From e845e203800e743e5aaa600a577330e96b14ecde Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <amuoz@ed.ac.uk>
Date: Wed, 29 Jun 2022 18:30:30 +0100
Subject: [PATCH] docs/feat(imageviewer):add outline transparency
---
aliby/utils/imageViewer.py | 42 +++++++++++++++++++++++++++++++++++++-
1 file changed, 41 insertions(+), 1 deletion(-)
diff --git a/aliby/utils/imageViewer.py b/aliby/utils/imageViewer.py
index 5341f469..6b158a32 100644
--- a/aliby/utils/imageViewer.py
+++ b/aliby/utils/imageViewer.py
@@ -274,10 +274,50 @@ class remoteImageViewer:
skip_outlines: bool = False,
norm: str = None,
ncols: int = None,
+ local_colours: bool = True,
img_plot_kwargs: dict = {},
- lbl_plot_kwargs: dict = {},
+ lbl_plot_kwargs: dict = {"alpha": 0.8},
**kwargs,
):
+ """Wrapper to plot time-lapses of individual traps
+
+ Use Cells and Tiler to generate images of cells with their resulting
+ outlines.
+
+ Parameters
+ ----------
+ trap_id : int
+ Identifier of trap
+ channels : Union[str, int]
+ Channels to use
+ trange : t.Union[range, t.Collection[int]]
+ Range or collection indicating the time-points to use.
+ remove_axis : bool
+ None, "off", or "x". Determines whether to remove the x-axis, both
+ axes or none.
+ savefile : str
+ Saves file to a location.
+ skip_outlines : bool
+ Do not add overlay with outlines
+ norm : str
+ Normalise signals
+ ncols : int
+ Number of columns to plot.
+ local_colours : bool
+ Bypass label indicators to guarantee that colours are not repeated
+ (TODO implement)
+ img_plot_kwargs : dict
+ Arguments to pass to plt.imshow used for images.
+ lbl_plot_kwargs : dict
+ Keyword arguments to pass to label plots.
+ **kwargs : dict
+ Additional keyword arguments passed to ImageViewer.get_images.
+
+ Examples
+ --------
+ FIXME: Add docs.
+
+ """
if ncols is None:
ncols = len(trange)
nrows = int(np.ceil(len(trange) / ncols))
--
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