added computation of wavelet/LoG filtered images for comparison with …

…CERR

Unit_Testing/tests_for_cerr/pyFeatureExtraction.py

@@ -2,72 +2,88 @@
 
 from __future__ import print_function
 import SimpleITK as sitk
+import numpy
+import scipy
+#import matplotlib
+import matlab
+#import matlab.engine
 import six
 from radiomics import getTestCase, imageoperations, featureextractor, getTestCase
 from radiomics.featureextractor import RadiomicsFeaturesExtractor
 
 
-def extract(imagePath, maskPath, paramfilepath, *args):
+def extract(imagePath, maskPath, paramfilepath, preprocessingFilter):
   r"""
   RKP - 3/20/2018
   Wrapper class for calculation of a radiomics features using pyradiomics.
 
   """
 
-  # testWaveletFilter = False
-  # testLoGFilter = False
 
   image, mask = RadiomicsFeaturesExtractor().loadImage(imagePath, maskPath)
 
   if imagePath is None or maskPath is None:  # Something went wrong, in this case PyRadiomics will also log an error
-    print('Error getting testcase!')
     exit()
 
   params = paramfilepath
-  extractor = featureextractor.RadiomicsFeaturesExtractor(params)
 
-
-  result = extractor.execute(imagePath, maskPath)
-  for key, val in six.iteritems(result):
-     strval = str(key)
-     if strval.find("-") == -1:
-       continue
-     else:
-       strval = strval.replace("-", "_")
-       result[strval] = result.pop(key)
-
-
-  if len(args) == 1 and args[0] == 'LoG':
+#if wavelet or LoG specified in argument, return only the preprocessed image arrays
+  if preprocessingFilter == 'LoG':
     resultdict = {}
-    for decompositionImage, decompositionName, inputKwargs in imageoperations.getLoGImage(image):
-      resultArray = sitk.GetArrayFromImage(decompositionImage)
+    extractor = featureextractor.RadiomicsFeaturesExtractor(params)
+    result = extractor.execute(imagePath, maskPath)
+    sigmaValues = [1.0]
+    for logImage, imageTypeName, inputKwargs in imageoperations.getLoGImage(image, sigma=sigmaValues):
+      resultArray = sitk.GetArrayFromImage(logImage)
+      resultArray = matlab.double(resultArray.tolist())
       # imgName = decompositionName + '.nrrd'
       # sitk.WriteImage(decompositionImage, imgName)
-      resultdict[decompositionName] = resultArray
-    return resultdict
+      #resultdict[decompositionName] = resultArray
+    return resultArray
 
-  elif len(args) == 1 and args[0] == 'wavelet':
+  elif preprocessingFilter == 'wavelet':
     resultdict = {}
-    for decompositionImage, decompositionName, inputKwargs in imageoperations.getWaveletImage(image):
+    for decompositionImage in imageoperations.getWaveletImage(image):
       resultArray=sitk.GetArrayFromImage(decompositionImage)
       # imgName = decompositionName+'.nrrd'
       # sitk.WriteImage(decompositionImage,imgName)
+      resultArray = matlab.double(resultArray.tolist())
       resultdict[decompositionName] = resultArray
-    return resultdict
+    for key, val in six.iteritems(resultdict):
+      strval = str(key)
+      if strval.find("-") == -1:
+        continue
+      else:
+        strval = strval.replace("-", "_")
+        strval = strval.replace("-", "_")
+        resultdict[strval] = resultdict.pop(key)
 
-  else:
+    return resultdict
+#perform feature extraction on original images and return the result
+  else:    
+    extractor = featureextractor.RadiomicsFeaturesExtractor(params)
+
+    result = extractor.execute(imagePath, maskPath)
+    for key, val in six.iteritems(result):
+      strval = str(key)
+      if strval.find("-") == -1:
+        continue
+      else:
+        strval = strval.replace("-", "_")
+        strval = strval.replace("-", "_")
+        result[strval] = result.pop(key)
     return result
 
 #
-# def main():
-#
-#   imagePath = 'C:\\Users\\pandyar1\\AppData\\Local\\Temp\\scan.nrrd'
-#   maskPath = 'C:\\Users\\pandyar1\\AppData\\Local\\Temp\\mask.nrrd'
-#   paramFilePath = 'W:\\Rutu\\CERR-testing\\Unit_Testing\\tests_for_cerr\pyradParams.yaml'
-#   result = extract(imagePath, maskPath, paramFilePath)
-#
-#
-# main()
+def main():
+
+  imagePath = 'C:\\Users\\pandyar1\\AppData\\Local\\Temp\\scan.nrrd'
+  maskPath = 'C:\\Users\\pandyar1\\AppData\\Local\\Temp\\mask.nrrd'
+  paramFilePath = 'W:\\Rutu\\CERR-testing\\Unit_Testing\\tests_for_cerr\pyradParams.yaml'
+  result = extract(imagePath, maskPath, paramFilePath, 'LoG')
+
+
+main()