A visualizer and related tools for Anna's thylakoid simulation data.
- Clone this repo and navigate to its top-level directory.
- Install wx for your platform: http://www.wxpython.org/download.php
- Install other dependencies:
pip install -r requirements.txt
On the command line, run ./pygs/visualizer.py
A GUI should appear.
Click "open files" and select particle coordinate files.
A sample configuration file is at tests/data/particle_config_L400.dat.
Clicking on a particle will toggle its tagged state, and write the particle identity to the terminal.
You can quit by clicking the close button, or by control-C on the command line.
- play: Play a movie starting from the current timepoint.
- draw PS frame: Draw the current screen as a postscript file.
- layers: Toggle the visibility of the bottom, top, and overlay views.
- movie controls > zoom: Set the zoom level of the view.
- initialize data > open files: Select particle coordinate files to load.
- initialize data > width / height: Set the width and height of the box, in nanometers. (This may be automatically set from the configuration file name.)
- colors: Set the base colors of tagged and untagged LHCII and PSII particles.
- color schemes: Toggle other color schemes. Play around with this one!
- tag within a rectangle: Tag all particles within a rectangle enclosed by xmin, xmax, ymin, and ymax, in nanometers.
- tag within a circle: Tag all particles within a circle centered on x, y with radius radius, in nanometers.