From 95675a7e44f434122494b61b8e1b75946aac8a59 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Sat, 7 Jan 2023 00:36:22 +0000
Subject: [PATCH] [WIP]feat(tiler): support metaless local expts
---
src/aliby/tile/tiler.py | 29 +++++++++++++++--------------
1 file changed, 15 insertions(+), 14 deletions(-)
diff --git a/src/aliby/tile/tiler.py b/src/aliby/tile/tiler.py
index f36492e0..f022971c 100644
--- a/src/aliby/tile/tiler.py
+++ b/src/aliby/tile/tiler.py
@@ -231,16 +231,16 @@ class Tiler(ProcessABC):
super().__init__(parameters)
self.image = image
self._metadata = metadata
- self.channels = metadata["channels"]
+ self.channels = metadata.get(
+ "channels", list(range(metadata["size_c"]))
+ )
self.ref_channel = self.get_channel_index(parameters.ref_channel)
self.trap_locs = trap_locs
try:
self.z_perchannel = {
- ch: metadata["zsectioning/nsections"] if zsect else 1
- for zsect, ch in zip(
- metadata["channels"], metadata["channels/zsect"]
- )
+ ch: zsect
+ for ch, zsect in zip(self.channels, metadata["zsections"])
}
except Exception as e:
print(f"Warning:Tiler: No z_perchannel data: {e}")
@@ -555,20 +555,21 @@ class Tiler(ProcessABC):
def ref_channel_index(self):
return self.get_channel_index(self.parameters.ref_channel)
- def get_channel_index(self, item):
+ def get_channel_index(self, channel: str or int):
"""
Find index for channel using regex. Returns the first matched string.
Parameters
----------
- item: string
- The channel
- """
- channel = find_channel_index(self.channels, item)
- if channel is None:
- raise Warning(
- f"Reference channel {channel} not in the available channels: {self.channels}"
- )
+ channel: string or int
+ The channel or index to be used
+ """
+ if isinstance(channel, str):
+ channel = find_channel_index(self.channels, channel)
+ if channel is None:
+ raise Warning(
+ f"Reference channel {channel} not in the available channels: {self.channels}"
+ )
return channel
@staticmethod
--
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