http://imagej.273.s1.nabble.com/Trouble-Calling-Variables-in-Macro-for-the-Image-Calculator-tp3687586p3687592.html
you. Fortunately or unfortunately this was merely a copy-paste error in
my email. I was making the change in the macro, and the errors I was
the windows. But thanks for taking a close look at it.
On 14 Jul 2010, at 17:49, Zwick, Ari A. wrote:
> Hi,
>
> Okay so here's my second amendment. I spoke too soon about the
> redundancy. By some happenstance my macro made it through 50
> iterations
> and then crashed again after about 5 after that. So I looked into
> macro
> timing and inserted wait(10) between each command and wait(100)
> between
> the problematic areas. I'm now employing multiple levels of
> redundancy
> in conjunction with wait and my macro has now made it through 400
> iterations seamlessly. I am certain that the macro was getting
> ahead of
> itself with assigning titles, but the Image ID's are actually getting
> miss-assigned too, however they are being convoluted by calling by
> hybrid title/imageID macro. The obvious solution would be to use all
> Image ID's, except that the macro still gets ahead of itself and can't
> find image ID's. So even if I run selectWindow or getImageID 5 times,
> it will still result in errors. I don't even have to run the print
> log
> because I can see my windows getting mislabeled and ImageID's "not
> existing", so that tells me that my commands are getting assigned
> to the
> wrong windows even when I build in the redundancy. So the ultimate
> fix
> is actually the wait command, and perhaps it would be getImageID if I
> used it exclusively, but I think I'd still have the problem. Right
> now
> my paranoia level is set to about 9/10, so I'm going to leave my
> sloppy
> macro with all the redundancies in place and keep the American ideals
> up: "If it aint broke, don't fix it." Ironically (to me at least)
> with
> the wait command, the macro has never run faster. There's almost no
> visible lag.
>
> I am running in "batch mode": z = m*random() *451; // 451 = Number of
> slices.
>
> Although my bugs are not occurring in batch mode. I extract a random
> sample (1 window) from my stack and then analyze that sample, and
> that's
> where my errors are coming in. The batch sampling process has worked
> seamlessly from the beginning, so I think it's just a macro calling
> problem. Maybe a future bug fix for ImageJ would be to have a default
> wait(10) command built into ImageJ to avoid these call errors,
> although
> something tells me that ImageJ programmers would have some beef with
> that. That's my two cents anyway. Thanks again for your help and
> advice. It's people like you that have fueled my transition to
> dedicated Linux for my next computer purchase in 2 weeks.
>
> Ari Zwick
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
> Ben Tupper
> Sent: Tuesday, July 13, 2010 6:35 PM
> To:
[hidden email]
> Subject: Re: Trouble Calling Variables in Macro for the Image
> Calculator
>
> Hi,
>
> On Jul 13, 2010, at 5:52 PM, Zwick, Ari A. wrote:
>
>> Hi Ben,
>>
>> Stunning.
>
> I haven't been called that before! This one is getting taped to the
> ol' refrigerator.
>
>> Unfortunately that did not exclusively solve my problem, but
>> it did certainly help. The ultimate cure was actually redundancy.
>> Now
>> before I close that problematic window I run:
>>
>> selectImage(id);
>> selectwindow(Mask3.tif);
>> close();
>>
>> It made it through 50 iterations without crashing.
>
> That stumps me. I know that others have had luck by inserting a small
> wait(100), but I thought use of image IDs obviated the need for that.
> I am curious if you can demonstrate that the title of the image
> selected by id really is "mask3.tif". I might be that you are creating
> an image (somewhere) that is not being properly disposed of. Perhaps
> you could try the following for debugging purposes.
>
> selectImage(id);
> print("id has a title of " + getTitle());
> selectwindow("Mask3.tif");
> print("Mask3.tif has id of " + getImageID());
> close();
>
> Also, are you running in batch mode?
>
>
>>
>> Ari Zwick
>>
>> -----Original Message-----
>> From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
>> Ben Tupper
>> Sent: Tuesday, July 13, 2010 1:52 PM
>> To:
[hidden email]
>> Subject: Re: Trouble Calling Variables in Macro for the Image
>> Calculator
>>
>> Hi,
>>
>> I think your best bet is to keep track of images by ID rather than by
>> name. Right after you instantiate/open/create/whatever an image use
>> the getImageID() function to get that image's unique identifier. For
>> most subsequent commands that operate on that image be sure to use
>> the
>> command selectImage(id). Note that the Image Calculator command (and
>> perhaps others) will accept an image ID instead of image name, which
>> is very handy.
>>
>> I will be surprised if that doesn't resolve the issue for you.
>>
>> Cheers,
>> Ben
>>
>>
>> On Jul 13, 2010, at 2:33 PM, Zwick, Ari A. wrote:
>>
>>> Dear ImageJ Community,
>>>
>>>
>>>
>>> I'm writing a macro that will loop ~800 times, and I'm getting a few
>>> glitches with my macro calling functions out of the order that I've
>>> written them in. My solution to this problem is to give individual
>>> titles to 1 set of problematic images (the rest use the same title
>>> for
>>> each iteration). So I was thinking of something simple such as
>>> naming
>>> my problematic image equal to the value of i (number of
>>> iterations). So
>>> I can rename the image rename(i) and the title works, however I
>>> can't
>>> get the Image Calculator to call the value of i, which will change
>>> for
>>> each iteration.
>>>
>>>
>>>
>>> Can I define a variable such as: p = getTitle(CurrentImage) to call
>>> in
>>> the Image Calculator? I was also thinking about the print command,
>>> but
>>> it doesn't seem clear to me that the value is easily accessible in
>>> the
>>> macro. I've been having problems with syntax, so I'd really
>>> appreciate
>>> any suggestions about how to call the variable properly, or any
>>> other
>>> work around. Below is a bit of the script that I'm trying to work
>>> with:
>>>
>>>
>>>
>>> width = getWidth();
>>>
>>> height = getHeight();
>>>
>>> work = 10;
>>>
>>> for (i=1; i<=work ; i++) {
>>>
>>>
>>>
>>> m = i/i;
>>>
>>> x = m*random() *(width-356);
>>>
>>> y = m*random() *(height-356);
>>>
>>> z = m*random() *451;
>>>
>>> (let p [ getTitle(getCurrentImage)])
>>>
>>>
>>>
>>> //I know that syntax for p is wrong, found it off a Fiji Wiki
>>>
>>> //Later...
>>>
>>>
>>>
>>> selectWindow("Sample");
>>>
>>> makePolygon(356,0,236,0,236,236,0,236,0,356,356,356);
>>>
>>> run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00
>>> show=Masks exclude");
>>>
>>> saveAs("Tiff", "/ecor/azwick/Macro/Mask3.tif");
>>>
>>> rename(i);
>>>
>>>
>>>
>>> imageCalculator("Add", "Mask2",p);
>>>
>>> rename("Edge Count");
>>>
>>>
>>>
>>> //Error
>>>
>>> //Later
>>>
>>>
>>>
>>> selectWindow("Mask3.tif");
>>>
>>> close();
>>>
>>>
>>>
>>> //Error Mask3.tif does not exit. (This is before I tried the i/p
>>> titles; the error that I'm trying to work around currently)
>>>
>>>
>>>
>>> I know this is kind of sloppy macro writing, but this is my first
>>> time
>>> actually modifying macro script rather than just recording. The
>>> saveAs
>>> Tiff is another attempt to prevent Mask3 from escaping my commands.
>>> My
>>> logic is that this problem probably won't go away, but if I can
>>> rename
>>> each file per iteration, then there won't be any overlap of files
>>> that
>>> don't get closed and mistakenly called in later iterations. I'm
>>> also
>>> aware that the CurrentImage command will cause some serious
>>> problems,
>>> because I have about 4 other windows open. I'd appreciate any help
>>> with
>>> this and thanks in advance.
>>>
>>>
>>>
>>> Ari Zwick
>>>
>>>
>>>
>>>