WhiskiWrap 1.2.2

Whisk package wrapper created by cxrodgers

WhiskiWrap

WhiskiWrap provides tools for running whisk more easily and efficiently.

My goal is to improve whisk in the following ways:

1. Make it more flexible about reading various input files. In my experience whisk has trouble reading certain input videos. Instead, WhiskiWrap uses your system's ffmpeg to read input files (because ffmpeg can typically read almost anything) and to generate simple tiff stacks which whisk can reliably read.
2. Make it faster, by calling many instances of trace in parallel on non-overlapping chunks of the input video.
3. Make it more cross-platform and memory-efficient, by converting whisk's output files into HDF5 files which can be read by multiple programs (Python, Matlab) on any operating system. Importantly, HDF5 files can also be read partially to avoid overflowing your system's memory.

Example

Note: The current best pipeline for running trace is interleaved_reading_and_trace, but the command pipeline_trace is the only one configured to run measure.

First start the interactive python environment by typing ipython at the terminal.

Import WhiskiWrap so it can be used:

import WhiskiWrap

Set the path to the input file. There are some test videos in this repository that you can use. Usually it's best to copy this file to a new directory, because a lot of temporary files will be created in the same directory.

mkdir ~/whiski_wrap_session
cp ~/dev/WhiskiWrap/test_video2.mp4 ~/whiski_wrap_session/test_video2.mp4
input_video = '~/whiski_wrap_session/test_video2.mp4'

Choose where you want the output HDF5 file to be.

output_file = 'output.hdf5'

Run the trace. Here we use 4 parallel processes.

WhiskiWrap.pipeline_trace(input_video, output_file, n_trace_processes=4)

If you go to the session directory, you'll see a bunch of tiff stacks and whiskers files that were generated by every instance of trace. There's also a combined HDF5 file with all the data combined. You can read it into Python like so:

import tables
import pandas
with tables.open_file(output_file) as fi:`
  test_result = pandas.DataFrame.from_records(
    fi.root.summary.read())     

This just reads the "summary": the tip and follicle of every whisker in every frame. The HDF5 file also contains the x- and y-coordinates of every pixel in every whisker, but you probably don't want to read all of this in at once.

More detail on how WhiskiWrap works

1. Split the entire video into epochs of about 100K frames (~100MB of data). The entire epoch will be read into memory, so the epoch size cannot be too big.
2. For each epoch:
3. Split it into chunks of about 1000 frames, each of which will be traced separately. The frames can optionally be cropped at this point.
4. Write each chunk to disk as a tiff stack (note: these files are quite large).
5. Trace each chunk with parallel instances of trace. A whiskers file is generated for each chunk.
6. Parse in order each chunk's whiskers file and append the results to an output HDF5 file.
7. (Optional) delete the intermediate chunk files here.

The following parameters must be chosen:

• n_trace_processes - the number of parallel instances of trace to run at the same time. The most efficient choice is the number of CPUs on your system.
• epoch_sz_frames - the number of frames per epoch. It is most efficient to make this value as large as possible. However, it should not be so large that you run out of memory when reading in the entire epoch of video. 100000 is a reasonable choice.
• chunk_sz_frames - the size of each chunk. Ideally, this should be epoch_size / n_trace_processes, so that all the processes complete at about the same time. It could also be epoch_size / (N * n_trace_processes) where N is an integer.

You may also add optional parameters to run the measure command

• measure=True - run measure command, default is False
• face='right' - run measure with face on right side, can also specify to 'left' side

Installation

WhiskiWrap is written in Python and relies on ffmpeg for reading input videos, tifffile for writing tiff stacks, whisk for tracing whiskers in the tiff stacks, and pytables for creating HDF5 files with all of the results. Also make sure that you have installed ffmpeg-python>=0.2.0.

Installing ffmpeg

First install ffmpeg and ensure it is available on your system path -- that is, you should be able to type ffmpeg in the terminal and it should find it and run it.

Installing whisk

Next install whisk. There are several ways to do this:

1. Download the pre-built binary. This is the easiest path because it doesn't require compiling anything. However, you still need to make a few changes to the Python code that is downloaded in order to make it work with WhiskiWrap.
2. Build whisk from source, using my lightly customized fork. This will probably require more trouble-shooting to make sure all of its parts are working.

To use the pre-built binary (preferred):

1. Download the zipped binary:
   1. Windows: Download whisk-1.1.0d-win32.exe or whisk-1.1.0d-win64.exe install adding to the PATH.
   2. Linux: Unpack with tar -xzf whisk-1.1.0d-64bit-Linux.tar.gz. Rename the unpacked directory to [Path-to-WhiskiWrap-Cloned-Repo]/whisk.Add to echo 'export WHISKPATH=[WhiskiWrap-Cloned-Path]/whisk' >> ~/.bashrc
   3. Mac: Unpack with tar -xzf whisk-1.1.0d-64bit-Linux.tar.gz. Rename the unpacked directory to [Path-to-WhiskiWrap-Cloned-Repo]/whisk. Add to echo 'export WHISKPATH=[WhiskiWrap-Cloned-Path]/whisk' >> ~/.bash_profile
2. Add the binaries to your system path so that you can run trace from the command line.
3. Install whisk package:
   1. git clone https://github.com/aiporre/whisk.git
   2. Copy recursively [Path-to-WhiskiWrap-Cloned-Repo]/whisk/lib/whisk/ to [Path-to-whisk-Cloned-Repo]/whisk/
   3. Install whisk package cd [Path-to-whisk-Cloned-Repo] && pip install .
4. In the WhiskiWrap repo install now this package with: uv pip install . (or pip install . if not using uv)
5. Test that everything worked by opening python or ipython and running import WhiskiWrap

To build from source:

1. Install required dependencies (gl.h, etc)
2. Download the source from my lightly modified fork, which makes the __init__ changes described above.
3. cd ~/dev
4. git clone https://github.com/aiporre/whisk.git
5. cd whisk
6. mkdir build && cd build
7. cmake ..
8. make
9. Copy a library into an expected location: [Path-to-whisk-Cloned-Repo]/bin
   1. In Windows: append to the PATH environmental variable [Path-to-whisk-Cloned-Repo]/bin
   2. In Linux: echo 'export WHISKPATH=[Path-to-whisk-Cloned-Repo]/bin/' >> ~/.bashrc
   3. In MacOS: echo 'export WHISKPATH=[Path-to-whisk-Cloned-Repo]/bin/' >> ~/.profile_bash
10. copy cp libwhisk.so ../whisk in Linux or mac, and copy whisk.dll ..\whisk in windows.
11. 'cd ..'
12. When you create your conda environment you should add whisk with uv pip install . (or pip install . if not using uv)
13. Test that everything worked by opening python or ipython and running from whisk import traj, trace
14. You need to the binaries to then environmental variables WHISKPATH and/or PATH

Installing Python modules

Recommended: Using uv (Modern Python Package Manager)

The easiest and fastest way to install WhiskiWrap is using uv, a modern Python package manager. This project now includes a pyproject.toml file that makes installation with uv straightforward.

Requirements:

• Python 3.10 or higher
• Some dependencies may require compilation. If you encounter build errors:
  • On Debian/Ubuntu: sudo apt-get install python3-dev build-essential
  • On Fedora/RHEL: sudo dnf install python3-devel gcc
  • On macOS: xcode-select --install
  • On Windows: Install Microsoft C++ Build Tools

1. First, install uv if you haven't already:

   For Windows, you can download the installer from the uv releases page. For Linux and macOS, you can use the following command to install uv:

   curl -LsSf https://astral.sh/uv/install.sh | sh
   

2. Option A: Install in an isolated virtual environment (Recommended)

   Create and activate a virtual environment, then install WhiskiWrap:

   uv venv
   source .venv/bin/activate  # On Windows: .venv\Scripts\activate
   uv pip install -e .
   

   This keeps WhiskiWrap and its dependencies isolated from your system Python and other projects.

3. Option B: Install globally (simpler but less isolated)

   Install WhiskiWrap system-wide:

   uv pip install -e .  # Development mode
   # or
   uv pip install .     # Normal installation
   

   This makes WhiskiWrap available everywhere but may cause dependency conflicts with other projects.

The pyproject.toml file will automatically handle all the dependencies, including matplotlib and easygui.

Important: If you chose Option A (virtual environment), you'll need to activate the environment each time you want to use WhiskiWrap:

source .venv/bin/activate  # On Windows: .venv\Scripts\activate

Then you can use WhiskiWrap as described in the examples above.

Alternative: Using conda (Traditional Method)

If you prefer using conda to manage and install Python modules:

1. Create conda environment: conda create -n WhiskiWrap python=3.10 pip (conda automatically installs required build dependencies)

2. Activate with: conda activate WhiskiWrap

3. Install WhiskiWrap: pip install . in the directory of this project

4. Install additional packages if needed:

   conda install scipy matplotlib
   pip install tifffile easygui
   

Note: When using conda, you should not have anything on your $PYTHONPATH, and there shouldn't be any installed modules in your ~/.local.