[Insight-users] Image index limits

Tue Jan 12 20:44:09 EST 2010

Hi Robert,

I confirm that CVS version works much better than ITK-3.16
but still it looks like ImageFileReader has
an issue with Analyze75 format.

Regards,

Alex

Robert.Atwood at diamond.ac.uk wrote:
> 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.
>>>
>>>
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