can't load moderately big files

[Rodrigo Gonçalves]

Dear all,
I'm trying to open a simple sequence of images:https://www.dropbox.com/s/tus90ojkm3p3hd1/video_002.zip?dl=0
It consists of 1812 PNG files, with a total size of 50 MB. Each png file is a RGB image, 864 x 720px.
Something I still don't fully understand: when trying to open the image sequence, ImageJ tells me I'll need 4300 MB (864 x 720 x 1812) instead of 50 MB, what's the math behind? Also, in the past I remember opening sequences of much larger than 50MB with ImageJ without changing the available memory, with no problem.

Fiji (and ImageJ as well) either tells me "all available memory has been used" or the computer gets directly unresponsive. I've tried several things without success- using virtual stack- convert to 8-bits to get rid of some megabytes (I don't need color)
- increasing the allowed memory in Edit-Options from 999MB to 3000 MB- Use TIF instead of PNG- install fresh copies of Fiji and ImageJ
I even tried converting the images to a video using another program, and ImageJ runs out of memory (using import video with FFMPEG and also the built-in import video as AVI) just as when it tries to load the sequence.

Most likely the problem is in my computer/setup because I'm almost sure it would have worked well some months ago (a 50MB image sequence is rather "small", isn't it?).. but I ran out of ideas :)
I'm using
Fiji (ImageJ 1.49k - Java 1.6.0_24; 64-bit)
ImageJ (ImageJ 1.49k12 - java 1.6.0_10; 32-bit)on Windows 7 professional in a intel Core i5 64-bit with 4GB RAM

Any suggestion?
 ________________________
Rodrigo Gonçalves 

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

[Saalfeld, Stephan]

PNG is a compression scheme, but in order to work with the pixels in
memory they have to be decompressed, i.e. each pixel gets the smae place
in memory, the image get fully deflated.  For RGB this is 4 bytes for
each pixel,

864 * 720 * 1,812 * 4 Bytes = 4,508,835,840 Bytes ~ 4,300 MB

You can use a virtual stack, split your work otherwise, or buy more RAM.

Best,
Stephan




On Mon, 2014-11-10 at 19:38 +0000, Rodrigo Gonçalves wrote:

> Dear all,
> I'm trying to open a simple sequence of images:https://www.dropbox.com/s/tus90ojkm3p3hd1/video_002.zip?dl=0
> It consists of 1812 PNG files, with a total size of 50 MB. Each png file is a RGB image, 864 x 720px.
> Something I still don't fully understand: when trying to open the image sequence, ImageJ tells me I'll need 4300 MB (864 x 720 x 1812) instead of 50 MB, what's the math behind? Also, in the past I remember opening sequences of much larger than 50MB with ImageJ without changing the available memory, with no problem.
>
> Fiji (and ImageJ as well) either tells me "all available memory has been used" or the computer gets directly unresponsive. I've tried several things without success- using virtual stack- convert to 8-bits to get rid of some megabytes (I don't need color)
> - increasing the allowed memory in Edit-Options from 999MB to 3000 MB- Use TIF instead of PNG- install fresh copies of Fiji and ImageJ
> I even tried converting the images to a video using another program, and ImageJ runs out of memory (using import video with FFMPEG and also the built-in import video as AVI) just as when it tries to load the sequence.
>
> Most likely the problem is in my computer/setup because I'm almost sure it would have worked well some months ago (a 50MB image sequence is rather "small", isn't it?).. but I ran out of ideas :)
> I'm using
> Fiji (ImageJ 1.49k - Java 1.6.0_24; 64-bit)
> ImageJ (ImageJ 1.49k12 - java 1.6.0_10; 32-bit)on Windows 7 professional in a intel Core i5 64-bit with 4GB RAM
>
> Any suggestion?
>  ________________________
> Rodrigo Gonçalves
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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

[Rasband, Wayne (NIH/NIMH) [E]]

On Nov 10, 2014, at 2:38 PM, Rodrigo Gonçalves <[hidden email]> wrote:
>
> Dear all,
> I'm trying to open a simple sequence of images:https://www.dropbox.com/s/tus90ojkm3p3hd1/video_002.zip?dl=0
> It consists of 1812 PNG files, with a total size of 50 MB. Each png file is a RGB image, 864 x 720px.
> Something I still don't fully understand: when trying to open the image sequence, ImageJ tells me I'll need 4300 MB (864 x 720 x 1812) instead of 50 MB, what's the math behind? Also, in the past I remember opening sequences of much larger than 50MB with ImageJ without changing the available memory, with no problem.

These 1812 compressed PNG files require 2.4MB each (4.2GB total) when opened in ImageJ and uncompressed. I am able to open the sequence as a stack on an 8GB machine with 7GB allocated to ImageJ. The sequence will open faster and use less memory if you enable the “Use virtual stack” option. The easiest way to open an image sequence is to drag and drop the folder onto the “ImageJ” window.

-wayne

> Fiji (and ImageJ as well) either tells me "all available memory has been used" or the computer gets directly unresponsive. I've tried several things without success- using virtual stack- convert to 8-bits to get rid of some megabytes (I don't need color)
> - increasing the allowed memory in Edit-Options from 999MB to 3000 MB- Use TIF instead of PNG- install fresh copies of Fiji and ImageJ
> I even tried converting the images to a video using another program, and ImageJ runs out of memory (using import video with FFMPEG and also the built-in import video as AVI) just as when it tries to load the sequence.
>
> Most likely the problem is in my computer/setup because I'm almost sure it would have worked well some months ago (a 50MB image sequence is rather "small", isn't it?).. but I ran out of ideas :)
> I'm using
> Fiji (ImageJ 1.49k - Java 1.6.0_24; 64-bit)
> ImageJ (ImageJ 1.49k12 - java 1.6.0_10; 32-bit)on Windows 7 professional in a intel Core i5 64-bit with 4GB RAM
>
> Any suggestion?
>  ________________________
> Rodrigo Gonçalves
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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