From 13344669dd24040011f1d71d3ac9c32b6ea0fdad Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Tue, 28 Jun 2022 19:49:40 +0100
Subject: [PATCH] fix(imageViewer): passing tps, channels,cells.tp
---
aliby/utils/imageViewer.py | 18 +++++++++++-------
1 file changed, 11 insertions(+), 7 deletions(-)
diff --git a/aliby/utils/imageViewer.py b/aliby/utils/imageViewer.py
index c76ae14d..f252f331 100644
--- a/aliby/utils/imageViewer.py
+++ b/aliby/utils/imageViewer.py
@@ -211,17 +211,20 @@ class remoteImageViewer:
self,
trap_id: int,
tps: t.Union[range, t.Collection[int]],
+ channels=None,
+ concatenate=True,
**kwargs,
) -> t.Tuple[np.array]:
- imgs = self.get_pos_timepoints(tps, **kwargs)
+ """
+ Core method to fetch traps and labels together
+ """
+ imgs = self.get_pos_timepoints(tps, channels=channels, **kwargs)
imgs_list = [x[trap_id] for x in imgs.values()]
outlines = [
self.cells.at_time(tp, kind="edgemask").get(trap_id, [])
for tp in tps
]
- lbls = [
- self.cells.labels_at_time(tp - 1).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
@@ -230,9 +233,10 @@ class remoteImageViewer:
else np.zeros_like(imgs_list[0]).astype(bool)
for maskset, lblset in zip(outlines, lbls)
]
- outline_concat = np.concatenate(lbld_outlines, axis=1)
- img_concat = np.concatenate(imgs_list, axis=1)
- return outline_concat, img_concat
+ if concatenate:
+ lbld_outlines = np.concatenate(lbld_outlines, axis=1)
+ imgs_list = np.concatenate(imgs_list, axis=1)
+ return lbld_outlines, imgs_list
def get_images(self, trap_id, trange, channels, **kwargs):
"""
--
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