Troubleshooting: analysis

Q: My crowd movies are empty and the movies are 0 bytes in size but I don't see any errors, why?
A: You likely are using the wrong version of ffmpeg, or don't have the proper movie encoders. Make sure you download ffmpeg like so: conda install -c anaconda ffmpeg.

Q: Why do I get an OpenMP error when trying to install MoSeq2-model on a Mac?
A: This is an issue with the Mac supplied version of gcc. Install the latest gcc using homebrew then set your gcc and gxx to use the homebrew version.

brew install gcc
export CC=/usr/local/bin/gcc-7
export CXX=/usr/local/bin/g++-7
cd ~/python_repos/moseq2-model/
pip install -e . --process-dependency-links

Q: Why do I see a bunch of Numpy warnings about binary incompatibility?
A: This a known issue with the latest version of Numpy. As far as we know this warning is benign. The simplest way to supress this message is to downgrade Numpy to 1.14.5. See this issue.

pip install numpy==1.14.5

Q: How do I load the raw data in Python or MATLAB?
A: The depth frames are saved as binary data in 16-bit little Endian format. See this function to load in raw data in Python. In MATLAB use the following code:

width=512;
height=424;
start_point=1; % start frame
frames_to_read=100; % frames to read

fid=fopen(PATH_TO_DATA, 'rb');

bytes_per_frame = height * width * 2; %2 bytes per int16
offset = bytes_per_frame * (start_point - 1);
fseek(fid, offset, 'bof'); % seek to the correct point

% note that width and height are permuted here
raw_frames = reshape(fread(fid, (width * height) * frames_to_read, '*int16'), [width height frames_to_read]);