Isyntax (#111)

* Support for isyntax file using pyisyntax * Read barcode from isyntax * Update changelog * Update readme * Skip isyntax test on mac * Do not include icc profile from isyntax as it is not useable
imi-bigpicture · Jan 29, 2025 · 74da149 · 74da149
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diff --git a/.github/workflows/pytest.yaml b/.github/workflows/pytest.yaml
@@ -92,7 +92,7 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install poetry
       - name: Install Application
-        run: python -m poetry install
+        run: python -m poetry install --all-extras
 
       - name: Lint with flake8
         run: |

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Added
+
+- Support for reading isyntax files using pyisyntax.
+
 ### Fixed
 
 - Reading correct image size in pyramid series in Bioformats reader.

diff --git a/README.md b/README.md
@@ -14,7 +14,7 @@
 - Aperio svs (lossless)
 - Hamamatsu ndpi (lossless)
 - Philips tiff (lossless)
-- Zeiss czi (lossy, only base level)
+- Zeiss czi (lossy)
 - Optional: Formats supported by Bioformats (lossy)
 
 With the `openslide` extra the following formats are also supported:
@@ -28,6 +28,10 @@ With the `openslide` extra the following formats are also supported:
 
 The `bioformats` extra by default enables lossy support for the [BSD-licensed Bioformat formats](https://docs.openmicroscopy.org/bio-formats/6.12.0/supported-formats.html).
 
+The `isyntax` extra enables lossy single-thread support for isynax files.
+
+For czi and isyntax only the base level is read from file. To produce a conversion with full levels, use `add_missing_levels` in the `save()` method.
+
 ## Installation
 
 ***Install wsidicomizer from pypi***

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -27,11 +27,13 @@ tiffslide = "^2.4.0"
 openslide-python = { version = "^1.3.0", optional = true }
 scyjava = { version = "^1.8.1", optional = true }
 ome-types = {version = "^0.5.0", optional = true }
+pyisyntax = {version = "^0.1.2", optional = true }
 imagecodecs = { version = "^2024.12.30",  optional = true }
 
 [tool.poetry.extras]
 openslide = ["openslide-python"]
 bioformats = ["scyjava", "ome-types"]
+isyntax = ["pyisyntax"]
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^7.2.0"

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -31,6 +31,7 @@
     "svs": {
         "CMU-1/CMU-1.svs": {
             "convert": True,
+            "openslide": True,
             "include_levels": [0, 1, 2],
             "lowest_included_pyramid_level": 0,
             "photometric_interpretation": "RGB",
@@ -73,6 +74,7 @@
         },
         "svs1/input.svs": {
             "convert": True,
+            "openslide": True,
             "include_levels": [0, 1, 2],
             "lowest_included_pyramid_level": 0,
             "photometric_interpretation": "RGB",
@@ -117,6 +119,7 @@
     "czi": {
         "czi1/input.czi": {
             "convert": False,
+            "openslide": False,
             "include_levels": [0],
             "lowest_included_pyramid_level": 0,
             "tile_size": 512,
@@ -144,6 +147,7 @@
     "mirax": {
         "CMU-1/CMU-1.mrxs": {
             "convert": True,
+            "openslide": True,
             "include_levels": [4, 6],
             "lowest_included_pyramid_level": 4,
             "tile_size": 1024,
@@ -197,6 +201,7 @@
     "ndpi": {
         "CMU-1/CMU-1.ndpi": {
             "convert": True,
+            "openslide": True,
             "include_levels": [2, 3],
             "lowest_included_pyramid_level": 4,
             "tile_size": 1024,
@@ -244,6 +249,7 @@
         },
         "ndpi1/input.ndpi": {
             "convert": True,
+            "openslide": True,
             "include_levels": [2, 3],
             "lowest_included_pyramid_level": 4,
             "tile_size": 1024,
@@ -358,6 +364,7 @@
     "philips_tiff": {
         "philips1/input.tif": {
             "convert": True,
+            "openslide": True,
             "include_levels": [4, 5, 6],
             "lowest_included_pyramid_level": 4,
             "photometric_interpretation": "YBR_FULL_422",
@@ -408,6 +415,40 @@
             ],
         }
     },
+    "isyntax": {
+        "isyntax1/testslide.isyntax": {
+            "convert": False,
+            "openslide": False,
+            "include_levels": [0],
+            "lowest_included_pyramid_level": 0,
+            "photometric_interpretation": "YBR_FULL_422",
+            "image_coordinate_system": {"x": 0.0, "y": 0.0},
+            "icc_profile": False,
+            "read_region": [
+                {
+                    "location": {"x": 18000, "y": 39000},
+                    "level": 0,
+                    "size": {"width": 200, "height": 200},
+                    "md5": "47d0eea527c6203817350a5b38c34a85",
+                },
+                {
+                    "location": {"x": 20000, "y": 40000},
+                    "level": 0,
+                    "size": {"width": 200, "height": 200},
+                    "md5": "3690f9decbd78ef83ed0b5c949050a15",
+                },
+                {
+                    "location": {"x": 20500, "y": 40300},
+                    "level": 0,
+                    "size": {"width": 200, "height": 200},
+                    "md5": "abb552d51b81feaf0768067708b1c169",
+                },
+            ],
+            "read_thumbnail": [],
+            "read_region_openslide": [],
+            "skip_hash_test_platforms": ["Darwin"],
+        }
+    },
 }
 
 

diff --git a/tests/download_test_images.py b/tests/download_test_images.py
@@ -61,6 +61,10 @@
         },
         "zip": True,
     },
+    "isyntax/isyntax1/testslide.isyntax": {
+        "url": "https://zenodo.org/record/5037046/files/testslide.isyntax",  # NOQA
+        "md5": {"testslide.isyntax": "d762ed9e13d4c47549672a54777f40e3"},
+    },
 }
 
 DEFAULT_SLIDE_FOLDER = "tests/testdata/slides"

diff --git a/tests/test_convert.py b/tests/test_convert.py
@@ -13,6 +13,7 @@
 #    limitations under the License.
 
 import os
+import platform
 from hashlib import md5
 from pathlib import Path
 from tempfile import TemporaryDirectory
@@ -136,13 +137,20 @@ def test_focal_plane_not_found(self, wsi: WsiDicom):
             wsi.read_tile(0, (0, 0), z=1.0)
 
     @pytest.mark.parametrize(
-        ["file_format", "file", "region", "lowest_included_level"],
+        [
+            "file_format",
+            "file",
+            "region",
+            "lowest_included_level",
+            "skip_hash_test_platforms",
+        ],
         [
             (
                 file_format,
                 file,
                 region,
                 file_parameters["lowest_included_pyramid_level"],
+                file_parameters.get("skip_hash_test_platforms", []),
             )
             for file_format, format_files in test_parameters.items()
             for file, file_parameters in format_files.items()
@@ -156,9 +164,12 @@ def test_read_region_from_converted_file_should_match_hash(
         file: str,
         region: Dict[str, Any],
         lowest_included_level: int,
+        skip_hash_test_platforms: List[str],
         wsi: WsiDicom,
     ):
         # Arrange
+        if platform.system() in skip_hash_test_platforms:
+            pytest.skip(f"Skipping hash test for {platform.system()}.")
         level = region["level"] - lowest_included_level
 
         # Act
@@ -174,19 +185,31 @@ def test_read_region_from_converted_file_should_match_hash(
         ), f"{file_format}: {file} lowest level {lowest_included_level} {region}"
 
     @pytest.mark.parametrize(
-        ["file_format", "file", "thumbnail"],
+        ["file_format", "file", "thumbnail", "skip_hash_test_platforms"],
         [
-            (file_format, file, thumbnail)
+            (
+                file_format,
+                file,
+                thumbnail,
+                file_parameters.get("skip_hash_test_platforms", []),
+            )
             for file_format, format_files in test_parameters.items()
             for file, file_parameters in format_files.items()
             for thumbnail in file_parameters["read_thumbnail"]
         ],
         scope="module",
     )
     def test_read_thumbnail_from_converted_file_should_match_hash(
-        self, file_format: str, file: str, thumbnail: Dict[str, Any], wsi: WsiDicom
+        self,
+        file_format: str,
+        file: str,
+        thumbnail: Dict[str, Any],
+        wsi: WsiDicom,
+        skip_hash_test_platforms: List[str],
     ):
         # Arrange
+        if platform.system() in skip_hash_test_platforms:
+            pytest.skip(f"Skipping hash test for {platform.system()}.")
 
         # Act
         im = wsi.read_thumbnail(
@@ -199,17 +222,25 @@ def test_read_thumbnail_from_converted_file_should_match_hash(
         ), f"{file_format}: {file} {thumbnail}"
 
     @pytest.mark.parametrize(
-        ["file_format", "file", "region", "lowest_included_level"],
+        [
+            "file_format",
+            "file",
+            "region",
+            "lowest_included_level",
+            "skip_hash_test_platforms",
+        ],
         [
             (
                 file_format,
                 file,
                 region,
                 file_parameters["lowest_included_pyramid_level"],
+                file_parameters.get("skip_hash_test_platforms", []),
             )
             for file_format, format_files in test_parameters.items()
             for file, file_parameters in format_files.items()
             for region in file_parameters["read_region_openslide"]
+            if file_parameters["openslide"]
         ],
         scope="module",
     )
@@ -219,10 +250,13 @@ def test_read_region_from_converted_file_should_match_openslide(
         file: str,
         region: Dict[str, Any],
         lowest_included_level: int,
+        skip_hash_test_platforms: List[str],
         wsi_file: Path,
         wsi: WsiDicom,
     ):
         # Arrange
+        if platform.system() in skip_hash_test_platforms:
+            pytest.skip(f"Skipping hash test for {platform.system()}.")
         level = region["level"] - lowest_included_level
         with OpenSlide(wsi_file) as openslide_wsi:
             scale: float = openslide_wsi.level_downsamples[region["level"]]
@@ -269,10 +303,11 @@ def test_read_region_from_converted_file_should_match_openslide(
             for file_format, format_files in test_parameters.items()
             for file, file_parameters in format_files.items()
             for thumbnail in file_parameters["read_thumbnail"]
+            if file_parameters["openslide"]
         ],
         scope="module",
     )
-    def test_read_thumbnail_from_converted_file_should_almost_match_thumbnail(
+    def test_read_thumbnail_from_converted_file_should_almost_match_openslide_thumbnail(
         self,
         file_format: str,
         file: str,
@@ -324,6 +359,7 @@ def test_photometric_interpretation(
             (file_format, file)
             for file_format, format_files in test_parameters.items()
             for file in format_files.keys()
+            if format_files[file]["convert"]
         ],
         scope="module",
     )

diff --git a/wsidicomizer/config.py b/wsidicomizer/config.py
@@ -20,9 +20,19 @@ class Settings:
     global variable settings."""
 
     def __init__(self) -> None:
+        self._default_tile_size = 512
         self._czi_block_cache_size = 8
         self._insert_icc_profile_if_missing = True
 
+    @property
+    def default_tile_size(self) -> int:
+        """Default tile size to use."""
+        return self._default_tile_size
+
+    @default_tile_size.setter
+    def default_tile_size(self, value: int) -> None:
+        self._default_tile_size = value
+
     @property
     def czi_block_cache_size(self) -> int:
         """Size of block cache to use for czi files."""