Package: edtools
edtoolsCollection of tools for automated processing and clustering of batch 3-dimensional electron diffraction (3D ED) datasets.The source for this project is available here.InstallationInstall usingpip install edtools. Installation should take less than 20 seconds on a normal desktop.Find the latestreleasesfor the versions that have been tested on.OS RequirementWindows 10 or newer.Software RequirementsPython 3.6+ includingnumpy,scipy,matplotlib, andpandaslibrariessginfoorcctbx.pythonmust be available on the system path foredtools.make_shelxAccess toWSLXDS package must be installed properly under WSLPackage dependenciesCheckpyproject.tomlfor the full dependency list and versions.DocumentationSee the documentation athttps://edtools.readthedocs.io.Pipeline toolsAt any step, runedtools.xxx -hfor help with possible arguments.autoindex.pyLooks for files matchingXDS.INPin all subdirectories and runs them usingXDS.In:  XDS.INP
Out: XDS data processing on all filesUsage:edtools.autoindexextract_xds_info.pyLooks files matchingCORRECT.LPin all subdirectories and extracts unit cell/integration info. Summarizes the unit cells in the excel filecells.xlsxandcells.yaml. XDS_ASCII.HKL files matching the completeness / CC(1/2) criteria are listed infilelist.txt. Optionally, gathers the correspondingXDS_ASCII.HKLfiles in the local directory. Thecells.yamlfile can be used as input for further processing.In:  CORRECT.LP
Out: cells.yaml
     cells.xlsx
     filelist.txtUsage:edtools.extract_xds_infofind_cell.pyThis program a cells.yaml file and shows histogram plots with the unit cell parameters. This program mimicksCELLPARMand 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--clustercommand, in which a dendrogram is shown. The cluster cutoff can be selected by clicking in the dendrogram. The clusters will be written tocells_cluster_#.yaml.In:  cells.yaml
Out: mean cell parameters
     cells_*.yaml (clustering only)Usage:edtools.find_cell cells.yaml --clustermake_xscale.pyPrepares an input fileXSCALE.INPforXSCALEand correspondingXDSCONV.INPforXDSCONV. Takes acells.yamlfile or a series ofXDS_ASCII.HKLfiles as input, and uses those to generate theXSCALE.INPfile.In:  cells.yaml / XDS_ASCII.HKL
Out: XSCALE.INPUsage:edtools.make_xscale cells.yaml -c 10.0 20.0 30.0 90.0 90.0 90.0 -s Cmmmcluster.pyParses theXSCALE.LPfile 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 newXSCALE.LPfiles to subdirectoriescluster_#, and runXSCALEon 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.clusterHelper toolsmake_shelx.pyCreates a shelx input file. Requiressginfoto be available on the system path to generate the SYMM/LATT cards.In:  cell, space group, composition
Out: shelx.insUsage:edtools.make_shelx -c 10.0 20.0 30.0 90.0 90.0 90.0 -s Cmmm -m Si180 O360run_pointless.pyLooks 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 processingupdate_xds.pyLooks files matchingCORRECT.LPin all subdirectories, and updates the cell parameters / space group as specified.In:  XDS.INP
Out: XDS.INPUsage:edtools.update_xds -c 10.0 20.0 30.0 90.0 90.0 90.0 -s Cmmmfind_rotation_axis.pyFinds 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 readsXDS.INPto get information about the wavelength, pixelsize, oscillation angle, and beam center, andSPOT.XDS(generated by COLSPOT) for the peak positions. If theXDS.INPfile is not specified, the program will try to look for it in the current directory.In:  XDS.INP, SPOT.XDS
Out: Rotation axisUsage:edtools.find_rotation_axis [XDS.INP]Demo of using edtools to process batch 3D electron diffraction datasetsSee the demo athttps://edtools.readthedocs.io/en/latest/examples/edtools_demo.html.