Update PyRadiomics Logging

bin/Notebooks/helloRadiomics.ipynb

@@ -40,6 +40,13 @@
     "## Setting up logging"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Regulate verbosity of PyRadiomics (outputs to stderr)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 2,
@@ -48,20 +55,35 @@
    },
    "outputs": [],
    "source": [
-    "logger = logging.getLogger('radiomics')  # Parent logger for the radiomics package\n",
+    "# Uncomment line below to output debug and info log messaging to stderr (is added to Jupyter notbook output)\n",
+    "# radiomics.debug()  # Switch on radiomics logging to stderr output from level=DEBUG (default level=WARNING)\n",
     "\n",
-    "# Enable writing out the log using radiomics logger\n",
-    "radiomics.debug()  # Switch on radiomics logging from level=DEBUG (default level=WARNING)\n",
-    "# Alternative; set logging to a specific level\n",
-    "# logger.setLevel(logging.INFO)\n",
-    "\n",
-    "# Prevent radiomics logger from printing out log entries with level < WARNING to the console\n",
-    "logger.handlers[0].setLevel(logging.WARNING)  # This limits the log messages printed to stdErr to level warning or higher\n",
-    "logger.propagate = False  # Do not pass log messages on to root logger\n",
+    "# Alternative: regulate verbosity with radiomics.verbosity\n",
+    "# radiomics.setVerbosity(logging.INFO)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Set up logging to a log file"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "# Get the PyRadiomics logger (default log-level = INFO)\n",
+    "logger = radiomics.logger\n",
+    "logger.setLevel(logging.DEBUG)  # set level to DEBUG to include debug log messages in log file\n",
     "\n",
-    "# Write out all log entries to a file, overwrite previous log\n",
+    "# Write out all log entries to a file\n",
     "handler = logging.FileHandler(filename='testLog.txt', mode='w')\n",
-    "formatter = logging.Formatter(\"%(levelname)s:%(name)s: %(message)s\")  # This determines how a log message should be formatted\n",
+    "formatter = logging.Formatter(\"%(levelname)s:%(name)s: %(message)s\")\n",
     "handler.setFormatter(formatter)\n",
     "logger.addHandler(handler)"
    ]
@@ -86,7 +108,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 4,
    "metadata": {
     "collapsed": false
    },
@@ -119,7 +141,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 5,
    "metadata": {
     "collapsed": false
    },
@@ -144,7 +166,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 6,
    "metadata": {
     "collapsed": false
    },
@@ -188,9 +210,9 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 7,
    "metadata": {
-    "collapsed": true
+    "collapsed": false
    },
    "outputs": [],
    "source": [
@@ -213,7 +235,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 8,
    "metadata": {
     "collapsed": false,
     "scrolled": true
@@ -412,7 +434,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 9,
    "metadata": {
     "collapsed": false
    },
@@ -422,14 +444,13 @@
      "output_type": "stream",
      "text": [
       "Calculating features\n",
-      "\t\tComputing firstorder\n",
       "Computed general_info_BoundingBox: (162; 84; 11; 47; 70; 7)\n",
-      "Computed general_info_GeneralSettings: {'additionalInfo': True; 'verbose': True; 'binWidth': 25; 'enableCExtensions': True; 'label': 1; 'interpolator': 'sitkBSpline'; 'resampledPixelSpacing': None; 'padDistance': 5}\n",
+      "Computed general_info_GeneralSettings: {'normalize': False; 'additionalInfo': True; 'verbose': True; 'removeOutliers': None; 'binWidth': 25; 'enableCExtensions': True; 'label': 1; 'interpolator': 'sitkBSpline'; 'resampledPixelSpacing': None; 'padDistance': 5; 'normalizeScale': 1}\n",
       "Computed general_info_ImageHash: 5c9ce3ca174f0f8324aa4d277e0fef82dc5ac566\n",
       "Computed general_info_ImageSpacing: (0.7812499999999999; 0.7812499999999999; 6.499999999999998)\n",
       "Computed general_info_InputImages: {'Original': {}}\n",
       "Computed general_info_MaskHash: 9dc2c3137b31fd872997d92c9a92d5178126d9d3\n",
-      "Computed general_info_Version: v1.0.1.post69.dev0+gc00bfe2\n",
+      "Computed general_info_Version: 1.1.0.post9.dev0+g409cdcd\n",
       "Computed general_info_VolumeNum: 2\n",
       "Computed general_info_VoxelNum: 4137\n",
       "Computed original_firstorder_InterquartileRange: 253.0\n",
@@ -461,6 +482,15 @@
     "for featureName in featureVector.keys():\n",
     "  print(\"Computed %s: %s\" % (featureName, featureVector[featureName]))"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": []
   }
  ],
  "metadata": {

bin/Params.yaml

@@ -22,7 +22,6 @@ setting:
   label: 1
   interpolator: 'sitkBSpline' # This is an enumerated value, here None is not allowed
   resampledPixelSpacing: # This disables resampling, as it is interpreted as None, to enable it, specify spacing in x, y, z as [x, y , z]
-  verbose: True
   weightingNorm: # If no value is specified, it is interpreted as None
 
 # Input images to use: original for unfiltered image and/or any other filters, see documentation of featureextractor.py

bin/addClassToBaseline.py

@@ -16,8 +16,7 @@ def main():
 
   testCases = []
 
-  kwargs = {'verbose': False,
-            'binWidth': 25,
+  kwargs = {'binWidth': 25,
             'interpolator': None,
             'resampledPixelSpacing': None,
             'padDistance': 5,

bin/batchExamples/batchprocessing.py

@@ -20,29 +20,29 @@ def main():
   outputFilepath = outPath + os.path.sep + "radiomics_features.csv"
   progress_filename = outPath + os.path.sep + "pyrad_log.txt"
 
