Dicomdir (#127)

* Add support for opening files in dicomdir

CHANGELOG.md

@@ -7,6 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Added
+
+- Support for opening DICOMDIR files using `open_dicomdir()`.
+
 ## [0.13.0] - 2023-11-11
 
 ### Added

README.md

@@ -53,6 +53,14 @@ from wsidicom import WsiDicom
 slide = WsiDicom.open([file_stream_1, file_stream_2, ... ])
 ```
 
+***Or load a WSI dataset from a DICOMDIR.***
+
+```python
+from wsidicom import WsiDicom
+
+slide = WsiDicom.open_dicomdir(path_to_dicom_dir)
+```
+
 ***Or load a WSI dataset from DICOMWeb.***
 
 ```python

wsidicom/file/wsidicom_file_source.py

@@ -14,13 +14,17 @@
 
 """A source for reading WSI DICOM files."""
 
-from collections import defaultdict
 import io
 import logging
+from collections import defaultdict
 from pathlib import Path
 from typing import BinaryIO, Dict, Iterable, List, Optional, Tuple, Union
 
-from pydicom.uid import UID
+from pydicom import dcmread
+from pydicom.errors import InvalidDicomError
+from pydicom.filereader import _read_file_meta_info, read_preamble
+from pydicom.fileset import FileSet
+from pydicom.uid import UID, MediaStorageDirectoryStorage
 
 from wsidicom.errors import (
     WsiDicomNotFoundError,
@@ -33,8 +37,6 @@
 from wsidicom.instance import ImageType, TileType, WsiDataset, WsiInstance
 from wsidicom.source import Source
 from wsidicom.uid import ANN_SOP_CLASS_UID, WSI_SOP_CLASS_UID, SlideUids
-from pydicom.filereader import read_preamble, _read_file_meta_info
-from pydicom.errors import InvalidDicomError
 
 
 class WsiDicomFileSource(Source):
@@ -160,6 +162,27 @@ def contains_levels(self) -> bool:
         """Returns true source has one level that can be read with WsiDicom."""
         return len(self.image_files) > 0
 
+    @classmethod
+    def open_dicomdir(cls, path: Union[str, Path]):
+        """Open a DICOMDIR file and return a WsiDicomFileSource for contained files.
+
+        Parameters
+        ----------
+        path: Union[str, Path]
+            Path to DICOMDIR file.
+
+        Returns
+        ----------
+        WsiDicomFileSource
+            Source for files in DICOMDIR.
+        """
+        dicomdir = dcmread(path)
+        if dicomdir.file_meta.MediaStorageSOPClassUID != MediaStorageDirectoryStorage:
+            raise ValueError()
+        fileset = FileSet(dicomdir)
+        files = [file.path for file in fileset]
+        return cls(files)
+
     @staticmethod
     def _open_file(file: Union[Path, BinaryIO]) -> Tuple[BinaryIO, Optional[Path]]:
         """Open stream if file is path. Return stream and optional filepath."""

wsidicom/wsidicom.py

@@ -151,6 +151,33 @@ def open_web(
         )
         return cls(source, label, True)
 
+    @classmethod
+    def open_dicomdir(
+        cls, path: Union[str, Path], label: Optional[Union[PILImage, str, Path]] = None
+    ) -> "WsiDicom":
+        """Open WSI DICOM files in DICOMDIR and return a WsiDicom object.
+
+        Parameters
+        ----------
+        path: Union[str, Path]
+            Path to DICOMDIR file or directory with a DICOMDIR file.
+        label: Optional[Union[PILImage, str, Path]] = None
+            Optional label image to use instead of label found in path.
+
+        Returns
+        ----------
+        WsiDicom
+            WsiDicom created from WSI DICOM files in DICOMDIR.
+        """
+        if isinstance(path, str):
+            path = Path(path)
+        if path.is_dir():
+            path = path.joinpath("DICOMDIR")
+        if not path.is_file() or not path.exists():
+            raise FileNotFoundError(f"DICOMDIR file {path} not found.")
+        source = WsiDicomFileSource.open_dicomdir(path)
+        return cls(source, label, True)
+
     def __enter__(self):
         return self