Fit2DLoader.java

/*
 * Copyright (c) 2012 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.analysis.io;

import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileReader;
import java.io.IOException;
import java.util.HashMap;
import java.util.Map;

import org.eclipse.dawnsci.analysis.api.io.ScanFileHolderException;
import org.eclipse.january.IMonitor;
import org.eclipse.january.dataset.Dataset;
import org.eclipse.january.dataset.DatasetFactory;
import org.eclipse.january.dataset.FloatDataset;
import org.eclipse.january.dataset.ILazyDataset;
import org.eclipse.january.metadata.Metadata;

/**
 * This class should be used to load fit2d datafiles created by fit2d
 * into the ScanFileHolder object. This has not been tested on general fit2d datafiles.
 * <p>
 * <b>Note</b>: the header data from this loader is left as strings
 * 
 * 
 */
public class Fit2DLoader extends AbstractFileLoader {

	private Map<String, String> textMetadata = new HashMap<String, String>();
	private static final String DATA_NAME = "Fit2D Data";

	/**
	 * @param fileName
	 */
	public Fit2DLoader(String fileName) {
		this.fileName = fileName;
	}

	@Override
	protected void clearMetadata() {
		metadata = null;
		textMetadata.clear();
	}

	@Override
	public DataHolder loadFile() throws ScanFileHolderException {
		return loadFile(null);
	}
	
	@Override
	public DataHolder loadFile(IMonitor mon) throws ScanFileHolderException {
		ILazyDataset data = null;
		final DataHolder output = new DataHolder();
		File f = null;
		FileInputStream fi = null;
		BufferedReader br = null;
		try {

			f = new File(fileName);
			fi = new FileInputStream(f);

			br = new BufferedReader(new FileReader(f));
			String line = br.readLine();
			
			// If the first line is not a { then we fail this loader.
			if (line == null || !line.trim().startsWith("\\")) {
				throw new ScanFileHolderException("Fit2D File should start with \\ !");
			}

			// Read the meta data
			int index = readMetaData(br, line.length()+1, mon);

			// Now read the data
			int[] shape = new int[] {Integer.parseInt(textMetadata.get("Dim_2")), Integer.parseInt(textMetadata.get("Dim_1"))};
			if (loadLazily) {
				data = createLazyDataset(DATA_NAME, Dataset.FLOAT32, shape, new Fit2DLoader(fileName));
			} else {
				data = DatasetFactory.zeros(FloatDataset.class, shape);
				Utils.readLeFloat(fi, (FloatDataset) data, index);
			}
				
		} catch (Exception e) {
			throw new ScanFileHolderException("File failed to load " + fileName, e);
		} finally {
			if (br != null) {
				try {
					br.close();
				} catch (IOException ex) {
					// do nothing
				}
			}
			if (fi != null) {
				try {
					fi.close();
				} catch (IOException ex) {
					// do nothing
				}
				fi = null;
			}
		}

		metadata = new Metadata();
		metadata.initialize(textMetadata);
		metadata.setFilePath(fileName);
		metadata.addDataInfo(DATA_NAME, Integer.parseInt(textMetadata.get("Dim_2")),
				Integer.parseInt(textMetadata.get("Dim_1")));
		output.addDataset(DATA_NAME, data);
		if (loadMetadata) {
			data.setMetadata(metadata);
			output.setMetadata(metadata);
		}
		return output;
	}

	private int readMetaData(final BufferedReader br, int index, final IMonitor mon) throws Exception {
		
		textMetadata.clear();
		String headerEnd = "\\data_array:";
		
		String line = br.readLine();
		if (line == null)
			return index;

		index += line.length()+1;
		
		while (!line.contains(headerEnd)) {
			if (!monitorIncrement(mon)) {
				throw new ScanFileHolderException("Loader cancelled during reading!");
			}
			
			addValuesToMetaData(line);
			
			line = br.readLine();
			if (line == null)
				break;
			index += line.length()+1;
		}
		if (line != null)
			addValuesToMetaData(line);
		
		return index;
	}
	
	private void addValuesToMetaData(String line) throws ScanFileHolderException {
		
		int index = line.indexOf(':')+1;
		
		String key = line.substring(1,index);
		boolean notArray = line.substring(index,index+8).contains("00000000");
		
		if (notArray) {
			switch (line.charAt(index + 8)) {
				case 's':
					
					String hex = line.substring(index+9,index+17);
					int stringSize = Integer.valueOf(hex, 16);
					
					textMetadata.put(key,line.substring(index+17,index+17+stringSize));
					
					return;
				case 'r':
					
					String hexr = line.substring(index+9,index+17);
					Integer intSize = Integer.valueOf(hexr, 16);
					textMetadata.put(key, intSize.toString());
					
					return;
			}
		} else {
			if (!line.substring(index+8,index+10).contains("ar")) throw new ScanFileHolderException("Image data not found");
			
			//There is other stuff here...
			//Dont know what it means
			//String hexr = line.substring(index+10,index+18);
			//Integer first = Integer.valueOf(hexr, 16);
			
			//hexr = line.substring(index+18,index+26);
			//Integer second = Integer.valueOf(hexr, 16);
			
			String hexr = line.substring(index+26,index+34);
			Integer x = Integer.valueOf(hexr, 16);
			
			textMetadata.put("Dim_1", x.toString());
			
			hexr = line.substring(index+34,index+42);
			Integer y = Integer.valueOf(hexr, 16);
			textMetadata.put("Dim_2", y.toString());
		}
	}
}