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

/*
    Copyright © 2005 by Duke University. All rights reserved.
 
    Permission to copy, use, and modify this software and accompanying documentation for educational and research
    purposes is hereby granted, without fee and without a signed licensing agreement, provided that the above copyright
    notice, this paragraph and the following two paragraphs appear in all copies including derivatives of the software.
    The copyright holder is free to make upgraded or improved versions of the software, provided that they are made readily
    available to others on these same terms without fee or any other charge. Contact the copyright holder at
    barbo013@mc.duke.edu for commercial licensing opportunities.
 
    IN NO EVENT SHALL THE COPYRIGHT HOLDER BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR
    CONSEQUENTIAL DAMAGES, OF ANY KIND WHATSOEVER, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF
    HE HAS BEEN ADVISED OF THE POSSIBILITY
    OF SUCH DAMAGE.
 
    THE COPYRIGHT HOLDER SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
    MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE SOFTWARE AND ACCOMPANYING DOCUMENTATION IS PROVIDED "AS IS".
    THE COPYRIGHT HOLDER HAS NO OBLIGATION TO PROVIDE MAINTENANCE, SUPPORT, UPDATES, ENHANCEMENTS, OR MODIFICATIONS.

    This latest version mimics the FolderOpener class, which implements the 
    File/Import/Image Sequence command, which opens a folder of images as a stack.

 */

public class Import_Dicom_Sequence implements PlugIn {
    
    private static boolean convertToGrayscale, convertToRGB;
    private static double scale = 100.0;
    private int n, start, increment;
    private String filter;
    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(Import_Dicom_Sequence.class);
        list = sortFileList(list);
        if (IJ.debugMode) IJ.log("Import_Dicom_Sequence: "+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++) {
                if (list[i].endsWith(".txt"))
                    continue;
                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 (list[i].indexOf(filter)>=0)
                        filteredImages++;
                    else
                        list[i] = null;
                }
                if (filteredImages==0) {
                    IJ.error("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 (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;
            for (int i=start-1; i<list.length; i++) {
                if (list[i].endsWith(".txt"))
                    continue;
                if ((counter++%increment)!=0)
                    continue;
                Opener opener = new Opener();
                opener.setSilentMode(true);
                IJ.redirectErrorMessages();
                ImagePlus 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 (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) {
                    if (!list[i].startsWith("."))
                        IJ.log(list[i] + ": unable to open");
                    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;
                    stack.addSlice(label2, ip);
                }
                if (count>=n)
                    break;
                if (IJ.escapePressed())
                {IJ.beep(); break;}
                //System.gc();
            }
        } catch(OutOfMemoryError e) {
            IJ.outOfMemory("Import_Dicom_Sequence");
            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);
            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;
        IDSDialog gd = new IDSDialog("Sequence Options", imp, list);
        gd.addNumericField("Number of Images:", fileCount, 0);
        gd.addNumericField("Starting Image:", 1, 0);
        gd.addNumericField("Increment:", 1, 0);
        //gd.addMessage("");
        gd.addStringField("File Name Contains:", "");
        gd.addNumericField("Scale Images:", scale, 0, 4, "%");
        gd.addCheckbox("Convert to 8-bit Grayscale", convertToGrayscale);
        gd.addCheckbox("Convert_to_RGB", convertToRGB);
        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();
        convertToGrayscale = gd.getNextBoolean();
        convertToRGB = gd.getNextBoolean();
        return true;
    }
    
    String[] sortFileList(String[] list) {
        int listLength = list.length;
        int first = listLength>1?1:0;
        if ((list[first].length()==list[listLength-1].length())&&(list[first].length()==list[listLength/2].length()))
        {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];
            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;
        }
    }
    
}

class IDSDialog extends GenericDialog {
    ImagePlus imp;
    int fileCount;
    boolean eightBits, rgb;
    String[] list;
    
    public IDSDialog(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;
            //TextField tf = (TextField)numberField.elementAt(0);
            //tf.setText(""+nImages);
        }
        if (inc<1)
            inc = 1;
        TextField tf = (TextField)stringField.elementAt(0);
        String filter = tf.getText();
        // IJ.write(nImages+" "+startingImage);
        if (!filter.equals("") && !filter.equals("*")) {
            int n2 = 0;
            for (int i=0; i<list.length; i++) {
                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 = (n*depth)/inc;
        if (n2<0)
            n2 = 0;
        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;
    }
    
}