gda.device.detector.countertimer.TFGScalerWithRatio.java Source code

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Here is the source code for gda.device.detector.countertimer.TFGScalerWithRatio.java

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/*-
 * Copyright  2010 Diamond Light Source Ltd.
 *
 * This file is part of GDA.
 *
 * GDA is free software: you can redistribute it and/or modify it under the
 * terms of the GNU General Public License version 3 as published by the Free
 * Software Foundation.
 *
 * GDA is distributed in the hope that it will be useful, but WITHOUT ANY
 * WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
 * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
 * details.
 *
 * You should have received a copy of the GNU General Public License along
 * with GDA. If not, see <http://www.gnu.org/licenses/>.
 */

package gda.device.detector.countertimer;

import gda.device.DeviceException;
import gda.device.detector.DarkCurrentDetector;

import org.apache.commons.lang.ArrayUtils;

/**
 * Temporary class for B18.
 * <p>
 * For when the drain currents are being fed into the TFG Scaler rather than the ion chamber output. When using drain
 * current then only It/I0 is required. This class should be used in place of TFGScalerWithLogValues for counterTimer01.
 */
public class TFGScalerWithRatio extends TfgScalerWithDarkCurrent implements DarkCurrentDetector {

    private boolean outputRatio = false; // add ln(I0/It) and ln(I0/Iref) to the output

    public TFGScalerWithRatio() {
        super();
    }

    /**
     * @return Returns the outputLogValues.
     */
    public boolean isOutputRatio() {
        return outputRatio;
    }

    /**
     * When set to true I0/It will be added to the output columns
     * 
     * @param outputRatio
     *            The outputLogValues to set.
     */

    public void setOutputRatio(boolean outputRatio) {
        this.outputRatio = outputRatio;
    }

    @Override
    public int getTotalChans() throws DeviceException {
        int cols = scaler.getDimension()[0];
        if (numChannelsToRead != null) {
            cols = numChannelsToRead;
        }
        if (timeChannelRequired) {
            cols++;
        }
        if (outputRatio) {
            cols += 2;
        }
        if (isTFGv2()) {
            cols--;
        }
        return cols;
    }

    @Override
    public double[] readout() throws DeviceException {
        double[] output = super.readout();

        if (getDarkCurrent() != null) {
            output = adjustForDarkCurrent(output, getCollectionTime());
        }

        if (outputRatio) {
            Double ratio = new Double(0);
            // find which col is which I0, It and Iref
            Double[] values = getI0It(output);

            ratio = values[1] / values[0];

            // always return a numerical value
            if (ratio.isInfinite() || ratio.isNaN()) {
                ratio = 0.0;
            }

            // append to output array
            output = correctCounts(output, values);
            output = ArrayUtils.add(output, ratio);
        }
        return output;
    }

    /*
     * This should only be called when outputLogValues is set to true.
     */
    private Double[] getI0It(double[] data) {
        if (timeChannelRequired) {
            return new Double[] { data[1], data[2] };
        }
        return new Double[] { data[0], data[1] };
    }

    private double[] correctCounts(final double[] output, final Double[] counts) {
        final int outIndex = (timeChannelRequired) ? 1 : 0;
        for (int i = 0; i < counts.length; i++) {
            output[i + outIndex] = counts[i];
        }
        return output;
    }
}