Merge branch 'release/0.4.0'

* release/0.4.0: (55 commits)
  Update Makefile and Pipfile to streamline dependencies and improve documentation
  Bump version: 0.4.0-dev -> 0.4.0
  Bump version: 0.3.13-dev -> 0.4.0-dev
  Update release checklist to correct git flow command for starting a release
  Fix InstanceNumber check to handle empty string and ensure proper type conversion for scheduled protocol index
  streamline DICOM attribute setting and improve type keyword handling
  Add method to retrieve scheduled protocol code in OrthodonticPhotograph class and enhance unit tests
  Refactor logging configuration and clean up whitespace in test_photography.py
  Add properties for series number and instance number in DicomBase
  Update lock file.
  Fix test cases to use 'test.dcm' instead of 'd90.dcm'
  Moved fhir2dicom4ortho to its own repository.
  Remove unused JPEG UID imports in model.py for cleaner code
  Fix condition in set_image to require either input_image_filename or input_image_bytes
  Add assertion for successful response status in e2e tests
  Fix username parameter to pacs_wado_username
  Rename process_bundle to build_and_send_dicom_image for clarity in DICOM image processing
  Refactor task processing to use build_and_send_dicom_image and add utility for extracting Scheduled Protocol from Basic resource
  Remove extension from ImagingStudy and add subject reference to Basic.
  Enhance DICOM handling and task status management in FHIR API integration
  ...

.bumpversion.cfg

@@ -2,7 +2,7 @@
 commit = True
 tag = True
 tag_name = v{new_version}
-current_version = 0.3.12
+current_version = 0.4.0
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+))?
 message = Bump version: {current_version} -> {new_version}
 serialize = 
@@ -11,7 +11,7 @@ serialize =
 
 [bumpversion:file:dicom4ortho/config.py]
 
-[bumpversion:file:setup.py]
+[bumpversion:file:pyproject.toml]
 
 [bumpversion:file:README.md]
 

.gitignore

@@ -8,3 +8,4 @@ build
 modules/dicom3tools
 docs/.buildinfo
 .test*
+*.sqlite

.python-version

@@ -0,0 +1 @@
+3.11

Makefile

@@ -28,7 +28,6 @@ default: clean build
 
 .PHONY: lint
 lint:
-	$(LINTER) setup.py
 	$(LINTER) $(MAIN)
 
 .PHONY: test
@@ -53,7 +52,7 @@ $(DIST):
 
 .PHONY: build
 build: lint test $(DIST) update_resources
-	python3 -m setup sdist
+	python3 -m build
 
 .PHONY: update_resources
 update_resources:

Pipfile

@@ -10,17 +10,24 @@ twine = "*"
 autopep8 = "*"
 bumpversion = "*"
 pytest = "*"
+build = "*"
+prettytable = "*"
 
 [packages]
 pydicom = "*"
 # There is a vulnerability flaw in <8.2.0 of Pillow.
 pillow = ">=9.2.0"
 pynetdicom = "*"
-dicom-photo = {path = ".", editable = true}
 # There is a vulnerability flaw in <1.26.5 of urllib3.
 urllib3 = ">=1.26.5"
 sphinx = "*"
 numpy = "*"
+fastapi = "*"
+"fhir.resources" = "*"
+pydantic = "*"
+uvicorn = "*"
+apscheduler = "*"
+
 
 [requires]
-python_version = "3"
+python_version = ">3.10"

README.md

@@ -12,7 +12,7 @@
     <img src="https://raw.githubusercontent.com/open-ortho/dicom4ortho/master/images/open-ortho.png" alt="Logo" width="80" height="80">
   </a>
 
-  <h3 align="center">dicom4ortho 0.3.12</h3>
+  <h3 align="center">dicom4ortho 0.4.0</h3>
 
   <p align="center">
     A Python library to create fully defined orthodontic photographs in DICOM.
@@ -137,6 +137,10 @@ then use dicom4ortho like this:
 Where `filename` should be a `.csv` file. Passing a single image file with
 metadata through arguments is planned for future implementations.
 
+generate a new UID for DICOM usage with this root:
+
+    $ d4o_generate
+
 ## Known Issues
 
 Please check the [Implementation Status](docs/IMPLEMENTATION_STATUS.md)

dicom4ortho/__init__.py

@@ -6,6 +6,3 @@
 import dicom4ortho.config
 
 __version__ = dicom4ortho.config.VERSION
-__url__ = 'https://github.com/open-ortho/dicom4ortho'
-__author__ = 'Toni Magni'
-__email__ = '[email protected]'

dicom4ortho/__main__.py

@@ -14,6 +14,7 @@
 
 import dicom4ortho.config as config
 import dicom4ortho.controller as controller
+from dicom4ortho.utils import generate_dicom_uid
 
 LIST_IMAGE_TYPES = 'list-image-types'
 
