fix: Fix bug in the wrong order of axis saved in napari contribution (#…

…972)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

package/PartSegCore/napari_plugins/save_tiff_layer.py

@@ -15,7 +15,7 @@ def napari_write_labels(path: str, data: Any, meta: dict) -> Optional[str]:
     image = Image(
         data,
         np.divide(meta["scale"], DEFAULT_SCALE_FACTOR)[-scale_shift:],
-        axes_order="TZXY"[-data.ndim :],
+        axes_order="TZYX"[-data.ndim :],
         channel_names=[meta["name"]],
         shift=np.divide(meta["translate"], DEFAULT_SCALE_FACTOR)[-scale_shift:],
         name="ROI",

package/tests/test_PartSegCore/test_napari_plugins.py

@@ -6,12 +6,14 @@
 import pytest
 from napari.layers import Image, Labels, Layer
 
+from PartSegCore.mask.io_functions import LoadROIFromTIFF
 from PartSegCore.napari_plugins.load_image import napari_get_reader as napari_get_reader_image
 from PartSegCore.napari_plugins.load_mask_project import napari_get_reader as napari_get_reader_mask
 from PartSegCore.napari_plugins.load_masked_image import napari_get_reader as napari_get_reader_mask_image
 from PartSegCore.napari_plugins.load_roi_project import napari_get_reader as napari_get_reader_roi
 from PartSegCore.napari_plugins.loader import project_to_layers
 from PartSegCore.napari_plugins.save_mask_roi import napari_write_labels
+from PartSegCore.napari_plugins.save_tiff_layer import napari_write_labels as napari_write_labels_tiff
 
 
 def test_project_to_layers_analysis(analysis_segmentation):
@@ -91,3 +93,12 @@ def test_write_labels(tmp_path):
 
     assert napari_write_labels(str(tmp_path / "test.txt"), data, {"scale": [10, 10]}) is None
     assert not (tmp_path / "test.txt").exists()
+
+
+def test_save_load_axis_order(tmp_path):
+    data = np.zeros((1, 10, 20, 30), dtype=np.uint8)
+    layer = Labels(data)
+    data_path = str(tmp_path / "test.tif")
+    assert napari_write_labels_tiff(data_path, *layer.as_layer_data_tuple()[:2])
+    proj = LoadROIFromTIFF.load([data_path])
+    assert proj.roi_info.roi.shape == data.shape