Merge pull request #44 from pchoisel/improve_usage_instructions

DOC: Improve usage instrucion

Author: pchoisel

.gitignore

@@ -5,5 +5,4 @@ __pycache__
 build
 *.egg-info
 .python-version
-# Ignore Pipfile.lock, since different versions of python and OS produce different hashes
-Pipfile.lock
+dist

README.md

@@ -3,7 +3,8 @@
 Python package to anonymize DICOM files.
 The anonymization answer to the standard . More information about dicom fields for anonymization can be found [here](https://dicom.nema.org/medical/dicom/current/output/html/part15.html#table_E.1-1).
 
-The default behaviour of this package is to anonymize DICOM fields referenced in [dicomfields](dicomanonymizer/dicomfields.py).
+The default behaviour of this package is to anonymize DICOM fields referenced in the 2023e DICOM standard. These fields are referenced in [dicomfields](dicomanonymizer/dicom_anonymization_databases/dicomfields_2023.py).  
+Another standard can be selected, see *Change the DICOM anonymization standard*. 
 
 Dicom fields are separated into different groups. Each groups will be anonymized in a different way.
 
@@ -142,6 +143,16 @@ Example 3: Change the tag value with an arbitrary value
 python anonymizer.py InputFilePath OutputFilePath -t '(0x0010, 0x0010)' 'replace_with_value' 'new_value'
 ```
 
+### DICOMDIR
+
+> DICOMDIR anonymization is not specified. It is therefore discouraged and it is recommended to regenerate new DICOMDIR files after anonymizing the original DICOM files.
+
+DICOMDIR files can have a `(0x0004, 0x1220)  Directory Record Sequence` tag that can contain patient information.  
+However, this tag is not part of the standard tag to anonymize set. If you still want dicom-anonymizer to anonymize it, you have to instruct it explicitly:
+
+```python
+python anonymizer.py InputFilePath OutputFilePath -t '(0x0004, 0x1220)' replace
+```
 
 ## Custom rules with dictionary file
 
@@ -194,6 +205,8 @@ def main():
     )
     args = parser.parse_args()
 
+    deletePrivateTags = False
+
     input_dicom_path = args.input
     output_dicom_path = args.output
 
@@ -305,3 +318,17 @@ You can also add `extra_anonymization_rules` as above:
 ** VR: Value Representation
 
 Work originally done by Edern Haumont
+
+# Change the DICOM anonymization standard
+
+You can customize the DICOM standard that will be used to anonymize the dataset by giving an argument `base_rules_gen` to the function `anonymize_dicom_file` or `anonymize_dataset`.  
+The value should be a function returning a dict of anonymization rules. Use the function `initialize_actions` to create such dict from a anonymization database from the folder `dicomanonymizer/dicom_anonymization_databases`.
+
+Example:
+```python
+from dicomanonymizer.simpledicomanonymizer import anonymize_dataset, initialize_actions
+
+anonymize_dataset(
+    dataset, base_rules_gen=lambda: initialize_actions("dicomfields_2024b")
+)
+```

dicomanonymizer/dicom_anonymization_databases/dicomfields_2023.py

@@ -1,6 +1,6 @@
 # Tags anonymized in DICOM standard
 # Documentation for groups meaning can be found in default associated actions.
-# http://dicom.nema.org/dicom/2023/output/chtml/part15/chapter_E.html#table_E.1-1
+# https://dicom.nema.org/medical/dicom/2023e/output/chtml/part15/chapter_E.html#table_E.1-1
 
 # Replaced tags
 D_TAGS = [

dicomanonymizer/dicom_anonymization_databases/dicomfields_2024b.py

@@ -1,6 +1,6 @@
 # Tags anonymized in DICOM standard
 # Documentation for groups meaning can be found in default associated actions.
-# https://dicom.nema.org/medical/dicom/current/output/chtml/part15/chapter_e.html
+# https://dicom.nema.org/medical/dicom/2024b/output/chtml/part15/chapter_E.html#table_E.1-1
 
 # Replaced tags
 D_TAGS = [