/*=========================================================================
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://oncora1.lyon.fnclcc.fr
+ - Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
This software is distributed WITHOUT ANY WARRANTY; without even
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+===========================================================================**/
+
#ifndef CLITKCOMMON_CXX
#define CLITKCOMMON_CXX
-/**
- -------------------------------------------------
- * @file clitkCommon.cxx
- * @author David Sarrut <david.sarrut@creatis.insa-lyon.fr>
- * @date 17 May 2006 07:59:06
- *
- * @brief
- *
- *
- -------------------------------------------------*/
+#include <itksys/SystemTools.hxx>
+
+#ifdef _WIN32
+ #define _USE_MATH_DEFINES
+ #include <cmath>
+ const double M_PI = std::acos(-1.0);
+#endif
+
+// clitk include
#include "clitkCommon.h"
+
+// std include
#include <fstream>
#include <iomanip>
#include <sstream>
+#include <cerrno>
//------------------------------------------------------------------
// skip line which begin with a sharp '#'
-void clitk::skipComment(std::istream & is)
+void clitk::skipComment(std::istream & is)
{
char c;
char line[1024];
if (is.eof()) return;
- is >> c ;
+ is >> c ;
while (is && (c == '#')) {
- is.getline (line, 1024);
- is >> c;
- if (is.eof()) return;
+ is.getline (line, 1024);
+ is >> c;
+ if (is.eof()) return;
}
- is.unget();
+ if (!(is.fail()) && c != '\n')
+ is.unget();
} ////
//------------------------------------------------------------------
-
+
//------------------------------------------------------------------
// linear (rough) conversion from Hounsfield Unit to density
-double clitk::HU2density(double HU)
+double clitk::HU2density(double HU)
{
return (HU+1000.0)/1000.0;
} ////
//------------------------------------------------------------------
// Return filename extension
-std::string clitk::GetExtension(const std::string& filename)
+std::string clitk::GetExtension(const std::string& filename)
{
// This assumes that the final '.' in a file name is the delimiter
// for the file's extension type
- const std::string::size_type it = filename.find_last_of( "." );
+ const std::string::size_type it = filename.find_last_of( "." );
// This determines the file's type by creating a new string
// who's value is the extension of the input filename
// eg. "myimage.gif" has an extension of "gif"
- std::string fileExt( filename, it+1, filename.length() );
+ std::string fileExt( filename, it+1, filename.length() );
return( fileExt );
} ////
//------------------------------------------------------------------
+
+//------------------------------------------------------------------
+// Return filename splitting in 1 or 2 parts : directory name (if exists) & filename
+std::vector<std::string> clitk::SplitFilename(const std::string& filename)
+{
+ std::vector<std::string> dirname;
+ std::string path = itksys::SystemTools::GetFilenamePath(filename);
+ std::vector<std::string> pathComponents;
+ itksys::SystemTools::SplitPath(filename.c_str(), pathComponents);
+ std::string fileName = pathComponents.back();
+ if (path != "")
+ dirname.push_back(path);
+ dirname.push_back(fileName);
+ return( dirname );
+} ////
+//------------------------------------------------------------------
+
+
//------------------------------------------------------------------
// Display progression
void clitk::VerboseInProgress(const int nb, const int current, const int percentage)
{
static int previous = -1;
const int rounded = (100*current)/nb;
- if (previous==rounded) return;
+ if (previous==rounded) return;
previous = rounded;
std::ostringstream oss;
oss << std::setw(4) << rounded << '%';
std::cout << oss.str() << std::flush;
- for (unsigned int i=0; i<oss.str().length(); ++i)
- std::cout << "\b" << std::flush;
+ for (unsigned int i=0; i<oss.str().length(); ++i)
+ std::cout << "\b" << std::flush;
}
//------------------------------------------------------------------
