ENH: Refactor code to remove six usage in iteration syntax.

This commit replaces `six.iteritems()` with Python 3's native `dict.items()` for iterating over dictionary items. The now unnecessary `six` import is removed, aligning the codebase with modern Python practices and enhancing maintainability.

Support for Python2 was removed many years ago.  Clean up the codebase
by removing the conditional behaviors encoded with six.

Author: hjmjohnson

CHANGES.rst

@@ -830,11 +830,6 @@ Bug fixes
 - Fix datatype error when calling ``SimpleITK.ResampleImageFilter.SetSize()`` (only causes error in python 3,
   `#205 <https://github.com/AIM-Harvard/pyradiomics/pull/205>`_)
 
-Requirements
-############
-
-- Add requirement for ``six>=1.10.0``, needed to make PyRadiomics compatible with both python 2 and 3.
-
 Documentation
 #############
 
@@ -865,8 +860,7 @@ Internal API
   feature classes and filters at initialization of the toolbox, and ensures feature classes are imported at
   initialization. (`#190 <https://github.com/AIM-Harvard/pyradiomics/pull/190>`_,
   `#198 <https://github.com/AIM-Harvard/pyradiomics/pull/198>`_)
-- Python 3 Compatibility. Add support for compatibility with python 2.7 and python >= 3.4. This is achieved using
-  package ``six``.
+- Python 3 Compatibility is required
 - Standardize function names for calculating matrices in python and with C extensions to ``_calculateMatrix`` and
   ``_calculateCMatrix``, respectively.
 - Make C code consistent with C89 convention. All variables (pointers for python objects) are initialized at top of each

README.md

@@ -152,7 +152,6 @@ available [here](https://github.com/AIM-Harvard/SlicerRadiomics).
 - numpy (Feature calculation)
 - PyWavelets (Wavelet filter)
 - pykwalify (Enabling yaml parameters file checking)
-- six (Python 3 Compatibility)
 - scipy (Only for LBP filter, install separately to enable this filter)
 - scikit-image (Only for LBP filter, install separately to enable this filter)
 - trimesh (Only for LBP filter, install separately to enable this filter)

bin/DatasetHierarchyReader.py

@@ -5,8 +5,6 @@
 import glob
 import os
 
-import six
-
 
 class DatasetHierarchyReader(object):
   def __init__(self, inputDatasetDirectory, filetype='.nrrd'):
@@ -105,7 +103,7 @@ def findImageAndLabelPair(self, imageFilepaths, maskFilepaths, keywordSettings):
     """
 
     keywordSettings = {k: [str(keyword.strip()) for keyword in v.split(',')]
-                       for (k, v) in six.iteritems(keywordSettings)}
+                       for (k, v) in keywordSettings.items()}
 
     matchedImages = []
     for imageFilepath in imageFilepaths:

bin/GenerateInputCSV_Filename.py

@@ -3,8 +3,6 @@
 import csv
 import os
 
-import six
-
 SqDic = {}
 SqDic['T2-TSE-TRA'] = 't2tra'
 SqDic['T2-TRA'] = 't2tra'
@@ -43,16 +41,16 @@ def main():
   print("Found %s patients, writing csv" % (len(datasetHierarchyDict.keys())))
 
   try:
-    with open(outputFile, 'wb') as outFile:
+    with open(outputFile, 'w') as outFile:
       cw = csv.writer(outFile, lineterminator='\n')
       cw.writerow(['Patient', 'Sequence', 'Reader', 'Image', 'Mask'])
 
-      for patient, Studies in sorted(six.iteritems(datasetHierarchyDict), key=lambda t: t[0]):
-        for Study, im_fileList in sorted(six.iteritems(Studies['reconstructions']), key=lambda t: t[0]):
+      for patient, Studies in sorted(datasetHierarchyDict.items(), key=lambda t: t[0]):
+        for Study, im_fileList in sorted(Studies['reconstructions'].items(), key=lambda t: t[0]):
           for i_idx, im_file in enumerate(im_fileList):
 
