std::ostream& operator<<(std::ostream& os, const clitk::GateAsciiImageIO::GateAsciiHeader& header)
{
- os << "matrix_size=[" << header.matrix_size[0] << "," << header.matrix_size[1] << "," << header.matrix_size[2] << "]" << endl;
- os << "resolution=[" << header.resolution[0] << "," << header.resolution[1] << "," << header.resolution[2] << "]" << endl;
- os << "voxel_size=[" << header.voxel_size[0] << "," << header.voxel_size[1] << "," << header.voxel_size[2] << "]" << endl;
- os << "nb_value=" << header.nb_value << endl;
- return os;
+ os << "matrix_size=[" << header.matrix_size[0] << "," << header.matrix_size[1] << "," << header.matrix_size[2] << "]" << endl;
+ os << "resolution=[" << header.resolution[0] << "," << header.resolution[1] << "," << header.resolution[2] << "]" << endl;
+ os << "voxel_size=[" << header.voxel_size[0] << "," << header.voxel_size[1] << "," << header.voxel_size[2] << "]" << endl;
+ os << "nb_value=" << header.nb_value << endl;
+ return os;
}
//--------------------------------------------------------------------
// Read Image Information
void clitk::GateAsciiImageIO::ReadImageInformation()
{
- FILE* handle = fopen(m_FileName.c_str(),"r");
- if (!handle) {
- itkGenericExceptionMacro(<< "Could not open file (for reading): " << m_FileName);
- return;
- }
-
- GateAsciiHeader header;
- if (!ReadHeader(handle,header)) {
- itkGenericExceptionMacro(<< "Could not read header: " << m_FileName);
- fclose(handle);
- return;
- }
+ FILE* handle = fopen(m_FileName.c_str(),"r");
+ if (!handle) {
+ itkGenericExceptionMacro(<< "Could not open file (for reading): " << m_FileName);
+ return;
+ }
+
+ GateAsciiHeader header;
+ if (!ReadHeader(handle,header)) {
+ itkGenericExceptionMacro(<< "Could not read header: " << m_FileName);
fclose(handle);
-
- int real_length = -1;
- double real_spacing = 0;
- for (int kk=0; kk<3; kk++) {
- if (header.resolution[kk]>1) {
- if (real_length>0) {
- itkGenericExceptionMacro(<< "Could not image dimension: " << m_FileName);
- return;
- }
- real_length = header.resolution[kk];
- real_spacing = header.voxel_size[kk];
- }
+ return;
+ }
+ fclose(handle);
+
+ int real_length = -1;
+ double real_spacing = 0;
+ for (int kk=0; kk<3; kk++) {
+ if (header.resolution[kk]>1) {
+ if (real_length>0) {
+ itkGenericExceptionMacro(<< "Could not image dimension: " << m_FileName);
+ return;
+ }
+ real_length = header.resolution[kk];
+ real_spacing = header.voxel_size[kk];
}
- assert(real_length == header.nb_value);
-
- // Set image information
- SetNumberOfDimensions(2);
- SetDimensions(0, real_length);
- SetDimensions(1, 1);
- SetSpacing(0, real_spacing);
- SetSpacing(1, 1);
- SetOrigin(0, 0);
- SetOrigin(1, 0);
- SetComponentType(itk::ImageIOBase::DOUBLE);
+ }
+ assert(real_length == header.nb_value);
+
+ // Set image information
+ SetNumberOfDimensions(2);
+ SetDimensions(0, real_length);
+ SetDimensions(1, 1);
+ SetSpacing(0, real_spacing);
+ SetSpacing(1, 1);
+ SetOrigin(0, 0);
+ SetOrigin(1, 0);
+ SetComponentType(itk::ImageIOBase::DOUBLE);
}
//--------------------------------------------------------------------
bool clitk::GateAsciiImageIO::CanReadFile(const char* FileNameToRead)
{
- std::string filename(FileNameToRead);
+ std::string filename(FileNameToRead);
- { // check extension
- std::string filenameext = GetExtension(filename);
- if (filenameext != "txt") return false;
- }
+ {
+ // check extension
+ std::string filenameext = GetExtension(filename);
+ if (filenameext != "txt") return false;
+ }
- { // check header
- FILE* handle = fopen(filename.c_str(),"r");
- if (!handle) return false;
+ {
+ // check header
+ FILE* handle = fopen(filename.c_str(),"r");
+ if (!handle) return false;
- GateAsciiHeader header;
- if (!ReadHeader(handle,header)) { fclose(handle); return false; }
- fclose(handle);
+ GateAsciiHeader header;
+ if (!ReadHeader(handle,header)) {
+ fclose(handle);
+ return false;
}
+ fclose(handle);
+ }
- return true;
+ return true;
}
//--------------------------------------------------------------------
// Read Line in file
bool clitk::GateAsciiImageIO::ReadLine(FILE* handle, std::string& line)
{
- std::stringstream stream;
- while (true)
- {
- char item;
- if (ferror(handle)) return false;
- if (fread(&item,1,1,handle) != 1) return false;
