margrietpalm/visgrid3d-python

Original python-based version of VisGrid3D

Visualizing 3D grid data

Installation

Dependencies

• Python 2.7
• Numpy
• Matplotlib
• VTK with Python bindings
• im2movie installed as library in the python path (only needed for creating movies)

Set up as command line program

1. Make script executable: chmod +x visualizer.py
2. Create a link to visualizer.py in a folder in your PATH. For example, when you have a bin folder in your home that is in your PATH: ln -s /path/to/VisGrid3D/visualizer.py /home/USERNAME/bin/visgrid3D
3. Now you can run the script with visgrid3D

Python library

Place VisGrid3D folder in the python path and have a look at the documentation.

Generating VTK files in Morpheus

Morpheus can generate VTK files with the VtkPlotter analysis plugin. Set up this plugin to write ascii files and to store the cell id and cell type:

<VtkPlotter mode="ascii" time-step="10">
	<Channel symbol-ref="cell.id"/>
	<Channel symbol-ref="cell.type"/>
</VtkPlotter>

Note that VTK files can become quite large. So keep the number of output files low during testing, or remove them.

Usage

To animate the results you must at least specify the folder containing the vtk files (-i) and the cell types to animate (-t). All other command line arguments are optimal and use defaults if not specify.

Examples

• Plot cell types 0 and 2 for results in morphesu/3d_migration_138/:

visgrid3D -i morpheus/3d_migration_138/ -t 0 2

• Colors and opacity can be defined per cell type:

visgrid3D -i morpheus/3d_migration_138/ -t 0 2 -c red grey -a 1 0.1

• Static (frozen) cell types can be defined such that they are only rendered once:

visgrid3D -i morpheus/3d_migration_138/ -t 0 2 -c red grey -a 1 0.1 --static 2

• Save snapshots and make movie from those snapshots when the visualization windows is closed

visgrid3D -i morpheus/3d_migration_138/ -t 0 2 -c red grey -a 1 0.1 --static 2 -s -m

Help

visgrid3D -h
usage: animate_morpheus_3D [-h] -i SIMDIR [-w WINSIZE WINSIZE] -t
                           [CELLTYPES [CELLTYPES ...]]
                           [-c [COLORS [COLORS ...]]] [-a [ALPHA [ALPHA ...]]]
                           [--static [STATIC [STATIC ...]]]
                           [--bboxcolor BBOXCOLOR BBOXCOLOR BBOXCOLOR]
                           [--bgcolor BGCOLOR BGCOLOR BGCOLOR]
                           [--camposition CAMPOSITION CAMPOSITION CAMPOSITION]
                           [--camfocus CAMFOCUS CAMFOCUS CAMFOCUS]
                           [--steps [STEPS [STEPS ...]]] [-f FPS] [-o OUTDIR]
                           [-p IMPREFIX] [-s] [-m] [--win] [--mp4]

optional arguments:
  -h, --help            show this help message and exit
  -i SIMDIR, --simdir SIMDIR
                        Simulation folder
  -w WINSIZE WINSIZE, --winsize WINSIZE WINSIZE
                        window size
  -t [CELLTYPES [CELLTYPES ...]], --celltypes [CELLTYPES [CELLTYPES ...]]
                        cell types to animate
  -c [COLORS [COLORS ...]], --colors [COLORS [COLORS ...]]
                        colors or the cell types
  -a [ALPHA [ALPHA ...]], --alpha [ALPHA [ALPHA ...]]
                        opacity of the cell types
  --static [STATIC [STATIC ...]]
                        static cell types (will NOT be updated during
                        animation)
  --bboxcolor BBOXCOLOR BBOXCOLOR BBOXCOLOR
                        bounding box color
  --bgcolor BGCOLOR BGCOLOR BGCOLOR
                        background color
  --camposition CAMPOSITION CAMPOSITION CAMPOSITION
                        camera position
  --camfocus CAMFOCUS CAMFOCUS CAMFOCUS
                        camera focal point
  --steps [STEPS [STEPS ...]]
                        steps to animate, all steps will be shown if this is
                        not specified
  -f FPS, --fps FPS     frames per second
  -o OUTDIR, --outdir OUTDIR
                        output directory
  -p IMPREFIX, --imprefix IMPREFIX
                        image prefix
  -s, --saveim          save images
  -m, --movie           make movie
  --readall             read all data at once before the visualization starts
  --savemem             reread vtk file every time it is used instead of
                        keeping it in memory  
  --win                 make movie windows compatible
  --mp4                 make mp4 movie