diff --git a/src/aliby/io/dataset.py b/src/aliby/io/dataset.py index e0f3b968856153cbb2cecb856722fc126efcfe3e..00e0fb02d1e48dffff6f25d0fe9bb6418b7f8ceb 100644 --- a/src/aliby/io/dataset.py +++ b/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")} diff --git a/src/aliby/io/image.py b/src/aliby/io/image.py index be15ae1b6a630aca0aaf4a9bec5d20d9736526aa..fca64f5dfa3e9cb16100b73e43d17d724f9885c2 100644 --- a/src/aliby/io/image.py +++ b/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]): diff --git a/src/aliby/tile/tiler.py b/src/aliby/tile/tiler.py index cddb2152262ddba9bb3cde5f94d49d69044b5d0f..f36492e010ec8b4349cb6bb29cd1820d5436b931 100644 --- a/src/aliby/tile/tiler.py +++ b/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, ):