Closed amcrab closed 2 years ago
Wow, okay, I figured it out. (I'm such a noob, sorry!) It won't show on the Terminal without a plt.show()
command thrown in. For some reason, I didn't expect it to work like pyplot in that respect.
import squidpy as sq
import matplotlib.pyplot as plt
adata = sq.datasets.mibitof()
img = sq.im.ImageContainer(adata.uns["spatial"]["point16"]["images"]["hires"], library_id="point16")
img.show("image")
plt.show() # shows image on Terminal, yay!
-Angela
Great work on this awesome tool! I am eager to implement it in my WSI analysis workflow, but I've encountered a setback. The tutorial to show layers of the ImageContainer (
examples/image/compute_show.py
), won't show the image through the Terminal but does show the image when run in Jupyter Notebook.Viewing data from loop starting on line 26 works perfectly. However, running any
squidpy.im.ImageContainer.show()
function (lines 45 and 49) does not run correctly through MacOS terminal. A window (normally displaying a python-generated image) appears and disappears immediately.To reproduce the issue:
Any ideas would be much appreciated!
-Angela
My computer & conda env info MacOS: Big Sur v11.6.5 Processor 2.6 GHz 6-Core Intel Core i7 Python version: Python 3.9.12 SquidPy version: 1.2.2 MatPlotLib version: 3.5.2