-  # Enable writing out the log using radiomics logger
-  logging.getLogger().setLevel(logging.INFO)  # Prints out log messages in this script
+  # Configure logging
+  rLogger = logging.getLogger('radiomics')
 
-  # Write out all log entries to log file
+  # Set logging level
+  # rLogger.setLevel(logging.INFO)  # Not needed, default log level of logger is INFO
+
+  # Create handler for writing to log file
   handler = logging.FileHandler(filename=progress_filename, mode='w')
-  formatter = logging.Formatter("%(levelname)s:%(name)s: %(message)s")
-  handler.setFormatter(formatter)
-  logging.getLogger().addHandler(handler)
+  handler.setFormatter(logging.Formatter("%(levelname)s:%(name)s: %(message)s"))
+  rLogger.addHandler(handler)
 
-  # Package logging
-  # radiomics.debug()  # Switch on radiomics logging from level=DEBUG (default level=WARNING)
-  # Alternative: specify level
-  radiomics.logger.setLevel(logging.INFO)
+  # Initialize logging for batch log messages
+  logger = rLogger.getChild('batch')
 
-  # Prevent radiomics logger from printing out log entries with level < WARNING to the console
-  radiomics.logger.handlers[0].setLevel(logging.WARNING)
+  # Set verbosity level for output to stderr (default level = WARNING)
+  # radiomics.setVerbosity(logging.INFO)
 
-  logging.info('Loading CSV')
+  logger.info('Loading CSV')
   print("Loading CSV")
 
   flists = []
   try:
-    with open(inputCSV, 'rb') as inFile:
+    with open(inputCSV, 'r') as inFile:
       cr = csv.reader(inFile, lineterminator='\n')
       flists = [row for row in cr]
   except Exception:
@@ -55,20 +55,22 @@ def main():
   kwargs['binWidth'] = 25
   kwargs['resampledPixelSpacing'] = None  # [3,3,3]
   kwargs['interpolator'] = sitk.sitkBSpline
-  kwargs['verbose'] = True
   kwargs['enableCExtensions'] = False
 
-  logging.info('pyradiomics version: %s', radiomics.__version__)
-  logging.info('Extracting features with kwarg settings: %s', str(kwargs))
+  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})
+
+  headers = None
+
   for idx, entry in enumerate(flists, start=1):
 
     print("(%d/%d) Processing Patient: %s, Study: %s, Reader: %s" % (idx, len(flists), entry[0], entry[1], entry[2]))
-    logging.info("(%d/%d) Processing Patient: %s, Study: %s, Reader: %s", idx, len(flists), entry[0], entry[1],
-                 entry[2])
+    logger.info("(%d/%d) Processing Patient: %s, Study: %s, Reader: %s", idx, len(flists), entry[0], entry[1],
+                entry[2])
 
     imageFilepath = entry[3]
     maskFilepath = entry[4]
@@ -84,12 +86,18 @@ def main():
       try:
         featureVector.update(extractor.execute(imageFilepath, maskFilepath))
 
-        with open(outputFilepath, 'ab') as outputFile:
+        with open(outputFilepath, 'a') as outputFile:
           writer = csv.writer(outputFile, lineterminator='\n')
-          if idx == 1: writer.writerow(featureVector.keys())
-          writer.writerow(featureVector.values())
+          if headers is None:
+            headers = list(featureVector.keys())
+            writer.writerow(headers)
+
+          row = []
+          for h in headers:
+            row.append(featureVector.get(h, "N/A"))
+          writer.writerow(row)
       except Exception:
-        logging.error('FEATURE EXTRACTION FAILED:\n%s', traceback.format_exc())
-
+        logger.error('FEATURE EXTRACTION FAILED:\n%s', traceback.format_exc())
 
-main()
+if __name__ == '__main__':
+  main()

bin/helloFeatureClass.py

@@ -35,8 +35,7 @@
 # Can be enabled by setting 'resampledPixelSpacing' to a list of 3 floats (new voxel size in mm for x, y and z)
 kwargs = {'binWidth': 25,
           'interpolator': sitk.sitkBSpline,
-          'resampledPixelSpacing': None,
-          'verbose': True}
+          'resampledPixelSpacing': None}
 
 #
 # If enabled, resample image (resampled image is automatically cropped.

bin/helloRadiomics.py

@@ -23,13 +23,28 @@
   print('Error: problem finding input labelmap', maskName)
   exit()
 
+# Uncomment line below to output debug and info log messaging to stderr
+# radiomics.debug()  # Switch on radiomics logging to stderr output from level=DEBUG (default level=WARNING)
+
+# Alternative: 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)
+
 # 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
-kwargs['verbose'] = True
 
 # Initialize wrapperClass to generate signature
 extractor = featureextractor.RadiomicsFeaturesExtractor(**kwargs)
@@ -46,20 +61,6 @@
 # Only enable mean and skewness in firstorder
 extractor.enableFeaturesByName(firstorder=['Mean', 'Skewness'])
 
-# Enable writing out the log using radiomics logger
-radiomics.debug()  # Switch on radiomics logging from level=DEBUG (default level=WARNING)
-
-# Prevent radiomics logger from printing out log entries with level < WARNING to the console
-logger = logging.getLogger('radiomics')
-logger.handlers[0].setLevel(logging.WARNING)
-logger.propagate = False  # Do not pass log messages on to root logger
-
-# 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)
-
 print("Active features:")
 for cls, features in six.iteritems(extractor.enabledFeatures):
   if len(features) == 0:

data/paramSchema.yaml

@@ -6,8 +6,6 @@ mapping:
   setting: &settings
     type: map
     mapping:
-      verbose:
-        type: bool
       enableCExtensions:
         type: bool
       additionalInfo: