Tag: PhysiCell_Friday

PhysiCell Tools : PhysiCell-povwriter

As PhysiCell matures, we are starting to turn our attention to better training materials and an ecosystem of open source PhysiCell tools. PhysiCell-povwriter is is designed to help transform your 3-D simulation results into 3-D visualizations like this one:

PhysiCell-povwriter transforms simulation snapshots into 3-D scenes that can be rendered into still images using POV-ray: an open source software package that uses raytracing to mimic the path of light from a source of illumination to a single viewpoint (a camera or an eye). The result is a beautifully rendered scene (at any resolution you choose) with very nice shading and lighting.

If you repeat this on many simulation snapshots, you can create an animation of your work.

What you’ll need

This workflow is entirely based on open source software:

Setup

Building PhysiCell-povwriter

After you clone PhysiCell-povwriter or download its source from a release, you’ll need to compile it. In the project’s root directory, compile the project by:

make

(If you need to set up a C++ PhysiCell development environment, click here for OSX or here for Windows.)

Next, copy povwriter (povwriter.exe in Windows) to either the root directory of your PhysiCell project, or somewhere in your path. Copy ./config/povwriter-settings.xml to the ./config directory of your PhysiCell project.

Editing resolutions in POV-ray

PhysiCell-povwriter is intended for creating “square” images, but POV-ray does not have any pre-created square rendering resolutions out-of-the-box. However, this is straightforward to fix.

  1. Open POV-Ray
  2. Go to the “tools” menu and select “edit resolution INI file”
  3. At the top of the INI file (which opens for editing in POV-ray), make a new profile:
    [1080x1080, AA]
    Width=480
    Height=480
    Antialias=On
    

  4. Make similar profiles (with unique names) to suit your preferences. I suggest one at 480×480 (as a fast preview), another at 2160×2160, and another at 5000×5000 (because they will be absurdly high resolution). For example:
    [2160x2160 no AA]
    Width=2160
    Height=2160
    Antialias=Off
    

    You can optionally make more profiles with antialiasing on (which provides some smoothing for areas of high detail), but you’re probably better off just rendering without antialiasing at higher resolutions and the scaling the image down as needed. Also, rendering without antialiasing will be faster.

  5. Once done making profiles, save and exit POV-Ray.
  6. The next time you open POV-Ray, your new resolution profiles will be available in the lefthand dropdown box.

Configuring PhysiCell-povwriter

Once you have copied povwriter-settings.xml to your project’s config file, open it in a text editor. Below, we’ll show the different settings.

Camera settings

<camera>
	<distance_from_origin units="micron">1500</distance_from_origin>
	<xy_angle>3.92699081699</xy_angle> <!-- 5*pi/4 -->
	<yz_angle>1.0471975512</yz_angle> <!-- pi/3 -->
</camera>

For simplicity, PhysiCell-POVray (currently) always aims the camera towards the origin (0,0,0), with “up” towards the positive z-axis. distance_from_origin sets how far the camera is placed from the origin. xy_angle sets the angle \(\theta\) from the positive x-axis in the xy-plane. yz_angle sets the angle \(\phi\) from the positive z-axis in the yz-plane. Both angles are in radians.

Options

<options>
	<use_standard_colors>true</use_standard_colors>
	<nuclear_offset units="micron">0.1</nuclear_offset>
	<cell_bound units="micron">750</cell_bound>
	<threads>8</threads>
</options>

use_standard_colors (if set to true) uses a built-in “paint-by-numbers” color scheme, where each cell type (identified with an integer) gets XML-defined colors for live, apoptotic, and dead cells. More on this below. If use_standard_colors is set to false, then PhysiCell-povwriter uses the my_pigment_and_finish_function in ./custom_modules/povwriter.cpp to color cells.

The nuclear_offset is a small additional height given to nuclei when cropping to avoid visual artifacts when rendering (which can cause some “tearing” or “bleeding” between the rendered nucleus and cytoplasm). cell_bound is used for leaving some cells out of bound: any cell with |x|, |y|, or |z| exceeding cell_bound will not be rendered. threads is used for parallelizing on multicore processors; note that it only speeds up povwriter if you are converting multiple PhysiCell outputs to povray files.

