Re: Help with ImageJ macro code

Posted by Wayne Rasband on Feb 01, 2008; 9:10pm
URL: http://imagej.273.s1.nabble.com/Help-with-ImageJ-macro-code-tp3697312p3697322.html

On Windows, try deleting the configuration file (ImageJ.cfg) and  
restarting ImageJ. The ImageJ launcher (ImageJ.exe) will detect that  
ImageJ.cfg is missing and generate a replacement. If the ImageJ/jre  
directory is missing, it will detect the latest installed Java and  
setup ImageJ.cfg to use that instead. It will set the memory limit to  
2/3 of installed memory or 640MB, whichever is lower. You will only be  
able to use 63MB of you launch ImageJ by double clicking on ij.jar.

-wayne

On Feb 1, 2008, at 1:13 PM, crieken wrote:

> Now the whole thing is messed up and when I try to open ImageJ.exe, I  
> get an
> error message that says, "Could not create the java virtual machine".  
> I can
> run the ij.jar, but then I get the 63MB error.
> Chris
>
>
> crieken wrote:
>>
>> 1.39q is confused and telling me that I've run out of memory (63MB)  
>> when I
>> have it set to 1500MB.  Hmmm, maybe I'll try a version that's a bit
>> older...
>>
>>
>> crieken wrote:
>>>
>>> Aha!  I'm using 1.38x - I'll check for a newer version and let you  
>>> know
>>> how it goes.  Thanks!
>>> Chris
>>>
>>>
>>> Michael Schmid-3 wrote:
>>>>
>>>> Hi Chris,
>>>>
>>>> maybe also this is a multithreading problem with the
>>>> foreground image not being set fast enough?
>>>>
>>>> There was a bug in ImageJ versions before 1.39f that has caused
>>>> such problems - maybe you have an old version?
>>>>
>>>> Otherwise, adding a short delay before close() could help, e.g.
>>>> wait(200);
>>>> It's not an elegant solution, only a workaround...
>>>>
>>>>
>>>> Michael
>>>> ________________________________________________________________
>>>>
>>>> On 1 Feb 2008, at 13:16, crieken wrote:
>>>>
>>>>> Hi Michael,
>>>>> Thanks for the advice.  I have rewritten the code as you have
>>>>> suggested, but
>>>>> I'm still getting errors.  The good news is, I think I know why,
>>>>> but the bad
>>>>> is that I have no idea how to solve it.  When I run the macro and
>>>>> open my
>>>>> images, I notice that the active image window (the one on top) will
>>>>> not
>>>>> remain consistent from run to run.  I therefore believe that  
>>>>> ImageJ is
>>>>> closing some of the channels I want to retain (A, C, D, etc...) and
>>>>> keeping
>>>>> some of the junk channels I want to discard, thus causing errors in
>>>>> the back
>>>>> end because the imageID that I direct ImageJ to no longer exists.
>>>>> I will
>>>>> try rewriting the code so that no channels are closed, but how can
>>>>> I be sure
>>>>> that I'm getting the correct imageID when I don't know how to
>>>>> control which
>>>>> window is active?  I could try to identify the windows based on  
>>>>> their
>>>>> original window names using a string search (ie 402nm ch:1), but
>>>>> then I run
>>>>> back into the problem that these window names are being reset to  
>>>>> "1".
>>>>> Aaargh!  Sorry to be such a bother, but does anyone have a good fix
>>>>> for
>>>>> this?  Many thanks!
>>>>> Chris
>>>>>
>>>>>
>>>>>
>>>>> Michael Schmid-3 wrote:
>>>>>>
>>>>>> Hi Chris,
>>>>>>
>>>>>> you are right that ImageIDs are negative numbers. They stay
>>>>>> valid until an image is closed. A new image that you open gets
>>>>>> a new ID that is the last ID used minus one.
>>>>>> (strictly speaking, "image" means the ImagePlus class of ImageJ)
>>>>>>
>>>>>> See the selectImage(id) and getImageID entries on
>>>>>>    http://rsb.info.nih.gov/ij/developer/macro/functions.html
>>>>>>
>>>>>> It might be that your problems are caused by
>>>>>>    run("Put Behind [tab]");
>>>>>> since some operations on Windows happen in a different thread
>>>>>> that may be slower than the thread executing the macro.
>>>>>>
>>>>>> Therefore, to access the images created I would simply try:
>>>>>>    Z = getImageID();
>>>>>>    W = getImageID()+1; //the image created before Z
>>>>>>
>>>>>>
>>>>>> Michael
>>>>>> ________________________________________________________________
>>>>>>
>>>>>> On 1 Feb 2008, at 01:42, crieken wrote:
>>>>>>
>>>>>>> Hi Justin,
>>>>>>> Unfortunately, it doesn't appear that each image is getting a
>>>>>>> unique ID...
>>>>>>> unless I'm not using the code correctly.  In the end I need to  
>>>>>>> have
>>>>>>> the
>>>>>>> windows named "A, C, D, E, F, gamma, W, Z" in order to do  
>>>>>>> particle
>>>>>>> analysis.
>>>>>>> I keep getting errors, so I printed the image IDs and there is
>>>>>>> always a
>>>>>>> repeat, but it seems to vary.  Are the image IDs usually  
>>>>>>> expressed
>>>>>>> like"-10", "-71", etc.?  Thanks for your advice.
>>>>>>> Chris
>>>>>>>
>>>>>>>
>>>>>>> //Selects directory to save files to
>>>>>>> dir = getDirectory("Select save directory");
>>>>>>>
>>>>>>> //Prompt for 402nm image
>>>>>>> var violet = "Open a 402nm image";
>>>>>>> requires("1.34m");
>>>>>>>   title = "Untitled";
>>>>>>>   width=512; height=512;
>>>>>>>   Dialog.create("402nm");
>>>>>>>   Dialog.addMessage(violet);
>>>>>>>   Dialog.show();
>>>>>>>
>>>>>>> //Run ICS opener
>>>>>>> run("ICS/IDS... ");
>>>>>>>
>>>>>>> //Closes 402 unassigned, 402 background
>>>>>>> close();
>>>>>>> close();
>>>>>>> Z = getImageID();
>>>>>>> run("Put Behind [tab]");
>>>>>>> W = getImageID();
>>>>>>>
>>>>>>> //Prompt for 488nm image
>>>>>>> var blue = "Open a 488nm image";
>>>>>>> requires("1.34m");
>>>>>>>   title = "Untitled";
>>>>>>>   width=512; height=512;
>>>>>>>   Dialog.create("488nm");
>>>>>>>   Dialog.addMessage(blue);
>>>>>>>   Dialog.show();
>>>>>>>
>>>>>>> //Run ICS opener
>>>>>>> run("ICS/IDS... ");
>>>>>>>
>>>>>>> //Converts stack to images
>>>>>>> run("Convert Stack to Images");
>>>>>>>
>>>>>>> //Closes 488 unassigned, 488 background, E_488
>>>>>>> close();
>>>>>>> close();
>>>>>>> close();
>>>>>>> D = getImageID();
>>>>>>> run("Put Behind [tab]");
>>>>>>> C = getImageID();
>>>>>>> run("Put Behind [tab]");
>>>>>>> A = getImageID();
>>>>>>>
>>>>>>>
>>>>>>> //Prompt for 561nm image
>>>>>>> var green = "Open a 561nm image";
>>>>>>> requires("1.34m");
>>>>>>>   title = "Untitled";
>>>>>>>   width=512; height=512;
>>>>>>>   Dialog.create("561nm");
>>>>>>>   Dialog.addMessage(green);
>>>>>>>   Dialog.show();
>>>>>>>
>>>>>>> //Run ICS opener
>>>>>>> run("ICS/IDS... ");
>>>>>>>
>>>>>>> //Converts stack to images
>>>>>>> run("Convert Stack to Images");
>>>>>>>
>>>>>>> //Closes 561 unassigned, 561 background
>>>>>>> close();
>>>>>>> close();
>>>>>>> gamma = getImageID();
>>>>>>> run("Put Behind [tab]");
>>>>>>> F = getImageID();
>>>>>>> run("Put Behind [tab]");
>>>>>>> E = getImageID();
>>>>>>>
>>>>>>> //Prints image IDs
>>>>>>> print(A);
>>>>>>> print(C);
>>>>>>> print(D);
>>>>>>> print(E);
>>>>>>> print(F);
>>>>>>> print(gamma);
>>>>>>> print(W);
>>>>>>> print(Z);
>>>>>>>
>>>>>>>
>>>>>>> //Renames windows
>>>>>>> selectWindow(A);
>>>>>>> rename("A");
>>>>>>> selectWindow(C);
>>>>>>> rename("C");
>>>>>>> selectWindow(D);
>>>>>>> rename("D");
>>>>>>> selectWindow(E);
>>>>>>> rename("E");
>>>>>>> selectWindow(F);
>>>>>>> rename("F");
>>>>>>> selectWindow(gamma);
>>>>>>> rename("gamma");
>>>>>>> selectWindow(W);
>>>>>>> rename("W");
>>>>>>> selectWindow(Z);
>>>>>>> rename("Z");
>>>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
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