X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=common%2FclitkGateAsciiImageIO.cxx;h=589c30cfb783b0a9d0ae7d43a1a3609e1a7d8a8b;hb=fe401a1eebf96ce5a94c424d53d7c58486f4bf55;hp=f3d4a8d49211670def30995457eb484651210c4e;hpb=8d8e16a85eb4b10e69c9d987fa997191aa0fbceb;p=clitk.git

diff --git a/common/clitkGateAsciiImageIO.cxx b/common/clitkGateAsciiImageIO.cxx
index f3d4a8d..589c30c 100644
--- a/common/clitkGateAsciiImageIO.cxx
+++ b/common/clitkGateAsciiImageIO.cxx
@@ -17,7 +17,6 @@
 ===========================================================================**/
 
 // std include
-#include <regex.h>
 #include <cstdio>
 #include <sstream>
 #include <iostream>
@@ -33,246 +32,238 @@ using std::endl;
 
 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' or 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;
     }
-}
 
-std::string ExtractMatch(const std::string& base, const regmatch_t& match) 
-{
-    return base.substr(match.rm_so,match.rm_eo-match.rm_so);
+    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
+clitk::GateAsciiImageIO::FindRegularExpressionNextLine(itksys::RegularExpression &reg, std::string &s, FILE* handle)
+{
+  std::string line;
+  if(!ReadLine(handle,line))  return false;
+  if(!reg.compile(s.c_str())) return false;
+  return reg.find(line.c_str());
 }
 
 //--------------------------------------------------------------------
 // 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,"^#.+$",REG_EXTENDED|REG_NEWLINE);
-	assert(ret == 0);
-	ret = regcomp(&re_matrix_size,"^# +Matrix *Size *= +\\(([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*)\\)$",REG_EXTENDED|REG_NEWLINE);
-	assert(ret == 0);
-	ret = regcomp(&re_resol,"^# +Resol *= +\\(([0-9]+),([0-9]+),([0-9]+)\\)$",REG_EXTENDED|REG_NEWLINE);
-	assert(ret == 0);
-	ret = regcomp(&re_voxel_size,"^# +Voxel *Size *= +\\(([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*),([0-9]+\\.?[0-9]*)\\)$",REG_EXTENDED|REG_NEWLINE);
-	assert(ret == 0);
-	ret = regcomp(&re_nb_value,"^# +nbVal *= +([0-9]+)$",REG_EXTENDED|REG_NEWLINE);
-	assert(ret == 0);
-    }
+  assert(handle);
+
+  std::string regexstr[6] = {
+    "^#.+$",
+    "^# +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]*)\\)$",
+    "^# +nbVal *= +([0-9]+)$"
+  };
 
-    if (!ReadLine(handle,line)) return false;
-    if (regexec(&re_comment,line.c_str(),1,matches,0) == REG_NOMATCH) return false;
+  itksys::RegularExpression regex;
 
-    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(!FindRegularExpressionNextLine(regex, regexstr[0], handle)) return false;
 
-    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(!FindRegularExpressionNextLine(regex, regexstr[1], handle)) return false;
+  header.matrix_size[0] = ConvertFromString<double>(regex.match(1));
+  header.matrix_size[1] = ConvertFromString<double>(regex.match(2));
+  header.matrix_size[2] = ConvertFromString<double>(regex.match(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(!FindRegularExpressionNextLine(regex, regexstr[2], handle)) return false;
+  header.resolution[0] = ConvertFromString<int>(regex.match(1));
+  header.resolution[1] = ConvertFromString<int>(regex.match(2));
+  header.resolution[2] = ConvertFromString<int>(regex.match(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(!FindRegularExpressionNextLine(regex, regexstr[3], handle)) return false;
+  header.voxel_size[0] = ConvertFromString<double>(regex.match(1));
+  header.voxel_size[1] = ConvertFromString<double>(regex.match(2));
+  header.voxel_size[2] = ConvertFromString<double>(regex.match(3));
 
-    if (!ReadLine(handle,line)) return false;
-    if (regexec(&re_comment,line.c_str(),1,matches,0) == REG_NOMATCH) return false;
+  if(!FindRegularExpressionNextLine(regex, regexstr[4], handle)) return false;
+  header.nb_value = ConvertFromString<int>(regex.match(1));
 
-    return true;
+  if(!FindRegularExpressionNextLine(regex, regexstr[0], handle)) return false;
+
+  return true;
 }
 
 //--------------------------------------------------------------------
 // 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);
 }