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<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Bill,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>I tested it and it works
perfectly now, so you can close the bug issue.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Thanks a lot!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Sebastien<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><b><font size=2 face=Tahoma><span lang=EN-US
style='font-size:10.0pt;font-family:Tahoma;font-weight:bold'>From:</span></font></b><font
size=2 face=Tahoma><span lang=EN-US style='font-size:10.0pt;font-family:Tahoma'>
Bill Lorensen [mailto:bill.lorensen@gmail.com] <br>
<b><span style='font-weight:bold'>Sent:</span></b> vendredi 14 décembre 2007
14:36<br>
<b><span style='font-weight:bold'>To:</span></b> Sébastien Fricker<br>
<b><span style='font-weight:bold'>Cc:</span></b> Xabier Artaechevarria Artieda;
insight-users@itk.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Insight-users]
Overwriting TIFF files</span></font><span lang=EN-US><o:p></o:p></span></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Sebastien,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
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<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Please update and try one more time. I had forgotten to remove the
dummy TIFFClose that was in TIFFImageIO.cxx. I'm not sure why my test worked.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Bill<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On Dec 14, 2007 4:06 AM, Sébastien Fricker <<a
href="mailto:sebastien.fricker@phaseview.net">sebastien.fricker@phaseview.net</a>>
wrote:<o:p></o:p></span></font></p>
<div vlink=blue link=blue>
<div>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'>Bill,</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'>I updated itkTIFFImageIO.cxx and tested it. Now I
get an error message when the tiff file cannot be written, which is good. </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'>The other problem is still present though: I
can't modify the file in-place because after calling
inputImageReader->Update() the file remains open. </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'>To me it looks like TIFFClose</span></font><font
size=2 face="Courier New"><span lang=EN-GB style='font-size:10.0pt;font-family:
"Courier New"'> </span></font><font size=2 color=navy face=Arial><span
lang=EN-GB style='font-size:10.0pt;font-family:Arial;color:navy'>does not do
what it's supposed to do (i.e. close the file…).</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'>After TIFFClose is being called during
inputImageReader->Update(), if I try to open the file with another
application such as Microsoft Document Imaging, it says the file is already in
use by another application, meaning ITK did not unlock it. </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'>But maybe I'm doing something wrong…</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'>Could you please check it out?</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'>Thanks a lot.</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span lang=EN-GB style='font-size:10.0pt;
font-family:Arial;color:navy'>Sebastien</span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'> </span></font><o:p></o:p></p>
<p><font size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:
Arial;color:navy'> </span></font><o:p></o:p></p>
<div>
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face="Times New Roman"><span lang=EN-US style='font-size:12.0pt'>
<hr size=2 width="100%" align=center>
</span></font></div>
<p><b><font size=2 face=Tahoma><span lang=EN-US style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span lang=EN-US style='font-size:10.0pt;font-family:Tahoma'> Bill
Lorensen [mailto:<a href="mailto:bill.lorensen@gmail.com" target="_blank">bill.lorensen@gmail.com</a>]
<br>
<b><span style='font-weight:bold'>Sent:</span></b> jeudi 13 décembre 2007 21:13<br>
<b><span style='font-weight:bold'>To:</span></b> Sébastien Fricker<br>
<b><span style='font-weight:bold'>Cc:</span></b> Xabier Artaechevarria Artieda;
<a href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org</a>
<o:p></o:p></span></font></p>
<div>
<div>
<p class=MsoNormal><font size=2 face=Tahoma><span lang=EN-US style='font-size:
10.0pt;font-family:Tahoma'><br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [Insight-users]
Overwriting TIFF files<o:p></o:p></span></font></p>
</div>
</div>
</div>
<div>
<div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>Sebastien,<o:p></o:p></span></font></p>
</div>
<div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>Thanks
for submitting the bug report. It was pretty easy to fix.<o:p></o:p></span></font></p>
</div>
<div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'><a
href="http://public.kitware.com/Bug/view.php?id=6159" target="_blank">http://public.kitware.com/Bug/view.php?id=6159</a><o:p></o:p></span></font></p>
</div>
<div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>Please
update itkTIFFImageIO.cxx and see if it fixes your problem. If it does, I'll
close the bug.<o:p></o:p></span></font></p>
</div>
<div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>Bill<o:p></o:p></span></font></p>
</div>
<div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'><br>
<br>
<o:p></o:p></span></font></p>
</div>
<div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>On Dec
13, 2007 1:17 PM, Bill Lorensen <<a href="mailto:bill.lorensen@gmail.com"
target="_blank">bill.lorensen@gmail.com</a>> wrote: <o:p></o:p></span></font></p>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>Sebastien,<br>
<br>
This looks like a bug to me. I can't see itkTIFFImageIO closing the file. Also,
the write should not silently fail. <br>
Please enter a bug report: <br>
<a href="http://public.kitware.com/Bug/my_view_page.php" target="_blank">http://public.kitware.com/Bug/my_view_page.php</a><br>
<font color="#888888"><span style='color:#888888'><br>
Bill</span></font> <o:p></o:p></span></font></p>
<div>
<div>
<p style='margin-bottom:12.0pt'><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>On Dec
13, 2007 12:56 PM, Sébastien Fricker <<a
href="mailto:sebastien.fricker@phaseview.net" target="_blank">sebastien.fricker@phaseview.net
</a>> wrote:<o:p></o:p></span></font></p>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>Thank you
Xabi,<br>
I have already tested writing to a different name and it works just fine. <br>
Only when input name == output name do I get a problem: the original file is <br>
not modified.<br>
<br>
The part of the code that fails is in Itktiffimageio.cxx, in the<br>
TIFFImageIO::InternalWrite function.<br>
The problem appears at the following piece of code: <br>
<br>
TIFF *tif = TIFFOpen(m_FileName.c_str(), "w"); <br>
if ( !tif )<br>
{<br>
itkDebugMacro( << "Returning" );<br>
return;<br>
}<br>
<br>
In my case !tif == true because the image was already open at the beginning <br>
of the pipeline.<br>
<br>
Surprisingly it works with BMP images though. Does this mean TIFF files <br>
cannot be modified in-place?<br>
<br>
Sebastien<o:p></o:p></span></font></p>
<div>
<div>
<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'><br>
-----Original Message-----<br>
From: insight-users-bounces+sebastien.fricker=<a
href="mailto:phaseview.net@itk.org" target="_blank">phaseview.net@itk.org </a><br>
[mailto:<a
href="mailto:insight-users-bounces+sebastien.fricker=phaseview.net@itk.org"
target="_blank"> insight-users-bounces+sebastien.fricker=phaseview.net@itk.org </a>]
On<br>
Behalf Of Xabier Artaechevarria Artieda <br>
Sent: jeudi 13 décembre 2007 18:21<br>
To: <a href="mailto:insight-users@itk.org" target="_blank">insight-users@itk.org
</a><br>
Subject: Re: [Insight-users] Overwriting TIFF files<br>
<br>
Hi Sébastien,<br>
I think I have done this, sometimes without even realising :( <br>
Try writing with a different name to see if that is the problem.<br>
Good luck, <br>
Xabi<br>
<br>
--<br>
Xabier Artaechevarria<br>
Cancer Imaging Laboratory <br>
Centre for Applied Medical Research<br>
<a href="http://www.cima.es/" target="_blank">www.cima.es</a><br>
<br>
<br>
<br>
Sébastien Fricker <<a href="mailto:sebastien.fricker@phaseview.net"
target="_blank"> sebastien.fricker@phaseview.net </a>> ha escrito:<br>
<br>
> Dear ITK users,<br>
><br>
> I wrote a program that opens an image, transforms it via the Resample <br>
image<br>
> filter and writes the result to the original image file (see code fragment
<br>
> below).<br>
><br>
> This works fine when I use BMP images.<br>
><br>
> It does not work when I use TIF images: the original image is not <br>
modified.<br>
> What happens is that the writer at the end does not do anything: <br>
apparently<br>
> it cannot open the image for writing, probably because the same image was<br>
> open for reading at the beginning of the pipeline. <br>
><br>
><br>
><br>
> Is this a bug or am I doing something wrong? <br>
><br>
> How can I modify a TIF file in-place?<br>
><br>
><br>
><br>
> Thanks for any hint.<br>
><br>
><br>
><br>
> Sebastien <br>
><br>
><br>
><br>
> CODE FRAGMENT:<br>
><br>
><br>
><br>
> --------------------------------------------------------<br>
><br>
><br>
><br>
> //DEFINE IMAGE TYPES<br>
><br>
> const unsigned int Dimension = 2; <br>
><br>
> typedef unsigned short PixelType;<br>
> <br>
> typedef double InternalPixelType;<br>
><br>
> typedef itk::Image< PixelType, Dimension > ImageType;<br>
><br>
> typedef itk::Image< InternalPixelType, Dimension >
InternalImageType; <br>
><br>
><br>
><br>
> //READ INPUT IMAGE<br>
><br>
> typedef itk::ImageFileReader< ImageType > ImageReaderType;<br>
><br>
> ImageReaderType::Pointer inputImageReader =
ImageReaderType::New();<br>
><br>
> <br>
><br>
> inputImageReader->SetFileName( fileName );<br>
><br>
> inputImageReader->Update();<br>
><br>
> ImageType::Pointer inputImage = inputImageReader->GetOutput();<br>
><br>
><br>
><br>
> <br>
><br>
> //RESAMPLE IMAGE<br>
><br>
> //Define filter, create one instance<br>
><br>
> typedef itk::ResampleImageFilter< InternalImageType, InternalImageType
><br>
> ResampleFilterType; <br>
><br>
> ResampleFilterType::Pointer resampler = ResampleFilterType::New();<br>
><br>
><br>
><br>
> resampler->SetInput( inputImage );<br>
><br>
><br>
><br>
> //MORE CODE HERE TO SET RESAMPLER PARAMETERS … <br>
><br>
><br>
><br>
><br>
><br>
> //CAST IMAGE TO OUTPUT TYPE<br>
><br>
> typedef itk::CastImageFilter<<br>
><br>
>
InternalImageType,<br>
><br>
>
ImageType > CastFilterType; <br>
><br>
> CastFilterType::Pointer caster = CastFilterType::New();<br>
><br>
><br>
><br>
> caster->SetInput( resampler->GetOutput() );<br>
><br>
><br>
><br>
> //WRITE OUTPUT FILE<br>
><br>
> typedef itk::ImageFileWriter< ImageType > WriterType; <br>
><br>
> WriterType::Pointer writer = WriterType::New();<br>
><br>
><br>
><br>
> writer->SetFileName( fileName );<br>
><br>
> writer->SetInput( caster->GetOutput() );<br>
><br>
> writer->Update(); <br>
><br>
><br>
><br>
> --------------------------------------------------------<br>
><br>
><br>
><br>
><br>
><br>
><br>
<br>
<br>
<br>
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<p><font size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
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