1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
5 - University of LYON http://www.universite-lyon.fr/
6 - Léon Bérard cancer center http://www.centreleonberard.fr
7 - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
9 This software is distributed WITHOUT ANY WARRANTY; without even
10 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
11 PURPOSE. See the copyright notices for more information.
13 It is distributed under dual licence
15 - BSD See included LICENSE.txt file
16 - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
17 ===========================================================================**/
23 #include "clitkPortability.h"
25 #include "clitkExceptionObject.h"
27 // itk include (include std)
28 #include <itkContinuousIndex.h>
30 #include <itkImageRegionConstIterator.h>
31 #include <itkImageRegionIterator.h>
36 // Include for "rusage"
38 #if defined(unix) || defined(__APPLE__)
39 # include <sys/time.h>
40 # include <sys/resource.h>
46 //--------------------------------------------------------------------
49 typedef unsigned char uchar;
50 typedef unsigned short ushort;
51 typedef unsigned int uint;
53 #define CLITK_TRY_CATCH_EXIT(func) \
57 catch (const itk::ExceptionObject& e) { \
61 catch (const std::exception& e) { \
62 std::cout << e.what() << std::endl; \
66 std::cout << "Unknown excpetion" << std::endl; \
71 //--------------------------------------------------------------------
72 // when everything goes wrong
73 #define WHEREAMI "[ " << __FILE__ << " ] line " << __LINE__
74 #define FATAL(a) std::cerr << "ERROR in " << WHEREAMI << ": " << a; exit(0);
76 //--------------------------------------------------------------------
77 // GGO with modified struct name
78 #define GGO(ggo_filename, args_info) \
79 args_info_##ggo_filename args_info; \
80 cmdline_parser_##ggo_filename##2(argc, argv, &args_info, 1, 1, 0); \
81 if (args_info.config_given) \
82 cmdline_parser_##ggo_filename##_configfile (args_info.config_arg, &args_info, 0, 0, 1); \
83 else cmdline_parser_##ggo_filename(argc, argv, &args_info);
85 //--------------------------------------------------------------------
87 void skipComment(std::istream & is);
89 //--------------------------------------------------------------------
90 // linear (rough) conversion from Hounsfield Unit to density
91 double HU2density(double HU);
93 //--------------------------------------------------------------------
94 // Return filename extension
95 std::string GetExtension(const std::string& filename);
97 //--------------------------------------------------------------------
98 // Convert float, double ... to string
99 template<class T> std::string toString(const T & t);
100 template<class T> std::string toStringVector(const T * t, const int n);
101 template<class T> std::string toStringVector(const T & t, const int n);
102 template<class T> std::string toStringVector(const std::vector<T> & t);
103 template <class T> bool fromString(T& t,
104 const std::string& s,
105 std::ios_base& (*f)(std::ios_base&)=std::dec);
107 //--------------------------------------------------------------------
108 // Display a progress %
109 void VerboseInProgress(const int nb, const int current, const int percentage);
110 void VerboseInProgressInPercentage(const int nb, const int current, const int percentage);
112 //--------------------------------------------------------------------
113 // Convert a pixel type to another (downcast)
114 template<class TPixelUp, class TPixelDown>
115 TPixelDown PixelTypeDownCast(const TPixelUp & x);
117 float PixelTypeDownCast(const double & x);
119 //--------------------------------------------------------------------
120 // Return the indexes of sorted values in a vector
121 template<class Type> struct vectorComparisonLowerThan;
122 template<class Type> struct vectorComparisonGreaterThan;
124 void GetSortedIndex(const std::vector<Type> & toSort, std::vector<int> & index, bool increasing=true);
126 //--------------------------------------------------------------------
127 // Return the name of a type as a string
128 template<class TPixel>
129 std::string GetTypeAsString();
131 //--------------------------------------------------------------------
132 // Convert radian / degree
133 double rad2deg(double anglerad);
134 double deg2rad(double anglerad);
136 //--------------------------------------------------------------------
137 int GetTypeSizeFromString(const std::string & type);
139 //--------------------------------------------------------------------
140 // Special case to handle "signed_char = schar" ...
