diff --git a/aliby/utils/imageViewer.py b/aliby/utils/imageViewer.py index 3ab41aaaaf28ce02643e0b96868c08a242e31d4e..11f6649211bdca15ab1b4649daede59d4952a82c 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