TEST: Add test baseline for shape2D

Add testing of shape 2D, using all 5 radiomics testcases. As shape2D only works with single slice segmentations, add new largest slice segmentations for each test case, and update code to allow adding of a "_2D" suffix to the testcase, indicating this 2D label should be returned as mask.

Additionally update the getTestCase function to raise an error instead of returning None in case the test case could not be obtained.

data/baseline/baseline_shape2D.csv

@@ -0,0 +1,42 @@
+featureName,brain1_shape2D,brain2_shape2D,breast1_shape2D,lung1_shape2D,lung2_shape2D
+diagnostics_Image-original_Maximum,3057.0,1523.0,248.0,3071.0,1671.0
+diagnostics_Mask-original_CenterOfMass,"(43.13548018292683, 20.012385670731703, 26.000000000000014)","(57.44906387665198, -22.31087860241864, -10.700000762939446)","(-99.99007990243902, -1.789887073170732, 28.35000000000003)","(-21.721181556195972, -120.73608609510089, -612.4999999999998)","(53.84355387019346, -97.05089679126613, -249.9999999999999)"
+diagnostics_Mask-corrected_VolumeNum,1,1,1,1,1
+diagnostics_Mask-corrected_Size,"(256, 256, 25)","(256, 256, 23)","(45, 120, 21)","(512, 512, 48)","(512, 512, 61)"
+diagnostics_Mask-corrected_Mean,859.3841463414634,422.5947136563877,131.1829268292683,-51.518731988472624,17.4510550996483
+diagnostics_Image-original_Minimum,0.0,0.0,6.0,-1024.0,-1024.0
+diagnostics_Mask-corrected_Spacing,"(0.7812499999999999, 0.7812499999999999, 6.499999999999998)","(0.7812499999999999, 0.7812499999999999, 6.499999999999998)","(0.664062, 0.664062, 2.1)","(0.5703125, 0.5703125, 5.0)","(0.6269531, 0.6269531, 5.0)"
+diagnostics_Versions_Numpy,1.15.1,1.15.1,1.15.1,1.15.1,1.15.1
+diagnostics_Mask-corrected_CenterOfMass,"(43.13548018292683, 20.012385670731703, 26.000000000000014)","(57.44906387665198, -22.31087860241864, -10.700000762939446)","(-99.99007990243902, -1.789887073170732, 28.35000000000003)","(-21.721181556195972, -120.73608609510089, -612.4999999999998)","(53.84355387019346, -97.05089679126613, -249.9999999999999)"
+diagnostics_Mask-corrected_CenterOfMassIndex,"(182.71341463414635, 101.88414634146342, 16.0)","(214.33480176211455, 160.9339207048458, 8.0)","(24.926829268292682, 69.8048780487805, 9.0)","(217.9135446685879, 358.1613832853026, 33.0)","(357.8314771395076, 362.784876905041, 22.0)"
+diagnostics_Mask-corrected_BoundingBox,"(162, 84, 16, 45, 32, 1)","(205, 155, 8, 20, 14, 1)","(21, 64, 9, 9, 12, 1)","(206, 347, 33, 24, 22, 1)","(321, 334, 22, 72, 65, 1)"
+diagnostics_Versions_SimpleITK,1.1.0,0.9.1,0.9.1,0.9.1,0.9.1
+diagnostics_Mask-original_CenterOfMassIndex,"(182.71341463414635, 101.88414634146342, 0.0)","(214.33480176211455, 160.9339207048458, 0.0)","(24.926829268292682, 69.8048780487805, 0.0)","(217.9135446685879, 358.1613832853026, 0.0)","(357.8314771395076, 362.784876905041, 0.0)"
+diagnostics_Configuration_EnabledImageTypes,{'Original': {}},{'Original': {}},{'Original': {}},{'Original': {}},{'Original': {}}
+diagnostics_Image-original_Hash,5c9ce3ca174f0f8324aa4d277e0fef82dc5ac566,f2b8fbc4d5d1da08a1a70e79a301f8a830139438,016951a8f9e8e5de21092d9d62b77262f92e04a5,34dca4200809a5e76c702d6b9503d958093057a3,14f57fd04838eb8c9cca2a0dd871d29971585975
+diagnostics_Versions_PyWavelet,0.5.1,0.5.2,0.5.2,0.5.2,0.5.2
+diagnostics_Mask-original_Size,"(256, 256, 1)","(256, 256, 1)","(45, 120, 1)","(512, 512, 1)","(512, 512, 1)"
+diagnostics_Mask-original_VoxelNum,984,227,82,347,3412
+diagnostics_Versions_Python,3.5.3,2.7.11,2.7.11,2.7.11,2.7.11
+diagnostics_Mask-corrected_Maximum,1261.0,729.0,162.0,106.0,108.0
+diagnostics_Image-original_Size,"(256, 256, 25)","(256, 256, 23)","(45, 120, 21)","(512, 512, 48)","(512, 512, 61)"
