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Re: handling very large images

Posted by Aryeh Weiss on Dec 03, 2015; 3:20pm
URL: http://imagej.273.s1.nabble.com/handling-very-large-images-tp5015116p5015125.html

Hi Mark

Thank you for your reply. I indeed have the individual images and can
read a subset of them, and then mosaic them. However, I really need to
stitch them (which I can do), and my first choice is  to read in the
stitched image that  I already have.

I run with a 12GB memory limit, so that should be sufficient.

Best regards
--aryeh


On 03/12/2015 4:13 PM, Mark J. Chopping wrote:

> Hi Aryeh,
>
> I have put some pretty large (>4GB) mosaics together using Image
> Sequence with the "use" (virtual memory) option, followed by Make
> Montage, by running ImageJ from the commandline: change directory to
> (for example,) /Applications/ImageJ_148 (or wherever your ImageJ
> binary is), with:
>
> java -jar -Xmx5120m ImageJ64_148.app/Contents/Resources/Java/ij.jar
>
> -- where the number after Xmx is the desired memory limit in MB.
>
> Macro code:
>
> print("Mosaicing the "+numfiles+" ("+xLocations+" x "+ NumSlices +")
> images...");
>
> run("Image Sequence...", "open="+sampleTIFF+" number="+numfiles+"
> starting=1 increment=1 scale=100 file=.tif sort use");
>
> print("Image Sequence run; doing Make Montage...");
>
> run("Make Montage...", "columns="+xLocations+" rows="+ NumSlices +"
> scale=1 first=1 last="+numfiles+" increment=1 border=0");
>
> saveAs("Tiff", outDir+"CAN_"+base+".tif");
>
> -- where xLocations and NumSlices are the number of images in X and Y,
> respectively; and sampleTIFF is one of a series of TIFFs that are
> tiles, numbered sequentially (_0000.tif, _0001.tif, _0002.tif and so on)
>
> This is the only way I could avoid the NegativeArraySizeException erorr.
>
> HTH.
>
>   Mark
>
>  Mark Chopping, Ph.D.
>  Montclair State University, Montclair, NJ 07043
>  http://www.montclair.edu/csam/remote-sensing-lab/
>
> ----
>> Date: Thu, 3 Dec 2015 14:34:39 +0200
>> From: Aryeh Weiss <[hidden email]>
>> To: [hidden email]
>> Subject: handling very large images
>>
>> I have a very large image (25x30 images, each is 1600x1200 pixels)
>> that I want to load into imagej.
>>
>> This produces the java.lang.NegativeArraySizeException that was
>> discussed in the following thread:
>> imagej.1557.x6.nabble.com/Montage-java-lang-NegativeArraySizeException-td5014201.html
>>
>>
>> In this thread, Curtis refers to a FAQ entry
>> http://imagej.net/FAQ#I_got_a_NegativeArraySizeException._What_caused_it.3F 
>>
>> but I did not find it in the FAQ after following the link.
>>
>> This image is not a stack, so I cannot use virtual stack.
>> I tried to use the crop on import option, and asked for a 12000x12000
>> section.
>> It started off ok , and reported that it is verifying the cropping.
>> Memory monitor reported that about 6.7GB were being used.
>> It ran for about 45 minutes, and then finally threw the
>> NegativeArraySizeException.
>>
>> Now I am trying it with a 5000x5000 crop, which should be no problem
>> to load. memory monitor claims
>> 6.4 GB are in use. Again, no image has appeared even after about 20
>> minutes.
>>
>> Is there a work around to load it?
>> Alternatively, is there a way to subsample it?
>>
>> --aryeh
>>
>> --
>> Aryeh Weiss
>> Faculty of Engineering
>> Bar Ilan University
>> Ramat Gan 52900 Israel
>>
>> Ph:  972-3-5317638
>> FAX: 972-3-7384051
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>


--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: 972-3-7384051

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html