script to compare features between CERR and pyradiomics

Unit_Testing/tests_for_cerr/compareCerrWithPyrad.m

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+% compareCerrWithPyrad.m
+%
+% Compares CERR and pyRaiomics features
+%
+% APA, 9/4/2019
+
+pradParamFileName = 'C:\Users\aptea\Desktop\PyradParamsComparison.yaml';
+cerrParamFileName = 'C:\Users\aptea\Desktop\CERR_ParamsComparison.json';
+nrrdSaveDir = 'C:\Users\aptea\Desktop';
+
+global planC
+indexS = planC{end};
+
+structNum = 1;
+scanNum = getStructureAssociatedScan(structNum,planC);
+
+scan3M = double(planC{indexS.scan}(scanNum).scanArray) - planC{indexS.scan}(scanNum).scanInfo(1).CTOffset;
+mask3M = getUniformStr(structNum,planC);
+[xV, yV, zV] = getScanXYZVals(planC{indexS.scan}(1));
+pixelspacing = [abs(mean(diff(xV))) abs(mean(diff(yV))) abs(mean(diff(zV)))]*10;
+origin = [0 0 0];
+encoding = 'raw';
+mask3M = cast(mask3M,'uint8');
+% Write scan and mask to nrrd
+scanFilename = fullfile(nrrdSaveDir,'scan.nrrd');
+maskFilename = fullfile(nrrdSaveDir,'mask.nrrd');
+ok1 = nrrdWriter(scanFilename, scan3M, pixelspacing, origin, encoding);
+ok2 = nrrdWriter(maskFilename, mask3M, pixelspacing, origin, encoding);
+
+pyradCallStr = ['pyradiomics ', scanFilename, ' ', maskFilename, ' --param ', pradParamFileName];
+system(pyradCallStr)
+
+delete(scanFilename)
+delete(maskFilename)
+
+% CERR radiomics
+paramS = getRadiomicsParamTemplate(cerrParamFileName);
+cerrFeatS = calcGlobalRadiomicsFeatures(scanNum, structNum, paramS, planC);
+cerrFeatS.Original.glcmFeatS.AvgS
+
+