FigureFirst

FigureFirst is a python 3.5+ library to decorate and parse SVG files so they can serve as layout documents for matplotlib figures. In principle FigureFirst works on python 2.7, but it is not officially supported.

• See our github page for readme and examples: http://flyranch.github.io/figurefirst/
• Read the docs: https://figurefirst.readthedocs.io/en/latest/index.html
• Read our Scipy 2017 proceedings: http://conference.scipy.org/proceedings/scipy2017/lindsay.html

If you use FigureFirst, please cite the above paper to help others find FigureFirst.

Installation

Install figurefirst using pip

pip install figurefirst

Installing figurefirst inkscape extensions

This package includes a console script, figurefirst_ext to install inkscape extensions. It tries to infer the default installation path for your OS (do figurefirst_ext --help to see what they are), or you can pass a path in manually, e.g..

figurefirst_ext ~/.config/inkscape/extensions

Quickstart

See http://flyranch.github.io/figurefirst/ for more detail, or follow the tutorial notebook: https://github.com/FlyRanch/figurefirst/blob/master/examples/tutorial/tutorial.ipynb

1. Create your figure template in Inkscape.
   • Make a rectangle for each panel, tag the panel using extensions > figurefirst > tagaxis, e.g. A or B
   • Group the rectangles (select all, ctrl-g), tag the group using extensions > figurefirst > tagfigure, e.g. fig1
   • Save your template, e.g. fifi_template.svg
2. In Python use the following commands to load, plot, and save:
   • import figurefirst as fifi
   • layout = fifi.svg_to_axes.FigureLayout('fifi_template.svg', autogenlayers=True, make_mplfigures=True, hide_layers=[])
   • For each axis, grab the axis handle using: ax = layout.axes[('fig1', 'B')]
   • Plot on that axis using matplotlib as usual
   • After you have plotted all panels, optionally update the aesthetics:
     • fifi.mpl_functions.adjust_spines(ax, ['left', 'bottom'])
     • fifi.mpl_functions.set_fontsize(ax, 6)
   • Add your figure to the layout using layout.append_figure_to_layer(layout.figures['fig1'], 'fig1', cleartarget=True)
   • Save your figure to the svg using layout.write_svg('fifi_template.svg'). Use a new name if you wish not to overwrite the template.
3. Note that you can have multiple figurefirst "figures" in a single svg file. Each figure will appear as a new layer.
4. If working in a jupyter notebook, you can display the figure using
   • from IPython.display import display,SVG
   • display(SVG('fifi_template.svg'))

Use with Inkscape

FigureFirst is developed and tested with Inkscape. Some versions and settings of Inkscape are very slow. Try Inkscape 0.92: https://inkscape.org/en/release/0.92.3/

Installing Inkscape 0.92 on Ubuntu

You can install Inkscape 0.92 using ppa:

• sudo add-apt-repository ppa:inkscape.dev/stable
• sudo apt update
• sudo apt install inkscape

Optimizing Inkscape settings

Try increasing the Rendering Tile Multiplier:

• Edit > Preference > Rending
• Rendering Tile Multiplier = 50 Restart Inkscape

Development

• Clone this repo
• Test locally by running pytest
  • To keep the test output files for inspection, add the --keep_files option
  • To test against all supported python versions, run tox
• Enable your github account with travis for continuous integration
• Raise a pull request