refactor(Image): Rename ImageLocal->ImageLocalOME

src/aliby/io/dataset.py

@@ -7,7 +7,7 @@ from typing import Union
 import omero
 from agora.io.bridge import BridgeH5
 
-from aliby.io.image import ImageLocal
+from aliby.io.image import ImageLocalOME
 from aliby.io.omero import BridgeOmero
 
 
@@ -42,7 +42,7 @@ class DatasetLocal:
 
     @property
     def date(self):
-        return ImageLocal(list(self.get_images().values())[0]).date
+        return ImageLocalOME(list(self.get_images().values())[0]).date
 
     def get_images(self):
         return {f.name: str(f) for f in self.fpath.glob("*.tif")}

src/aliby/io/image.py

@@ -62,6 +62,7 @@ class BaseLocalImage(ABC):
         return self
 
     def format_data(self, img):
+        # Format image using x and y size from metadata.
 
         self._formatted_img = da.rechunk(
             img,
@@ -207,7 +208,7 @@ class ImageDir(BaseLocalImage):
     - One folders per position.
     - Images are flat.
     - Channel, Time, z-stack and the others are determined by filenames.
-    - Provides Dimorder as TCZYX
+    - Provides Dimorder as it is set in the filenames, or expects order during instatiation
     """
 
     def __init__(self, path: t.Union[str, PosixPath]):

src/aliby/tile/tiler.py

@@ -30,7 +30,7 @@ from skimage.registration import phase_cross_correlation
 
 from agora.abc import ParametersABC, ProcessABC
 from agora.io.writer import BridgeH5
-from aliby.io.image import Image, ImageLocal, ImageDir
+from aliby.io.image import Image, ImageLocalOME, ImageDir
 from aliby.tile.traps import segment_traps
 
 
@@ -262,7 +262,7 @@ class Tiler(ProcessABC):
     @classmethod
     def from_h5(
         cls,
-        image: t.Union[Image, ImageLocal, ImageDir],
+        image: t.Union[Image, ImageLocalOME, ImageDir],
         filepath: t.Union[str, PosixPath],
         parameters: TilerParameters = None,
     ):