edtools
Collection of tools for automated processing and clustering of electron diffraction data
Science Score: 59.0%
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Low similarity (16.8%) to scientific vocabulary
Keywords
Repository
Collection of tools for automated processing and clustering of electron diffraction data
Basic Info
- Host: GitHub
- Owner: instamatic-dev
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: https://edtools.readthedocs.io
- Size: 461 KB
Statistics
- Stars: 11
- Watchers: 8
- Forks: 9
- Open Issues: 0
- Releases: 5
Topics
Metadata Files
readme.md
edtools
Collection of tools for automated processing and clustering of batch 3-dimensional electron diffraction (3D ED) datasets.
The source for this project is available here.
Installation
Install using pip install edtools. Installation should take less than 20 seconds on a normal desktop.
Find the latest releases for the versions that have been tested on.
OS Requirement
Windows 10 or newer.
Software Requirements
- Python 3.6+ including
numpy,scipy,matplotlib, andpandaslibraries sginfoorcctbx.pythonmust be available on the system path foredtools.make_shelx- Access to WSL
- XDS package must be installed properly under WSL
Package dependencies
Check pyproject.toml for the full dependency list and versions.
Documentation
See the documentation at https://edtools.readthedocs.io.
Pipeline tools
At any step, run edtools.xxx -h for help with possible arguments.
autoindex.py
Looks for files matching XDS.INP in all subdirectories and runs them using XDS.
In: XDS.INP
Out: XDS data processing on all files
Usage:
edtools.autoindex
extractxdsinfo.py
Looks files matching CORRECT.LP in all subdirectories and extracts unit cell/integration info. Summarizes the unit cells in the excel file cells.xlsx and cells.yaml. XDSASCII.HKL files matching the completeness / CC(1/2) criteria are listed in filelist.txt. Optionally, gathers the corresponding `XDSASCII.HKLfiles in the local directory. Thecells.yaml` file can be used as input for further processing.
In: CORRECT.LP
Out: cells.yaml
cells.xlsx
filelist.txt
Usage:
edtools.extract_xds_info
find_cell.py
This program a cells.yaml file and shows histogram plots with the unit cell parameters. This program mimicks CELLPARM and calculates the weighted mean lattice parameters, where the weight is typically the number of observed reflections (defaults to 1.0). For each lattice parameter, the mean is calculated in a given range (default range = median+-2). The range can be changed by dragging the cursor on the histogram plots.
Alternatively, the unit cells can be clustered by giving the --cluster command, in which a dendrogram is shown. The cluster cutoff can be selected by clicking in the dendrogram. The clusters will be written to cells_cluster_#.yaml.
In: cells.yaml
Out: mean cell parameters
cells_*.yaml (clustering only)
Usage:
edtools.find_cell cells.yaml --cluster
make_xscale.py
Prepares an input file XSCALE.INP for XSCALE and corresponding XDSCONV.INP for XDSCONV. Takes a cells.yaml file or a series of XDS_ASCII.HKL files as input, and uses those to generate the XSCALE.INP file.
In: cells.yaml / XDS_ASCII.HKL
Out: XSCALE.INP
Usage:
edtools.make_xscale cells.yaml -c 10.0 20.0 30.0 90.0 90.0 90.0 -s Cmmm
cluster.py
Parses the XSCALE.LP file for the correlation coefficients between reflection files to perform hierarchical cluster analysis (Giordano et al., Acta Cryst. (2012). D68, 649658). The cutoff threshold can be selected by clicking in the dendrogram window. The program will write new XSCALE.LP files to subdirectories cluster_#, and run XSCALE on them, and (if available), pointless.
In: XSCALE.LP
Out: cluster_n/
filelist.txt
*_XDS_ASCII.HKL
XSCALE processing
Pointless processing
shelx.hkl
shelx.ins (optional)
Usage:
edtools.cluster
Helper tools
make_shelx.py
Creates a shelx input file. Requires sginfo to be available on the system path to generate the SYMM/LATT cards.
In: cell, space group, composition
Out: shelx.ins
Usage:
edtools.make_shelx -c 10.0 20.0 30.0 90.0 90.0 90.0 -s Cmmm -m Si180 O360
run_pointless.py
Looks for XDS_ASCII.HKL files specified in the cells.yaml, or on the command line and runs Pointless on them.
In: cells.yaml / XDS_ASCII.HKL
Out: Pointless processing
update_xds.py
Looks files matching CORRECT.LP in all subdirectories, and updates the cell parameters / space group as specified.
In: XDS.INP
Out: XDS.INP
Usage:
edtools.update_xds -c 10.0 20.0 30.0 90.0 90.0 90.0 -s Cmmm
findrotationaxis.py
Finds the rotation axis and prints out the inputs for several programs (XDS, PETS, DIALS, Instamatic, and RED). Implements the algorithm from Gorelik et al. (Introduction to ADT/ADT3D. In Uniting Electron Crystallography and Powder Diffraction (2012), 337-347). The program reads XDS.INP to get information about the wavelength, pixelsize, oscillation angle, and beam center, and SPOT.XDS (generated by COLSPOT) for the peak positions. If the XDS.INP file is not specified, the program will try to look for it in the current directory.
In: XDS.INP, SPOT.XDS
Out: Rotation axis
Usage:
edtools.find_rotation_axis [XDS.INP]
Demo of using edtools to process batch 3D electron diffraction datasets
See the demo at https://edtools.readthedocs.io/en/latest/examples/edtools_demo.html.
Owner
- Name: Instamatic
- Login: instamatic-dev
- Kind: organization
- Repositories: 5
- Profile: https://github.com/instamatic-dev
GitHub Events
Total
- Create event: 2
- Release event: 2
- Issues event: 4
- Issue comment event: 5
- Push event: 4
- Pull request review event: 1
- Pull request event: 2
- Fork event: 2
Last Year
- Create event: 2
- Release event: 2
- Issues event: 4
- Issue comment event: 5
- Push event: 4
- Pull request review event: 1
- Pull request event: 2
- Fork event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Stef Smeets | s****s@m****e | 40 |
| Stef Smeets | s****s@t****l | 32 |
| TM | t****g@g****m | 16 |
| Stef Smeets | s****s | 15 |
| Bin Wang | w****7@s****m | 11 |
| Stef Smeets | s****s@e****l | 10 |
| binwang | b****g@v****m | 9 |
| BinWang | b****g@s****e | 7 |
| David Waterman | d****n@g****m | 3 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 7
- Total pull requests: 18
- Average time to close issues: 3 months
- Average time to close pull requests: about 19 hours
- Total issue authors: 5
- Total pull request authors: 5
- Average comments per issue: 1.86
- Average comments per pull request: 0.89
- Merged pull requests: 18
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 1
- Average time to close issues: about 13 hours
- Average time to close pull requests: 1 day
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 2.0
- Average comments per pull request: 4.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- dagewa (2)
- iverks (2)
- danielnrainer (1)
- stefsmeets (1)
- aurorateien (1)
Pull Request Authors
- asdfdsa (6)
- stefsmeets (6)
- Taimin (3)
- dagewa (2)
- iverks (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- pypi 57 last-month
- Total dependent packages: 0
- Total dependent repositories: 1
- Total versions: 6
- Total maintainers: 1
pypi.org: edtools
Collection of tools for automated processing and clustering of electron diffraction data.
- Documentation: https://edtools.readthedocs.io/
- License: bsd-3-clause
-
Latest release: 1.1.1
published 9 months ago