aorta_houghcircle

Generating aorta measurements from pulmonary artery view MRI using hough circles

Set up the python environment (installing all python package dependencies)

To ensure all required packages are installed, run the following command:

pip install -r requirements.txt

Package List:

cycler==0.10.0
decorator==4.4.2
future==0.18.2
imagecodecs==2020.2.18
imageio==2.8.0
kiwisolver==1.2.0
matplotlib==3.2.1
networkx==2.4
numpy==1.18.4
opencv-contrib-python-headless==4.2.0.32
pandas==1.0.3
Pillow==7.1.2
pydicom==1.4.2
pyparsing==2.4.7
python-dateutil==2.8.1
pytz==2020.1
PyWavelets==1.1.1
scikit-image==0.17.2
scipy==1.4.1
six==1.14.0
tifffile==2020.5.11
torch==1.5.0
torchvision==0.6.0

Running the code with an example

To see the process of segmentation and generating measurements in action, simply run the code:

python Ao_segment.py --root_dir test_data/zips --csv_data test_data/labels.csv --threads 1 --plot

Results

The segmentation of the examples would be like the images shown below:

Example 1:

Example 2:

Example 3: