[Insight-users] PGM from NII with ITK
Dženan Zukić
dzenanz at gmail.com
Fri Feb 28 05:03:38 EST 2014
I needed to compare results of my segmentation method with power
watersheds, so I modified one of ITK's image reading files to enable
natural support for PGM format.
#include "itkPGMImageIOFactory.h" //include it in the beginning of the main
file
//call in the main() function before any ITK-related read/write operations
take place
itk::ObjectFactoryBase::RegisterFactory( itk::PGMImageIOFactory::New() );
This makes .pgm supported just as well as .png or .mha. You can make your
own project "natively" support it. If you only want to convert a few
images, you can modify ITK's ImageReadWrite example.
On Thu, Feb 27, 2014 at 9:19 PM, Richard Beare <richard.beare at gmail.com>wrote:
> Hi,
> I'm assuming you really want a 3d watershed, since you are starting with
> nifti, rather than a series of 2D versions. If you are interested in a
> series of 2d versions, then you might try nifti to tiff with convert3d,
> then extract the tiff slices with tiffsplit, then tifftopgm with the image
> magick tools.
>
> The README with the power watershed code says that the 3d format is a
> very simple header followed by the data, so your best bet is to probably do
> it manually. Use convert3d, or equivalent tool to change the nii to a
> format that has separate data and header sections (or strip the nii header
> off), making sure that you have unsigned char data. Then manually construct
> the text header and join the two together. It appears that the text header
> should look like this:
>
> P5
> xsize ysize zsize
> 255
>
> Then do the reverse to get back to a nifti file. Seems that the extended
> pgm format doesn't know about voxel sizes, so you may get weird results if
> the data is highly anisotropic.
>
>
> On Fri, Feb 28, 2014 at 1:11 AM, Nicolas Cordier <nicolas.cordier at inria.fr
> > wrote:
>
>> Hello,
>>
>> There is a tool (Power Watershed) from ICCV 2009 which only accepts .ppm
>> images:
>> http://powerwatershed.sourceforge.net/
>>
>> It seems convert3d does not support this image format, which I suspect is
>> the following one:
>> <http://netpbm.sourceforge.net/doc/pgm.html>
>> http://netpbm.sourceforge.net/doc/pgm.html
>>
>> Is there an easy way to convert my .nii (3D images) to .pgm files? Apply
>> this tool and then convert the way back?
>>
>> Best regards,
>> --
>>
>> *Nicolas CORDIER*
>>
>> ASCLEPIOS <http://www-sop.inria.fr/asclepios/> PhD Candidate
>>
>>
>> *INRIA SOPHIA ANTIPOLIS - MEDITERRANEE
>> <http://www.inria.fr/centre/sophia/>*
>>
>> 2004 route des Lucioles, BP93, 06902 Sophia Antipolis Cedex, FR
>> Tel : +33 (0)4 92 38 79 26 - Fax : +33 (0)4 92 38 76 69
>>
>>
>>
>>
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>
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>
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#ifdef _MSC_VER
#pragma warning ( disable : 4786 )
#endif
#include <string>
#include <iterator>
#include "itkPGMImageIO.h"
#include "itkMacro.h"
#include "itkMetaDataObject.h"
#include "itkIOCommon.h"
#include "itksys/SystemTools.hxx"
#include <fstream>
#include <iomanip>
#include <ios>
typedef std::string::value_type char_t;
namespace itk {
bool PGMImageIO::SupportsDimension(unsigned long dim)
{
return dim==3 || dim==2; //2D + extension to 3D
}
void PGMImageIO::PrintSelf(std::ostream& os, Indent indent) const
{
Superclass::PrintSelf(os, indent);
}
bool PGMImageIO::CanReadFile( const char* filename )
{
// Check the extension first to avoid opening files that do not
// look like dats. The file must have an appropriate extension to be
// recognized.
std::string fname = filename;
if( fname == "" )
{
itkDebugMacro(<<"No filename specified.");
return false;
}
bool extensionFound = false;
std::string::size_type datPos = fname.rfind(".pgm");
if ((datPos != std::string::npos)
&& (datPos == fname.length() - 4))
{
extensionFound = true;
}
if( !extensionFound )
{
itkDebugMacro(<<"The filename extension is not recognized");
return false;
}
std::ifstream inputStream;
inputStream.open( filename, std::ios::in | std::ios::binary );
if( inputStream.fail() )
{
return false;
}
inputStream.close();
return true;
}
void PGMImageIO::ReadImageInformation()
{
std::ifstream in(this->GetFileName());
std::string s;
char buf[1000];
in>>s;
if (s!="P5")
{
ExceptionObject exception(__FILE__, __LINE__);
exception.SetDescription("P5 signature not found.");
throw exception;
}
in.getline(buf, 999); //read endline char
int xres, yres, zres, maxVal;
in>>xres>>yres;
this->SetComponentType(UCHAR);
this->SetPixelType( ImageIOBase::SCALAR );
this->SetNumberOfComponents(1);
in.getline(buf, 999);
if (buf[0]!=0)
{
this->SetNumberOfDimensions(3);
zres=atoi(buf);
this->SetDimensions(2, zres);
}
else
{
this->SetNumberOfDimensions(2);
}
this->SetDimensions(0, xres);
this->SetDimensions(1, yres);
in>>maxVal;
if (maxVal!=255)
itkWarningMacro (<<"Maximum value should be 255, not "<<maxVal);
in.close();
}
void PGMImageIO::Read(void* buffer)
{
size_t elems;
if (this->GetNumberOfDimensions()==3)
elems=this->GetDimensions(0)*this->GetDimensions(1)*this->GetDimensions(2);
else
elems=this->GetDimensions(0)*this->GetDimensions(1);
size_t esize=this->GetComponentSize();
std::ifstream in(this->GetFileName(), std::ios::binary);
in.getline((char *)buffer, 999);
in.getline((char *)buffer, 999);
in.getline((char *)buffer, 999);
in.read((char *)buffer, esize*elems);
if (in.bad()||in.gcount()!=esize*elems)
{
ExceptionObject exception(__FILE__, __LINE__);
exception.SetDescription("Error reading "+std::string(this->GetFileName()));
throw exception;
}
in.close();
}
bool PGMImageIO::CanWriteFile( const char * name )
{
std::string filename = name;
if( filename == "" )
{
return false;
}
std::string::size_type datPos = filename.rfind(".pgm");
if ((datPos != std::string::npos)
&& (datPos == filename.length() - 4))
return true;
return false;
}
void PGMImageIO::WriteImageInformation(void)
{
//nothing to do here
}
void PGMImageIO::Write( const void* buffer)
{
size_t elems;
if (this->GetNumberOfDimensions()==3)
elems=this->GetDimensions(0)*this->GetDimensions(1)*this->GetDimensions(2);
else
elems=this->GetDimensions(0)*this->GetDimensions(1);
std::ofstream f(this->GetFileName(), std::ios::binary);
f<<"P5\n";
f<<this->GetDimensions(0)<<' '<<this->GetDimensions(1);
if (this->GetNumberOfDimensions()==3)
f<<' '<<this->GetDimensions(2);
f<<"\n255\n";
f.write((char *)buffer, elems*this->GetComponentSize());
if (f.bad())
{
ExceptionObject exception(__FILE__, __LINE__);
exception.SetDescription("Error writing "+std::string(this->GetFileName()));
throw exception;
}
f.close();
}
} // end namespace itk
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#include "itkPGMImageIOFactory.h"
#include "itkCreateObjectFunction.h"
#include "itkPGMImageIO.h"
#include "itkVersion.h"
namespace itk
{
PGMImageIOFactory::PGMImageIOFactory()
{
this->RegisterOverride("itkImageIOBase",
"itkPGMImageIO",
"PGM Image IO",
1,
CreateObjectFunction<PGMImageIO>::New());
}
PGMImageIOFactory::~PGMImageIOFactory()
{
}
const char*
PGMImageIOFactory::GetITKSourceVersion(void) const
{
return ITK_SOURCE_VERSION;
}
const char*
PGMImageIOFactory::GetDescription() const
{
return "PGM ImageIO Factory, allows the loading of Netpbm PGM images into ITK";
}
} // end namespace itk
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