-
- if (item=='\n' || feof(handle)) {
- line = stream.str();
- return true;
- }
-
- stream << item;
+ std::stringstream stream;
+ while (true) {
+ char item;
+ if (ferror(handle)) return false;
+ if (fread(&item,1,1,handle) != 1) return false;
+
+ if (item=='\n' || feof(handle)) {
+ line = stream.str();
+ return true;
}
+
+ stream << item;
+ }
}
template <typename T>
T ConvertFromString(const std::string& value)
{
- std::stringstream stream;
- stream << value;
- T converted;
- stream >> converted;
- return converted;
+ std::stringstream stream;
+ stream << value;
+ T converted;
+ stream >> converted;
+ return converted;
}
bool
// Read Image Header
bool clitk::GateAsciiImageIO::ReadHeader(FILE* handle, GateAsciiHeader& header)
{
- assert(handle);
+ assert(handle);
- std::string regexstr[6] =
- {"^#.+$",
- "^# +Matrix *Size *= +\\(([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*)\\)$",
- "^# +Resol *= +\\(([0-9]+),([0-9]+),([0-9]+)\\)$",
- "^# +Voxel *Size *= +\\(([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*)\\)$",
- "^# +nbVal *= +([0-9]+)$"};
+ std::string regexstr[6] = {
+ "^#.+$",
+ "^# +Matrix *Size *= +\\(([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*)\\)$",
+ "^# +Resol *= +\\(([0-9]+),([0-9]+),([0-9]+)\\)$",
+ "^# +Voxel *Size *= +\\(([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*)\\)$",
+ "^# +nbVal *= +([0-9]+)$"
+ };
itksys::RegularExpression regex;
// Read Image Content
void clitk::GateAsciiImageIO::Read(void* abstract_buffer)
{
- FILE* handle = fopen(m_FileName.c_str(),"r");
- if (!handle) {
- itkGenericExceptionMacro(<< "Could not open file (for reading): " << m_FileName);
- return;
- }
-
- GateAsciiHeader header;
- if (!ReadHeader(handle,header)) {
- itkGenericExceptionMacro(<< "Could not read header: " << m_FileName);
- fclose(handle);
- return;
- }
-
- {
- double* buffer = static_cast<double*>(abstract_buffer);
- int read_count = 0;
- while (true) {
- std::string line;
- if (!ReadLine(handle,line)) break;
- *buffer = ConvertFromString<double>(line);
- read_count++;
- buffer++;
- }
- assert(read_count == header.nb_value);
+ FILE* handle = fopen(m_FileName.c_str(),"r");
+ if (!handle) {
+ itkGenericExceptionMacro(<< "Could not open file (for reading): " << m_FileName);
+ return;
+ }
+
+ GateAsciiHeader header;
+ if (!ReadHeader(handle,header)) {
+ itkGenericExceptionMacro(<< "Could not read header: " << m_FileName);
+ fclose(handle);
+ return;
+ }
+
+ {
+ double* buffer = static_cast<double*>(abstract_buffer);
+ int read_count = 0;
+ while (true) {
+ std::string line;
+ if (!ReadLine(handle,line)) break;
+ *buffer = ConvertFromString<double>(line);
+ read_count++;
+ buffer++;
}
+ assert(read_count == header.nb_value);
+ }
- fclose(handle);
+ fclose(handle);
}
//--------------------------------------------------------------------
bool clitk::GateAsciiImageIO::CanWriteFile(const char* FileNameToWrite)
{
- if (GetExtension(std::string(FileNameToWrite)) != "txt") return false;
- return true;
+ if (GetExtension(std::string(FileNameToWrite)) != "txt") return false;
+ return true;
}
void clitk::GateAsciiImageIO::WriteImageInformation()
{
- cout << GetNumberOfDimensions() << endl;
+ cout << GetNumberOfDimensions() << endl;
}
bool clitk::GateAsciiImageIO::SupportsDimension(unsigned long dim)
{
- if (dim==2) return true;
- return false;
+ if (dim==2) return true;
+ return false;
}
//--------------------------------------------------------------------
// Write Image
void clitk::GateAsciiImageIO::Write(const void* abstract_buffer)
{
- const unsigned long nb_value = GetDimensions(0)*GetDimensions(1);
- std::stringstream stream;
- stream << "######################" << endl;
- stream << "# Matrix Size= (" << GetSpacing(0)*GetDimensions(0) << "," << GetSpacing(1)*GetDimensions(1) << ",1)" << endl;
- stream << "# Resol = (" << GetDimensions(0) << "," << GetDimensions(1) << ",1)" << endl;
- stream << "# VoxelSize = (" << GetSpacing(0) << "," << GetSpacing(1) << ",1)" << endl;
- stream << "# nbVal = " << nb_value << endl;
- stream << "######################" << endl;
-
- const double* buffer = static_cast<const double*>(abstract_buffer);
- for (unsigned long kk=0; kk<nb_value; kk++) { stream << buffer[kk] << endl; }
-
