Merge branch 'main' into invalid-image-size-handling

CHANGELOG.md

@@ -11,6 +11,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Override image size for labels and overviews if it is likely to be wrong.
 
+### Changed
+
+- Use logger instead of issuing warnings.
+
+### Fixed
+
+- Error in documentation of read_overview() in readme.
+- Spellings.
+
 ## [0.10.0] - 2023-06-01
 
 ### Added
@@ -35,11 +44,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Support for opening DICOM WSI using DICOMWeb.
 - save() now takes the optional parameter add_missing_levels, that enables adding missing pyramid levels up to the single-tile level.
-- read_region(), read_region_mm(), and read_region_mpp() takes an optional parameter threads, that allows multiple threads to be used for stitching togheter the region.
+- read_region(), read_region_mm(), and read_region_mpp() takes an optional parameter threads, that allows multiple threads to be used for stitching together the region.
 
 ### Changed
 
-- WsiDicom is now initalized using a Source, that is responsible for provides the instances to view.
+- WsiDicom is now initialized using a Source, that is responsible for provides the instances to view.
 - Saving a WsiDicom is now handled by WsiDicomFileTarget.
 - Refactoring due to adding support for DICOMWeb and opening instances using Source and saving using Target.
 - Frame positions and tiling for levels are now parsed lazily, e.g. on first tile access.
@@ -85,7 +94,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-- Focal planes are considered equal if configurable withing threshold distance, see config.focal_plane_distance_threshold
+- Focal planes are considered equal if configurable within threshold distance, see config.focal_plane_distance_threshold
 - Option to read region defined in slide coordinate system for get_region_mm().
 
 ### Changed
@@ -113,7 +122,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Fixed
 
-- Order of paramaters for ConceptCode matches pydicom Code.
+- Order of parameters for ConceptCode matches pydicom Code.
 
 ## [0.3.0] - 2022-04-20
 

README.md

@@ -108,7 +108,7 @@ region_mpp = slide.read_region_mpp((0, 0), 0.01, (3, 3))
 ***Read a thumbnail of the whole slide with maximum dimensions 200x200 px.***
 
 ```python
-thumbnail = slide.read_thumbnail(200, 200)
+thumbnail = slide.read_thumbnail((200, 200))
 ```
 
 ***Read an overview image (if available).***
@@ -146,7 +146,7 @@ slide.close()
 An opened WsiDicom instance can be saved to a new path using the save()-method. The produced files will be:
 
 - Fully tiled. Any sparse tiles will be replaced with a blank tile with color depending on the photometric interpretation.
-- Have a basic offset table (or optionally an exteded offset table or no offset table).
+- Have a basic offset table (or optionally an extended offset table or no offset table).
 - Not be concatenated.
 
 The frames are copied as-is, i.e. without re-compression.
@@ -156,7 +156,7 @@ with WsiDicom.open(path_to_folder) as slide:
     slide.save(path_to_output)
 ```
 
-The output folder must already exists. Be careful to specify a unique folder folder to avoid mixing files from diferent images.
+The output folder must already exists. Be careful to specify a unique folder folder to avoid mixing files from different images.
 
 ## Settings
 
@@ -175,7 +175,7 @@ Annotations are structured in a hierarchy:
 - AnnotationInstance
     Represents a collection of AnnotationGroups. All the groups have the same frame of reference, i.e. annotations are from the same wsi stack.
 - AnnotationGroup
-    Represents a group of annotations. All annotations in the group are of the same type (e.g. PointAnnotation), have the same label, description and category and type. The category and type are codes that are used to define the annotated feature. A good resource for working with codes is avaiable [here](https://qiicr.gitbook.io/dcmqi-guide/opening/coding_schemes).
+    Represents a group of annotations. All annotations in the group are of the same type (e.g. PointAnnotation), have the same label, description and category and type. The category and type are codes that are used to define the annotated feature. A good resource for working with codes is available [here](https://qiicr.gitbook.io/dcmqi-guide/opening/coding_schemes).
 - Annotation
     Represents a annotation. An Annotation has a geometry (currently Point, Polyline, Polygon) and an optional list of Measurements.
 - Measurement
@@ -257,7 +257,7 @@ To watch unit tests use:
 poetry run pytest-watch -- -m unittest
 ```
 
-The integration tests uses test images from nema.org thats needs to be downloaded. The location of the test images can be changed from the default tests\testdata\slides using the enviroment variable WSIDICOM_TESTDIR. Download the images using the supplied script:
+The integration tests uses test images from nema.org that's needs to be downloaded. The location of the test images can be changed from the default tests\testdata\slides using the environment variable WSIDICOM_TESTDIR. Download the images using the supplied script:
 
 ```console
 python .\tests\download_test_images.py
@@ -285,7 +285,7 @@ A WSI DICOM pyramid is in *wsidicom* represented by a hierarchy of objects of di
 
 Labels and overviews are structured similarly to levels, but with somewhat different properties and restrictions. For DICOMWeb the WsiDicomFile\* classes are replaced with WsiDicomWeb\* classes.
 
-A Source is used to create WsiInstances, either from files (*WsiDicomFileSource*) or DICOMWeb (*WsiDicomWebSource*), and can be used to to initate a *WsiDicom* object. A source is easiest created with the open() and open_web() helper functions, e.g.:
+A Source is used to create WsiInstances, either from files (*WsiDicomFileSource*) or DICOMWeb (*WsiDicomWebSource*), and can be used to to Initiate a *WsiDicom* object. A source is easiest created with the open() and open_web() helper functions, e.g.:
 
 ```python
 slide = WsiDicom.open(path_to_folder)
@@ -342,4 +342,4 @@ Our aim is to provide constructive and positive code reviews for all submissions
 
 *wsidicom*: Copyright 2021 Sectra AB, licensed under Apache 2.0.
 
-This project is part of a project that has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 945358. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. IMI website: www.imi.europa.eu
+This project is part of a project that has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 945358. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. IMI website: <www.imi.europa.eu>

pyproject.toml

@@ -32,6 +32,7 @@ pycodestyle = "^2.8.0"
 black = "^23.1.0"
 flake8 = "^4.0.1"
 parameterized = "^0.8.1"
+codespell = "^2.2.5"
 
 [build-system]
 requires = ["poetry-core>=1.2.0"]

tests/download_test_images.py

@@ -19,62 +19,62 @@
 from typing import Any, Dict
 
 
-FILESERVER = 'medical.nema.org'
-FILESERVER_SLIDE_PATH = Path('MEDICAL/Dicom/DataSets/WG26')
+FILESERVER = "medical.nema.org"
+FILESERVER_SLIDE_PATH = Path("MEDICAL/Dicom/DataSets/WG26")
 
 SLIDES: Dict[str, Dict[str, Any]] = {
-    'FULL_WITH_BOT': {
-        'name':  r'Histech^Samantha [1229631]',
-        'parentpath': r'WG26Demo2020_PV',
-        'subpath': r'20190104 140000 [Case S - Colon polyps]/Series 000 [SM]',
-        'files': {
-            '2.25.173648596820938096199028939965251554503.dcm': '865538d55fce37ae6d91d85aebe29029',  # NOQA
-            '2.25.181487944453580109633363498147571426374.dcm': '7ff4acf3c71572236ce968e06e79d8db',  # NOQA
-            '2.25.191907898033754830752233761154920949936.dcm': '596183ec0444fedaba981de2f94652cb',  # NOQA
-            '2.25.209236321826383427842899333369775338594.dcm': 'f7fe907553f036ec6d2a68443f006fd4',  # NOQA
-            '2.25.222943316513786317622687980099326639180.dcm': 'ec1db6ca69c7d6fe8c4dacb04051ff11',  # NOQA
-            '2.25.251277550657103455222613143487830679046.dcm': '03399b8332c967a9a97e67bffdd70fb9',  # NOQA
-            '2.25.253973508129488054885063915385651983009.dcm': 'ac85a6f618ed0ca2bdf921be429fa185',  # NOQA
-            '2.25.259312801889857550164526960213815274816.dcm': 'b7c64d1ed975b42f2b1b4d917c4ba8c0',  # NOQA
-            '2.25.264278491200307498225194538752823371217.dcm': '0cc906dbeb22e10bff65f9b6d8961fa7',  # NOQA
-            '2.25.290884199110265475119989552423006928136.dcm': 'b8faf60dc44e4cb9aa5e7ab92a706b88',  # NOQA
-            '2.25.315427219625170954090644500893748466389.dcm': '84cca002af2e6263f25913b2896e36db',  # NOQA
-            '2.25.339652625381363485545547336547695948130.dcm': '52ea8ec41f3f86368d50542c9ed41975',  # NOQA
-            '2.25.98447601926716844575918590187306802549.dcm': '382e1b6780404efb7f44c65444694b05'  # NOQA
-        }
+    "FULL_WITH_BOT": {
+        "name": r"Histech^Samantha [1229631]",
+        "parentpath": r"WG26Demo2020_PV",
+        "subpath": r"20190104 140000 [Case S - Colon polyps]/Series 000 [SM]",
+        "files": {
+            "2.25.173648596820938096199028939965251554503.dcm": "865538d55fce37ae6d91d85aebe29029",  # NOQA
+            "2.25.181487944453580109633363498147571426374.dcm": "7ff4acf3c71572236ce968e06e79d8db",  # NOQA
+            "2.25.191907898033754830752233761154920949936.dcm": "596183ec0444fedaba981de2f94652cb",  # NOQA
+            "2.25.209236321826383427842899333369775338594.dcm": "f7fe907553f036ec6d2a68443f006fd4",  # NOQA
+            "2.25.222943316513786317622687980099326639180.dcm": "ec1db6ca69c7d6fe8c4dacb04051ff11",  # NOQA
+            "2.25.251277550657103455222613143487830679046.dcm": "03399b8332c967a9a97e67bffdd70fb9",  # NOQA
+            "2.25.253973508129488054885063915385651983009.dcm": "ac85a6f618ed0ca2bdf921be429fa185",  # NOQA
+            "2.25.259312801889857550164526960213815274816.dcm": "b7c64d1ed975b42f2b1b4d917c4ba8c0",  # NOQA
+            "2.25.264278491200307498225194538752823371217.dcm": "0cc906dbeb22e10bff65f9b6d8961fa7",  # NOQA
+            "2.25.290884199110265475119989552423006928136.dcm": "b8faf60dc44e4cb9aa5e7ab92a706b88",  # NOQA
+            "2.25.315427219625170954090644500893748466389.dcm": "84cca002af2e6263f25913b2896e36db",  # NOQA
+            "2.25.339652625381363485545547336547695948130.dcm": "52ea8ec41f3f86368d50542c9ed41975",  # NOQA
+            "2.25.98447601926716844575918590187306802549.dcm": "382e1b6780404efb7f44c65444694b05",  # NOQA
+        },
+    },
+    "SPARSE_NO_BOT": {
+        "name": r"MoticWangjie^Professer [100001]",
+        "parentpath": r"WG26Demo2019_PV",
+        "subpath": r"20190903 102029 [200001]\Series 000 [SM]",
+        "files": {
+            "1.2.276.0.7230010.3.1.4.1145362585.2096.1567753444.778.dcm": "4463e99bea080b14591f0665a6e84559",  # NOQA
+            "1.2.276.0.7230010.3.1.4.1145362585.2096.1567753447.783.dcm": "0b48b76e46c754fc75b13d6fbf682a19",  # NOQA
+            "1.2.276.0.7230010.3.1.4.1145362585.2096.1567753450.788.dcm": "75452d5f811f5c8c8f4475fbac6665bb",  # NOQA
+            "1.2.276.0.7230010.3.1.4.1145362585.2096.1567753451.793.dcm": "3bf4fee344571bda7005d9735b5bd699",  # NOQA
+            "1.2.276.0.7230010.3.1.4.1145362585.2096.1567753451.798.dcm": "84f2b3ba111ec09beb8846d17ddcd9e5",  # NOQA
+            "1.2.276.0.7230010.3.1.4.1145362585.2096.1567753451.803.dcm": "d2e565d600a573685ca1be48d96a0ef4",  # NOQA
+            "1.2.276.0.7230010.3.1.4.1145362585.2096.1567753451.808.dcm": "aedbe1f7ba9f15754078e3c8a9077fee",  # NOQA
+            "1.2.276.0.7230010.3.1.4.1145362585.2096.1567753451.813.dcm": "3533d30ef5e9abe3b8ee6e1c7bc0fb17",  # NOQA
+        },
     },
-    'SPARSE_NO_BOT': {
-        'name':  r'MoticWangjie^Professer [100001]',
-        'parentpath': r'WG26Demo2019_PV',
-        'subpath': r'20190903 102029 [200001]\Series 000 [SM]',
-        'files': {
-            '1.2.276.0.7230010.3.1.4.1145362585.2096.1567753444.778.dcm': '4463e99bea080b14591f0665a6e84559',  # NOQA
-            '1.2.276.0.7230010.3.1.4.1145362585.2096.1567753447.783.dcm': '0b48b76e46c754fc75b13d6fbf682a19',  # NOQA
-            '1.2.276.0.7230010.3.1.4.1145362585.2096.1567753450.788.dcm': '75452d5f811f5c8c8f4475fbac6665bb',  # NOQA
-            '1.2.276.0.7230010.3.1.4.1145362585.2096.1567753451.793.dcm': '3bf4fee344571bda7005d9735b5bd699',  # NOQA
-            '1.2.276.0.7230010.3.1.4.1145362585.2096.1567753451.798.dcm': '84f2b3ba111ec09beb8846d17ddcd9e5',  # NOQA
-            '1.2.276.0.7230010.3.1.4.1145362585.2096.1567753451.803.dcm': 'd2e565d600a573685ca1be48d96a0ef4',  # NOQA
-            '1.2.276.0.7230010.3.1.4.1145362585.2096.1567753451.808.dcm': 'aedbe1f7ba9f15754078e3c8a9077fee',  # NOQA
-            '1.2.276.0.7230010.3.1.4.1145362585.2096.1567753451.813.dcm': '3533d30ef5e9abe3b8ee6e1c7bc0fb17'  # NOQA
-        }
-    }
 }
 
 
 def cwd_to_folder(ftp, folder: Path):
-    ftp.cwd('/')
+    ftp.cwd("/")
     for subfolder in folder.parts:
         ftp.cwd(str(subfolder))
 
 
 def download_file(ftp: FTP, file: str, filename: Path):
-    with open(filename, 'wb') as fp:
-        ftp.retrbinary(f'RETR {file}', fp.write)
+    with open(filename, "wb") as fp:
+        ftp.retrbinary(f"RETR {file}", fp.write)
 
 
 def get_slide_dir() -> Path:
-    DEFAULT_DIR = 'tests/testdata'
-    SLIDE_DIR = 'slides'
+    DEFAULT_DIR = "tests/testdata"
+    SLIDE_DIR = "slides"
     test_data_path = os.environ.get("DICOM_TESTDIR")
     if test_data_path is None:
         test_data_dir = Path(DEFAULT_DIR)
@@ -89,15 +89,13 @@ def get_slide_dir() -> Path:
 
 
 def get_or_check_slide(slide_dir: Path, slide: Dict[str, Any], ftp: FTP):
-    path = slide_dir.joinpath(slide['name'], slide['subpath'])
+    path = slide_dir.joinpath(slide["name"], slide["subpath"])
     ftp_path = FILESERVER_SLIDE_PATH.joinpath(
-        slide['parentpath'],
-        slide['name'],
-        slide['subpath']
+        slide["parentpath"], slide["name"], slide["subpath"]
     )
     os.makedirs(path, exist_ok=True)
     cwd_to_folder(ftp, ftp_path)
-    for file, checksum in slide['files'].items():
+    for file, checksum in slide["files"].items():
         file_path = path.joinpath(file)
         if not file_path.exists():
             print(
@@ -111,7 +109,7 @@ def get_or_check_slide(slide_dir: Path, slide: Dict[str, Any], ftp: FTP):
 
 
 def check_checksum(file_path: Path, checksum: str):
-    with open(file_path, 'rb') as saved_file:
+    with open(file_path, "rb") as saved_file:
         data = saved_file.read()
         file_checksum = md5(data).hexdigest()
         if checksum != file_checksum:

tests/test_save.py

@@ -111,7 +111,6 @@ def _get_encoded_tile(self, tile: Point, z: float, path: str) -> bytes:
 
