Examples with IMapPathModel org.eclipse.scanning.api.points.models.IMapPathModel used on opensource projects

Example 1 with IMapPathModel

use of org.eclipse.scanning.api.points.models.IMapPathModel in project gda-core by openGDA.

the class ScanRequestConverter method convertToScanRequest.

/**
 * Convert an IMappingExperimentBean to a ScanRequest so that it can be run by the
 * GDA9 scanning framework.
 * <p>
 * This will include setting the mapping scan axes with the names from the mapping axis manager.
 * <p>
 * This method is made <code>public</code> to allow testing.
 *
 * @param mappingBean
 *            the IMappingExperimentBean to be converted
 * @return the ScanRequest
 */
public ScanRequest convertToScanRequest(IMappingExperimentBean mappingBean) {
    final ScanRequest scanRequest = new ScanRequest();
    final IMappingScanRegion scanRegion = mappingBean.getScanDefinition().getMappingScanRegion();
    final IMapPathModel mapPath = getMapPathAndConfigureScanAxes(scanRegion);
    // Build the list of models for the scan
    // first get the models for any outer scannables to be included
    final List<IScanPointGeneratorModel> models = mappingBean.getScanDefinition().getOuterScannables().stream().filter(IScanModelWrapper<IScanPointGeneratorModel>::isIncludeInScan).map(IScanModelWrapper<IScanPointGeneratorModel>::getModel).filter(Objects::nonNull).collect(// use array list as we're going to add an element
    toCollection(ArrayList::new));
    // then add the actual map path model last, it's the inner most model
    models.add(mapPath);
    // Convert the list of models into a compound model
    final CompoundModel compoundModel = new CompoundModel(models);
    // Add the ROI for the mapping region
    final ScanRegion region = new ScanRegion(scanRegion.getRegion().toROI(), mapPath.getxAxisName(), mapPath.getyAxisName());
    // Convert to a List of ScanRegion<IROI> containing one item to avoid unsafe varargs warning
    compoundModel.setRegions(Arrays.asList(region));
    // Set the model on the scan request
    scanRequest.setCompoundModel(compoundModel);
    // set the scan start position (scannables not in the scan that are set to a certain value before the scan starts)
    final Map<String, Object> beamlineConfiguration = mappingBean.getBeamlineConfiguration();
    if (beamlineConfiguration != null) {
        scanRequest.setStartPosition(new MapPosition(beamlineConfiguration));
    }
    // add the required detectors to the scan
    for (IScanModelWrapper<IDetectorModel> detectorWrapper : mappingBean.getDetectorParameters()) {
        if (detectorWrapper.isIncludeInScan()) {
            IDetectorModel detectorModel = detectorWrapper.getModel();
            scanRequest.putDetector(detectorModel.getName(), detectorModel);
        }
    }
    // set the per-scan and per-point monitors according to the mapping bean
    configureMonitors(mappingBean, scanRequest);
    // set the scripts to run before and after the scan, if any
    if (mappingBean.getScriptFiles() != null) {
        final IScriptFiles scriptFiles = mappingBean.getScriptFiles();
        scanRequest.setBeforeScript(createScriptRequest(scriptFiles.getBeforeScanScript()));
        scanRequest.setAfterScript(createScriptRequest(scriptFiles.getAfterScanScript()));
        scanRequest.setAlwaysRunAfterScript(scriptFiles.isAlwaysRunAfterScript());
    }
    // add the sample metadata
    if (mappingBean.getSampleMetadata() != null) {
        setSampleMetadata(mappingBean, scanRequest);
    }
    // Add required processing
    Map<String, Collection<Object>> processingRequest = mappingBean.getProcessingRequest();
    ProcessingRequest r = new ProcessingRequest();
    r.setRequest(processingRequest);
    scanRequest.setProcessingRequest(r);
    // Add template files
    final List<TemplateFileWrapper> templateFiles = mappingBean.getTemplateFiles();
    if (templateFiles != null && !templateFiles.isEmpty()) {
        final Set<String> existingTemplateFilePaths = scanRequest.getTemplateFilePaths();
        final Set<String> allTemplateFilePaths = new TreeSet<>();
        Optional.ofNullable(existingTemplateFilePaths).ifPresent(allTemplateFilePaths::addAll);
        templateFiles.stream().filter(TemplateFileWrapper::isActive).forEach(fp -> allTemplateFilePaths.add(fp.getFilePath()));
        scanRequest.setTemplateFilePaths(allTemplateFilePaths);
    }
    // Add alternative output directory if selected and valid
    if (mappingBean.isUseAlternativeDirectory()) {
        final String outputDirString = mappingBean.getAlternativeDirectory();
        final File outputDir = new File(outputDirString);
        if (outputDir.isDirectory()) {
            scanRequest.setFilePath(outputDirString);
        } else {
            logger.warn("Cannot write output to {}: it is not a directory", outputDirString);
        }
    }
    return scanRequest;
}

Example 2 with IMapPathModel

use of org.eclipse.scanning.api.points.models.IMapPathModel in project gda-core by openGDA.

the class ScanRequestConverter method getMapPathAndConfigureScanAxes.

private IMapPathModel getMapPathAndConfigureScanAxes(IMappingScanRegion scanRegion) {
    // check the scan path is an IMapPathModel
    if (!(scanRegion.getScanPath() instanceof IMapPathModel)) {
        final String message = "Could not set fast and slow axis. The scan path is not an instance of IMapPathModel.";
        logger.error(message);
        throw new IllegalArgumentException(message);
    }
    // get the fast and slow axis of the scan.
    final IMapPathModel mapPath = (IMapPathModel) scanRegion.getScanPath();
    if (mappingStageInfo != null) {
        // If the mapping stage is set, use these axis, and update the default map path with them
        String xAxisName = mappingStageInfo.getPlotXAxisName();
        String yAxisName = mappingStageInfo.getPlotYAxisName();
        mapPath.setxAxisName(xAxisName);
        mapPath.setyAxisName(yAxisName);
        ScannableMotionUnits xAxis = Finder.find(xAxisName);
        Optional.ofNullable(xAxis).ifPresent(axis -> mapPath.setxAxisUnits(axis.getHardwareUnitString()));
        ScannableMotionUnits yAxis = Finder.find(yAxisName);
        Optional.ofNullable(yAxis).ifPresent(axis -> mapPath.setyAxisUnits(axis.getHardwareUnitString()));
    } else {
        // Otherwise we use the default axis in the map path model
        logger.warn("No mapping axis manager is set - the scan request will use default axis names and uni!");
    }
    return mapPath;
}

Example 3 with IMapPathModel

use of org.eclipse.scanning.api.points.models.IMapPathModel in project gda-core by openGDA.

the class ScanRequestConverter method checkMapModelAndUpdateMappingStage.

private IMapPathModel checkMapModelAndUpdateMappingStage(final CompoundModel compoundModel) {
    final List<IScanPointGeneratorModel> models = compoundModel.getModels();
    // check that the inner most model is an IMapPathModel, i.e. for a mapping scan
    final IScanPointGeneratorModel innerModelObj = models.get(models.size() - 1);
    if (!(innerModelObj instanceof IMapPathModel)) {
        throw new IllegalArgumentException("The inner most model is not a map model. This is not mapping scan");
    }
    final IMapPathModel mapPath = (IMapPathModel) innerModelObj;
    // update the mapping bean with axes in the mapping path
    if (mappingStageInfo != null) {
        mappingStageInfo.setPlotXAxisName(mapPath.getxAxisName());
        mappingStageInfo.setPlotYAxisName(mapPath.getyAxisName());
    }
    return mapPath;
}

Example 4 with IMapPathModel

use of org.eclipse.scanning.api.points.models.IMapPathModel in project gda-core by openGDA.

the class ScanRequestConverter method mergeIntoMappingBean.

/**
 * Merge a scan request into an existing mapping bean so that it can be viewed
 * and possibly modified in the Mapping Experiment Setup view.
 * The reason for merging into an existing mapping bean is so that we don't remove
 * detectors and processing steps that we not selected when this scan was run -
 * when creating the scan request from the mapping bean a detector is only added if
 * {@link IScanModelWrapper#isIncludeInScan()} is true. The mapping bean reconstructed
 * from the scan request still needs to include this detector.
 *
 * @param scanRequest the {@link ScanRequest}
 * @param mappingBean the {@link IMappingExperimentBean} to merge into
 */
public void mergeIntoMappingBean(ScanRequest scanRequest, IMappingExperimentBean mappingBean) {
    final CompoundModel compoundModel = scanRequest.getCompoundModel();
    final Collection<ScanRegion> regions = compoundModel.getRegions();
    if (regions.size() != 1) {
        throw new IllegalArgumentException("The scan request must have exactly one region, has " + regions.size());
    }
    // Check that the scannable names in the scan region are the same as in the mapping stage
    final IMapPathModel mapPath = checkMapModelAndUpdateMappingStage(compoundModel);
    // recreate the outer scannable wrappers from the scan request
    mergeOuterScannables(compoundModel, mappingBean);
    // set the scan path to the last child model of the compound model
    final IScanDefinition scanDefinition = mappingBean.getScanDefinition();
    final IMappingScanRegion scanRegion = scanDefinition.getMappingScanRegion();
    scanRegion.setScanPath(mapPath);
    // convert the ROI to a mapping scan region shape
    final ScanRegion region = regions.iterator().next();
    final IMappingScanRegionShape shape = convertROItoRegionShape(region.getRoi());
    scanRegion.setRegion(shape);
    // recreate the beamline configuration from the scan start position
    if (scanRequest.getStartPosition() != null) {
        mappingBean.setBeamlineConfiguration(new LinkedHashMap<>(scanRequest.getStartPosition().getValues()));
    }
    // recreate the detector models and processing steps (included in the same map of detectors in the scan request)
    mergeDetectorAndProcessing(scanRequest, mappingBean);
    // recreate the scripts to run before and after the scan, if any
    if (scanRequest.getBeforeScript() != null || scanRequest.getAfterScript() != null) {
        ScriptFiles scriptFiles = new ScriptFiles();
        if (scanRequest.getBeforeScript() != null) {
            scriptFiles.setBeforeScanScript(scanRequest.getBeforeScript().getFile());
        }
        if (scanRequest.getAfterScript() != null) {
            scriptFiles.setAfterScanScript(scanRequest.getAfterScript().getFile());
        }
        scriptFiles.setAlwaysRunAfterScript(scanRequest.isAlwaysRunAfterScript());
        mappingBean.setScriptFiles(scriptFiles);
    }
    // recreate the sample metadata from the metadata in the scan request
    mergeSampleMetadata(scanRequest, mappingBean);
    mergeTemplateFiles(scanRequest, mappingBean);
    mergeProcessingRequest(scanRequest, mappingBean);
}

Example 5 with IMapPathModel

use of org.eclipse.scanning.api.points.models.IMapPathModel in project gda-core by openGDA.

the class FocusScanConverter method convertToScanRequest.

public ScanRequest convertToScanRequest(FocusScanBean focusScanBean) {
    logger.debug("Converting focusScanBean to scan request");
    final ScanRequest scanRequest = new ScanRequest();
    final IMapPathModel lineModel = createLineModel(focusScanBean);
    final ILineMappingRegion lineRegion = focusScanBean.getLineRegion();
    final ScanRegion scanRegion = new ScanRegion(lineRegion.toROI(), lineModel.getxAxisName(), lineModel.getyAxisName());
    final AxialStepModel focusModel = createFocusPathModel(focusScanBean);
    final CompoundModel compoundModel = new CompoundModel(Arrays.asList(focusModel, lineModel));
    compoundModel.setRegions(Arrays.asList(scanRegion));
    scanRequest.setCompoundModel(compoundModel);
    // add detectors
    final IDetectorModel detectorModel = focusScanBean.getDetector();
    final Map<String, IDetectorModel> detectorsMap = new HashMap<>();
    detectorsMap.put(detectorModel.getName(), detectorModel);
    scanRequest.setDetectors(detectorsMap);
    return scanRequest;
}