DescriptionStringCoder.java

package edu.mbl.jif.imagej;

/*
 * Image/J Plugins
 * Copyright (C) 2002,2003 Jarek Sacha
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 *
 * This library 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
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with this library; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
 *
 * Latest release available at http://sourceforge.net/projects/ij-plugins/
 */

import ij.ImagePlus;
import ij.io.FileInfo;
import ij.io.TiffDecoder;
import ij.measure.Calibration;

import java.io.*;
import java.util.Properties;

/**
 *  Decodes and encodes description strings used by ImageJ to store extra image
 *  info in TIFF description field.
 *
 * @author     Jarek Sacha
 * @created    March 23, 2002
 * @version    $Revision: 1.3 $
 */

public class DescriptionStringCoder {

  private DescriptionStringCoder() {
  }


  /**
   *  Creates an optional image description string for saving calibration data.
   *  For stacks, also saves the stack size so ImageJ can open the stack without
   *  decoding an IFD for each slice.
   *
   * @param  imp  Image for which the decription string should be created.
   * @return      Description string.
   */
  public static String encode(ImagePlus imp) {
    FileInfo fi = imp.getFileInfo();
    StringBuffer sb = new StringBuffer(100);
    sb.append("ImageJ=" + ij.ImageJ.VERSION + "\n");
    if (fi.nImages > 1) {
      sb.append("images=" + fi.nImages + "\n");
    }
    if (fi.unit != null) {
      sb.append("unit=" + fi.unit + "\n");
    }
    if (fi.valueUnit != null) {
      sb.append("cf=" + fi.calibrationFunction + "\n");
      if (fi.coefficients != null) {
        for (int i = 0; i < fi.coefficients.length; i++) {
          sb.append("c" + i + "=" + fi.coefficients[i] + "\n");
        }
      }
      sb.append("vunit=" + fi.valueUnit + "\n");
    }
    if (fi.nImages > 1) {
      if (fi.pixelDepth != 0.0 && fi.pixelDepth != 1.0) {
        sb.append("spacing=" + fi.pixelDepth + "\n");
      }
      if (fi.frameInterval != 0.0) {
        double fps = 1.0 / fi.frameInterval;
        if ((int) fps == fps) {
          sb.append("fps=" + (int) fps + "\n");
        }
        else {
          sb.append("fps=" + fps + "\n");
        }
      }
    }
    sb.append("");
    return sb.toString();
  }


  /**
   *  Decode the ImageDescription tag. ImageJ saves spatial and density
   *  calibration data in this string. For stacks, it also saves the number of
   *  images to avoid having to decode an IFD for each image.
   *
   * @param  description    Description string.
   * @param  imp            Image that will be adjusted using information stored
   *      in the decription string.
   * @exception  Exception  If information stored in the decription string is
   *      inconsistent with image size.
   */
  public static void decode(String description, ImagePlus imp)
       throws Exception {

    if (description == null || !description.startsWith("ImageJ")) {
      return;
    }

    Properties props = new Properties();
    InputStream is = new ByteArrayInputStream(description.getBytes());
    try {
      props.load(is);
      is.close();
    }
    catch (IOException e) {
      return;
    }

    FileInfo fi = new FileInfo();

    fi.unit = props.getProperty("unit", "");

    Integer n_cf = getInteger(props, "cf");
    if (n_cf != null) {
      fi.calibrationFunction = n_cf.intValue();
    }

    double c[] = new double[5];
    int coefficientsCount = 0;
    for (int i = 0; i < 5; i++) {
      Double n_ci = getDouble(props, "c" + i);
      if (n_ci == null) {
        break;
      }
      c[i] = n_ci.doubleValue();
      coefficientsCount++;
    }
    if (coefficientsCount >= 2) {
      fi.coefficients = new double[coefficientsCount];
      for (int i = 0; i < coefficientsCount; i++) {
        fi.coefficients[i] = c[i];
      }
    }
    fi.valueUnit = props.getProperty("vunit");

    Integer n_images = getInteger(props, "images");
    if (n_images != null && n_images.intValue() > 1) {
      fi.nImages = n_images.intValue();
      if (fi.nImages != imp.getStackSize()) {
        throw new Exception("Number of images in description string ("
            + fi.nImages + ") does not match number if slices in the image ("
            + imp.getStackSize() + ").");
      }
    }

    Calibration calib = imp.getCalibration();
    if (calib == null) {
      calib = new Calibration(imp);
    }
    calib.setFunction(fi.calibrationFunction, fi.coefficients, fi.valueUnit);
    calib.setUnit(fi.unit);

    if (fi.nImages > 1) {
      Double n_spacing = getDouble(props, "spacing");
      if (n_spacing != null && n_spacing.doubleValue() != 0.0) {
        calib.pixelDepth = n_spacing.doubleValue();
      }
      Double n_fps = getDouble(props, "fps");
      if (n_fps != null && n_fps.doubleValue() != 0.0) {
        calib.frameInterval = 1.0 / n_fps.doubleValue();
      }
    }

    imp.setCalibration(calib);
  }


  /*
   *
   */
  private static Double getDouble(Properties props, String key) {
    String s = props.getProperty(key);
    if (s != null) {
      try {
        return Double.valueOf(s);
      }
      catch (NumberFormatException e) {
      }
    }
    return null;
  }


  /*
   *
   */
  private static Integer getInteger(Properties props, String key) {
    String s = props.getProperty(key);
    if (s != null) {
      try {
        return Integer.valueOf(s);
      }
      catch (NumberFormatException e) {
      }
    }
    return null;
  }
}