 
 @pytest.mark.save
-@pytest.mark.filterwarnings("ignore")
 class WsiDicomFileSaveTests(unittest.TestCase):
     @classmethod
     def setUpClass(cls):
@@ -177,7 +176,7 @@ def _get_relative_path(slide_path: Path) -> Path:
     def create_test_dataset(frame_count: int, image_data: WsiDicomTestImageData):
         dataset = Dataset()
         dataset.SOPClassUID = WSI_SOP_CLASS_UID
-        dataset.ImageType = ["ORGINAL", "PRIMARY", "VOLUME", "NONE"]
+        dataset.ImageType = ["ORIGINAL", "PRIMARY", "VOLUME", "NONE"]
         dataset.NumberOfFrames = frame_count
         dataset.SOPInstanceUID = generate_uid()
         dataset.StudyInstanceUID = generate_uid()

tests/test_wsidicom_file_target.py

@@ -26,7 +26,6 @@
 
 
 @pytest.mark.integration
-@pytest.mark.filterwarnings("ignore")
 class WsiDicomFileTargetIntegrationTests(unittest.TestCase):
     @classmethod
     def setUpClass(cls):

tests/test_wsidicom_integration.py

@@ -25,7 +25,6 @@
 
 
 @pytest.mark.integration
-@pytest.mark.filterwarnings("ignore")
 @parameterized_class(
     [
         {"input_type": WsiInputType.FILE},

wsidicom/conceptcode.py

@@ -228,7 +228,7 @@ def _from_cid(cls, meaning: str) -> Code:
         for code in cls.cid.values():
             if code.meaning == meaning:
                 return code
-        raise ValueError("Unsupported code")
+        raise ValueError(f"Unsupported code with meaning {meaning}.")
 
     @classmethod
     def list(cls) -> List[str]:
@@ -254,6 +254,7 @@ def from_code_value(
             code.meaning, code.value, code.scheme_designator, code.scheme_version
         )
 
+
 class UnitCode(SingleConceptCode):
     """Code for concepts representing units according to UCUM scheme"""
 

wsidicom/errors.py

@@ -38,14 +38,14 @@ def __str__(self):
 
 
 class WsiDicomMatchError(Exception):
-    """Raised if item in group that should match doesnt match."""
+    """Raised if item in group that should match does not match."""
 
     def __init__(self, item: str, group: str):
         self.item = item
         self.group = group
 
     def __str__(self):
-        return f"{self.item} doesnt match {self.group}"
+        return f"{self.item} does not match {self.group}"
 
 
 class WsiDicomUidDuplicateError(Exception):
@@ -89,7 +89,7 @@ class WsiDicomRequirementError(Exception):
     """Raised if required attribute is missing."""
 
 
-class WsiDicomNoResultionError(Exception):
+class WsiDicomNoResolutionError(Exception):
     """Raised if method is not possible as resolution is missing in image
     data."""
 

wsidicom/file/wsidicom_file.py

@@ -366,7 +366,7 @@ def _read_sequence_delimiter(self):
         TAG_BYTES = 4
         self._file.seek(-TAG_BYTES, 1)
         if self._file.read_tag() != SequenceDelimiterTag:
-            raise WsiDicomFileError(self._file, "No sequence delimeter tag")
+            raise WsiDicomFileError(self._file, "No sequence delimiter tag")
 
     def read_frame(self, frame_index: int) -> bytes:
         """Return frame data from pixel data by frame index.
@@ -411,11 +411,11 @@ def _parse_pixel_data(self) -> Tuple[List[Tuple[int, int]], OffsetTableType]:
         then not be empty. A BOT most always be the first item in the Pixel
         data, but can be empty (zero length). If EOT is used BOT should be empty.
 
-        First seach to pixel data position, which is either EOT tag or PixelData tag.
+        First search to pixel data position, which is either EOT tag or PixelData tag.
         If EOT read the EOT. For all cases validate that the filepointer now is at the
         PixelData tag. If BOT read the BOT, otherwise skip the BOT. If EOT nor BOT has
         been read, parse frame positions from pixel data. Otherwise parse frame
-        positions from EOT or BOT. Finaly check that the number of read frames equals
+        positions from EOT or BOT. Finally check that the number of read frames equals
         the specified number of frames, otherwise frames are fragmented which we dont
         support.
 

wsidicom/file/wsidicom_file_image_data.py

@@ -68,7 +68,7 @@ def transfer_syntax(self) -> UID:
 
     def _get_file(self, frame_index: int) -> WsiDicomFile:
         """
-        Return file contaning frame index.
+        Return file containing frame index.
 
         Raises WsiDicomNotFoundError if frame is not found.