Merge pull request #173 from JoostJM/update-for-first-release

Update for first release

data/paramSchema.yaml

@@ -55,19 +55,11 @@ mapping:
           min: 0
   featureClass:
     type: map
+    func: checkFeatureClass
+    matching-rule: 'any'
     mapping:
-      # Possible feature classes, each can have a list of enabled features, empyt list or none value signifies
-      # that all features must be enabled
-      shape: &featurelist
-        seq:
-          - type: str
-            unique: True
-      firstorder: *featurelist
-      glcm: *featurelist
-      gldm: *featurelist
-      ngtdm: *featurelist
-      glrlm: *featurelist
-      glszm: *featurelist
+      regex;(.+):
+        type: any
 
   inputImage:
     type: map

data/schemaFuncs.py

@@ -1,4 +1,7 @@
 import pywt
+from radiomics.featureextractor import RadiomicsFeaturesExtractor
+
+featureClasses = RadiomicsFeaturesExtractor.getFeatureClasses()
 
 
 def checkWavelet(value, rule_obj, path):
@@ -44,3 +47,21 @@ def checkWeighting(value, rule_obj, path):
   else:
     raise TypeError('WeightingNorm not expected type (str or None)')
   return True
+
+
+def checkFeatureClass(value, rule_obj, path):
+  global featureClasses
+  if value is None:
+    raise TypeError('featureClass dictionary cannot be None value')
+  for className, features in value.iteritems():
+    if className not in featureClasses.keys():
+      raise ValueError(
+        'Feature Class %s is not recognized. Available feature classes are %s' % (className, featureClasses.keys()))
+    if features is not None:
+      if not isinstance(features, list):
+        raise TypeError('Value of feature class %s not expected type (list)' % (className))
+      unrecognizedFeatures = set(features) - set(featureClasses[className].getFeatureNames())
+      if len(unrecognizedFeatures) > 0:
+        raise ValueError('Feature Class %s contains unrecognized features: %s' % (className, str(unrecognizedFeatures)))
+
+  return True

docs/radiomics.rst

@@ -59,28 +59,6 @@ radiomics.glcm module
     :show-inheritance:
     :member-order: bysource
 
-.. _radiomics-gldm-label:
-
-radiomics.gldm module
----------------------
-
-.. automodule:: radiomics.gldm
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :member-order: bysource
-
-.. _radiomics-gldzm-label:
-
-radiomics.gldzm module
-----------------------
-
-.. automodule:: radiomics.gldzm
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :member-order: bysource
-
 .. _radiomics-glszm-label:
 
 radiomics.glszm module
@@ -103,17 +81,6 @@ radiomics.glrlm module
     :show-inheritance:
     :member-order: bysource
 
-.. _radiomics-ngtdm-label:
-
-radiomics.ngtdm module
-----------------------
-
-.. automodule:: radiomics.ngtdm
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :member-order: bysource
-
 .. _radiomics-shape-label:
 
 radiomics.shape module
@@ -136,18 +103,6 @@ radiomics.imageoperations module
     :show-inheritance:
     :member-order: bysource
 
-.. _radiomics-test-label:
-
-test module
-------------
-
-.. automodule:: test
-    :members:
-    :undoc-members:
-    :show-inheritance:
-    :member-order: bysource
-
-
 Module contents
 ---------------
 

radiomics/featureextractor.py

@@ -561,7 +561,8 @@ def getInputImageTypes(self):
     """
     return [member[9:] for member in dir(self) if member.startswith('generate_')]
 
-  def getFeatureClasses(self):
+  @classmethod
+  def getFeatureClasses(cls):
     """
     Iterates over all modules of the radiomics package using pkgutil and subsequently imports those modules.