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توضیحات

Collection of tools for automated processing and clustering of electron diffraction data.

ویژگی	مقدار
سیستم عامل	-
نام فایل	edtools-1.0.4
نام	edtools
نسخه کتابخانه	1.0.4
نگهدارنده	['Stef Smeets']
ایمیل نگهدارنده	['s.smeets@esciencecenter.nl']
نویسنده	Stef Smeets
ایمیل نویسنده	s.smeets@esciencecenter.nl
آدرس صفحه اصلی	http://github.com/instamatic-dev/edtools
آدرس اینترنتی	https://pypi.org/project/edtools/
مجوز	BSD-3-Clause

[![GitHub Workflow Status](https://img.shields.io/github/workflow/status/instamatic-dev/edtools/build)](https://github.com/instamatic-dev/edtools/actions) [![PyPI - Python Version](https://img.shields.io/pypi/pyversions/edtools)](https://pypi.org/project/edtools/) [![PyPI](https://img.shields.io/pypi/v/edtools.svg?style=flat)](https://pypi.org/project/edtools/) [![PyPI - Downloads](https://img.shields.io/pypi/dm/edtools)](https://pypi.org/project/edtools/) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5727188.svg)](https://doi.org/10.5281/zenodo.5727188) # 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][src]. [src]: https://github.com/instamatic-dev/edtools ## Installation Install using `pip install edtools`. Installation should take less than 20 seconds on a normal desktop. Find the latest [releases](https://github.com/instamatic-dev/edtools/releases) for the versions that have been tested on. ## OS Requirement Windows 10 or newer. ## Software Requirements - Python 3.6+ including `numpy`, `scipy`, `matplotlib`, and `pandas` libraries - [`sginfo`](https://github.com/rwgk/sginfo) or [`cctbx.python`](https://cctbx.github.io/installation.html#installation) must be available on the system path for `edtools.make_shelx` - Access to [WSL](https://en.wikipedia.org/wiki/Windows_Subsystem_for_Linux) - XDS package must be installed properly under WSL ## Package dependencies Check [pyproject.toml](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 ``` ### extract_xds_info.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`. XDS_ASCII.HKL files matching the completeness / CC(1/2) criteria are listed in `filelist.txt`. Optionally, gathers the corresponding `XDS_ASCII.HKL` files in the local directory. The `cells.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`](http://xds.mpimf-heidelberg.mpg.de/html_doc/cellparm_program.html) 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, 649–658). 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 ``` ### find_rotation_axis.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.

نیازمندی

مقدار	نام
>=1.18.2	numpy
>=3.2.1	matplotlib
>=1.4.1	scipy
>=1.0.3	pandas
>=3.1.2	uncertainties
>=5.4.1	PyYAML
>=3.0.10	openpyxl

زبان مورد نیاز

مقدار	نام
>=3.6.1	Python

نحوه نصب

نصب پکیج whl edtools-1.0.4:

pip install edtools-1.0.4.whl

نصب پکیج tar.gz edtools-1.0.4:

pip install edtools-1.0.4.tar.gz