From 7206793a086d8d203cab702f39118cd96e7873a2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Thu, 5 Jan 2023 23:27:14 +0000
Subject: [PATCH] refactor(Image): Rename ImageLocal->ImageLocalOME
---
src/aliby/io/dataset.py | 4 ++--
src/aliby/io/image.py | 3 ++-
src/aliby/tile/tiler.py | 4 ++--
3 files changed, 6 insertions(+), 5 deletions(-)
diff --git a/src/aliby/io/dataset.py b/src/aliby/io/dataset.py
index e0f3b968..00e0fb02 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 be15ae1b..fca64f5d 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 cddb2152..f36492e0 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,
):
--
GitLab