From ce07a3333920de29d40ccb675792a43d6a66b52d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Wed, 4 Jan 2023 13:55:36 +0000
Subject: [PATCH] [WIP]feat(meta): bring back default get_data_lazy
---
src/aliby/io/image.py | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
diff --git a/src/aliby/io/image.py b/src/aliby/io/image.py
index 2f6132d5..35d454d7 100644
--- a/src/aliby/io/image.py
+++ b/src/aliby/io/image.py
@@ -332,3 +332,30 @@ class UnsafeImage(Image):
except Exception as e:
print(f"ERROR: Failed fetching image from server: {e}")
self.conn.connect(False)
+
+
+def get_data_lazy(image) -> da.Array:
+ """
+ Get 5D dask array, with delayed reading from OMERO image.
+ """
+ nt, nc, nz, ny, nx = [getattr(image, f"getSize{x}")() for x in "TCZYX"]
+ pixels = image.getPrimaryPixels()
+ dtype = PIXEL_TYPES.get(pixels.getPixelsType().value, None)
+ # using dask
+ get_plane = delayed(lambda idx: pixels.getPlane(*idx))
+
+ def get_lazy_plane(zct):
+ return da.from_delayed(get_plane(zct), shape=(ny, nx), dtype=dtype)
+
+ # 5D stack: TCZXY
+ t_stacks = []
+ for t in range(nt):
+ c_stacks = []
+ for c in range(nc):
+ z_stack = []
+ for z in range(nz):
+ z_stack.append(get_lazy_plane((z, c, t)))
+ c_stacks.append(da.stack(z_stack))
+ t_stacks.append(da.stack(c_stacks))
+
+ return da.stack(t_stacks)
--
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