@@ -125,22 +126,6 @@ def main(argv=None):
             default='EV01',
             metavar='<image_type>',
         )
-        parser.add_argument(
-            "--teeth",
-            dest="teeth",
-            nargs="*",
-            help="Add this tooth to image. Tooth should be clearly visible. \
-            Use ISO tooth numbering. Add as many as necessary, divided by a \
-            space, like: '--teeth 18 17 16'.",
-        )
-        parser.add_argument(
-            "--add-max-allowed-teeth",
-            dest="add_max_allowed_teeth",
-            action="store_true",
-            help="Adds the maximum allowed teeth for each image type. Assumes \
-            adult patient with all teeth present and clearly visible for the \
-            specified image type.",
-        )
         parser.add_argument(
             "--validate",
             dest="validate",
@@ -177,24 +162,17 @@ def main(argv=None):
         c = controller.OrthodonticController(
             url_codes=args.url_codes,
             url_views=args.url_views)
-        if args.add_max_allowed_teeth:
-            teeth = config.ADD_MAX_ALLOWED_TEETH
-        elif args.teeth:
-            teeth = args.teeth
-        else:
-            teeth = []
 
         if args.validate is True:
             c.validate_dicom_file(args.input_filename)
             return 0
         elif args.input_filename.lower().endswith('.csv'):
-            c.bulk_convert_from_csv(args.input_filename, teeth=teeth)
+            c.bulk_convert_from_csv(args.input_filename)
             return 0
         else:
             c.convert_image_to_dicom4orthograph_and_save({
                 'image_type': args.image_type,
                 'input_image_filename': args.input_filename,
-                'teeth': teeth,
                 'output_image_filename': args.output_filename})
             c.photo.print()
             return 0
@@ -204,5 +182,8 @@ def main(argv=None):
         return 120
 
 
+def generate_uid():
+    print(generate_dicom_uid())
+
 if __name__ == "__main__":
     sys.exit(main(sys.argv[1:]))

dicom4ortho/config.py

@@ -6,7 +6,7 @@
 from pathlib import Path
 import importlib.resources as importlib_resources
 
-VERSION = '0.3.12'
+VERSION = '0.4.0'
 PROJECT_NAME = 'dicom4ortho'
 __url__ = 'https://github.com/open-ortho/dicom4ortho'
 __author__ = 'Toni Magni'
@@ -54,8 +54,6 @@
 # The default IDs used for SeriesNumber StudyID and InstanceNumber
 IDS_NUMBERS = '000'
 
-ADD_MAX_ALLOWED_TEETH = 'ALL'
-
 # This is populated by controller.OrthodonticController._load_image_types()
 image_types = {}
 

dicom4ortho/controller.py

@@ -4,6 +4,7 @@
 import os
 import csv
 from pathlib import Path
+from pydicom.dataset import Dataset
 
 from dicom4ortho.config import DICOM3TOOLS_PATH
 from dicom4ortho.model import DicomBase
@@ -14,7 +15,6 @@
 import logging
 logger = logging.getLogger(__name__)
 
-
 class OrthodonticController(object):
     """ Controller
 
@@ -37,13 +37,12 @@ def __init__(self, **kwargs):
             url_codes=kwargs.get('url_codes'),
             url_views=kwargs.get('url_views'))
 
-    def bulk_convert_from_csv(self, csv_input, teeth=None):
+    def bulk_convert_from_csv(self, csv_input):
         with open(csv_input, mode='r') as csv_file:
             csv_reader = csv.DictReader(csv_file, delimiter=',')
             for row in csv_reader:
                 row['input_image_filename'] = (
                     Path(csv_input).parent / row['input_image_filename'])
-                row['teeth'] = teeth
                 self.convert_image_to_dicom4orthograph_and_save(metadata=row)
 
     def convert_image_to_dicom4orthograph(self, metadata) -> OrthodonticPhotograph:
@@ -67,9 +66,6 @@ def convert_image_to_dicom4orthograph(self, metadata) -> OrthodonticPhotograph:
                                             - "Posttreatment"
             days_after_event            : number of days from treatment_event_type
             burned_in_annotation        : 'YES' or 'NO'. Default = 'NO'.
-            teeth                       : array of teeth visible in the photograph.
-                                          Use ISO notation in string. Example:
-                                          teeth=['24','25','26','27','28','34','35','36','37','38']
             output_image_filename       : filename to write dicom image into.
                                           Default is the same name as the input file name with replaced
                                           extension.
@@ -81,17 +77,27 @@ def convert_image_to_dicom4orthograph(self, metadata) -> OrthodonticPhotograph:
 
         self.photo = OrthodonticPhotograph(**metadata)
 
-        # TODO: check if metadata['teeth'] contains teeth and add
-        # What teeth are shown in the images is something we cannot guess from
-        # what image type is taken, and shold be entered manually or
-        # automtaicaly by the implementing software. Therefore, i would like
-        # the controller to have an option to add teeth and provide this option
-        # to the end user which, in this case, is the CLI, and the CSV import
-        # file.
-        # if metadata['teeth']
-
         return self.photo
 
