> Thank you for the reply!
>
> You are correct that I am using the LSM Toolbox. Unfortunately, when
> I try either of the methods you suggested, I receive the following
> exception:
>
> java.lang.IllegalArgumentException: Argument out of range: 3
> at ij.ImageStack.setSliceLabel(ImageStack.java:222)
> at LSM_Reader.readStack(LSM_Reader.java:753)
> at LSM_Reader.open(LSM_Reader.java:554)
> at LSM_Reader.open(LSM_Reader.java:139)
> at LSM_Reader.open(LSM_Reader.java:111)
> at LSM_Reader.run(LSM_Reader.java:95)
> at ij.IJ.runUserPlugIn(IJ.java:158)
> at ij.IJ.runPlugIn(IJ.java:124)
> at ij.IJ.runPlugIn(IJ.java:113)
> at HandleExtraFileTypes.tryPlugIn(HandleExtraFileTypes.java:282)
> at HandleExtraFileTypes.tryOpen(HandleExtraFileTypes.java:151)
> at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:246)
> at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37)
> at ij.IJ.runUserPlugIn(IJ.java:158)
> at ij.IJ.runPlugIn(IJ.java:124)
> at ij.IJ.runPlugIn(IJ.java:113)
> at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:304)
> at ij.io.Opener.openImage(Opener.java:233)
> at ij.io.Opener.openImage(Opener.java:249)
> at ij.io.Opener.open(Opener.java:116)
> at ij.io.Opener.open(Opener.java:55)
> at ij.plugin.Commands.run(Commands.java:23)
> at ij.IJ.runPlugIn(IJ.java:131)
> at ij.Executer.runCommand(Executer.java:104)
> at ij.Executer.run(Executer.java:58)
> at java.lang.Thread.run(Thread.java:619)
>
> I am working with linescan .lsm files. I would be happy to post one
> if that would be of assistance.
>
> Thanks for your help!
>
> Mike
>
>
>
> Rasband Wayne wrote:
>> I suspect you are using the LSM_Toolbox to open the files. It opens
>> an LSM file in a separate thread, returning before it has finished.
>> Switching to the LSM_Reader at
>>
http://rsb.info.nih.gov/ij/plugins/lsm-reader.html>> should fix the problem. You will need to remove LSM_Toolbox.jar from
>> the plugins folder since the open() macro function will use it if it
>> is present. Or upgrade to the latest Handle_Extra_File_Types plugin
>> at
>>
http://rsb.info.nih.gov/ij/plugins/file-handler.html>> which gives priority to the LSM_Reader.
>> -wayne
>> On Apr 21, 2008, at 4:36 PM, Mike Myerburg wrote:
>>> I made a macro to scale/calibrate, threshold, apply gaussian blur,
>>> change the LUT, and rename images(to blind myself). This macro
>>> (“ASLCalibration”) is within a macro (“BatchProcessFolders”) that
>>> processes all of the images in a folder. It also provides the
>>> option to
>>> batch process/measure all the files, otherwise I measure the height
>>> of
>>> an object on each image, and then the macro continues to the next
>>> image.
>>>
>>> Unless I add multiple wait() commands throughout the above steps, the
>>> image becomes locked, the command is called prior to the image
>>> opening,
>>> or I get unexpected errors. The necessary wait times vary from
>>> computer to computer, which makes it difficult to use and has
>>> required a lot of
>>> debugging to get it to work. These wait times add up and slow the
>>> routine down, so it is not a good solution.
>>>
>>> I have added setOption("QueueMacros",true) as I thought that this
>>> might
>>> help. This has made no difference. Is this a known bug or am I
>>> missing
>>> something? Any help or suggestions would be appreciated.
>>>
>>> Below are the portions of the macro that are giving me difficulty (if
>>> you need the whole thing I can post it, but it gets a bit long). I
>>> have
>>> this macro as a toolset if that makes any difference.
>>>
>>> Thanks, Mike
>>>
>>> ________________________________________________
>>> //Global Variables
>>> var measurecount=0; //Number of ASL measurements
>>> var linecount=0; //Number of ASL line measurements
>>> var ASLLine=newArray(3); //Array containing line measurements
>>> var ShowThreshold=0; //Toggle for showing threshold
>>> automaticaly
>>> enabled by ASLCalibration
>>> var ImageName; //Image Name prior to renaming the window
>>> var ImagesProcessed=0; //Count of imgaes proccessed helopful
>>> for resume
>>> var dir;
>>>
>>> //Options
>>> var AutoMode=0; //Toggle for Full Automatic mode - User
>>> is
>>> asked when starting BatchMode
>>> var Blinded=1; //Toggle to enable blinded mode - User
>>> is
>>> asked when starting BatchMode
>>> var expertmode=1; //Change to set the expertmode
>>> var PicX=30; //Set Snapshot Dimentions X in um
>>> var PicY=30; //Set Snapshot Dimentions Y in um
>>> var scaleFactor=2; //Scale Factor
>>>
>>> macro "ASLCalibration" { //Calibrates and filters image, sets
>>> threshold and LUT
>>> measurecount=0; //sets all the counts to zero as well
>>> linecount=0;
>>> ASLLine=newArray(3);
>>> getVoxelSize(pWidth, pHeight, pDepth, unit);
>>> pHeight=pDepth; //Corrects
>>> for LSM file format
>>> setVoxelSize(pWidth, pHeight, pDepth, unit);
>>> run("Gaussian Blur...", "sigma=2");
>>>
>>> if (AutoMode==0) { //Scales Image and sets LUT
>>> width=getWidth();
>>> height=getHeight();
>>> scaleCorrection=((1/pWidth)*scaleFactor);
>>> xCorrection=(scaleCorrection*pWidth);
>>> yCorrection=(scaleCorrection*pHeight);
>>> delFile=getImageID();
>>> run("Scale...", "x="+xCorrection+" y="+yCorrection+"
>>> width="+(width*xCorrection)+" height="+(height*yCorrection)+"
>>> interpolate create title=calibrated_"+ImageName);
>>> selectImage(delFile);
>>> close();
>>> selectWindow("calibrated_"+ImageName);
>>> run("Flip Vertically");
>>> run("Fire");
>>> }
>>> setAutoThreshold();
>>> ShowThreshold=1;
>>> }
>>>
>>> macro "BatchProcessFolders" { //This is the
>>> Batch process routine
>>> requires("1.33s");
>>> dir = getDirectory("Choose a Directory ");
>>> count = 0;
>>> countFiles(dir);
>>> n = 0;
>>> first=0;
>>> run("Set Measurements...", "area bounding area_fraction");
>>> if (expertmode==1) {
>>> //Expermode options
>>> Dialog.create("Batch Mode Options");
>>> Dialog.addCheckbox("Automatic Batch Mode",AutoMode); //Set
>>> AutoMode
>>> Dialog.addCheckbox("Blinded Mode",Blinded); //Set
>>> BlindMode
>>> Dialog.addNumber("Start at file#",0);
>>> Dialog.show();
>>> AutoMode = Dialog.getCheckbox;
>>> Blinded = Dialog.getCheckbox;
>>> StartFile = Dialog.getNumber();
>>> ImagesProcessed=StartFile;
>>> }
>>>
>>> setOption("QueueMacros",true); //option to put in
>>> QueueMacro mode
>>>
>>> if (AutoMode==1) { //Put in batch mode if desired
>>> setBatchMode(true);
>>> }else setBatchMode(false);
>>>
>>> processFiles(dir);
>>> //print(count+" files processed");
>>>
>>> function countFiles(dir) {
>>> list = getFileList(dir);
>>> for (i=0; i<list.length; i++) {
>>> if (endsWith(list[i], "/"))
>>> countFiles(""+dir+list[i]);
>>> else
>>> count++;
>>> }
>>> }
>>>
>>> function processFiles(dir) { //Also sets ImageName
>>> list = getFileList(dir);
>>> for (i=0; i<list.length; i++) {
>>> if (i>=StartFile) {
>>> if (endsWith(list[i], "/")) {
>>> ImageName=list[i]; //Set ImageName for the image
>>> processFiles(""+dir+list[i]);
>>> }
>>> else {
>>> showProgress(n++, count);
>>> path = dir+list[i];
>>> ImageName=list[i]; //Set ImageName for the image
>>> processFile(path);
>>> }
>>> }
>>> }
>>> }
>>>
>>> function processFile(path) { //This is the batch
>>> function
>>> if (endsWith(path, ".lsm")) {
>>>
>>> if (AutoMode==0) setBatchMode(true); //Batchmode is used to
>>> manipulate the image and change the name
>>> open(path); // prior to showing
>>> it on
>>> the screen
>>>
>>> if (first==0) { //Make it wait for 2 sec
>>> to
>>> load first image
>>> first++;
>>> wait(2000);
>>> }
>>>
>>> wait(300);
>>> run("ASLCalibration");
>>> wait(300);
>>> if ((Blinded==1) && (AutoMode==0)) { //Has a long
>>> wait that
>>> should be removed - it is necessary to keep blinded when ImageJ auto
>>> zooms
>>> wait(500);
>>> rename("blank");
>>> }
>>>
>>> if (AutoMode==0) setBatchMode(false); //BatchMode is
>>> disabled if
>>> not in AutoMode
>>>
>>> if (AutoMode==1) {
>>> ASLheight = ASLAutoMeasure();
>>> ASLHeightLogger(ASLheight,"AutoMode");
>>> }
>>> else{
>>> while (measurecount<3) wait(10); //Wait for the user to
>>> take
>>> three measurements
>>> }
>>>
>>> close();
>>> ImagesProcessed++;
>>> }
>>> }
>>>
>>> AutoMode=0;
>>> }
>>>
>