How can I show the pictures from folder figures in google colab inline in a markdown cell?
I have the following structure of notebooks on my local drive.
figures
- pic1.png
- pic2.png
- ...
Notebook1.ipynb
Notebook2.ipynb
etc.
After opening a Notebook in google colab and uploading the figures folder, I checked that the folder with pictures is actually uploaded. It is.
I then tried the following in a markdown cell:
This apparently doesn't work in google colab.
How did Jake VanderPlas do this here? Apparently he didn't even upload the pictures into a folder "figures" but still uses the following line in markdown
 in the above link (scroll down to see a picture on numpy arrays).
Any help is appreciated!
Thanks!
GitHib image references are resolved relative to the repo.
For notebooks stored in Drive, you'll need to embed the image in the notebook. Here's an example:
https://colab.research.google.com/drive/1jWHKR6rhhyZtUulttBD6Pxd_AJhgtVaV
The key bit is the Image display helper, applied to a local file–
from IPython.display import Image
Image('220px-TensorFlowLogo.svg.png')
Here is another way to show it.
##markdown Fig.1. Pic1 demo
import matplotlib.pyplot as plt
pic_name = '/content/drive/MyDrive/pic1.png'
image=plt.imread(pic_name)
fig=plt.figure(figsize=(20,30))
_=plt.imshow(image)
_=plt.axis('off')
Markdown tag shows text, which allows code hiding from the report (if that is your end goal).
Once you upload your local image to your Google Colab filesystem (click the folder icon on the upper left of your notebook that says "files", then upload it), you can use the IPython code to display it. You get the path link by right-clicking on the image after you uploaded it that says "copy path". Put the whole link in quotes.
from IPython import display
display.Image("/content/my-image.png")
Related
I have a Jupyter notebook with some images in the attachment that look like this:
<img src="attachment:media/image20.png" style="width:2.83in;height:2.85in" />
I wanted to use this image elsewhere, but I couldn't find the image file image20.png or the media folder anywhere on the hard drive. I guess the image file is somewhere inside the .ipynb itself.
My question is:
How to export the image file referenced by attachment:media/... to an actual .png file on the disk?
Note: I searched around on SO, and only found answers to export the output of a cell. e.g.
Jupyter Notebook: automatically saves all images
(, ... or saving the output of a maplotlib plot function.)
But the images above are not from the output of any code cell or code. I can see the image in the notebook, but not the actual .png file in the file system.
I am running Python 3.7 on Windows using pycharm. I have a jupyter notebook and I would like to embed an image into the notebook. I know all the ways of doing standard embedding with markdown language, BUT ideally what I want is:
a. Embed the image via markdown language, i.e. the notebook cell is in 'markdown' state, not 'Code' state, AND ALSO
b. Have it able to export to HTML and retain that image in the HTML file. i.e. on the notebook. I want to click File -> Download as -> HTML (.html), save the notebook file in .html format, and then when I send it to my buddy, the image that I attached is in the notebook, and he sees it.
I know i could do this in a cell ('code'):
from IPython.display import Image
Image(filename="myfile.jpg")
but I do not want to use 'Code', since when I send to my buddy, he will see the In [] code statement and the Out [] of the image in the notebook html file.
Note: This would be an image that was on my laptop that I would want in the html formatted exported notebook. It is NOT on the web where he could refer to it with a www type statement. Unless I'm crazy, there is no way to do this with markdown command in a cell, the only way to do it (with the image embedded 'permanently' into the .html format of the notebook), would be via a cell that was in 'Code' celltype.
When you use a code cell to show an image and then export the notebook to an HTML file, the image is converted to Base64 and the code directly used in the src attribute of the <img> tag. You can apply the same procedure with images included in markdown cells.
First, encode your image as Base64, e.g. by using one of the online enocders.
Create a markdown cell and include an <img> tag which uses your Base64 code, e.g.:
<img src="data:image/png;base64,CODE_FOLLOWS_HERE" />
Evaluate the cell and you should already see your image.
If you now export your notebook to HTML, the image should be included in the file the same way as images from code cells.
The only disadvantage with this approach is that your markdown cell gets cluttered with the (probably long) Base64 code. However, this is manageable by e.g. using a markdown cell dedicated solely to the image without other content.
You can install the Unofficial Jupyter Notebook Extensions.
It has some interesting extensions (e.g. spell checker, collapsible headings, ...). One of the extensions is Export HTML With Embedded Images which exactly does what you want.
To install Nbextensions using pip do the following:
$ pip install jupyter_contrib_nbextensions
$ pip install jupyter_nbextensions_configurator
$ jupyter contrib nbextension install --user
$ jupyter nbextensions_configurator enable --user
Then you will see in your Jupyter homepage a new tab (Nbextensions), where you can enable and configure different extension.
After enabling the "Export HTML With Embedded Images", you will see the corresponding option in the "File-Download as" menu.
My complete solution is based on Milania and
encoding-an-image-file-with-base64
how-to-base64-encode-an-image-using-python
BytesIO.getvalue
the code
import base64, io, IPython
from PIL import Image as PILImage
image = PILImage.open(image_path)
output = io.BytesIO()
image.save(output, format='PNG')
encoded_string = base64.b64encode(output.getvalue()).decode()
html = '<img src="data:image/png;base64,{}"/>'.format(encoded_string)
IPython.display.HTML(html)
For me, on Visual Studio Code, something like this did the trick (in a markdown cell, as you requested, and a image that you want to embed in your notebook and further be exported to the html output):
<figure>
<img src="./notebook_img/diptera_taxat_yes_no.jpg" width="200"/>
<figcaption>Limit the search on Diptera</figcaption>
</figure>
Where the image is located in "./notebook_img" relative to the location of the notebook (in this sense, the notebook is located in .)
Your buddy will not see the code from above when reading the HTML exported file, so that should satisfy the requested need as far as I understand. He will also not need the folder "notebook_img".
I'm working with Jupyter notebook and have a question in mind:
If I want to markdown an HTML file or any website, I can just simply do
[name-of-the-website](address-here)
and it will create a link to the page that I want to reference
My question is
Are there any markdown code for PDF reference
IS the code the same with HTML reference (whenver I click into the markdown link, It will create a new tab which can download the file to the computer)
P/s: I'm not talking about coverting the notebook into PDF file
I have found out an answer:
Go to the file PDF that you want to download, for example I want to download this PDF file
Ideas:
Because there should be a HTML link to download the document, if one can find this link, then can proceed to normal markdown HTML file in Jupyter Notebook
Steps:
On the browser, right-click that PDF download link, and then choose Inspect Element (Q) (on Firefox or any browser in use)
It is then open the console that will shown the download HTML file like shown:
href="http://www.montefiore.ulg.ac.be/services/stochastic/pubs/2009/DMWG09/dumont-visapp09-shortpaper.pdf"
One can proceed with normal markdown in Jupyter Notebook
This works for me:
ref.
This is a relative path to the file.
I have an ipython notebook with an embedded image from my local drive. I was expecting it to be embedded in the JSON along with the output of code cells, but when I distributed the notebook, the image did not appear to users. What is the recommended way (or ways) to embed an image in a Notebook, so that it doesn't disappear if users rerun code cells, clear cell output, etc.?
The notebook system caches images included with , but they last only until the python "kernel" serving the notebook is restarted. If I rename the image file on disk, I can close and reopen the notebook and it still shows the image; but it disappears when I restart the kernel.
Edit: If I generate an image as code cell output and then export the notebook to html, the image is embedded in the html as encoded data. Surely there must be a way to hook into this functionality and load the output into a markdown (or better yet "raw nbconvert") cell?
from IPython.display import Image
Image(filename='imagename.png')
will be exported (with ipython nbconvert) to html that contains the following:
<div class="output_png output_subarea output_execute_result">
<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAnAAAAFgCAYAAAA...
</div>
However, even when I manually embedded this snippet into a markdown cell, I couldn't get the image to display. What am I doing wrong?
Update (2020)
Apparently, the problem has (finally!) been addressed in the newer notebook / Jupyter versions: as of 2018 (thanks for the link #Wayne), the html sanitizer will accept an embedded html image, as in <img src="data:image/png;base64,iV...> . Markdown image syntax also accepts images as embedded data, so there are two ways to do this. Details in these helpful answers:
markdown image syntax (answer by #id01)
html element syntax (in answer by #tel -- note that it works now!)
Are you happy to use an extra code cell to display the image? If so, use this:
from IPython.display import Image
Image(filename="example.png")
The output cell will have the raw image data embedded in the .ipynb file so you can share it and the image will be retained.
