README

Quick guide - install (macOS/linux)

Download this repository using git

mkdir -p ~/code & git clone https://github.com/alonsoJASL/imatools ~/code/imatools

Environments

Option 1 (Recommended). Use Conda + Poetry

Poetry is a tool for dependency management. We create the environment with Anaconda and manage dependencies with Poetry.

1. Install Poetry in your computer
2. Install Anaconda
3. Create a new environment with the file provided: conda env create -f environment.yaml
4. Activate the environment conda activate imatools
5. Install the dependencies using Poetry poetry install --only main.

Poetry will read from the poetry.lock file and install the exact dependencies used to develop this project.

If you want to experiment with dependencies versions, delete the lock file and modify the pyproject.toml before poetry install --only main

Option 2. Only use CONDA

Anaconda is useful, but it can be slow at managing dependencies. It is recommended to use poetry.

Setup conda environment

You only need to do this once

Download anaconda, then on a terminal type:

conda create -n imatools python=3.9 -y & conda activate imatools

Copy the following to install the python dependencies of this project

conda install -c conda-forge vtk=9.2.6 simpleitk numpy scipy=1.9.2 matplotlib pandas seaborn networkx scikit-image nibabel pydicom -n imatools -y

Adjust PYTHONPATH

Sometimes you will need to set the PYTHONPATH variable, do this by opening a termina, changing into imatools directory cd /path/to/imatools and pasting the following:

export PYTHONPATH=$PYTHONPATH:$(pwd)

Example: Calculate volume & area of vtk file

Open a Terminal. Navigate to the code folder:

cd ~/code/imatools

Activate the anaconda environment

conda activate imatools

Run the volume code by typing

python calculate_volume.py /path/to/file.vtk

You can type python calculate_volume.py + SPACE and then drag the file from Finder into the terminal window if you do not know the path.

Some minimal tutorials:

• Create surface meshes from your multilabel segmentations

Alternative minimal setup#

While this is OK, it is not necessary as we use VTK 9.2.6, which allows to specify the version of Legacy VTK ASCII files. To use with VTK 8.1 to save vtk meshes in legacy VTK Writer 4.2.

conda create -n vtk81 python=3.6 -y
conda activate vtk81
conda install -c conda-forge vtk=8.1 -y
conda install -c conda-forge numpy -n vtk81 -y  
conda install -c conda-forge itk