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MexConv3D

Matlab mex implementation (with both CPU and GPU version) of the basic operations for 3D (volume) ConvNet. Potential use: video, volume data (CT, MR), etc. The APIs and conventions are consistent with matconvnet.

Overview

mex_conv3d.m is provided for 3D convoluation, while mex_maxpool3d.m for 3D max pooling. Their calling conventions are consistent with vl_nnconv.m and vl_nnpool.m in matconvnet, respectively.

In this project only the most basic building blocks are provided. For a ready-to-use 3D ConvNet in Matlab, one needs a high-level wrapper like the vl_simplenn.m in matconvnet or MatConvDAG

Install

Step by step:

  • Run make_all.m in root directory to make the mex files
    • CUDA toolkit needed if enabling GPU
  • Run setup_path.m in root directory to add path
  • (Optional) CD to folder unittest and run run_all.m to verify everything works well

MexConv3D has been tested in the following environment:

  • Matlab R2014a + Windows 8.1 + Visual Studio 2012 + CUDA Toolkit 6.5 (if enabling GPU)
  • Matlab R2014a + Ubuntu 12.04 + GCC 4.8.2 + CUDA Toolkit 6.5 (if enabling GPU)

Usage

For 3D Convolution:

%% data
szX = [9,8,5, 5,9];  % input size: 3D volume + #feature maps + #instances
szF = [3,3,3, 5,4];  % filter size: 3D volume + #input feature maps + #output feature maps
szB = [1, szF(end)]; % bias size: #output feature maps
X = gpuArray.rand(szX, 'single');
F = gpuArray.rand(szF, 'single');
B = gpuArray.rand(szB, 'single');

pad    = [1,2, 2,1, 3,4]; % 3D higher/lower padding
stride = [2,3,5];         % 3D stride
%% fprop
Y = mex_conv3d(X,F,B, 'pad', pad, 'stride',stride);
%% bprop
dZdY = rand(size(Y), 'like', Y);
[dZdX,dZdF,dZdB] = mex_conv3d(X,F,B, dZdY, 'pad',pad, 'stride',stride);

For 3D Max Pooling:

%% data
sz = [7,8,5, 5,9]; % size for 3D volume + #feature maps + #instances
pool   = [3,2,4];          % 3D pooling window size
stride = [2,1,2];          % 3D stride 
pad    = [1,1,  0,0, 2,1]; % 3D higher/lower padding
x = gpuArray.rand(sz, 'single'); % Input data/feature maps
%% fprop
[y, ind] = mex_maxpool3d(x,...
  'pool',pool, 'stride',stride, 'pad',pad);
%% bprop
dzdy = rand(size(y),'like',y);
xx = mex_maxpool3d(dzdy,ind,size(x),...
  'pool',pool, 'stride',stride, 'pad',pad);

Example

See more scripts in directory example. Type help mex_conv3d or help mex_maxpool3d for doc. See README.md in each folder (if any) to understand the folder layout and the purpose.

See example/example_simplenet for an example of doing fprop/bprop over a simple 3D convnet (which is based on the code of Sushma Rudra).