//------------------------------------------------------------------
//------------------------------------------------------------------
-double clitk::rad2deg(const double anglerad) {
+// Convert a pixel type without casting
+template<>
+double clitk::PixelTypeDownCast(const double & x)
+{
+ return x;
+}
+//------------------------------------------------------------------
+
+//------------------------------------------------------------------
+double clitk::rad2deg(const double anglerad)
+{
return (anglerad/M_PI*180.0);
}
//------------------------------------------------------------------
//------------------------------------------------------------------
-double clitk::deg2rad(const double angledeg) {
+double clitk::deg2rad(const double angledeg)
+{
return (angledeg*(M_PI/180.0));
}
//------------------------------------------------------------------
//------------------------------------------------------------------
-int clitk::GetTypeSizeFromString(const std::string & type) {
+int clitk::GetTypeSizeFromString(const std::string & type)
+{
#define RETURN_SIZEOF_PIXEL(TYPENAME, TYPE) \
if (type == #TYPENAME) return sizeof(TYPE);
RETURN_SIZEOF_PIXEL(char, char);
//------------------------------------------------------------------
template<>
-bool clitk::IsSameType<signed char>(std::string t) {
- if ((t==GetTypeAsString<signed char>()) || (t == "schar")) return true; else return false;
+bool clitk::IsSameType<signed char>(std::string t)
+{
+ if ((t==GetTypeAsString<signed char>()) || (t == "schar")) return true;
+ else return false;
}
template<>
-bool clitk::IsSameType<char>(std::string t) {
- if ((t==GetTypeAsString<char>()) || (t == "char")) return true; else return false;
+bool clitk::IsSameType<char>(std::string t)
+{
+ if ((t==GetTypeAsString<char>()) || (t == "char")) return true;
+ else return false;
}
template<>
-bool clitk::IsSameType<unsigned char>(std::string t) {
- if ((t==GetTypeAsString<unsigned char>()) || (t == "uchar")) return true; else return false;
+bool clitk::IsSameType<unsigned char>(std::string t)
+{
+ if ((t==GetTypeAsString<unsigned char>()) || (t == "uchar")) return true;
+ else return false;
}
template<>
-bool clitk::IsSameType<unsigned short>(std::string t) {
- if ((t==GetTypeAsString<unsigned short>()) || (t == "ushort")) return true; else return false;
+bool clitk::IsSameType<unsigned short>(std::string t)
+{
+ if ((t==GetTypeAsString<unsigned short>()) || (t == "ushort")) return true;
+ else return false;
}
//------------------------------------------------------------------
//------------------------------------------------------------------
-void clitk::FindAndReplace(std::string & line,
- const std::string & tofind,
- const std::string & replacement) {
+void clitk::FindAndReplace(std::string & line,
+ const std::string & tofind,
+ const std::string & replacement)
+{
int pos = line.find(tofind);
while (pos!= (int)std::string::npos) {
line.replace(pos, tofind.size(), replacement);
//------------------------------------------------------------------
//------------------------------------------------------------------
-void clitk::FindAndReplace(std::string & line,
- const std::vector<std::string> & tofind,
- const std::vector<std::string> & toreplace) {
+void clitk::FindAndReplace(std::string & line,
+ const std::vector<std::string> & tofind,
+ const std::vector<std::string> & toreplace)
+{
for(unsigned int i=0; i<tofind.size(); i++) {
FindAndReplace(line, tofind[i], toreplace[i]);
}
//------------------------------------------------------------------
//------------------------------------------------------------------
-void clitk::FindAndReplace(std::ifstream & in,
- const std::vector<std::string> & tofind,
- const std::vector<std::string> & toreplace,
- std::ofstream & out) {
+void clitk::FindAndReplace(std::ifstream & in,
+ const std::vector<std::string> & tofind,
+ const std::vector<std::string> & toreplace,
+ std::ofstream & out)
+{
std::string line;
if (tofind.size() != toreplace.size()) {
std::cerr << "Error' tofind' is size=" << tofind.size() << std::endl;
//------------------------------------------------------------------
//------------------------------------------------------------------
-double clitk::ComputeEuclideanDistanceFromPointToPlane(const itk::ContinuousIndex<double, 3> point,
- const itk::ContinuousIndex<double, 3> pointInPlane,
- const itk::ContinuousIndex<double, 3> normalPlane) {
+double clitk::ComputeEuclideanDistanceFromPointToPlane(const itk::ContinuousIndex<double, 3> point,
+ const itk::ContinuousIndex<double, 3> pointInPlane,
+ const itk::ContinuousIndex<double, 3> normalPlane)
+{
// http://mathworld.wolfram.com/Plane.html
// http://mathworld.wolfram.com/Point-PlaneDistance.html
double a = normalPlane[0];
double d = -a*x0 - b*y0 - c*z0;
DD(d);
double distance = (a*x + b*y + c*z + d) / norm;
-
+
return distance;
}
//------------------------------------------------------------------
//--------------------------------------------------------------------
// Open a file for reading
-void clitk::openFileForReading(std::ifstream & is, const std::string & filename) {
- is.open(filename.c_str(), std::ios::in);
+void clitk::openFileForReading(std::ifstream & is, const std::string & filename)
+{
+ is.open(filename.c_str(), std::ios::in | std::ios::binary);
if ( is.fail() ) {
- itkGenericExceptionMacro(<< "Could not open file (for reading): " << filename);
+ clitkExceptionMacro("Could not open file for reading: "
+ << filename << ". Error is : <"
+ << strerror(errno) << ">");
}
}
//--------------------------------------------------------------------
-
+
//--------------------------------------------------------------------
// Open a file for writing
-void clitk::openFileForWriting(std::ofstream & os, const std::string & filename) {
+void clitk::openFileForWriting(std::ofstream & os, const std::string & filename)
+{
os.open(filename.c_str(), std::ios::out);
if ( os.fail() ) {
- itkGenericExceptionMacro(<< "Could not open file (for writing): " << filename);
+ clitkExceptionMacro("Could not open file for writing: "
+ << filename << ". Error is : <"
+ << strerror(errno) << ">");
}
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-double clitk::cotan(double i) { return(1.0 / tan(i)); }
-double clitk::invcotan(double x) {
+double clitk::cotan(double i)
+{
+ return(1.0 / tan(i));
+}
+double clitk::invcotan(double x)
+{
// http://mathworld.wolfram.com/InverseCotangent.html
double y;
if (x<0) {
y = -0.5*M_PI-atan(x);
- }
- else {
+ } else {
y = 0.5*M_PI-atan(x);
}
return y;
//--------------------------------------------------------------------
std::streambuf * clitk_stdcerr_backup;
-void clitk::disableStdCerr() {
+void clitk::disableStdCerr()
+{
clitk_stdcerr_backup = std::cerr.rdbuf();
std::stringstream oss;
std::cerr.rdbuf( oss.rdbuf() );
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-void clitk::enableStdCerr() {
+void clitk::enableStdCerr()
+{
std::cerr.rdbuf(clitk_stdcerr_backup);
}
//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+void clitk::readDoubleFromFile(const std::string & filename, std::vector<double> & list)
+{
+ std::ifstream is;
+ clitk::openFileForReading(is, filename);
+ list.clear();
+ while (is) {
+ clitk::skipComment(is);
+ double d;
+ is >> d;
+ if (is) list.push_back(d);
+ }
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::PrintMemoryUsed()
+{
+#if defined(unix) || defined(__APPLE__)
+ rusage usage;
+ getrusage(RUSAGE_SELF, &usage);
+ DD(usage.ru_maxrss); /* maximum resident set size */
+ // DD(usage.ru_ixrss); /* integral shared memory size */
+ // DD(usage.ru_idrss); /* integral unshared data size */
+ // DD(usage.ru_isrss); /* integral unshared stack size */
+#endif
+}
+//--------------------------------------------------------------------
+
+
#endif /* end #define CLITKCOMMON_CXX */
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