Suite of useful tools for manipulating medical images.
Project description
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.
There are two ways of installing I2T2 and its dependencies:
- Using
pip
:
conda create -n I2T2 python=3.7
conda activate I2T2
pip install I2T2
conda install -c conda-forge gdcm
- Via 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 I2T2
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.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')
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