
+	    },
+
+"featureClass": { 
+	    	    			"firstOrder": {"featureList": ["all"]}
+	                }
+
 
 }
diff --git a/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID6b.json b/cerr/datasets/radiomics_settings/IBSIsettings/IBSI2Phase2/IBSIPhase2-2ID6b.json
@@ -37,9 +37,14 @@
                    "firstOrder" :{ 
 				            "offsetForEnergy": 0,
                             "binWidthEntropy":0
-                            }
-
-
-	    }
+                            },
+
+                   "mapFeaturenamesToIBSI": "yes"
+
+	    },
+
+"featureClass": { 
+	    	    			"firstOrder": {"featureList": ["all"]}
+	                }
 
 }
diff --git a/cerr/datasets/referenceValuesForTests/IBSI2Phase2/IBSIphase2-2_CERR_features.csv b/cerr/datasets/referenceValuesForTests/IBSI2Phase2/IBSIphase2-2_CERR_features.csv
@@ -1,24 +1,24 @@
-family,feature_name,feature_tag,ibsi_identifier,1.A,1.B,2.A,2.B,3.A,3.B,4.A,4.B,5.A,5.B,6.A,6.B,7.A,7.B,8.A,8.B,9.A,9.B,10.A,10.B,11.A,11.B
-Diagnostic,Number of voxels in ROI before interpolation,diag_n_voxel,0,125256,125256,125256,125256,125256,125256,125256,125256,125256,125256,125256,125256,,,,,,,,,,
-Diagnostic,Number of voxels in intensity ROI-mask after interpolation and resegmentation,diag_n_voxel_interp_reseg,1,125238,357802,125238,357802,125238,357802,125238,357802,125238,357802,125238,357802,,,,,,,,,,
-Diagnostic,Mean intensity in intensity ROI-mask after interpolation and resegmentation,diag_mean_int_interp_reseg,2,-46.9756,-46.4075,-46.9756,-46.4075,-46.9756,-46.4075,-46.9756,-46.4075,-46.9756,-46.4075,-46.9756,-46.4075,,,,,,,,,,
-Diagnostic,Max intensity in intensity ROI-mask after interpolation and resegmentation,diag_max_int_interp_reseg,3,377,377,377,377,377,377,377,377,377,377,377,377,,,,,,,,,,
-Diagnostic,Min intensity in intensity ROI-mask after interpolation and resegmentation,diag_min_int_interp_reseg,4,-1000,-997,-1000,-997,-1000,-997,-1000,-997,-1000,-997,-1000,-997,,,,,,,,,,
-Statistics,Mean,stat_mean,Q4LE,-46.9756,-46.4075,-49.8816,-49.8926,-2.4409,-2.9424,148.258,141.8271,102.9942,40.24,-0.18505,-0.19165,,,,,,,,,,
-Statistics,Variance,stat_var,ECT3,53338.7497,52636.8857,46616.9379,44392.8445,555.6829,719.6975,17953.6433,11118.4954,1036.2306,230.562,427.2793,258.4748,,,,,,,,,,
-Statistics,Skewness,stat_skew,KE2A,-2.1668,-2.1794,-2.1266,-2.1286,0.2953,0.42212,0.87706,0.64455,1.314,1.5747,0.083694,0.15965,,,,,,,,,,
-Statistics,(Excess) kurtosis,stat_kurt,IPH6,3.6451,3.7126,3.5277,3.5863,7.0161,6.1333,-0.27877,-0.71065,2.8417,4.3373,7.7218,8.7531,,,,,,,,,,
-Statistics,Median,stat_median,Y12H,41,41,38.08,37.336,-0.58489,-0.91947,88.7164,113.1384,97.0368,37.1933,0.045594,0.058616,,,,,,,,,,
