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;
import ij.util.*;
public class FolderOpener implements PlugIn {
private static String[] excludedTypes = {".txt", ".lut", ".roi", ".pty", ".hdr", ".java", ".ijm", ".py", ".js", ".bsh", ".xml"};
private static boolean staticSortFileNames = true;
private static boolean staticOpenAsVirtualStack;
private boolean convertToRGB;
private boolean sortFileNames = true;
private boolean openAsVirtualStack;
private double scale = 100.0;
private int n, start, increment;
private String filter;
private String legacyRegex;
private FileInfo fi;
private String info1;
private ImagePlus image;
private boolean saveImage;
private long t0;
public static ImagePlus open(String path) {
return open(path, null);
}
public static ImagePlus open(String path, String options) {
FolderOpener fo = new FolderOpener();
fo.saveImage = true;
fo.openAsVirtualStack = options!=null && options.contains("virtual");
fo.run(path);
return fo.image;
}
public ImagePlus openFolder(String path) {
saveImage = true;
run(path);
return image;
}
public void run(String arg) {
boolean isMacro = Macro.getOptions()!=null;
String directory = null;
if (arg!=null && !arg.equals("")) {
directory = arg;
} else {
if (!isMacro) {
sortFileNames = staticSortFileNames;
openAsVirtualStack = staticOpenAsVirtualStack;
}
arg = null;
String title = "Open Image Sequence...";
String macroOptions = Macro.getOptions();
if (macroOptions!=null) {
directory = Macro.getValue(macroOptions, title, null);
if (directory!=null) {
directory = OpenDialog.lookupPathVariable(directory);
File f = new File(directory);
if (!f.isDirectory() && (f.exists()||directory.lastIndexOf(".")>directory.length()-5))
directory = f.getParent();
}
legacyRegex = Macro.getValue(macroOptions, "or", "");
if (legacyRegex.equals(""))
legacyRegex = null;
}
if (directory==null) {
if (Prefs.useFileChooser && !IJ.isMacOSX()) {
OpenDialog od = new OpenDialog(title, arg);
directory = od.getDirectory();
String name = od.getFileName();
if (name==null)
return;
} else
directory = IJ.getDirectory(title);
}
}
if (directory==null)
return;
String[] list = (new File(directory)).list();
if (list==null)
return;
String title = directory;
if (title.endsWith(File.separator) || title.endsWith("/"))
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, stackSize=1, bitDepth=0;
ImageStack stack = null;
double min = Double.MAX_VALUE;
double max = -Double.MAX_VALUE;
Calibration cal = null;
boolean allSameCalibration = true;
IJ.resetEscape();
Overlay overlay = null;
n = list.length;
start = 1;
increment = 1;
try {
if (isMacro) {
if (!showDialog(null, list))
return;
} else {
for (int i=0; i<list.length; i++) {
Opener opener = new Opener();
opener.setSilentMode(true);
IJ.redirectErrorMessages(true);
ImagePlus imp = opener.openImage(directory, list[i]);
IJ.redirectErrorMessages(false);
if (imp!=null) {
width = imp.getWidth();
height = imp.getHeight();
bitDepth = imp.getBitDepth();
if (arg==null) {
if (!showDialog(imp, list))
return;
}
break;
}
}
if (width==0) {
IJ.error("Sequence Reader", "This folder does not appear to contain\n"
+ "any TIFF, JPEG, BMP, DICOM, GIF, FITS or PGM files.\n \n"
+ " \""+directory+"\"");
return;
}
}
String pluginName = "Sequence Reader";
if (legacyRegex!=null)
pluginName += "(legacy)";
list = getFilteredList(list, filter, pluginName);
if (list==null)
return;
IJ.showStatus("");
t0 = System.currentTimeMillis();
if (sortFileNames)
list = StringSorter.sortNumerically(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;
boolean firstMessage = true;
boolean fileInfoStack = false;
for (int i=start-1; i<list.length; i++) {
if ((counter++%increment)!=0)
continue;
Opener opener = new Opener();
opener.setSilentMode(true);
IJ.redirectErrorMessages(true);
