FishFlow is a tool to compute the optical flow of moving particles. It loads images from a video file and outputs data and videos of the optical flow.

It works by detecting spatial and temporal correlations of pixel intensities.

It was built in order to extract the motion of schooling fish in a laboratory setting, hence the name. All the default parameters are tuned for these specific videos but they can be adjusted to meet other needs.

The build process is managed by CMake. The easiest way to build is to open in your terminal the root directory of the FishFlow repository and to type:

mkdir build
cd build
cmake ..
make

CMake Tips: You can use different generators. For instance to generate a Xcode project, use cmake -G Xcode ... You can also use the ncurses interface to cmake with ccmake ...

But first you need to make sure that the following dependencies are installed on your computer:

• CMake for the build process
• OpenCV for the image processing
• HDF5 (including the C++ bindings) for the data output
• Boost (including Program Options) for the options input

FishFlow is a command line tool. If the executable is in your current directory, type ./fishFlow to run it.

You can show usage information and a list of options with ./fishFlow -h or ./fishFlow --help.

Note: If you want to drop the ./ prefix, you need to install the executable somewhere in your $PATH. For instance you can do cp fishFlow /usr/local/bin. After this, fishFlow -h will work from any directory. From now on, I will assume you installed it properly.

Options can be specified in three ways:

• On the command line
• In a config file
• On the standard input

Note for C++ Programmers: The options are handled by the Boost library Program Options. Please refer to Boost's documentation for more information.

Type fishFlow -h to see the list of options. An option looks like a list of words separated by dots. The first words can be seen as sections while the last word is the specific option within that section. For instance frame.count is the total number of frames from the input video that you want to process. You can specify it in a config file by writing:

frame.count = 100

or

[frame]
	count = 100

then run fishFlow my_config_file.ini (or fishFlow < my_config_file.ini).

Or you can write it directly on the command line like this:

fishFlow --frame.count 100

Have a look at config.ini for a more complete example of config file.

At the minimum, you need to provide an input file. If this is all you specify, FishFlow will produce an output data file in the same directory and with the same name as the input video (but with an additional .flow.h5 extension).

The source for FishFlow is released under the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.