Installation¶
Minimum requirements¶
We have tested PlantCV on the following systems:
- Linux: CentOS 7 x86 64-bit (RedHat Enterprise Linux)
- Linux: Ubuntu 12.04, 14.04, and 16.04
- Mac OSX 10.11
- Windows 10
A list of minimum tested software dependencies is listed below:
- Python 2.7
- argparse 1.1
- cv2 2.4
- matplotlib 1.5
- numpy 1.11
- pandas 0.18
- pytest 2.9
- python-dateutil 2.6
- scikit-image 0.12
- scipy 0.18
- setuptools 28.6
- OpenCV 2.4
- SQLite 3.7
- Git 1.8
Installation tutorials¶
The tutorials below require that you have administrator privileges. If you are not logged in as the root user you will need to execute the following commands with root authority by prepending all commands with the sudo command. If you do not have administrator privileges you will need to contact your system administrator or manually install the dependencies into your user directory.
RedHat Linux¶
We use Centos x86 64-bit minimal release 7.3 currently on our system. The minimal install is a bare-bones server installation with only necessary packages installed. More complete editions of CentOS, including those with a graphical user interface should work fine as well. After installation, connect to the server with SSH or a local terminal and execute the following commands to install PlantCV.
Install the developer tools (includes compilers and other tools)
sudo yum groupinstall "Development tools"
Install additional software dependencies
sudo yum install opencv opencv-devel opencv-python python-setuptools
Clone the PlantCV repository
git clone https://github.com/danforthcenter/plantcv.git
The default branch (master) is the latest release. If you want to check out a specific version:
# Switch to a stable release
cd plantcv
git checkout v1.1
Install PlantCV
sudo python setup.py install
Or to install to a local directory:
python setup.py install --prefix /home/username
If everything is working, the following should run without errors:
python -c 'import plantcv'
Or for more extensive tests:
cd plantcv
py.test -v tests/tests.py
Ubuntu Linux¶
Script-based installation¶
Clone the PlantCV repository:
git clone https://github.com/danforthcenter/plantcv.git
Note that the following may not be merged in the main repository at this time. The fallback may be this fork.
Run the setup script:
cd plantcv
bash scripts/setup.sh
The script guides you through the installation steps. Successful completion ends with a usage report.
The script has been tested on Ubuntu x86_64-bit 16_04 server edition.
Manual¶
We tested Ubuntu x86 64-bit 14.04 server edition.
After installation, connect to the server with SSH or a local terminal and execute the following commands
to install PlantCV.
Install software dependencies
sudo apt-get install git libopencv-dev python-opencv sqlite3 python-setuptools libpython2.7-dev python-pip
Add the OpenCV distribution for Python to find it:
export PYTHONPATH=/usr/lib/python2.7/dist-packages
Clone the PlantCV repository into your home directory
git clone https://github.com/danforthcenter/plantcv.git
Install the minimum dependencies:
pip install -r requirements.txt
The default branch (master) is the latest release. If you want to check out a specific version:
# Switch to a stable release
cd plantcv
git checkout v1.1
Install PlantCV
sudo python setup.py install
Or to install to a local directory:
python setup.py install --prefix /home/username
If everything is working, the following should run without errors:
python -c 'import plantcv'
Or for more extensive tests:
cd plantcv
py.test -v tests/tests.py
Mac OSX¶
Tested on OSX 10.11.
With MacPorts¶
Clone the PlantCV repository:
git clone https://github.com/danforthcenter/plantcv.git
Note that the following may not be merged in the main repository at this time. The fallback may be this fork.
Run the setup script:
cd plantcv
bash scripts/setup.sh
The script should guide you through the installation steps. Successful completion ends with a usage report.
With Brew¶
Procedure modified from here.
Install Homebrew by following the instructions here.
Install OpenCV with Homebrew
brew tap homebrew/science
brew install opencv
Add OpenCV to your PYTHONPATH. Use your favorite editor to edit ~/.bash_profile
(or .bashrc or .profile) and
add the following line:
export PYTHONPATH=$PYTHONPATH:/usr/local/lib/python2.7/site-packages
Clone the PlantCV repository into your home directory
git clone https://github.com/danforthcenter/plantcv.git
The default branch (master) is the latest release. If you want to check out a specific version:
# Switch to a stable release
cd plantcv
git checkout v1.1
Install PlantCV
sudo python setup.py install
Or to install to a local directory:
python setup.py install --prefix /home/username
If everything is working, the following should run without errors:
python -c 'import plantcv'
Or for more extensive tests:
cd plantcv
py.test -v tests/tests.py
Python virtual environment¶
Install OpenCV as documented for your system.
Create a Python virtual environment (assumes OpenCV is already installed in the system).
virtualenv plantcv-venv --system-site-packages
Install PlantCV into the virtual environment.
cd plantcv-venv
# Activate the virtual environment
source bin/activate
# Clone PlantCV
git clone https://github.com/danforthcenter/plantcv.git
# Install PlantCV
cd plantcv
python setup.py install
Windows¶
Tested on Windows 10.
The easiest way to get PlantCV working on Windows is to use Anaconda. An alternate approach might be to use the new Linux subsystem for Windows, but we have not tested that yet.
Install Anaconda (tested with 4.3.1) from here. Download and install the Python 2.7 version that is appropriate for your system (we used the 64-bit installer).
Run the Anaconda Prompt application and update Anaconda:
conda update -q conda
Install prerequisite Python packages (most are already installed by default):
pip install argparse
pip install matplotlib
pip install numpy
pip install pandas
pip install pytest
pip install python-dateutil
pip install scikit-image
pip install scipy
Use Anaconda to install OpenCV and SQLite3:
conda install -c menpo opencv=2.4.11
conda install -c blaze sqlite3
Clone the PlantCV repository and install it in the Anaconda environment:
git clone https://github.com/danforthcenter/plantcv.git
cd plantcv
python setup.py install
If everything is working, the following should run without errors:
python -c 'import plantcv'
Or for more extensive tests:
cd plantcv
py.test -v tests/tests.py
Cloud9 IDE¶
Cloud9 is a development environment in the cloud that works with Chromebooks or other thin clients. The IDE workspaces are powered by Docker Ubuntu containers within a web browser.
After signing up for an account create a new workspace and choose a Python template.
Install update
sudo apt-get update
Install software dependencies
sudo apt-get install git libopencv-dev python-opencv python-numpy python-matplotlib sqlite3
Clone the PlantCV repository into your home directory
git clone https://github.com/danforthcenter/plantcv.git
The default branch (master) is the latest release. If you want to check out a specific version:
# Switch to a stable release
cd plantcv
git checkout v1.1
Install PlantCV
sudo python setup.py install
After installation test with the following:
python -c 'import plantcv'
You will be given the following error:
libdc1394 error: Failed to initialize libdc1394
libdc1394 allows a program to interface with cameras that work on the ieee1394 standard(firewire). Due to no option to enable USB access in the Cloud9 workspace this error will keep occuring when running a pipeline. This error will have no effect on the output of your pipelines and can continue working despite the warning.
To temporarily remove the driver and error use:
sudo ln /dev/null /dev/raw1394
Test import again and you should see no more errors. Restarting workspace will require input to remove libdc1394 error again.
python -c 'import plantcv'