===========================================================================**/
// std include
-#include <stdio.h>
+#include <regex.h>
+#include <cstdio>
+#include <sstream>
+#include <iostream>
+using std::cout;
+using std::endl;
// clitk include
#include "clitkGateAsciiImageIO.h"
// itk include
#include <itkMetaDataObject.h>
+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;
+}
+
//--------------------------------------------------------------------
// Read Image Information
void clitk::GateAsciiImageIO::ReadImageInformation()
itkGenericExceptionMacro(<< "Could not open file (for reading): " << m_FileName);
- /* Convert hnd to ITK image information */
- SetNumberOfDimensions(2);
- //SetDimensions(0, hnd.SizeX);
- //SetDimensions(1, hnd.SizeY);
- //SetSpacing(0, hnd.dIDUResolutionX);
- //SetSpacing(1, hnd.dIDUResolutionY);
- //SetOrigin(0, -0.5*(hnd.SizeX-1)*hnd.dIDUResolutionX); //SR: assumed centered
- //SetOrigin(1, -0.5*(hnd.SizeY-1)*hnd.dIDUResolutionY); //SR: assumed centered
- //SetComponentType(itk::ImageIOBase::UINT);
+ /* Convert hnd to ITK image information */
+ SetNumberOfDimensions(2);
+ //SetDimensions(0, hnd.SizeX);
+ //SetDimensions(1, hnd.SizeY);
+ //SetSpacing(0, hnd.dIDUResolutionX);
+ //SetSpacing(1, hnd.dIDUResolutionY);
+ //SetOrigin(0, -0.5*(hnd.SizeX-1)*hnd.dIDUResolutionX); //SR: assumed centered
+ //SetOrigin(1, -0.5*(hnd.SizeY-1)*hnd.dIDUResolutionY); //SR: assumed centered
+ //SetComponentType(itk::ImageIOBase::UINT);
- /* Store important meta information in the meta data dictionary */
- //itk::EncapsulateMetaData<double>(this->GetMetaDataDictionary(), "dCTProjectionAngle", hnd.dCTProjectionAngle);
- //itk::ExposeMetaData<double>( this->GetMetaDataDictionary(), &(hnd.dCTProjectionAngle), "dCTProjectionAngle");
+ /* Store important meta information in the meta data dictionary */
+ //itk::EncapsulateMetaData<double>(this->GetMetaDataDictionary(), "dCTProjectionAngle", hnd.dCTProjectionAngle);
+ //itk::ExposeMetaData<double>( this->GetMetaDataDictionary(), &(hnd.dCTProjectionAngle), "dCTProjectionAngle");
}
//--------------------------------------------------------------------
bool clitk::GateAsciiImageIO::CanReadFile(const char* FileNameToRead)
{
- std::string filename(FileNameToRead);
- std::string filenameext = GetExtension(filename);
- if (filenameext != std::string("hnd")) return false;
- return true;
+ std::string filename(FileNameToRead);
+
+ { // check extension
+ std::string filenameext = GetExtension(filename);
+ if (filenameext != std::string("txt")) 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);
+ }
+
+ 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' or feof(handle)) {
+ line = stream.str();
+ return true;
+ }
+
+ stream << item;
+ }
+}
+
+std::string ExtractMatch(const std::string& base, const regmatch_t& match)
+{
+ return base.substr(match.rm_so,match.rm_eo-match.rm_so);
+}
+
+template <typename T>
+T ConvertFromString(const std::string& value)
+{
+ std::stringstream stream;
+ stream << value;
+ T converted;
+ stream >> converted;
+ return converted;
+}
+
+//--------------------------------------------------------------------
+// Read Image Header
+bool clitk::GateAsciiImageIO::ReadHeader(FILE* handle, GateAsciiHeader& header)
+{
+ assert(handle);
+ std::string line;
+
+ regex_t re_comment;
+ regex_t re_matrix_size;
+ regex_t re_resol;
+ regex_t re_voxel_size;
+ regex_t re_nb_value;
+ regmatch_t matches[4];
+
+ { // build regex
+ int ret = 0;
+ ret = regcomp(&re_comment,"^#.+$",REG_EXTENDED|REG_NEWLINE);
+ assert(ret);
+ ret = regcomp(&re_matrix_size,"^# +Matrix *Size *= +\\(([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*)\\)$",REG_EXTENDED|REG_NEWLINE);
+ assert(ret);
+ ret = regcomp(&re_resol,"^# +Resol *= +\\(([0-9]+),([0-9]+),([0-9]+)\\)$",REG_EXTENDED|REG_NEWLINE);
+ assert(ret);
+ ret = regcomp(&re_voxel_size,"^# +Voxel *Size *= +\\(([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*)\\)$",REG_EXTENDED|REG_NEWLINE);
+ assert(ret);
+ ret = regcomp(&re_nb_value,"^# +nbVal *= +([0-9]+)$",REG_EXTENDED|REG_NEWLINE);
+ assert(ret);
+ }
+
+ if (!ReadLine(handle,line)) return false;
+ if (regexec(&re_comment,line.c_str(),1,matches,0) == REG_NOMATCH) return false;
+
+ if (!ReadLine(handle,line)) return false;
+ if (regexec(&re_matrix_size,line.c_str(),4,matches,0) == REG_NOMATCH) return false;
+ header.matrix_size[0] = ConvertFromString<double>(ExtractMatch(line,matches[1]));
+ header.matrix_size[1] = ConvertFromString<double>(ExtractMatch(line,matches[2]));
+ header.matrix_size[2] = ConvertFromString<double>(ExtractMatch(line,matches[3]));
+
+ if (!ReadLine(handle,line)) return false;
+ if (regexec(&re_resol,line.c_str(),4,matches,0) == REG_NOMATCH) return false;
+ header.resolution[0] = ConvertFromString<int>(ExtractMatch(line,matches[1]));
+ header.resolution[1] = ConvertFromString<int>(ExtractMatch(line,matches[2]));
+ header.resolution[2] = ConvertFromString<int>(ExtractMatch(line,matches[3]));
+
+ if (!ReadLine(handle,line)) return false;
+ if (regexec(&re_voxel_size,line.c_str(),4,matches,0) == REG_NOMATCH) return false;
+ header.voxel_size[0] = ConvertFromString<double>(ExtractMatch(line,matches[1]));
+ header.voxel_size[1] = ConvertFromString<double>(ExtractMatch(line,matches[2]));
+ header.voxel_size[2] = ConvertFromString<double>(ExtractMatch(line,matches[3]));
+
+ if (!ReadLine(handle,line)) return false;
+ if (regexec(&re_nb_value,line.c_str(),2,matches,0) == REG_NOMATCH) return false;
+ header.nb_value = ConvertFromString<int>(ExtractMatch(line,matches[1]));
+
+ if (!ReadLine(handle,line)) return false;
+ if (regexec(&re_comment,line.c_str(),1,matches,0) == REG_NOMATCH) return false;
+
+ return true;
}
//--------------------------------------------------------------------
#include "itkVersion.h"
namespace clitk {
-
- //====================================================================
- // Factory for reading GateAscii Image file format
- class GateAsciiImageIOFactory: public itk::ObjectFactoryBase
- {
- public:
- /** Standard class typedefs. */
- typedef GateAsciiImageIOFactory Self;
- typedef itk::ObjectFactoryBase Superclass;
- typedef itk::SmartPointer<Self> Pointer;
- typedef itk::SmartPointer<const Self> ConstPointer;
-
- /** Class methods used to interface with the registered factories. */
- const char* GetITKSourceVersion(void) const {
- return ITK_SOURCE_VERSION;
- }
-
- const char* GetDescription(void) const {
- return "GateAscii ImageIO Factory, allows the loading of gate ascii images into insight";
- }
-
- /** Method for class instantiation. */
- itkFactorylessNewMacro(Self);
-
- /** Run-time type information (and related methods). */
- itkTypeMacro(GateAsciiImageIOFactory, ObjectFactoryBase);
-
- /** Register one factory of this type */
- static void RegisterOneFactory(void) {
- ObjectFactoryBase::RegisterFactory( Self::New() );
- }
-
- protected:
- GateAsciiImageIOFactory();
- ~GateAsciiImageIOFactory() {};
- typedef GateAsciiImageIOFactory myProductType;
- const myProductType* m_MyProduct;
-
- private:
- GateAsciiImageIOFactory(const Self&); //purposely not implemented
- void operator=(const Self&); //purposely not implemented
- };
+
+ //====================================================================
+ // Factory for reading GateAscii Image file format
+ class GateAsciiImageIOFactory: public itk::ObjectFactoryBase
+ {
+ public:
+ /** Standard class typedefs. */
+ typedef GateAsciiImageIOFactory Self;
+ typedef itk::ObjectFactoryBase Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Class methods used to interface with the registered factories. */
+ const char* GetITKSourceVersion(void) const {
+ return ITK_SOURCE_VERSION;
+ }
+
+ const char* GetDescription(void) const {
+ return "GateAscii ImageIO Factory, allows the loading of gate ascii images into insight";
+ }
+
+ /** Method for class instantiation. */
+ itkFactorylessNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(GateAsciiImageIOFactory, ObjectFactoryBase);
+
+ /** Register one factory of this type */
+ static void RegisterOneFactory(void) {
+ ObjectFactoryBase::RegisterFactory( Self::New() );
+ }
+
+ protected:
+ GateAsciiImageIOFactory();
+ ~GateAsciiImageIOFactory() {};
+
+ private:
+ GateAsciiImageIOFactory(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+ };
} // end namespace
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff