TEST: Use different Notebooks while testing in CircleCI

Update the config.yml to test the hello* notebooks and the PyRadiomicsExample.ipynb, which more extensively tests different parts of the toolbox and different ways the toolbox can be used.

.circleci/config.yml

@@ -38,20 +38,12 @@ jobs:
           command: |
             source activate root
             nosetests
-      - run:
-          name: Install test data
-          command: |
-            cp -r data /tmp/example_data
-            cp examples/exampleSettings/Params.yaml /tmp
-            cp -r examples/Notebooks/*.ipynb /tmp
-            # helloFeatureClass is not ready for inclusion yet, so isn't being tested
-            rm -f /tmp/hello*.ipynb
       - run:
           name: test notebooks in python 2 and 3
           command: |
-            jupyter nbconvert --ExecutePreprocessor.kernel_name=python2 --ExecutePreprocessor.timeout=-1 --to notebook --execute /tmp/RadiomicsExample.ipynb /tmp/FeatureVisualization.ipynb /tmp/FeatureVisualizationWithClustering.ipynb /tmp/FilteringEffects.ipynb
+            jupyter nbconvert --ExecutePreprocessor.kernel_name=python2 --ExecutePreprocessor.timeout=-1 --to notebook --output-dir /tmp --execute notebooks/HelloRadiomics.ipynb notebooks/HelloFeatureClass.ipynb notebooks/PyRadiomicsExample.ipynb
 
-            jupyter nbconvert --ExecutePreprocessor.kernel_name=python3 --ExecutePreprocessor.timeout=-1 --to notebook --execute  /tmp/RadiomicsExample.ipynb /tmp/FeatureVisualization.ipynb /tmp/FeatureVisualizationWithClustering.ipynb /tmp/FilteringEffects.ipynb
+            jupyter nbconvert --ExecutePreprocessor.kernel_name=python3 --ExecutePreprocessor.timeout=-1 --to notebook --output-dir /tmp --execute  notebooks/HelloRadiomics.ipynb notebooks/HelloFeatureClass.ipynb notebooks/PyRadiomicsExample.ipynb
 
 
 

Dockerfile

@@ -28,11 +28,11 @@ RUN /bin/bash -c "source activate python2 \
 
 # Install sample data and notebooks
 ADD data/ /home/jovyan/work/example_data/
-ADD bin/Notebooks/RadiomicsExample.ipynb /home/jovyan/work/
-ADD bin/Notebooks/FeatureVisualization.ipynb /home/jovyan/work/
-ADD bin/Notebooks/FeatureVisualizationWithClustering.ipynb /home/jovyan/work/
-ADD bin/Notebooks/FilteringEffects.ipynb /home/jovyan/work/
-ADD bin/Params.yaml /home/jovyan/work/
+ADD notebooks/RadiomicsExample.ipynb /home/jovyan/work/
+ADD notebooks/FeatureVisualization.ipynb /home/jovyan/work/
+ADD notebooks/FeatureVisualizationWithClustering.ipynb /home/jovyan/work/
+ADD notebooks/FilteringEffects.ipynb /home/jovyan/work/
+ADD examples/exampleSettings/Params.yaml /home/jovyan/work/
 
 # Make a global directory and link it to the work directory
 RUN mkdir /data

examples/batchExamples/batchProcessingPandas.py → examples/batchProcessingWithPandas.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 
 from __future__ import print_function
 
@@ -12,11 +13,12 @@
 
 
 def main():
-  outPath = r'E:\Git-Repos\PyRadiomicsNKI\pyradiomics-API'
+  outPath = r''
 
-  inputCSV = outPath + os.path.sep + "TestCases.csv"
-  outputFilepath = outPath + os.path.sep + "radiomics_features.csv"
-  progress_filename = outPath + os.path.sep + "pyrad_log.txt"
+  inputCSV = os.path.join(outPath, 'testCases.csv')
+  outputFilepath = os.path.join(outPath, 'radiomics_features.csv')
+  progress_filename = os.path.join(outPath, 'pyrad_log.txt')
+  params = os.path.join(outPath, 'exampleSettings', 'Params.yaml')
 
   # Configure logging
   rLogger = logging.getLogger('radiomics')
@@ -26,7 +28,7 @@ def main():
 
   # Create handler for writing to log file
   handler = logging.FileHandler(filename=progress_filename, mode='w')
-  handler.setFormatter(logging.Formatter("%(levelname)s:%(name)s: %(message)s"))
+  handler.setFormatter(logging.Formatter('%(levelname)s:%(name)s: %(message)s'))
   rLogger.addHandler(handler)
 
