http://imagej.273.s1.nabble.com/Trouble-Calling-Variables-in-Macro-for-the-Image-Calculator-tp3687586p3687593.html
On 17 Jul 2010, at 00:59, Zwick, Ari A. wrote:
> Hi Michael,
>
> You are indeed correct that there was an error in the code that I
> showed
> 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
> getting occurred in the Image Calculator before it had a chance to
> close
> the windows. But thanks for taking a close look at it.
>
> Ari
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of
> Michael Schmid
> Sent: Friday, July 16, 2010 5:12 AM
> To:
[hidden email]
> Subject: Re: Trouble Calling Variables in Macro for the Image
> Calculator
>
> Hi Ari,
>
> from your code:
>
>
>> saveAs("Tiff", "/ecor/azwick/Macro/Mask3.tif");
>>
>> rename(i);
>>
> ...
>
>> selectWindow("Mask3.tif");
>>
>> close();
>>
>
> It seems that you image "Mask3.tif" should be renamed to the number
> contained in variable 'i', so why should it ever work? Did I miss
> something?
>
> Michael
> ________________________________________________________________
>
> 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
>>>>
>>>>
>>>>
>>>>
>>>>