I2T2 0.0.3

Suite of useful tools for manipulating medical images.

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

There are two ways of installing I2T2 and its dependencies:

1. Without explicit github download, using pip:

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

2. With github download

git clone https://github.com/UCSF-intelligent-imaging/I2T2/
cd I2T2/
conda env create -f environment.yml

Test your installation

conda activate I2T2
python
>>> import I2T4

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

How to use

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

data_path = '../data/knee/'
try:
    array = dcm2array(path_to_dicom_dir = data_path, sort_by_slice_location=True)
    plt.imshow(array[:,:,0])
    plt.show()
except:
    print('could not load array')