   # Initialize logging for batch log messages
@@ -35,6 +37,7 @@ def main():
   # Set verbosity level for output to stderr (default level = WARNING)
   radiomics.setVerbosity(logging.INFO)
 
+  logger.info('pyradiomics version: %s', radiomics.__version__)
   logger.info('Loading CSV')
 
   # ####### Up to this point, this script is equal to the 'regular' batchprocessing script ########
@@ -45,24 +48,27 @@ def main():
     # the input cases
     flists = pandas.read_csv(inputCSV).T
   except Exception:
-    logging.error('CSV READ FAILED', exc_info=True)
+    logger.error('CSV READ FAILED', exc_info=True)
     exit(-1)
 
-  logging.info('Loading Done')
-  logging.info('Patients: %d', len(flists))
+  logger.info('Loading Done')
+  logger.info('Patients: %d', len(flists.columns))
 
-  kwargs = {}
-  kwargs['binWidth'] = 25
-  kwargs['resampledPixelSpacing'] = None  # [3,3,3]
-  kwargs['interpolator'] = sitk.sitkBSpline
-  kwargs['enableCExtensions'] = True
+  if os.path.isfile(params):
+    extractor = featureextractor.RadiomicsFeaturesExtractor(params)
+  else:  # Parameter file not found, use hardcoded settings instead
+    settings = {}
+    settings['binWidth'] = 25
+    settings['resampledPixelSpacing'] = None  # [3,3,3]
+    settings['interpolator'] = sitk.sitkBSpline
+    settings['enableCExtensions'] = True
 
-  logger.info('pyradiomics version: %s', radiomics.__version__)
-  logger.info('Extracting features with kwarg settings: %s', str(kwargs))
+    extractor = featureextractor.RadiomicsFeaturesExtractor(**settings)
+    # extractor.enableInputImages(wavelet= {'level': 2})
 
-  extractor = featureextractor.RadiomicsFeaturesExtractor(**kwargs)
-  # extractor.enableInputImages(Original={}) # Original enabled by default
-  # extractor.enableInputImages(wavelet= {'level': 2})
+  logger.info('Enabled input images types: %s', extractor.inputImages)
+  logger.info('Enabled features: %s', extractor.enabledFeatures)
+  logger.info('Current settings: %s', extractor.kwargs)
 
   # Instantiate a pandas data frame to hold the results of all patients
   results = pandas.DataFrame()

examples/batchExamples/batchprocessing.py → examples/batchprocessing.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 
 from __future__ import print_function
 
@@ -13,11 +14,12 @@
 
 
 def main():
-  outPath = r'E:\Git-Repos\PyRadiomicsNKI\pyradiomics-API'
+  outPath = r''
 
-  inputCSV = outPath + os.path.sep + "TestCases.csv"
-  outputFilepath = outPath + os.path.sep + "radiomics_features.csv"
-  progress_filename = outPath + os.path.sep + "pyrad_log.txt"
+  inputCSV = os.path.join(outPath, 'testCases.csv')
+  outputFilepath = os.path.join(outPath, 'radiomics_features.csv')
+  progress_filename = os.path.join(outPath, 'pyrad_log.txt')
+  params = os.path.join(outPath, 'exampleSettings', 'Params.yaml')
 
   # Configure logging
   rLogger = logging.getLogger('radiomics')
@@ -27,7 +29,7 @@ def main():
 
   # Create handler for writing to log file
   handler = logging.FileHandler(filename=progress_filename, mode='w')
-  handler.setFormatter(logging.Formatter("%(levelname)s:%(name)s: %(message)s"))
+  handler.setFormatter(logging.Formatter('%(levelname)s:%(name)s: %(message)s'))
   rLogger.addHandler(handler)
 
   # Initialize logging for batch log messages
@@ -36,6 +38,7 @@ def main():
   # Set verbosity level for output to stderr (default level = WARNING)
   radiomics.setVerbosity(logging.INFO)
 
+  logger.info('pyradiomics version: %s', radiomics.__version__)
   logger.info('Loading CSV')
 
   flists = []
@@ -44,23 +47,26 @@ def main():
       cr = csv.DictReader(inFile, lineterminator='\n')
       flists = [row for row in cr]
   except Exception:
-    logging.error('CSV READ FAILED', exc_info=True)
+    logger.error('CSV READ FAILED', exc_info=True)
 
   logger.info('Loading Done')
   logger.info('Patients: %d', len(flists))
 
-  kwargs = {}
-  kwargs['binWidth'] = 25
-  kwargs['resampledPixelSpacing'] = None  # [3,3,3]
-  kwargs['interpolator'] = sitk.sitkBSpline
-  kwargs['enableCExtensions'] = False
-
-  logger.info('pyradiomics version: %s', radiomics.__version__)
-  logger.info('Extracting features with kwarg settings: %s', str(kwargs))
-
-  extractor = featureextractor.RadiomicsFeaturesExtractor(**kwargs)
-  extractor.enableInputImages(Original={})
-  # extractor.enableInputImages(wavelet= {'level': 2})
+  if os.path.isfile(params):
+    extractor = featureextractor.RadiomicsFeaturesExtractor(params)
+  else:  # Parameter file not found, use hardcoded settings instead
+    settings = {}
+    settings['binWidth'] = 25
+    settings['resampledPixelSpacing'] = None  # [3,3,3]
+    settings['interpolator'] = sitk.sitkBSpline
+    settings['enableCExtensions'] = True
+
+    extractor = featureextractor.RadiomicsFeaturesExtractor(**settings)
+    # extractor.enableInputImages(wavelet= {'level': 2})
+
+  logger.info('Enabled input images types: %s', extractor.inputImages)
+  logger.info('Enabled features: %s', extractor.enabledFeatures)
+  logger.info('Current settings: %s', extractor.kwargs)
 
   headers = None
 

examples/helloFeatureClass.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 
 from __future__ import print_function
 

examples/helloRadiomics.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 
 from __future__ import print_function
 
@@ -97,13 +98,13 @@ def __exit__(self, exc_type, exc_value, tb):
 
 # Define settings for signature calculation
 # These are currently set equal to the respective default values
-kwargs = {}
-kwargs['binWidth'] = 25
-kwargs['resampledPixelSpacing'] = None  # [3,3,3] is an example for defining resampling (voxels with size 3x3x3mm)
-kwargs['interpolator'] = sitk.sitkBSpline
+settings = {}
+settings['binWidth'] = 25
+settings['resampledPixelSpacing'] = None  # [3,3,3] is an example for defining resampling (voxels with size 3x3x3mm)
+settings['interpolator'] = sitk.sitkBSpline
 
-# Initialize wrapperClass to generate signature
-extractor = featureextractor.RadiomicsFeaturesExtractor(**kwargs)
+# Initialize feature extractor
+extractor = featureextractor.RadiomicsFeaturesExtractor(**settings)
 
 # By default, only original is enabled. Optionally enable some filters:
 # extractor.enableInputImages(Original={}, LoG={}, Wavelet={})
@@ -117,20 +118,12 @@ def __exit__(self, exc_type, exc_value, tb):
 # Only enable mean and skewness in firstorder
 extractor.enableFeaturesByName(firstorder=['Mean', 'Skewness'])
 
-# Uncomment on of these functions to show how PyRadiomics can use the 'tqdm' or 'click' package to report progress when
+# Uncomment one of these functions to show how PyRadiomics can use the 'tqdm' or 'click' package to report progress when
 # running in full python mode. Assumes the respective package is installed (not included in the requirements)
 
 # tqdmProgressbar()
 # clickProgressbar()
 
-print("Active features:")
-for cls, features in six.iteritems(extractor.enabledFeatures):
-  if len(features) == 0:
-    features = extractor.getFeatureNames(cls)
-  for f in features:
-    print(f)
-    print(getattr(extractor.featureClasses[cls], 'get%sFeatureValue' % f).__doc__)
-
 print("Calculating features")
 featureVector = extractor.execute(imageName, maskName)
 

