Substrate heatmaps in SVGs, defined in config file

[drbergman]

This extends the functionality of plotting substrate heatmaps on SVG output:

• Allows for all colormaps permitted in studio for visualizing substrate concentrations
• Allows for configuration of this heatmap in the XML configuration file
• updates all sample projects so that they can use this functionality just by enabling SVG substrate plots in the XML

To utilize this, open a new project with the herein-modified template project and skip to Step 3 below. To make use of this in an existing project, do the following:

1. Add the following line in main.cpp. Immediately after defining cell_coloring_function works.

std::string (*substrate_coloring_function)(double, double, double) = paint_by_density_percentage;

2. Replace calls of SVG_plot in main.cpp with the following. There are likely 3 calls to replace.

SVG_plot( filename , microenvironment, 0.0 , PhysiCell_globals.current_time, cell_coloring_function, substrate_coloring_function );

3. Replace the <SVG> node with the following block to the configuration file, e.g. config/PhysiCell_settings.xml. The colormap element can be any of YlOrRd, viridis, turbo, jet, plasma, original, or any of these with _r appended to reverse the colormap.

		<SVG>
			<interval units="min">60</interval>
			<enable>true</enable>
			<plot_substrate enabled="true" limits="false">
				<substrate>substrate</substrate>
				<min_conc>0</min_conc>
				<max_conc>1</max_conc>
				<colormap>viridis_r</colormap>
			</plot_substrate>
		</SVG>

[drbergman]

Including previous discussions from PR #204 here:

Original PR message:

Two main changes being suggested here:

Make SVG plots with substrates easier: Add the substrate_coloring_function to the template main.cpp and pass it into the three calls to SVG_plot so that all projects starting from there can include the substrate plot in SVGs just by configuring via xml or studio. If it is not set, SVG_plot already cleverly ignores all this, even if not specified. In other words, it should not cause errors. Make SVG plots with substrates more configurable: Allow users to specify the colormap used in plotting the substrate in SVGs. Options include all those included in studio as well as their reverse values. Marco Ruscone's original colormap is included as original. Default, however, is YlOrRd. The list of colormap names is then {"original","YlOrRd","viridis","turbo","jet","plasma"} as well as any of these with a "_r" appended to indicate it is reversed. Minor change: substrate_coloring_function originally returned a vector of 4 strings, probably because it started from the cell_coloring_function template which uses four colors. However, only one of substrate_coloring_function were used, so that is now reflected in the code.

Most of the lines added are simply the specifications for turbo, jet, and plasma. These have higher resolution because it was when I was adding those that I realized I could easily get Matlab to print out what I needed to specify these colormaps to arbitrary precision.

Update on studio implementation

Follow up: the implementation in studio is already done and passed preliminary testing (just me).

Inclusion of other PR changes

Changes made in #216 included here as well.