STYLE: Prefer python3.9+ syntax recommendations

hjmjohnson · hjmjohnson · commit ff50ec4626ef · 2025-05-10T13:23:39.000-05:00
```bash
pip install pyupgrade
git ls-files '*.py' \
   | xargs pyupgrade --py39-plus \
                     --exit-zero-even-if-changed
```
diff --git a/bin/DatasetHierarchyReader.py b/bin/DatasetHierarchyReader.py
@@ -1,12 +1,9 @@
-# -*- coding: utf-8 -*-
-from __future__ import print_function
-
 import collections
 import glob
 import os
 
 
-class DatasetHierarchyReader(object):
+class DatasetHierarchyReader:
     def __init__(self, inputDatasetDirectory, filetype=".nrrd"):
         self.inputDatasetDirectory = inputDatasetDirectory
         self.filetype = filetype
diff --git a/bin/GenerateInputCSV_Datasethierarchy.py b/bin/GenerateInputCSV_Datasethierarchy.py
@@ -1,5 +1,3 @@
-from __future__ import print_function
-
 import csv
 import os
 
diff --git a/bin/GenerateInputCSV_Filename.py b/bin/GenerateInputCSV_Filename.py
@@ -1,5 +1,3 @@
-from __future__ import print_function
-
 import csv
 import os
 
diff --git a/docs/conf.py b/docs/conf.py
@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # pyradiomics documentation build configuration file, created by
 # sphinx-quickstart on Tue Jun 28 13:27:28 2016.
@@ -12,7 +11,6 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-from __future__ import print_function
 
 import sys
 import os
diff --git a/examples/batchProcessingWithPandas.py b/examples/batchProcessingWithPandas.py
@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 
-from __future__ import print_function
 
 import logging
 import os
diff --git a/examples/batchprocessing.py b/examples/batchprocessing.py
@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 
-from __future__ import print_function
 
 import collections
 import csv
@@ -43,7 +42,7 @@ def main():
 
     flists = []
     try:
-        with open(inputCSV, "r") as inFile:
+        with open(inputCSV) as inFile:
             cr = csv.DictReader(inFile, lineterminator="\n")
             flists = [row for row in cr]
     except Exception:
diff --git a/examples/batchprocessing_parallel.py b/examples/batchprocessing_parallel.py
@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 
-from __future__ import print_function
 
 from collections import OrderedDict
 import csv
@@ -63,7 +62,7 @@
 # loggers.
 class info_filter(logging.Filter):
     def __init__(self, name):
-        super(info_filter, self).__init__(name)
+        super().__init__(name)
         self.level = logging.WARNING
 
     def filter(self, record):
@@ -201,7 +200,7 @@ def _writeResults(featureVector):
     # Extract List of cases
     cases = []
     try:
-        with open(INPUTCSV, "r") as inFile:
+        with open(INPUTCSV) as inFile:
             cr = csv.DictReader(inFile, lineterminator="\n")
             cases = []
             for row_idx, row in enumerate(cr, start=1):
diff --git a/examples/helloFeatureClass.py b/examples/helloFeatureClass.py
@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 
-from __future__ import print_function
 
 import numpy
 import SimpleITK as sitk
@@ -169,7 +168,7 @@
         logFirstorderFeatures.enableAllFeatures()
         results = logFirstorderFeatures.execute()
         for key, val in results.items():
-            laplacianFeatureName = "%s_%s" % (imageTypeName, key)
+            laplacianFeatureName = "{}_{}".format(imageTypeName, key)
             print("  ", laplacianFeatureName, ":", val)
 #
 # Show FirstOrder features, calculated on a wavelet filtered image
@@ -187,5 +186,5 @@
         results = waveletFirstOrderFeaturs.execute()
         print("Calculated firstorder features with wavelet ", decompositionName)
         for key, val in results.items():
-            waveletFeatureName = "%s_%s" % (str(decompositionName), key)
+            waveletFeatureName = "{}_{}".format(str(decompositionName), key)
             print("  ", waveletFeatureName, ":", val)
diff --git a/examples/helloRadiomics.py b/examples/helloRadiomics.py
@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 
-from __future__ import print_function
 
 import logging
 
@@ -64,4 +63,4 @@
 featureVector = extractor.execute(imageName, maskName)
 
 for featureName in featureVector.keys():
-    print("Computed %s: %s" % (featureName, featureVector[featureName]))
+    print("Computed {}: {}".format(featureName, featureVector[featureName]))
diff --git a/examples/helloRadiomicsWithSettings.py b/examples/helloRadiomicsWithSettings.py
@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 
-from __future__ import print_function
 
 import logging
 import os
@@ -58,4 +57,4 @@
 featureVector = extractor.execute(imageName, maskName)
 
 for featureName in featureVector.keys():
-    print("Computed %s: %s" % (featureName, featureVector[featureName]))
+    print("Computed {}: {}".format(featureName, featureVector[featureName]))
diff --git a/examples/helloVoxel.py b/examples/helloVoxel.py
@@ -1,6 +1,5 @@
 #!/usr/bin/env python
 
-from __future__ import print_function
 
 import logging
 import os
@@ -136,9 +135,11 @@ def __exit__(self, exc_type, exc_value, tb):
 
 for featureName, featureValue in featureVector.items():
     if isinstance(featureValue, sitk.Image):
-        sitk.WriteImage(featureValue, "%s_%s.nrrd" % (testCase, featureName))
+        sitk.WriteImage(featureValue, "{}_{}.nrrd".format(testCase, featureName))
         print(
-            'Computed %s, stored as "%s_%s.nrrd"' % (featureName, testCase, featureName)
+            'Computed {}, stored as "{}_{}.nrrd"'.format(
+                featureName, testCase, featureName
+            )
         )
     else:
-        print("%s: %s" % (featureName, featureValue))
+        print("{}: {}".format(featureName, featureValue))
diff --git a/radiomics/__init__.py b/radiomics/__init__.py
@@ -170,7 +170,7 @@ def getTestCase(testCase, dataDirectory=None):
         )
 
     im_name = "%s_image.nrrd" % testCase
-    ma_name = "%s_label%s.nrrd" % (testCase, "_2D" if label2D else "")
+    ma_name = "{}_label{}.nrrd".format(testCase, "_2D" if label2D else "")
 
     def get_or_download(fname):
         target = os.path.join(dataDirectory, fname)
@@ -225,7 +225,7 @@ def getParameterValidationFiles():
     return schemaFile, schemaFuncs
 
 
-class _DummyProgressReporter(object):
+class _DummyProgressReporter:
     """
     This class represents the dummy Progress reporter and is used for where progress reporting is implemented, but not
     enabled (when the progressReporter is not set or verbosity level > INFO).
diff --git a/radiomics/base.py b/radiomics/base.py
@@ -8,7 +8,7 @@
 from radiomics import getProgressReporter, imageoperations
 
 
-class RadiomicsFeaturesBase(object):
+class RadiomicsFeaturesBase:
     """
     This is the abstract class, which defines the common interface for the feature classes. All feature classes inherit
     (directly of indirectly) from this class.
diff --git a/radiomics/featureextractor.py b/radiomics/featureextractor.py
@@ -1,6 +1,3 @@
-# -*- coding: utf-8 -*-
-from __future__ import print_function
-
 import collections
 from itertools import chain
 import json
@@ -65,7 +62,7 @@ def __init__(self, *args, **kwargs):
             isinstance(args[0], str) or isinstance(args[0], pathlib.PurePath)
         ):
             if not os.path.isfile(args[0]):
-                raise IOError("Parameter file %s does not exist." % args[0])
+                raise OSError("Parameter file %s does not exist." % args[0])
             logger.info("Loading parameter file %s", str(args[0]))
             self._applyParams(paramsFile=args[0])
         else:
@@ -492,7 +489,7 @@ def compute(shape_type):
                     shapeClass.enableFeatureByName(feature)
 
             for featureName, featureValue in shapeClass.execute().items():
-                newFeatureName = "original_%s_%s" % (shape_type, featureName)
+                newFeatureName = "original_{}_{}".format(shape_type, featureName)
                 featureVector[newFeatureName] = featureValue
 
         Nd = mask.GetDimension()
@@ -576,7 +573,7 @@ def computeFeatures(self, image, mask, imageTypeName, **kwargs):
                         featureClass.enableFeatureByName(feature)
 
                 for featureName, featureValue in featureClass.execute().items():
-                    newFeatureName = "%s_%s_%s" % (
+                    newFeatureName = "{}_{}_{}".format(
                         imageTypeName,
                         featureClassName,
                         featureName,
diff --git a/radiomics/firstorder.py b/radiomics/firstorder.py
@@ -29,14 +29,14 @@ class RadiomicsFirstOrder(base.RadiomicsFeaturesBase):
     """
 
     def __init__(self, inputImage, inputMask, **kwargs):
-        super(RadiomicsFirstOrder, self).__init__(inputImage, inputMask, **kwargs)
+        super().__init__(inputImage, inputMask, **kwargs)
 
         self.pixelSpacing = inputImage.GetSpacing()
         self.voxelArrayShift = kwargs.get("voxelArrayShift", 0)
         self.discretizedImageArray = self._applyBinning(self.imageArray.copy())
 
     def _initVoxelBasedCalculation(self):
-        super(RadiomicsFirstOrder, self)._initVoxelBasedCalculation()
+        super()._initVoxelBasedCalculation()
 
         kernelRadius = self.settings.get("kernelRadius", 1)
 
diff --git a/radiomics/glcm.py b/radiomics/glcm.py
@@ -98,7 +98,7 @@ class RadiomicsGLCM(base.RadiomicsFeaturesBase):
   """
 
     def __init__(self, inputImage, inputMask, **kwargs):
-        super(RadiomicsGLCM, self).__init__(inputImage, inputMask, **kwargs)
+        super().__init__(inputImage, inputMask, **kwargs)
 
         self.symmetricalGLCM = kwargs.get("symmetricalGLCM", True)
         self.weightingNorm = kwargs.get(
diff --git a/radiomics/gldm.py b/radiomics/gldm.py
@@ -64,7 +64,7 @@ class RadiomicsGLDM(base.RadiomicsFeaturesBase):
   """
 
     def __init__(self, inputImage, inputMask, **kwargs):
-        super(RadiomicsGLDM, self).__init__(inputImage, inputMask, **kwargs)
+        super().__init__(inputImage, inputMask, **kwargs)
 
         self.gldm_a = kwargs.get("gldm_a", 0)
 
diff --git a/radiomics/glrlm.py b/radiomics/glrlm.py
@@ -73,7 +73,7 @@ class RadiomicsGLRLM(base.RadiomicsFeaturesBase):
   """
 
     def __init__(self, inputImage, inputMask, **kwargs):
-        super(RadiomicsGLRLM, self).__init__(inputImage, inputMask, **kwargs)
+        super().__init__(inputImage, inputMask, **kwargs)
 
         self.weightingNorm = kwargs.get(
             "weightingNorm", None
diff --git a/radiomics/glszm.py b/radiomics/glszm.py
@@ -55,7 +55,7 @@ class RadiomicsGLSZM(base.RadiomicsFeaturesBase):
   """
 
     def __init__(self, inputImage, inputMask, **kwargs):
-        super(RadiomicsGLSZM, self).__init__(inputImage, inputMask, **kwargs)
+        super().__init__(inputImage, inputMask, **kwargs)
 
         self.P_glszm = None
         self.imageArray = self._applyBinning(self.imageArray)
diff --git a/radiomics/imageoperations.py b/radiomics/imageoperations.py
@@ -1,5 +1,3 @@
-from __future__ import print_function
-
 import logging
 
 import numpy
@@ -906,14 +904,14 @@ def getWaveletImage(inputImage, inputMask, **kwargs):
             if idx == 1:
                 inputImageName = "wavelet-%s" % (decompositionName)
             else:
-                inputImageName = "wavelet%s-%s" % (idx, decompositionName)
+                inputImageName = "wavelet{}-{}".format(idx, decompositionName)
             logger.debug("Yielding %s image", inputImageName)
             yield decompositionImage, inputImageName, kwargs
 
     if len(ret) == 1:
         inputImageName = "wavelet-%s" % ("L" * len(axes))
     else:
-        inputImageName = "wavelet%s-%s" % (len(ret), ("L" * len(axes)))
+        inputImageName = "wavelet{}-{}".format(len(ret), ("L" * len(axes)))
     logger.debug("Yielding approximation (%s) image", inputImageName)
     yield approx, inputImageName, kwargs
 
diff --git a/radiomics/ngtdm.py b/radiomics/ngtdm.py
@@ -84,7 +84,7 @@ class RadiomicsNGTDM(base.RadiomicsFeaturesBase):
   """
 
     def __init__(self, inputImage, inputMask, **kwargs):
-        super(RadiomicsNGTDM, self).__init__(inputImage, inputMask, **kwargs)
+        super().__init__(inputImage, inputMask, **kwargs)
 
         self.P_ngtdm = None
         self.imageArray = self._applyBinning(self.imageArray)
diff --git a/radiomics/schemas/schemaFuncs.py b/radiomics/schemas/schemaFuncs.py
@@ -12,7 +12,7 @@ def checkWavelet(value, rule_obj, path):
     wavelist = pywt.wavelist()
     if value not in wavelist:
         raise ValueError(
-            'Wavelet "%s" not available in pyWavelets %s' % (value, wavelist)
+            'Wavelet "{}" not available in pyWavelets {}'.format(value, wavelist)
         )
     return True
 
@@ -35,7 +35,9 @@ def checkInterpolator(value, rule_obj, path):
         }
         if value not in enum:
             raise ValueError(
-                'Interpolator value "%s" not valid, possible values: %s' % (value, enum)
+                'Interpolator value "{}" not valid, possible values: {}'.format(
+                    value, enum
+                )
             )
     elif isinstance(value, int):
         if value < 1 or value > 10:
diff --git a/radiomics/scripts/__init__.py b/radiomics/scripts/__init__.py
@@ -264,7 +264,7 @@ def _processInput(self):
         if self.args.input.endswith(".csv"):
             self.logger.debug('Loading batch file "%s"', self.args.input)
             self.relative_path_start = os.path.dirname(self.args.input)
-            with open(self.args.input, mode="r") as batchFile:
+            with open(self.args.input) as batchFile:
                 cr = csv.DictReader(batchFile, lineterminator="\n")
 
                 # Check if required Image and Mask columns are present
diff --git a/radiomics/scripts/segment.py b/radiomics/scripts/segment.py
@@ -24,7 +24,7 @@ def extractSegment(case_idx, case, extractor, **kwargs):
     filename = os.path.join(out_dir, "features_%s.csv" % case_idx)
     if os.path.isfile(filename):
         # Output already generated, load result (prevents re-extraction in case of interrupted process)
-        with open(filename, "r") as outputFile:
+        with open(filename) as outputFile:
             reader = csv.reader(outputFile)
             headers = next(reader)
             values = next(reader)
@@ -124,7 +124,7 @@ def _configureParallelExtraction(logging_config, add_info_filter=True):
         # other loggers.
         class info_filter(logging.Filter):
             def __init__(self, name):
-                super(info_filter, self).__init__(name)
+                super().__init__(name)
                 self.level = logging.WARNING
 
             def filter(self, record):
diff --git a/radiomics/scripts/voxel.py b/radiomics/scripts/voxel.py
@@ -107,7 +107,7 @@ def _configureParallelExtraction(logging_config, add_info_filter=True):
         # other loggers.
         class info_filter(logging.Filter):
             def __init__(self, name):
-                super(info_filter, self).__init__(name)
+                super().__init__(name)
                 self.level = logging.WARNING
 
             def filter(self, record):
diff --git a/radiomics/shape.py b/radiomics/shape.py
@@ -41,7 +41,7 @@ def __init__(self, inputImage, inputMask, **kwargs):
         assert (
             inputMask.GetDimension() == 3
         ), "Shape features are only available in 3D. If 2D, use shape2D instead"
-        super(RadiomicsShape, self).__init__(inputImage, inputMask, **kwargs)
+        super().__init__(inputImage, inputMask, **kwargs)
 
     def _initVoxelBasedCalculation(self):
         raise NotImplementedError(
diff --git a/radiomics/shape2D.py b/radiomics/shape2D.py
@@ -46,7 +46,7 @@ class RadiomicsShape2D(base.RadiomicsFeaturesBase):
     """
 
     def __init__(self, inputImage, inputMask, **kwargs):
-        super(RadiomicsShape2D, self).__init__(inputImage, inputMask, **kwargs)
+        super().__init__(inputImage, inputMask, **kwargs)
 
     def _initVoxelBasedCalculation(self):
         raise NotImplementedError(
diff --git a/tests/add_baseline.py b/tests/add_baseline.py
@@ -53,7 +53,7 @@ def process_testcase(self, test, featureClassName):
             if cMat is not None:
                 numpy.save(
                     os.path.join(
-                        self.baselineDir, "%s_%s.npy" % (test, featureClassName)
+                        self.baselineDir, "{}_{}.npy".format(test, featureClassName)
                     ),
                     cMat,
                 )
@@ -67,7 +67,7 @@ def process_testcase(self, test, featureClassName):
         self.new_baselines[featureClassName].configuration[test].update(versions)
 
         self.new_baselines[featureClassName].baseline[test] = {
-            "%s_%s_%s" % (imageTypeName, featureClassName, key): val
+            "{}_{}_{}".format(imageTypeName, featureClassName, key): val
             for key, val in featureClass.featureValues.items()
         }
 
diff --git a/tests/testUtils.py b/tests/testUtils.py
diff --git a/tests/test_exampleSettings.py b/tests/test_exampleSettings.py
diff --git a/tests/test_features.py b/tests/test_features.py
diff --git a/tests/test_matrices.py b/tests/test_matrices.py

Original file line number	Diff line number	Diff line change
`@@ -1,5 +1,3 @@`
`1`		`-from __future__ import print_function`
`2`		`-`
`3`	`1`	`import csv`
`4`	`2`	`import os`
`5`	`3`