-            if Studies['segmentations'].has_key(Study):
-              for Reader, seg_fileList in sorted(six.iteritems(Studies['segmentations'][Study]), key=lambda t: t[0]):
+            if Study in Studies['segmentations']:
+              for Reader, seg_fileList in sorted(Studies['segmentations'][Study].items(), key=lambda t: t[0]):
                 for s_idx, seg_file in enumerate(sorted(seg_fileList)):
 
                   i_name = Study
@@ -75,22 +73,22 @@ def scanpatients(f, filetype):
       if (fname[0:3] == "Pt-") & (fname.endswith(filetype)):
         PtNo = fname[3:7]
 
-        if not outputDict.has_key(PtNo):
+        if PtNo not in outputDict:
           outputDict[PtNo] = {'reconstructions': {}}
           outputDict[PtNo]['segmentations'] = {}
 
-        for SqKey, SqVal in six.iteritems(SqDic):
+        for SqKey, SqVal in SqDic.items():
           if ("ROI_" + SqVal) in fname:
-            for ReaderKey, ReaderVal in six.iteritems(LabelDic):
+            for ReaderKey, ReaderVal in LabelDic.items():
               if (ReaderKey + '_') in fname:
-                if not outputDict[PtNo]['segmentations'].has_key(SqVal):
+                if SqVal not in outputDict[PtNo]['segmentations']:
                   outputDict[PtNo]['segmentations'][SqVal] = {}
-                if not outputDict[PtNo]['segmentations'][SqVal].has_key(ReaderVal):
+                if ReaderVal not in outputDict[PtNo]['segmentations'][SqVal]:
                   outputDict[PtNo]['segmentations'][SqVal][ReaderVal] = set()
                 outputDict[PtNo]['segmentations'][SqVal][ReaderVal].add(os.path.join(dirpath, fname))
                 break
           elif SqKey in fname:
-            if not outputDict[PtNo]['reconstructions'].has_key(SqVal):
+            if SqVal not in outputDict[PtNo]['reconstructions']:
               outputDict[PtNo]['reconstructions'][SqVal] = set()
             outputDict[PtNo]['reconstructions'][SqVal].add(os.path.join(dirpath, fname))
             break

conda/meta.yaml

@@ -22,14 +22,12 @@ requirements:
     - pykwalify >=1.6.0
     - pywavelets >=0.4.0
     - SimpleITK !=1.1.0
-    - six >=1.10.0
   run:
     - python
     - numpy >=1.9.2
     - pykwalify >=1.6.0
     - pywavelets >=0.4.0
     - SimpleITK !=1.1.0
-    - six >=1.10.0
     - scipy
     - scikit-learn
     - trimesh

docs/developers.rst

@@ -184,7 +184,6 @@ Using feature classes directly
 
      from radiomics import firstorder, glcm, imageoperations, shape, glrlm, glszm, getTestCase
      import SimpleITK as sitk
-     import six
      import sys, os
 
 * Set up a data directory variable::
@@ -204,7 +203,7 @@ Using feature classes directly
      firstOrderFeatures = firstorder.RadiomicsFirstOrder(image,mask)
      firstOrderFeatures.enableAllFeatures()  # On the feature class level, all features are disabled by default.
      firstOrderFeatures.calculateFeatures()
-     for (key,val) in six.iteritems(firstOrderFeatures.featureValues):
+     for (key,val) in firstOrderFeatures.featureValues.items():
        print("\t%s: %s" % (key, val))
 
 * See the :ref:`radiomics-features-label` section for more features that you can calculate.

docs/index.rst

@@ -107,7 +107,6 @@ and filters, thereby enabling fully reproducible feature extraction. For more in
 * numpy (Feature calculation)
 * PyWavelets (Wavelet filter)
 * pykwalify (Enabling yaml parameters file checking)
-* six (Python 3 Compatibility)
 
 See also the `requirements file <https://github.com/Radiomics/pyradiomics/blob/master/requirements.txt>`_.
 

docs/usage.rst

@@ -127,7 +127,6 @@ Interactive Use
      import os
 
      import SimpleITK as sitk
-     import six
 
      from radiomics import featureextractor, getTestCase
 
@@ -152,13 +151,13 @@ Interactive Use
 * Calculate the features (segment-based)::
 
     result = extractor.execute(imageName, maskName)
-    for key, val in six.iteritems(result):
+    for key, val in result.items():
       print("\t%s: %s" %(key, val))
 
 * Calculate the features (voxel-based)::
 
     result = extractor.execute(imageName, maskName, voxelBased=True)
-    for key, val in six.iteritems(result):
+    for key, val in result.items():
       if isinstance(val, sitk.Image):  # Feature map
         sitk.WriteImage(val, key + '.nrrd', True)
         print("Stored feature %s in %s" % (key, key + ".nrrd"))

examples/helloFeatureClass.py

@@ -4,7 +4,6 @@
 
 import numpy
 import SimpleITK as sitk
-import six
 
 from radiomics import firstorder, getTestCase, glcm, glrlm, glszm, imageoperations, shape
 
@@ -65,7 +64,7 @@
 print('done')
 
 print('Calculated first order features: ')
-for (key, val) in six.iteritems(results):
+for (key, val) in results.items():
   print('  ', key, ':', val)
 
 #
@@ -84,7 +83,7 @@
 print('done')
 
 print('Calculated Shape features: ')
-for (key, val) in six.iteritems(results):
+for (key, val) in results.items():
   print('  ', key, ':', val)
 
 #
@@ -103,7 +102,7 @@
 print('done')
 
 print('Calculated GLCM features: ')
-for (key, val) in six.iteritems(results):
+for (key, val) in results.items():
   print('  ', key, ':', val)
 
 #
@@ -122,7 +121,7 @@
 print('done')
 
 print('Calculated GLRLM features: ')
-for (key, val) in six.iteritems(results):
+for (key, val) in results.items():
   print('  ', key, ':', val)
 
 #
@@ -141,7 +140,7 @@
 print('done')
 
 print('Calculated GLSZM features: ')
-for (key, val) in six.iteritems(results):
+for (key, val) in results.items():
   print('  ', key, ':', val)
 
 #
@@ -153,7 +152,7 @@
     logFirstorderFeatures = firstorder.RadiomicsFirstOrder(logImage, mask, **inputKwargs)
     logFirstorderFeatures.enableAllFeatures()
     results = logFirstorderFeatures.execute()
-    for (key, val) in six.iteritems(results):
+    for (key, val) in results.items():
       laplacianFeatureName = '%s_%s' % (imageTypeName, key)
       print('  ', laplacianFeatureName, ':', val)
 #
@@ -165,6 +164,6 @@
     waveletFirstOrderFeaturs.enableAllFeatures()
     results = waveletFirstOrderFeaturs.execute()
     print('Calculated firstorder features with wavelet ', decompositionName)
-    for (key, val) in six.iteritems(results):
+    for (key, val) in results.items():
       waveletFeatureName = '%s_%s' % (str(decompositionName), key)
       print('  ', waveletFeatureName, ':', val)

examples/helloRadiomicsWithSettings.py

@@ -5,8 +5,6 @@
 import logging
 import os
 
-import six
-
 import radiomics
 from radiomics import featureextractor, getFeatureClasses
 
@@ -41,9 +39,9 @@
 featureClasses = getFeatureClasses()
 
 print("Active features:")
-for cls, features in six.iteritems(extractor.enabledFeatures):
+for cls, features in extractor.enabledFeatures.items():
   if features is None or len(features) == 0:
-    features = [f for f, deprecated in six.iteritems(featureClasses[cls].getFeatureNames()) if not deprecated]
+    features = [f for f, deprecated in featureClasses[cls].getFeatureNames().items() if not deprecated]
   for f in features:
     print(f)
     print(getattr(featureClasses[cls], 'get%sFeatureValue' % f).__doc__)