STYLE: Prefer modern f-strings formatting

hjmjohnson · hjmjohnson · commit dc49019048fa · 2025-05-10T13:27:47.000-05:00
```bash
pip install flynt
git ls-files '*.py' \
| xargs flynt
```
diff --git a/bin/GenerateInputCSV_Datasethierarchy.py b/bin/GenerateInputCSV_Datasethierarchy.py
@@ -21,7 +21,7 @@ def main():
     datasetReader = DatasetHierarchyReader(inputDirectory, filetype=filetype)
     datasetHierarchyDict = datasetReader.ReadDatasetHierarchy()
 
-    print("Found %s patients, writing csv" % (str(len(datasetHierarchyDict.keys()))))
+    print(f"Found {str(len(datasetHierarchyDict.keys()))} patients, writing csv")
 
     try:
         with open(outputFile, "wb") as outFile:
diff --git a/bin/GenerateInputCSV_Filename.py b/bin/GenerateInputCSV_Filename.py
@@ -36,7 +36,7 @@ def main():
 
     datasetHierarchyDict = scanpatients(inputDirectory, filetype)
 
-    print("Found %s patients, writing csv" % (len(datasetHierarchyDict.keys())))
+    print(f"Found {len(datasetHierarchyDict.keys())} patients, writing csv")
 
     try:
         with open(outputFile, "w") as outFile:
@@ -60,11 +60,11 @@ def main():
 
                                     i_name = Study
                                     if i_idx > 0:
-                                        i_name += " (%s)" % (str(i_idx + 1))
+                                        i_name += f" ({str(i_idx + 1)})"
 
                                     s_name = Reader
                                     if s_idx > 0:
-                                        s_name += " (%s)" % (str(s_idx + 1))
+                                        s_name += f" ({str(s_idx + 1)})"
 
                                     cw.writerow(
                                         [patient, i_name, s_name, im_file, seg_file]
diff --git a/bin/testParams.py b/bin/testParams.py
@@ -26,7 +26,7 @@ def main(paramsFile):
             % (params["featureClass"], params["imageType"], params["setting"])
         )
     except Exception as e:
-        print("Parameter validation failed!\n%s" % e.message)
+        print(f"Parameter validation failed!\n{e.message}")
 
 
 if __name__ == "__main__" and len(sys.argv) > 1:
diff --git a/examples/helloFeatureClass.py b/examples/helloFeatureClass.py
@@ -68,7 +68,7 @@
 print("Will calculate the following first order features: ")
 for f in firstOrderFeatures.enabledFeatures.keys():
     print("  ", f)
-    print(getattr(firstOrderFeatures, "get%sFeatureValue" % f).__doc__)
+    print(getattr(firstOrderFeatures, f"get{f}FeatureValue").__doc__)
 
 print("Calculating first order features...")
 results = firstOrderFeatures.execute()
@@ -87,7 +87,7 @@
 print("Will calculate the following Shape features: ")
 for f in shapeFeatures.enabledFeatures.keys():
     print("  ", f)
-    print(getattr(shapeFeatures, "get%sFeatureValue" % f).__doc__)
+    print(getattr(shapeFeatures, f"get{f}FeatureValue").__doc__)
 
 print("Calculating Shape features...")
 results = shapeFeatures.execute()
@@ -106,7 +106,7 @@
 print("Will calculate the following GLCM features: ")
 for f in glcmFeatures.enabledFeatures.keys():
     print("  ", f)
-    print(getattr(glcmFeatures, "get%sFeatureValue" % f).__doc__)
+    print(getattr(glcmFeatures, f"get{f}FeatureValue").__doc__)
 
 print("Calculating GLCM features...")
 results = glcmFeatures.execute()
@@ -125,7 +125,7 @@
 print("Will calculate the following GLRLM features: ")
 for f in glrlmFeatures.enabledFeatures.keys():
     print("  ", f)
-    print(getattr(glrlmFeatures, "get%sFeatureValue" % f).__doc__)
+    print(getattr(glrlmFeatures, f"get{f}FeatureValue").__doc__)
 
 print("Calculating GLRLM features...")
 results = glrlmFeatures.execute()
@@ -144,7 +144,7 @@
 print("Will calculate the following GLSZM features: ")
 for f in glszmFeatures.enabledFeatures.keys():
     print("  ", f)
-    print(getattr(glszmFeatures, "get%sFeatureValue" % f).__doc__)
+    print(getattr(glszmFeatures, f"get{f}FeatureValue").__doc__)
 
 print("Calculating GLSZM features...")
 results = glszmFeatures.execute()
@@ -168,7 +168,7 @@
         logFirstorderFeatures.enableAllFeatures()
         results = logFirstorderFeatures.execute()
         for key, val in results.items():
-            laplacianFeatureName = "{}_{}".format(imageTypeName, key)
+            laplacianFeatureName = f"{imageTypeName}_{key}"
             print("  ", laplacianFeatureName, ":", val)
 #
 # Show FirstOrder features, calculated on a wavelet filtered image
@@ -186,5 +186,5 @@
         results = waveletFirstOrderFeaturs.execute()
         print("Calculated firstorder features with wavelet ", decompositionName)
         for key, val in results.items():
-            waveletFeatureName = "{}_{}".format(str(decompositionName), key)
+            waveletFeatureName = f"{str(decompositionName)}_{key}"
             print("  ", waveletFeatureName, ":", val)
diff --git a/examples/helloRadiomics.py b/examples/helloRadiomics.py
@@ -63,4 +63,4 @@
 featureVector = extractor.execute(imageName, maskName)
 
 for featureName in featureVector.keys():
-    print("Computed {}: {}".format(featureName, featureVector[featureName]))
+    print(f"Computed {featureName}: {featureVector[featureName]}")
diff --git a/examples/helloRadiomicsWithSettings.py b/examples/helloRadiomicsWithSettings.py
@@ -51,10 +51,10 @@
         ]
     for f in features:
         print(f)
-        print(getattr(featureClasses[cls], "get%sFeatureValue" % f).__doc__)
+        print(getattr(featureClasses[cls], f"get{f}FeatureValue").__doc__)
 
 print("Calculating features")
 featureVector = extractor.execute(imageName, maskName)
 
 for featureName in featureVector.keys():
-    print("Computed {}: {}".format(featureName, featureVector[featureName]))
+    print(f"Computed {featureName}: {featureVector[featureName]}")
diff --git a/examples/helloVoxel.py b/examples/helloVoxel.py
@@ -128,18 +128,14 @@ def __exit__(self, exc_type, exc_value, tb):
         ]
     for f in features:
         print(f)
-        print(getattr(featureClasses[cls], "get%sFeatureValue" % f).__doc__)
+        print(getattr(featureClasses[cls], f"get{f}FeatureValue").__doc__)
 
 print("Calculating features")
 featureVector = extractor.execute(imageName, maskName, voxelBased=True)
 
 for featureName, featureValue in featureVector.items():
     if isinstance(featureValue, sitk.Image):
-        sitk.WriteImage(featureValue, "{}_{}.nrrd".format(testCase, featureName))
-        print(
-            'Computed {}, stored as "{}_{}.nrrd"'.format(
-                featureName, testCase, featureName
-            )
-        )
+        sitk.WriteImage(featureValue, f"{testCase}_{featureName}.nrrd")
+        print(f'Computed {featureName}, stored as "{testCase}_{featureName}.nrrd"')
     else:
-        print("{}: {}".format(featureName, featureValue))
+        print(f"{featureName}: {featureValue}")
diff --git a/labs/pyradiomics-dcm/pyradiomics-dcm.py b/labs/pyradiomics-dcm/pyradiomics-dcm.py
@@ -359,7 +359,7 @@ def addMeasurement(
             return
 
         try:
-            measurement["value"] = "%E" % Decimal(float(value))
+            measurement["value"] = f"{Decimal(float(value)):E}"
         except Exception as e:
             scriptlogger.error("Exception formatting %s as Decimal: %s", value, str(e))
             scriptlogger.error("type of value: %s", type(value))
diff --git a/radiomics/__init__.py b/radiomics/__init__.py
@@ -159,7 +159,7 @@ def getTestCase(testCase, dataDirectory=None):
         testCase = testCase[:-3]
 
     if testCase not in testCases:
-        raise ValueError('Testcase "%s" not recognized!' % testCase)
+        raise ValueError(f'Testcase "{testCase}" not recognized!')
 
     logger.debug("Getting test case %s", testCase)
 
@@ -169,8 +169,8 @@ def getTestCase(testCase, dataDirectory=None):
             'No data directory specified, using temporary directory "%s"', dataDirectory
         )
 
-    im_name = "%s_image.nrrd" % testCase
-    ma_name = "{}_label{}.nrrd".format(testCase, "_2D" if label2D else "")
+    im_name = f"{testCase}_image.nrrd"
+    ma_name = f"{testCase}_label{'_2D' if label2D else ''}.nrrd"
 
     def get_or_download(fname):
         target = os.path.join(dataDirectory, fname)
diff --git a/radiomics/base.py b/radiomics/base.py
@@ -259,7 +259,7 @@ def _calculateFeatures(self, voxelCoordinates=None):
             if enabled:
                 try:
                     # Use getattr to get the feature calculation methods, then use '()' to evaluate those methods
-                    yield True, feature, getattr(self, "get%sFeatureValue" % feature)()
+                    yield True, feature, getattr(self, f"get{feature}FeatureValue")()
                 except DeprecationWarning as deprecatedFeature:
                     # Add a debug log message, as a warning is usually shown and would entail a too verbose output
                     self.logger.debug(
diff --git a/radiomics/featureextractor.py b/radiomics/featureextractor.py
@@ -62,7 +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 OSError("Parameter file %s does not exist." % args[0])
+                raise OSError(f"Parameter file {args[0]} does not exist.")
             logger.info("Loading parameter file %s", str(args[0]))
             self._applyParams(paramsFile=args[0])
         else:
@@ -355,7 +355,7 @@ def execute(
             )
             imageGenerators = chain(
                 imageGenerators,
-                getattr(imageoperations, "get%sImage" % imageType)(image, mask, **args),
+                getattr(imageoperations, f"get{imageType}Image")(image, mask, **args),
             )
 
         logger.debug("Extracting features")
@@ -489,7 +489,7 @@ def compute(shape_type):
                     shapeClass.enableFeatureByName(feature)
 
             for featureName, featureValue in shapeClass.execute().items():
-                newFeatureName = "original_{}_{}".format(shape_type, featureName)
+                newFeatureName = f"original_{shape_type}_{featureName}"
                 featureVector[newFeatureName] = featureValue
 
         Nd = mask.GetDimension()
@@ -573,11 +573,7 @@ def computeFeatures(self, image, mask, imageTypeName, **kwargs):
                         featureClass.enableFeatureByName(feature)
 
                 for featureName, featureValue in featureClass.execute().items():
-                    newFeatureName = "{}_{}_{}".format(
-                        imageTypeName,
-                        featureClassName,
-                        featureName,
-                    )
+                    newFeatureName = f"{imageTypeName}_{featureClassName}_{featureName}"
                     featureVector[newFeatureName] = featureValue
 
         return featureVector
diff --git a/radiomics/imageoperations.py b/radiomics/imageoperations.py
@@ -58,8 +58,7 @@ def getMask(mask, **kwargs):
         raise ValueError("No labels found in this mask (i.e. nothing is segmented)!")
     if label not in labels:
         raise ValueError(
-            "Label (%g) not present in mask. Choose from %s"
-            % (label, labels[labels != 0])
+            f"Label ({label:g}) not present in mask. Choose from {labels[labels != 0]}"
         )
 
     return mask
@@ -254,7 +253,7 @@ def checkMask(imageNode, maskNode, **kwargs):
         # If lsif fails, and mask is corrected, it includes a check whether the label is present. Therefore, perform
         # this test here only if lsif does not fail on the first attempt.
         if label not in lsif.GetLabels():
-            raise ValueError("Label (%g) not present in mask" % label)
+            raise ValueError(f"Label ({label:g}) not present in mask")
     except RuntimeError as e:
         # If correctMask = True, try to resample the mask to the image geometry, otherwise return None ("fail")
         if not kwargs.get("correctMask", False):
@@ -704,7 +703,7 @@ def resegmentMask(imageNode, maskNode, **kwargs):
         raise ValueError("resegmentRange is None.")
     if len(resegmentRange) == 0 or len(resegmentRange) > 2:
         raise ValueError(
-            "Length %i is not allowed for resegmentRange" % len(resegmentRange)
+            f"Length {len(resegmentRange)} is not allowed for resegmentRange"
         )
 
     logger.debug("Resegmenting mask (range %s, mode %s)", resegmentRange, resegmentMode)
@@ -727,7 +726,7 @@ def resegmentMask(imageNode, maskNode, **kwargs):
         logger.debug("Resegmenting in sigma mode, mean %g, std %g", mean_gl, sd_gl)
         thresholds = [mean_gl + sd_gl * th for th in sorted(resegmentRange)]
     else:
-        raise ValueError("Resegment mode %s not recognized." % resegmentMode)
+        raise ValueError(f"Resegment mode {resegmentMode} not recognized.")
 
     # Apply lower threshold
     logger.debug("Applying lower threshold (%g)", thresholds[0])
@@ -843,7 +842,7 @@ def getLoGImage(inputImage, inputMask, **kwargs):
                 lrgif = sitk.LaplacianRecursiveGaussianImageFilter()
                 lrgif.SetNormalizeAcrossScale(True)
                 lrgif.SetSigma(sigma)
-                inputImageName = "log-sigma-%s-mm-3D" % (str(sigma).replace(".", "-"))
+                inputImageName = f"log-sigma-{str(sigma).replace('.', '-')}-mm-3D"
                 logger.debug("Yielding %s image", inputImageName)
                 yield lrgif.Execute(inputImage), inputImageName, kwargs
             else:
@@ -902,16 +901,16 @@ def getWaveletImage(inputImage, inputMask, **kwargs):
             logger.info("Computing Wavelet %s", decompositionName)
 
             if idx == 1:
-                inputImageName = "wavelet-%s" % (decompositionName)
+                inputImageName = f"wavelet-{decompositionName}"
             else:
-                inputImageName = "wavelet{}-{}".format(idx, decompositionName)
+                inputImageName = f"wavelet{idx}-{decompositionName}"
             logger.debug("Yielding %s image", inputImageName)
             yield decompositionImage, inputImageName, kwargs
 
     if len(ret) == 1:
-        inputImageName = "wavelet-%s" % ("L" * len(axes))
+        inputImageName = f"wavelet-{'L' * len(axes)}"
     else:
-        inputImageName = "wavelet{}-{}".format(len(ret), ("L" * len(axes)))
+        inputImageName = f"wavelet{len(ret)}-{'L' * len(axes)}"
     logger.debug("Yielding approximation (%s) image", inputImageName)
     yield approx, inputImageName, kwargs
 
diff --git a/radiomics/schemas/schemaFuncs.py b/radiomics/schemas/schemaFuncs.py
@@ -11,9 +11,7 @@ def checkWavelet(value, rule_obj, path):
         raise TypeError("Wavelet not expected type (str)")
     wavelist = pywt.wavelist()
     if value not in wavelist:
-        raise ValueError(
-            'Wavelet "{}" not available in pyWavelets {}'.format(value, wavelist)
-        )
+        raise ValueError(f'Wavelet "{value}" not available in pyWavelets {wavelist}')
     return True
 
 
@@ -35,9 +33,7 @@ def checkInterpolator(value, rule_obj, path):
         }
         if value not in enum:
             raise ValueError(
-                'Interpolator value "{}" not valid, possible values: {}'.format(
-                    value, enum
-                )
+                f'Interpolator value "{value}" not valid, possible values: {enum}'
             )
     elif isinstance(value, int):
         if value < 1 or value > 10:
@@ -56,8 +52,7 @@ def checkWeighting(value, rule_obj, path):
         enum = ["euclidean", "manhattan", "infinity", "no_weighting"]
         if value not in enum:
             raise ValueError(
-                'WeightingNorm value "%s" not valid, possible values: %s'
-                % (value, enum)
+                f'WeightingNorm value "{value}" not valid, possible values: {enum}'
             )
     else:
         raise TypeError("WeightingNorm not expected type (str or None)")
@@ -77,7 +72,7 @@ def checkFeatureClass(value, rule_obj, path):
         if features is not None:
             if not isinstance(features, list):
                 raise TypeError(
-                    "Value of feature class %s not expected type (list)" % (className)
+                    f"Value of feature class {className} not expected type (list)"
                 )
             unrecognizedFeatures = set(features) - set(
                 featureClasses[className].getFeatureNames()
diff --git a/radiomics/scripts/__init__.py b/radiomics/scripts/__init__.py
@@ -537,7 +537,7 @@ def parse_value(value, value_type):
             elif value_type == "bool":
                 return value == "1" or value.lower() == "true"
             else:
-                raise ValueError('Cannot understand value_type "%s"' % value_type)
+                raise ValueError(f'Cannot understand value_type "{value_type}"')
 
         for setting in self.args.setting:  # setting = "setting_key:setting_value"
             if ":" not in setting:
@@ -695,5 +695,5 @@ def parse_args():
         logging.getLogger().error(
             "Error executing PyRadiomics command line!", exc_info=True
         )
-        print("Error executing PyRadiomics command line!\n%s" % e)
+        print(f"Error executing PyRadiomics command line!\n{e}")
         return 4
diff --git a/radiomics/scripts/segment.py b/radiomics/scripts/segment.py
@@ -21,7 +21,7 @@ def extractSegment(case_idx, case, extractor, **kwargs):
     if out_dir is None:
         return _extractFeatures(case_idx, case, extractor)
 
-    filename = os.path.join(out_dir, "features_%s.csv" % case_idx)
+    filename = os.path.join(out_dir, f"features_{case_idx}.csv")
     if os.path.isfile(filename):
         # Output already generated, load result (prevents re-extraction in case of interrupted process)
         with open(filename) as outputFile:
@@ -93,7 +93,7 @@ def _extractFeatures(case_idx, case, extractor):
 def extractSegment_parallel(args, logging_config=None, **kwargs):
     try:
         # set thread name to patient name
-        threading.current_thread().name = "case %s" % args[0]  # args[0] = case_idx
+        threading.current_thread().name = f"case {args[0]}"  # args[0] = case_idx
 
         if logging_config is not None:
             _configureParallelExtraction(logging_config)
diff --git a/radiomics/scripts/voxel.py b/radiomics/scripts/voxel.py
@@ -25,7 +25,7 @@ def extractVoxel(case_idx, case, extractor, **kwargs):
         if out_dir is None:
             out_dir = "."
         elif not os.path.isdir(out_dir):
-            caseLogger.debug("Creating output directory at %s" % out_dir)
+            caseLogger.debug(f"Creating output directory at {out_dir}")
             os.makedirs(out_dir)
 
         caseLogger.info("Processing case %s", case_idx)
@@ -76,7 +76,7 @@ def extractVoxel(case_idx, case, extractor, **kwargs):
 def extractVoxel_parallel(args, logging_config=None, **kwargs):
     try:
         # set thread name to patient name
-        threading.current_thread().name = "case %s" % args[0]  # args[0] = case_idx
+        threading.current_thread().name = f"case {args[0]}"  # args[0] = case_idx
 
         if logging_config is not None:
             _configureParallelExtraction(logging_config)
diff --git a/tests/add_baseline.py b/tests/add_baseline.py
diff --git a/tests/testUtils.py b/tests/testUtils.py
diff --git a/tests/test_docstrings.py b/tests/test_docstrings.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
`@@ -26,7 +26,7 @@ def main(paramsFile):`
`26`	`26`	`% (params["featureClass"], params["imageType"], params["setting"])`
`27`	`27`	`)`
`28`	`28`	`except Exception as e:`
`29`		`- print("Parameter validation failed!\n%s" % e.message)`
	`29`	`+ print(f"Parameter validation failed!\n{e.message}")`
`30`	`30`
`31`	`31`
`32`	`32`	`if __name__ == "__main__" and len(sys.argv) > 1:`