Training code of Faster R-CNN used in knee staging prediction

Disclaimer

This repository is build on a fork of https://github.com/rbgirshick/py-faster-rcnn by Shaoqing Ren, Kaiming He, Ross Girshick, Jian Sun (Microsoft Research).

License

This code is released under the MIT License (refer to the LICENSE file for details).

Contents

1. Requirements: software
2. Requirements: hardware
3. Basic installation
4. Demo
5. Beyond the demo: training and testing
6. Usage

Requirements: software

NOTE If you are having issues compiling and you are using a recent version of CUDA/cuDNN, please consult this issue for a workaround

1. Requirements for Caffe and pycaffe (see: Caffe installation instructions)

Note: Caffe must be built with support for Python layers!

# In your Makefile.config, make sure to have this line uncommented
WITH_PYTHON_LAYER := 1
# Unrelatedly, it's also recommended that you use CUDNN
USE_CUDNN := 1

You can download my Makefile.config for reference. 2. Python packages you might not have: cython, python-opencv, easydict 3. [Optional] MATLAB is required for official PASCAL VOC evaluation only. The code now includes unofficial Python evaluation code.

Requirements: hardware

1. For training smaller networks (ZF, VGG_CNN_M_1024) a good GPU (e.g., Titan, K20, K40, ...) with at least 3G of memory suffices
2. For training Fast R-CNN with VGG16, you'll need a K40 (~11G of memory)
3. For training the end-to-end version of Faster R-CNN with VGG16, 3G of GPU memory is sufficient (using CUDNN)

Installation (sufficient for the demo)

1. Clone the Faster R-CNN repository

# Make sure to clone with --recursive
git clone --recursive https://github.com/stanfordnmbl/knee_OA_staging_training.git

2. We'll call the directory that you cloned Faster R-CNN into FRCN_ROOT

   Ignore notes 1 and 2 if you followed step 1 above.

   Note 1: If you didn't clone Faster R-CNN with the --recursive flag, then you'll need to manually clone the caffe-fast-rcnn submodule:

   git submodule update --init --recursive

   Note 2: The caffe-fast-rcnn submodule needs to be on the faster-rcnn branch (or equivalent detached state). This will happen automatically if you followed step 1 instructions.

3. Build the Cython modules

   cd $FRCN_ROOT/lib
   make

4. Build Caffe and pycaffe

   cd $FRCN_ROOT/caffe-fast-rcnn
   # Now follow the Caffe installation instructions here:
   #   http://caffe.berkeleyvision.org/installation.html
   
   # If you're experienced with Caffe and have all of the requirements installed
   # and your Makefile.config in place, then simply do:
   make -j8 && make pycaffe

5. Download pre-computed Faster R-CNN detectors

   cd $FRCN_ROOT
   ./data/scripts/fetch_faster_rcnn_models.sh

   This will populate the $FRCN_ROOT/data folder with faster_rcnn_models. See data/README.md for details. These models were trained on VOC 2007 trainval.

Demo

After successfully completing basic installation, you'll be ready to run the demo.

To run the demo

cd $FRCN_ROOT
./tools/demo.py

The demo performs detection using a VGG16 network trained for detection on PASCAL VOC 2007.

Beyond the demo: installation for training and testing models

1. It should have this basic structure

   $VOCdevkit/                           
   $VOCdevkit/VOC2007                    # image sets, annotations, etc.
   # ... and several other directories ...

2. Create symlinks for the dataset

   cd $FRCN_ROOT/data
   ln -s $VOCdevkit VOCdevkit2007

3. Follow the next sections to download pre-trained ImageNet models

Download pre-trained ImageNet models

Pre-trained ImageNet models can be downloaded for the three networks described in the paper: ZF and VGG16.

cd $FRCN_ROOT
./data/scripts/fetch_imagenet_models.sh

VGG16 comes from the Caffe Model Zoo, but is provided here for your convenience. ZF was trained at MSRA.

Usage

To train and test a Faster R-CNN detector using the alternating optimization algorithm from our NIPS 2015 paper, use experiments/scripts/faster_rcnn_alt_opt.sh. Output is written underneath $FRCN_ROOT/output.

cd $FRCN_ROOT
./experiments/scripts/faster_rcnn_alt_opt.sh [GPU_ID] [NET] [--set ...]
# GPU_ID is the GPU you want to train on
# NET in {ZF, VGG_CNN_M_1024, VGG16} is the network arch to use
# --set ... allows you to specify fast_rcnn.config options, e.g.
#   --set EXP_DIR seed_rng1701 RNG_SEED 1701

("alt opt" refers to the alternating optimization training algorithm described in the NIPS paper.)

To train and test a Faster R-CNN detector using the approximate joint training method, use experiments/scripts/faster_rcnn_end2end.sh. Output is written underneath $FRCN_ROOT/output.

cd $FRCN_ROOT
./experiments/scripts/faster_rcnn_end2end.sh [GPU_ID] [NET] [--set ...]
# GPU_ID is the GPU you want to train on
# NET in {ZF, VGG_CNN_M_1024, VGG16} is the network arch to use
# --set ... allows you to specify fast_rcnn.config options, e.g.
#   --set EXP_DIR seed_rng1701 RNG_SEED 1701

This method trains the RPN module jointly with the Fast R-CNN network, rather than alternating between training the two. It results in faster (~ 1.5x speedup) training times and similar detection accuracy. See these slides for more details.

Artifacts generated by the scripts in tools are written in this directory.

Trained Fast R-CNN networks are saved under:

output/<experiment directory>/<dataset name>/

Test outputs are saved under:

output/<experiment directory>/<dataset name>/<network snapshot name>/