+diagnostics_Configuration_Settings,"{'additionalInfo': True, 'interpolator': 'sitkBSpline', 'minimumROISize': None, 'force2D': True, 'minimumROIDimensions': 2, 'preCrop': False, 'resegmentRange': None, 'correctMask': True, 'normalize': False, 'distances': [1], 'removeOutliers': None, 'label': 1, 'resampledPixelSpacing': None, 'normalizeScale': 1, 'force2Ddimension': 0, 'padDistance': 5}","{'distances': [1], 'additionalInfo': True, 'force2D': True, 'interpolator': 'sitkBSpline', 'resampledPixelSpacing': None, 'label': 1, 'normalizeScale': 1, 'normalize': False, 'force2Ddimension': 0, 'removeOutliers': None, 'minimumROISize': None, 'minimumROIDimensions': 2, 'correctMask': True, 'preCrop': False, 'resegmentRange': None, 'padDistance': 5}","{'distances': [1], 'additionalInfo': True, 'force2D': True, 'interpolator': 'sitkBSpline', 'resampledPixelSpacing': None, 'label': 1, 'normalizeScale': 1, 'normalize': False, 'force2Ddimension': 0, 'removeOutliers': None, 'minimumROISize': None, 'minimumROIDimensions': 2, 'correctMask': True, 'preCrop': False, 'resegmentRange': None, 'padDistance': 5}","{'distances': [1], 'additionalInfo': True, 'force2D': True, 'interpolator': 'sitkBSpline', 'resampledPixelSpacing': None, 'label': 1, 'normalizeScale': 1, 'normalize': False, 'force2Ddimension': 0, 'removeOutliers': None, 'minimumROISize': None, 'minimumROIDimensions': 2, 'correctMask': True, 'preCrop': False, 'resegmentRange': None, 'padDistance': 5}","{'distances': [1], 'additionalInfo': True, 'force2D': True, 'interpolator': 'sitkBSpline', 'resampledPixelSpacing': None, 'label': 1, 'normalizeScale': 1, 'normalize': False, 'force2Ddimension': 0, 'removeOutliers': None, 'minimumROISize': None, 'minimumROIDimensions': 2, 'correctMask': True, 'preCrop': False, 'resegmentRange': None, 'padDistance': 5}"
+diagnostics_Configuration_TestCase,brain1_2D,brain2_2D,breast1_2D,lung1_2D,lung2_2D
+diagnostics_Mask-corrected_Minimum,546.0,206.0,106.0,-506.0,-677.0
+diagnostics_Mask-original_Spacing,"(0.7812499999999999, 0.7812499999999999, 6.499999999999998)","(0.7812499999999999, 0.7812499999999999, 6.499999999999998)","(0.664062, 0.664062, 2.1)","(0.5703125, 0.5703125, 5.0)","(0.6269531, 0.6269531, 5.0)"
+diagnostics_Versions_PyRadiomics,2.1.0.post17.dev0+gba07b03,2.1.0.post17.dev0+gba07b03,2.1.0.post17.dev0+gba07b03,2.1.0.post17.dev0+gba07b03,2.1.0.post17.dev0+gba07b03
+diagnostics_Mask-original_Hash,c686d815c4383f3ca71a1afb07d6f871172a7dac,1d3b86cb29e4ab89fd40c0fdaddea1110ca21bfc,378ace5e4d190eaeb0d69fdc80b2b7eaeb61ffd6,1c84c30b5030441c864b3569b88919459344af9a,0094f5cfe799b0bd5603f6b7cafdc6387be39d66
+diagnostics_Mask-corrected_VoxelNum,984,227,82,347,3412
+diagnostics_Image-original_Spacing,"(0.7812499999999999, 0.7812499999999999, 6.499999999999998)","(0.7812499999999999, 0.7812499999999999, 6.499999999999998)","(0.664062, 0.664062, 2.1)","(0.5703125, 0.5703125, 5.0)","(0.6269531, 0.6269531, 5.0)"
+diagnostics_Mask-original_VolumeNum,1,1,1,1,1
+diagnostics_Image-original_Mean,385.6564080810547,236.20217696480128,63.380440917107585,-577.9148241678873,-433.28809775680793
+diagnostics_Mask-original_BoundingBox,"(162, 84, 0, 45, 32, 1)","(205, 155, 0, 20, 14, 1)","(21, 64, 0, 9, 12, 1)","(206, 347, 0, 24, 22, 1)","(321, 334, 0, 72, 65, 1)"
+original_shape2D_MeshSurface,600.28076171875,138.244628906,35.9397346973,112.701324463,1340.95895182
+original_shape2D_PixelSurface,600.5859374999998,138.54980468749994,36.160223867208,112.86395263671875,1341.1554869138695
+original_shape2D_Perimeter,101.0913825153671,48.0908978016,23.6116203532,43.4485541519,156.412404051
+original_shape2D_PerimeterSurfaceRatio,0.16840683387206656,0.347868110191,0.656978148339,0.385519463581,0.116642201343
+original_shape2D_Sphericity,0.8591480496460207,0.8666947794872987,0.9000498705600878,0.8661520010380676,0.8299300366556801
+original_shape2D_MaximumDiameter,35.579054802299055,16.3129789202,8.39979371027,16.3113363151,46.3182155834
+original_shape2D_MajorAxisLength,33.85279086841539,16.570640783628463,8.259750107622313,16.33412649719061,45.38958860924436
+original_shape2D_MinorAxisLength,23.785948973581707,10.963260379640587,5.729800201543435,8.986202904129604,38.4309041153114
+original_shape2D_Elongation,0.7026288930220511,0.6616075094978898,0.6937013985757058,0.5501489721948207,0.8466898531766884

radiomics/__init__.py

@@ -135,53 +135,63 @@ def getTestCase(testCase, dataDirectory=None):
 
   If the test case has been found or downloaded successfully, this function returns a tuple of two strings:
   ``(path/to/image.nrrd, path/to/mask.nrrd)``. In case of an error ``(None, None)`` is returned.
+
+  .. note::
+    To get the testcase with the corresponding single-slice label, append "_2D" to the testCase.
+
   """
   global logger, testCases
+  label2D = False
+  testCase = testCase.lower()
+  if testCase.endswith('_2d'):
+    label2D = True
+    testCase = testCase[:-3]
+
   if testCase not in testCases:
-    logger.error('Testcase "%s" not recognized!', testCase)
-    return None, None
+    raise ValueError('Testcase "%s" not recognized!' % testCase)
 
   logger.debug('Getting test case %s', testCase)
 
   if dataDirectory is None:
     dataDirectory = os.path.join(tempfile.gettempdir(), 'pyradiomics', 'data')
     logger.debug('No data directory specified, using temporary directory "%s"', dataDirectory)
 
-  # Check if test case has already been downloaded.
-  imageFile = os.path.join(dataDirectory, '%s_image.nrrd' % testCase)
-  maskFile = os.path.join(dataDirectory, '%s_label.nrrd' % testCase)
-  if os.path.isfile(imageFile) and os.path.isfile(maskFile):
-    logger.info('Test case already downloaded')
-    return imageFile, maskFile
+  im_name = '%s_image.nrrd' % testCase
+  ma_name = '%s_label%s.nrrd' % (testCase, '_2D' if label2D else '')
+
+  def get_or_download(fname):
+    target = os.path.join(dataDirectory, fname)
+    if os.path.exists(target):
+      logger.debug('File %s already downloaded', fname)
+      return target
 
-  # Test case not found, so try to download it
-  logger.info("Test case %s not available locally, downloading test case...", testCase)
+    # Test case file not found, so try to download it
+    logger.info("Test case file %s not available locally, downloading from github...", fname)
 
