From 29a51323da9f703e9226ea14424d3611b882f9fa Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Fri, 25 Mar 2022 18:45:50 +0000
Subject: [PATCH] bugfix methods imageviewer
---
aliby/utils/imageViewer.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/aliby/utils/imageViewer.py b/aliby/utils/imageViewer.py
index 32281a11..50e5b088 100644
--- a/aliby/utils/imageViewer.py
+++ b/aliby/utils/imageViewer.py
@@ -89,7 +89,7 @@ class remoteImageViewer:
with OImage(self.image_id, **server_info) as image:
self.tiler.image = image.data
- return self.tiler.get_tc(tp, riv.tiler.ref_channel)
+ return self.tiler.get_tc(tp, self.tiler.ref_channel)
def get_trap_timepoints(self, trap_id, tps, server_info=None):
server_info = server_info or self.server_info
@@ -110,9 +110,9 @@ class remoteImageViewer:
imgs = self.get_trap_timepoints(trap_id, tps)
imgs_list = [x[trap_id] for x in imgs.values()]
outlines = [
- riv.cells.at_time(tp, kind="edgemask").get(trap_id, []) for tp in tps
+ self.cells.at_time(tp, kind="edgemask").get(trap_id, []) for tp in tps
]
- lbls = [riv.cells.labels_at_time(tp).get(trap_id, []) for tp in tps]
+ lbls = [self.cells.labels_at_time(tp).get(trap_id, []) for tp in tps]
lbld_outlines = [
np.dstack([mask * lbl for mask, lbl in zip(maskset, lblset)]).max(axis=2)
if len(lblset)
@@ -133,7 +133,7 @@ class remoteImageViewer:
:trange: list list of time points to fetch
"""
nrows = len(trange) // ncols
- width = riv.tiler.tile_size * ncols
+ width = self.tiler.tile_size * ncols
out, img = self.get_labeled_trap(trap_id, trange)
# dilation makes outlines easier to see
--
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