Package ij.plugin

Source Code of ij.plugin.FolderOpenerDialog

package ij.plugin;
import java.awt.*;
import java.io.*;
import java.awt.event.*;
import java.awt.image.ColorModel;
import ij.*;
import ij.io.*;
import ij.gui.*;
import ij.process.*;
import ij.measure.Calibration;

/** Implements the File/Import/Image Sequence command, which
opens a folder of images as a stack. */
public class FolderOpener implements PlugIn {

  private static boolean convertToGrayscale, convertToRGB;
  private static boolean sortFileNames = true;
  private static double scale = 100.0;
  private static boolean virtualStack;
  private int n, start, increment;
  private String filter;
  private boolean isRegex;
  private FileInfo fi;
  private String info1;

  public void run(String arg) {
    OpenDialog od = new OpenDialog("Open Image Sequence...", arg);
    String directory = od.getDirectory();
    String name = od.getFileName();
    if (name==null)
      return;
    String[] list = (new File(directory)).list();
    if (list==null)
      return;
    String title = directory;
    if (title.endsWith(File.separator))
      title = title.substring(0, title.length()-1);
    int index = title.lastIndexOf(File.separatorChar);
    if (index!=-1) title = title.substring(index + 1);
    if (title.endsWith(":"))
      title = title.substring(0, title.length()-1);
   
    IJ.register(FolderOpener.class);
    list = trimFileList(list);
    if (list==null) return;
    if (IJ.debugMode) IJ.log("FolderOpener: "+directory+" ("+list.length+" files)");
    int width=0,height=0,depth=0,bitDepth=0;
    ImageStack stack = null;
    double min = Double.MAX_VALUE;
    double max = -Double.MAX_VALUE;
    Calibration cal = null;
    boolean allSameCalibration = true;
    IJ.resetEscape();   
    try {
      for (int i=0; i<list.length; i++) {
        IJ.redirectErrorMessages();
        ImagePlus imp = (new Opener()).openImage(directory, list[i]);
        if (imp!=null) {
          width = imp.getWidth();
          height = imp.getHeight();
          bitDepth = imp.getBitDepth();
          fi = imp.getOriginalFileInfo();
          if (!showDialog(imp, list))
            return;
          break;
        }
      }
      if (width==0) {
        IJ.error("Import Sequence", "This folder does not appear to contain any TIFF,\n"
        + "JPEG, BMP, DICOM, GIF, FITS or PGM files.");
        return;
      }

      if (filter!=null && (filter.equals("") || filter.equals("*")))
        filter = null;
      if (filter!=null) {
        int filteredImages = 0;
          for (int i=0; i<list.length; i++) {
          if (isRegex&&list[i].matches(filter))
            filteredImages++;
          else if (list[i].indexOf(filter)>=0)
            filteredImages++;
           else
             list[i] = null;
         }
          if (filteredImages==0) {
            if (isRegex)
              IJ.error("Import Sequence", "None of the file names match the regular expression.");
            else
               IJ.error("Import Sequence", "None of the "+list.length+" files contain\n the string '"+filter+"' in their name.");
           return;
          }
          String[] list2 = new String[filteredImages];
          int j = 0;
          for (int i=0; i<list.length; i++) {
           if (list[i]!=null)
             list2[j++] = list[i];
         }
          list = list2;
        }
      if (sortFileNames)
        list = sortFileList(list);