Save

<save> <!-- done -->
	<folder>output</folder> <!-- use . for root -->
	<filebase>output</filebase>
	<time_index>3696</time_index>
</save>

Use folder to tell PhysiCell-povwriter where the data files are stored. Use filebase to tell how the outputs are named. Typically, they have the form output########_cells_physicell.mat; in this case, the filebase is output. Lastly, use time_index to set the output number. For example if your file is output00000182_cells_physicell.mat, then filebase = output and time_index = 182.

Below, we’ll see how to specify ranges of indices at the command line, which would supersede the time_index given here in the XML.

Clipping planes

PhysiCell-povwriter uses clipping planes to help create cutaway views of the simulations. By default, 3 clipping planes are used to cut out an octant of the viewing area.

Recall that a plane can be defined by its normal vector and a point p on the plane. With these, the plane can be defined as all points satisfying

\[  \left( \vec{x} -\vec{p} \right) \cdot \vec{n} = 0 \]

These are then written out as a plane equation

\[ a x + by + cz + d = 0, \]

where

\[ (a,b,c) = \vec{n} \hspace{.5in} \textrm{ and  } \hspace{0.5in} d = \: – \vec{n} \cdot \vec{p}. \]

As of Version 1.0.0, we are having some difficulties with clipping planes that do not pass through the origin (0,0,0), for which \( d = 0 \).

In the config file, these planes are written as \( (a,b,c,d) \):

<clipping_planes> <!-- done --> 
	<clipping_plane>0,-1,0,0</clipping_plane>
	<clipping_plane>-1,0,0,0</clipping_plane>
	<clipping_plane>0,0,1,0</clipping_plane>
</clipping_planes>

Note that cells “behind” the plane (where \( ( \vec{x} – \vec{p} ) \cdot \vec{n} \le 0 \)) are rendered, and cells in “front” of the plane (where \( (\vec{x}-\vec{p}) \cdot \vec{n} > 0 \)) are not rendered. Cells that intersect the plane are partially rendered (using constructive geometry via union and intersection commands in POV-ray).

Cell color definitions

Within <cell_color_definitions>, you’ll find multiple <cell_colors> blocks, each of which defines the live, dead, and necrotic colors for a specific cell type (with the type ID indicated in the attribute). These colors are only applied if use_standard_colors is set to true in options. See above.

The live colors are given as two rgb (red,green,blue) colors for the cytoplasm and nucleus of live cells. Each element of this triple can range from 0 to 1, and not from 0 to 255 as in many raw image formats. Next, finish specifies ambient (how much highly-scattered background ambient light illuminates the cell), diffuse (how well light rays can illuminate the surface), and specular (how much of a shiny reflective splotch the cell gets).

See the POV-ray documentation for for information on the finish.

This is repeated to give the apoptotic and necrotic colors for the cell type.

<cell_colors type="0">
	<live>
		<cytoplasm>.25,1,.25</cytoplasm> <!-- red,green,blue --> 
		<nuclear>0.03,0.125</nuclear>
		<finish>0.05,1,0.1</finish> <!-- ambient,diffuse,specular -->
	</live>
	<apoptotic>
		<cytoplasm>1,0,0</cytoplasm> <!-- red,green,blue --> 
		<nuclear>0.125,0,0</nuclear>
		<finish>0.05,1,0.1</finish> <!-- ambient,diffuse,specular -->
	</apoptotic>
	<necrotic>
		<cytoplasm>1,0.5412,0.1490</cytoplasm> <!-- red,green,blue --> 
		<nuclear>0.125,0.06765,0.018625</nuclear>
		<finish>0.01,0.5,0.1</finish> <!-- ambient,diffuse,specular -->
	</necrotic>
</cell_colors>

Use multiple cell_colors blocks (each with type corresponding to the integer cell type) to define the colors of multiple cell types.

Using PhysiCell-povwriter

Use by the XML configuration file alone

The simplest syntax:

physicell$ ./povwriter

(Windows users: povwriter or povwriter.exe) will process ./config/povwriter-settings.xml and convert the single indicated PhysiCell snapshot to a .pov file.

If you run POV-writer with the default configuration file in the povwriter structure (with the supplied sample data), it will render time index 3696 from the immunotherapy example in our 2018 PhysiCell Method Paper:

physicell$ ./povwriter

povwriter version 1.0.0
================================================================================

Copyright (c) Paul Macklin 2019, on behalf of the PhysiCell project
OSI License: BSD-3-Clause (see LICENSE.txt)

Usage:
================================================================================
povwriter : run povwriter with config file ./config/settings.xml

povwriter FILENAME.xml : run povwriter with config file FILENAME.xml

povwriter x:y:z : run povwriter on data in FOLDER with indices from x
to y in incremenets of z

Example: ./povwriter 0:2:10 processes files:
./FOLDER/FILEBASE00000000_physicell_cells.mat
./FOLDER/FILEBASE00000002_physicell_cells.mat
...
./FOLDER/FILEBASE00000010_physicell_cells.mat
(See the config file to set FOLDER and FILEBASE)

povwriter x1,...,xn : run povwriter on data in FOLDER with indices x1,...,xn

Example: ./povwriter 1,3,17 processes files:
./FOLDER/FILEBASE00000001_physicell_cells.mat
./FOLDER/FILEBASE00000003_physicell_cells.mat
./FOLDER/FILEBASE00000017_physicell_cells.mat
(Note that there are no spaces.)
(See the config file to set FOLDER and FILEBASE)

Code updates at https://github.com/PhysiCell-Tools/PhysiCell-povwriter

Tutorial & documentation at http://MathCancer.org/blog/povwriter
================================================================================

Using config file ./config/povwriter-settings.xml ...
Using standard coloring function ...
Found 3 clipping planes ...
Found 2 cell color definitions ...
Processing file ./output/output00003696_cells_physicell.mat...
Matrix size: 32 x 66978
Creating file pov00003696.pov for output ...
Writing 66978 cells ...
done!

Done processing all 1 files!

The result is a single POV-ray file (pov00003696.pov) in the root directory.

Now, open that file in POV-ray (double-click the file if you are in Windows), choose one of your resolutions in your lefthand dropdown (I’ll choose 2160×2160 no antialiasing), and click the green “run” button.

You can watch the image as it renders. The result should be a PNG file (named pov00003696.png) that looks like this:

Cancer immunotherapy sample image, at time index 3696

Using command-line options to process multiple times (option #1)

Now, suppose we have more outputs to process. We still state most of the options in the XML file as above, but now we also supply a command-line argument in the form of start:interval:end. If you’re still in the povwriter project, note that we have some more sample data there. Let’s grab and process it:

physicell$ cd output
physicell$ unzip more_samples.zip
Archive: more_samples.zip
inflating: output00000000_cells_physicell.mat
inflating: output00000001_cells_physicell.mat
inflating: output00000250_cells_physicell.mat
inflating: output00000300_cells_physicell.mat
inflating: output00000500_cells_physicell.mat
inflating: output00000750_cells_physicell.mat
inflating: output00001000_cells_physicell.mat
inflating: output00001250_cells_physicell.mat
inflating: output00001500_cells_physicell.mat
inflating: output00001750_cells_physicell.mat
inflating: output00002000_cells_physicell.mat
inflating: output00002250_cells_physicell.mat
inflating: output00002500_cells_physicell.mat
inflating: output00002750_cells_physicell.mat
inflating: output00003000_cells_physicell.mat
inflating: output00003250_cells_physicell.mat
inflating: output00003500_cells_physicell.mat
inflating: output00003696_cells_physicell.mat

physicell$ ls

citation and license.txt
more_samples.zip
output00000000_cells_physicell.mat
output00000001_cells_physicell.mat
output00000250_cells_physicell.mat
output00000300_cells_physicell.mat
output00000500_cells_physicell.mat
output00000750_cells_physicell.mat
output00001000_cells_physicell.mat
output00001250_cells_physicell.mat
output00001500_cells_physicell.mat
output00001750_cells_physicell.mat
output00002000_cells_physicell.mat
output00002250_cells_physicell.mat
output00002500_cells_physicell.mat
output00002750_cells_physicell.mat
output00003000_cells_physicell.mat
output00003250_cells_physicell.mat
output00003500_cells_physicell.mat
output00003696.xml
output00003696_cells_physicell.mat

Let’s go back to the parent directory and run povwriter:

physicell$ ./povwriter 0:250:3500

povwriter version 1.0.0
================================================================================

Copyright (c) Paul Macklin 2019, on behalf of the PhysiCell project
OSI License: BSD-3-Clause (see LICENSE.txt)