-Statistics,Minimum,stat_min,1GSF,-1000,-997,-888.92,-906.176,-178.0502,-172.907,15.452,28.4672,31.3725,9.5348,-245.1464,-143.9796,,,,,,,,,,
-Statistics,10th percentile,stat_p10,QG58,-434,-427,-402.364,-389.3224,-27.102,-32.1572,26.877,35.5697,68.8025,24.6298,-18.8451,-14.1429,,,,,,,,,,
-Statistics,90th percentile,stat_p90,8DWT,93,92,79.84,77.248,13.2345,17.391,346.961,292.6233,144.5656,59.2863,17.7175,12.4719,,,,,,,,,,
-Statistics,Maximum,stat_max,84IY,377,377,334.16,316.312,190.6673,204.2998,672.2096,524.8028,353.6986,174.5559,201.6358,154.4726,,,,,,,,,,
-Statistics,Interquartile range,stat_iqr,SALO,69,67,82,92.584,8.7437,11.4459,219.2627,187.655,37.1797,17.3522,15.7707,9.8874,,,,,,,,,,
-Statistics,Range,stat_range,2OJQ,1377,1374,1223.08,1222.488,368.7175,377.2068,656.7576,496.3355,322.3261,165.0212,446.7822,298.4521,,,,,,,,,,
-Statistics,Mean absolute deviation,stat_mad,4FUA,160.0892,158.9223,152.5869,149.3422,13.1507,15.4966,116.0725,92.4481,24.2066,11.2782,13.0301,9.5143,,,,,,,,,,
-Statistics,Robust mean absolute deviation,stat_rmad,1128,64.4227,63.5967,67.7311,68.1352,4.9768,6.3688,92.892,75.9196,15.7577,7.3098,6.8152,4.4259,,,,,,,,,,
-Statistics,Median absolute deviation,stat_medad,N72L,121.7435,120.5444,115.8276,113.8108,12.9032,15.2606,110.7334,90.813,23.7017,10.9943,13.0283,9.5107,,,,,,,,,,
-Statistics,Coefficient of variation,stat_cov,7TET,-4.9164,-4.9438,-4.3284,-4.223,-9.6576,-9.1174,0.90377,0.74347,0.31255,0.37734,-111.7049,-83.8886,,,,,,,,,,
-Statistics,Quartile coefficient of dispersion,stat_qcod,9S40,1,0.94366,1.8502,2.9728,-2.9306,-2.3389,0.77305,0.69926,0.18686,0.22554,491.1043,-156.1466,,,,,,,,,,
-Statistics,Energy,stat_energy,N8CA,6956402357,19604163821,6149826557,16774513585,70338761.75,260607009.4,5001263504,11175381810,1458276196,661870210,53515894.29,92495949.33,,,,,,,,,,
-Statistics,Root mean square,stat_rms,5ZWQ,235.6808,234.0738,221.5967,216.5228,23.699,26.9881,199.8351,176.7298,107.9075,43.0096,20.6716,16.0783,,,,,,,,,,
+family,feature_name,feature_tag,ibsi_identifier,1a,1b,2a,2b,3a,3b,4a,4b,5a,5b,6a,6b
+Diagnostic,Number of voxels in ROI before interpolation,diag_n_voxel,0,125256,125256,125256,125256,125256,125256,125256,125256,125256,125256,125256,125256
+Diagnostic,Number of voxels in intensity ROI-mask after interpolation and resegmentation,diag_n_voxel_interp_reseg,1,125238,357802,125238,357802,125238,357802,125238,357802,125238,357802,125238,357802
+Diagnostic,Mean intensity in intensity ROI-mask after interpolation and resegmentation,diag_mean_int_interp_reseg,2,-46.9756,-46.4075,-46.9756,-46.4075,-46.9756,-46.4075,-46.9756,-46.4075,-46.9756,-46.4075,-46.9756,-46.4075
+Diagnostic,Max intensity in intensity ROI-mask after interpolation and resegmentation,diag_max_int_interp_reseg,3,377,377,377,377,377,377,377,377,377,377,377,377
