[Insight-users] Image index limits

Tue Jan 12 12:56:12 EST 2010

Hi,
I updated my copy of ITK at about 15:30 today (Jan 12 2010)  and
performed some tests.

Note: I get the following warning from Alex's program:

WARNING: In
/dls_test/i12/robert/sources/ITK_cvs/Insight/Code/IO/itkAnalyzeImageIO.c
xx, line 1307
AnalyzeImageIO (0x8d25790): ERROR: Analyze 7.5 File Format Only Allows
RPI, PIR, and RIP Orientation

However it does not stop the execution of the program.

Results:

1. Write cubes as .mhd, then run JustReadWrite using .mhd input and .mhd
output: correct
2. Write cubes as .mhd, then run JustReadWrite using .mhd input and .hdr
output: correct
3. Write cubes as .hdr, then run JustReadWrite using .hdr input and .hdr
output: INCORRECT
4. Write cubes as .hdr, then run JustReadWrite using .hdr input and .mhd
output: INCORRECT

Conclusion:
The problem lies in the reading of the .hdr format and is still present
in the current CVS version. Writing of .hdr files seems unaffected. 

I suspect the problem lies here:
   1
/*======================================================================
===
   2
   3   Program:   Insight Segmentation & Registration Toolkit
   4   Module:    $RCSfile: itkAnalyzeImageIO.cxx,v $
   5   Language:  C++
   6   Date:      $Date: 2009-12-23 20:15:06 $
   7   Version:   $Revision: 1.102 $

....

 681 void AnalyzeImageIO::Read(void* buffer)
 682 {
 683   unsigned int dim;
 684   const unsigned int dimensions = this->GetNumberOfDimensions();
 685   unsigned int numberOfPixels = 1;
//////<<<<<<<<<<<<<<<<<<<<<<<<<<<< UNSIGNED INT ???? 
 686   for(dim=0; dim< dimensions; dim++ )
 687     {
 688     numberOfPixels *= m_Dimensions[ dim ];
 689     }

I hope this helps,

Robert

-----Original Message-----
From: Bill Lorensen [mailto:bill.lorensen at gmail.com] 
Sent: 12 January 2010 17:25
To: Oleksandr Dzyubak
Cc: Atwood, Robert (DLSLtd,RAL,DIA); insight-users at itk.org;
luis.ibanez at kitware.com
Subject: Re: [Insight-users] Image index limits

We have been making passes through the io's to add the proper types for
offsets. etc.

Try the cvs version and see if your test works with .mdh.

Bill

On Tue, Jan 12, 2010 at 11:42 AM, Oleksandr Dzyubak <adzyubak at gmail.com>
wrote:
>
> Hi Robert,
>
> Thanks for your help in studying this problem.
>
> Following your advise, I tested both
>
> ImageFill_Cube test.mhd
> and
> ImageFill_Cube test.hdr
>
> and in both images I see that
> the first cube stays where it should but the second one disappeared!
> The only reason for such different behavior on your and my machines I 
> can think of is that on my server I am using ITK 3.16 released on 
> September 15, 2009 vs your ITK CVS Nov 4, 2009.
>
> Does that mean that IOFactory was updated somehow between these two 
> releases?
> Well, if it was, I have to give the CVS version a try.
>
> But anyway, according to your findings, this issue was not fixed in 
> ImageFileReader for all formats though (or, in particular, for 
> Analyze75 format), right?
>
> Unfortunately all my input images are in the Analyze75 format, thus 
> any conversion would still require the Analyze75 support in
ImageFileReader.
>
> I see that we are getting close.
>
> Regards,
>
> Alex
>
> On Tue, Jan 12, 2010 at 6:06 AM, <Robert.Atwood at diamond.ac.uk> wrote:
>>
>> Hi Kevin:
>>
>> Which image format did you use for your tests? I observed (see my 
>> other
>> post) that problem using .hdr format (as described by Oleksander's 
>> original post) but not with .mhd format. I believe I observed a 
>> similar problem before with .tif stack but not with a series of .tif 
>> (or .mhd)
>>
>> Do you observe the problem if you use .hdr format?
>>
>> Thanks
>>
>> Robert
>>
>>
>> -----Original Message-----
>> From: insight-users-bounces at itk.org
>> [mailto:insight-users-bounces at itk.org] On Behalf Of Kevin H. Hobbs
>> Sent: 11 January 2010 15:01
>> To: adzyubak at gmail.com
>> Cc: insight-users at itk.org; Luis Ibanez
>> Subject: Re: [Insight-users] Image index limits
>>
>> On 01/07/2010 05:28 PM, Oleksandr Dzyubak wrote:
>> >
>> > ****** End JustReadWrite.cxx ***
>> >
>>
>> When I run this pair of programs I get two cubes in the output of the

>> second program.
>>
>> I am using ITK from CVS on a 64 bit Linux workstation with 12 
>> gigabytes of RAM (bubbles.hooperlab on the dashboard).
>>
>> I tried running ImageCompare on the input and output images but the 
>> machine started swapping and I cancelled the comparison.
>>
>>
>> --
>> 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
>>
>>
>>
>>
>
>
> _____________________________________
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at 
> http://www.kitware.com/opensource/opensource.html
>
> Kitware offers ITK Training Courses, for more information visit:
> http://www.kitware.com/products/protraining.html
>
> Please keep messages on-topic and check the ITK FAQ at:
> http://www.itk.org/Wiki/ITK_FAQ
>
> Follow this link to subscribe/unsubscribe:
> http://www.itk.org/mailman/listinfo/insight-users
>
>

-- 
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