Usage:
================================================================================
povwriter : run povwriter with config file ./config/settings.xml

povwriter FILENAME.xml : run povwriter with config file FILENAME.xml

povwriter x:y:z : run povwriter on data in FOLDER with indices from x
to y in incremenets of z

Example: ./povwriter 0:2:10 processes files:
./FOLDER/FILEBASE00000000_physicell_cells.mat
./FOLDER/FILEBASE00000002_physicell_cells.mat
...
./FOLDER/FILEBASE00000010_physicell_cells.mat
(See the config file to set FOLDER and FILEBASE)

povwriter x1,...,xn : run povwriter on data in FOLDER with indices x1,...,xn

Example: ./povwriter 1,3,17 processes files:
./FOLDER/FILEBASE00000001_physicell_cells.mat
./FOLDER/FILEBASE00000003_physicell_cells.mat
./FOLDER/FILEBASE00000017_physicell_cells.mat
(Note that there are no spaces.)
(See the config file to set FOLDER and FILEBASE)

Code updates at https://github.com/PhysiCell-Tools/PhysiCell-povwriter

Tutorial & documentation at http://MathCancer.org/blog/povwriter
================================================================================

Using config file ./config/povwriter-settings.xml ...
Using standard coloring function ...
Found 3 clipping planes ...
Found 2 cell color definitions ...
Matrix size: 32 x 18317
Processing file ./output/output00000000_cells_physicell.mat...
Creating file pov00000000.pov for output ...
Writing 18317 cells ...
Processing file ./output/output00002000_cells_physicell.mat...
Matrix size: 32 x 33551
Creating file pov00002000.pov for output ...
Writing 33551 cells ...
Processing file ./output/output00002500_cells_physicell.mat...
Matrix size: 32 x 43440
Creating file pov00002500.pov for output ...
Writing 43440 cells ...
Processing file ./output/output00001500_cells_physicell.mat...
Matrix size: 32 x 40267
Creating file pov00001500.pov for output ...
Writing 40267 cells ...
Processing file ./output/output00003000_cells_physicell.mat...
Matrix size: 32 x 56659
Creating file pov00003000.pov for output ...
Writing 56659 cells ...
Processing file ./output/output00001000_cells_physicell.mat...
Matrix size: 32 x 74057
Creating file pov00001000.pov for output ...
Writing 74057 cells ...
Processing file ./output/output00003500_cells_physicell.mat...
Matrix size: 32 x 66791
Creating file pov00003500.pov for output ...
Writing 66791 cells ...
Processing file ./output/output00000500_cells_physicell.mat...
Matrix size: 32 x 114316
Creating file pov00000500.pov for output ...
Writing 114316 cells ...
done!

Processing file ./output/output00000250_cells_physicell.mat...
Matrix size: 32 x 75352
Creating file pov00000250.pov for output ...
Writing 75352 cells ...
done!

Processing file ./output/output00002250_cells_physicell.mat...
Matrix size: 32 x 37959
Creating file pov00002250.pov for output ...
Writing 37959 cells ...
done!

Processing file ./output/output00001750_cells_physicell.mat...
Matrix size: 32 x 32358
Creating file pov00001750.pov for output ...
Writing 32358 cells ...
done!

Processing file ./output/output00002750_cells_physicell.mat...
Matrix size: 32 x 49658
Creating file pov00002750.pov for output ...
Writing 49658 cells ...
done!

Processing file ./output/output00003250_cells_physicell.mat...
Matrix size: 32 x 63546
Creating file pov00003250.pov for output ...
Writing 63546 cells ...
done!

done!

done!

done!

Processing file ./output/output00001250_cells_physicell.mat...
Matrix size: 32 x 54771
Creating file pov00001250.pov for output ...
Writing 54771 cells ...
done!

done!

done!

done!

Processing file ./output/output00000750_cells_physicell.mat...
Matrix size: 32 x 97642
Creating file pov00000750.pov for output ...
Writing 97642 cells ...
done!

done!

Done processing all 15 files!

Notice that the output appears a bit out of order. This is normal: povwriter is using 8 threads to process 8 files at the same time, and sending some output to the single screen. Since this is all happening simultaneously, it’s a bit jumbled (and non-sequential). Don’t panic. You should now have created pov00000000.povpov00000250.pov, … , pov00003500.pov.

