/show

Primary LanguagePython

This project provides a Python script show for visualizing 3D image volume, tensor field, vector field, large number of curves, and meshes.

It can be useful for people who analyze medical images in Matlab but would like to visualize data efficiently elsewhere.

The basic work flow is to

- save data in `Matlab` in `mat` format
- run `show` in a terminal or in a `ipython` interpreter to visualize the data

Install Mayavi

As of Feb 24, 2022,

  • Mayavi is not surpported on M1 Mac 2021;
  • I met the black screen problem in installing Mayavi via conda/mamba on Ubuntu Mate 20.04, which is solved by following the pip approach for installation.

Install dependency pyvtk (for viewing tensor only)

git clone https://github.com/hakostra/pyvtk
git checkout hakostra/tensor-out-encoding-fix
cd pyvtk
pip install .

(If pyvtk is installed by pip install pyvtk, an error will occur in saving tensor: _"TypeError: sequence item 1: expected str instance, bytes found"_

save data in matlab

load('test_data')

savePaths4mayaviRGBchu('~/f', fibers)
saveTensorScalarSlices4mayavi('~/t', noise_free_data, 10)
saveImageVolum3d4mayavi('~/i', noise_free_data.intensity, 1)
saveVectors4mayavi('~/v', test_data, 1) % single color

to use show

  • on command line

    $ show -ft f.mat
$ show -t t.mat
$ show -i i.mat
$ show -fl f.mat -i i.mat -t t.mat

  • in ipython interpreter

    In [1]: %run show_with_full_path -i i.mat

Note: user interaction with Mayavi window can be recorded as Python code, which could be useful for later use, e.g., creating other functions.