16-bit raw images - how to preserve absolute value?

[robert atwood]

Hi;
I've been using ImageJ to prepare data files for some of my own
routines, because I can create shapes interactively in the interface or
by macro. However, now when I try to load a file which is 16-bit raw
data, containing values that are only small integers (0,1,2,3) , then
change (for example ) areas of '0' to '1' using flood-fill, then save as
raw data, then import it again, I find that the values are rescaled such
that 1 becomes 256, 2 becomes 512, and 3 becomes 768  

How do I avoid this ? I need the values to remain exactly as I assign
them!

 Thanks
Robert

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[Michael Schmid]

Hi Robert,

it seems to be either a problem of incorrectly giving little endian/
big endian byte order or the offset to the first image is wrong in  
the import dialog (it should be 0 for raw files written by ImageJ)

Edit>Options>IO Options allows you to set whether to write raw files  
in Intel (=little endian) format.

Michael
________________________________________________________________

On 8 Apr 2010, at 12:21, Robert Atwood wrote:

> Hi;
> I've been using ImageJ to prepare data files for some of my own
> routines, because I can create shapes interactively in the  
> interface or
> by macro. However, now when I try to load a file which is 16-bit raw
> data, containing values that are only small integers (0,1,2,3) , then
> change (for example ) areas of '0' to '1' using flood-fill, then  
> save as
> raw data, then import it again, I find that the values are rescaled  
> such
> that 1 becomes 256, 2 becomes 512, and 3 becomes 768
>
> How do I avoid this ? I need the values to remain exactly as I assign
> them!
>
>  Thanks
> Robert

[robert atwood]

Hi, Michael:

That appears to be the correct problem.

I am confused because 'save as raw' does not provide the option at the
time of exporting the data,  but 'import raw' does provide the option at
the time of importing the data. I did not know about the Edit>Options>IO
Options setting for this parameter. Also I note that the name of the
byte order is 'Intel byte order' in the dialog you mention , but the
Import>Raw dialog box refers to 'Little-Endian byte order', the more
usual and brand-agnostic designation!

Many Thanks
Robert
 

> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On
> Behalf Of Michael Schmid
> Sent: 08 April 2010 15:03
> To: [hidden email]
> Subject: Re: 16-bit raw images - how to preserve absolute value?
>
> Hi Robert,
>
> it seems to be either a problem of incorrectly giving little
> endian/ big endian byte order or the offset to the first
> image is wrong in the import dialog (it should be 0 for raw
> files written by ImageJ)
>
> Edit>Options>IO Options allows you to set whether to write raw files
> in Intel (=little endian) format.
>
> Michael
> ________________________________________________________________
>
> On 8 Apr 2010, at 12:21, Robert Atwood wrote:
>
> > Hi;
> > I've been using ImageJ to prepare data files for some of my own
> > routines, because I can create shapes interactively in the
> interface
> > or by macro. However, now when I try to load a file which is 16-bit
> > raw data, containing values that are only small integers
> (0,1,2,3) ,
> > then change (for example ) areas of '0' to '1' using
> flood-fill, then
> > save as raw data, then import it again, I find that the values are
> > rescaled such that 1 becomes 256, 2 becomes 512, and 3 becomes 768
> >
> > How do I avoid this ? I need the values to remain exactly
> as I assign
> > them!
> >
> >  Thanks
> > Robert
>

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This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom