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

Example 6 with IPosition

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

the class ScannableNexusWrapper method setPosition.

@Override
public Object setPosition(Object value, IPosition scanPosition) throws ScanningException {
    try {
        final Scannable scannable = getScannable();
        if (value != null) {
            final int index = (scanPosition == null ? -1 : scanPosition.getIndex(getName()));
            final IPosition position = new Scalar<Object>(getName(), index, value);
            positionDelegate.firePositionWillPerform(position);
            logger.debug("Moving scannable {} to position {} at {}", scannable.getName(), value, scanPosition);
            scannable.moveTo(value);
            positionDelegate.firePositionPerformed(getLevel(), position);
        } else {
            logger.debug("Ignoring request to move scannable {} to position {} at {}", scannable.getName(), value, scanPosition);
        }
        if (scanPosition != null && getScannableNexusDevice(false) != null) {
            // It stops it being read again.
            return getScannableNexusDevice(false).writePosition(value, scanPosition);
        }
    } catch (Exception e) {
        throw new ScanningException("Could not set position of scannable " + getName(), e);
    }
    // new position.
    return null;
}

Example 7 with IPosition

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

the class HklAdapter method getAnglesForEachPoint.

private List<Map<String, Double>> getAnglesForEachPoint(List<IPosition> positions, Set<String> axisNames) {
    Map<String, Double> current = getCurrentAnglePositions();
    List<Map<String, Double>> allAnglePositions = new ArrayList<>();
    for (IPosition pos : positions) {
        Map<String, Double> thisPoint = new HashMap<>(current);
        axisNames.stream().filter(current::containsKey).forEach(n -> thisPoint.put(n, pos.getValue(n)));
        allAnglePositions.add(thisPoint);
    }
    return allAnglePositions;
}

Example 8 with IPosition

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

the class ScanRequestFactory method createInterpolatedCompoundModel.

/**
 * Implementation based on {@code org.eclipse.scanning.test.scan.nexus.MalcolmMultiScanTest}
 *
 * @param acquisitionTemplate
 * @return
 */
private CompoundModel createInterpolatedCompoundModel(AcquisitionTemplate acquisitionTemplate) {
    final var multiScanModel = new InterpolatedMultiScanModel();
    // --- Preparation ---
    // Each new multiscanModel must set this start position and image type
    // --- Positions List ---
    final List<IPosition> interpolationPositions = new ArrayList<>();
    // --- Images Type ---
    final List<ImageType> imageTypes = new ArrayList<>();
    // --- Flat Positions ---
    // Note - The shutter "close" position is added by the ScanningAcquisitionController
    final IPosition flatPos = createPositionMap(getFlatCalibration().getPosition());
    // --- Dark Positions ---
    // Note - The shutter "close" position is added by the ScanningAcquisitionController
    final IPosition darkPos = createPositionMap(getDarkCalibration().getPosition());
    // --- Steps estimation
    ScannableTrackDocument trackDocument = getScanpathDocument().getScannableTrackDocuments().get(0);
    // darks and flats should be (step / 2) before the start of the main scan, and the same after
    final double posBeforeMainScan = trackDocument.getStart() - trackDocument.calculatedStep() / 2;
    final double posAfterMainScan = trackDocument.getStop() + trackDocument.calculatedStep() / 2;
    // Flat Before Acquisition
    if (getFlatCalibration().isBeforeAcquisition() && getFlatCalibration().getNumberExposures() > 0) {
        var preScanFlats = getCalibrationModel(trackDocument.getScannable(), posBeforeMainScan, getFlatCalibration().getNumberExposures());
        multiScanModel.addModel(preScanFlats);
        addPosition(flatPos, interpolationPositions::add);
        imageTypes.add(ImageType.FLAT);
    }
    // Dark Before Acquisition
    if (getDarkCalibration().isBeforeAcquisition() && getDarkCalibration().getNumberExposures() > 0) {
        var preScanDarks = getCalibrationModel(trackDocument.getScannable(), posBeforeMainScan, getDarkCalibration().getNumberExposures());
        multiScanModel.addModel(preScanDarks);
        addPosition(darkPos, interpolationPositions::add);
        imageTypes.add(ImageType.DARK);
    }
    // Acquisition
    addPosition(createStartPosition(), interpolationPositions::add);
    multiScanModel.addModel(acquisitionTemplate.getIScanPointGeneratorModel());
    imageTypes.add(ImageType.NORMAL);
    // Flat After Acquisition
    if (getFlatCalibration().isAfterAcquisition() && getFlatCalibration().getNumberExposures() > 0) {
        var postScanFlats = getCalibrationModel(trackDocument.getScannable(), posAfterMainScan, getFlatCalibration().getNumberExposures());
        multiScanModel.addModel(postScanFlats);
        addPosition(flatPos, interpolationPositions::add);
        imageTypes.add(ImageType.FLAT);
    }
    // Dark After Acquisition
    if (getDarkCalibration().isAfterAcquisition() && getDarkCalibration().getNumberExposures() > 0) {
        var posScanDarks = getCalibrationModel(trackDocument.getScannable(), posAfterMainScan, getDarkCalibration().getNumberExposures());
        multiScanModel.addModel(posScanDarks);
        addPosition(darkPos, interpolationPositions::add);
        imageTypes.add(ImageType.DARK);
    }
    multiScanModel.setContinuous(Optional.ofNullable(getScanpathDocument().getMutators().containsKey(Mutator.CONTINUOUS)).orElse(false));
    multiScanModel.setInterpolatedPositions(interpolationPositions);
    multiScanModel.setImageTypes(imageTypes);
    return new CompoundModel(multiScanModel);
}

