diff --git a/Modules/IOExt/Internal/mitkParRecFileReader.cpp b/Modules/IOExt/Internal/mitkParRecFileReader.cpp
index 87998a1165..c76470e697 100644
--- a/Modules/IOExt/Internal/mitkParRecFileReader.cpp
+++ b/Modules/IOExt/Internal/mitkParRecFileReader.cpp
@@ -1,278 +1,280 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#include "mitkParRecFileReader.h"
#include <itkImageFileReader.h>
#include <mitkLocaleSwitch.h>
#ifdef __GNUC__
#define stricmp strcasecmp
#endif
void mitk::ParRecFileReader::GenerateOutputInformation()
{
mitk::Image::Pointer output = this->GetOutput();
if ((output->IsInitialized()) && (this->GetMTime() <= m_ReadHeaderTime.GetMTime()))
return;
itkDebugMacro(<< "Reading PAR file for GenerateOutputInformation()" << m_FileName);
// Check to see if we can read the file given the name or prefix
//
if (m_FileName == "" && m_FilePrefix == "")
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "One of FileName or FilePrefix must be non-empty");
}
m_RecFileName = "";
if (m_FileName != "")
{
int extPos = m_FileName.find_last_of(".");
if (extPos >= -1)
{
const char *ext = m_FileName.c_str() + extPos + 1;
if (stricmp(ext, "par") == 0)
m_RecFileName = m_FileName.substr(0, extPos);
else
m_RecFileName = m_FileName;
}
else
m_RecFileName = m_FileName;
m_RecFileName.append(".rec");
bool headerRead = false;
bool signedCharType = true;
unsigned int dimension = 0;
unsigned int dimensions[4] = {0, 0, 1, 1};
float sliceThickness = 0.0;
float sliceGap = 0.0;
float sliceSpacing = 0.0;
mitk::Vector3D thickness;
thickness.Fill(1.0);
mitk::Vector3D gap;
gap.Fill(0.0);
mitk::Vector3D spacing;
FILE *f;
f = fopen(m_FileName.c_str(), "r");
if (f != nullptr)
{
while (!feof(f))
{
char s[300], *p;
- fgets(s, 200, f);
+ if (fgets(s, 200, f) == nullptr)
+ throw itk::ImageFileReaderException(__FILE__, __LINE__, "Could not read header");
if (strstr(s, "Max. number of cardiac phases"))
{
p = strchr(s, ':') + 1;
dimensions[3] = atoi(p);
if (dimensions[3] > 1)
dimension = 4;
}
else if (strstr(s, "Max. number of slices/locations"))
{
p = strchr(s, ':') + 1;
dimensions[2] = atoi(p);
if (dimension == 0)
{
if (dimensions[2] > 1)
dimension = 3;
else
dimension = 2;
}
}
else if (strstr(s, "Image pixel size"))
{
p = strchr(s, ':') + 1;
int bpe = atoi(p);
if (bpe != 8)
signedCharType = false;
}
else if (strstr(s, "Recon resolution"))
{
p = s + strcspn(s, "0123456789");
sscanf(p, "%u %u", dimensions, dimensions + 1);
}
else if (strstr(s, "FOV (ap,fh,rl) [mm]"))
{
p = s + strcspn(s, "0123456789");
mitk::LocaleSwitch localeSwitch("C");
sscanf(p, "%lf %lf %lf", &thickness[0], &thickness[1], &thickness[2]);
}
else if (strstr(s, "Slice thickness [mm]"))
{
p = s + strcspn(s, "0123456789");
mitk::LocaleSwitch localeSwitch("C");
sscanf(p, "%f", &sliceThickness);
}
else if (strstr(s, "Slice gap [mm]"))
{
p = s + strcspn(s, "-0123456789");
mitk::LocaleSwitch localeSwitch("C");
sscanf(p, "%f", &sliceGap);
}
}
fclose(f);
// C:\home\ivo\data\coronaries\ucsf-wholeheart-2.par
sliceSpacing = sliceThickness + sliceGap;
if ((dimension > 0) && (dimensions[0] > 0) && (dimensions[1] > 0) && (sliceThickness > 0) && (sliceSpacing > 0))
{
headerRead = true;
if (fabs(thickness[0] / dimensions[2] - sliceSpacing) < 0.0001)
thickness[0] = thickness[1];
else if (fabs(thickness[1] / dimensions[2] - sliceSpacing) < 0.0001)
thickness[1] = thickness[0];
thickness[2] = sliceSpacing;
thickness[0] /= dimensions[0];
thickness[1] /= dimensions[1];
spacing = thickness + gap;
}
}
if (headerRead == false)
{
itk::ImageFileReaderException e(__FILE__, __LINE__);
std::ostringstream msg;
msg << " Could not read file " << m_FileName.c_str();
e.SetDescription(msg.str().c_str());
throw e;
return;
}
// define types
mitk::PixelType SCType = mitk::MakeScalarPixelType<signed char>();
mitk::PixelType SSType = mitk::MakeScalarPixelType<signed short>();
if (signedCharType)
output->Initialize(SCType, dimension, dimensions);
else
output->Initialize(SSType, dimension, dimensions);
output->GetSlicedGeometry()->SetSpacing(spacing);
// output->GetSlicedGeometry()->SetPlaneGeometry(mitk::Image::BuildStandardPlanePlaneGeometry(output->GetSlicedGeometry(),
// dimensions).GetPointer(), 0);
output->GetSlicedGeometry()->SetEvenlySpaced();
}
m_ReadHeaderTime.Modified();
}
void mitk::ParRecFileReader::GenerateData()
{
mitk::Image::Pointer output = this->GetOutput();
// Check to see if we can read the file given the name or prefix
//
if (m_RecFileName == "")
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "FileName for rec-file empty");
}
if (m_RecFileName != "")
{
FILE *f = fopen(m_RecFileName.c_str(), "r");
if (f == nullptr)
{
throw itk::ImageFileReaderException(__FILE__, __LINE__, "Could not open rec-file.");
}
int zstart, zmax;
int tstart, tmax;
zstart = output->GetRequestedRegion().GetIndex(2);
tstart = output->GetRequestedRegion().GetIndex(3);
zmax = zstart + output->GetRequestedRegion().GetSize(2);
tmax = tstart + output->GetRequestedRegion().GetSize(3);
int sliceSize = output->GetDimension(0) * output->GetDimension(1) * output->GetPixelType().GetBpe() / 8;
void *data = malloc(sliceSize);
bool ignore4Dtopogram = false;
{
int slicePlusTimeSize = output->GetDimension(0) * output->GetDimension(1) * output->GetDimension(3) *
output->GetPixelType().GetBpe() / 8;
if (output->GetDimension(3) > 1)
ignore4Dtopogram = true;
int z, t;
for (t = tstart; t < tmax; ++t)
for (z = zstart; z < zmax; ++z)
{
if (ignore4Dtopogram)
fseek(f, slicePlusTimeSize * z + (sliceSize + 1) * t, SEEK_SET);
else
fseek(f, slicePlusTimeSize * z + sliceSize * t, SEEK_SET);
- fread(data, sliceSize, 1, f);
+ if(fread(data, sliceSize, 1, f) < 1)
+ throw itk::ImageFileReaderException(__FILE__, __LINE__, "Could not read slice.");
output->SetSlice(data, z, t, 0);
}
}
// else
//{
// for(;z<zmax;++z)
// {
// fseek(f,sliceSize*z,SEEK_SET);
// fread(data, sliceSize, 1, f);
// output->SetSlice(data,z,0,0);
// }
//}
free(data);
fclose(f);
}
}
bool mitk::ParRecFileReader::CanReadFile(const std::string filename,
const std::string /*filePrefix*/,
const std::string /*filePattern*/)
{
// First check the extension
if (filename == "")
{
// MITK_INFO<<"No filename specified."<<std::endl;
return false;
}
bool extensionFound = false;
std::string::size_type PARPos = filename.rfind(".par");
if ((PARPos != std::string::npos) && (PARPos == filename.length() - 4))
{
extensionFound = true;
}
PARPos = filename.rfind(".PAR");
if ((PARPos != std::string::npos) && (PARPos == filename.length() - 4))
{
extensionFound = true;
}
if (!extensionFound)
{
// MITK_INFO<<"The filename extension is not recognized."<<std::endl;
return false;
}
return true;
}
mitk::ParRecFileReader::ParRecFileReader() : m_FileName(""), m_FilePrefix(""), m_FilePattern("")
{
}
mitk::ParRecFileReader::~ParRecFileReader()
{
}