Add ZarrTIFFWSIReader class.

Author: aacic

requirements/requirements.txt

@@ -1,5 +1,6 @@
 # torch installation
 --extra-index-url https://download.pytorch.org/whl/cu118; sys_platform != "darwin"
+aiohttp>=3.8.1
 albumentations>=1.3.0
 bokeh>=3.1.1, <3.6.0
 Click>=8.1.3

tests/zarrtiff/__init__.py

@@ -0,0 +1 @@
+"""Test files meant for testing zarr tiff json files."""

tests/zarrtiff/tiff_fsspec.py

@@ -0,0 +1,147 @@
+"""Module for processing SVS metadata and generating fsspec JSON file."""
+
+from __future__ import annotations
+
+import json
+import sys
+from datetime import datetime
+from pathlib import Path
+from typing import TYPE_CHECKING, Any
+
+from tifffile import TiffFile, TiffPages, tiff2fsspec
+
+if TYPE_CHECKING:
+    from numbers import Number
+
+# Constants
+EXPECTED_KEY_VALUE_PAIRS = 2
+EXPECTED_ARG_COUNT = 4
+URL_PLACEHOLDER = "https://replace.me/"
+
+
+def _parse_svs_metadata(pages: TiffPages) -> dict[str, Any]:
+    # Copy/paste from TIFFWSIReader._parse_svs_metadata, extract to the util method.
+    """Extract SVS-specific metadata."""
+    raw = {}
+    mpp: list[float] | None = None
+    objective_power: float | None = None
+    vendor = "Aperio"
+
+    description = pages[0].description
+    raw["Description"] = description
+    parts = description.split("|")
+    description_headers, key_value_pairs = parts[0], parts[1:]
+    description_headers = description_headers.split(";")
+
+    software, photometric_info = description_headers[0].splitlines()
+    raw["Software"] = software
+    raw["Photometric Info"] = photometric_info
+
+    def parse_svs_tag(string: str) -> tuple[str, Number | str | datetime]:
+        """Parse SVS key-value string."""
+        pair = string.split("=")
+        if len(pair) != EXPECTED_KEY_VALUE_PAIRS:
+            invalid_metadata_msg = (
+                "Invalid metadata. Expected string of the format 'key=value'."
+            )
+            raise ValueError(invalid_metadata_msg)
+
+        key, value_string = pair
+        key = key.strip()
+        value_string = value_string.strip()
+
+        def us_date(string: str) -> datetime:
+            """Return datetime parsed according to US date format."""
+            return datetime.strptime(string, r"%m/%d/%y").astimezone()
+
+        def time(string: str) -> datetime:
+            """Return datetime parsed according to HMS format."""
+            return datetime.strptime(string, r"%H:%M:%S").astimezone()
+
+        casting_precedence = [us_date, time, int, float]
+        value: Number | str | datetime = value_string
+        for cast in casting_precedence:
+            try:
+                value = cast(value_string)
+                break
+            except ValueError:
+                continue
+
+        return key, value
+
+    svs_tags = dict(parse_svs_tag(string) for string in key_value_pairs)
+    raw["SVS Tags"] = svs_tags
+    mpp = [svs_tags.get("MPP")] * 2 if svs_tags.get("MPP") is not None else None
+    objective_power = svs_tags.get("AppMag")
+
+    return {
+        "objective_power": objective_power,
+        "vendor": vendor,
+        "mpp": mpp,
+        "raw": raw,
+    }
+
+
+def convert_metadata(metadata: dict) -> dict:
+    """Convert metadata to JSON-compatible format."""
+    if isinstance(metadata, dict):
+        return {key: convert_metadata(value) for key, value in metadata.items()}
+    if isinstance(metadata, list):
+        return [convert_metadata(item) for item in metadata]
+    if isinstance(metadata, datetime):
+        return metadata.isoformat()  # Convert datetime to ISO 8601 string
+    return metadata
+
+
+def replace_url(
+    data: dict[str, Any], output_path: Path, old_url: str, new_url: str
+) -> None:
+    """Replace URL in the JSON file."""
+    for value in data.values():
+        if isinstance(value, list) and value[0] == old_url:
+            value[0] = new_url
+
+    with output_path.open("w") as json_file:
+        json.dump(data, json_file, indent=2)
+
+
+def main(svs_file_path: str, json_file_path: str, final_url: str) -> None:
+    """Main function to handle SVS file processing."""
+    url_to_replace = f"{URL_PLACEHOLDER}{Path(svs_file_path).name}"
+
+    tiff_file_pages = TiffFile(svs_file_path).pages
+
+    # Generate fsspec JSON
+    tiff2fsspec(svs_file_path, url=URL_PLACEHOLDER, out=json_file_path)
+
+    # Parse SVS metadata
+    metadata = _parse_svs_metadata(pages=tiff_file_pages)
+
+    # Convert metadata to JSON-compatible format
+    metadata_serializable = convert_metadata(metadata)
+
+    # Read the JSON data from the file
+    json_path = Path(json_file_path)
+    with json_path.open() as file:
+        json_data = json.load(file)
+
+    # Decode `.zattrs` JSON string into a dictionary
+    zattrs = json.loads(json_data[".zattrs"])
+
+    # Update metadata into `.zattrs`
+    if "multiscales" in zattrs and isinstance(zattrs["multiscales"], list):
+        zattrs["multiscales"][0]["metadata"] = metadata_serializable
+
+    # Convert back to a JSON string
+    json_data[".zattrs"] = json.dumps(zattrs)
+
+    # Replace URLs in the JSON file
+    replace_url(json_data, json_path, url_to_replace, final_url)
+
+
+if __name__ == "__main__":
+    if len(sys.argv) != EXPECTED_ARG_COUNT:
+        msg = " Usage: python script.py <svs_file_path> <json_file_path> <final_url>"
+        raise ValueError(msg)
+
+    main(sys.argv[1], sys.argv[2], sys.argv[3])

tests/zarrtiff/tileserver.py

@@ -0,0 +1,20 @@
+"""Module to run TileServer for testing purpose."""
+
+from flask_cors import CORS
+
+from tiatoolbox.visualization import TileServer
+from tiatoolbox.wsicore import WSIReader
+
+svs = "/path/to/fsspec.json"
+
+reader = WSIReader.open(svs)
+
+# Initialize and run the TileServer
+tile_server = TileServer(
+    title="Tiatoolbox TileServer",
+    layers={"layer": reader},
+)
+CORS(tile_server, send_wildcard=True)
+
+
+tile_server.run(host="127.0.0.1", port=5000)