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https://github.com/jberry47/ddpsc_phenotypercv

Header-only C++11 library using OpenCV for high-throughput image-based plant phenotyping
https://github.com/jberry47/ddpsc_phenotypercv

charuco color-correction high-throughput image-processing machine-learning opencv plant-phenotyping

Last synced: 2 months ago
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Header-only C++11 library using OpenCV for high-throughput image-based plant phenotyping

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README 

        



# DDPSC PhenotyperCV

PhenotyperCV is a header-only C++11 library that has a large range of functionality for image-based plant phenotyping. 



Included is a single source file that, when built, has workflows for many pratical applications. The created executable has multiple features that are selected for using `-m` flag indicating the "mode" you'd like execute. As development continues, new modes will become available to expand the use of this program to problems outside the framework of Bellwether platform. Futher information can be found using the `-h` flag. 



Custom workflows, with the aid of functions in this library, are also made possible and are intended to ease the difficulty in processing images from any source. A common bottleneck of image processing is not knowing how to perform specific tasks and this library is designed with that in mind.



### Usage

Visit [the wiki page](https://github.com/jberry47/ddpsc_phenotypercv/wiki) for more info on how to use included source file and how to create your own custom workflows. 



### Building the program on a local computer

PhenotyperCV is dependent on two packages: OpenCV and Eigen3. Additionally, the OpenCV installation must have been with the extra modules enabled, namely: aruco, ml, and ximgproc. This program must be compiled from source and is made easier with `cmake`



##### (Mac Only) Installing Homebew

```bash 

/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

```



##### Installing CMake

For Ubuntu users:

```bash

sudo apt-get install cmake

```

For MacOSX users:

```bash

brew install cmake

```



##### Making a directory for all builds

```bash

mkdir big_build && cd big_build

export my_path=$(pwd)

```



##### Getting Eigen3 and installing

```bash

wget "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.bz2" -O"eigen-3.3.7.tar"

tar -xf eigen-3.3.7.tar && cd eigen-3.3.7

mkdir build && cd build

cmake -DCMAKE_INSTALL_PREFIX=/usr/local ..

sudo make install

sudo cp -r /usr/local/include/eigen3/Eigen /usr/local/include/

cd $my_path

```



##### Getting OpenCV extra modules

```bash

wget https://github.com/opencv/opencv_contrib/archive/4.5.2.tar.gz -O"opencv_contrib-4.5.2.tar.gz"

tar -xzf opencv_contrib-4.5.2.tar.gz

cd opencv_contrib-4.5.2/modules

rm -rv !("aruco"|"ximgproc") 

cd $my_path

```



##### Getting OpenCV and installing

```bash

wget https://github.com/opencv/opencv/archive/4.5.2.tar.gz -O"opencv-4.5.2.tar.gz"

tar -xzf opencv-4.5.2.tar.gz

cd opencv-4.5.2

mkdir build && cd build

cmake .. -DOPENCV_EXTRA_MODULES_PATH=$my_path/opencv_contrib-4.5.2/modules

make -j8

sudo make install

cd $my_path

```

##### Getting ZBar and installing

For Ubuntu users:

```bash

sudo apt-get install libzbar-dev libzbar0

```

For MacOSX users:

```bash

brew install zbar

```



##### Getting PhenotyperCV and building

```bash

git clone https://github.com/jberry47/ddpsc_phenotypercv

cd ddpsc_phenotypercv && mkdir build && cd build

cmake ..

make

export PATH=$PATH:$my_path/ddpsc_phenotypercv/build

```



### Building the program on DDPSC Infrastructure

Both OpenCV and Eigen3 depedencies are in unconventional locations that are not found with cmake. To build the program on the infrastructure, there is a bash script in the misc directory of this repo that links to everything needed, and can be run with: 

```bash 

cd ddpsc_phenotypercv/misc

./pull_compile_phenocv.sh

cd ../../

```

Alternatively, a pre-built executable exists already in `/home/jberry/programs/PhenotyperCV`.



After a successful build, you need to include the libraries to OpenCV and ZBar in your LD_LIBRARY_PATH

```bash

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/shares/bioinfo/installs/opencv-3.3.0/install/lib:/bioinfo/lib

```

It is recommended that you add this line to your bash_profile or bash_rc so you don't have to add the libraries every time you want to use PhenotyperCV.



### Testing the build

After you create the executable, test to make sure it can be used by running `PhenotyperCV -h` which should display a help page. 



### DDPSC Datasci Cluster Usage

Example condor job file and accompanying executable for processing images on the DDPSC infrastructure can be found in the `misc` directory

* **phenotypercv.submit** - condor submit file that MUST BE EDITED to your file paths and image location

* **run_phenocv.sh** - the executable that the job file calls and MUST BE EDITED to your file paths and image location