Polynomial1DXYBgSubtraction.java example

Explorer
scisoft-core-master
/*-
 * Copyright 2016 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 org.dawnsci.surfacescatter;

import java.util.Arrays;

import org.dawnsci.surfacescatter.AnalaysisMethodologies.Methodology;
import org.eclipse.dawnsci.analysis.dataset.roi.RectangularROI;
import org.eclipse.january.dataset.Dataset;
import org.eclipse.january.dataset.DatasetFactory;
import org.eclipse.january.dataset.IDataset;
import org.eclipse.january.dataset.IndexIterator;
import org.eclipse.january.dataset.Maths;

public class Polynomial1DXYBgSubtraction {
	
	private int[] len;
	private int[] pt;
	private RectangularROI box;

	
	
	public IDataset Polynomial1DXYBgSubtraction1 (SuperModel sm, 
												 IDataset input, 
												 ExampleModel model, 
												 DataModel dm, 
												 int k,
												 int selection,
												 AnalaysisMethodologies.Methodology am) {

		len = sm.getInitialLenPt()[0];
		pt = sm.getInitialLenPt()[1];

		
		RectangularROI box = sm.getBackgroundBox();
		
		Dataset in1 = BoxSlicerRodScanUtilsForDialog.rOIBox(input, len, pt);
		
		IDataset[] background = new IDataset[2];
				
		background[0] = BoxSlicerRodScanUtilsForDialog.iBelowOrRightBox(input, 
																		len, 
																		pt,
																		model.getBoundaryBox(), 
																		am);
		
		background[1] = BoxSlicerRodScanUtilsForDialog.iAboveOrLeftBox(input, 
																	   len, 
																	   pt,
																	   model.getBoundaryBox(), 
																	   am);
		
		
		Dataset in1Background = DatasetFactory.zeros(in1.getShape(), Dataset.FLOAT64);
		
		in1Background = BackgroundSetting.rOIBackground1(background, 
														 in1Background,
														 len,
														 pt, 
														 model.getBoundaryBox(), 
														 AnalaysisMethodologies.toInt(model.getFitPower()), 
														 am);
		
		
		if(Arrays.equals(in1Background.getShape(),(new int[] {2,2}))){
			return (IDataset) in1Background;
		}
		
		IndexIterator it = in1Background.getIterator();
		
		while (it.hasNext()) {
			double v = in1Background.getElementDoubleAbs(it.index);
			if (v < 0) {
				in1Background.setObjectAbs(it.index, 0);
			}
		}

		Dataset pBackgroundSubtracted = Maths.subtract(in1, in1Background, null);

		pBackgroundSubtracted.setName("PBackgroundSubtracted");

		
		IndexIterator it1 = pBackgroundSubtracted.getIterator();
		
		while (it1.hasNext()) {
			double q = pBackgroundSubtracted.getElementDoubleAbs(it1.index);
			if (q < 0){
			           pBackgroundSubtracted.setObjectAbs(it1.index, 0);
			}
		}
		
		
		double[] location = new double[] { (double) sm.getInitialLenPt()[1][1], 
				   							(double) sm.getInitialLenPt()[1][0], 
				   							(double) (sm.getInitialLenPt()[1][1] + sm.getInitialLenPt()[0][1]), 
				   							(double) (sm.getInitialLenPt()[1][0]),
				   							(double) sm.getInitialLenPt()[1][1], 
				   							(double) sm.getInitialLenPt()[1][0] + sm.getInitialLenPt()[0][0], 
				   							(double) (sm.getInitialLenPt()[1][1] + sm.getInitialLenPt()[0][1]), 
				   							(double) (sm.getInitialLenPt()[1][0] + sm.getInitialLenPt()[0][0]) };

		sm.addLocationList(selection, location);
	
		dm.addBackgroundDatArray(in1Background);
		dm.addLocationList(model.getDatImages().getShape()[0], k, location);
		
		return pBackgroundSubtracted;

	}
}