[vtkusers] Bug in vtkTIFFReader reading multi-paged tiff file

[David Gobbi]

One other thing about the DRR: maybe you need to use a log lookup
table, e.g. if you have a lookup table, try SetScaleToLog10().

On Fri, Nov 8, 2013 at 3:25 PM, David Gobbi <david.gobbi at gmail.com> wrote:
> On Fri, Nov 8, 2013 at 2:35 PM, Maarten Beek <beekmaarten at yahoo.com> wrote:
>> Hi David,
>>
>> Using VTK 6.0.0, sorry ;-)
>
> My tiff patch didn't make it into VTK 6.0, either.  Just master. (And
> eventually, VTK 6.1 and maybe even VTK 5.10.2).
>
>> Should I send you the tiff file so you can play with it?
>
> Sure.  I always like having more images to play with.  Is it a true
> TIFF, or is it converted from LSM (Zeiss)?
>
>> Now I seem to have your attention:
>>
>> - How do I display a multi-page tif? I don't seem to see the different
>> images using a vtkImageSlice.
>
> Ideally, it should load as a 3D volume, just like any other 3D image
> format, and the only special thing you have to do is set the
> DataSpacing.
>
> However, one of the other bugs I fixed at the same time as the
> OutputExtent segfault was a frame indexing error, which caused some
> frames to be missing when the file was loaded.  Also, even after the
> patches that I made, the TIFF reader still didn't behave properly for
> all images.  I can't remember exactly what the problems were, because
> it was several months ago.
>
>> - What would be good values for the window and level parameters? I am using
>> window = range[1]-range[0] and level = 0.5*(range[0]+range[1]) which works
>> ok for this multi-page tif, but gets me nowhere when I try to display a drr.
>
> I wrote a class called vtkImageHistogramStatistics to help me out with
> Window/Level.  It is included with VTK 5.10 and VTK 6.  It works like
> this:
>
> 1) set the input of vtkImageHistogramStatistics to your image
> 2) call Update()
> 3) call GetAutoRange(range) to get a good window/level range
>
> The AutoRange gives a range based on the threshold for the 99th
> percentile of the image histogram, which gives much better results
> than using the full range (i.e. the full range will often make the
> image look way too dark, whereas the 99th percentile gives something
> much more reasonable).
>
>   David
>
>
>> Thanks - Maarten
>>
>>
>>
>>
>>
>>
>> On Friday, November 8, 2013 4:23:23 PM, David Gobbi <david.gobbi at gmail.com>
>> wrote:
>> Hi Maarten,
>>
>> Which version of VTK are you using?  I believe that this bug has been
>> fixed in the master branch by a commits in the following topic merge:
>> http://vtk.org/gitweb?p=VTK.git;a=commitdiff;h=7e3d5270
>>
>> It was not fixed in time for VTK 5.10, however.
>>
>>   David
>>
>>
>> On Fri, Nov 8, 2013 at 2:12 PM, Maarten Beek <beekmaarten at yahoo.com> wrote:
>>> Hi all,
>>>
>>> vtkTIFFReader crashed for me while loading a multi-paged tiff file.
>>>
>>> The crash occured in vtkTIFFReader::ReadGenericImage(), because
>>> this->OutputExtent was not set (still NULL).
>>> The scalar type for the image I was loading was unsigned short, so it
>>> happened at line 1368.
>>>
>>> I changed void vtkTIFFReader::ReadVolume(void* buffer) into void
>>> vtkTIFFReader::ReadVolume(void* buffer, int outExt[6]) and added the line
>>> this->outputExtent = outExt.
>>>
>>> This solved my crash.
>>> I am not sure I am on to something, but thought to let you know.
>>>
>>> Maarten
>>
>>