search

ComputationalCryoEM / ASPIRE-Python

Algorithms for Single Particle Reconstruction
http://spr.math.princeton.edu
GNU General Public License v3.0
46 stars 21 forks source link

Unified input and output for star and mrc files #141

Open junchaoxia opened 4 years ago

junchaoxia commented 4 years ago

Our ASPIRE Python package defines the IO operations for the output star file and mrc files using the function save_star as below: https://github.com/ComputationalCryoEM/ASPIRE-Python/blob/master/src/aspire/io/starfile.py#L164

It generates a new star file for the input ImageSource object and multiple MRC files based on the batch size. It is not clean that it is fully consistent with RELION format. For example RELION uses the project folder as default root path and all MRC files and folders created by different submodules and job tasks are referring to this project folder. We need to have similar thing for all submodules and make it easy to exchangable with RELION. There might be two things to follow: 1) format consistent with RELION; 2) better organization to follow for different ImageSource Classes.

junchaoxia commented 3 years ago

In a comment of PR #337, we think it is better to re-implement save function in the ImageSource class with two separate parts, save_metadata using star files and save_images using mrc files. For the derived ImageSource Classes, we can override save function for different options to save star files and/or mrc files.