saving binary as 1 bit-per-pixel tif

[Jan Eglinger-5]

Dear all,

I tried to save a binary mask as a 1-bit-per-pixel file using "File>Save
As>Compressed TIFF ...".
After confirming that I want to save it using 1 bit per pixel, I get the
following error message:


java.lang.IllegalArgumentException: Input ByteProcessor has to have
index color model with map size of 2, got 256.
   at
net.sf.ij.jaiio.BufferedImageCreator.createBinary(BufferedImageCreator.java:102)
   at
net.sf.ij.jaiio.BufferedImageCreator.create(BufferedImageCreator.java:77)
   at net.sf.ij.jaiio.JAIWriter.write(JAIWriter.java:143)
   at
net.sf.ij.plugin.ImageIOSaveAsPlugin.write(ImageIOSaveAsPlugin.java:237)
   at net.sf.ij.plugin.ImageIOSaveAsPlugin.run(ImageIOSaveAsPlugin.java:207)
[...]


I already tried editing the LUT to contain only 2 colours, and choosing
different compression methods... I guess the problem is that the image
still has 256 grey levels (of which only 0 and 255 are used).

How can I reduce the map size to 2?

Is there any other memory-saving way of saving big binary images?

Thanks,
Jan

[dscho]

Hi,

On Sun, 6 Sep 2009, Jan Eglinger wrote:

> I already tried editing the LUT to contain only 2 colours, and choosing
> different compression methods... I guess the problem is that the image
> still has 256 grey levels (of which only 0 and 255 are used).
>
> How can I reduce the map size to 2?

I think you have to use "Image>Type>RGB" followed by "Image>Type>8-bit
Color" (where you choose 2 channels only).

Hth,
Dscho

[Jan Eglinger-5]

Hi,

Johannes Schindelin wrote:
>> How can I reduce the map size to 2?
>
> I think you have to use "Image>Type>RGB" followed by "Image>Type>8-bit
> Color" (where you choose 2 channels only).
thx, I didn't think of that option via "8-bit Color" yet. However, that
doesn't eliminate but only changes the error message when I try to save
as 1-bit-per-pixel tiff. Now it reads:

java.lang.IllegalStateException: Internal error: wrong size of destPixels.
        at
net.sf.ij.jaiio.BufferedImageCreator.createBinary(BufferedImageCreator.java:116)


Any ideas?

Jan

[Gluender-3]

Just curious:

Where did you find the command: "File>Save As>Compressed TIFF ..."

(I'm using "ImageJ 1.43g daily built" and can't find it.)

>Dear all,
>
>I tried to save a binary mask as a 1-bit-per-pixel file using "File>Save
>As>Compressed TIFF ...".
>After confirming that I want to save it using 1 bit per pixel, I get the
>following error message:
>
>
>java.lang.IllegalArgumentException: Input ByteProcessor has to have
>index color model with map size of 2, got 256.
>    at
>net.sf.ij.jaiio.BufferedImageCreator.createBinary(BufferedImageCreator.java:102)
>    at
>net.sf.ij.jaiio.BufferedImageCreator.create(BufferedImageCreator.java:77)
>    at net.sf.ij.jaiio.JAIWriter.write(JAIWriter.java:143)
>    at
>net.sf.ij.plugin.ImageIOSaveAsPlugin.write(ImageIOSaveAsPlugin.java:237)
>    at net.sf.ij.plugin.ImageIOSaveAsPlugin.run(ImageIOSaveAsPlugin.java:207)
>[...]
>
>
>I already tried editing the LUT to contain only 2 colours, and choosing
>different compression methods... I guess the problem is that the image
>still has 256 grey levels (of which only 0 and 255 are used).
>
>How can I reduce the map size to 2?
>
>Is there any other memory-saving way of saving big binary images?
>
>Thanks,
>Jan

AFAIK ImageJ uses minimum 8bit per pixel.

