Support for python 3.12, pyproject.toml, minor naming cleanups

README.md

@@ -141,9 +141,10 @@ If you want to use the **regexp** action in a dictionary:
 
 Here is a small example which keeps all metadata but updates the series description
 by adding a suffix passed as a parameter.
+
 ```python
 import argparse
-from dicomanonymizer import *
+from dicomanonymizer import ALL_TAGS, anonymize, keep
 
 def main():
     parser = argparse.ArgumentParser(add_help=True)
@@ -155,84 +156,58 @@ def main():
     input_dicom_path = args.input
     output_dicom_path = args.output
 
-    extraAnonymizationRules = {}
+    extra_anonymization_rules = {}
 
-    def setupSeriesDescription(dataset, tag):
+    def setup_series_description(dataset, tag):
         element = dataset.get(tag)
         if element is not None:
-            element.value = element.value + '-' + args.suffix
+            element.value = f'{element.value}-{args.suffix}'
 
     # ALL_TAGS variable is defined on file dicomfields.py
     # the 'keep' method is already defined into the dicom-anonymizer
     # It will overrides the default behaviour
-    for i in allTags:
-        extraAnonymizationRules[i] = keep
+    for i in ALL_TAGS:
+        extra_anonymization_rules[i] = keep
 
     if args.suffix:
-        extraAnonymizationRules[(0x0008, 0x103E)] = setupSeriesDescription
+        extra_anonymization_rules[(0x0008, 0x103E)] = setup_series_description
 
     # Launch the anonymization
-    anonymize(input_dicom_path, output_dicom_path, extraAnonymizationRules)
+    anonymize(input_dicom_path, output_dicom_path, extra_anonymization_rules, delete_private_tags=False)
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     main()
 ```
 
+See the full application in the `examples` folder.
+
 In your own file, you'll have to define:
 - Your custom functions. Be careful, your functions always have in inputs a dataset and a tag
 - A dictionary which map your functions to a tag
 
-## Anonymize dicom tags without dicom file
+## Anonymize dicom tags for a dataset
 
-If for some reason, you need to anonymize dicom fields without initial dicom file (extracted from a database for example). Here is how you can do it:
+You can also anonymize dicom fields in-place for pydicom's DataSet using `anonymize_dataset`. See this example:
 ```python
-from dicomanonymizer import *
+from dicomanonymizer import anonymize_dataset
+from pydicom.data import get_testdata_file
+from pydicom import dcmread
 
 def main():
-
-  # Create a list of tags object that should contains id, type and value
-  fields = [
-    { # Replaced by Anonymized
-      'id': (0x0040, 0xA123),
-      'type': 'LO',
-      'value': 'Annie de la Fontaine',
-    },
-    { # Replaced with empty value
-      'id': (0x0008, 0x0050),
-      'type': 'TM',
-      'value': 'bar',
-    },
-    { # Deleted
-      'id': (0x0018, 0x4000),
-      'type': 'VR',
-      'value': 'foo',
-    }
-  ]
-
-  # Create a readable dataset for pydicom
-  data = pydicom.Dataset()
-
-  # Add each field into the dataset
-  for field in fields:
-    data.add_new(field['id'], field['type'], field['value'])
-
-  anonymize_dataset(data)
+    data_ds = dcmread(get_testdata_file("CT_small.dcm"))
+    anonymize_dataset(data_ds, delete_private_tags=True) # Anonymization is done in-place
 
 if __name__ == "__main__":
     main()
 ```
-For more information about the pydicom's Dataset, please refer [here](https://github.com/pydicom/pydicom/blob/995ac6493188313f6a2e6355477baba9f543447b/pydicom/dataset.py).
-You can also add a dictionary as previously :
-```python
-    dictionary = {}
 
-    def newMethod(dataset, tag):
-        element = dataset.get(tag)
-        if element is not None:
-            element.value = element.value + '- generated with new method'
+See the full application in the `examples` folder.
+
+For more information about the pydicom's Dataset, please refer [here](https://pydicom.github.io/pydicom/stable/reference/generated/pydicom.dataset.Dataset.html).
 
