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 #define VTK_EXCLUDE_STRSTREAM_HEADERS
48 //--------------------------------------------------------------------
51 typedef unsigned char uchar;
52 typedef unsigned short ushort;
53 typedef unsigned int uint;
55 #define CLITK_TRY_CATCH_EXIT(func) \
59 catch (const itk::ExceptionObject& e) { \
63 catch (const std::exception& e) { \
64 std::cout << e.what() << std::endl; \
68 std::cout << "Unknown excpetion" << std::endl; \
73 //--------------------------------------------------------------------
74 // when everything goes wrong
75 #define WHEREAMI "[ " << __FILE__ << " ] line " << __LINE__
76 #define FATAL(a) { std::cerr << "ERROR in " << WHEREAMI << ": " << a; exit(0); }
78 //--------------------------------------------------------------------
79 // GGO with modified struct name
80 #define GGO(ggo_filename, args_info) \
81 args_info_##ggo_filename args_info; \
82 cmdline_parser_##ggo_filename##2(argc, argv, &args_info, 1, 1, 0); \
83 if (args_info.config_given) \
84 cmdline_parser_##ggo_filename##_configfile (args_info.config_arg, &args_info, 0, 0, 1); \
85 else cmdline_parser_##ggo_filename(argc, argv, &args_info);
87 //--------------------------------------------------------------------
89 void skipComment(std::istream & is);
91 //--------------------------------------------------------------------
92 // linear (rough) conversion from Hounsfield Unit to density
93 double HU2density(double HU);
95 //--------------------------------------------------------------------
96 // Return filename extension
97 std::string GetExtension(const std::string& filename);
99 //--------------------------------------------------------------------
100 // Convert float, double ... to string
101 template<class T> std::string toString(const T & t);
102 template<class T> std::string toStringVector(const T * t, const int n);
103 template<class T> std::string toStringVector(const T & t, const int n);
104 template<class T> std::string toStringVector(const std::vector<T> & t);
105 template <class T> bool fromString(T& t,
106 const std::string& s,
107 std::ios_base& (*f)(std::ios_base&)=std::dec);
109 //--------------------------------------------------------------------
110 // Display a progress %
111 void VerboseInProgress(const int nb, const int current, const int percentage);
112 void VerboseInProgressInPercentage(const int nb, const int current, const int percentage);
114 //--------------------------------------------------------------------
115 // Convert a pixel type to another (downcast)
116 template<class TPixelUp, class TPixelDown>
117 TPixelDown PixelTypeDownCast(const TPixelUp & x);
119 float PixelTypeDownCast(const double & x);
121 double PixelTypeDownCast(const double & x);
123 //--------------------------------------------------------------------
124 // Return the indexes of sorted values in a vector
125 template<class Type> struct vectorComparisonLowerThan;
126 template<class Type> struct vectorComparisonGreaterThan;
128 void GetSortedIndex(const std::vector<Type> & toSort, std::vector<int> & index, bool increasing=true);
130 //--------------------------------------------------------------------
131 // Return the name of a type as a string
132 template<class TPixel>
133 std::string GetTypeAsString();
135 //--------------------------------------------------------------------
136 // Convert radian / degree
137 double rad2deg(double anglerad);
138 double deg2rad(double anglerad);
140 //--------------------------------------------------------------------
141 int GetTypeSizeFromString(const std::string & type);
143 //--------------------------------------------------------------------
144 // Special case to handle "signed_char = schar" ...