      if (n<1)
        n = list.length;
      if (start<1 || start>list.length)
        start = 1;
      if (start+n-1>list.length)
        n = list.length-start+1;
      int count = 0;
      int counter = 0;
      ImagePlus imp = null;
      for (int i=start-1; i<list.length; i++) {
        if ((counter++%increment)!=0)
          continue;
        Opener opener = new Opener();
        opener.setSilentMode(true);
        IJ.redirectErrorMessages();
        if (!virtualStack||stack==null)
          imp = opener.openImage(directory, list[i]);
        if (imp!=null && stack==null) {
          width = imp.getWidth();
          height = imp.getHeight();
          depth = imp.getStackSize();
          bitDepth = imp.getBitDepth();
          cal = imp.getCalibration();
          if (convertToRGB) bitDepth = 24;
          if (convertToGrayscale) bitDepth = 8;
          ColorModel cm = imp.getProcessor().getColorModel();
          if (virtualStack)
            stack = new VirtualStack(width, height, cm, directory);
          else if (scale<100.0)           
            stack = new ImageStack((int)(width*scale/100.0), (int)(height*scale/100.0), cm);
          else
            stack = new ImageStack(width, height, cm);
          info1 = (String)imp.getProperty("Info");
        }
        if (imp==null)
          continue;
        if (imp.getWidth()!=width || imp.getHeight()!=height) {
          IJ.log(list[i] + ": wrong size; "+width+"x"+height+" expected, "+imp.getWidth()+"x"+imp.getHeight()+" found");
          continue;
        }
        String label = imp.getTitle();
        if (depth==1) {
          String info = (String)imp.getProperty("Info");
          if (info!=null)
            label += "\n" + info;
        }
        if (imp.getCalibration().pixelWidth!=cal.pixelWidth)
          allSameCalibration = false;
        ImageStack inputStack = imp.getStack();
        for (int slice=1; slice<=inputStack.getSize(); slice++) {
          ImageProcessor ip = inputStack.getProcessor(slice);
          int bitDepth2 = imp.getBitDepth();
          if (convertToRGB) {
            ip = ip.convertToRGB();
            bitDepth2 = 24;
          } else if(convertToGrayscale) {
            ip = ip.convertToByte(true);
            bitDepth2 = 8;
          }
          if (bitDepth2!=bitDepth) {
            if (bitDepth==8) {
              ip = ip.convertToByte(true);
              bitDepth2 = 8;
            } else if (bitDepth==24) {
              ip = ip.convertToRGB();
              bitDepth2 = 24;
            }
          }
          if (bitDepth2!=bitDepth) {
            IJ.log(list[i] + ": wrong bit depth; "+bitDepth+" expected, "+bitDepth2+" found");
            break;
          }
          if (slice==1) count++;
          IJ.showStatus(count+"/"+n);
          IJ.showProgress(count, n);
          if (scale<100.0)
            ip = ip.resize((int)(width*scale/100.0), (int)(height*scale/100.0));
          if (ip.getMin()<min) min = ip.getMin();
          if (ip.getMax()>max) max = ip.getMax();
          String label2 = label;
          if (depth>1) label2 = ""+slice;
          if (virtualStack) {
            if (slice==1) ((VirtualStack)stack).addSlice(list[i]);
          } else
            stack.addSlice(label2, ip);
        }
        if (count>=n)
          break;
        if (IJ.escapePressed())
          {IJ.beep(); break;}
        //System.gc();
      }
    } catch(OutOfMemoryError e) {
      IJ.outOfMemory("FolderOpener");
      if (stack!=null) stack.trim();
    }
    if (stack!=null && stack.getSize()>0) {
      if (info1!=null && info1.lastIndexOf("7FE0,0010")>0)
        stack = (new DICOM_Sorter()).sort(stack);
      ImagePlus imp2 = new ImagePlus(title, stack);
      if (imp2.getType()==ImagePlus.GRAY16 || imp2.getType()==ImagePlus.GRAY32)
        imp2.getProcessor().setMinAndMax(min, max);
      if (fi==null)
        fi = new FileInfo();
      fi.fileFormat = FileInfo.UNKNOWN;
      fi.fileName = "";
      fi.directory = directory;
      imp2.setFileInfo(fi); // saves FileInfo of the first image
      if (allSameCalibration)
        imp2.setCalibration(cal); // use calibration from first image
      if (imp2.getStackSize()==1 && info1!=null)
        imp2.setProperty("Info", info1);
      imp2.show();
    }
    IJ.showProgress(1.0);
  }
 
  boolean showDialog(ImagePlus imp, String[] list) {
    int fileCount = list.length;
    FolderOpenerDialog gd = new FolderOpenerDialog("Sequence Options", imp, list);
    gd.addNumericField("Number of Images:", fileCount, 0);
    gd.addNumericField("Starting Image:", 1, 0);
    gd.addNumericField("Increment:", 1, 0);
    gd.addNumericField("Scale Images:", scale, 0, 4, "%");
    gd.addStringField("File Name Contains:", "", 10);
    gd.addStringField("or Enter Pattern:", "", 10);
    gd.addCheckbox("Convert to 8-bit Grayscale", convertToGrayscale);
    gd.addCheckbox("Convert_to_RGB", convertToRGB);
    gd.addCheckbox("Sort Names Numerically", sortFileNames);
    gd.addCheckbox("Use Virtual Stack", virtualStack);
    gd.addMessage("10000 x 10000 x 1000 (100.3MB)");
    gd.showDialog();
    if (gd.wasCanceled())
      return false;
    n = (int)gd.getNextNumber();
    start = (int)gd.getNextNumber();
    increment = (int)gd.getNextNumber();
    if (increment<1)
      increment = 1;
    scale = gd.getNextNumber();
    if (scale<5.0) scale = 5.0;
    if (scale>100.0) scale = 100.0;
    filter = gd.getNextString();
    String regex = gd.getNextString();
    if (!regex.equals("")) {
      filter = regex;
      isRegex = true;
    }
    convertToGrayscale = gd.getNextBoolean();
    convertToRGB = gd.getNextBoolean();
    sortFileNames = gd.getNextBoolean();
    virtualStack = gd.getNextBoolean();
    if (virtualStack) {
      convertToGrayscale = false;
      convertToRGB = false;
      scale = 100.0;
    }
    return true;
  }

  /** Removes names that start with "." or end with ".db". ".txt", ".lut", "roi" or ".pty". */
  public String[] trimFileList(String[] rawlist) {
    int count = 0;
    for (int i=0; i< rawlist.length; i++) {
      String name = rawlist[i];
      if (name.startsWith(".")||name.equals("Thumbs.db")||name.endsWith(".txt")||name.endsWith(".lut")||name.endsWith(".roi")||name.endsWith(".pty"))
        rawlist[i] = null;
      else
        count++;
    }
    if (count==0) return null;
    String[] list = rawlist;
    if (count<rawlist.length) {
      list = new String[count];
      int index = 0;
      for (int i=0; i< rawlist.length; i++) {
        if (rawlist[i]!=null)
          list[index++] = rawlist[i];
      }
    }
    return list;
  }

  /** Sorts the file names into numeric order. */
  public String[] sortFileList(String[] list) {
    int listLength = list.length;
    boolean allSameLength = true;
    int len0 = list[0].length();
    for (int i=0; i<listLength; i++) {
      if (list[i].length()!=len0) {
        allSameLength = false;
        break;
      }
    }
    if (allSameLength)
      {ij.util.StringSorter.sort(list); return list;}
    int maxDigits = 15;   
    String[] list2 = null
    char ch; 
    for (int i=0; i<listLength; i++) {
      int len = list[i].length();
      String num = "";
      for (int j=0; j<len; j++) {
        ch = list[i].charAt(j);
        if (ch>=48&&ch<=57) num += ch;
      }
      if (list2==null) list2 = new String[listLength];
      if (num.length()==0) num = "aaaaaa";
      num = "000000000000000" + num; // prepend maxDigits leading zeroes
      num = num.substring(num.length()-maxDigits);
      list2[i] = num + list[i];
    }
    if (list2!=null) {
      ij.util.StringSorter.sort(list2);
      for (int i=0; i<listLength; i++)
        list2[i] = list2[i].substring(maxDigits);
      return list2; 
    } else {
      ij.util.StringSorter.sort(list);
      return list;  
   
  }

} // FolderOpener

class FolderOpenerDialog extends GenericDialog {
  ImagePlus imp;
  int fileCount;
   boolean eightBits, rgb;
   String[] list;
   boolean isRegex;

  public FolderOpenerDialog(String title, ImagePlus imp, String[] list) {
    super(title);
    this.imp = imp;
    this.list = list;
    this.fileCount = list.length;
  }

  protected void setup() {
     eightBits = ((Checkbox)checkbox.elementAt(0)).getState();
     rgb = ((Checkbox)checkbox.elementAt(1)).getState();
    setStackInfo();
  }
  
  public void itemStateChanged(ItemEvent e) {
    Checkbox item = (Checkbox)e.getSource();
    Checkbox grayscaleCB = (Checkbox)checkbox.elementAt(0);
    Checkbox rgbCB = (Checkbox)checkbox.elementAt(1);
    if (item==grayscaleCB) {
      eightBits = item.getState();
      if (eightBits) {
       rgbCB.setState(false);
       rgb = false;
      }
    }
    if (item==rgbCB) {
      rgb = item.getState();
      if (rgb) {
        grayscaleCB.setState(false);
        eightBits = false;
      }
    }
     setStackInfo();
  }
 
  public void textValueChanged(TextEvent e) {
     setStackInfo();
  }

  void setStackInfo() {
    int width = imp.getWidth();
    int height = imp.getHeight();
    int depth = imp.getStackSize();
    int bytesPerPixel = 1;
     int n = getNumber(numberField.elementAt(0));
    int start = getNumber(numberField.elementAt(1));
    int inc = getNumber(numberField.elementAt(2));
    double scale = getNumber(numberField.elementAt(3));
    if (scale<5.0) scale = 5.0;
    if (scale>100.0) scale = 100.0;
   
    if (n<1) n = fileCount;
    if (start<1 || start>fileCount) start = 1;
    if (start+n-1>fileCount)
      n = fileCount-start+1;
    if (inc<1) inc = 1;
     TextField tf = (TextField)stringField.elementAt(0);
     String filter = tf.getText();
    tf = (TextField)stringField.elementAt(1);
      String regex = tf.getText();
    if (!regex.equals("")) {
      filter = regex;
      isRegex = true;
    }
     if (!filter.equals("") && !filter.equals("*")) {
       int n2 = 0;
      for (int i=0; i<list.length; i++) {
        if (isRegex&&list[i].matches(filter))
          n2++;
        else if (list[i].indexOf(filter)>=0)
          n2++;
      }
      if (n2<n) n = n2;
     }
    switch (imp.getType()) {
      case ImagePlus.GRAY16:
        bytesPerPixel=2;break;
      case ImagePlus.COLOR_RGB:
      case ImagePlus.GRAY32:
        bytesPerPixel=4; break;
    }
    if (eightBits)
      bytesPerPixel = 1;
    if (rgb)
      bytesPerPixel = 4;
    width = (int)(width*scale/100.0);
    height = (int)(height*scale/100.0);
    int n2 = ((fileCount-start+1)*depth)/inc;
    if (n2<0) n2 = 0;
    if (n2>n) n2 = n;
    double size = ((double)width*height*n2*bytesPerPixel)/(1024*1024);
     ((Label)theLabel).setText(width+" x "+height+" x "+n2+" ("+IJ.d2s(size,1)+"MB)");
  }

  public int getNumber(Object field) {
    TextField tf = (TextField)field;
    String theText = tf.getText();
    double value;
    Double d;
    try {d = new Double(theText);}
    catch (NumberFormatException e){
      d = null;
    }
    if (d!=null)
      return (int)d.doubleValue();
    else
      return 0;
      }

} // FolderOpenerDialog

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