| Generated on: | Fri Jun 20 03:53:22 2014 |
| Number of Control Plugins: | 117 |
| Number of Execution Plugins: | 155 |
| Number of Others Plugins: | 28 |
| EDPluginBioSaxsAsciiExportv1_0 | Control for Bio Saxs ascii export of integrated data : * Wait for the file to arrive * Retrieve metadata from the header * export as 3-column ascii file (EDPluginSaxsCurvesv1_0) * rewrite metadata |
| EDPluginBioSaxsAsciiExportv1_1 | Control for Bio Saxs ascii export of integrated data : * Wait for the file to arrive * Retrieve metadata from the header * export as 3-column ascii file (EDPluginSaxsCurvesv1_0) * rewrite metadata |
| EDPluginBioSaxsAveragev1_0 | Control for Bio Saxs Averaging of spectra in : * wait for azimuthally integrated files to arrive (EDPluginWaitMultiFile) * sum & divide spectra (EDPluginSaxsMCv1_0) * export as spec-file (EDPluginBioSaxsAsciiExportv1_0) |
| EDPluginBioSaxsAzimutIntv1_0 | Control for Bio Saxs azimuthal integration: * wait for normalized file to arrive (EDPluginWaitFile) * retrieve and update metadata (EDPluginBioSaxsMetadatav1_1) * apply mask (EDPluginSaxsAddv1_0) * Write metadata (EDPluginBioSaxsMetadatav1_1) * integrate (EDPluginSaxsAnglev1_0) * export as spec-file (EDPluginAsciiExportv1_0) |
| EDPluginBioSaxsAzimutIntv1_1 | Control for Bio Saxs azimuthal integration; suppose the mask is already applied by BioSaxsNormalizev1.1 : * wait for normalized file to arrive (EDPluginWaitFile) * retrieve and update metadata (EDPluginBioSaxsMetadatav1_0) * integrate (EDPluginSaxsAnglev1_0) * export as spec-file (EDPluginAsciiExportv1_1) TODO: switch the metadata from flat to more structured (sample/experiment setup) |
| EDPluginBioSaxsAzimutIntv1_2 | Control for Bio Saxs azimuthal integration; suppose the mask is already applied by BioSaxsNormalizev1.1 : * wait for normalized file to arrive (EDPluginWaitFile) * retrieve and update metadata (EDPluginBioSaxsMetadatav1_0) * integrate (EDPluginSaxsAnglev1_0) * export as 3-column ascii-file is done here to allow more precise header |
| EDPluginBioSaxsAzimutIntv1_3 | Control for Bio Saxs azimuthal integration; suppose the mask is already applied by BioSaxsNormalizev1.1 : * wait for normalized file to arrive (EDPluginWaitFile) * retrieve and update metadata (EDPluginBioSaxsMetadatav1_0) * integrate (directly vi pyFAI) * export as 3-column ascii-file is done here to allow more precise header Changelog since v1.2: use PyFAI instead of saxs_angle from Peter Boesecke |
| EDPluginBioSaxsFlushHPLCv1_0 | plugin that just flushes the HPLC data to disk |
| EDPluginBioSaxsHPLCv1_0 | plugin for processing Saxs data coming from HPLC runs subsequently: *ProcessOneFile, *subtraction of buffer *SaxsAnalysis todo: only store references: Wait for flush to construct HDF5 file and (possibly) web pages with PNG graphs |
| EDPluginBioSaxsMetadatav1_0 | Plugin for reading, updating and writing Metadata. |
| EDPluginBioSaxsNormalizev1_0 | Wait for the file to appear then do the normalization of the raw data by ring current and BeamStopDiode Finally append all metadata to the file (in post-processing). |
| EDPluginBioSaxsNormalizev1_1 | Wait for the file to appear then apply mask ; do the normalization of the raw data by ring current and BeamStopDiode and finally append all metadata to the file EDF. All "processing" are done with Numpy, Input/Output is handled by Fabio |
| EDPluginBioSaxsProcessOneFilev1_0 | Control plugin that does subsequent execution of: * EDPluginBioSaxsNormalizev1_1 * EDPluginBioSaxsAzimutIntv1_1 |
| EDPluginBioSaxsProcessOneFilev1_1 | Control plugin that does subsequent execution of: * EDPluginBioSaxsNormalizev1_1 * EDPluginBioSaxsAzimutIntv1_2 |
| EDPluginBioSaxsProcessOneFilev1_2 | Control plugin that does subsequent execution of: * EDPluginBioSaxsNormalizev1_1 * EDPluginBioSaxsAzimutIntv1_3 |
| EDPluginBioSaxsReduceFileSeriev1_0 | Control plugin that does: * n times processOneFile * synchronize plugins * smart merge at the end |
| EDPluginBioSaxsReprocessv1_0 | Control plugin that does what was in the Reprocess function in the original program |
| EDPluginBioSaxsSingleSamplev1_0 | Plugin that does the processing a sample: - 1 protein - 1 concentration - 2+ serie of buffer files: each file is individually reduced to 1D data - 1+ serie of sample files: each file is individually reduced to 1D data * Each serie is merged using smart merge * All buffer are averages (regardless to radiation damage) * All Samples are averages (they are at the same concentration) * buffer is subtracted from sample to obtain the final result |
| EDPluginBioSaxsSmartMergev1_0 | This plugin takes a set of input data files (1D SAXS) measure their differences (versus previous and versus first) and merge those which are equivalent Controled plugins: - Execplugins/WaitMultifile - EdnaSaxs/Atsas/DatCmp - EdnaSaxs/Atsas/DatAver |
| EDPluginBioSaxsSmartMergev1_1 | This plugin takes a set of input data files (1D SAXS) measure their differences (versus previous and versus first) and merge those which are equivalent v1.1 adds information from AutoRg Controlled plugins: - Execplugins/WaitMultifile - EdnaSaxs/Atsas/DatCmp - EdnaSaxs/Atsas/DatAver - EdnaSaxs/Atsas/AutoRg |
| EDPluginBioSaxsSmartMergev1_2 | This plugin takes a set of input data files (1D SAXS) measure their differences (versus previous and versus first) and merge those which are equivalent v1.1 adds information from AutoRg Controlled plugins: - Execplugins/WaitMultifile - EdnaSaxs/Atsas/DatCmp - EdnaSaxs/Atsas/DatAver - EdnaSaxs/Atsas/AutoRg |
| EDPluginBioSaxsSmartMergev1_3 | This plugin takes a set of input data files (1D SAXS) measure their differences (versus previous and versus first) and merge those which are equivalent v1.1 adds information from AutoSub Controlled plugins: - Execplugins/WaitMultifile - EdnaSaxs/Atsas/DatCmp - EdnaSaxs/Atsas/DatAver - EdnaSaxs/Atsas/AutoSub |
| EDPluginBioSaxsSmartMergev1_4 | This plugin takes a set of input data files (1D SAXS) measure their differences (versus previous and versus first) and merge those which are equivalent v1.1 adds information from AutoSub Controlled plugins: - Execplugins/WaitMultifile - EdnaSaxs/Atsas/DatCmp - EdnaSaxs/Atsas/DatAver - EdnaSaxs/Atsas/AutoSub - EdnaSaxs/SaxsAnalysis |
| EDPluginBioSaxsSubtractv1_0 | This plugin takes a set of input data files (1D SAXS) measure their differences (versus previous and versus first) and merge those which are equivalent v1.1 adds information from AutoSub Controlled plugins: - Execplugins/WaitMultifile - EdnaSaxs/Atsas/DatCmp - EdnaSaxs/Atsas/DatAver - EdnaSaxs/Atsas/AutoSub |
| EDPluginBioSaxsToSASv1_0 | This is basically just a wrapper for Irakli's SAS pipeline, but with parameters optimized for ESRF |
| EDPluginBioSaxsMetadatav1_1 | Plugin for reading, updating and writing Metadata. |
| EDPluginControlCopyUnitCellMTZtoPDBv10 | This is the Edna plugin control that runs subsequently the two execution plugins called MTZDUMPUnitCellSpaceGroupv10 and PDBSETUnitCellv10 -MTZDUMP to extract the Unit Cell parameters and the space group of an MTZ file -PDBSET to set the unit cell formerly extracted into the given PDB file. @author: Mark Basham, Jérôme Kieffer @copyright: CCP4 team, DLS & ESRF collaboration @license: GPLv3 or above |
| EDPluginExecMTZDUMPUnitCellSpaceGroupv10 | [To be replaced with a description of EDPluginExecProcessScriptTemplatev10] |
| EDPluginExecPDBSETUnitCellv10 | [To be replaced with a description of EDPluginExecProcessScriptTemplatev10] |
| EDPluginControlDLSArchiverv10 | DLS Archiver plugin |
| EDPluginExecICATIngesterv10 | DLS Archiver plugin |
| EDPluginExecSRBRegisterv10 | DLS Archiver plugin |
| EDPluginControlDCTPowderIntegrationv1_0 | This is the plugin-control for Diffraction Contrast Tomography for doing the azimutal integration of |
| EDPluginControlDCTPowderIntegrationv1_1 | This is the plugin-control for Diffraction CT for doing the azimuthal integration of images |
| EDPluginControlDCTReadHeaderv1_0 | [To be replaced with a description of EDPluginControlTemplatev1_0] |
| EDPluginControlDiffractionCTv1_0 | This is the EDNA control plug-in for diffraction contrast tomography. It is intented to run 2D integration provided by Fit2D for example and .... |
| EDPluginControlDiffractionCTv1_1 | This is the EDNA control plug-in for diffraction contrast tomography. It is intented to run 2D integration provided by Fit2D for example and .... |
| EDPluginControlDiffractionCTv1_2 | This is the EDNA control plug-in for diffraction contrast tomography. It is intented to run 2D integration provided by SPD for example and create a sinogram as a 3D array in HDF5.... |
| EDPluginDCTWriteSinogramv1_0 | This plugin is a part of the DiffractionCT project. It takes as input the path to a CIF file containing integrated intensities as well as the necessary header information. The CIF file could for example be the result of a 2D azimuthal integration performed by the plugin EDPluginControlDCTPowderIntegration-v1.0. It also takes as input the path to the directory where the sinogram images are (or will be if they don't exist) stored, as well as a sinogram file name prefix. The EDPluginDCTWriteSinogramv1_0 plugin produces one or several sinogram images depending on the header information in the CIF file. The XSDataResultWriteSinogram object contains a list of paths to these images. |
| EDPluginControlDIMPLECopySpaceGroupPDBtoMTZv10 | A plugin to copy the spacegroup name from a PDB file to an MTZ. |
| EDPluginControlDIMPLECopyUnitCellMTZtoPDBv10 | [To be replaced with a description of EDPluginControlTemplatev10] |
| EDPluginControlDIMPLEPipelineCalcDiffMapv10 | A pipeline to compute a difference map from an intensity data file from e.g. fast_dp and a putative correct structure. Aim is for ligand identification. |
| EDPluginControlDIMPLEPrepareMTZFileForRefinementv10 | A plugin to prepare the input reflection file from fast_dp for refinement with refmac. This will do the following: query pdb, get sequence (nres -> truncate) (spacegroup -> reindex) query mtz, get unit cell (+ spacegroup -> unique, freerflag) run truncate, copy in free column. |
| EDPluginControlDIMPLERefmacRigidBodyPhaserv10 | A control plugin that uses 2 exec plugins (RefmacRigidBody and Phaser) and returns a XYZ file depending on the values found in the input files (HKL and XYZ) |
| EDPluginExecDIMPLECADv10 | A wrapper for the CCP4 program CAD, with primary purpose: adding columns from two MTZ files together. |
| EDPluginExecDIMPLECheckValidHKLv10 | An EDNA plugin to check for the validity of mtz files |
| EDPluginExecDIMPLECheckValidXYZv10 | [To be replaced with a description of EDPluginExecTemplatev10] |
| EDPluginExecDIMPLEFREERFLAGv10 | An EDNA plugin to wrap the CCP4 program freerflag, which randomly assigns a give fraction (typically 5%) of the unique reflections to a free set, for validation. |
| EDPluginExecDIMPLEMTZDUMPv10 | [To be replaced with a description of EDPluginExecProcessScriptTemplatev10] |
| EDPluginExecDIMPLEPDBDUMPv10 | An EDNA plugin to dump some metadata from a PDB file to allow comparison with metadata in an MTX file. In particular, returns information about the unit cell, space group and amino acid sequence. |
| EDPluginExecDIMPLEPDBSETv10 | An EDNA plugin for the CCP4 program PDBSET |
| EDPluginExecDIMPLEPHASERv10 | An EDNA plugin for the CCP4 program Phaser |
| EDPluginExecDIMPLEPointlessOriginv10 | An EDNA plugin for the CCP4 program Pointless, to determine the correct origin for an input MTZ file with respect to an input PDB file. |
| EDPluginExecDIMPLEREFMACRigidBodyv10 | An EDNA plugin for the CCP4 program refmac5 for rigid body refinement. |
| EDPluginExecDIMPLEREINDEXv10 | An EDNA plugin for the CCP4 program reindex. |
| EDPluginExecDIMPLERefmacMonomerCheckv10 | A plugin to verify that an input PDB file is fine. |
| EDPluginExecDIMPLETRUNCATETESTv10 | An EDNA plugin for the CCP4 program truncate. |
| EDPluginExecDIMPLETRUNCATEv10 | An EDNA plugin for the CCP4 program truncate. |
| EDPluginExecDIMPLEUNIQUEv10 | A plugin to run the CCP4 program UNIQUE, which will calculate a list of Miller indices in an MTZ file from a unit cell, space group and resolution limit. |
| EDPluginExecDIMPLEREFMACRestrainedRefinementv10 |
| EDPluginAutoSubv1_0 | This is an EDNA plugin that tries to mimic the behavour of autosub: - find the best buffer (usually the merged one) - subtract data with the best buffer |
| EDPluginControlSaxsAnalysisv1_0 | Executes the pipeline: * AutoRg -> Extract the Guinier region and measure Rg, I0 * DatGnom -> transformation from reciprocal to direct space. measure Dmax. * DatPorod -> calculates the volume of the protein using the porod formula. |
| EDPluginControlSaxsPipelinev1_0 | Execute saxs reduce file serie and pipes it to autoRg. |
| EDPluginExecAutoRgv1_0 | Execution plugin for AutoRg (part of Atsas package) |
| EDPluginExecDamaverv0_1 | Execution plugin running DAMAVER pipeline for alignment of input pdb models, selecting the most typical one and building an averaged model |
| EDPluginExecDamfiltv0_1 | Execution plugin for ab-initio model determination using Damfilt |
| EDPluginExecDammifv0_1 | Execution plugin for ab-initio model determination using DAMMIF |
| EDPluginExecDamminv0_1 | Execution plugin for ab-initio model determination using DAMMIN |
| EDPluginExecDamstartv0_1 | Execution plugin for ab-initio model determination using Damstart |
| EDPluginExecDatGnomv1_0 | Plugin that simply runs datgnom; a clever version of gnom; on a 1D curve. |
| EDPluginExecDatPorodv1_0 | Plugin that simply runs datporod on a gnom file to calculate the volume according to the porod formula: VP = 2π2I(0)/Q where Q = ∫s2[I(s) - K]ds where K is a constant determined to ensure the asymptotical intensity decay proportional to s-4 at higher angles |
| EDPluginExecDataverv1_0 | Execution plugin that does the (basic) data averaging , part from Atsas package |
| EDPluginExecDatcmpv1_0 | Execution plugin to run datcmp: evaluation of the Similarity of two curves (in a 2-3 column ascii file) |
| EDPluginExecDatopv1_0 | Plugin that simply performs an operation on a (couple of) curves. operations can be ADD, SUB, MUL, DIV |
| EDPluginExecGnomv0_1 | Execution plugin for small angle scattering data processing using GNOM |
| EDPluginExecGnomv0_2 | Execution plugin for small angle scattering data processing using GNOM |
| EDPluginExecSupcombv0_1 | Execution plugin for ab-initio model determination using Supcomb |
| EDPluginControlMedianFilterImagev1_0 | Apply a median Filter from frames -with/2 to frame -with/2, pixel by pixel. |
| EDPluginControlStitchImagev1_0 | Control plugin doing automatic image alignment and stitching. |
| EDPluginWaitMultiFile | Plugins that waits for a set of files to be written and reach a certain minimum size |
| EDPluginChiToEDFv1_0 | This plugin reads the header of an EDF (ESRF Data File) and returns the header values as a python Dictionary. |
| EDPluginEDFReadHeaderv1_0 | This plugin reads the header of an EDF (ESRF Data File) and returns the header values as a XSDataDitcionary. |
| EDPluginExecCommandLinev10 | This is execution plugin that will create a shell script, running the command line program with the given options and filename and puts the processed file in the output directory |
| EDPluginExecEpydocv1_0 | EDPluginExecEpydocv1_0 is a plugin running Epydoc, an automatic API documentation generator |
| EDPluginExecMeasureOffsetv1_0 | An exec plugin that taked two images and measures the offset between the two. |
| EDPluginExecMeasureOffsetv2_0 | An exec plugin that taked two images and measures the offset between the two using the SIFT algorithm. |
| EDPluginExecMedianFilterv1_0 | Calculate the median image of a set of images, pixel by pixel. |
| EDPluginExecNormalizeImagev1_0 | Plugin that normalizes an image (subtract dark current and divide by flat-field image, taking into account the exposure time) |
| EDPluginExecNormalizeImagev1_1 | Plugin that normalizes an image (subtract dark current and divide by flat-field image, taking into account the exposure time) v1.1 is compatible with EDShare -> lower memory footprint |
| EDPluginExecNormalizeImagev1_2 | Plugin that normalizes an image (subtract dark current and divide by flat-field image, taking into account the exposure time) v1.1 is compatible with EDShare -> lower memory footprint v1.2 allows the scaling of images with a scale-factor |
| EDPluginExecPyFAIv1_0 | This is the basic plugin of PyFAI for azimuthal integration |
| EDPluginExecPyHSTv10 | [To be replaced with a description of EDPluginExecTemplatev10] |
| EDPluginExecRsync | Execution plugin that does the synchronization of two directories using rsync |
| EDPluginExecSaxsAddMetadatav1_0 | Wrapper for program /sware/exp/saxs/bin/edfheaderdelkey /sware/exp/saxs/edf/ubuntu1004/edfheaderdelkey <level> <verbose> <block> <chain> <key> [<filename>] EXAMPLE: Delete header key SampleConcentration (level=0|1|2|..., verbose=0|1|2, block and chain are usually 1, key="string") edfheaderdelkey 0 1 1 1 SampleConcentration *ccd Append or modify a metadata called key and set the value Value. verbose is set to 2 if EDVerbose.isVerboseDebug |
| EDPluginExecSaxsAddv1_0 | Execution plugin for Sacs Add: multiply and add constant to images (or set of images) |
| EDPluginExecSaxsAnglev1_0 | Execution plugins running the saxs_angle program |
| EDPluginExecSaxsCurvesv1_0 | Execution plugin for Sacs Curves: multiply and add constant to images (or set of images) |
| EDPluginExecSaxsCurvesv1_1 | Numpy implementation of Saxs Curves |
| EDPluginExecSaxsDelMetadatav1_0 | Wrapper for program /sware/exp/saxs/bin/edfheaderdelkey /sware/exp/saxs/edf/ubuntu1004/edfheaderdelkey <level> <verbose> <block> <chain> <key> [<filename>] EXAMPLE: Delete header key SampleConcentration (level=0|1|2|..., verbose=0|1|2, block and chain are usually 1, key="string") edfheaderdelkey 0 1 1 1 SampleConcentration *ccd Remove a metadata called key. verbose is set to 2 if EDVerbose.isVerboseDebug |
| EDPluginExecSaxsMacv1_0 | Execution plugin for Sacs Mac: multiply and add constant to images (or set of images) |
| EDPluginExecShiftImagev1_0 | Shift image by a given value |
| EDPluginExecShiftImagev1_1 | Shift image by a given value. New in version 1.1: shift on a wider canvas (defined in configuration file) |
| EDPluginExecSiftDescriptorv1_0 | Runs "autopano-sift" to retrive the SIFT descriptor of the image |
| EDPluginExecSiftOffsetv1_0 | Simple implementation based on SIFT to measure the offset of two images |
| EDPluginExecStitchOffsetedImagev1_0 | plugin that shifts a set of images and merge them togeather. |
| EDPluginExecThumbnailv10 | This is the excution plugin called Thumbnail that creates a JPEG (or PNG) thumbnail image from a CCD image It makes use of both Fabio, PIL and Numpy libraries. So please check that those three libraries, all located at $EDNA_HOME/libraries have been compiled for your computer. |
| EDPluginExecVideov10 | This is an execution plugin arround mencoder to create a video from a set of images |
| EDPluginExportAsciiPowderv1_0 | Plugin to extract the data from an 1D powder diffraction pattern created with SPD. |
| EDPluginFIT2DCakev1_0 | The purpose of this plugin is to use FIT2D to do "cake" integration, i.e. azimutal integration of powder diffraction images. |
| EDPluginFIT2DCakev1_1 | The purpose of this plugin is to use FIT2D to do "cake" integration, i.e. azimutal integration of powder diffraction images. version 1.1 correspond to the first trial to get rid of the null-X-server |
| EDPluginSPDCakev1_0 | The purpose of this plugin is to use SPD to do "cake" azimuthal integration, i.e. azimutal integration of powder diffraction images. The version 1.0 of EDPluginSPDCake will just call spd as strand alone version of the program, so this implementation is far from being optimal in performances. Few tips and tricks about SPD ... * When doing azimuthal integration, spd keeps the first axis in length (meter of detector) and not in 2Theta as expected (or Fit2D does). This is why there is a numpy transformation with ArcTan in the post process with a subsequent rebinning. * I did not manage to make spd do a full 2pi azimuthal integration. This is why 360 cakes of 1 degree are generated and subsequently summed in the postprocess * Last but not least, there is currently NO tilt, only spline distortion of the image |
| EDPluginSPDCakev1_1 | The purpose of this plugin is to use SPD to do "cake" azimuthal integration, i.e. azimutal integration of powder diffraction images. The version 1.0 of EDPluginSPDCake will just call spd as strand alone version of the program, so this implementation is far from being optimal in performances. Few tips and tricks about SPD ... * When doing azimuthal integration, spd keeps the first axis in length (meter of detector) and not in 2Theta as expected (or Fit2D does). This is why there is a numpy transformation with ArcTan in the post process with a subsequent rebinning. * This version includes a full 2pi azimuthal integration from SPD. This is the main difference with plugin v1_0 * Last but not least, there is currently NO tilt, only spline distortion of the image |
| EDPluginSPDCorrectv10 | The purpose of this execution plugin is to use SPD to do 2D image correction using a spline and/or a tilt, Few tips and tricks about SPD ... * the tilt implementation is done in python and applied to the orthonormmal spline distortion of the image. |
| EDPluginAccumulatorv1_0 | Accumulate items and checks for fulfilled queries. items should be strings, queries are list of strings. EDPluginAccumulatorv1_0 is an simple plugin because: * it is not a control plugin (as it controls nothing) * it is not an execution plugin as it does not need to take a CPU (via SemaphoreNbCPU) |
| EDPluginHDF5 | This is a common part for all EDNA plugin writing HDF5. most methods are class methods |
| EDPluginHDF5MapOfSpectrav10 | This plugin is made for putting together 1D spectra comming from a 2D scan in a 3D cube, read using various libraries ... , and put them together in an NeXus/HDF5 file |
| EDPluginHDF5StackImagesv10 | This plugin is made for putting together many images in a 3D cube as a stack of images, and put them together in an NeXus/HDF5 file |
| EDPluginSPDCakev1_5 | The purpose of this plugin is to use SPD to do "cake" azimuthal integration, i.e. azimuthal integration of powder diffraction images. Most of the code is in EDPluginSPDCorrectv10 |
| EDPluginWaitFile | Plugins that waits for a file to be written and reach a certain size |
| EDPluginControlAlignStackv1_0 | This control plugin aligns a stack on images in a single HDF5 3D-structure |
| EDPluginControlFullFieldXASv1_0 | Plugin to control Full Field XRay Absorption Spectroscopy Experiment, ID21 ESRF |
| EDPluginExecProcess | The super class for all plugins that execute a process This class manages the process to be launched: - Process time out management (configurable by EDPlugin ) - Process executable to be invoked (configurable, Default 'cat') - Process command line to be launched (Default: empty) The ExecProcess plugin is required to have a configuration in order to be executed in a plugin execution test case. |
| EDPluginExecProcessScript | The super class for all EDNA plugins that execute a task using a script. This class manages the process script to be executed: - Configuration options: - execProcessScriptShell : The shell that will execute the script, written into the top line of the script, for example : - execProcessScriptExecutor : If defined, this command is used for launching the shell. It can be used for example to launch the shell using a grid engine. (Note that the example to launch the shell using a grid engine. (Note that the execProcessScriptExecutor will be replaced by execProcessExecutable) - execProcessScriptExecutable : The path to the third-party executable that will be launched in the script. - execProcessScriptSetupCCP4 : Path to CCP4 setup file (if required) - execProcessScriptVersionString : A string which describes the version of the execProcessScriptExecutable, which should match the version string written into the program log, for example: "Version 7.0.1 for Image plate and CCD data 20th August 2007" (Note that this configuration option will be moved to EDPluginExecProcess) - The list of compatible 3rd party executable version the plugin should support (should be move up to EDPluginExecProcess) - The list of pre-execution commands - The script command line that invokes the executable, which is written into the script (the EDPluginExecProcess command line is not used, but will be in the future: It will consist of the execProcessExecutable and the path to the script file.) - The list of execution commands for the execProcessScriptExecutable - The list of post-execution commands - The script base name (<date>-<random number>-<base name>) - The script file name - The script file path - The standard output log file name - The error output file log file name - The poll sleep time for checking if the process has finished (set to 1 s). |
| EDPluginExecProcessXIA2CORE |
| EDPlugin | This is the EDNA plugin main class An EDNA plugin class: - is a configurable entity - has a base name (<date>-<random number>-<base name>) - handles input/output data (setter, getter, checker) - has warning and error messages - has a base and a working directory (both are configurable) The working directory is the folder from which the plugin is launched and should contain all associated files with the plugin execution (edna xml input/output, 3rd party output files) The base directory is the parent directory of the working directory. Example: the working directory of a control plugin is the base directory of the plugins that it invokes, i.e. the plugins working directories has the control plugin working directory as parent. - defines the method that generates an executive summary (user-related output summary) that sub-classes should implement |
| EDPluginControl | An EDPluginControl is a plugin that is responsible for a EDPluginExec or EDPluginControl plugin execution: It is responsible for: - The EDPluginExec or EDPluginControl Workflow - The data propagation between the EDPluginExec - The translation between generic and specific data models via EDHandler classes - The error/warning propagation - The executive summaries propagation - Execution of an "action cluster": a set of plugins can be added to a so called "action cluster" with the method "addPluginToActionCluster". All the plugins in the cluster can then be executed simultaneously with the method "executeActionCluster" and synchronized with the method "synchronizeActionCluster". The number of threads used by the action cluster is by default the number of processors available on the computer, but this value can be changed either by calling the method "setClusterSize" or by using the configuration parameter "clusterSize". |
| EDPluginExec | Super class for all plugins that execute something. For now, does nothing. |
| EDPluginTestPluginFactory |
| EDPluginControlAutoproc | Runs the part of the autoproc pipeline that has to be run on the cluster. |
| EDPluginControlAutoprocImport | |
| EDPluginControlFileConversion | |
| EDPluginControlRunXds | Runx XDS 3 times like Max's autoproc does. 1. First run is a vanilla run 2. Second run set JOB to DEFPIX INTEGRATE CORRECT 3. Third run set JOB to ALL, maxproc to 4 and maxjobs to 1 4. Final run set JOB to DEFPIX INTEGRATE CORRECT and maxproc and maxjobs like the 3rd run |
| EDPluginControlRunXdsFastProc | Run XDS up to three times, extending the SPOT_RANGE after each failure. |
| EDPluginControlXdsBurnStrategy | This plugin runs XDS with the specified input file, unit cell constants and spacegroup |
| EDPluginControlXscaleGenerate | Uses the XScale plugin to generate merged and unmerged and w/ and w/out anom |
| EDPluginXDSGenerate |
| EDPluginBackground3Dv1_0 | This plugin runs the Background3D program written by Sasha Popov |
| EDPluginBestv10 | |
| EDPluginBestv1_1 | |
| EDPluginBestv1_2 | |
| EDPluginDistlSignalStrengthThinClientv1_1 | This plugin runs the labelit.distl command for pre-screening reference images. |
| EDPluginDistlSignalStrengthv1_1 | This plugin runs the labelit.distl command for pre-screening reference images. |
| EDPluginDozorv1_0 | This plugin runs the Dozor program written by Sasha Popov |
| EDPluginExecAimless | |
| EDPluginExecMinimalXds | |
| EDPluginExecMtz2Variousv1_0 | [To be replaced with a description of EDPluginExecTemplatev10] |
| EDPluginExecPlotGlev1_0 | [To be replaced with a description of EDPluginExecTemplatev10] |
| EDPluginExecPointless | |
| EDPluginExecTruncate | |
| EDPluginExecUniqueify | |
| EDPluginExecXdsToSca | |
| EDPluginExecXscale | |
| EDPluginISPyBGetSampleInformationv1_4 | Plugin to store workflow status in an ISPyB database using web services |
| EDPluginISPyBGroupDataCollectionsv1_4 | Plugin to store workflow status in an ISPyB database using web services |
| EDPluginISPyBRetrieveDataCollectionv1_3 | Plugin to retrieve results in an ISPyB database using web services |
| EDPluginISPyBRetrieveDataCollectionv1_4 | Plugin to retrieve results in an ISPyB database using web services |
| EDPluginISPyBSetBestWilsonPlotPathv1_4 | Plugin to store motor positions (for grid scans) |
| EDPluginISPyBSetDataCollectionPositionv1_4 | Plugin to store sample position (for grid scans) |
| EDPluginISPyBSetDataCollectionsPositionsv1_4 | Plugin to store sample position (for grid scans) |
| EDPluginISPyBSetImagesPositionsv1_4 | Plugin to store sample position (for grid scans) |
| EDPluginISPyBStoreAutoProcStatusv1_4 | Plugin to store results in an ISPyB database using web services |
| EDPluginISPyBStoreAutoProcv1_3 | Plugin to store results in an ISPyB database using web services |
| EDPluginISPyBStoreAutoProcv1_4 | Plugin to store results in an ISPyB database using web services |
| EDPluginISPyBStoreDataCollectionv1_3 | Plugin to store results in an ISPyB database using web services |
| EDPluginISPyBStoreDataCollectionv1_4 | Plugin to store results in an ISPyB database using web services |
| EDPluginISPyBStoreGridInfov1_4 | Plugin to store workflow status in an ISPyB database using web services |
| EDPluginISPyBStoreImageQualityIndicatorsv1_3 | Plugin to store results in an ISPyB database using web services |
| EDPluginISPyBStoreImageQualityIndicatorsv1_4 | Plugin to store results in an ISPyB database using web services |
| EDPluginISPyBStoreListOfImageQualityIndicatorsv1_4 | Plugin to store results in an ISPyB database using web services |
| EDPluginISPyBStoreMotorPositionv1_4 | Plugin to store motor positions (for grid scans) |
| EDPluginISPyBStoreScreeningv1_4 | Plugin to store results in an ISPyB database using web services |
| EDPluginISPyBStoreWorkflowMeshv1_4 | Plugin to store workflow status in an ISPyB database using web services |
| EDPluginISPyBStoreWorkflowv1_4 | Plugin to store workflow status in an ISPyB database using web services |
| EDPluginISPyBUpdateDataCollectionGroupWorkflowIdv1_4 | Plugin to store workflow id status in a data collection group given an image path |
| EDPluginISPyBUpdateWorkflowStatusv1_4 | Plugin to store workflow status in an ISPyB database using web services |
| EDPluginISPyBv10 | Plugin to store results in an ISPyB database using the DNA/ISPyB dbserver |
| EDPluginISPyBv1_1 | Plugin to store results in an ISPyB database using the DNA/ISPyB dbserver |
| EDPluginISPyBv1_2 | Plugin to store results in an ISPyB database using the DNA/ISPyB dbserver |
| EDPluginLabelitv10 | This plugin runs the labelit.screen command for indexing reference images. If the labelit.sceen command is successful, the labelit.mosflm_scripts command is run for generating the orientation matrices (in MOSFLM format). The plugin requires that the path to the Labelit "setpath.sh" script is configured using the configuration keyword "pathToLabelitSetpathScript". |
| EDPluginLabelitv1_1 | This is an abstract class to be subclassed by all Labelit plugins. It takes care of common configuration parameters. |
| EDPluginMOSFLMv10 | |
| EDPluginMxv1ParamsToXMLv1_0 | Plugin to convert a string of parameters into a proper XSDataInputInterface object |
| EDPluginRBins | |
| EDPluginRaddosev10 | |
| EDPluginRdfitv1_0 | This plugin runs the rdfit program written by Sasha Popov: There is the help for RDFIT rdfit --help RDFIT can read xml file after BEST burn strategy and also write results in xml format and create GLE files. For EDNA one can run rdfit as: rdfit -d best_htm.file -glr rdfit_graph.gle -xml out_xml.file [ xds.HKL files] For GLE It will make 3 data files with fixed names : B2D.dat, I2D.dat, S2D.dat. To run RDFIT need to set (like for BEST) setenv rdfithome rdfit_directory - can be used the BEST directory where must be file - symop.lib |
| EDPluginSTACv10 | |
| EDPluginSTACv2_0 | |
| EDPluginSolveContent | |
| EDPluginXDSSpotSearchv1_1 | |
| EDPluginXDSv1_0 |
| EDPluginLabelitDistlv1_1 | This plugin runs the labelit.distl command for pre-screening reference images. |
| EDPluginLabelitIndexingv1_1 | This plugin runs the labelit.screen command for indexing reference images. If the labelit.sceen command is successful, the labelit.mosflm_scripts command is run for generating the orientation matrices (in MOSFLM format). The plugin requires that the path to the Labelit "setpath.sh" script is configured using the configuration keyword "pathToLabelitSetpathScript". |
| EDPluginMOSFLMGeneratePredictionv10 | |
| EDPluginMOSFLMIndexingv10 | |
| EDPluginMOSFLMIntegrationv10 | |
| EDPluginParseXdsOutput | |
| EDPluginParseXscaleOutput | |
| EDPluginResCutoff | |
| EDPluginSTACAlignmentv10 | Calculates xtal reorientations using a configured and calibrated STAC installation INPUT : XSDataInputBest OUTPUT : kappa_alignment_response EXECSUMM: table of orientation vectors and the necessary Omega-Kappa-Phi Datums Current limitations: + static predefined request + assupmtion of collecting the original orientation at the datum (0;0;0) |
| EDPluginSTACAlignmentv2_0 | Calculates xtal reorientations using a configured and calibrated STAC installation INPUT : XSDataInputBest; XSDataMXv2.XSDataCollection; kappa_alignment_request OUTPUT : kappa_alignment_response EXECSUMM: table of orientation vectors and the necessary Omega-Kappa-Phi Datums Current limitations: + static predefined request |
| EDPluginSTACOrientationv2_0 | Suggests xtal orientations using a configured and calibrated STAC installation INPUT : XSDataInputBest; XSDataMXv2.XSDataCollection; XSFastOrientationType OUTPUT : kappa_Orientation_request EXECSUMM: table of orientation vectors suggested for the requested type Current limitations: |
| EDPluginSTACStrategyv10 | Calculates multi-sweep data collection strategy for different orientations using a configured and calibrated STAC installation INPUT : kappa_strategy_request OUTPUT : kappa_strategy_response EXECSUMM: table of Omega scan strategies with different Kappa-Phi Datums Current limitations: + assupmtion of collecting the original orientation at the datum (0;0;0) + do not print exposure time and resolution to be used |
| EDPluginSTACStrategyv2_0 | Calculates multi-sweep data collection strategy for different orientations using a configured and calibrated STAC installation INPUT : kappa_strategy_request; XSDataMXv2.XSDataCollection; XSDataInputStrategy OUTPUT : kappa_strategy_response EXECSUMM: table of Omega scan strategies with different Kappa-Phi Datums Current limitations: + do not print exposure time, osc. width and resolution to be used |
| EDPluginXDSGenerateBackgroundImagev1_0 | |
| EDPluginXDSIndexingv1_0 |
| EDPluginControlBackground3Dv1_0 | This plugin runs the Background3D program written by Sasha Popov |
| EDPluginControlCCP4iv10 | This is the plugin interface to launch the characterisation from an ccp4i gui. |
| EDPluginControlCCP4iv1_1 | This is the plugin interface to launch the characterisation from an ccp4i gui. |
| EDPluginControlCharacterisationv10 | The Plugin that controls the whole characterisation. |
| EDPluginControlCharacterisationv1_1 | The Plugin that controls the whole characterisation. |
| EDPluginControlCharacterisationv1_2 | [To be replaced with a description of EDPluginControlTemplatev10] |
| EDPluginControlCharacterisationv1_3 | [To be replaced with a description of EDPluginControlTemplatev10] |
| EDPluginControlDozorv1_0 | This plugin runs the Dozor program written by Sasha Popov |
| EDPluginControlGeneratePredictionv10 | The Plugin that control the plugin that generates the prediction. If several images are available the execution of the plugin which generates the prediction is performed in parallel. |
| EDPluginControlGridScreeningv1_0 | This plugin is a "light-weight" characterisation to be used for processing images from grid scans. |
| EDPluginControlISPyB | [To be replaced with a description of EDPluginControlTemplatev10] |
| EDPluginControlISPyBv1_0 | This plugin controls the ISPyB execution plugin. |
| EDPluginControlISPyBv1_1 | This plugin controls the ISPyB execution plugin. |
| EDPluginControlISPyBv1_4 | This plugin controls the ISPyB v1.4 execution plugin. |
| EDPluginControlImageQualityIndicatorsv1_0 | This plugin that control the plugin that generates the image quality indicators. |
| EDPluginControlImageQualityIndicatorsv1_1 | This plugin that control the plugin that generates the image quality indicators. |
| EDPluginControlImageQualityIndicatorsv1_2 | This plugin that control the plugin that generates the image quality indicators. |
| EDPluginControlImageQualityIndicatorsv1_3 | This plugin that control the plugin that generates the image quality indicators. |
| EDPluginControlImageQualityIndicatorsv1_4 | This plugin that control the plugin that generates the image quality indicators. |
| EDPluginControlIndexingIndicatorsv10 | This control plugin will launch in parallel indexing with MOSFLM (EDPluginControlIndexingMOSFLMv1_0) and the EDPluginControlImageQualityIndicators. The idea is to run labelit.distl at the same time as the MOSFLM indexing in order to not loose time for obtaining the image quality indicators. - Input (same as current XSDataIndexingInput) : * dataCollection (XSDataCollection) 1..1 * crystal (XSDataCrystal) 0..1 * refinedExperimentalCondition (XSDataExperimentalCondition) 0..1 - Output : * indexingResult : XSDataIndexingResult 0..1 * imageQualityIndicators (XSDataImageQualityIndicators) 0..* |
| EDPluginControlIndexingLabelitv10 | This plugin is derived from EDPluginControlIndexingv10, and implements only the specific parts needed for executing the Labelit execution plugin. |
| EDPluginControlIndexingMOSFLMv10 | This plugin is derived from EDPluginControlIndexingv10, and implements only the specific parts needed for executing the MOSFLM execution plugin. |
| EDPluginControlIndexingParallelv10 | This plugin can launch several control indexing plugins in parallel. Although the parallel execution is functional, there's yet to implementation of a ranking of the indexing results, hence this plugin is not yet operational. |
| EDPluginControlIndexingv10 | The plugin which controls the indexing execution plugins. Note that this plugin is not controlling the execution plugins directly, it is using separate specialised plugins which controls e.g. MOSFLM indexing, which are derived from this plugin class. This plugin accepts several sub-wedges with one or several images each. The indexing is performed on all images together. One image with prediction is generated for each input image. |
| EDPluginControlInducedRadiationProcessv10 | The Plugin that controls the whole characterisation. |
| EDPluginControlIntegrationv10 | The Plugin that controls the MOSFLM integration. |
| EDPluginControlInterfaceToMXCuBEv1_2 | This is the plugin interface to launch the MXv1 characterisation from an MXCuBE gui. It is for the moment a wrapper for the EDPluginControlCCP4iv1_1 plugin, which also runs the ISPyB control plugin if a data collection id is available. |
| EDPluginControlInterfaceToMXCuBEv1_3 | This is the plugin interface to launch the MXv1 characterisation from an MXCuBE gui. It is for the moment a wrapper for the EDPluginControlCCP4iv1_1 plugin, which also runs the ISPyB control plugin if a data collection id is available. |
| EDPluginControlInterfacev10 | This is the common class to all plugins managing user interfaces |
| EDPluginControlInterfacev1_1 | This is the common class to all plugins managing user interfaces |
| EDPluginControlInterfacev1_2 | This is the common class to all plugins managing user interfaces |
| EDPluginControlMXCuBEWrapperv1_3 | The purpose of this plugin is to run the EDPluginControlInterfaceToMXCuBEv1_3 in a new process. |
| EDPluginControlPyarchThumbnailGeneratorParallelv1_0 | This control plugin runs the EDPluginControlPyarchThumbnailGeneratorv1_0 in parallel for many images |
| EDPluginControlPyarchThumbnailGeneratorv1_0 | This control plugin uses EDPluginExecThumbnailv10 for creating two JPEG images from a diffraction image: one 1024x1024 (imagename.jpeg) and one 256x256 (imagename.thumb.jpeg). |
| EDPluginControlReadImageHeaderv10 | |
| EDPluginControlStrategyv10 | The Plugin that controls the strategy step |
| EDPluginControlStrategyv1_1 | The Plugin that controls the strategy step |
| EDPluginControlStrategyv1_2 | The Plugin that controls the strategy step |
| EDPluginControlSubWedgeAssemblev10 | This plugin takes as input a list of paths to images. It executes the EDPluginReadImageHeaderv10 plugin for each image path in order to read the image header data and produce a XSDataSubWedge instance for each image. It then executes the EDPluginSubWedgeMergev10 plugin for, if possible, merging these subwedges. |
| EDPluginControlSubWedgeAssemblev1_1 | This plugin takes as input a list of paths to images. It executes the EDPluginReadImageHeaderv1_1 plugin for each image path in order to read the image header data and produce a XSDataSubWedge instance for each image. It then executes the EDPluginSubWedgeMergev1_1 plugin for, if possible, merging these subwedges. |
| EDPluginControlXDSGenerateBackgroundImagev1_0 | [To be replaced with a description of EDPluginControlTemplatev10] |
| EDPluginExecCreateDNAFilesDirectoryv1_0 | [To be replaced with a description of EDPluginExecTemplatev10] |
| EDPluginExecEvaluationIndexingv10 | This plugin evaluates the results of the indexing and image quality indicators. The "indexingSuccess" output is of type XSDataBoolean The "indexingComments" output is of type XSDataString |
| EDPluginExecOutputHTMLv1_0 | This plugin does not need any input data, it can use its directory hierarchy for providing the necessary "--run_basename" for EDNA2html. However, if inputs are provided, then these will be used instead. There are three optional input parameters: "title" : The title to use for the strategy "basename" : The directory where the HTML should go ("_html" is automatically appended) "workingDir" : The directory containing the EDNA MXv1 application run files There are two output data items: "htmlFile" : Path to the generated HTML file "htmlDir" : Path to the generated HTML directory In order for this plugin to work the path to the "EDNA2html" package written by Peter Briggs should either be configured in the plugin configuration (name=EDNA2html,value=pathToEDNA2html) or the environment variable "EDNA2html" should be set to this path. |
| EDPluginExecReadImageHeaderADSCv10 | |
| EDPluginExecReadImageHeaderMARCCDv10 | |
| EDPluginExecReadImageHeaderPilatus2Mv10 | |
| EDPluginExecReadImageHeaderPilatus6Mv10 | |
| EDPluginExecSimpleHTMLPagev1_0 | This plugin launches the EDPluginExecOutputHTMLv1_0 for creating web pages for ISPyB |
| EDPluginSubWedgeMergev10 | This plugin takes as input a list of sub wedges and merges them (if possible) |
| EDPluginSubWedgeMergev1_1 | This plugin takes as input a list of sub wedges and merges them (if possible) |
| EDPluginControlCharAtNewOrientationv2_0 | The Plugin that controls the whole characterisation: Indexing-Integration-Strategy Just like mxv1 characterisation. === At the end we compare the statistics at this orientation to the statisticsa at the reference orientation. If the reference is much better, we suggest to go back, or chose the next possible orientation. Otherwise, we suggest to continue with collecting the data following the currently calculated strategy. |
| EDPluginControlCharForReorientInterfacev2_0 | This plugin is an extension of EDPluginControlInterfacev1_2 that uses a different characterisationPlugin |
| EDPluginControlCharForReorientationv2_0 | The Plugin that controls the whole characterisation: Indexing-Integration-(Kappa)Strategy Indexing-Integration is the same as mxv1 characterisation. KappaStrategy: Preferred Strategy is given at the initial orientation, but if KAPPA features are enabled, strategies are calculated to some alignments. === In case the XSDataCollection.diffractionPlan.kappaStrategyOption contains KAPPA related keywords, reorientation strategy is calculated after the Integration. If the beam is bigger then the xtal, the result is a full strategy in a new orientation, otherwise it generates a strategty for collecting extra reference images at the new orientation. |
| EDPluginControlCharacterisationv2_0 | The Plugin that controls the whole characterisation: Indexing-Integration-(Kappa)Strategy Indexing-Integration is the same as mxv1 characterisation. KappaStrategy: Preferred Strategy is given at the initial orientation, but if KAPPA features are enabled, strategies are calculated to some alignments. |
| EDPluginControlISPyBv2_0 | This plugin controls the ISPyB execution plugin. |
| EDPluginControlInterfacev2_0 | This plugin is an enhancement of EDPluginControlInterfacev1_2 |
| EDPluginControlInterfacev2_2 | This is the common class to all plugins managing user interfaces |
| EDPluginControlKappaReorientationStrategyv2_0 | The Plugin that controls the strategy step |
| EDPluginControlKappaStrategyv2_0 | The Plugin that controls the strategy step |
| EDPluginControlSubWedgeAssemblyv2_0 | This plugin takes as input a list of paths to images. It calls the old assembler. The result of that will be then converted to new DM and also extended by info fetched from DC (data collection) descriptior file created by the BCM next to the data images. For now, the OUTPUT is a LIST of + the old result + the new DC descriptor Old assembler: It executes the EDPluginReadImageHeaderv10 plugin for each image path in order to read the image header data and produce a XSDataSubWedge instance for each image. It then executes the EDPluginSubWedgeMergev10 plugin for, if possible, merging these subwedges. |
| EDPluginExecSimpleHTMLPagev2_0 | This plugin launches the EDPluginExecOutputHTMLv1_0 for creating web pages for ISPyB |
| EDPluginControlDevelopRawv1_0 | Control plugin that builds the pipeline |
| EDPluginCopyExifv1_0 | Copy the Exif metadata from input file to output file |
| EDPluginExecDcrawv1_0 | Plugin Exec to wrap dcraw |
| EDPluginControlID11v1_0 | Plugin specific to ID11 |
| EDPluginControlMatrixInvertFilev1_0 | [To be replaced with a description of EDPluginControlTemplatev10] |
| EDPluginExecFindv0_1 | [To be replaced with a description of EDPluginExecProcessScriptTemplatev10] |
| EDPluginExecMatrixInvertv1_0 | [To be replaced with a description of EDPluginExecTemplatev10] |
| EDPluginExecMatrixInvertv2_0 | Testing matix inversion from a shared array (via HDF5) |
| EDPluginExecMatrixReadv1_0 | [To be replaced with a description of EDPluginExecTemplatev10] |
| EDPluginExecMatrixWritev1_0 | [To be replaced with a description of EDPluginExecTemplatev10] |
| EDPluginExecPeakSearchv1_0 | Execution plugin for running the Fable program peaksearch.py |
| EDPluginPyarchThumbnailv10 | This is the excution plugin called Thumbnail that creates a JPEG (or PNG) thumbnail image from a CCD image It makes use of both Fabio, PIL and Numpy libraries. So please check that those three libraries, all located at $EDNA_HOME/libraries have been compiled for your computer. |
| EDPluginTestXIA2CORE | [To be replaced with a description of EDPluginExecTemplatev10] |
| EDPluginWrapperForJobScheduler | Wrapper for executing EDPlugins through job schedulers like OAR, Condor etc. |
| EDPluginControlSolutionScatteringv0_2 | Solution scattering control plugin for running GNOM->DAMMIF->DAMAVER pipeline Step 1: Running GNOM jobs in parallel to idenfity the optimal value for rMax input parameter Step 2: Running DAMMIF jobs in parallel to build series of ab-initio models Step 3: Run DAMAVER pipeline to calculate an averaged model |
| EDPluginControlSolutionScatteringv0_3 | Solution scattering control plugin for running GNOM->DAMMIF->DAMAVER pipeline Step 1: Running GNOM jobs in parallel to idenfity the optimal value for rMax input parameter Step 2: Running DAMMIF jobs in parallel to build series of ab-initio models Step 3: Run DAMAVER pipeline to calculate an averaged model |
| EDPluginControlSolutionScatteringv0_4 | Solution scattering control plugin for running GNOM->DAMMIF->DAMAVER pipeline Step 1: Running GNOM jobs in parallel to idenfity the optimal value for rMax input parameter Step 2: Running DAMMIF jobs in parallel to build series of ab-initio models Step 3: Run DAMAVER pipeline to calculate an averaged model |
| EDPluginControlSolutionScatteringv0_5 | Solution scattering control plugin for running GNOM->DAMMIF->DAMAVER pipeline Step 1: Run AutoRg to find the Guinier region Step 2: run DatGnom to measure Dmax Step 3: Running DAMMIF jobs in parallel to build series of ab-initio models Step 4: Run DAMAVER pipeline to calculate an averaged model |
| EDPluginControlTomographyv10 | [To be replaced with a description of EDPluginControlTemplatev10] |
| EDPluginExecTomographyv10 | [To be replaced with a description of EDPluginExecTemplatev10] |
| EDPluginControlTRExafsv1_0 | [To be replaced with a description of EDPluginControlTemplatev10] |
| EDPluginExecCalibrateEnergyv1_0 | This plugin reads an ascii file of DEXAFS data produced by the ID24 beamline at the ESRF. The energy calibration coefficients must be given as input. |
| EDPluginExecJesfv1_0 | Execution plugin for the program Jesf |
| EDPluginExecReadDataBM23v1_0 | This plugin reads an ascii file of DEXAFS data produced by the BM23 beamline at the ESRF. The energy calibration coefficients must be given as input. |
| EDPluginExecReadDataID24v1_0 | This plugin reads an ascii file of DEXAFS data produced by the ID24 beamline at the ESRF. The energy calibration coefficients must be given as input. |
| EDPluginExecWriteNexusFilev1_0 | This plugin writes a Nexus (HDF 5) file with the data given as input. |
| EDPluginControlAbsorptionv0_1 | [To be replaced with a description of EDPluginControlTemplatev10] |
| EDPluginControlXAFSDataBatchProcessingv0_1 | Solution scattering control plugin for running GNOM->DAMMIF->DAMAVER pipeline Step 1: Running GNOM jobs in parallel to idenfity the optimal value for rMax input parameter Step 2: Running DAMMIF jobs in parallel to build series of ab-initio models Step 3: Run DAMAVER pipeline to calculate an averaged model |
| EDPluginControlXAFSDataProcessingv0_1 | Solution scattering control plugin for running GNOM->DAMMIF->DAMAVER pipeline Step 1: Running GNOM jobs in parallel to idenfity the optimal value for rMax input parameter Step 2: Running DAMMIF jobs in parallel to build series of ab-initio models Step 3: Run DAMAVER pipeline to calculate an averaged model |
| EDPluginExecAbsCalcv0_1 | [To be replaced with a description of EDPluginExecTemplatev10] |
| EDPluginExecAtomsv0_1 | Execution plugin for ab-initio model determination using Ifeffit |
| EDPluginExecIfeffitv0_1 | Execution plugin for ab-initio model determination using Ifeffit |
| EDPluginParallelXNCFJobLauncher |