uk.ac.diamond.scisoft.ncd.reduction.LazyDataReduction.java Source code

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Here is the source code for uk.ac.diamond.scisoft.ncd.reduction.LazyDataReduction.java

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/*
 * Copyright 2011 Diamond Light Source Ltd.
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *   http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package uk.ac.diamond.scisoft.ncd.reduction;

import java.util.Arrays;

import javax.measure.unit.Unit;
import javax.measure.unit.UnitFormat;

import ncsa.hdf.hdf5lib.H5;
import ncsa.hdf.hdf5lib.HDF5Constants;
import ncsa.hdf.hdf5lib.exceptions.HDF5Exception;
import ncsa.hdf.hdf5lib.exceptions.HDF5LibraryException;

import org.apache.commons.beanutils.ConvertUtils;
import org.eclipse.dawnsci.analysis.dataset.impl.Dataset;

import uk.ac.diamond.scisoft.analysis.crystallography.ScatteringVector;
import uk.ac.diamond.scisoft.ncd.core.data.DetectorTypes;
import uk.ac.diamond.scisoft.ncd.core.utils.NcdNexusUtils;

public abstract class LazyDataReduction {

    protected Dataset qaxis;
    protected Unit<ScatteringVector> qaxisUnit;
    protected String detector;
    protected Dataset mask;

    public LazyDataReduction() {
    }

    public void setDetector(String detector) {
        this.detector = detector;
    }

    public void setQaxis(Dataset qaxis, Unit<ScatteringVector> unit) {
        this.qaxis = qaxis;
        this.qaxisUnit = unit;
    }

    public void setMask(Dataset mask) {
        this.mask = mask;
    }

    public void writeQaxisData(int dim, int datagroup_id) throws HDF5Exception {
        long[] qaxisShape = (long[]) ConvertUtils.convert(qaxis.getShape(), long[].class);

        UnitFormat unitFormat = UnitFormat.getUCUMInstance();
        String units = unitFormat.format(qaxisUnit);
        int qaxis_id = NcdNexusUtils.makeaxis(datagroup_id, "q", HDF5Constants.H5T_NATIVE_FLOAT, qaxisShape,
                new int[] { dim }, 1, units);

        int filespace_id = H5.H5Dget_space(qaxis_id);
        int type_id = H5.H5Dget_type(qaxis_id);
        int memspace_id = H5.H5Screate_simple(qaxis.getRank(), qaxisShape, null);
        H5.H5Sselect_all(filespace_id);
        H5.H5Dwrite(qaxis_id, type_id, memspace_id, filespace_id, HDF5Constants.H5P_DEFAULT, qaxis.getBuffer());

        H5.H5Sclose(filespace_id);
        H5.H5Sclose(memspace_id);
        H5.H5Tclose(type_id);
        H5.H5Dclose(qaxis_id);

        if (qaxis.hasErrors()) {
            long[] qaxisShapeError = (long[]) ConvertUtils.convert(qaxis.getShape(), long[].class);
            int qaxis_error_id = NcdNexusUtils.makedata(datagroup_id, "q_errors", HDF5Constants.H5T_NATIVE_DOUBLE,
                    qaxisShapeError, false, units);

            filespace_id = H5.H5Dget_space(qaxis_error_id);
            type_id = H5.H5Dget_type(qaxis_error_id);
            memspace_id = H5.H5Screate_simple(qaxis.getRank(), qaxisShapeError, null);
            H5.H5Sselect_all(filespace_id);
            H5.H5Dwrite(qaxis_error_id, type_id, memspace_id, filespace_id, HDF5Constants.H5P_DEFAULT,
                    qaxis.getError().getBuffer());

            H5.H5Sclose(filespace_id);
            H5.H5Sclose(memspace_id);
            H5.H5Tclose(type_id);
            H5.H5Dclose(qaxis_error_id);
        }

    }

    public void writeNcdMetadata(int datagroup_id)
            throws HDF5LibraryException, NullPointerException, HDF5Exception {
        String detType = DetectorTypes.REDUCTION_DETECTOR;
        int type = H5.H5Tcopy(HDF5Constants.H5T_C_S1);
        H5.H5Tset_size(type, detType.length());
        int metadata_id = NcdNexusUtils.makedata(datagroup_id, "sas_type", type, new long[] { 1 });

        int filespace_id = H5.H5Dget_space(metadata_id);
        int memspace_id = H5.H5Screate_simple(1, new long[] { 1 }, null);
        H5.H5Sselect_all(filespace_id);
        H5.H5Dwrite(metadata_id, type, memspace_id, filespace_id, HDF5Constants.H5P_DEFAULT, detType.getBytes());

        H5.H5Sclose(filespace_id);
        H5.H5Sclose(memspace_id);
        H5.H5Tclose(type);
        H5.H5Dclose(metadata_id);
    }

    protected Dataset flattenGridData(Dataset data, int dimension) {

        int dataRank = data.getRank();
        int[] dataShape = data.getShape();
        if (dataRank > (dimension + 1)) {
            int[] frameArray = Arrays.copyOf(dataShape, dataRank - dimension);
            int totalFrames = 1;
            for (int val : frameArray) {
                totalFrames *= val;
            }
            int[] newShape = Arrays.copyOfRange(dataShape, dataRank - dimension - 1, dataRank);
            newShape[0] = totalFrames;
            return data.reshape(newShape);
        }
        return data;
    }
}