From 2ed9a1f4576c1c07ec1101c9d7811fbcb196fd2e Mon Sep 17 00:00:00 2001
From: bugraoezdemir <91956472+bugraoezdemir@users.noreply.github.com>
Date: Mon, 6 May 2024 18:06:53 +0200
Subject: [PATCH 1/2] Improves `save_ij_tiff` by fixing the issue #671

---
 .../OpenIJTIFF/OpenIJTIFF/__init__.py         | 32 ++++++++++++++++---
 1 file changed, 28 insertions(+), 4 deletions(-)

diff --git a/functions/python_modules/OpenIJTIFF/OpenIJTIFF/__init__.py b/functions/python_modules/OpenIJTIFF/OpenIJTIFF/__init__.py
index 1fef722f..9c8eaf6f 100644
--- a/functions/python_modules/OpenIJTIFF/OpenIJTIFF/__init__.py
+++ b/functions/python_modules/OpenIJTIFF/OpenIJTIFF/__init__.py
@@ -6,6 +6,8 @@
 import numpy.typing as npt
 import requests
 import tifffile
+from skimage.io import imread
+import napari
 
 
 def _fetch_data(uri: str) -> Path:
@@ -173,9 +175,9 @@ def open_ij_tiff(
 def save_ij_tiff(
     tiffdest: Union[str, Path],
     image_array: np.ndarray,
-    ax_names: Sequence[str],
-    ax_scales: Sequence[float],
-    ax_units: Sequence[str],
+    ax_names: Optional[Sequence[str]] = None,
+    ax_scales: Optional[Sequence[float]] = None,
+    ax_units: Optional[Sequence[str]] = None,
     extra_metadata: Optional[dict] = None,
 ) -> Dict[str, Any]:
     """
@@ -195,15 +197,33 @@ def save_ij_tiff(
         Metadata dictionary
     """
 
+    _full_axes = 'TCZYX'
+    _full_units = ['Frame', 'na', 'Slice', 'Pixel', 'Pixel']
+
+    if ax_names is None:
+        ax_names = _full_axes[-image_array.ndim:]
+    if ax_units is None:
+        ax_units = _full_units[-image_array.ndim:]
+    if ax_scales is None:
+        ax_scales = [1] * image_array.ndim
+    ax_names = ax_names.upper()
+    assert len(ax_names) == image_array.ndim, f"The length of 'ax_names' must match the number of dimensions, which is {image_array.ndim}"
+    assert len(ax_units) == image_array.ndim, f"The length of 'ax_units' must match the number of dimensions, which is {image_array.ndim}"
+    assert len(ax_scales) == image_array.ndim, f"The length of 'ax_scales' must match the number of dimensions, which is {image_array.ndim}"
+
     metadata = {
         "axes": ax_names,
     }
 
+    if image_array.dtype == np.dtype(bool):
+        image_array = image_array.astype(np.uint8) * 255
+
     if "Y" in ax_names:
         y_idx = ax_names.index("Y")
+        metadata["unit"] = ax_units[y_idx]
     if "X" in ax_names:
         x_idx = ax_names.index("X")
-        metadata["unit"] = encode_unicode(ax_units[x_idx])
+        metadata["unit"] = ax_units[x_idx]
     if "Z" in ax_names:
         z_idx = ax_names.index("Z")
         if ax_units[z_idx] != "Slice":  ### TODO: This checkpoint might be improved
@@ -238,3 +258,7 @@ def save_ij_tiff(
         metadata=metadata,
     )
     return metadata
+
+
+
+

From fab78b7a0dbf8118f9a54eedf806e48ff5dfd937 Mon Sep 17 00:00:00 2001
From: bugraoezdemir <91956472+bugraoezdemir@users.noreply.github.com>
Date: Mon, 6 May 2024 18:09:19 +0200
Subject: [PATCH 2/2] Update __init__.py

---
 functions/python_modules/OpenIJTIFF/OpenIJTIFF/__init__.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/functions/python_modules/OpenIJTIFF/OpenIJTIFF/__init__.py b/functions/python_modules/OpenIJTIFF/OpenIJTIFF/__init__.py
index 9c8eaf6f..7b74f0dd 100644
--- a/functions/python_modules/OpenIJTIFF/OpenIJTIFF/__init__.py
+++ b/functions/python_modules/OpenIJTIFF/OpenIJTIFF/__init__.py
@@ -6,8 +6,7 @@
 import numpy.typing as npt
 import requests
 import tifffile
-from skimage.io import imread
-import napari
+
 
 
 def _fetch_data(uri: str) -> Path: