changed all mutable defaults to None

imgtools/io/loaders.py

@@ -30,8 +30,7 @@ def read_header(path):
 
 def read_dicom_series(path: str,
                       series_id: Optional[str] = None,
-                      recursive: bool = False,
-                      modality: str = "CT") -> Scan:
+                      recursive: bool = False) -> Scan:
     """Read DICOM series as SimpleITK Image.
 
     Parameters
@@ -70,72 +69,6 @@ def read_dicom_series(path: str,
     reader.LoadPrivateTagsOn()
 
     metadata = {}
-    # dicom_data = dcmread(dicom_names[0])
-    # if modality == 'CT':
-    #     if hasattr(dicom_data, 'KVP'):
-    #         metadata["KVP"] = str(dicom_data.KVP)
-    #     if hasattr(dicom_data, 'XRayTubeCurrent'):
-    #         metadata["XRayTubeCurrent"] = str(dicom_data.XRayTubeCurrent)
-    #     if hasattr(dicom_data, 'ScanOptions'):
-    #         metadata["ScanOptions"] = str(dicom_data.ScanOptions)
-    #     if hasattr(dicom_data, 'ReconstructionAlgorithm'):
-    #         metadata["ReconstructionAlgorithm"] = str(dicom_data.ReconstructionAlgorithm)
-    #     if hasattr(dicom_data, 'ContrastFlowRate'):
-    #         metadata["ContrastFlowRate"] = str(dicom_data.ContrastFlowRate)
-    #     if hasattr(dicom_data, 'ContrastFlowDuration'):
-    #         metadata["ContrastFlowDuration"] = str(dicom_data.ContrastFlowDuration)
-    #     # is this contrast type?
-    #     if hasattr(dicom_data, 'ContrastBolusAgent'):
-    #         metadata["ContrastType"] = str(dicom_data.ContrastBolusAgent)
-    # else: # MR
-    #     if hasattr(dicom_data, 'AcquisitionTime'):
-    #         metadata["AcquisitionTime"] = str(dicom_data.AcquisitionTime)
-    #     if hasattr(dicom_data, 'AcquisitionContrast'):
-    #         metadata["AcquisitionContrast"] = str(dicom_data.AcquisitionContrast)
-    #     if hasattr(dicom_data, 'AcquisitionType'):
-    #         metadata["AcquisitionType"] = str(dicom_data.AcquisitionType)
-    #     if hasattr(dicom_data, 'RepetitionTime'):
-    #         metadata["RepetitionTime"] = str(dicom_data.RepetitionTime)
-    #     if hasattr(dicom_data, 'EchoTime'):
-    #         metadata["EchoTime"] = str(dicom_data.EchoTime)
-    #     if hasattr(dicom_data, 'ImagingFrequency'):
-    #         metadata["ImagingFrequency"] = str(dicom_data.ImagingFrequency)
-    #     if hasattr(dicom_data, 'MagneticFieldStrength'):
-    #         metadata["MagneticFieldStrength"] = str(dicom_data.MagneticFieldStrength)
-
-    # # Number of Slices is avg. number slice?
-    # if hasattr(dicom_data, 'BodyPartExamined'):
-    #     metadata["BodyPartExamined"] = str(dicom_data.BodyPartExamined)
-    # if hasattr(dicom_data, 'DataCollectionDiameter'):
-    #     metadata["DataCollectionDiameter"] = str(dicom_data.DataCollectionDiameter)
-    # if hasattr(dicom_data, 'NumberofSlices'):
-    #     metadata["NumberofSlices"] = str(dicom_data.NumberofSlices)
-    # # Slice Thickness is avg. slice thickness?
-    # if hasattr(dicom_data, 'SliceThickness'):
-    #     metadata["SliceThickness"] = str(dicom_data.SliceThickness)
-    # if hasattr(dicom_data, 'ScanType'):
-    #     metadata["ScanType"] = str(dicom_data.ScanType)
-    # # Scan Progression Direction is Scan Direction?
-    # if hasattr(dicom_data, 'ScanProgressionDirection'):
-    #     metadata["ScanProgressionDirection"] = str(dicom_data.ScanProgressionDirection)
-    # if hasattr(dicom_data, 'PatientPosition'):
-    #     metadata["PatientPosition"] = str(dicom_data.PatientPosition)
-    # # is this contrast type?
-    # if hasattr(dicom_data, 'ContrastBolusAgent'):
-    #     metadata["ContrastType"] = str(dicom_data.ContrastBolusAgent)
-    # if hasattr(dicom_data, 'Manufacturer'):
-    #     metadata["Manufacturer"] = str(dicom_data.Manufacturer)
-    # # Scan Plane?
-    # if hasattr(dicom_data, 'ScanOptions'):
-    #     metadata["ScanOptions"] = str(dicom_data.ScanOptions)
-    # if hasattr(dicom_data, 'RescaleType'):
-    #     metadata["RescaleType"] = str(dicom_data.RescaleType)
-    # if hasattr(dicom_data, 'RescaleSlope'):
-    #     metadata["RescaleSlope"] = str(dicom_data.RescaleSlope)
-    # if hasattr(dicom_data, 'PixelSpacing') and hasattr(dicom_data, 'SliceThickness'):
-    #     pixel_size = copy.copy(dicom_data.PixelSpacing)
-    #     pixel_size.append(dicom_data.SliceThickness)
-    #     metadata["PixelSize"] = str(tuple(pixel_size))
 
     return Scan(reader.Execute(), metadata)
 
@@ -216,11 +149,18 @@ def get(self, subject_id, default=None):
 class ImageCSVLoader(BaseLoader):
     def __init__(self,
                  csv_path_or_dataframe,
-                 colnames=[],
-                 seriesnames=[],
+                 colnames=None,
+                 seriesnames=None,
                  id_column=None,
                  expand_paths=False,
-                 readers=[read_image]):
+                 readers=None):
+
+        if colnames is None:
+            colnames = []
+        if seriesnames is None:
+            seriesnames = []
+        if readers is None:
+            readers = [read_image] # no mutable defaults https://florimond.dev/en/posts/2018/08/python-mutable-defaults-are-the-source-of-all-evil/
 
         self.expand_paths = expand_paths
         self.readers = readers
@@ -270,8 +210,13 @@ def __init__(self,
                  root_directory,
                  get_subject_id_from="filename",
                  subdir_path=None,
-                 exclude_paths=[],
-                 reader=read_image):
+                 exclude_paths=None,
+                 reader=None):
+
+        if exclude_paths is None:
+            exclude_paths = []
+        if reader is None:
+            reader = read_image # no mutable defaults https://florimond.dev/en/posts/2018/08/python-mutable-defaults-are-the-source-of-all-evil/
 
         self.root_directory = root_directory
         self.get_subject_id_from = get_subject_id_from

imgtools/modules/dose.py

@@ -50,44 +50,6 @@ def from_dicom_rtdose(cls, path):
         img_dose = img_dose * factor
 
         metadata = {}
-        # metadata["DoseType"] = df.DoseType
-        #return cls(img_dose, df, metadata)
-        # if hasattr(df, 'BodyPartExamined'):
-        #     metadata["BodyPartExamined"] = str(df.BodyPartExamined)
-        # if hasattr(df, 'DataCollectionDiameter'):
-        #     metadata["DataCollectionDiameter"] = str(df.DataCollectionDiameter)
-        # # Number of Slices is avg. number slice?
-        # if hasattr(df, 'NumberofSlices'):
-        #     metadata["NumberofSlices"] = str(df.NumberofSlices)
-        # # Slice Thickness is avg. slice thickness?
-        # if hasattr(df, 'SliceThickness'):
-        #     metadata["SliceThickness"] = str(df.SliceThickness)
-        # if hasattr(df, 'ScanType'):
-        #     metadata["ScanType"] = str(df.ScanType)
-        # # Scan Progression Direction is Scan Direction?
-        # if hasattr(df, 'ScanProgressionDirection'):
-        #     metadata["ScanProgressionDirection"] = str(df.ScanProgressionDirection)
-        # if hasattr(df, 'PatientPosition'):
-        #     metadata["PatientPosition"] = str(df.PatientPosition)
-        # # is this contrast type?
-        # if hasattr(df, 'ContrastBolusAgent'):
-        #     metadata["ContrastType"] = str(df.ContrastBolusAgent)
-        # if hasattr(df, 'Manufacturer'):
-        #     metadata["Manufacturer"] = str(df.Manufacturer)
-        # # Which field of view?
-        # # if hasattr(df, 'FieldOfViewDescription'):
-        # #     metadata["FieldOfViewDescription"] = str(df.FieldOfViewDescription)
-        # # Scan Plane?
-        # if hasattr(df, 'ScanOptions'):
-        #     metadata["ScanOptions"] = str(df.ScanOptions)
-        # if hasattr(df, 'RescaleType'):
-        #     metadata["RescaleType"] = str(df.RescaleType)
-        # if hasattr(df, 'RescaleSlope'):
-        #     metadata["RescaleSlope"] = str(df.RescaleSlope)
-        # if hasattr(df, 'PixelSpacing') and hasattr(df, 'SliceThickness'):
-        #     pixel_size = copy.copy(df.PixelSpacing)
-        #     pixel_size.append(df.SliceThickness)
-        #     metadata["PixelSize"] = str(tuple(pixel_size))
 
         return cls(img_dose, df, metadata)
 

imgtools/modules/pet.py

@@ -64,51 +64,6 @@ def from_dicom_pet(cls, path,series_id=None,type="SUV"):
         img_pet = sitk.Abs(img_pet * factor)
 
         metadata = {}
-        # metadata["factor"] = df.factor
-
-        # if hasattr(pet, 'RescaleType'):
-        #     metadata["RescaleType"] = str(pet.RescaleType)
-        # if hasattr(pet, 'RescaleSlope'):
-        #     metadata["RescaleSlope"] = str(pet.RescaleSlope)
-        # if hasattr(pet, 'RadionuclideTotalDose'):
-        #     metadata["RadionuclideTotalDose"] = str(pet.RadionuclideTotalDose)
-        # if hasattr(pet, 'RadionuclideHalfLife'):
-        #     metadata["RadionuclideHalfLife"] = str(pet.RadionuclideHalfLife)
-
-        # if hasattr(pet, 'BodyPartExamined'):
-        #     metadata["BodyPartExamined"] = str(pet.BodyPartExamined)
-        # if hasattr(pet, 'DataCollectionDiameter'):
-        #     metadata["DataCollectionDiameter"] = str(pet.DataCollectionDiameter)
-        # # Number of Slices is avg. number slice?
-        # if hasattr(pet, 'NumberofSlices'):
-        #     metadata["NumberofSlices"] = str(pet.NumberofSlices)
-        # # Slice Thickness is avg. slice thickness?
-        # if hasattr(pet, 'SliceThickness'):
-        #     metadata["SliceThickness"] = str(pet.SliceThickness)
-        # if hasattr(pet, 'ScanType'):
-        #     metadata["ScanType"] = str(pet.ScanType)
-        # # Scan Progression Direction is Scan Direction?
-        # if hasattr(pet, 'ScanProgressionDirection'):
-        #     metadata["ScanProgressionDirection"] = str(pet.ScanProgressionDirection)
-        # if hasattr(pet, 'PatientPosition'):
-        #     metadata["PatientPosition"] = str(pet.PatientPosition)
-        # # is this contrast type?
-        # if hasattr(pet, 'ContrastBolusAgent'):
-        #     metadata["ContrastType"] = str(pet.ContrastBolusAgent)
-        # if hasattr(pet, 'Manufacturer'):
-        #     metadata["Manufacturer"] = str(pet.Manufacturer)
-        # # Scan Plane?
-        # if hasattr(pet, 'ScanOptions'):
-        #     metadata["ScanOptions"] = str(pet.ScanOptions)
-        # if hasattr(pet, 'RescaleType'):
-        #     metadata["RescaleType"] = str(pet.RescaleType)
-        # if hasattr(pet, 'RescaleSlope'):
-        #     metadata["RescaleSlope"] = str(pet.RescaleSlope)
-        # if hasattr(pet, 'PixelSpacing') and hasattr(pet, 'SliceThickness'):
-        #     pixel_size = copy.copy(pet.PixelSpacing)
-        #     pixel_size.append(pet.SliceThickness)
-        #     metadata["PixelSize"] = str(tuple(pixel_size))
-
         return cls(img_pet, df, factor, calc, metadata)
         # return cls(img_pet, df, factor, calc)
 

imgtools/ops/ops.py

@@ -142,10 +142,14 @@ class ImageCSVInput(BaseInput):
     """
     def __init__(self,
                  csv_path_or_dataframe: str,
-                 colnames: List[str] = [],
+                 colnames: List[str] = None,
                  id_column: Optional[str] = None,
                  expand_paths: bool = True,
-                 readers: List[LoaderFunction] = [read_image]):
+                 readers: List[LoaderFunction] = None): # no mutable defaults: https://florimond.dev/en/posts/2018/08/python-mutable-defaults-are-the-source-of-all-evil/
+        if colnames is None:
+            colnames = []
+        if readers is None:
+            readers = [read_image]
         self.csv_path_or_dataframe = csv_path_or_dataframe
         self.colnames = colnames
         self.id_column = id_column
@@ -195,8 +199,12 @@ def __init__(self,
                  root_directory: str,
                  get_subject_id_from: str = "filename",
                  subdir_path: Optional[str] = None,
-                 exclude_paths: Optional[List[str]] =[],
-                 reader: LoaderFunction =read_image):
+                 exclude_paths: Optional[List[str]] = None, # no mutable defaults https://florimond.dev/en/posts/2018/08/python-mutable-defaults-are-the-source-of-all-evil/
+                 reader: LoaderFunction = None):
+        if exclude_paths is None:
+            exclude_paths = []
+        if reader is None:
+            reader = read_image
         self.root_directory = root_directory
         self.get_subject_id_from = get_subject_id_from
         self.subdir_path = subdir_path