+Diagnostic,Min intensity in intensity ROI-mask after interpolation and resegmentation,diag_min_int_interp_reseg,4,-1000,-997,-1000,-997,-1000,-997,-1000,-997,-1000,-997,-1000,-997
+Statistics,Mean,stat_mean,Q4LE,-46.9756,-46.4075,-49.8816,-49.8926,-2.4409,-2.9424,148.258,141.8271,102.9942,40.24,-0.18505,-0.19165
+Statistics,Variance,stat_var,ECT3,53338.7497,52636.8857,46616.9379,44392.8445,555.6829,719.6975,17953.6433,11118.4954,1036.2306,230.562,427.2793,258.4748
+Statistics,Skewness,stat_skew,KE2A,-2.1668,-2.1794,-2.1266,-2.1286,0.2953,0.42212,0.87706,0.64455,1.314,1.5747,0.083694,0.15965
+Statistics,(Excess) kurtosis,stat_kurt,IPH6,3.6451,3.7126,3.5277,3.5863,7.0161,6.1333,-0.27877,-0.71065,2.8417,4.3373,7.7218,8.7531
+Statistics,Median,stat_median,Y12H,41,41,38.08,37.336,-0.58489,-0.91947,88.7164,113.1384,97.0368,37.1933,0.045594,0.058616
+Statistics,Minimum,stat_min,1GSF,-1000,-997,-888.92,-906.176,-178.0502,-172.907,15.452,28.4672,31.3725,9.5348,-245.1464,-143.9796
+Statistics,10th percentile,stat_p10,QG58,-434,-427,-402.364,-389.3224,-27.102,-32.1572,26.877,35.5697,68.8025,24.6298,-18.8451,-14.1429
+Statistics,90th percentile,stat_p90,8DWT,93,92,79.84,77.248,13.2345,17.391,346.961,292.6233,144.5656,59.2863,17.7175,12.4719
+Statistics,Maximum,stat_max,84IY,377,377,334.16,316.312,190.6673,204.2998,672.2096,524.8028,353.6986,174.5559,201.6358,154.4726
+Statistics,Interquartile range,stat_iqr,SALO,69,67,82,92.584,8.7437,11.4459,219.2627,187.655,37.1797,17.3522,15.7707,9.8874
+Statistics,Range,stat_range,2OJQ,1377,1374,1223.08,1222.488,368.7175,377.2068,656.7576,496.3355,322.3261,165.0212,446.7822,298.4521
+Statistics,Mean absolute deviation,stat_mad,4FUA,160.0892,158.9223,152.5869,149.3422,13.1507,15.4966,116.0725,92.4481,24.2066,11.2782,13.0301,9.5143
+Statistics,Robust mean absolute deviation,stat_rmad,1128,64.4227,63.5967,67.7311,68.1352,4.9768,6.3688,92.892,75.9196,15.7577,7.3098,6.8152,4.4259
+Statistics,Median absolute deviation,stat_medad,N72L,121.7435,120.5444,115.8276,113.8108,12.9032,15.2606,110.7334,90.813,23.7017,10.9943,13.0283,9.5107
+Statistics,Coefficient of variation,stat_cov,7TET,-4.9164,-4.9438,-4.3284,-4.223,-9.6576,-9.1174,0.90377,0.74347,0.31255,0.37734,-111.7049,-83.8886
+Statistics,Quartile coefficient of dispersion,stat_qcod,9S40,1,0.94366,1.8502,2.9728,-2.9306,-2.3389,0.77305,0.69926,0.18686,0.22554,491.1043,-156.1466
+Statistics,Energy,stat_energy,N8CA,6956402357,19604163821,6149826557,16774513585,70338761.75,260607009.4,5001263504,11175381810,1458276196,661870210,53515894.29,92495949.33
+Statistics,Root mean square,stat_rms,5ZWQ,235.6808,234.0738,221.5967,216.5228,23.699,26.9881,199.8351,176.7298,107.9075,43.0096,20.6716,16.0783