feat: add reading skew from czi files

package/PartSegCore/napari_plugins/loader.py

@@ -51,13 +51,13 @@ def add_color(image: Image, idx: int) -> dict:  # noqa: ARG001
         return {}
 
 
-def _image_to_layers(project_info, scale, translate):
+def _image_to_layers(project_info, scale, translate, shear):
     res_layers = []
     if project_info.image.name == "ROI" and project_info.image.channels == 1:
         res_layers.append(
             (
                 project_info.image.get_channel(0),
-                {"scale": scale, "name": project_info.image.channel_names[0], "translate": translate},
+                {"scale": scale, "name": project_info.image.channel_names[0], "translate": translate, "shear": shear},
                 "labels",
             )
         )
@@ -71,6 +71,7 @@ def _image_to_layers(project_info, scale, translate):
                     "blending": "additive",
                     "translate": translate,
                     "metadata": project_info.image.metadata,
+                    "shear": shear,
                     **add_color(project_info.image, i),
                 },
                 "image",
@@ -85,14 +86,15 @@ def project_to_layers(project_info: typing.Union[ProjectTuple, MaskProjectTuple]
     res_layers = []
     if project_info.image is not None and not isinstance(project_info.image, str):
         scale = project_info.image.normalized_scaling()
+        shear = project_info.image.shear
         translate = project_info.image.shift
         translate = (0,) * (len(project_info.image.axis_order.replace("C", "")) - len(translate)) + translate
-        res_layers.extend(_image_to_layers(project_info, scale, translate))
+        res_layers.extend(_image_to_layers(project_info, scale, translate, shear))
         if project_info.roi_info.roi is not None:
             res_layers.append(
                 (
                     project_info.image.fit_array_to_image(project_info.roi_info.roi),
-                    {"scale": scale, "name": "ROI", "translate": translate},
+                    {"scale": scale, "name": "ROI", "translate": translate, "shear": shear},
                     "labels",
                 )
             )
@@ -105,6 +107,7 @@ def project_to_layers(project_info: typing.Union[ProjectTuple, MaskProjectTuple]
                         "name": name,
                         "translate": translate,
                         "visible": False,
+                        "shear": shear,
                     },
                     "labels",
                 )
@@ -115,7 +118,7 @@ def project_to_layers(project_info: typing.Union[ProjectTuple, MaskProjectTuple]
             res_layers.append(
                 (
                     project_info.image.fit_array_to_image(project_info.mask),
-                    {"scale": scale, "name": "Mask", "translate": translate},
+                    {"scale": scale, "name": "Mask", "translate": translate, "shear": shear},
                     "labels",
                 )
             )

package/PartSegImage/image.py

@@ -224,6 +224,7 @@ def __init__(
         channel_info: list[ChannelInfo | ChannelInfoFull] | None = None,
         axes_order: str | None = None,
         shift: Spacing | None = None,
+        shear: np.ndarray | None = None,
         name: str = "",
         metadata_dict: dict | None = None,
     ):
@@ -243,6 +244,7 @@ def __init__(
         self._image_spacing = tuple(el if el > 0 else 10**-6 for el in self._image_spacing)
 
         self._shift = tuple(shift) if shift is not None else (0,) * len(self._image_spacing)
+        self._shear = shear
         self.name = name
 
         self.file_path = file_path
@@ -369,6 +371,10 @@ def _merge_channel_names(base_channel_names: list[str], new_channel_names: list[
             base_channel_names.append(new_name)
         return base_channel_names
 
+    @property
+    def shear(self) -> np.ndarray | None:
+        return self._shear
+
     @property
     def channel_info(self) -> list[ChannelInfoFull]:
         return [copy(x) for x in self._channel_info]

package/PartSegImage/image_reader.py

@@ -1,6 +1,7 @@
 import inspect
 import os.path
 import typing
+import warnings
 from abc import abstractmethod
 from contextlib import suppress
 from importlib.metadata import version
@@ -388,8 +389,36 @@ def read(self, image_path: typing.Union[str, BytesIO, Path], mask_path=None, ext
             axes_order=self.return_order(),
             metadata_dict=metadata,
             channel_info=self._get_channel_info(),
+            shear=self._read_shear(metadata),
         )
 
+    def _read_shear(self, metadata: dict):
+        skew = self._read_skew(metadata)
+        shear = np.diag([1.0] * len(skew))
+        for i, val in enumerate(skew):
+            if val == 0:
+                continue
+            shear[i, i + 1] = np.tan(np.radians(val))
+        return shear
+
+    @staticmethod
+    def _read_skew(metadata: dict):
+        dimensions = metadata["ImageDocument"]["Metadata"]["Information"]["Image"]["Dimensions"]
+        res = [0.0] * 4
+        for i, dim in enumerate("TZYX"):
+            if dim not in dimensions:
+                continue
+            if f"{dim}AxisShear" not in dimensions[dim]:
+                continue
+
+            shear_value = dimensions[dim][f"{dim}AxisShear"]
+            if not shear_value.startswith("Skew"):
+                warnings.warn(f"Unknown shear value {shear_value}", stacklevel=1)
+                continue
+            res[i] = float(shear_value[4:])
+
+        return res
+
     @classmethod
     def update_array_shape(cls, array: np.ndarray, axes: str):
         if "B" in axes: