Yi Jiang

Volume rendering fails if an array dimension is larger than 2048

2

**Describe the bug** I get an error message when visualizing a dataset with size of 2500x2500x100. After some trials, it seems that the error occurs if an array dimension is...

Reset center of rotation after transforms

3

The default rotation center is at the center of the matrix: If I do some transform that changes data size, say downsample by 2, then the rotation center often ends...

Add wrapper functions and an example script for an automatic parameter tuning workflow based on Bayesian optimization with Gaussian processes. These functions can be used with external python libraries and...

If diffraction patterns are removed based on p.avg_photon_threshold or p.avg_photon_threshold_ub, loading initial scan positions from .mat files will not work because the number of positions is different from the number...

It might be useful to do position correction on multiple object layers in multi-slice ptychography. One way is to calculate position updates using each object layer and then "average" them...

optimize sample thickness during multi-slice ptycho reconstruction

2

I think it's possible to make use of existing code to optimize sample thickness (delta_z) during GPU_MS reconstruction. Functions worth checking out: +GPU_MS/LSQML.m +GPU_MS/private/gradient_NF_propagation_solver.m +ML_MS/gradient_ptycho_MS.m +ML_MS/calc_ms_grad.c

The TV minimization in GPU engines currently uses the Chambolle algorithm, which seems to be too aggressive with the default parameters. It's worth testing some other TV algorithms. Here is...

implement coarse position correction

1

Currently the best way to correct large position errors in ptychography is to do low-resolution reconstruction using cropped data. However, sometimes reconstruction may fail if diffraction patterns are too small,...

In ptycho_solver.m, the loop "ll = 1:max(par.object_modes, par.Nscans)" for object constraints (e.g. apply_smoothness_constraint) will result in error if multiple scans share the same object. In this case, the number of...

method for reduce crosstalk in multi-slice ptychography

2

This could be useful for resolving layer structures in multi-slice ptychographic reconstruction https://arxiv.org/abs/2102.00869