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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Brad,<br>
<br>
I rebuilt ITK on ubuntu with ITK_USE_SYSTEM_TIFF unselected, and confirmed that the truncation problem is still there. It seems to be an ITK issue, as you suspected. Interesting (and problematic) that it occurs on Linux/ubuntu but not on Windows 7. I could
send a tiff file that manifests the problem to anyone who'd like to test it on their Linux system. The file (compressed tiff) is 95 MB.<br>
<br>
Gib<br>
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<div style="direction: ltr;" id="divRpF176316"><font color="#000000" face="Tahoma" size="2"><b>From:</b> Bradley Lowekamp [blowekamp@mail.nih.gov]<br>
<b>Sent:</b> Thursday, 6 March 2014 2:55 a.m.<br>
<b>To:</b> Gib Bogle<br>
<b>Cc:</b> community@itk.org<br>
<b>Subject:</b> Re: [ITK Community] Problem with multi-image tiff on Linux (ubuntu)<br>
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<div>Hello,
<div><br>
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<div>For windows to handle larger than 4GB image the CMake option ITK_USE_64BITS_IDS needs to be turned on. ( In this day and age it really should be turned on by default now. )</div>
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<div>I have had similar problems trying to convert large image to tiffs too. Specifically, I recall getting the same type of truncation when trying to convert the Visible Human cyro-slices to big tiff.</div>
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<div>I think some serious time needs to be spend looking at itkTIFFImageIO for 64-bit issues, as my casual looks have not turned up anything.</div>
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<div>Brad</div>
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<div>
<div>On Mar 5, 2014, at 3:28 AM, Gib Bogle <<a href="mailto:g.bogle@auckland.ac.nz" target="_blank">g.bogle@auckland.ac.nz</a>> wrote:</div>
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<div style="direction:ltr; font-family:Tahoma; font-size:10pt">I have recently started having to work with big multi-image tiff files, e.g. 4.5 GB. I discovered that ITK on Windows cannot handle such large images, so I am trying to use Linux (64-bit ubuntu
12.10). I managed to build ITK with libtiff5 (actually 4.0.2 I think) which does have bigtiff support, after downloading the latest source code with git, which contains a patch fix for a bug that prevented building. The patch was applied yesterday, so that
was a bit of luck.<br>
<br>
But there is something screwy happening when I read my multi-image tiff with ITK. After reading the image (which is compressed with Deflate) I look at each z-frame and compute the sum of pixel intensities. After z=346 all the intensities are 0, but I know
this is not correct. I can view the frames with Imagemagick's display program, and those at z>346 are not qualitatively different from the earlier ones.<br>
<br>
After reading the image in I am using a pointer to the buffer to access the data:<br>
<br>
p = (unsigned char *)(im->GetBufferPointer());<br>
<br>
then I access the voxel value at (x,y,z) as p[z*xysize+y*width+x]<br>
<br>
I have declared x, y, z, width and xysize = width*height all as long int.<br>
<br>
Another way to show the problem: When the compressed tiff that looks correct when viewed with Imagemagick-display is read with ITK and then written without compression, the uncompressed version has blank frames for z>346. This tiff has 693 frames, each 601x1380.
Exactly the same thing is seen with another tiff that has 693 frames each 779x1380 - again the uncompressed version is blank after frame 346.<br>
<br>
I'd be interested to know if anyone else is reading big tiffs with ITK, on Linux.<br>
<br>
Thanks<br>
Gib</div>
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