Name		Name	Last commit message	Last commit date
parent directory ..
Ermentrout2009		Ermentrout2009
LotkaVolterra		LotkaVolterra
SimpsonGoodhill		SimpsonGoodhill
boundaries		boundaries
docs		docs
gl_compute		gl_compute
pi		pi
qt		qt
schnakenberg		schnakenberg
screenshots		screenshots
wx		wx
CMakeLists.txt		CMakeLists.txt
README.md		README.md
anneal_asa.cpp		anneal_asa.cpp
anneal_asa.json		anneal_asa.json
bike256.png		bike256.png
bike256_64.png		bike256_64.png
bike256_65.png		bike256_65.png
bootstrap.cpp		bootstrap.cpp
bootstrap.json		bootstrap.json
cartgrid.cpp		cartgrid.cpp
cartgrid_colourbar_repeat.cpp		cartgrid_colourbar_repeat.cpp
colourbar.cpp		colourbar.cpp
colourbar_interactive.cpp		colourbar_interactive.cpp
colourmap_browser.cpp		colourmap_browser.cpp
colourmap_test.cpp		colourmap_test.cpp
colourmaps_cet.cpp		colourmaps_cet.cpp
colourmaps_crameri.cpp		colourmaps_crameri.cpp
colourmaps_desaturating.cpp		colourmaps_desaturating.cpp
colourmaps_hsv1d.cpp		colourmaps_hsv1d.cpp
colourmaps_lenthe.cpp		colourmaps_lenthe.cpp
colourmaps_matplotlib.cpp		colourmaps_matplotlib.cpp
colourmaps_mono.cpp		colourmaps_mono.cpp
colourmaps_other.cpp		colourmaps_other.cpp
cone.cpp		cone.cpp
convolve.cpp		convolve.cpp
convolve_rect.cpp		convolve_rect.cpp
curvytelly.cpp		curvytelly.cpp
curvytelly_chequered_pipe.cpp		curvytelly_chequered_pipe.cpp
curvytelly_pipe.cpp		curvytelly_pipe.cpp
cyclic_colour.cpp		cyclic_colour.cpp
draw_triangles.cpp		draw_triangles.cpp
duochrome.cpp		duochrome.cpp
fps.cpp		fps.cpp
geodesic.cpp		geodesic.cpp
geodesic_ce.cpp		geodesic_ce.cpp
graph1.cpp		graph1.cpp
graph1.py		graph1.py
graph1_nomx.cpp		graph1_nomx.cpp
graph_bar.cpp		graph_bar.cpp
graph_change_xaxis.cpp		graph_change_xaxis.cpp
graph_coords.cpp		graph_coords.cpp
graph_dynamic_sine.cpp		graph_dynamic_sine.cpp
graph_dynamic_sine_rescale.cpp		graph_dynamic_sine_rescale.cpp
graph_dynamic_x2.cpp		graph_dynamic_x2.cpp
graph_fouraxes.cpp		graph_fouraxes.cpp
graph_histo.cpp		graph_histo.cpp
graph_incoming_data.cpp		graph_incoming_data.cpp
graph_incoming_data_rescale.cpp		graph_incoming_data_rescale.cpp
graph_line.cpp		graph_line.cpp
graph_line_xcross.cpp		graph_line_xcross.cpp
graph_logist.cpp		graph_logist.cpp
graph_logist2.cpp		graph_logist2.cpp
graph_logist2.json		graph_logist2.json
graph_rightaxis.cpp		graph_rightaxis.cpp
graph_twinax.cpp		graph_twinax.cpp
grating.cpp		grating.cpp
grid_border.cpp		grid_border.cpp
grid_border2.cpp		grid_border2.cpp
grid_flat_dynamic.cpp		grid_flat_dynamic.cpp
grid_image.cpp		grid_image.cpp
grid_layout.cpp		grid_layout.cpp
grid_mnist.cpp		grid_mnist.cpp
grid_resampled_image.cpp		grid_resampled_image.cpp
grid_simple.cpp		grid_simple.cpp
grid_simple_rand.cpp		grid_simple_rand.cpp
gridct_image.cpp		gridct_image.cpp
gridct_simple.cpp		gridct_simple.cpp
hdfdata.cpp		hdfdata.cpp
healpix.cpp		healpix.cpp
helloversion.cpp		helloversion.cpp
helloworld.cpp		helloworld.cpp
helloworld_nomx.cpp		helloworld_nomx.cpp
hexgrid.cpp		hexgrid.cpp
hexgrid_image.cpp		hexgrid_image.cpp
hexgrid_image_onsphere.cpp		hexgrid_image_onsphere.cpp
hexgrid_image_rect.cpp		hexgrid_image_rect.cpp
horsehead_reduced.png		horsehead_reduced.png
hsvwheel.cpp		hsvwheel.cpp
icosahedron.cpp		icosahedron.cpp
izhikevich.cpp		izhikevich.cpp
izhikevich.json		izhikevich.json
izhikevich_alt.cpp		izhikevich_alt.cpp
izhikevich_alt.json		izhikevich_alt.json
izhikevich_ardin.json		izhikevich_ardin.json
jsonconfig.cpp		jsonconfig.cpp
lighting_test.cpp		lighting_test.cpp
line.cpp		line.cpp
lines.cpp		lines.cpp
linregr.cpp		linregr.cpp

README.md

Example programs

This folder contains a set of example morphologica programs to help new users to get started using the library.

These examples will build alongside the unit tests when you do a morphologica build like this:

# Clone morphologica if you didn't already
git clone [email protected]/ABRG-Models/morphologica
cd morphologica
mkdir build
cd build
cmake ..
make
cd ..

You'll find the example program binaries in build/examples.

The examples are almost all built on the morph::Visual environment, which means you can interact with the mouse. Right-button down allows you to drag, Left-button down allows you to rotate. Press 't' to change the axis of rotations. Press 'h' and have a look at stdout to see some other key presses. 'x' exits. 'a' Resets the view.

Computational and scientific model examples

These are examples of models that we've re-implemented from the literature. These examples make use of most of the basic facilities in morphologic; morph::Config, morph::HdfData and morph::Visual.

convolve.cpp

An example demonstrating the use of morph::HexGrid, its HexGrid::convolve function, the morph::Random class and a visualization of the input, the convolution kernel and the resulting output.

logisticmap.cpp

Computes the logistic map and displays with a morph::GraphVisual, using diamond shaped markers.

rosenbrock.cpp

This program find the minimum of the Rosenbrock banana function using the Nelder-Mead simplex optimization method (coded as the class morph::NMSimplex). The walk of the simplex down the function surface is animated. Note that the scaling of the colour map is set so that only the lowest part of the surface is resolved in the green to blue part of the map (which is Inferno)

Ermentrout2009

Contains an implementation of a Keller-Segel reaction diffusion system.

From the base of morphologica, run like this (the program needs to access the file ./boundaries/whiskerbarrels.svg):

/build/examples/Ermentrout2009/erm ./examples/Ermentrout2009/configs/erm.json

LotkaVolterra

Contains an implementation of the Lotka-Volterra population model cast as a reaction diffusion system.

SimpsonGoodhill

Contains an implementation of the model described in the paper 'A simple model can unify a broad range of phenomena in retinotectal map development', Biological Cybernetics, 2011, by Hugh Simpson and Geoffrey Goodhill. This one is notable because it is an agent based model, rather than a reaction diffusion model. Proof that morphologica is useful for many different types of model! The image shows results for the wildtype model, Figs 2B to 2D in the paper, with parameters exactly as given in the paper.

From the base of morphologica, run like this:

/build/examples/SimpsonGoodhill/sg ./examples/SimpsonGoodhill/sg.json

morph::Visual examples

These simple examples showcase the features in morphologica's morph::Visual code. They're a useful place to see what the code can do for data visualization.

visual.cpp

An example morph::Visual program which shows a morph::HexGrid and some text labels.

fps.cpp

A dynamic HexGrid program showing an animated surface

hexgrid.cpp

Example HexGridVisual

hexgrid_image

Creates a HexGrid, then uses HexGrid::resampleImage to load a picture.

cartgrid.cpp

Example Cartesian grid (CartGridVisual)

quiver.cpp

An example quiver plot using morph::QuiverVisual.

scatter.cpp

An example three dimensional scatter plot of spheres using morph::ScatterVisual. Note that in this example, the coordinate arrows are set within the scene (and so move with the model).

graph1.cpp to graph4.cpp

Various examples of the use of morph::GraphVisual.

twowindows.cpp

An example to show how to create two morph::Visuals, and hence two windows, in your program.

rods.cpp

An example of the very simple VisualModel, morph::RodVisual, which simply draws a polygonal rod. You can specify how many sides, so this can be used to draw rods of square section, or rods which appear to be cylindrical.

quads.cpp

An example of morph::QuadsVisual.

pointrows.cpp

An example of morph::PointRowsVisual, which is used to render a surface made of adjacent rows of points.

This program is also conditially compiled into the exectuable pointrows_mesh, which renders the same points as a ball-and-stick mesh.

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examples

examples

README.md

Example programs

Computational and scientific model examples

convolve.cpp

logisticmap.cpp

rosenbrock.cpp

Ermentrout2009

LotkaVolterra

SimpsonGoodhill

morph::Visual examples

visual.cpp

fps.cpp

hexgrid.cpp

hexgrid_image

cartgrid.cpp

quiver.cpp

scatter.cpp

graph1.cpp to graph4.cpp

twowindows.cpp

rods.cpp

quads.cpp

pointrows.cpp

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examples

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examples

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parent directory

README.md

Example programs

Computational and scientific model examples

convolve.cpp

logisticmap.cpp

rosenbrock.cpp

Ermentrout2009

LotkaVolterra

SimpsonGoodhill

morph::Visual examples

visual.cpp

fps.cpp

hexgrid.cpp

hexgrid_image

cartgrid.cpp

quiver.cpp

scatter.cpp

graph1.cpp to graph4.cpp

twowindows.cpp

rods.cpp

quads.cpp

pointrows.cpp