irAEMM/templates/segmentation3.json

{
 "setVariables":["__tempBase__","__segBase__","__roiFile__","__petFile__","__ctFile__","__segFile__","__modelName__","__suffix__"],
 "setVariablesComment":"this variables will get updated with local values like home and can be used to set variables further on",
 "__tempBase__":"__home__/temp/segmentation",
 "__segBase__":"/home/andrej/software/src/irAEMM/segmentation",
 "__roiFile__":"testMask",
 "__ctFile__":"testCT",
 "__petFile__":"testPET",
 "__segFile__":"segmentation",
 "__modelName__":"DM_defaults.DM_train_VISCERAL16_Fold1.final.2019-10-01.07.46.19.932616.model.ckpt",
 "__suffix__":"nii.gz",
 "tempBase":"__tempBase__",
 "model":"__model__",
 "project":"iPNUMMretro/Study",
 "targetSchema":"study",
 "targetQuery":"Imaging1",
 "participantField":"PatientId",
 "imageDir":"preprocessedImages",
 "segmentationSchema":"study",
 "segmentationQuery":"Segmentations",
 "version":"v3",
 "images":{
	"comment":"weight is coded as a sequence of intervals and [k,n] of linear function inbetween",
 	"crop":{
		"00":{
			"range":["0","0.5"],
			"axis":"2",
			"n":"NONE",
			"w":[
				{"range":["0.0","0.3333"],"n":"1"},
				{"range":["0.3333","0.4166"],"k":"-12","n":"5"},
				{"range":["0.4166","1"],"n":"0"}
			]
		},
		"01":{
			"range":["0.25","0.75"],
			"axis":"2",
			"n":"NONE",
			"w":[
				{"range":["0.0","0.3333"],"n":"0"},
				{"range":["0.3333","0.4166"],"k":"12","n":"-4"},
				{"range":["0.4166","0.5833"],"n":"1"},
				{"range":["0.5833","0.6666"],"k":"-12","n":"8"},
				{"range":["0.6666","1"],"n":"0"}
			]
		},
		"02":{
			"range":["0.5","1"],
			"axis":"2",
			"n":"NONE",
			"w":[
				{"range":["0.0","0.5833"],"n":"0"},
				{"range":["0.5833","0.6666"],"k":"12","n":"-7"},
				{"range":["0.6666","1"],"n":"1"}
			]
		}
	},
	"images":{
		"CT":{
			"queryField":"ctResampled",
			"tempFile":"__tempBase__/__ctFile__.__suffix__",
			"fileList":"__tempBase__/testChannels_CT.cfg"
		},
		"patientmask":{
			"queryField":"ROImask",
			"tempFile":"__tempBase__/__roiFile__.__suffix__",
			"fileList":"__tempBase__/testRoiMasks.cfg"
		},
		"segmentations":{
			"tempFile":"__segFile__.__suffix__",
			"fileList":"__tempBase__/testNamesOfPredictions.cfg"
		}
	}
 },
 "replacePattern":{
	 "__workDir__":"__tempBase__",
	 "__roi__":"__tempBase__/__roiFile__.__suffix__",
	 "__pet__":"__tempBase__/__petFile__.__suffix__",
	 "__ct__":"__tempBase__/__ctFile__.__suffix__",
	 "__seg__":"__segFile__.__suffix__",
	 "__model__":"__modelName__",
	 "__segmentBase__":"__segBase__",
	 "__sfx__":"__suffix__"
 },
 "deepmedic": {
	 "config":{
		 "model":{
		 	"template":"__segBase__/model/modelConfig.cfg.template",
		 	"out":"__tempBase__/modelConfig.cfg"
	 	},
	 	"test":{
			"template":"__segBase__/test/testConfig.cfg.template",
		 	"out":"__tempBase__/testConfig.cfg"
	 	}
	 }
 }


}