How to Save IPython.core.display.SVG as PNG in Jupyter Notebook

Discover the best methods to save `IPython.core.display.SVG` as PNG files in a Jupyter Notebook environment without the hassle of errors.
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This video is based on the question https://stackoverflow.com/q/67189346/ asked by the user 'Mohammad' ( https://stackoverflow.com/u/9668218/ ) and on the answer https://stackoverflow.com/a/67194322/ provided by the user 'Oliver Scott' ( https://stackoverflow.com/u/8720000/ ) at 'Stack Overflow' website. Thanks to these great users and Stackexchange community for their contributions.

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The Problem: Saving SVG as PNG in Jupyter Notebook

If you find yourself trying to save images generated in Jupyter Notebook using IPython.core.display.SVG and want to convert them into PNG format, you're not alone. Many users have faced similar challenges as they encounter various errors and obstacles along the way. As you attempt to save a variable with the SVG data type as a PNG, issues like TypeError: a bytes-like object is required, not 'str' or file corruption may arise.

Understanding the Issue

The main problem arises when you try to write SVG data directly to a PNG file without proper conversion. The usual approach seems straightforward—write the SVG data to a file and then convert it. However, this can lead to confusion due to file formats and encoding issues.

Attempted Solutions

Initially, you might try to save your SVG data directly:

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This results in a TypeError because the data property needs to be encoded correctly. Moving forward, users often encounter errors like:

File opening errors: “The file ‘file.png’ could not be opened. It may be damaged or use a format that Preview doesn’t recognize.”

Encoding errors during conversion: ValueError: unknown locale: UTF-8.

The Solution: Direct PNG Creation

Instead of converting SVG files to PNG, it can be more effective to generate PNG images directly from your molecular structures using RDKit. This avoids the SVG format altogether and provides a seamless solution when working in Jupyter Notebook.

Step-by-Step Guide

Here’s how you can create a PNG file directly from your molecular data in RDKit:

Create Your Molecule:
Begin by defining the molecule using SMILES notation and importing necessary libraries.

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Setting Up PNG Drawing:
Use RDKit's drawing capabilities to directly create a PNG.

[[See Video to Reveal this Text or Code Snippet]]

Save Your PNG File:
Now, save the generated PNG data to a file.

[[See Video to Reveal this Text or Code Snippet]]

Extending with CairoSVG (if needed)

If you prefer to continue using SVGs and convert them to PNGs, you can do so with the cairosvg library while addressing encoding issues. Here’s a refined method:

[[See Video to Reveal this Text or Code Snippet]]

Conclusion

With these methods, you can efficiently save IPython.core.display.SVG images as PNG files in Jupyter Notebook without running into common errors. Whether you choose to create PNG images directly or convert from SVG with CairoSVG, you can streamline your workflow and avoid frustration.

Try these solutions in your next Jupyter project, and say goodbye to file format conversion headaches!