examples/helloRadiomicsWithSettings.py

@@ -0,0 +1,120 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import logging
+import os
+
+import SimpleITK as sitk
+import six
+
+import radiomics
+from radiomics import featureextractor
+
+def tqdmProgressbar():
+  """
+  This function will setup the progress bar exposed by the 'tqdm' package.
+  Progress reporting is only used in PyRadiomics for the calculation of GLCM and GLSZM in full python mode, therefore
+  enable GLCM and full-python mode to show the progress bar functionality
+
+  N.B. This function will only work if the 'click' package is installed (not included in the PyRadiomics requirements)
+  """
+  global extractor
+  extractor.kwargs['enableCExtensions'] = False
+  # Enable the GLCM class to show the progress bar
+  extractor.enableFeatureClassByName('glcm')
+
+  radiomics.setVerbosity(logging.INFO)  # Verbosity must be at least INFO to enable progress bar
+
+  import tqdm
+  radiomics.progressReporter = tqdm.tqdm
+
+def clickProgressbar():
+  """
+  This function will setup the progress bar exposed by the 'click' package.
+  Progress reporting is only used in PyRadiomics for the calculation of GLCM and GLSZM in full python mode, therefore
+  enable GLCM and full-python mode to show the progress bar functionality.
+
+  Because the signature used to instantiate a click progress bar is different from what PyRadiomics expects, we need to
+  write a simple wrapper class to enable use of a click progress bar. In this case we only need to change the 'desc'
+  keyword argument to a 'label' keyword argument.
+
+  N.B. This function will only work if the 'click' package is installed (not included in the PyRadiomics requirements)
+  """
+  global extractor
+
+  extractor.kwargs['enableCExtensions'] = False
+  # Enable the GLCM class to show the progress bar
+  extractor.enableFeatureClassByName('glcm')
+
+  radiomics.setVerbosity(logging.INFO)  # Verbosity must be at least INFO to enable progress bar
+
+  import click
+
+  class progressWrapper():
+    def __init__(self, iterable, desc=''):
+      # For a click progressbar, the description must be provided in the 'label' keyword argument.
+      self.bar = click.progressbar(iterable, label=desc)
+
+    def __iter__(self):
+      return self.bar.__iter__()  # Redirect to the __iter__ function of the click progressbar
+
+    def __enter__(self):
+      return self.bar.__enter__()  # Redirect to the __enter__ function of the click progressbar
+
+    def __exit__(self, exc_type, exc_value, tb):
+      return self.bar.__exit__(exc_type, exc_value, tb)  # Redirect to the __exit__ function of the click progressbar
+
+  radiomics.progressReporter = progressWrapper
+
+# Get some test data
+
+# repositoryRoot points to the root of the repository. The following line gets that location if this script is run
+# from it's default location in \pyradiomics\bin. Otherwise, it will point to some (invalid) folder, causing the
+# getTestCase function to fail to find the test case in the repository. In that case, a test case will be downloaded to
+# temporary files and it's location is returned.
+repositoryRoot = os.path.abspath(os.path.join(os.getcwd(), ".."))
+imageName, maskName = radiomics.getTestCase('brain1', repositoryRoot)
+
+# Get the location of the example settings file
+paramsFile = os.path.abspath(r'exampleSettings\Params.yaml')
+
+if imageName is None or maskName is None:  # Something went wrong, in this case PyRadiomics will also log an error
+  print('Error getting testcase!')
+  exit()
+
+# Regulate verbosity with radiomics.verbosity
+# radiomics.setVerbosity(logging.INFO)
+
+# Get the PyRadiomics logger (default log-level = INFO
+logger = radiomics.logger
+logger.setLevel(logging.DEBUG)  # set level to DEBUG to include debug log messages in log file
+
+# Write out all log entries to a file
+handler = logging.FileHandler(filename='testLog.txt', mode='w')
+formatter = logging.Formatter("%(levelname)s:%(name)s: %(message)s")
+handler.setFormatter(formatter)
+logger.addHandler(handler)
+
+# Initialize feature extractor using the settings file
+extractor = featureextractor.RadiomicsFeaturesExtractor(paramsFile)
+
+# Uncomment one of these functions to show how PyRadiomics can use the 'tqdm' or 'click' package to report progress when
+# running in full python mode. Assumes the respective package is installed (not included in the requirements)
+
+# tqdmProgressbar()
+# clickProgressbar()
+
+print("Active features:")
+for cls, features in six.iteritems(extractor.enabledFeatures):
+  if len(features) == 0:
+    features = extractor.getFeatureNames(cls)
+  for f in features:
+    print(f)
+    print(getattr(extractor.featureClasses[cls], 'get%sFeatureValue' % f).__doc__)
+
+print("Calculating features")
+featureVector = extractor.execute(imageName, maskName)
+
+for featureName in featureVector.keys():
+  print("Computed %s: %s" % (featureName, featureVector[featureName]))

examples/helloResampling.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 
 import sys
 
@@ -8,7 +9,8 @@
 image = sitk.ReadImage(sys.argv[1])
 mask = sitk.ReadImage(sys.argv[2])
 
-(ii, im) = imageoperations.resampleImage(image, mask, [2, 2, 2])
+# Resamples and crops onto bounding box defined by the label
+(ii, im) = imageoperations.resampleImage(image, mask, [2, 2, 2], label=1, padDistance=5)
 
 sitk.WriteImage(ii, sys.argv[3])
 sitk.WriteImage(im, sys.argv[4])

examples/testCases.csv

@@ -0,0 +1,6 @@
+ID,Image,Mask
+brain1,..\data\brain1_image.nrrd,..\data\brain1_label.nrrd
+brain2,..\data\brain2_image.nrrd,..\data\brain2_label.nrrd
+breast1,..\data\breast1_image.nrrd,..\data\breast1_label.nrrd
+lung1,..\data\lung1_image.nrrd,..\data\lung1_label.nrrd
+lung2,..\data\lung2_image.nrrd,..\data\lung2_label.nrrd