From 0b9e6e72443fbd657d09b6ea2d34d3bf4747b846 Mon Sep 17 00:00:00 2001
From: Andrey Aristov <aaristov@pasteur.fr>
Date: Sat, 26 Mar 2022 23:30:47 +0100
Subject: [PATCH] auto names and channel axis
---
src/napari_segment/_reader.py | 11 +++++++----
1 file changed, 7 insertions(+), 4 deletions(-)
diff --git a/src/napari_segment/_reader.py b/src/napari_segment/_reader.py
index c86f0cd..063b83b 100644
--- a/src/napari_segment/_reader.py
+++ b/src/napari_segment/_reader.py
@@ -38,10 +38,11 @@ def napari_get_reader(path):
def read_nd2(path):
+ print(f"opening {path}")
data = nd2.ND2File(path)
ddata = data.to_dask()
try:
- channel_axis = list(d.sizes.keys()).index('C')
+ channel_axis = list(data.sizes.keys()).index("C")
except ValueError:
channel_axis = None
return [
@@ -49,9 +50,11 @@ def read_nd2(path):
ddata,
dict(
channel_axis=channel_axis,
- name=["BF", "fluo"],
- colormap=["gray", "green"],
- contrast_limits=[(8500, 35000), (150, 20000)],
+ name=[ch.channel.name for ch in data.metadata.channels],
+ # colormap=[hex(ch.channel.colorRGB)
+ # for ch in data.metadata.channels],
+ # scale=data.metadata.channels[0].volume.axesCalibration[:]
+ # contrast_limits=[(8500, 35000), (150, 20000)],
),
"image",
)
--
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