Best
--

                   Herbie

          ------------------------
          <http://www.gluender.de>

[Jan Eglinger-5]

Hi,

Gluender wrote:
> Just curious:
>
> Where did you find the command: "File>Save As>Compressed TIFF ..."
I just noticed that the function is residing in the ImageIO plugin by
Jerek Sacha:

http://ij-plugins.sourceforge.net/plugins/imageio/

Just filed the bug on the sourceforge page as well..


>> Is there any other memory-saving way of saving big binary images?
>
> AFAIK ImageJ uses minimum 8bit per pixel.
I was just wondering if there is a better way to save huge binary masks
than to waste 7/8 of the disk space.
During processing, it doesn't make any difference, since IJ is using
8bit per pixel minimum, that's right.

Best,
Jan

[Joachim Wesner]

Hi Jan,

if ImagIO really does **compressed** TIIFs, I would assume that the
compression algo is smart enough to
not waste 7/8 of disk space, i.e. that the final size of the compressed
TIFF is almost the same, be it a true
binary image or a "8-bit image" that only has 0 and 255 as pixel content.
Did you check that?

(Using another program that can do both kinds of compressed images)

Image compressing works on adapting the final code to the occurence
frequency of certain symbols and
would detect that there is only 0 and 255, I assume!)


Mit freundlichen Grüßen / Best regards

Joachim Wesner


Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht
Wetzlar  HRB 2432
Geschäftsführer:  Dr. Stefan Traeger | Dr. Wolf-Otto Reuter | Dr. David Roy
Martyr | Colin Davis
www.leica-microsystems.com



                                                                           
             Jan Eglinger                                                  
             <eglinger@MPI-CBG                                            
             .DE>                                                       An
             Gesendet von:              [hidden email]                
             ImageJ Interest                                         Kopie
             Group                                                        
             <[hidden email].                                       Thema
             GOV>                       Re: saving binary as 1            
                                        bit-per-pixel tif                  
                                                                           
             07.09.2009 12:03                                              
                                                                           
                                                                           
              Bitte antworten                                              
                    an                                                    
              ImageJ Interest                                              
                   Group                                                  
             <[hidden email].                                            
                   GOV>                                                    
                                                                           
                                                                           




Hi,

Gluender wrote:
> Just curious:
>
> Where did you find the command: "File>Save As>Compressed TIFF ..."
I just noticed that the function is residing in the ImageIO plugin by
Jerek Sacha:

http://ij-plugins.sourceforge.net/plugins/imageio/

Just filed the bug on the sourceforge page as well..


>> Is there any other memory-saving way of saving big binary images?
>
> AFAIK ImageJ uses minimum 8bit per pixel.
I was just wondering if there is a better way to save huge binary masks
than to waste 7/8 of the disk space.
During processing, it doesn't make any difference, since IJ is using
8bit per pixel minimum, that's right.

Best,
Jan



______________________________________________________________________
This email has been scanned by the MessageLabs Email Security System.
For more information please visit http://www.messagelabs.com/email 
______________________________________________________________________

[Wayne Rasband]

On Sep 7, 2009, at 6:03 AM, Jan Eglinger wrote:

> Hi,
>
> Gluender wrote:
>> Just curious:
>>
>> Where did you find the command: "File>Save As>Compressed TIFF ..."
> I just noticed that the function is residing in the ImageIO plugin by
> Jerek Sacha:
>
> http://ij-plugins.sourceforge.net/plugins/imageio/
>
> Just filed the bug on the sourceforge page as well..
>
>
>>> Is there any other memory-saving way of saving big binary images?
>>
>> AFAIK ImageJ uses minimum 8bit per pixel.
> I was just wondering if there is a better way to save huge binary  
> masks
> than to waste 7/8 of the disk space.
> During processing, it doesn't make any difference, since IJ is using
> 8bit per pixel minimum, that's right.

Use File>Save As ZIP. As a test, I saved a 4000x4000 binary mask in  
ZIP format and it was 300 times smaller (52K) compared to saving in  
uncompressed TIFF format (15.3MB). You can open ZIP files created by  
File>Save As>ZIP using File>Open or by drag and drop.

-wayne