uk.ac.diamond.scisoft.xpdf.operations.XPDFAzimuthalIntegrationOperation.java Source code

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Here is the source code for uk.ac.diamond.scisoft.xpdf.operations.XPDFAzimuthalIntegrationOperation.java

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/*-
 * Copyright 2015 Diamond Light Source Ltd.
 *
 * All rights reserved. This program and the accompanying materials
 * are made available under the terms of the Eclipse Public License v1.0
 * which accompanies this distribution, and is available at
 * http://www.eclipse.org/legal/epl-v10.html
 */

package uk.ac.diamond.scisoft.xpdf.operations;

import java.util.Arrays;
import java.util.Collections;
import java.util.List;

import org.apache.commons.lang.ArrayUtils;
import org.eclipse.dawnsci.analysis.api.dataset.IDataset;
import org.eclipse.dawnsci.analysis.api.dataset.Slice;
import org.eclipse.dawnsci.analysis.api.dataset.SliceND;
import org.eclipse.dawnsci.analysis.api.metadata.Reshapeable;
import org.eclipse.dawnsci.analysis.api.monitor.IMonitor;
import org.eclipse.dawnsci.analysis.api.processing.OperationData;
import org.eclipse.dawnsci.analysis.api.processing.OperationException;
import org.eclipse.dawnsci.analysis.api.processing.OperationRank;
import org.eclipse.dawnsci.analysis.dataset.impl.SliceIterator;
import org.eclipse.dawnsci.analysis.dataset.operations.AbstractOperation;
import org.eclipse.dawnsci.analysis.dataset.slicer.SliceFromSeriesMetadata;

import uk.ac.diamond.scisoft.analysis.processing.operations.powder.AzimuthalPixelIntegrationModel;
import uk.ac.diamond.scisoft.analysis.processing.operations.powder.AzimuthalPixelIntegrationOperation;
import uk.ac.diamond.scisoft.xpdf.metadata.XPDFMetadata;

/**
 * An operation to perform azimuthal integration while preserving the {@link XPDFMetadata} metadata associated with the data. 
 * @author Timothy Spain, timothy.spain@diamond.ac.uk
 *
 * @param <T> a subclass of{@link AzimuthalPixalIntegrationModel}.
 */
public class XPDFAzimuthalIntegrationOperation
        extends AbstractOperation<XPDFAzimuthalIntegrationModel, OperationData> {

    @Override
    public String getId() {
        return "uk.ac.diamond.scisoft.xpdf.operations.XPDFAzimuthalIntegration";
    }

    @Override
    protected OperationData process(IDataset input, IMonitor monitor) throws OperationException {

        // get the XPDF metadata
        XPDFMetadata xMeta = input.getFirstMetadata(XPDFMetadata.class);

        // create the Operation that will do the processing
        AzimuthalPixelIntegrationOperation<XPDFAzimuthalIntegrationInternalModel> internalOperation = new AzimuthalPixelIntegrationOperation<XPDFAzimuthalIntegrationInternalModel>();

        // create the fake model that will supply the parameters to the internal Operation
        XPDFAzimuthalIntegrationInternalModel internalModel = new XPDFAzimuthalIntegrationInternalModel(
                model.getAzimuthalRange(), model.getRadialRange(), model.isPixelSplitting(),
                model.getNumberOfBins());

        internalOperation.setModel(internalModel);

        // Resize the data to be more like it was in the execute() method
        SliceFromSeriesMetadata ssm = getSliceSeriesMetadata(input);
        // Get the dimensions in the original data
        int[] dataDims = ssm.getDataDimensions();
        int maxDimension = Collections.max(Arrays.asList(ArrayUtils.toObject(dataDims)));
        int[] newShape = new int[maxDimension + 1];
        int[] oldShape = input.getShape();
        // All elements of the new shape are 1
        Arrays.fill(newShape, 1);
        // except those that are in the data
        for (int dim = 0; dim < oldShape.length; dim++)
            newShape[dataDims[dim]] = oldShape[dim];

        IDataset reshapedInput = input.clone();
        // The reshaped data is now (hopefully) the same shape as input was in this.execute()
        reshapedInput.resize(newShape);

        OperationData output = internalOperation.execute(reshapedInput, monitor);

        // Set the axis coordinate to q
        if (xMeta != null) {
            xMeta.getSample().getTrace().setAxisAngle(false);
        }

        output.getData().addMetadata(xMeta);

        return output;

        //      OperationData superResult = super.process(input, monitor);
        //
        //      // The downstream processing relies on metadata to tell if the axis is 2 or q
        //      if (xMeta != null) {
        //         
        //         if (model.getAxisType() != XAxis.ANGLE)
        //            xMeta.getSample().getTrace().setAxisAngle(false);
        //      
        //         superResult.getData().setMetadata(xMeta);
        //      }
        //      return superResult;
    }

    @Override
    public OperationRank getInputRank() {
        return OperationRank.TWO;
    }

    @Override
    public OperationRank getOutputRank() {
        return OperationRank.ONE;
    }

}