Example 9 with IPosition

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

the class ScannableNexusWrapperScanTest method checkNexusFile.

private void checkNexusFile(final IRunnableDevice<ScanModel> scanner, int... sizes) throws Exception {
    final ScanModel scanModel = ((AbstractRunnableDevice<ScanModel>) scanner).getModel();
    assertThat(scanner.getDeviceState(), is(DeviceState.ARMED));
    final String filePath = ((AbstractRunnableDevice<ScanModel>) scanner).getModel().getFilePath();
    final NexusFile nf = org.eclipse.dawnsci.nexus.ServiceHolder.getNexusFileFactory().newNexusFile(filePath);
    nf.openToRead();
    final TreeFile nexusTree = NexusUtils.loadNexusTree(nf);
    final NXroot rootNode = (NXroot) nexusTree.getGroupNode();
    final NXentry entry = rootNode.getEntry();
    final NXinstrument instrument = entry.getInstrument();
    final NXsample sample = entry.getSample();
    // check the scan points have been written correctly
    assertDiamondScanGroup(entry, false, false, sizes);
    DataNode dataNode = null;
    IDataset dataset = null;
    int[] shape = null;
    // check metadata scannables
    checkMetadataScannables(scanModel, entry);
    checkAttributeScannable(instrument);
    checkBeamSizeScannable(sample);
    final IPosition pos = scanModel.getPointGenerator().iterator().next();
    final Collection<String> scannableNames = pos.getNames();
    final String dataGroupName = scanModel.getDetectors().get(0).getName();
    final NXdata nxData = entry.getData(dataGroupName);
    assertThat(nxData, is(notNullValue()));
    // Check axes
    final List<String> expectedAxesNames = Stream.concat(scannableNames.stream().map(x -> x + NexusConstants.FIELD_SEPERATOR + FIELD_NAME_VALUE_SET), Arrays.asList("real", "imaginary").stream()).collect(Collectors.toList());
    assertAxes(nxData, expectedAxesNames.toArray(new String[expectedAxesNames.size()]));
    final int[] defaultDimensionMappings = IntStream.range(0, sizes.length).toArray();
    int scannableIndex = -1;
    for (final String scannableName : scannableNames) {
        scannableIndex++;
        NXpositioner positioner = instrument.getPositioner(scannableName);
        final boolean inLocationMap = locationMap.containsKey(scannableName);
        if (inLocationMap) {
            final NXcollection scannablesCollection = (NXcollection) instrument.getGroupNode(COLLECTION_NAME_SCANNABLES);
            assertThat(scannablesCollection, is(notNullValue()));
            positioner = (NXpositioner) scannablesCollection.getGroupNode(scannableName);
        }
        assertThat(positioner, is(notNullValue()));
        assertThat(positioner.getGroupNodeNames(), is(empty()));
        assertThat(positioner.getNumberOfGroupNodes(), is(0));
        assertThat(positioner.getAttributeNames(), containsInAnyOrder(NXCLASS, ATTR_NAME_GDA_SCANNABLE_NAME, ATTR_NAME_GDA_SCAN_ROLE));
        assertThat(positioner.getNumberOfAttributes(), is(3));
        assertThat(positioner.getAttrString(null, ATTR_NAME_GDA_SCANNABLE_NAME), is(equalTo(scannableName)));
        assertThat(positioner.getAttrString(null, ATTR_NAME_GDA_SCAN_ROLE), is(equalTo(ScanRole.SCANNABLE.toString().toLowerCase())));
        final Scannable legacyScannable = getScannable(scannableName);
        final List<String> inputFieldNames = new ArrayList<>();
        inputFieldNames.addAll(Arrays.asList(legacyScannable.getInputNames()));
        inputFieldNames.addAll(Arrays.asList(legacyScannable.getExtraNames()));
        final List<String> outputFieldNames = new ArrayList<>(inputFieldNames);
        if (outputFieldNames.contains(scannableName)) {
            outputFieldNames.set(outputFieldNames.indexOf(scannableName), NXpositioner.NX_VALUE);
        }
        // check the number of data nodes, num fields of legacy scannable + name + demand_value
        final List<String> additionalDataNodeNames = Arrays.asList(NXpositioner.NX_NAME, FIELD_NAME_VALUE_SET, NXpositioner.NX_SOFT_LIMIT_MIN, NXpositioner.NX_SOFT_LIMIT_MAX);
        final String[] expectedDataNodeNames = Stream.of(outputFieldNames, additionalDataNodeNames).flatMap(Collection::stream).toArray(String[]::new);
        assertThat(positioner.getDataNodeNames(), containsInAnyOrder(expectedDataNodeNames));
        assertThat(positioner.getNumberOfDataNodes(), is(expectedDataNodeNames.length));
        assertThat(positioner.getNameScalar(), is(equalTo(scannableName)));
        // Demand values should be 1D
        dataNode = positioner.getDataNode(FIELD_NAME_VALUE_SET);
        dataset = dataNode.getDataset().getSlice();
        shape = dataset.getShape();
        assertThat(shape.length, is(1));
        assertThat(shape[0], is(sizes[scannableIndex]));
        String nxDataFieldName = scannableName + NexusConstants.FIELD_SEPERATOR + FIELD_NAME_VALUE_SET;
        assertThat(nxData.getDataNode(nxDataFieldName), is(sameInstance(dataNode)));
        assertIndices(nxData, nxDataFieldName, scannableIndex);
        assertTarget(nxData, nxDataFieldName, rootNode, "/entry/instrument/" + (inLocationMap ? COLLECTION_NAME_SCANNABLES + "/" : "") + scannableName + "/" + FIELD_NAME_VALUE_SET);
        final String[] paths = locationMap.containsKey(scannableName) ? ((SingleScannableWriter) locationMap.get(scannableName)).getPaths() : null;
        final String[] expectedUnits = getExpectedUnits(legacyScannable);
        assertThat(positioner.getNameScalar(), is(equalTo(scannableName)));
        final DataNode setValueDataNode = positioner.getDataNode(NXpositioner.NX_VALUE + "_set");
        assertThat(setValueDataNode, is(notNullValue()));
        dataset = setValueDataNode.getDataset().getSlice();
        shape = dataset.getShape();
        assertThat(shape, is(equalTo(new int[] { sizes[scannableIndex] })));
        assertThat(positioner.getSoft_limit_minScalar(), is(equalTo(((ScannableMotion) legacyScannable).getLowerGdaLimits()[0])));
        assertThat(positioner.getSoft_limit_maxScalar(), is(equalTo(((ScannableMotion) legacyScannable).getUpperGdaLimits()[0])));
        for (int fieldIndex = 0; fieldIndex < outputFieldNames.size(); fieldIndex++) {
            final String valueFieldName = outputFieldNames.get(fieldIndex);
            dataNode = positioner.getDataNode(valueFieldName);
            assertThat(valueFieldName, dataNode, is(notNullValue()));
            assertThat(dataNode.getAttribute(ATTR_NAME_LOCAL_NAME), is(notNullValue()));
            assertThat(valueFieldName, positioner.getAttrString(valueFieldName, ATTR_NAME_LOCAL_NAME), is(equalTo(scannableName + NexusConstants.FIELD_SEPERATOR + inputFieldNames.get(fieldIndex))));
            assertThat(dataNode.getAttribute(ATTR_NAME_GDA_FIELD_NAME), is(notNullValue()));
            assertThat(valueFieldName, positioner.getAttrString(valueFieldName, ATTR_NAME_GDA_FIELD_NAME), is(equalTo(inputFieldNames.get(fieldIndex))));
            // Actual values should be scanD
            dataset = dataNode.getDataset().getSlice();
            shape = dataset.getShape();
            assertThat(valueFieldName, shape, is(equalTo(sizes)));
            if (fieldIndex == 0) {
                // currently only the first field of a Scannable is linked to from an NXdata group,
                // this is probably incorrect, see JIRA DAQ-311
                nxDataFieldName = scannableName + NexusConstants.FIELD_SEPERATOR + valueFieldName;
                assertThat(nxData.getDataNode(nxDataFieldName), is(sameInstance(dataNode)));
                assertIndices(nxData, nxDataFieldName, defaultDimensionMappings);
                assertTarget(nxData, nxDataFieldName, rootNode, "/entry/instrument/" + (inLocationMap ? COLLECTION_NAME_SCANNABLES + "/" : "") + scannableName + "/" + valueFieldName);
                if (paths != null && paths.length > fieldIndex) {
                    // check the same datanode can also be found at the path for this fieldname in the location map
                    final DataNode expectedLinkedDataNode = NexusUtils.getDataNode(entry, paths[fieldIndex]);
                    assertThat(valueFieldName, expectedLinkedDataNode, is(sameInstance(dataNode)));
                    if (expectedUnits != null && expectedUnits.length > fieldIndex) {
                        // check the units attribute has been written according to the location map
                        final Attribute unitsAttribute = dataNode.getAttribute(ATTR_NAME_UNITS);
                        assertThat(unitsAttribute, is(notNullValue()));
                        assertThat(unitsAttribute.getFirstElement(), is(equalTo(expectedUnits[fieldIndex])));
                    }
                }
            }
        }
    }
}

Example 10 with IPosition

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

the class ScannableNexusWrapperTest method testNullSetPosition_withScanPosition.

@Test
public void testNullSetPosition_withScanPosition() throws Exception {
    // Note: nexus writing tested separately by ScannableNexusWrapperScanTest
    // Arrange
    final int scanIndex = 38;
    IPositionListener posListener = mock(IPositionListener.class);
    ((IPositionListenable) scannable).addPositionListener(posListener);
    final IPosition scanPosition = new Scalar<Double>("sax", scanIndex, null);
    assertThat(scannable.getPosition(), is(equalTo(3.7)));
    // Act
    scannable.setPosition(null, scanPosition);
    // Assert
    assertThat(scannable.getPosition(), is(equalTo(3.7)));
    ((IPositionListenable) scannable).removePositionListener(posListener);
    verifyZeroInteractions(posListener);
}