-    dictionary[(0x0008, 0x103E)] = newMethod
-    anonymize_dataset(data, dictionary)
+You can also add `extra_anonymization_rules` as above:
+```python
+    anonymize_dataset(data_ds, extra_anonymization_rules, delete_private_tags=True)
 ```
 
 # Actions list

dicomanonymizer/anonymizer.py

@@ -1,7 +1,7 @@
 import argparse
 import ast
+import importlib.metadata
 import json
-import pkg_resources
 import os
 import sys
 import tqdm
@@ -21,7 +21,7 @@ def isDICOMType(filePath):
         return False
 
 
-def anonymize(input_path: str, output_path: str, anonymization_actions: dict, deletePrivateTags: bool) -> None:
+def anonymize(input_path: str, output_path: str, anonymization_actions: dict, delete_private_tags: bool) -> None:
     """
     Read data from input path (folder or file) and launch the anonymization.
 
@@ -62,7 +62,7 @@ def anonymize(input_path: str, output_path: str, anonymization_actions: dict, de
 
     progress_bar = tqdm.tqdm(total=len(input_files_list))
     for cpt in range(len(input_files_list)):
-        anonymize_dicom_file(input_files_list[cpt], output_files_list[cpt], anonymization_actions, deletePrivateTags)
+        anonymize_dicom_file(input_files_list[cpt], output_files_list[cpt], anonymization_actions, delete_private_tags)
         progress_bar.update(1)
 
     progress_bar.close()
@@ -98,7 +98,7 @@ def generate_actions_dictionary(map_action_tag, defined_action_map = {}) -> dict
 
 
 def main(defined_action_map = {}):
-    version_info = pkg_resources.require("dicom_anonymizer")[0].version
+    version_info = importlib.metadata.version("dicom_anonymizer")
     parser = argparse.ArgumentParser(add_help=True)
     parser.add_argument('input', help='Path to the input dicom file or input directory which contains dicom files')
     parser.add_argument('output', help='Path to the output dicom file or output directory which will contains dicom files')

examples/.gitignore

@@ -0,0 +1,2 @@
+# Ignore Pipfile.lock to allow support across multiple Python and operating system versions.
+Pipfile.lock 

examples/Pipfile

@@ -0,0 +1,4 @@
+[packages]
+# dicom-anonymizer = "*" # For 'released' version 
+dicom-anonymizer = {file = ".."} # For local version
+pydicom = "*"

examples/README.md

@@ -0,0 +1,8 @@
+#DicomAnonymizer Examples
+
+This folder contains the following examples:
+- `anonymize_dataset.py`: Anonymize dicom tags for a dataset
+- `anonymize_extra_rules.py`: Anonymize dicom tags for a file with extra rules
+
+The supporting files are:
+- `Pipfile`: The [pipenv](https://packaging.python.org/en/latest/tutorials/managing-dependencies/) file.

examples/anonymize_dataset.py

@@ -0,0 +1,14 @@
+from dicomanonymizer import anonymize_dataset
+from pydicom.data import get_testdata_file
+from pydicom import dcmread
+
+def main():
+    original_ds = dcmread(get_testdata_file("CT_small.dcm"))
+    data_ds = original_ds.copy()
+    anonymize_dataset(data_ds, delete_private_tags=True) # Anonymization is done in-place
+    print("Examples of original -> anonymized values:")
+    for tt in ["PatientName", "PatientID", "StudyDate"]:
+        print(f"  {tt}: '{original_ds[tt].value}' -> '{data_ds[tt].value}'")
+
+if __name__ == "__main__":
+    main()

examples/anonymize_extra_rules.py

@@ -0,0 +1,34 @@
+import argparse
+from dicomanonymizer import ALL_TAGS, anonymize, keep
+
+def main():
+    parser = argparse.ArgumentParser(add_help=True)
+    parser.add_argument('input', help='Path to the input dicom file or input directory which contains dicom files')
+    parser.add_argument('output', help='Path to the output dicom file or output directory which will contains dicom files')
+    parser.add_argument('--suffix', action='store', help='Suffix that will be added at the end of series description')
+    args = parser.parse_args()
+
+    input_dicom_path = args.input
+    output_dicom_path = args.output
+
+    extra_anonymization_rules = {}
+
+    def setup_series_description(dataset, tag):
+        element = dataset.get(tag)
+        if element is not None:
+            element.value = f'{element.value}-{args.suffix}'
+
+    # ALL_TAGS variable is defined on file dicomfields.py
+    # the 'keep' method is already defined into the dicom-anonymizer
+    # It will overrides the default behaviour
+    for i in ALL_TAGS:
+        extra_anonymization_rules[i] = keep
+
+    if args.suffix:
+        extra_anonymization_rules[(0x0008, 0x103E)] = setup_series_description
+
+    # Launch the anonymization
+    anonymize(input_dicom_path, output_dicom_path, extra_anonymization_rules, delete_private_tags=False)
+
+if __name__ == '__main__':
+    main()

pyproject.toml

@@ -0,0 +1,40 @@
+[project]
+name = "dicom_anonymizer"
+version = "1.0.11"
+authors = [
+  { name="Laurenn Lam", email="[email protected]" },
+]
+description = "Program to anonymize dicom files with default and custom rules"
+readme = "README.md"
+requires-python = ">=3.10"
+classifiers = [
+        "Development Status :: 3 - Alpha",
+        "Intended Audience :: Science/Research",
+        "Topic :: Software Development :: Build Tools",
+        "License :: OSI Approved :: BSD License",
+        "Natural Language :: English",
+        "Programming Language :: Python"
+]
+keywords = ["dicom", "anonymizer" , "medical"]
+
+dependencies = [
+  "pydicom",
+  "tqdm",
+]
+
+[project.optional-dependencies]
+dev = [
+  "pytest",
+  "setuptools", # Needed to load pydicom's test files
+]
+
+[project.scripts]
+dicom-anonymizer = "dicomanonymizer.anonymizer:main"
+
+[project.urls]
+"Homepage" = "https://github.com/KitwareMedical/dicom-anonymizer"
+"Bug Tracker" = "https://github.com/KitwareMedical/dicom-anonymizer/issues"
+
+[tool.setuptools.packages]
+find = {}  # Scanning implicit namespaces is active by default
+