-  try:
     # First check if the folder is available
     if not os.path.isdir(dataDirectory):
       logger.debug('Creating data directory: %s', dataDirectory)
       os.makedirs(dataDirectory)
 
     # Download the test case files (image and label)
-    url = r'https://github.com/Radiomics/pyradiomics/releases/download/v1.0/%s_%s.nrrd'
+    url = r'https://github.com/Radiomics/pyradiomics/releases/download/v1.0/%s' % fname
 
-    logger.debug('Retrieving image at %s', url % (testCase, 'image'))
-    fname, headers = urllib.request.urlretrieve(url % (testCase, 'image'), imageFile)
-    if headers.get('status', '') == '404 Not Found':
-      logger.warning('Unable to download image file at %s!', url % (testCase, 'image'))
-      return None, None
+    logger.debug('Retrieving file at %s', url)
+    _, headers = urllib.request.urlretrieve(url, target)
 
-    logger.debug('Retrieving mask at %s', url % (testCase, 'label'))
-    fname, headers = urllib.request.urlretrieve(url % (testCase, 'label'), maskFile)
     if headers.get('status', '') == '404 Not Found':
-      logger.warning('Unable to download mask file at %s!', url % (testCase, 'label'))
+      raise ValueError('Unable to download image file at %s!', url)
+
+    logger.info('File %s downloaded', fname)
+    return target
+
+  logger.debug('Getting Image file')
+  imageFile = get_or_download(im_name)
+
+  logger.debug('Getting Mask file')
+  maskFile = get_or_download(ma_name)
 
-    logger.info('Test case %s downloaded', testCase)
-    return imageFile, maskFile
-  except Exception:
-    logger.error('Download failed!', exc_info=True)
-    return None, None
+  return imageFile, maskFile
 
 
 def getParameterValidationFiles():

tests/addTest.py

@@ -20,10 +20,13 @@ def main(argv=None):
 
   radiomics.logger.addHandler(handler)
 
+  testcases = list(radiomics.testCases)
+  testcases += [t + '_2D' for t in testcases]
+
   parser = argparse.ArgumentParser()
   parser.add_argument('TestName', type=str, help='Name for the new test, must not be already present in the baseline')
-  parser.add_argument('TestCase', type=str, choices=list(radiomics.testCases), help='Test image and segmentation to '
-                                                                                    'use in the new test')
+  parser.add_argument('TestCase', type=str, choices=testcases, help='Test image and segmentation to '
+                                                                    'use in the new test')
   parser.add_argument('Configuration', metavar='FILE', default=None,
                       help='Parameter file containing the settings to be used in extraction')
   parser.add_argument('--force', '-f', action='store_true', help='When the test is already known for the class, '
@@ -38,7 +41,7 @@ def main(argv=None):
     testutils = RadiomicsTestUtils()
 
     try:
-      assert args.TestCase in radiomics.testCases
+      assert args.TestCase.lower().replace('_2d', '') in radiomics.testCases
     except AssertionError:
       logger.error('Input not valid, cancelling addTest!')
       exit(1)

tests/testUtils.py

@@ -10,7 +10,7 @@
 import SimpleITK as sitk
 import six
 
-from radiomics import featureextractor, getTestCase, imageoperations, testCases
+from radiomics import featureextractor, getTestCase, imageoperations
 
 # Get the logger. This is done outside the class, as it is needed by both the class and the custom_name_func
 logger = logging.getLogger('radiomics.testing')
@@ -154,9 +154,8 @@ class or test case is changed, function returns True.
     if self._testCase != self._current_config['TestCase']:
       self._testCase = self._current_config['TestCase']
       self._logger.info("Reading the image and mask for test case %s", self._testCase)
-      assert self._current_config['TestCase'] in testCases
 
-      imageName, maskName = getTestCase(self._testCase)
+      imageName, maskName = getTestCase(self._testCase)  # Throws ValueError if test case is not recognized
 
       assert imageName is not None
       assert maskName is not None
@@ -419,7 +418,7 @@ def writeBaselineFile(self, baselineDir):
       header = ['featureName'] + cases
       csvWriter.writerow(header)
 
-      config = self.configuration[cases[1]].keys()
+      config = self.configuration[cases[0]].keys()
       self._configKeys += list(set(config) - set(self._configKeys))
       for c in self._configKeys:
         if c not in config: