From baa450a38ebe373a34b8cb9b27aada5e29620f22 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Fri, 17 Feb 2023 20:05:27 +0000
Subject: [PATCH] fix(tiler): Set default size_c metadata
---
src/aliby/tile/tiler.py | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/src/aliby/tile/tiler.py b/src/aliby/tile/tiler.py
index 34aa89d1..aaaa5474 100644
--- a/src/aliby/tile/tiler.py
+++ b/src/aliby/tile/tiler.py
@@ -232,8 +232,9 @@ class Tiler(StepABC):
self.image = image
self._metadata = metadata
self.channels = metadata.get(
- "channels", list(range(metadata["size_c"]))
+ "channels", list(range(metadata.get("size_c", 0)))
)
+
self.ref_channel = self.get_channel_index(parameters.ref_channel)
self.trap_locs = trap_locs
@@ -352,7 +353,10 @@ class Tiler(StepABC):
-------
full: an array of images
"""
- full = self.image[t, c].compute(scheduler="synchronous")
+ full = self.image[t, c]
+ if hasattr(full, "compute"): # If using dask fetch images here
+ full = full.compute(scheduler="synchronous")
+
return full
@property
--
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