Intelligent Imaging Tools and Tasks (I2T2)

Library of useful tools for Medical Imaging Handling

Instructions for installation and usage examples can be found below.

Install

It's highly recommended you install I2T2 and its dependencies in a virtual environment (conda or others), so that you don't interfere with system-wide python packages.

1. Installing via github download:

git clone https://github.com/UCSF-intelligent-imaging/I2T2/
cd I2T2
conda create -n I2T2 python=3.7
conda activate I2T2
pip install nbdev jupyter
pip install -e .
conda install -c conda-forge gdcm

2. Installing via pip (latest stable version)

conda create -n I2T2 python=3.7
conda activate I2T2
pip install nbdev jupyter
pip install I2T2
conda install -c conda-forge gdcm

Test your installation

conda activate I2T2
python
>>> import I2T2

NOTE:

I2T2 uses GDCM to uncompress some DICOMs.

Make sure to have GDCM installed in your conda environment via conda install -c conda-forge gdcm

conda activate I2T2
python
>>> import gdcm

Using I2T2

# example usage:
from I2T2.io import *
import matplotlib.pyplot as plt

data_path = '../data/knee/'
try:
    array = load_dcm(path_to_dicom_dir = data_path, sort_by_slice_location=True)
    plt.imshow(array[:,:,0])
    plt.show()
except:
    print('could not load array')