+    def convert_image_plus_mwl_to_dicom4orthograph(self, image_bytes, mwl:Dataset) -> OrthodonticPhotograph:
+        ''' Converts a PIL image into an OrthodonticPhotograph using a DICOM MWL for metadata.
+
+        The MWL is passed as a pydicom Dataset object, and should contain a single ScheduledProtocolCode.
+
+        Parameters:
+        image_bytes (bytes): Image bytes. Purposely set to raw bytes to avoid file I/O. Purposely avoiding PIL Image, because once in PIL Image, the image will be decoded and re-encoded even when saved as JPEG. This would result in loss of image quality.
+
+        mwl (Dataset): DICOM MWL object.
+
+        '''
+        metadata = {
+            'input_image_filename': None,
+            'input_image_bytes': image_bytes,
+            'dicom_mwl': mwl,
+        }
+        self.photo = OrthodonticPhotograph(**metadata)
+        pass
+
     def convert_image_to_dicom4orthograph_and_save(self, metadata):
         _photo = self.convert_image_to_dicom4orthograph(metadata=metadata)
         _photo.save()
@@ -141,14 +147,14 @@ def send(self, send_method, **kwargs):
         **kwargs: Additional keyword arguments depending on the send method:
 
             For send_method 'dimse':
-                pacs_ip (str): IP address of the PACS server.
-                pacs_port (int): Port of the PACS server.
-                pacs_aet (str): AE Title of the PACS server.
+                pacs_dimse_hostname (str): IP address of the PACS server.
+                pacs_dimse_port (int): Port of the PACS server.
+                pacs_dimse_aet (str): AE Title of the PACS server.
 
             For send_method 'wado':
-                dicomweb_url (str): URL of the DICOMweb server.
-                username (str, optional): Username for DICOMweb authentication.
-                password (str, optional): Password for DICOMweb authentication.
+                pacs_wado_url (str): URL of the DICOMweb server.
+                pacs_wado_username (str, optional): Username for DICOMweb authentication.
+                pacs_wado_password (str, optional): Password for DICOMweb authentication.
 
         Raises:
         ValueError: If an invalid send method is specified or required kwargs are missing.
@@ -157,40 +163,47 @@ def send(self, send_method, **kwargs):
         send(
             dicom_files=['path/to/output.dcm'],
             send_method='dimse',
-            pacs_ip='127.0.0.1',
-            pacs_port=104,
-            pacs_aet='PACS_AET'
+            pacs_dimse_hostname='127.0.0.1',
+            pacs_dimse_port=104,
+            pacs_dimse_aet='PACS_AET'
         )
 
         send(
             orthodontic_series=orthodontic_series,
             send_method='wado',
-            dicomweb_url='http://dicomweb-server.com/dicomweb/studies',
-            username='user',
-            password='pass'
+            pacs_wado_url='http://dicomweb-server.com/dicomweb/studies',
+            pacs_wado_username='user',
+            pacs_wado_password='pass'
         )
+
+        Returns either a DICOM Dateset or a response containing the response.
         """
 
         # Convert image to DICOM (assuming you have a function for this)
 
         # Send the DICOM file based on the specified method
         if send_method == 'dimse':
             return dimse.send(
+                dicom_datasets=kwargs.get('dicom_datasets', None),
                 dicom_files=kwargs.get('dicom_files', None),
                 orthodontic_series=kwargs.get('orthodontic_series', None),
-                pacs_ip=kwargs['pacs_ip'],
-                pacs_port=kwargs['pacs_port'],
-                pacs_aet=kwargs['pacs_aet'])
+                pacs_dimse_hostname=kwargs['pacs_dimse_hostname'],
+                pacs_dimse_port=kwargs['pacs_dimse_port'],
+                pacs_dimse_aet=kwargs['pacs_dimse_aet'])
 
         elif send_method == 'wado':
             return wado.send(
                 dicom_files=kwargs.get('dicom_files', None),
                 orthodontic_series=kwargs.get('orthodontic_series', None),
-                dicomweb_url=kwargs['dicomweb_url'],
-                username=kwargs.get('username'),
-                password=kwargs.get('password'),
+                pacs_wado_url=kwargs['pacs_wado_url'],
+                pacs_wado_username=kwargs.get('pacs_wado_username'),
+                pacs_wado_password=kwargs.get('pacs_wado_password'),
                 ssl_certificate=kwargs.get('ssl_certificate'),
                 ssl_verify=kwargs.get('ssl_verify'),
             )
         else:
             logger.error('Invalid send method specified.')
+
+
+    def get_image_view_code(self, ds:Dataset, code_system):
+        pass

dicom4ortho/defaults.py

@@ -6,5 +6,4 @@
 logger.warning("DEPRECATION WARNING: dicom4ortho.defaults is deprecated. Make use of dicom4orto.config and dicom4ortho.utils instead.")
 
 from dicom4ortho.utils import generate_dicom_uid
-from dicom4ortho.config import *
-from dicom4ortho.config import __author__, __creation_date__, __email__, __short_description__, __updated__, __url__
+from dicom4ortho.config import *