146 bool IsSameType(std::string t) { return (t==GetTypeAsString<T>()); }
147 template<> bool IsSameType<char>(std::string t);
148 template<> bool IsSameType<signed char>(std::string t);
149 template<> bool IsSameType<unsigned char>(std::string t);
150 template<> bool IsSameType<unsigned short>(std::string t);
152 //--------------------------------------------------------------------
154 std::string CreateListOfTypes(bool last=true) {
155 return GetTypeAsString<T1>();
158 template<class T1, class T2>
159 std::string CreateListOfTypes(bool last=true) {
160 if (last) return CreateListOfTypes<T1>()+" and "+CreateListOfTypes<T2>();
161 else return CreateListOfTypes<T1>()+", "+CreateListOfTypes<T2>();
164 template<class T1, class T2, class T3>
165 std::string CreateListOfTypes(bool last=true) {
166 if (last) return CreateListOfTypes<T1,T2>(false)+" and "+CreateListOfTypes<T3>();
167 else return CreateListOfTypes<T1,T2>(false)+", "+CreateListOfTypes<T3>();
170 template<class T1, class T2, class T3, class T4>
171 std::string CreateListOfTypes(bool last=true) {
172 if (last) return CreateListOfTypes<T1,T2,T3>(false)+" and "+CreateListOfTypes<T4>();
173 else return CreateListOfTypes<T1,T2,T3>(false)+", "+CreateListOfTypes<T4>();
176 template<class T1, class T2, class T3, class T4, class T5>
177 std::string CreateListOfTypes(bool last=true) {
178 if (last) return CreateListOfTypes<T1,T2,T3,T4>(false)+" and "+CreateListOfTypes<T5>();
179 else return CreateListOfTypes<T1,T2,T3,T4>(false)+", "+CreateListOfTypes<T5>();
182 template<class T1, class T2, class T3, class T4, class T5, class T6>
183 std::string CreateListOfTypes(bool last=true) {
184 if (last) return CreateListOfTypes<T1,T2,T3,T4,T5>(false)+" and "+CreateListOfTypes<T6>();
185 else return CreateListOfTypes<T1,T2,T3,T4,T5>(false)+", "+CreateListOfTypes<T6>();
188 template<class T1, class T2, class T3, class T4, class T5, class T6, class T7>
189 std::string CreateListOfTypes(bool last=true) {
190 if (last) return CreateListOfTypes<T1,T2,T3,T4,T5,T6>(false)+" and "+CreateListOfTypes<T7>();
191 else return CreateListOfTypes<T1,T2,T3,T4,T5,T6>(false)+", "+CreateListOfTypes<T7>();
194 template<class T1, class T2, class T3, class T4, class T5, class T6, class T7, class T8>
195 std::string CreateListOfTypes(bool last=true) {
196 if (last) return CreateListOfTypes<T1,T2,T3,T4,T5,T6,T7>(false)+" and "+CreateListOfTypes<T8>();
197 else return CreateListOfTypes<T1,T2,T3,T4,T5,T6,T7>(false)+", "+CreateListOfTypes<T8>();
199 //--------------------------------------------------------------------
201 //--------------------------------------------------------------------
202 void FindAndReplace(std::string & line, const std::string & tofind, const std::string & replacement);
203 void FindAndReplace(std::string & line, const std::vector<std::string> & tofind, const std::vector<std::string> & toreplace);
204 void FindAndReplace(std::ifstream & in, const std::vector<std::string> & tofind, const std::vector<std::string> & toreplace, std::ofstream & out);
205 //--------------------------------------------------------------------
207 //--------------------------------------------------------------------
208 double ComputeEuclideanDistanceFromPointToPlane(const itk::ContinuousIndex<double, 3> point,
209 const itk::ContinuousIndex<double, 3> pointInPlane,
210 const itk::ContinuousIndex<double, 3> normalPlane);
212 //--------------------------------------------------------------------
213 // Open a File for reading/writing
214 void openFileForReading(std::ifstream & is, const std::string & filename);
215 void openFileForWriting(std::ofstream & os, const std::string & filename);
217 //--------------------------------------------------------------------
218 void readDoubleFromFile(const std::string & filename, std::vector<double> & list);
220 //--------------------------------------------------------------------
221 double cotan(double i);
222 double invcotan(double i);
224 //--------------------------------------------------------------------
225 void disableStdCerr();
226 void enableStdCerr();
228 //--------------------------------------------------------------------
229 template<class ImageType>
230 void CloneImage(const typename ImageType::Pointer & input, typename ImageType::Pointer & output);
232 //--------------------------------------------------------------------
233 void PrintMemoryUsed();
235 //--------------------------------------------------------------------
236 // Convert a map to a vector
237 template <typename M, typename V>
238 void MapToVecFirst(const M & m, V & v);
239 template <typename M, typename V>
240 void MapToVecSecond(const M & m, V & v);
242 //--------------------------------------------------------------------
243 // Find/replace string
245 int inline findAndReplace(T& source, const T& find, const T& replace);
247 #include "clitkCommon.txx"
251 #endif /* end #define CLITKCOMMON_H */