Skip to content

Latest commit

 

History

History
20 lines (18 loc) · 1.32 KB

README.md

File metadata and controls

20 lines (18 loc) · 1.32 KB
Raw

BOTalign

This is an algorithm for aligning three-dimensional objects represented as three dimensional arrays $V_1,V_2\in \mathbb{R}^{L\times L\times L}$. More details can be found in our manuscript https://arxiv.org/pdf/2305.12310.pdf.

Dependencies

The algorithm requires the following packages:

  • ASPIRE
  • numpy
  • scipy
  • mrcfile
  • pymanopt

Usage

The user can simply download the files utils_BO.py and wemd.py. The main alignment algorithm can be found in utils_BO.py as align_BO, which takes in the two volumes $V_1,V_2$ to be aligned and four parameters:

  • Loss type: 'wemd' or 'eu'
  • Downsampling level: an integer
  • Number of iterations: an integer
  • Whether to perform refinement: True or False

The data folder contains one test volume (more can be found on EMDB). The test_BOTalign.py conducts a comparison on four combinations of the parameters that we illustrated in the manuscript.

Comparisons

To reproduce the comparison results in the manuscript, install the EMalign and the alignOT packages, and run test_comparison.py. For alignOT, one needs to download all the files in their alignOT folder and put them in the same directory as test_comparison.py.