# Name

sxresample - calculate resampled 3D reconstructions

TO BE WRITTEN

## Usage

*Usage in command lines*:

sxbootstrap_bigdisk.py prj_stack wgtfile outdir bufprefix --nvol --nbufvol --seedbase --snr --genbuf --CTF --ngroup --npad --zero_wgts --MPI --core --verbose

*Usage in python programming*:

bootstrap_bigdisk(prj_stack, wgtfile, outdir, bufprefix, nvol, nbufvol, seedbase, snr, genbuf, sharebuf)

## Input

- prj_stack
- projection stack file
- wgtfile
the weight of each projection. This is a text file with the weights of projections int he first column. The weights is proportional to the probability of a projection to be selected in bootstrap calculation. This file is generated using sxbootstrap_calcwgts.py.

- buf_prefix
the prefix for the buffer file. These files were generated using sxbootstrap_genbuf.py.

- nvol
- number of bootstrap volumes to be generated
- nbufvol
- number of fftvols in the memory
- genbuf
- whether generate the buffer
- ngroup
- how many groups to use (each group will share a buffer)
- zero_wgts
- Percentage of maximum weights to be set to zero (default 0.0)
- seedbase
- random seed base
- core
- keep projections with high weights without resampling
- verbose
- verbose level: 0 no, 1 yes

## Output

- outdir
- bootstrap volumes will be in put in this directory with names "bsvolxxxx.hdf", where xxxx is the rank of CPU. Warning: If the output directory already exists, the program will crash. Please change the name of directory and restart the program.

## Options

- nvol
- number of bootstrap volumes to be generated
- nbufvol
- number of volumes to be generated simultaneously. It depend on how much memory there is available for each CPU and the image size in pixels. A single 3D reconstruction will require 0.000512*nx^3 MB of memory. Thus, if image size is 75, one reconstruction will take 216 MB of memory. If image size is 64, it will take 134 MB of memory. The nbufvol is computed by dividing the total memory available for a CPU by the memory required for one 3D reconstruction. Note on a cluster memory per CPU is typically memory available on a node divided by the number of CPUs.
- CTF
- use CTF in reconstruction
- snr
- Signal to Noise ratio
- seedbase
- seed for the random number generator. If in order to compute sufficient number of bootstrap volumes the program is ran multiple times the seedbase has to be modified (increased by the number of volumes already generated).

# Description

This is third and the most time consuming step of real-space variance calculations.

# Method

# Reference

# Author / Maintainer

Wei Zhang

# Keywords

- category 1
- APPLICATIONS

# Files

applications.py, sxbootstrap_bigdisk.py

# See also

# Maturity

- stable
- works for most people, has been tested; test cases/examples available.

# Bugs

None. It is perfect.