Large black and white images

[Sarel Botha]

Hi Everyone

We're using ImageJ to open some huge engineering drawings and memory
usage is currently a concern.

The images are black and white TIFF images and can be 23000 x 12000
pixels. The way ImageJ currently works is that every pixel takes up a
byte of memory. For an image of this size ImageJ would need 263MB of RAM
to keep the image in memory. In the uncompressed TIFF format the image
only takes up about 32MB because each pixel is 1 bit, so you can store 8
pixels in a byte.

Would it be practical and possible to store the data as 1 bit per pixel
and as it is needed turn it into 1 byte per pixel or does ImageJ rely
heavily upon having access to all the pixels as bytes in an array?

Some pointers in the right direction would be much appreciated.

Thanks,
Sarel

[Albert Cardona]

Sarel:

If you can program in java, take the BitVector class from the colt.jar package
(a very nice high performance java computation package) and use it in a
BitProcessor (that would extend ByteProcessor) to store your pixels, and then
adapt the Tiff opener class to load the data from the stream into the
BitVector in the BitProcessor. Then, any call to getPixel() and putPixel()
can be redirected (by overriding these methods), in the BitProcessor class,
to the proper values in the BitVector.
I don't have a solution for the getPixels() which returns the byte[], you'd
have to make it return null and flag a warning or something. Which means, for
saving a file you'll need an special, extended ij.io.TiffEncoder as well.
I believe you can use most ImageJ plugins and commands on such a setup because
they call the getPixel() and putPixel() methods, not the getPixels() that
returns the byte[].

Hope it helped.

--
Albert Cardona
Molecular Cell Developmental Biology
University of California Los Angeles
Tel [phone]
Programming: http://www.pensament.net/java/
Research: http://www.mcdb.ucla.edu/Research/Hartenstein/
Web design: http://www.pixelets.com

[Sarel Botha]

Thank you very much, Albert.

That's what I was looking for.

Sarel

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
Albert Cardona
Sent: Tuesday, March 21, 2006 12:27 AM
To: [hidden email]
Subject: Re: Large black and white images

Sarel:

If you can program in java, take the BitVector class from the colt.jar
package
(a very nice high performance java computation package) and use it in a
BitProcessor (that would extend ByteProcessor) to store your pixels, and
then
adapt the Tiff opener class to load the data from the stream into the
BitVector in the BitProcessor. Then, any call to getPixel() and
putPixel()
can be redirected (by overriding these methods), in the BitProcessor
class,
to the proper values in the BitVector.
I don't have a solution for the getPixels() which returns the byte[],
you'd
have to make it return null and flag a warning or something. Which
means, for
saving a file you'll need an special, extended ij.io.TiffEncoder as
well.
I believe you can use most ImageJ plugins and commands on such a setup
because
they call the getPixel() and putPixel() methods, not the getPixels()
that
returns the byte[].

Hope it helped.

--
Albert Cardona
Molecular Cell Developmental Biology
University of California Los Angeles
Tel [phone]
Programming: http://www.pensament.net/java/
Research: http://www.mcdb.ucla.edu/Research/Hartenstein/
Web design: http://www.pixelets.com

[Till Bretschneider]

Dear list,

I have two questions:

1: although the virtual stack opener is recordable it always opens a
dialog box when used in a macro, for example as in

run("Virtual Stack Opener", "open="+ redDir + " number="+redfiles+ " starting=1 increment=1 file=.tif");

2: I would like to open a file list, either from a text file or an array, into a virtual stack. Is this possible using a macro.


Cheers,

Till


--
Dr. Till Bretschneider
AG Celldynamics (Gerisch)
Max-Planck-Institut fuer Biochemie
Am Klopferspitz 18a
D-82152 Martinsried, Germany

Tel: [phone]
Fax: [phone]
E-mail: [hidden email]
WWW: http://www.till-bretschneider.de