[vtkusers] ComputeTransformedOrigin bug in vtkImageReader.cxx

[Mathieu Malaterre]

Josh,

	Could you provide us with a sample code that reproduce the problem ?

Thanks
Mathieu

Josh Snyder wrote:
> Making this change fixed my problem. Could someone verify this and check 
> it in?
> 
> Josh
> 
> Josh Snyder wrote:
> 
>> I've run into a problem using vtkImageReader with the SetTransform 
>> functionality, and I think it's due to the line of code referenced in 
>> the post below (line 495 in the current CVS version). It seems to me 
>> that the older version (w/out the +1) was correct. My understanding is 
>> that if the Transform specifies an axis reversal, the order of the 
>> voxels along that axis needs to be reversed, and the origin coordinate 
>> for that axis needs to be shifted so that the voxels originally 
>> occurring at negative locations become positive and vice versa. The 
>> former step is handled by the inverse transform of the increments 
>> during the vtkImageReaderUpdate2 method, and the latter by the code 
>> mentioned below. I think the +1 addition is a bug. For example, 
>> consider the case where the extent in the y direction consists of a 
>> single voxel situated at y = -1, and the Transform specifies that this 
>> axis be reversed. This line should translate the origin to +1, so that 
>> the voxel is newly situated at +1.
>>
>> In this case, the variables would be set as follows:
>> original origin[1] = -1
>> original spacing[1] = 1
>>
>> Transform =
>> 1 0 0 0
>> 0 -1 0 0
>> 0 0 1 0
>> 0 0 0 1
>>
>> yields
>>
>> transformedOrigin[1] = 1
>> transformedSpacing[1] = -1
>>
>> transformedExtent[3] = 0
>> transformedExtent[2] = 0
>> i = 1
>>
>> The current code:
>> origin[i] = transformedOrigin[i] + 
>> transformedSpacing[i]*(transformedExtent[i*2+1] -  
>> transformedExtent[i*2] + 1)
>> = 1 + (-1 * (0 - 0 + 1)) = 1 - 1 = 0
>>
>> The old (correct?) code:
>> origin[i] = transformedOrigin[i] + 
>> transformedSpacing[i]*(transformedExtent[i*2+1] -  
>> transformedExtent[i*2])
>> = 1 + (-1 * (0 - 0)) = 1 + 0 = 1
>>
>> Is my understanding of this correct, or is there something I'm missing?
>>
>> Josh
>>
>>> Simon,
>>>
>>> I checked in your corrections this morning. I also fixed 
>>> graphics/vtkVolume16Reader. Its logic was
>>> also flawed.
>>>
>>> Thanks,
>>>
>>> Bill
>>>
>>> -----Original Message-----
>>> From: Simon Warfield [mailto:warfield at bwh.harvard.edu 
>>> <mailto:warfield%20at%20bwh.harvard.edu>]
>>> Sent: Sunday, July 08, 2001 7:09 PM
>>> To: vtkusers at public.kitware.com 
>>> <mailto:vtkusers%20at%20public.kitware.com>
>>> Subject: [vtkusers] bug in vtkImageReader.cxx ?
>>>
>>>
>>>
>>> I notice that if I read some image data using vtkImageReader and 
>>> transform
>>> it to correct for patient orientation using the 
>>> vtkImagerReader::SetTransform
>>> function, then the new origin is at an unexpected location.
>>>
>>> I get data looking like:
>>> # vtk DataFile Version 3.0
>>> vtk output
>>> BINARY
>>> DATASET STRUCTURED_POINTS
>>> DIMENSIONS 256 256 90
>>> SPACING 0.703125 0.703125 1.5
>>> ORIGIN -90 -89.2969 -67.5
>>> CELL_DATA 5787225
>>> POINT_DATA 5898240
>>>
>>> When I expect to get data looking like:
>>> # vtk DataFile Version 3.0
>>> vtk output
>>> BINARY
>>> DATASET STRUCTURED_POINTS
>>> DIMENSIONS 256 256 90
>>> SPACING 0.703125 0.703125 1.5
>>> ORIGIN -90 -90 -67.5
>>> CELL_DATA 5787225
>>> POINT_DATA 5898240
>>>
>>>  I think the problem is that line 936 of imaging/vtkImageReader.cxx 
>>> should not
>>> read
>>>          (transformedExtent[i*2+1] -  transformedExtent[i*2]);
>>> but instead should be:
>>>          (transformedExtent[i*2+1] -  transformedExtent[i*2]+1);
>>>
>>>  This part of vtkImageReader.cxx in the latest vtk nightly is doing a 
>>> shift of the origin when an axis is reflected, but seems to be using 
>>> one less
>>> than the width of the data to compute the new origin. I think the width
>>> of the data should be used.
>>>
>>>  Could someone check this, and make the change to the CVS repository 
>>> if it
>>> should be fixed ?
>>>
>>> -- 
>>> Simon Warfield, Ph.D. warfield at bwh.harvard.edu 
>>> <mailto:warfield%20at%20bwh.harvard.edu> Phone:617-732-7090
>>> http://www.spl.harvard.edu/~warfield 
>>> <http://www.spl.harvard.edu/%7Ewarfield>           FAX:  617-582-6033
>>> Thorn 329, Brigham and Women's Hospital, Harvard Medical School
>>> Department of Radiology, 75 Francis St, Boston, MA, 02115
>>>
>>
>> _______________________________________________
>> This is the private VTK discussion list. Please keep messages 
>> on-topic. Check the FAQ at: <http://public.kitware.com/cgi-bin/vtkfaq>
>> Follow this link to subscribe/unsubscribe:
>> http://www.vtk.org/mailman/listinfo/vtkusers
> 
> 
> _______________________________________________
> This is the private VTK discussion list. Please keep messages on-topic. 
> Check the FAQ at: <http://public.kitware.com/cgi-bin/vtkfaq>
> Follow this link to subscribe/unsubscribe:
> http://www.vtk.org/mailman/listinfo/vtkusers
>