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documents:101029imagej_cui_lifconversion [2010/10/29 15:35] – kotadocuments:101029imagej_cui_lifconversion [2020/11/26 09:11] (current) – external edit 127.0.0.1
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 </sxh> </sxh>
 +
 +===== ImpProps.java =====
 +
 +Accessing Image Physical Properties. Compiled class should be copied to the imageJ plugin folder. [[http://rsbweb.nih.gov/ij/plugins/imp-props.html|Original java code]] was modified to access image properties scales and dimensions. 
 +
 +<sxh java>
 +import ij.*;
 +import ij.measure.Calibration;
 +//import java.lang.Double;
 +/**
 + * This simple class can be called from an ImageJ macro via the "call" mechanism to
 + * get and set the (string) properties of the active image (ImagePlus). 
 + *
 + * call("ImpProps.setProperty", "<key>", "<value>");
 + * set property <key> to <value>, returns <value> if successful, 
 + * "" otherwise (no active image)
 + *
 + * call("ImpProps.getProperty", "<key>");
 + * returns value of property <key> if set, "" otherwise (not found or no active image)
 + *
 + * @see    ij.ImagePlus#setProperty
 + * @see    ij.ImagePlus#getProperty
 + *
 + * @author Joachim Wesner
 + * @author Leica Microsystems CMS GmbH
 + * @author joachim.wesner@leica-microsystems.com
 + * @version 2008-3-15
 + * 
 + * @author Kota Miura
 + * cmci, embl
 + * added methods for setting image dimension sizes and pixel scales. 
 + * this was done for setting these values in headless mode. 
 + * @version 2010-10-28
 + * This class can be compiled with ImageJ's Plugins>Compile and Run command.
 + */
 +
 +public class ImpProps {
 +
 + //kota
 + public static String getProperties() {
 + ImagePlus imp = WindowManager.getCurrentImage();
 + if (imp == null)
 + return "";
 + Object prop = imp.getProperties();
 + if (prop != null && prop instanceof String)
 + return (String)prop;
 + else
 + return "";
 + }
 +
 + public static String setProperty(String arg1, String arg2) {
 + ImagePlus imp = WindowManager.getCurrentImage();
 + if (imp == null)
 + return "";
 + imp.setProperty(arg1, arg2);
 + imp.updateAndDraw();
 + return arg2;
 + }
 +
 + public static String getProperty(String arg1) {
 + ImagePlus imp = WindowManager.getCurrentImage();
 + if (imp == null)
 + return "";
 + Object prop = imp.getProperty(arg1);
 + if (prop != null && prop instanceof String)
 + return (String)prop;
 + else
 + return "";
 + }
 +
 + //kota
 + public static int setCalibration(String unit, String spixelWidth, String spixelHeight, String spixelDepth){
 + double pixelWidth = java.lang.Double.parseDouble(spixelWidth);
 + double pixelHeight = java.lang.Double.parseDouble(spixelHeight);
 + double pixelDepth = java.lang.Double.parseDouble(spixelDepth);
 + ImagePlus imp = WindowManager.getCurrentImage();
 + if (imp == null)
 + return -1;
 + Calibration cal = imp.getCalibration();
 + cal.setUnit(unit);
 + cal.pixelWidth = pixelWidth;
 + cal.pixelHeight = pixelHeight;
 + cal.pixelDepth = pixelDepth;
 + imp.setCalibration(cal);
 + WindowManager.repaintImageWindows();
 + return 1;
 + }
 +
 + //kota
 + public static int setCalibration(
 + String schannels, String sslices, 
 + String sframes, String unit, 
 + String spixelWidth, String spixelHeight, 
 + String spixelDepth) {
 + int channels = java.lang.Integer.parseInt(schannels);
 + int slices   = java.lang.Integer.parseInt(sslices);
 + int frames   = java.lang.Integer.parseInt(sframes);
 + double pixelWidth  = java.lang.Double.parseDouble(spixelWidth);
 + double pixelHeight = java.lang.Double.parseDouble(spixelHeight);
 + double pixelDepth  = java.lang.Double.parseDouble(spixelDepth);
 +
 + ImagePlus imp = WindowManager.getCurrentImage();
 + if (imp == null)
 + return -1;
 + int stackSize = imp.getImageStackSize();
 + if (channels*slices*frames==stackSize)
 +  imp.setDimensions(channels, slices, frames);
 +  else
 +  IJ.error("Properties", "The product of channels ("+channels+"), slices ("+slices
 +  +")\n and frames ("+frames+") must equal the stack size ("+stackSize+").");
 + Calibration cal = imp.getCalibration();
 + cal.setUnit(unit);
 + //cal.setTimeUnit(IJ.micronSymbol + "sec");
 + cal.pixelWidth = pixelWidth;
 + cal.pixelHeight = pixelHeight;
 + cal.pixelDepth = pixelDepth;
 + imp.setCalibration(cal);
 + WindowManager.repaintImageWindows();
 + return 1;
 + }
 +}
 +</sxh>
 +===== bfconvert help =====
 +
 +<blockquote>
 +To convert a file between formats, run:
 +  bfconvert [-debug] [-stitch] [-separate] [-merge] [-expand]
 +    [-bigtiff] [-compression codec] [-series series] [-map id]
 +    in_file out_file
 +
 +      -debug: turn on debugging output
 +     -stitch: stitch input files with similar names
 +   -separate: split RGB images into separate channels
 +      -merge: combine separate channels into RGB image
 +     -expand: expand indexed color to RGB
 +    -bigtiff: force BigTIFF files to be written
 +-compression: specify the codec to use when saving images
 +     -series: specify which image series to convert
 +        -map: specify file on disk to which name should be mapped
 +
 +If any of the following patterns are present in out_file, they will
 +be replaced with the indicated metadata value from the input file.
 +
 +   Pattern:     Metadata value:
 +   ---------------------------
 +   %s           series index
 +   %n           series name
 +   %c           channel index
 +   %w           channel name
 +   %z           Z index
 +   %t           T index
 +
 +If any of these patterns are present, then the images to be saved
 +will be split into multiple files.  For example, if the input file
 +contains 5 Z sections and 3 timepoints, and out_file is
 +
 +  converted_Z%z_T%t.tiff
 +
 +then 15 files will be created, with the names
 +
 +  converted_Z0_T0.tiff
 +  converted_Z0_T1.tiff
 +  converted_Z0_T2.tiff
 +  converted_Z1_T0.tiff
 +  ...
 +  converted_Z4_T2.tiff
 +
 +Each file would have a single image plane.
 +</blockquote>
 +
 +===== LifOpenerCUI.ijm =====
 +
 +ImageJ macro for converting LIF stack series to multiple tiff stacks, together with setting physical parameters. 
 +<code>
 +// converts LIF file to channel-separated tif stacks. 
 +// output files will be saved under the folder <LIF file name>_tifStack
 +
 +//bach command example
 +/*
 +/usr/struct/bin/java -cp /g/almf/software/ij/headless.jar:/g/almf/software/ij/ij-1.44h.jar -Djava.awt.headless=true ij.ImageJ -ijpath /g/almf/software/ij -batch /g/almf/software/ij/LifOpenerCUI.ijm /g/almf/miura/lif/laminedapi23012.lif
 +*/
 +// TODO: scale should be set as the propertiy of tiff file. 
 +// reading out of the scale from LIF is somehow not working, unlike it was done in 2009
 +// metadata of .lif file would be saved as <filename.lif>.meta.txt
 +//will be saved in the same directory. 
 +// TODO: program might return error if sequence is terminated abruptly. 
 +
 +// for setting scale, plugin " ImpProp.class" is required.
 +
 + srcfile = getArgument(); //cui
 +// srcfile = File.openDialog("Select a LIF File"); //gui
 + requires("1.43d");
 + run("Bio-Formats Macro Extensions");
 +
 + path = srcfile;
 + name = File.getName(path);
 + dir = File.getParent(path);
 + DAPIch = 0;//getNumber("DAPI ch=?", 0);
 + FISHch = 1;//getNumber("FISH ch=?", 1);
 + metaname = name + ".meta.txt";
 +
 + q = File.separator; //090912
 + metafullpath = dir+q+metaname;
 + metastr = File.openAsString(metafullpath);
 + workdir = File.getParent(srcfile);  //getDirectory("Choose a work space directory to save resulting files");
 +
 + //create "tiffStack" folder under the gene folder (tiff stacks will have series No. and channel so no overlaps)
 + pathtifstack = workdir + q + name+ "_tifStack"; print(pathtifstack );
 + if (File.isDirectory(pathtifstack)==0) File.makeDirectory(pathtifstack);
 +
 + Ext.setId(path);
 + Ext.getSeriesCount(seriesCount);
 + Ext.getCurrentFile(file);
 + Ext.close();
 + print("File:"+ file);
 + print("series total number" + seriesCount);
 +
 + for (s=0; s<seriesCount; s++) {
 +
 + seriesNum = s;
 + //Ext.setId(path); //out 090925 v4n
 + //Ext.setSeries(seriesNum);
 + //Ext.getSeriesName(seriesName);
 + //Ext.close(); //out 090925 v4n
 +
 + if (s>0) refresh =0;
 +
 + seriesName = OpenLIFSeriesOneChannel(path, name, seriesNum, DAPIch, 0, metastr); //modified 090925
 + G_GID = getImageID();
 + savepath = pathtifstack + q+getTitle();
 + print(savepath);
 + saveAs("tiff", savepath);
 + close();
 +
 + OpenLIFSeriesOneChannel(path, name, seriesNum, FISHch, 0, metastr);
 + G_RID = getImageID(); 
 + savepath = pathtifstack  + q+ getTitle();
 + print(savepath);
 + saveAs("tiff", savepath);
 + close();
 + }
 +
 +
 +//working  maybe memory flashing problem, but not sure. 
 +/* 090907 
 + 090908
 + - save tif file in a specified directory
 + - problem with DAPI appearance in the resulting window.  ---> seperate 2D analysis files in other macro?
 +*/
 +function OpenLIFSeriesOneChannel(id, name, seriesNum, ch, datasetOpened, metastr){
 + run("Bio-Formats Macro Extensions");
 +
 + //if (datasetOpened ==0) Ext.setId(id);
 + Ext.setId(id);
 + Ext.setSeries(seriesNum);
 + Ext.getSeriesName(seriesName); print(seriesName);
 + Ext.getSizeZ(sizeZ);
 + Ext.getSizeC(sizeC);
 + Ext.getSizeT(sizeT);
 + Ext.getImageCount(imageCount);
 + print("ImageCount:"+imageCount);
 + calculatedCount = sizeZ*sizeC*sizeT;
 + print("...calculated"+sizeZ*sizeC*sizeT);
 + if (imageCount != calculatedCount) {
 + print();
 + exit();
 + }
 + sizeT = imageCount/sizeC/sizeZ;
 + print("C:"+sizeC+" Z:"+sizeZ+" T:"+sizeT);
 + newname = name+"_"+seriesNum+"_ch"+ch+".tif";
 + setBatchMode(true);
 + for (j=0; j<sizeT; j++){
 + for (i=0; i<sizeZ; i++){
 + currentZch0 = i*sizeC;
 + currentPlane = j*sizeZ*sizeC + i*sizeC;
 + Ext.openImage("t"+j+"_z"+i, currentPlane+ch);
 + if ((i==0) && (j==0))
 + stackID=getImageID();
 + else {
 + run("Copy");
 + close;
 + selectImage(stackID);
 + run("Add Slice");
 + run("Paste");
 + }
 + //print(currentPlane);
 + }
 + }
 + rename(newname);
 + xscale = returnXscale(metastr);
 + yscale = returnYscale(metastr);
 + zscale = returnZscale(metastr);
 + tscale = 1;//returnTscale(metastr);
 + xscalemicron = parseFloat(xscale) * pow(10, 6);
 + yscalemicron = parseFloat(yscale) * pow(10, 6);
 + zscalemicron = parseFloat(zscale) * pow(10, 6);
 + op = "channels=1 slices="+sizeZ+" frames="+sizeT+" unit=micron pixel_width="+xscalemicron +" pixel_height="+yscalemicron +" voxel_depth="+zscalemicron +" frame=[0 sec] origin=0,0";
 + //since run("Properties...", op); cannot be used (AWT problem in headless)
 + //follwoing is a new plugin for setting image properties. 
 + // ImpProp.class
 + SsizeC = ""+1;
 + SsizeZ = ""+sizeZ;
 + SsizeT = ""+sizeT;
 + Sxscalemicron = ""+xscalemicron;
 + Syscalemicron = ""+yscalemicron;
 + Szscalemicron = ""+zscalemicron;
 + call("ImpProps.setCalibration", 
 + SsizeC, SsizeZ, SsizeT, "micron", 
 + Sxscalemicron, Syscalemicron, Szscalemicron);
 +
 + setBatchMode(false);
 + //if (datasetOpened ==0) Ext.close();
 + Ext.close();
 + return seriesName;
 +}
 +
 +//zscale in micron
 +function returnZscale(metastr){
 + metaA = split(metastr, "\n");
 + zscale = 1;
 + for (i=0; i<metaA.length; i++){
 + if (startsWith(metaA[i], "HardwareSetting|ScannerSettingRecord|dblStepSize")){
 + lineA = split(metaA[i], " ");
 + //for (j=0; j<lineA.length; j++)print(lineA[j]);
 + if (lineA.length>=3) {
 + zscale = parseFloat(lineA[2]);
 + print(zscale);
 + }
 + }
 + }
 + return zscale;  
 +}
 +
 +//Xscale in micron
 +function returnXscale(metastr){
 + metaA = split(metastr, "\n");
 + xscale = 1;
 + for (i=0; i<metaA.length; i++){
 + if (startsWith(metaA[i], "HardwareSetting|ScannerSettingRecord|dblVoxelX")){
 + lineA = split(metaA[i], " ");
 + //for (j=0; j<lineA.length; j++)print(lineA[j]);
 + if (lineA.length>=3) { 
 + xscale = parseFloat(lineA[2]);
 + print(xscale);
 + }
 + }
 + }
 + return xscale;  
 +}
 +
 +function returnYscale(metastr){
 + metaA = split(metastr, "\n");
 + yscale = 1;
 + for (i=0; i<metaA.length; i++){
 + if (startsWith(metaA[i], "HardwareSetting|ScannerSettingRecord|dblVoxelY")){
 + lineA = split(metaA[i], " ");
 + //for (j=0; j<lineA.length; j++)print(lineA[j]);
 + if (lineA.length>=3){
 + yscale = parseFloat(lineA[2]);
 + print(yscale);
 + }
 + }
 + }
 + return yscale;  
 +}
 +
 +function returnTscale(){
 + metaA = split(metastr, "\n");
 + for (i=0; i<metaA.length; i++){
 + if (startsWith(metaA[i], "HardwareSetting|ScannerSettingRecord|dblStepSize")){
 + lineA = split(metaA[i], " ");
 + //for (j=0; j<lineA.length; j++)print(lineA[j]);
 + if (lineA.length>=3) print(parseFloat(lineA[2]));
 + }
 + }  
 +}
 +</code> 
 +
 +
documents/101029imagej_cui_lifconversion.1288366501.txt.gz · Last modified: 2016/05/24 12:46 (external edit)
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