Merge pull request #100 from KitwareMedical/release_2_0

Release version 2.0.0 with Pydicom>3 and Python>=3.10

Author: pchoisel

.github/workflows/ci.yml

@@ -10,11 +10,7 @@ jobs:
 
     strategy:
       matrix:
-        # Tracked via issue #77
-        # 3.6: Not available on ubuntu-22.04
-        # 3.7: Results in failures in `test_cli.py`
-        # 3.12: pkg_resources not supported
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
 
     steps:
       - uses: actions/checkout@v4

dicomanonymizer/dicom_anonymization_databases/dicomfields_2026c.py

@@ -52,12 +52,12 @@ The sources files can be packaged by using:
 `python ./setup.py bdist_wheel`
 
 This command will generate a wheel package in `dist` folder which can be then installed as a python package using
-`pip install ./dist/dicom_anonymizer-1.0.13-1-py2.py3-none-any.whl`
+`pip install ./dist/dicom_anonymizer-2.0.0-py2.py3-none-any.whl`
 
 On Windows, if you see a warning message
-`'./dist/dicom_anonymizer-1.0.13-1-py2.py3-none-any.whl' looks like a filename, but the file does not exist`,
+`'./dist/dicom_anonymizer-2.0.0-py2.py3-none-any.whl' looks like a filename, but the file does not exist`,
 this could be due to pip not being able to handle relative path (See issue https://github.com/pypa/pip/issues/10808). As a work-around, change directory to `dist` and then install it using
-`pip install dicom_anonymizer-1.0.13-1-py2.py3-none-any.whl`
+`pip install dicom_anonymizer-2.0.0-py2.py3-none-any.whl`
 
 
 Installing this package will also install an executable named `dicom-anonymizer`. In order to use it, please refer to the next section.

doc/Setup_build_test.md

@@ -3,6 +3,7 @@
 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
+- `anonymize_with_different_standard.py`: Anonymize dicom file with a different NEMA standard
 
 The supporting files are:
 - `Pipfile`: The [pipenv](https://packaging.python.org/en/latest/tutorials/managing-dependencies/) file.

examples/README.md

@@ -1,11 +1,14 @@
-from dicomanonymizer import anonymize_dataset
-from pydicom.data import get_testdata_file
+import copy
+
 from pydicom import dcmread
+from pydicom.data import get_testdata_file
+
+from dicomanonymizer import anonymize_dataset
 
 
 def main():
     original_ds = dcmread(get_testdata_file("CT_small.dcm"))
-    data_ds = original_ds.copy()
+    data_ds = copy.deepcopy(original_ds)
     anonymize_dataset(
         data_ds, delete_private_tags=True
     )  # Anonymization is done in-place

examples/anonymize_dataset.py

@@ -1,7 +1,7 @@
 import argparse
 
-from dicomanonymizer.dicom_anonymization_databases.dicomfields_2023 import ALL_TAGS
 from dicomanonymizer import anonymize, keep
+from dicomanonymizer.dicom_anonymization_databases.dicomfields_2023 import ALL_TAGS
 
 
 def main():

examples/anonymize_extra_rules.py

@@ -0,0 +1,26 @@
+import copy
+
+from pydicom import dcmread
+from pydicom.data import get_testdata_file
+
+from dicomanonymizer import anonymize_dataset
+from dicomanonymizer.simpledicomanonymizer import initialize_actions
+
+
+def initialize_actions_2026c():
+    return initialize_actions("dicomfields_2026c")
+
+
+def main():
+    original_ds = dcmread(get_testdata_file("CT_small.dcm"))
+    data_ds = copy.deepcopy(original_ds)
+    anonymize_dataset(
+        data_ds, delete_private_tags=True, base_rules_gen=initialize_actions_2026c
+    )  # 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_with_different_standard.py

@@ -115,7 +115,7 @@ def create_DICOM_fields(profiles):
 
 def main(
     url="https://dicom.nema.org/medical/dicom/current/output/chtml/part15/chapter_e.html",
-    output_path="dicomanonymizer/dicomfields_2024b.py",
+    output_path="dicomanonymizer/dicom_anonymization_databases/dicomfields_2024b.py",
 ):
     # As of 2024.05.14, the current version of DICOM spec is 2024b.
     profiles = scrap_profiles(url)

scripts/scrap_DICOM_fields.py

@@ -12,7 +12,7 @@
 
 setup(
     name="dicom_anonymizer",  # Required
-    version="1.0.13-1",  # Required
+    version="2.0.0",  # Required
     author="Laurenn Lam",
     author_email="laurenn.lam@kitware.com",
     description="Program to anonymize dicom files with default and custom rules",
@@ -31,7 +31,7 @@
         "Programming Language :: Python",
     ],
     keywords=["dicom", "anonymizer", "medical"],
-    python_requires=">=3.6",
+    python_requires=">=3.10",
     packages=find_packages(),  # Required
     # Define an executable calls dicom-anonymizer from a specific file
     entry_points={
@@ -44,7 +44,5 @@
     # For an analysis of "install_requires" vs pip's requirements files see:
     # https://packaging.python.org/en/latest/guides/distributing-packages-using-setuptools/
     install_requires=["pydicom", "tqdm"],  # Optional
-    extras_require={
-        "dev": ["pytest", "bs4", "fire", "requests", "pre-commit", "ruff===0.12.10"]
-    },
+    extras_require={"dev": ["pytest", "bs4", "fire", "requests", "pre-commit", "ruff"]},
 )