From a499fc367beaadf23cbbb426ac56c8ce340b1b22 Mon Sep 17 00:00:00 2001
From: ktsitsi <kostas.t@tiledb.com>
Date: Thu, 10 Nov 2022 13:18:50 +0200
Subject: [PATCH 1/2] Initial Skeleton for Isyntax files

---
 setup.py                        |  6 ++++-
 tiledbimg/converters/isyntax.py | 46 +++++++++++++++++++++++++++++++++
 2 files changed, 51 insertions(+), 1 deletion(-)
 create mode 100644 tiledbimg/converters/isyntax.py

diff --git a/setup.py b/setup.py
index 50dfb49b..be73b003 100644
--- a/setup.py
+++ b/setup.py
@@ -8,7 +8,10 @@
     "tifffile@git+https://github.com/TileDB-Inc/tifffile.git@gsa/python-3.7",
     "imagecodecs",
 ]
-full = sorted({*zarr, *openslide, *tiff})
+
+isyntax = ["openphi"]
+
+full = sorted({*zarr, *openslide, *tiff, *isyntax})
 
 setuptools.setup(
     setup_requires=["setuptools_scm"],
@@ -21,6 +24,7 @@
     extras_require={
         "zarr": zarr,
         "openslide": openslide,
+        "isyntax": isyntax,
         "tiff": tiff,
         "full": full,
     },
diff --git a/tiledbimg/converters/isyntax.py b/tiledbimg/converters/isyntax.py
new file mode 100644
index 00000000..f483a47c
--- /dev/null
+++ b/tiledbimg/converters/isyntax.py
@@ -0,0 +1,46 @@
+from typing import Any, Dict, cast
+
+import numpy as np
+import openphi as op
+
+from .base import Axes, ImageConverter, ImageReader, ImageWriter
+
+
+class ISyntaxReader(ImageReader):
+    def __init__(self, input_path: str):
+        self._ophi = op.OpenPhi(input_path)
+
+    def __exit__(self, exc_type: Any, exc_val: Any, exc_tb: Any) -> None:
+        self._ophi.close()
+
+    @property
+    def level_count(self) -> int:
+        return cast(int, self._ophi.level_count)
+
+    def level_axes(self, level: int) -> Axes:
+        return Axes("YXC")
+
+    def level_metadata(self, level: int) -> Dict[str, Any]:
+        return {}
+
+    @property
+    def group_metadata(self) -> Dict[str, Any]:
+        return {}
+
+    def level_image(self, level: int) -> np.ndarray:
+        dims = self._ophi.level_dimensions[level]
+        # image is in (width, height, channel) == XYC
+        image = self._ophi.read_region((0, 0), level, dims).convert("RGB")
+        # np.asarray() transposes it to (height, width, channel) == YXC
+        # https://stackoverflow.com/questions/49084846/why-different-size-when-converting-pil-image-to-numpy-array
+        return np.asarray(image)
+
+
+class ISyntaxConverter(ImageConverter):
+    """Converter of OpenSlide-supported images to TileDB Groups of Arrays"""
+
+    def _get_image_reader(self, input_path: str) -> ImageReader:
+        return ISyntaxReader(input_path)
+
+    def _get_image_writer(self, input_path: str, output_path: str) -> ImageWriter:
+        raise NotImplementedError

From 96ab7c6da41d1b39d0c231500005685b1b9f1372 Mon Sep 17 00:00:00 2001
From: ktsitsi <kostas.t@tiledb.com>
Date: Thu, 10 Nov 2022 16:26:23 +0200
Subject: [PATCH 2/2] Adding group metadata from ophi

---
 tiledbimg/converters/isyntax.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tiledbimg/converters/isyntax.py b/tiledbimg/converters/isyntax.py
index f483a47c..fb2f64f6 100644
--- a/tiledbimg/converters/isyntax.py
+++ b/tiledbimg/converters/isyntax.py
@@ -25,7 +25,7 @@ def level_metadata(self, level: int) -> Dict[str, Any]:
 
     @property
     def group_metadata(self) -> Dict[str, Any]:
-        return {}
+        return cast(Dict[str, Any], self._ophi.properties)
 
     def level_image(self, level: int) -> np.ndarray:
         dims = self._ophi.level_dimensions[level]