OpenVessel is an open-source Flask app that segments out portions of DICOM files using machine learning hosted on celery workers, and displays the result as a 3D objects using VTK.
git clone https://github.com/OpenVessel/Vessel-app.git
python3 -m venv vessel_env
vessel_env\Script\activate
pip3 install -r requirements.txt
If you do not have npm and nodeJS, follow this guide: Directions to install npm
Then, type this in the terminal starting at the Vessel-app
cd Back-end\vessel_app\static
npm install
npm run build
To run JavaScript for debugging, run
npm run watch
One of the main dependencies for the project is a tool called VTK, short for The Visualization Toolkit. It allows us to render 3D images of DICOM files.
Directions to install VTK on Windows
Our machine learning happens on various workers with the help of celery. Celery is included in requirements.txt, however it needs a Redis server to work off of.
Once you have Redis installed, you need to point to the the URL that the Redis broker is located at.
Open config.py and find these lines
class Config:
...
### Celery Workers ##########
CELERY_BROKER_URL='redis://localhost:6379/0'
CELERY_RESULT_BACKEND='redis://localhost:6379/0'
Change the redis://localhost:6379/0 to whatever port your Redis server is running on.
git clone https://github.com/OpenVessel/Vessel-app.git
python3 -m venv vessel_env
source vessel_env/bin/activate
pip3 install -r requirements.txt
If you do not have npm and nodeJS, follow this guide: Directions to install npm
Then, type this in the terminal starting at the Vessel-app
cd Back-end/vessel_app/static
npm install
npm run build
To run JavaScript for debugging, run
npm run watch
One of the main dependencies for the project is a tool called VTK, short for The Visualization Toolkit. It allows us to render 3D images of dicom files.
In this subsection, you will learn how to install VTK and it's dependancies for macOS.
-
Homebrew
-
Python 3.X
-
CMake
If you don't have Homebrew installed on your Mac, install it by going to Homebrew's website or by entering the command below in your Terminal.
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install.sh)"
Now, we'll use Homebrew to install VTK.
Enter the following into your Terminal.
brew install vtk
Install Kitware's CMake tool to download VTK's dependancies.
Go here to get the latest version.
Follow the steps below to download everything you'll need to run VTK.
-
Open CMake
-
Go to Tools > How to Install for Command Line Use
-
Click on "How to Install for Command Line Use"
-
Follow the instructions in the dialogue box that opens
To make sure that everything has gone smoothly, enter the following in the Terminal.
which cmake
If this works correctly, enter the following to make sure you have the latest version installed.
cmake --version
Our machine learning happens on various workers with the help of celery. Celery is included in requirements.txt, however it needs a Redis server to work off of.
In order to install Redis for MacOS enter the following commands into a command prompt:
brew install redis
brew services start redis
brew services stop redis
brew services restart redis
Once you have Redis installed, you need to point to the the URL that the Redis broker is located at.
Open config.py and find these lines
class Config:
...
### Celery Workers ##########
CELERY_BROKER_URL='redis://localhost:6379/0'
CELERY_RESULT_BACKEND='redis://localhost:6379/0'
Change the redis://localhost:6379/0 to whatever port your Redis server is running on.
We use Flask-SQLAlchemy to connect to our SQLite database, and Flask-Migrate by Miguel Grinberg to update the database as we make changes.
In order to run the Flask app you need to have a database.
First make your current working directory the Back-end folder in the repo.
cd Vessel-app/vessel_app/Back-end
Run these commands to initialize the database.
flask db init
flask db migrate
flask db upgrade
-
Make a new terminal
-
Go into the virtual environment
-
cd into Back_end
-
Run the command:
celery -A vessel_app.file_pipeline.celery_tasks.celery worker --loglevel=info -P gevent
Make sure you are in the Back-end directory then run
flask run
and the website will run on a local port for you!
git clone https://github.com/OpenVessel/Vessel-app.git
python3 -m venv vessel_env
vessel_env\Script\activate
pip3 install -r requirements.txt
One of the main dependencies for the project is a tool called VTK, short for The Visualization Toolkit. It allows us to render 3D images of DICOM files.
Directions to install VTK on Windows
Our machine learning happens on various workers with the help of celery. Celery is included in requirements.txt, however it needs a Redis server to work off of.
Once you have Redis installed, you need to point to the the URL that the Redis broker is located at.
Open config.py and find these lines
class Config:
...
### Celery Workers ##########
CELERY_BROKER_URL='redis://localhost:6379/0'
CELERY_RESULT_BACKEND='redis://localhost:6379/0'
Change the redis://localhost:6379/0 to whatever port your Redis server is running on.
git clone https://github.com/OpenVessel/Vessel-app.git
python3 -m venv vessel_env
source vessel_env/bin/activate
pip3 install -r requirements.txt
One of the main dependencies for the project is a tool called VTK, short for The Visualization Toolkit. It allows us to render 3D images of dicom files.
brew install vtk
Our machine learning happens on various workers with the help of celery. Celery is included in requirements.txt, however it needs a Redis server to work off of.
Install Redis
brew install redis
Once you have Redis installed, you need to point to the the URL that the Redis broker is located at.
Open config.py and find these lines
class Config:
...
### Celery Workers ##########
CELERY_BROKER_URL='redis://localhost:6379/0'
CELERY_RESULT_BACKEND='redis://localhost:6379/0'
Change the redis://localhost:6379/0 to whatever port your Redis server is running on.
We use Flask-SQLAlchemy to connect to our SQLite database, and Flask-Migrate by Miguel Grinberg to update the database as we make changes.
In order to run the Flask app you need to have a database. First make your current working directory the Back-end folder in the repo.
cd Vessel-app/vessel_app/Back-end
Run these commands to initialize the database.
flask db init
flask db migrate
flask db upgrade
Make sure you are in the Back-end directory then run
flask run
and the website will run on a local port for you!