142 bool IsSameType(std::string t) { return (t==GetTypeAsString<T>()); }
143 template<> bool IsSameType<char>(std::string t);
144 template<> bool IsSameType<signed char>(std::string t);
145 template<> bool IsSameType<unsigned char>(std::string t);
146 template<> bool IsSameType<unsigned short>(std::string t);
148 //--------------------------------------------------------------------
150 std::string CreateListOfTypes(bool last=true) {
151 return GetTypeAsString<T1>();
154 template<class T1, class T2>
155 std::string CreateListOfTypes(bool last=true) {
156 if (last) return CreateListOfTypes<T1>()+" and "+CreateListOfTypes<T2>();
157 else return CreateListOfTypes<T1>()+", "+CreateListOfTypes<T2>();
160 template<class T1, class T2, class T3>
161 std::string CreateListOfTypes(bool last=true) {
162 if (last) return CreateListOfTypes<T1,T2>(false)+" and "+CreateListOfTypes<T3>();
163 else return CreateListOfTypes<T1,T2>(false)+", "+CreateListOfTypes<T3>();
166 template<class T1, class T2, class T3, class T4>
167 std::string CreateListOfTypes(bool last=true) {
168 if (last) return CreateListOfTypes<T1,T2,T3>(false)+" and "+CreateListOfTypes<T4>();
169 else return CreateListOfTypes<T1,T2,T3>(false)+", "+CreateListOfTypes<T4>();
172 template<class T1, class T2, class T3, class T4, class T5>
173 std::string CreateListOfTypes(bool last=true) {
174 if (last) return CreateListOfTypes<T1,T2,T3,T4>(false)+" and "+CreateListOfTypes<T5>();
175 else return CreateListOfTypes<T1,T2,T3,T4>(false)+", "+CreateListOfTypes<T5>();
178 template<class T1, class T2, class T3, class T4, class T5, class T6>
179 std::string CreateListOfTypes(bool last=true) {
180 if (last) return CreateListOfTypes<T1,T2,T3,T4,T5>(false)+" and "+CreateListOfTypes<T6>();
181 else return CreateListOfTypes<T1,T2,T3,T4,T5>(false)+", "+CreateListOfTypes<T6>();
184 template<class T1, class T2, class T3, class T4, class T5, class T6, class T7>
185 std::string CreateListOfTypes(bool last=true) {
186 if (last) return CreateListOfTypes<T1,T2,T3,T4,T5,T6>(false)+" and "+CreateListOfTypes<T7>();
187 else return CreateListOfTypes<T1,T2,T3,T4,T5,T6>(false)+", "+CreateListOfTypes<T7>();
190 template<class T1, class T2, class T3, class T4, class T5, class T6, class T7, class T8>
191 std::string CreateListOfTypes(bool last=true) {
192 if (last) return CreateListOfTypes<T1,T2,T3,T4,T5,T6,T7>(false)+" and "+CreateListOfTypes<T8>();
193 else return CreateListOfTypes<T1,T2,T3,T4,T5,T6,T7>(false)+", "+CreateListOfTypes<T8>();
195 //--------------------------------------------------------------------
197 //--------------------------------------------------------------------
198 void FindAndReplace(std::string & line, const std::string & tofind, const std::string & replacement);
199 void FindAndReplace(std::string & line, const std::vector<std::string> & tofind, const std::vector<std::string> & toreplace);
200 void FindAndReplace(std::ifstream & in, const std::vector<std::string> & tofind, const std::vector<std::string> & toreplace, std::ofstream & out);
201 //--------------------------------------------------------------------
203 //--------------------------------------------------------------------
204 double ComputeEuclideanDistanceFromPointToPlane(const itk::ContinuousIndex<double, 3> point,
205 const itk::ContinuousIndex<double, 3> pointInPlane,
206 const itk::ContinuousIndex<double, 3> normalPlane);
208 //--------------------------------------------------------------------
209 // Open a File for reading/writing
210 void openFileForReading(std::ifstream & is, const std::string & filename);
211 void openFileForWriting(std::ofstream & os, const std::string & filename);
213 //--------------------------------------------------------------------
214 void readDoubleFromFile(const std::string & filename, std::vector<double> & list);
216 //--------------------------------------------------------------------
217 double cotan(double i);
218 double invcotan(double i);
220 //--------------------------------------------------------------------
221 void disableStdCerr();
222 void enableStdCerr();
224 //--------------------------------------------------------------------
225 template<class ImageType>
226 void CloneImage(const typename ImageType::Pointer & input, typename ImageType::Pointer & output);
228 //--------------------------------------------------------------------
229 void PrintMemoryUsed();
231 //--------------------------------------------------------------------
232 // Convert a map to a vector
233 template <typename M, typename V>
234 void MapToVecFirst(const M & m, V & v);
235 template <typename M, typename V>
236 void MapToVecSecond(const M & m, V & v);
238 #include "clitkCommon.txx"
242 #endif /* end #define CLITKCOMMON_H */