How can I display an image from a file in Jupyter Notebook?

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I would like to use an IPython notebook as a way to interactively analyze some genome charts I am making with Biopython"s GenomeDiagram module. While there is extensive documentation on how to use matplotlib to get graphs inline in IPython notebook, GenomeDiagram uses the ReportLab toolkit which I don"t think is supported for inline graphing in IPython.

I was thinking, however, that a way around this would be to write out the plot/genome diagram to a file and then open the image inline which would have the same result with something like this:

gd_diagram.write("test.png", "PNG")
display(file="test.png")

However, I can"t figure out how to do this - or know if it"s possible. So does anyone know if images can be opened/displayed in IPython?

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How can I display an image from a file in Jupyter Notebook? around: Questions

Removing white space around a saved image in matplotlib

2 answers

I need to take an image and save it after some process. The figure looks fine when I display it, but after saving the figure, I got some white space around the saved image. I have tried the "tight" option for savefig method, did not work either. The code:

  import matplotlib.image as mpimg
  import matplotlib.pyplot as plt

  fig = plt.figure(1)
  img = mpimg.imread(path)
  plt.imshow(img)
  ax=fig.add_subplot(1,1,1)

  extent = ax.get_window_extent().transformed(fig.dpi_scale_trans.inverted())
  plt.savefig("1.png", bbox_inches=extent)

  plt.axis("off") 
  plt.show()

I am trying to draw a basic graph by using NetworkX on a figure and save it. I realized that without a graph it works, but when added a graph I get white space around the saved image;

import matplotlib.image as mpimg
import matplotlib.pyplot as plt
import networkx as nx

G = nx.Graph()
G.add_node(1)
G.add_node(2)
G.add_node(3)
G.add_edge(1,3)
G.add_edge(1,2)
pos = {1:[100,120], 2:[200,300], 3:[50,75]}

fig = plt.figure(1)
img = mpimg.imread("image.jpg")
plt.imshow(img)
ax=fig.add_subplot(1,1,1)

nx.draw(G, pos=pos)

extent = ax.get_window_extent().transformed(fig.dpi_scale_trans.inverted())
plt.savefig("1.png", bbox_inches = extent)

plt.axis("off") 
plt.show()
228

Answer #1

You can remove the white space padding by setting bbox_inches="tight" in savefig:

plt.savefig("test.png",bbox_inches="tight")

You"ll have to put the argument to bbox_inches as a string, perhaps this is why it didn"t work earlier for you.


Possible duplicates:

Matplotlib plots: removing axis, legends and white spaces

How to set the margins for a matplotlib figure?

Reduce left and right margins in matplotlib plot

228

Answer #2

I cannot claim I know exactly why or how my “solution” works, but this is what I had to do when I wanted to plot the outline of a couple of aerofoil sections — without white margins — to a PDF file. (Note that I used matplotlib inside an IPython notebook, with the -pylab flag.)

plt.gca().set_axis_off()
plt.subplots_adjust(top = 1, bottom = 0, right = 1, left = 0, 
            hspace = 0, wspace = 0)
plt.margins(0,0)
plt.gca().xaxis.set_major_locator(plt.NullLocator())
plt.gca().yaxis.set_major_locator(plt.NullLocator())
plt.savefig("filename.pdf", bbox_inches = "tight",
    pad_inches = 0)

I have tried to deactivate different parts of this, but this always lead to a white margin somewhere. You may even have modify this to keep fat lines near the limits of the figure from being shaved by the lack of margins.

We hope this article has helped you to resolve the problem. Apart from How can I display an image from a file in Jupyter Notebook?, check other around-related topics.

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Walter Chamberlet

London | 2022-12-07

I was preparing for my coding interview, thanks for clarifying this - How can I display an image from a file in Jupyter Notebook? in Python is not the simplest one. Will use it in my bachelor thesis

Chen OConnell

San Francisco | 2022-12-07

I was preparing for my coding interview, thanks for clarifying this - How can I display an image from a file in Jupyter Notebook? in Python is not the simplest one. I am just not quite sure it is the best method

Marie Lehnman

Munchen | 2022-12-07

Thanks for explaining! I was stuck with How can I display an image from a file in Jupyter Notebook? for some hours, finally got it done 🤗. Checked yesterday, it works!

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