if ("RoiSet.zip".equals(list[i])) {
IJ.open(directory+list[i]);
imp = null;
} else if (!openAsVirtualStack||stack==null) {
imp = opener.openImage(directory, list[i]);
stackSize = imp!=null?imp.getStackSize():1;
}
IJ.redirectErrorMessages(false);
if (imp!=null && stack==null) {
width = imp.getWidth();
height = imp.getHeight();
bitDepth = imp.getBitDepth();
fi = imp.getOriginalFileInfo();
ImageProcessor ip = imp.getProcessor();
min = ip.getMin();
max = ip.getMax();
cal = imp.getCalibration();
if (convertToRGB) bitDepth = 24;
ColorModel cm = imp.getProcessor().getColorModel();
if (openAsVirtualStack) {
if (stackSize>1) {
stack = new FileInfoVirtualStack();
fileInfoStack = true;
} else
stack = new VirtualStack(width, height, cm, directory);
((VirtualStack)stack).setBitDepth(bitDepth);
} 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 (stackSize==1) {
String info = (String)imp.getProperty("Info");
if (info!=null)
label += "\n" + info;
}
if (Math.abs(imp.getCalibration().pixelWidth-cal.pixelWidth)>0.0000000001)
allSameCalibration = false;
ImageStack inputStack = imp.getStack();
Overlay overlay2 = imp.getOverlay();
if (overlay2!=null && !openAsVirtualStack) {
if (overlay==null)
overlay = new Overlay();
for (int j=0; j<overlay2.size(); j++) {
Roi roi = overlay2.get(j);
int position = roi.getPosition();
if (position==0)
roi.setPosition(count+1);
overlay.add(roi);
}
}
if (openAsVirtualStack) {
if (fileInfoStack)
openAsFileInfoStack((FileInfoVirtualStack)stack, directory+list[i]);
else
((VirtualStack)stack).addSlice(list[i]);
} else {
for (int slice=1; slice<=stackSize; slice++) {
int bitDepth2 = imp.getBitDepth();
String label2 = label;
ImageProcessor ip = null;
if (stackSize>1) {
String sliceLabel = inputStack.getSliceLabel(slice);
if (sliceLabel!=null)
label2=sliceLabel;
else if (label2!=null && !label2.equals(""))
label2 += ":"+slice;
}
ip = inputStack.getProcessor(slice);
if (convertToRGB) {
ip = ip.convertToRGB();
bitDepth2 = 24;
}
if (bitDepth2!=bitDepth) {
if (bitDepth==8 && bitDepth2==24) {
ip = ip.convertToByte(true);
bitDepth2 = 8;
} else if (bitDepth==32) {
ip = ip.convertToFloat();
bitDepth2 = 32;
} 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 (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();
stack.addSlice(label2, ip);
}
}
count++;
IJ.showStatus(count+"/"+n);
IJ.showProgress(count, n);
if (count>=n)
break;
if (IJ.escapePressed())
{IJ.beep(); break;}
}
} catch(OutOfMemoryError e) {
IJ.outOfMemory("FolderOpener");
if (stack!=null) stack.trim();
}
if (stack!=null && stack.getSize()>0) {
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); imp2.setOverlay(overlay);
if (allSameCalibration) {
if (scale!=100.0 && cal.scaled()) {
cal.pixelWidth /= scale/100.0;
cal.pixelHeight /= scale/100.0;
}
if (cal.pixelWidth!=1.0 && cal.pixelDepth==1.0)
cal.pixelDepth = cal.pixelWidth;
imp2.setCalibration(cal);
}
if (info1!=null && info1.lastIndexOf("7FE0,0010")>0) {
stack = DicomTools.sort(stack);
imp2.setStack(stack);
double voxelDepth = DicomTools.getVoxelDepth(stack);
if (voxelDepth>0.0) {
if (IJ.debugMode) IJ.log("DICOM voxel depth set to "+voxelDepth+" ("+cal.pixelDepth+")");
cal.pixelDepth = voxelDepth;
imp2.setCalibration(cal);
}
}
if (imp2.getStackSize()==1) {
imp2.setProperty("Label", list[0]);
if (info1!=null)
imp2.setProperty("Info", info1);
}
if (arg==null && !saveImage) {
String time = (System.currentTimeMillis()-t0)/1000.0 + " seconds";
imp2.show(time);
if (stack.isVirtual()) {
overlay = stack.getProcessor(1).getOverlay();
if (overlay!=null)
imp2.setOverlay(overlay);
}
}
if (saveImage)
image = imp2;
}
IJ.showProgress(1.0);
}
private void openAsFileInfoStack(FileInfoVirtualStack stack, String path) {
FileInfo[] info = Opener.getTiffFileInfo(path);
if (info==null || info.length==0)
return;
int n =info[0].nImages;
if (info.length==1 && n>1) {
long size = fi.width*fi.height*fi.getBytesPerPixel();
for (int i=0; i<n; i++) {
FileInfo fi = (FileInfo)info[0].clone();
fi.nImages = 1;
fi.longOffset = fi.getOffset() + i*(size + fi.gapBetweenImages);
stack.addImage(fi);
}
} else
stack.addImage(info[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.setInsets(0,45,0);
gd.addMessage("(enclose regex in parens)", null, Color.darkGray);
gd.addCheckbox("Convert_to_RGB", convertToRGB);
gd.addCheckbox("Sort names numerically", sortFileNames);
gd.addCheckbox("Use virtual stack", openAsVirtualStack);
gd.addMessage("10000 x 10000 x 1000 (100.3MB)");
gd.addHelp(IJ.URL+"/docs/menus/file.html#seq1");
gd.setSmartRecording(true);
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();
if (legacyRegex!=null)
filter = "("+legacyRegex+")";
convertToRGB = gd.getNextBoolean();
sortFileNames = gd.getNextBoolean();
openAsVirtualStack = gd.getNextBoolean();
if (openAsVirtualStack)
scale = 100.0;
if (!IJ.macroRunning()) {
staticSortFileNames = sortFileNames;
staticOpenAsVirtualStack = openAsVirtualStack;
}
return true;
}
public static String[] getFilteredList(String[] list, String filter, String title) {
boolean isRegex = false;
if (filter!=null && (filter.equals("") || filter.equals("*")))
filter = null;
if (list==null || filter==null)
return list;
if (title==null) {
String[] list2 = new String[list.length];
for (int i=0; i<list.length; i++)
list2[i] = list[i];
list = list2;
}
if (filter.length()>=2 && filter.startsWith("(")&&filter.endsWith(")")) {
filter = filter.substring(1,filter.length()-1);
isRegex = true;
}
int filteredImages = 0;
for (int i=0; i<list.length; i++) {
if (isRegex && containsRegex(list[i],filter,title!=null&&title.contains("(legacy)")))
filteredImages++;
else if (list[i].contains(filter))
filteredImages++;
else
list[i] = null;
}
if (filteredImages==0) {
if (title!=null) {
if (isRegex)
IJ.error(title, "None of the file names contain the regular expression '"+filter+"'.");
else
IJ.error(title, "None of the "+list.length+" files contain '"+filter+"' in the name.");
}
return null;
}
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;
return list;
}
private static boolean containsRegex(String name, String regex, boolean legacy) {
boolean contains = false;
try {
if (legacy)
contains = name.matches(regex);
else
contains = name.replaceAll(regex,"").length()!=name.length();
IJ.showStatus("");
} catch(Exception e) {
String msg = e.getMessage();
int index = msg.indexOf("\n");
if (index>0)
msg = msg.substring(0,index);
IJ.showStatus("Regex error: "+msg);
contains = true;
}
return contains;
}
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")||excludedFileType(name))
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;
}
public static boolean excludedFileType(String name) {
if (name==null) return true;
for (int i=0; i<excludedTypes.length; i++) {
if (name.endsWith(excludedTypes[i]))
return true;
}
return false;
}
public void openAsVirtualStack(boolean b) {
openAsVirtualStack = b;
}
public void sortFileNames(boolean b) {
sortFileNames = b;
}
public String[] sortFileList(String[] list) {
return StringSorter.sortNumerically(list);
}
class FolderOpenerDialog extends GenericDialog {
ImagePlus imp;
int fileCount;
boolean eightBits, rgb;
String[] list;
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) {
}
public void textValueChanged(TextEvent e) {
setStackInfo();
}
void setStackInfo() {
if (imp==null)
return;
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();
int n3 = Integer.MAX_VALUE;
String[] filteredList = getFilteredList(list, filter, null);
if (filteredList!=null)
n3 = filteredList.length;
else
n3 = 0;
if (n3<n)
n = n3;
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;
}
}
}