- FILE* handle = fopen(m_FileName.c_str(),"w");
- if (!handle) {
- itkGenericExceptionMacro(<< "Could not open file (for writing): " << m_FileName);
- return;
- }
-
- fwrite(stream.str().c_str(),1,stream.str().size(),handle);
-
- fclose(handle);
+ const unsigned long nb_value = GetDimensions(0)*GetDimensions(1);
+ std::stringstream stream;
+ stream << "######################" << endl;
+ stream << "# Matrix Size= (" << GetSpacing(0)*GetDimensions(0) << "," << GetSpacing(1)*GetDimensions(1) << ",1)" << endl;
+ stream << "# Resol = (" << GetDimensions(0) << "," << GetDimensions(1) << ",1)" << endl;
+ stream << "# VoxelSize = (" << GetSpacing(0) << "," << GetSpacing(1) << ",1)" << endl;
+ stream << "# nbVal = " << nb_value << endl;
+ stream << "######################" << endl;
+
+ const double* buffer = static_cast<const double*>(abstract_buffer);
+ for (unsigned long kk=0; kk<nb_value; kk++) {
+ stream << buffer[kk] << endl;
+ }
+
+ FILE* handle = fopen(m_FileName.c_str(),"w");
+ if (!handle) {
+ itkGenericExceptionMacro(<< "Could not open file (for writing): " << m_FileName);
+ return;
+ }
+
+ fwrite(stream.str().c_str(),1,stream.str().size(),handle);
+
+ fclose(handle);
}
/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
#include <stdint.h>
#endif
-namespace clitk {
-
- //====================================================================
- // Class for reading gate ascii Image file format
- class GateAsciiImageIO: public itk::ImageIOBase
- {
- public:
- /** Standard class typedefs. */
- typedef GateAsciiImageIO Self;
- typedef itk::ImageIOBase Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef signed short int PixelType;
-
- struct GateAsciiHeader {
- double matrix_size[3];
- int resolution[3];
- double voxel_size[3];
- int nb_value;
- };
-
- GateAsciiImageIO():Superclass() {;}
-
- /** Method for creation through the object factory. */
- itkNewMacro(Self);
-
- /** Run-time type information (and related methods). */
- itkTypeMacro(GateAsciiImageIO, ImageIOBase);
-
- /*-------- This part of the interface deals with reading data. ------ */
- virtual void ReadImageInformation();
- virtual bool CanReadFile( const char* FileNameToRead );
- virtual void Read(void * buffer);
-
- /*-------- This part of the interfaces deals with writing data. ----- */
- virtual void WriteImageInformation();
- virtual bool CanWriteFile(const char* filename);
- virtual void Write(const void* buffer);
-
- virtual bool SupportsDimension(unsigned long dim);
-
- protected:
- static bool ReadHeader(FILE* handle, GateAsciiHeader& header);
- static bool ReadLine(FILE* handle, std::string& line);
- static bool FindRegularExpressionNextLine(itksys::RegularExpression ®, std::string &s, FILE* handle);
-
- }; // end class GateAsciiImageIO
+namespace clitk
+{
+
+//====================================================================
+// Class for reading gate ascii Image file format
+class GateAsciiImageIO: public itk::ImageIOBase
+{
+public:
+ /** Standard class typedefs. */
+ typedef GateAsciiImageIO Self;
+ typedef itk::ImageIOBase Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef signed short int PixelType;
+
+ struct GateAsciiHeader {
+ double matrix_size[3];
+ int resolution[3];
+ double voxel_size[3];
+ int nb_value;
+ };
+
+ GateAsciiImageIO():Superclass() {}
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(GateAsciiImageIO, ImageIOBase);
+
+ /*-------- This part of the interface deals with reading data. ------ */
+ virtual void ReadImageInformation();
+ virtual bool CanReadFile( const char* FileNameToRead );
+ virtual void Read(void * buffer);
+
+ /*-------- This part of the interfaces deals with writing data. ----- */
+ virtual void WriteImageInformation();
+ virtual bool CanWriteFile(const char* filename);
+ virtual void Write(const void* buffer);
+
+ virtual bool SupportsDimension(unsigned long dim);
+
+protected:
+ static bool ReadHeader(FILE* handle, GateAsciiHeader& header);
+ static bool ReadLine(FILE* handle, std::string& line);
+ static bool FindRegularExpressionNextLine(itksys::RegularExpression ®, std::string &s, FILE* handle);
+
+}; // end class GateAsciiImageIO
} // end namespace
// explicit template instantiation
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff