From 5b53094c6dee8b533ed6e132bde49dd353debefb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Wed, 29 Jun 2022 18:19:21 +0100
Subject: [PATCH] feat(image): Add ImageDirectory class
---
aliby/io/image.py | 44 ++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)
diff --git a/aliby/io/image.py b/aliby/io/image.py
index 83571b3e..257f5f6b 100644
--- a/aliby/io/image.py
+++ b/aliby/io/image.py
@@ -121,6 +121,50 @@ class ImageLocal:
return self._formatted_img
+class ImageDirectory(ImageLocal):
+ """
+ Image class for case where 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:
+ - Assumes individual folders for individual channels. If only one path provided it assumes it to be brightfield.
+ - Assumes that images are flat.
+ - Provides Dimorder as TCZYX
+ """
+
+ def __init__(self, path: t.Union[str, t.Dict[str, str]], *args, **kwargs):
+ if isinstance(path, str):
+ path = {"Brightfield": path}
+
+ self.path = path
+ self.image_id = str(path)
+ self._meta = dict(channels=path.keys(), name=list(path.values())[0])
+
+ # Parse name if necessary
+ # Build lazy-loading array using dask?
+
+ def get_data_lazy_local(self) -> da.Array:
+ """Return 5D dask array. For lazy-loading local multidimensional tiff files"""
+
+ img = da.stack([imread(v) for v in self.path.values()])
+ if (
+ img.ndim < 5
+ ): # Files do not include z-stack: Add and swap with time dimension.
+ img = da.stack((img,)).swapaxes(0, 2)
+
+ # TODO check whether x and y swap is necessary
+
+ # Use images to redefine axes
+ for i, dim in enumerate(("t", "c", "z", "y", "x")):
+ self._meta["size_" + dim] = img.shape[i]
+
+ self._formatted_img = da.rechunk(
+ img,
+ chunks=(1, 1, 1, self._meta["size_y"], self._meta["size_x"]),
+ )
+ return self._formatted_img
+
+
class Image(Argo):
"""
Loads images from OMERO and gives access to the data and metadata.
--
GitLab