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

Question

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

User · Answer

Note  until now posted solutions only work for png and jpg   If you want it even easier without importing further libraries or you want to display an animated or not animated GIF File in your Ipython Notebook  Transform the line where you want to display it to markdown and use this nice short hack     alt text  test gif  Title

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Courtesy of this page  I found this worked when the suggestions above didn t   import PIL Image from cStringIO import StringIO import IPython display import numpy as np def showarray a  fmt  png        a   np uint8 a      f   StringIO       PIL Image fromarray a  save f  fmt      IPython display display IPython display Image data f getvalue

User · Answer

Courtesy of this post  you can do the following   from IPython display import Image Image filename  test png       official docs

User · Answer

If you want to efficiently display big number of images I recommend using IPyPlot package  import ipyplot  ipyplot plot images images array  max images 20  img width 150      There are some other useful functions in that package where you can display images in interactive tabs  separate tab for each label class  which is very helpful for all the ML classification tasks

User · Answer

from IPython display import Image  Image filename  r C  user path    I ve seen some solutions and some wont work because of the raw directory  when adding codes like the one above  just remember to add  r  before the directory  this should avoid this kind of error   unicode error   unicodeescape  codec can t decode bytes in position 2-3  truncated  UXXXXXXXX escape

User · Answer

You could use in html code in markdown section  example     lt img src  https   www tensorflow org images colab logo 32px png    gt

User · Answer

If you are trying to display an Image in this way inside a loop  then you need to wrap the Image constructor in a display method   from IPython display import Image  display  listOfImageNames      path to images 1 png                         path to images 2 png    for imageName in listOfImageNames      display Image filename imageName

User · Answer

This will import and display a  jpg image in Jupyter  tested with Python 2 7 in Anaconda environment   from IPython display import display from PIL import Image   path   path to image jpg  display Image open path     You may need to install PIL  in Anaconda this is done by typing  conda install pillow

User · Answer

A cleaner Python3 version that use standard numpy  matplotlib and PIL  Merging the answer for opening from URL   import matplotlib pyplot as plt from PIL import Image import numpy as np  pil im   Image open  image png    Take jpg   png    Uncomment to open from URL  import requests  r   requests get  https   www vegvesen no public webkamera kamera id 131206    pil im   Image open BytesIO r content   im array   np asarray pil im  plt imshow im array  plt show

User · Answer

When using GenomeDiagram with Jupyter  iPython   the easiest way to display images is by converting the GenomeDiagram to a PNG image  This can be wrapped using an IPython display Image object to make it display in the notebook   from Bio Graphics import GenomeDiagram from Bio SeqFeature import SeqFeature  FeatureLocation from IPython display import display  Image gd diagram   GenomeDiagram Diagram  Test diagram   gd track for features   gd diagram new track 1  name  Annotated Features   gd feature set   gd track for features new set   gd feature set add feature SeqFeature FeatureLocation 25  75   strand  1   gd diagram draw format  linear   orientation  landscape   pagesize  A4                   fragments 1  start 0  end 100  Image gd diagram write to string  PNG       See Notebook

User · Answer

Another option for plotting inline from an array of images could be  import IPython def showimg a       IPython display display PIL Image fromarray a    where a is an array a shape  720  1280  3

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

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