Fully automated tracking of single rows of whiskers in high-speed video.
Project description
Janelia Whisker tracking
Fully automated tracking of single rows of whiskers in high-speed video.
The original source code repository is https://github.com/nclack/whisk/.
The original website for this program is now accessible here.
A copy of the instructions and the tutorial are available here.
Downloading
Pre-built binaries are available on this forked repository. Binaries are built against FFmpeg 6.0.
Binary and library file can simply be installed from Pypi, with pip install whisk-janelia
.
Note that on Linux, if not root, you may need to make some of the binary files executable, e.g.
chmod +x /path/to/whisk/bin/trace
. You can also use the post-installation scriptupdate_permissions.py
to make all files in thewhisk/bin
directory executable.
Check which version of FFmpeg is installed, just typeffmpeg
in a terminal.
You can also check which version of required libraries likelibavdevice
are installed with:
for dir in $(echo $LD_LIBRARY_PATH | tr ":" "\n"); do find $dir -name 'libavdevice.so*' 2>/dev/null; done
.
See also the README on the whisk-dockerfile repo, in whisk-base
section.
Building
Updated build files are found here.
This package uses a Cmake based build system. The basic build steps are similar under Windows, OS X, and Linux.
The build requirements are cmake
gcc-12.2+
FFmpeg
.
For Unix-y systems:
- Install CMake 2.8+, a C++ compiler and other build tools.
sudo apt update
sudo apt install cmake pkg-config bison gawk
sudo apt install g++ gdb make ninja-build rsync zip
- Install FFmpeg libraries
sudo apt install libavdevice-dev libavfilter-dev libavformat-dev libavcodec-dev libswresample-dev libswscale-dev libavutil-dev
- -- Alternatively --
Build FFmpeg from source.
First, install the necessary dependencies:sudo apt-get install -y autoconf automake build-essential cmake libass-dev libfreetype6-dev libsdl2-dev libtool libva-dev libvdpau-dev libvorbis-dev libxcb1-dev libxcb-shm0-dev libxcb-xfixes0-dev pkg-config texinfo zlib1g-dev yasm libx264-dev libx265-dev libnuma-dev libvpx-dev libfdk-aac-dev libmp3lame-dev libopus-dev
Then, download the FFmpeg source code:wget https://FFmpeg.org/releases/ffmpeg-6.0.tar.bz2 tar xjf ffmpeg-6.0.tar.bz2 cd ffmpeg-6.0
Configure and compile FFmpeg with shared libraries (note the--enable-pic
,--enable-shared
, and--disable-static
flags):CFLAGS="-fPIC" CXXFLAGS="-fPIC" ./configure \ --enable-gpl \ --enable-version3 \ --enable-nonfree \ --enable-small \ --enable-libmp3lame \ --enable-libx264 \ --enable-libx265 \ --enable-libvpx \ --enable-libfdk-aac \ --enable-libopus \ --enable-pic \ --enable-shared \ --disable-static make -j$(nproc)
Finally, install FFmpeg:sudo make install
If cmake still fails because of it can't find FFmpeg libraries libavdevice;libavfilter;libavformat;libavcodec;libswresample;libswscale;libavutil
, you need to have them somewhere, and make it find it, e.g. export PKG_CONFIG_PATH=/home/$USER/ffmpeg_build/lib/pkgconfig
.
If you built FFmpeg from source, you can add /usr/local/lib
to LD_LIBRARY_PATH
and update the dynamic linker cache with sudo ldconfig
:
echo 'export LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH' >> ~/.bashrc
source ~/.bashrc
echo "/usr/local/lib" | sudo tee /etc/ld.so.conf.d/FFmpeg.conf
sudo ldconfig
- Install Qt5 and Qt5Svg
sudo apt install qtbase5-dev libqt5svg5-dev
- Check installation with
qmake -v
. - Set
Qt5_DIR
andQt5Svg_DIR
environment variables if cmake asks for it.
- Start in the root of the source directory (in a terminal).
- Type these commands (or use VSCode's CMake extension to configure and build):
mkdir build
cd build
cmake ..
make
For WSL systems, this page may be helpful:
https://devblogs.microsoft.com/cppblog/build-and-debug-c-with-wsl-2-distributions-and-visual-studio-2022/
For Windows systems (ignore VS Code instructions if not using it):
- Install Visual Studio Code.
- Install the C/C++ extension for VS Code.
- Install Mingw-w64 via MSYS2. Prefer installing MSYS2 in a directory without space (e.g., not C:/Program Files/ ...). That will save you a lot of headaches.
- Launch a MSYS2 terminal for the UCRT64 environment as an administrator and install the following:
- Install gcc as mentioned in MSYS2 installation page:
pacman -S mingw-w64-ucrt-x86_64-gcc
- Install the Mingw-w64 toolchain:
pacman -S --needed base-devel mingw-w64-x86_64-toolchain
- Install cmake and generators (ninja ... make is installed with the toolchain above, ):
pacman -S mingw-w64-x86_64-cmake
- Install the FFmpeg libraries for the 64-bit MinGW toolchain:
To install the most recent version instead, run
pacman -S mingw-w64-x86_64-ffmpeg
.
If using python (see packageswhisk-janelia
andwhiskiwrap
), you need to ensure compatibility between the FFmpeg version used to build whisk (currently, version 6.0) and the FFmpeg library files that python will call with the packagectypes
. Tarballs are available for download on MSYS2's package page, or runwget https://mirror.msys2.org/mingw/mingw64/mingw-w64-x86_64-ffmpeg-6.0-7-any.pkg.tar.zst
. Then, install the package withpacman -U mingw-w64-x86_64-ffmpeg-6.0-7-any.pkg.tar.zst
. - Update the PKG_CONFIG_PATH environment variable to include the path to the FFmpeg library .pc files. In the MSYS2 terminal, run:
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:/mingw64/lib/pkgconfig
, and add it to~/.bashrc
as well to make this change permanent.
- Open a terminal, navigate to the
whisk
repository directory. - Run the following commands:
mkdir build
cd build
cmake ..
ninja
CMake works by building the Makefile, or other required project files, in the "build" directory you created. You don't have to use a Makefile; XCode projects, Eclipse projects, Visual Studio projects, etc ... can be generated. To generate these other project types replace the "cmake .." step with "cmake-gui ..". The GUI will show available options. See the CMake documentation for more details.
File formats
Whiskers
Whiskers can be stored in either a text or binary format. There is a command line utility, whisker_convert
, provided to convert between different
supported formats. batch.py
can be used to speed up the process of converting many files.
The most detailed description of each format can be found in the corresponding whisker_io_*.c
files implimenting the readers/writers for each format.
In general, each whisker segment in a file is comprised of a unique id and a number of data points describing the shape as output from the tracing program.
Measurements
The measurements file stores the features of traced curves used for classification, such as follicle position, angle and whisker length. Additionally, after classification, this file records the determined identity of each traced curve.
Graphical interface
See ui/README for instructions on how to use the graphical user interface.
ui2.py --help
Community
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for whisk_janelia-1.1.10-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 44b86715e4b62a41413c414f719cd18ce78b5257b78760bba8eddab393946134 |
|
MD5 | 2fbd11701392ff07f7fce4ccf7fb34a1 |
|
BLAKE2b-256 | 46accda5282237fc88fb437a602349b90dc376b23f1d9dfe7deee74c317b6671 |