Czifile v2026

napari_czifile2/_reader.py

@@ -24,7 +24,7 @@ def reader_function(paths):
         num_scenes = CZISceneFile.get_num_scenes(path)
         for scene_index in range(num_scenes):
             with CZISceneFile(path, scene_index) as f:
-                data = f.as_tzcyx0_array(max_workers=cpu_count())
+                data = f.as_tzcyx0_array(maxworkers=cpu_count())
                 # https://github.com/BodenmillerGroup/napari-czifile2/issues/5
                 contrast_limits = None
                 if data.dtype == np.uint16:

napari_czifile2/io.py

@@ -1,77 +1,74 @@
+from functools import cached_property
 from pathlib import Path
-from typing import Iterable, List, Optional, Union
+from typing import List, Optional, Union
 from xml.etree import ElementTree
 
 import numpy as np
-from czifile import CziFile, DimensionEntryDV1, DirectoryEntryDV
-from tifffile import lazyattr
+from czifile import CziDirectoryEntryDV, CziFile
 
 
 class CZISceneFile(CziFile):
     @staticmethod
     def get_num_scenes(path: Union[str, Path], *args, **kwargs) -> int:
         with CziFile(path, *args, **kwargs) as czi_file:
-            if "S" in czi_file.axes:
-                return czi_file.shape[czi_file.axes.index("S")]
-            return 1
+            return len(czi_file.scenes)
 
     def __init__(self, path: Union[str, Path], scene_index: int, *args, **kwargs):
         super(CZISceneFile, self).__init__(str(path), *args, **kwargs)
         self.scene_index = scene_index
+        self.axes = list(self.scenes[self.scene_index].sizes.keys())
 
-    @lazyattr
+    def _get_start(self, dim: str) -> int:
+        try:
+            return self.scenes[self.scene_index].start[self.axes.index(dim)]
+        except ValueError:
+            return 0
+
+    @cached_property
     def pos_x_um(self) -> float:
-        return self.scale_x_um * min(
-            (dim_entry.start for dim_entry in self._iter_dim_entries("X")), default=0.0
-        )
+        return self.scale_x_um * self._get_start("X")
 
-    @lazyattr
+    @cached_property
     def pos_y_um(self) -> float:
-        return self.scale_y_um * min(
-            (dim_entry.start for dim_entry in self._iter_dim_entries("Y")), default=0.0
-        )
+        return self.scale_y_um * self._get_start("Y")
 
-    @lazyattr
+    @cached_property
     def pos_z_um(self) -> float:
-        return self.scale_z_um * min(
-            (dim_entry.start for dim_entry in self._iter_dim_entries("Z")), default=0.0
-        )
+        return self.scale_z_um * self._get_start("Z")
 
-    @lazyattr
+    @cached_property
     def pos_t_seconds(self) -> float:
-        return self.scale_t_seconds * min(
-            (dim_entry.start for dim_entry in self._iter_dim_entries("T")), default=0.0
-        )
+        return self.scale_t_seconds * self._get_start("T")
 
-    @lazyattr
+    @cached_property
     def scale_x_um(self) -> float:
         return self._get_scale("X", multiplier=10.0**6)
 
-    @lazyattr
+    @cached_property
     def scale_y_um(self) -> float:
         return self._get_scale("Y", multiplier=10.0**6)
 
-    @lazyattr
+    @cached_property
     def scale_z_um(self) -> float:
         return self._get_scale("Z", multiplier=10.0**6)
 
-    @lazyattr
+    @cached_property
     def scale_t_seconds(self) -> float:
         return self._get_scale("T")
 
-    @lazyattr
+    @cached_property
     def channel_names(self) -> Optional[List[str]]:
         if "C" in self.axes:
             channel_elements = self._metadata_xml.findall(
                 ".//Metadata/Information/Image/Dimensions/Channels/Channel"
             )
-            if len(channel_elements) == self.shape[self.axes.index("C")]:
+            if len(channel_elements) == self.scenes[self.scene_index].sizes["C"]:
                 return [c.attrib.get("Name", c.attrib["Id"]) for c in channel_elements]
         return None
 
-    @lazyattr
+    @cached_property
     def is_rgb(self) -> bool:
-        return "0" in self.axes and self.shape[self.axes.index("0")] > 1
+        return "0" in self.axes and self.scenes[self.scene_index].sizes["0"] > 1
 
     def as_tzcyx0_array(self, *args, **kwargs) -> np.ndarray:
         data = self.asarray(*args, **kwargs)
@@ -105,12 +102,6 @@ def as_tzcyx0_array(self, *args, **kwargs) -> np.ndarray:
         data.shape = data.shape[:6]
         return data
 
-    def _iter_dim_entries(self, dimension: str) -> Iterable[DimensionEntryDV1]:
-        for dir_entry in self.filtered_subblock_directory:
-            for dim_entry in dir_entry.dimension_entries:
-                if dim_entry.dimension == dimension:
-                    yield dim_entry
-
     def _get_scale(self, dimension: str, multiplier: float = 1.0):
         scale_element = self._metadata_xml.find(
             f'.//Metadata/Scaling/Items/Distance[@Id="{dimension}"]/Value'
@@ -121,12 +112,12 @@ def _get_scale(self, dimension: str, multiplier: float = 1.0):
                 return scale * multiplier
         return 1.0
 
-    @lazyattr
+    @cached_property
     def _metadata_xml(self) -> ElementTree.Element:
         return ElementTree.fromstring(self.metadata())
 
-    @lazyattr
-    def filtered_subblock_directory(self) -> List[DirectoryEntryDV]:
+    @cached_property
+    def filtered_subblock_directory(self) -> List[CziDirectoryEntryDV]:
         dir_entries = super(CZISceneFile, self).filtered_subblock_directory
         return list(
             filter(
@@ -136,13 +127,6 @@ def filtered_subblock_directory(self) -> List[DirectoryEntryDV]:
         )
 
     @staticmethod
-    def _get_scene_index(dir_entry: DirectoryEntryDV) -> int:
-        scene_indices = {
-            dim_entry.start
-            for dim_entry in dir_entry.dimension_entries
-            if dim_entry.dimension == "S"
-        }
-        if len(scene_indices) == 0:
-            return 0
-        assert len(scene_indices) == 1
-        return scene_indices.pop()
+    def _get_scene_index(dir_entry: CziDirectoryEntryDV) -> int:
+        scene_index = dir_entry.scene_index
+        return 0 if scene_index == -1 else scene_index

setup.cfg

@@ -28,7 +28,7 @@ project_urls =
 [options]
 include_package_data = True
 install_requires =
-    czifile
+    czifile >= 2026
     imagecodecs
     numpy
     tifffile