Merge pull request #4 from den-sq/main

Address TIFF file loading.

Author: den-sq

.github/workflows/pr-coverage.yml

@@ -3,6 +3,11 @@ on:
   pull_request:
     branches:
       - main
+
+env: 
+  GH_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
+  GITHUB_TOKEN: "${{ secrets.GITHUB_TOKEN }}"
+
 jobs:
   coverage:
     runs-on: ubuntu-latest

python/ouroboros/helpers/files.py

@@ -94,7 +94,7 @@ def get_sorted_tif_files(directory):
     files = os.listdir(directory)
 
     # Filter to include only .tif files and sort them numerically
-    tif_files = sorted((file for file in files if file.endswith(".tif")))
+    tif_files = sorted((file for file in files if file.endswith((".tif", ".tiff"))))
 
     return tif_files
 

python/ouroboros/pipeline/backproject_pipeline.py

@@ -91,7 +91,7 @@ def _process(self, input_data: any) -> tuple[any, None] | tuple[None, any]:
 
             # Save the straightened volume to a new tif file
             with tifffile.TiffWriter(new_straightened_volume_path) as tif:
-                if straightened_volume_path.endswith(".tif"):
+                if straightened_volume_path.endswith((".tif", ".tiff")):
                     # Read the single tif file
                     with tifffile.TiffFile(straightened_volume_path) as tif_in:
                         for i in range(len(tif_in.pages)):

python/test/helpers/test_files.py

@@ -1,4 +1,5 @@
 import os
+from pathlib import Path
 from tifffile import imwrite
 from ouroboros.helpers.files import (
     format_backproject_output_file,
@@ -22,9 +23,16 @@ def test_load_and_save_tiff_from_slices(tmp_path):
     slices_folder = tmp_path / "slices"
     slices_folder.mkdir()
 
+    input_names = [slices_folder / f"slice_{i:03d}.tif" for i in range(5)]
+
+    # Change some names to .tiff to ensure both .tif and .tiff are read.
+    from random import randrange
+    for i in [randrange(5) for j in range(2)]:
+        input_names[i] = input_names[i].with_suffix('.tiff')
+
     # Create some sample tiff files
-    for i in range(5):
-        imwrite(slices_folder / f"slice_{i:03d}.tif", data=[[i]])
+    for name in input_names:
+        imwrite(name, data=[[i]])
 
     output_file_path = tmp_path / "output.tif"
     load_and_save_tiff_from_slices(
@@ -44,36 +52,46 @@ def test_load_and_save_tiff_from_slices(tmp_path):
 
 
 def test_get_sorted_tif_files(tmp_path):
+    import random
+
     # Generate some sample tiff files
-    filenames = [f"{i:03d}.tif" for i in range(101)]
-    original_filenames = filenames.copy()
+    filenames = [Path(tmp_path, f"{i:03d}.tif") for i in range(101)]
 
-    # Randomize the order
-    import random
+    # Ensure both .tif and .tiff files are handled.
+    for i in [random.randrange(101) for j in range(35)]:
+        filenames[i] = filenames[i].with_suffix('.tiff')
+
+    original_filenames = [path.name for path in filenames]
 
+    # Randomize the order
     random.shuffle(filenames)
 
     # Create the files
-    for filename in filenames:
-        (tmp_path / filename).touch()
+    for path in filenames:
+        path.touch()
 
     sorted_files = get_sorted_tif_files(str(tmp_path))
     assert sorted_files == original_filenames
 
 
 def test_get_sorted_tif_files_prefix(tmp_path):
+    import random
+
     # Generate some sample tiff files
-    filenames = [f"slice_{i:03d}.tif" for i in range(101)]
-    original_filenames = filenames.copy()
+    filenames = [Path(tmp_path, f"slice_{i:03d}.tif") for i in range(101)]
 
-    # Randomize the order
-    import random
+    # Ensure both .tif and .tiff files are handled.
+    for i in [random.randrange(101) for j in range(35)]:
+        filenames[i] = filenames[i].with_suffix('.tiff')
+
+    original_filenames = [path.name for path in filenames]
 
+    # Randomize the order
     random.shuffle(filenames)
 
     # Create the files
-    for filename in filenames:
-        (tmp_path / filename).touch()
+    for path in filenames:
+        path.touch()
 
     sorted_files = get_sorted_tif_files(str(tmp_path))
     assert sorted_files == original_filenames

src/renderer/src/components/MenuPanel/components/FileExplorer/components/DraggableEntry/DraggableEntry.tsx

@@ -20,7 +20,7 @@ function DraggableEntry({
 	handleChange: (event: InputEvent) => void
 }): JSX.Element {
 	// Determine the type of the entry
-	const type = node.children ? 'folder' : node.name.endsWith('.tif') ? 'image' : 'file'
+	const type = node.children ? 'folder' : (node.name.endsWith('.tif') || node.name.endsWith('.tiff')) ? 'image' : 'file'
 	const isFolder = type === 'folder'
 	const isEmpty = !node.children || Object.keys(node.children).length === 0