You are correct that I am using the LSM Toolbox. Unfortunately, when I
I am working with linescan .lsm files. I would be happy to post one if
> 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;
>> }
>>
>