Now, go into POV-ray, and choose “queue.” Click “Add File” and select all 15 .pov files you just created:

Hit “OK” to let it render all the povray files to create PNG files (pov00000000.png, … , pov00003500.png).

Using command-line options to process multiple times (option #2)

You can also give a list of indices. Here’s how we render time indices 250, 1000, and 2250:

physicell$ ./povwriter 250,1000,2250

povwriter version 1.0.0
================================================================================

Copyright (c) Paul Macklin 2019, on behalf of the PhysiCell project
OSI License: BSD-3-Clause (see LICENSE.txt)

Usage:
================================================================================
povwriter : run povwriter with config file ./config/settings.xml

povwriter FILENAME.xml : run povwriter with config file FILENAME.xml

povwriter x:y:z : run povwriter on data in FOLDER with indices from x
to y in incremenets of z

Example: ./povwriter 0:2:10 processes files:
./FOLDER/FILEBASE00000000_physicell_cells.mat
./FOLDER/FILEBASE00000002_physicell_cells.mat
...
./FOLDER/FILEBASE00000010_physicell_cells.mat
(See the config file to set FOLDER and FILEBASE)

povwriter x1,...,xn : run povwriter on data in FOLDER with indices x1,...,xn

Example: ./povwriter 1,3,17 processes files:
./FOLDER/FILEBASE00000001_physicell_cells.mat
./FOLDER/FILEBASE00000003_physicell_cells.mat
./FOLDER/FILEBASE00000017_physicell_cells.mat
(Note that there are no spaces.)
(See the config file to set FOLDER and FILEBASE)

Code updates at https://github.com/PhysiCell-Tools/PhysiCell-povwriter

Tutorial & documentation at http://MathCancer.org/blog/povwriter
================================================================================

Using config file ./config/povwriter-settings.xml ...
Using standard coloring function ...
Found 3 clipping planes ...
Found 2 cell color definitions ...
Processing file ./output/output00002250_cells_physicell.mat...
Matrix size: 32 x 37959
Creating file pov00002250.pov for output ...
Writing 37959 cells ...
Processing file ./output/output00001000_cells_physicell.mat...
Matrix size: 32 x 74057
Creating file pov00001000.pov for output ...
Processing file ./output/output00000250_cells_physicell.mat...
Matrix size: 32 x 75352
Writing 74057 cells ...
Creating file pov00000250.pov for output ...
Writing 75352 cells ...
done!

done!

done!

Done processing all 3 files!

This will create files pov00000250.povpov00001000.pov, and pov00002250.pov. Render them in POV-ray just as before.

Advanced options (at the source code level)

If you set use_standard_colors to false, povwriter uses the function my_pigment_and_finish_function (at the end of  ./custom_modules/povwriter.cpp). Make sure that you set colors.cyto_pigment (RGB) and colors.nuclear_pigment (also RGB). The source file in povwriter has some hinting on how to write this. Note that the XML files saved by PhysiCell have a legend section that helps you do determine what is stored in each column of the matlab file.

Optional postprocessing

Image conversion / manipulation with ImageMagick

Suppose you want to convert the PNG files to JPEGs, and scale them down to 60% of original size. That’s very straightforward in ImageMagick:

physicell$ magick mogrify -format jpg -resize 60% pov*.png

Creating an animated GIF with ImageMagick

Suppose you want to create an animated GIF based on your images. I suggest first converting to JPG (see above) and then using ImageMagick again. Here, I’m adding a 20 ms delay between frames:

physicell$ magick convert -delay 20 *.jpg out.gif

Here’s the result:

Animated GIF created from raytraced still images. (You have to click the image to see the animation.)

Creating a compressed movie with Mencoder

Syntax coming later.

Closing thoughts and future work

In the future, we will probably allow more control over the clipping planes and a bit more debugging on how to handle planes that don’t pass through the origin. (First thoughts: we need to change how we use union and intersection commands in the POV-ray outputs.)

We should also look at adding some transparency for the cells. I’d prefer something like rgba (red-green-blue-alpha), but POV-ray uses filters and transmission, and we want to make sure to get it right.

Lastly, it would be nice to find a balance between the current very simple camera setup and better control.

Thanks for reading this PhysiCell Friday tutorial! Please do give PhysiCell at try (at http://PhysiCell.org) and read the method paper at PLoS Computational Biology.

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