From ff7e211ffe04538fe280f508a00d414c029c0a93 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Thu, 23 Jun 2022 13:59:05 +0100
Subject: [PATCH] hide internal imageviewer method and blackify
---
aliby/utils/imageViewer.py | 28 +++++++++++++++++++---------
1 file changed, 19 insertions(+), 9 deletions(-)
diff --git a/aliby/utils/imageViewer.py b/aliby/utils/imageViewer.py
index 3ab41aaa..11f66492 100644
--- a/aliby/utils/imageViewer.py
+++ b/aliby/utils/imageViewer.py
@@ -157,11 +157,14 @@ class remoteImageViewer:
imgs = self.get_trap_timepoints(trap_id, tps, **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
+ self.cells.at_time(tp, kind="edgemask").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)
+ np.dstack([mask * lbl for mask, lbl in zip(maskset, lblset)]).max(
+ axis=2
+ )
if len(lblset)
else np.zeros_like(imgs_list[0]).astype(bool)
for maskset, lblset in zip(outlines, lbls)
@@ -174,21 +177,24 @@ class remoteImageViewer:
"""
Wrapper to fetch images
"""
+ out = None
imgs = {}
- for ch in self.find_channels(channels):
+ for ch in self._find_channels(channels):
out, imgs[ch] = self.get_labeled_trap(
trap_id, trange, channels=[ch], **kwargs
)
return out, imgs
- def plot_labeled_zstacks(self, trap_id, channels, trange, z=None, **kwargs):
+ def plot_labeled_zstacks(
+ self, trap_id, channels, trange, z=None, **kwargs
+ ):
# if z is None:
# z =
- out, images = self.get_imgs(trap_id, trange, channels, z=z, **kwargs)
+ out, images = self.get_images(trap_id, trange, channels, z=z, **kwargs)
def plot_labeled_channelrows(self, trap_id, channels, trange, **kwargs):
- out, images = self.get_imgs(trap_id, trange, channels, **kwargs)
+ out, images = self.get_images(trap_id, trange, channels, **kwargs)
# dilation makes outlines easier to see
out = dilation(out).astype(float)
@@ -207,14 +213,18 @@ class remoteImageViewer:
interpolation=None,
)
plt.yticks(
- ticks=[self.tiler.tile_size * (i + 0.5) for i in range(len(channels))],
+ ticks=[
+ self.tiler.tile_size * (i + 0.5) for i in range(len(channels))
+ ],
labels=[
self.tiler.channels[ch] if isinstance(ch, int) else ch
for ch in channels
],
)
plt.xticks(
- ticks=[self.tiler.tile_size * (i + 0.5) for i in range(len(trange))],
+ ticks=[
+ self.tiler.tile_size * (i + 0.5) for i in range(len(trange))
+ ],
labels=[t for t in trange],
)
plt.show()
@@ -227,7 +237,7 @@ class remoteImageViewer:
remove_axis=False,
savefile=False,
skip_outlines=False,
- **kwargs
+ **kwargs,
):
"""
Wrapper to plot a single trap over time
--
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