Sparse Pattern INDexing toolkit

Installation

First, install some necessary tools. For CentOS users, just use the following command,

sudo yum install -y git wget bzip2

Then download SPIND package,

git clone https://github.com/LiuLab-CSRC/indexing.git

To integrate SPIND into CrystFEL, we add SPIND module to CrystFEL-0.6.2. See detailed installation instructions here.

SPIND is implemented using Python, you do not have to do standard configure, make, make install, just install necessary dependencies.

SPIND package has the following dependencies,

To make life easier, anaconda is highly recommended for Python-related library management.

Download anaconda for Python2.7 by

wget https://repo.continuum.io/archive/Anaconda2-5.0.1-Linux-x86_64.sh

Install anaconda,

bash Anaconda2-5.0.1-Linux-x86_64.sh

Accept the license then wait minutes for installation.

After the installation, make the installer prepend anaconda location to PATH in your .bashrc file.

Then source ~/.bashrc.

Finally, install SPIND dependencies using

conda install mpi4py yaml docopt tqdm

Installation is done! Congratulations!

2023-11-29

build a diagnosis tool for comparing the experimental pattern with the predicted from the SPIND-proposed soultion.

Name		Name	Last commit message	Last commit date
Latest commit History 84 Commits
docs		docs
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
SPIND.py		SPIND.py
SPIND_v2.py		SPIND_v2.py
config.yml		config.yml
crystfel_spind.tar		crystfel_spind.tar
extract_peaks.py		extract_peaks.py
gen_hkl_table_v2.py		gen_hkl_table_v2.py
generate_table.py		generate_table.py
index.py		index.py
merge.py		merge.py
preprocessing.py		preprocessing.py
simple_viewer.py		simple_viewer.py
util.py		util.py