From 1ebd37bd479fdf82f00902233fe3f946cd3927ac Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Tue, 3 Jan 2023 14:30:26 +0000
Subject: [PATCH] tweak(meta): Create ABC for ImageLocal
---
src/aliby/io/image.py | 50 ++++++++++++++++++++++++++++---------------
1 file changed, 33 insertions(+), 17 deletions(-)
diff --git a/src/aliby/io/image.py b/src/aliby/io/image.py
index 3cedb17b..290d5d80 100644
--- a/src/aliby/io/image.py
+++ b/src/aliby/io/image.py
@@ -47,9 +47,22 @@ def get_image_class(source: t.Union[str, int, t.Dict[str, str], PosixPath]):
return instatiator
-class ImageLocal:
+class BaseLocalImage:
+ """
+ Base class to set path and provide context management method.
+ """
+
+ def __init__(self, path: t.Union[str, PosixPath]):
+ # If directory, assume contents are naturally sorted
+ self.path = Path(path)
+
+ def __enter__(self):
+ return self
+
+
+class ImageLocal(BaseLocalImage):
def __init__(self, path: str, dimorder=None):
- self.path = path
+ super().__init__(path)
self._id = str(path)
meta = dict()
@@ -154,16 +167,26 @@ class ImageLocal:
reshaped, range(len(reshaped.shape)), target_order
)
- self._formatted_img = da.rechunk(
- img,
- chunks=(1, 1, 1, self._meta["size_y"], self._meta["size_x"]),
- )
+ return self.format_data(img)
+
+ def format_data(self, img):
+
+ self._formatted_img = da.rechunk(
+ img,
+ chunks=(
+ 1,
+ 1,
+ 1,
+ *[self._meta[f"size_{n}"] for n in self.dimorder[-2:]],
+ ),
+ )
return self._formatted_img
class ImageDir(ImageLocal):
"""
- Image class for case where all images are split in one or multiple folders with time-points and channels as independent files.
+ Image class for the case in which all images are split in one or
+ multiple folders with time-points and channels as independent files.
It inherits from Imagelocal so we only override methods that are critical.
Assumptions:
@@ -174,9 +197,7 @@ class ImageDir(ImageLocal):
"""
def __init__(self, path: t.Union[str, PosixPath]):
-
- # Assume they are naturally sorted
- self.path = Path(path)
+ super().__init__(path)
self.image_id = str(self.path.stem)
filenames = list(self.path.glob("*.tiff"))
@@ -220,13 +241,8 @@ class ImageDir(ImageLocal):
img = img[..., 0]
self._meta["size_x"], self._meta["size_y"] = img.shape[-2:]
- reshaped = da.reshape(img, (*self._dim_shapes, *img.shape[1:]))
-
- self._formatted_img = da.rechunk(
- reshaped,
- chunks=(1, 1, 1, self._meta["size_y"], self._meta["size_x"]),
- )
- return self._formatted_img
+ img = da.reshape(img, (*self._dim_shapes, *img.shape[1:]))
+ return self.format_data(img)
class Image(BridgeOmero):
--
GitLab