Note that the Image class also has a url keyword, but this will only link to the image unless you also specify embed=True (see the documentation for details). So it's safer to use the filename keyword unless you are referring to an image on a remote server.
I'm not sure if there is an easy solution if you require the image to be included in a Markdown cell, i.e. without a separate code cell to generate the embedded image data. You may be able to use the python markdown extension which allows dynamically displaying the contents of Python variables in markdown cells. However, the extension generates the markdown cells dynamically, so in order to retain the output when sharing the notebook you will need to run ipython nbconvert --to notebook original_notebook.ipynb --output preprocessed_notebook using the preprocessor pymdpreprocessor.py as mentioned in the section "Installation". The generated notebook then has the data embedded in the markdown cell as an HTML tag of the form <img src="data:image/png;base64,..."> so you can delete the corresponding code cell from preprocessed_notebook.ipynb. Unfortunately, when I tried this the contents of the <img> tag weren't actually displayed in the browser, so not sure if this is a viable solution. :-/
A different option would be to use the Image class in a code cell to generate the image as above, and then use nbconvert with a custom template to remove code input cells from the notebook. See this thread for details. However, this will strip all code cells from the converted notebook, so it may not be what you want.
The reason why the
<img src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAnAAAAFgCAYAAAA...
tag doesn't do anything when you put it in a markdown cell is because IPython uses an HTML sanitizer (something called Google Caja) that screens out this type of tag (and many others) before it can be rendered.
The HTML sanitizer in IPython can be completely disabled by adding the following line to your custom.js file (usually located at ~/.ipython/profile_default/static/custom/custom.js):
iPython.security.sanitize_html = function (html) { return html; };
It's not a great solution though, as it does create a security risk, and it doesn't really help that much with distribution.
Postscript:
The ability to render base64 encoded strings as images != obvious security concern, so there should be a way for the Caja people to eventually allow this sort of thing through (although the related feature request ticket was first opened back in 2012, so don't hold your breath).
I figured out that replacing the image URL in the  with a base64 URL, similar to the ones found above, can embed an image in a markdown container.
Example markdown:
If using the IPython HTML() function to output raw HTML, you can embed a linked image in base64 inside an <img> tag using the following method:
import base64
import requests
from IPython.core.display import HTML
def embedded_image(url):
response = requests.get(url)
uri = ("data:" +
response.headers['Content-Type'] + ";" +
"base64," + str(base64.b64encode(response.content).decode('utf-8')))
return uri
# Here is a small example. When you export the notebook as HTML,
# the image will be embedded in the HTML file
html = f'<img src="{embedded_image("https://upload.wikimedia.org/wikipedia/commons/5/56/Kosaciec_szczecinkowaty_Iris_setosa.jpg")}" />'
HTML(html)
UPDATE: As pointed out by #alexis, this doesn't actually answer the question correctly, this will not allow users to re-run cells and have images persist (this solution only allows one to embed the images into exports).
As of Jupyter Notebook 5, you can attach image data to cells, and refer to them from the cell via attachment:<image-file-name>. See the menu Edit > Insert Image, or use drag and drop.
Unfortunately, when converting notebooks with attached (embedded) images to HTML, those images will not show up.
To get them into the HTML code, you can use (for instance) nbtoolbelt.
It will replace those attachment: references by data: with the image data embedded in the img tag.
Dear ipython notebook users,
I want to insert a link to a local file located in the notebook directory, and no, it is not an image (the only example I've found). I want to insert this link within a markdown cell.
When clicked on the link, the file is to be opened with a local application (in this case, a molecule viewer)
I've tried to come up with the correct syntax, but no luck. Please, any help is greatly appreciated.
I want to insert a link to a local file located in the notebook directory
I want to insert this link within a markdown cell.
The path need to be relative to where the server has been started, and prefixed with files/.
e.g: [my molecule](files/molecules/ethanol.mol)
the file is to be opened with a local application (in this case, a molecule viewer)
Not possible unless your application support custom links protocol like the itunes:// or apt-get:// one. the best that can append is that on link click you will be prompted to download the file. (keep in mind that the server can be on a different machine thant your browser)
completenting the answer of Matt, it will work only in you import FileLink
from IPython.display import FileLink, FileLinks
FileLink('path_to_file/filename.extension')
Then in a markdown cell insert your links waterBox30.pdb