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FolderOpener |
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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 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 (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 (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.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.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(); 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; 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(); 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 = ((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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FolderOpener |
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