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://oncora1.lyon.fnclcc.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 "clitkConfiguration.h"
24 #include "clitkPortability.h"
26 // itk include (include std)
27 #include <itkContinuousIndex.h>
29 #include <itkImageRegionConstIterator.h>
30 #include <itkImageRegionIterator.h>
34 //--------------------------------------------------------------------
37 typedef unsigned char uchar;
38 typedef unsigned short ushort;
39 typedef unsigned int uint;
41 //--------------------------------------------------------------------
43 #define DD(a) std::cout << #a " = [ " << a << " ]" << std::endl;
44 #define DDV(a,n) { std::cout << #a " = [ "; for(unsigned int _i_=0; _i_<n; _i_++) { std::cout << a[_i_] << " "; }; std::cout << " ]" << std::endl;}
46 void _print_container(T const& a)
47 { for(typename T::const_iterator i=a.begin();i!=a.end();++i) { std::cout << *i << " "; };}
48 #define DDS(a) { std::cout << #a " = [ "; _print_container(a) ; std::cout << " ]" << std::endl;}
50 //--------------------------------------------------------------------
51 // when everything goes wrong
52 #define WHEREAMI "[ " << __FILE__ << " ] line " << __LINE__
53 #define FATAL(a) std::cerr << "ERROR in " << WHEREAMI << ": " << a; exit(0);
55 //--------------------------------------------------------------------
56 // GGO with modified struct name
57 #define GGO(ggo_filename, args_info) \
58 args_info_##ggo_filename args_info; \
59 cmdline_parser_##ggo_filename##2(argc, argv, &args_info, 1, 1, 0); \
60 if (args_info.config_given) \
61 cmdline_parser_##ggo_filename##_configfile (args_info.config_arg, &args_info, 0, 0, 1); \
62 else cmdline_parser_##ggo_filename(argc, argv, &args_info);
64 //--------------------------------------------------------------------
66 void skipComment(std::istream & is);
68 //--------------------------------------------------------------------
69 // linear (rough) conversion from Hounsfield Unit to density
70 double HU2density(double HU);
72 //--------------------------------------------------------------------
73 // Return filename extension
74 std::string GetExtension(const std::string& filename);
76 //--------------------------------------------------------------------
77 // Convert float, double ... to string
78 template<class T> std::string toString(const T & t);
79 template<class T> std::string toStringVector(const T * t, const int n);
80 template<class T> std::string toStringVector(const T & t, const int n);
81 template<class T> std::string toStringVector(const std::vector<T> & t);
83 //--------------------------------------------------------------------
84 // Display a progress %
85 void VerboseInProgress(const int nb, const int current, const int percentage);
86 void VerboseInProgressInPercentage(const int nb, const int current, const int percentage);
88 //--------------------------------------------------------------------
89 // Convert a pixel type to another (downcast)
90 template<class TPixelUp, class TPixelDown>
91 TPixelDown PixelTypeDownCast(const TPixelUp & x);
93 float PixelTypeDownCast(const double & x);
95 //--------------------------------------------------------------------
96 // Return the indexes of sorted values in a vector
97 template<class Type> struct vectorComparisonLowerThan;
98 template<class Type> struct vectorComparisonGreaterThan;
100 void GetSortedIndex(const std::vector<Type> & toSort, std::vector<int> & index, bool increasing=true);
102 //--------------------------------------------------------------------
103 // Return the name of a type as a string
104 template<class TPixel>
105 std::string GetTypeAsString();
107 //--------------------------------------------------------------------
108 // Convert radian / degree
109 double rad2deg(double anglerad);
110 double deg2rad(double anglerad);
112 //--------------------------------------------------------------------
113 int GetTypeSizeFromString(const std::string & type);
115 //--------------------------------------------------------------------
116 // Special case to handle "signed_char = schar" ...
118 bool IsSameType(std::string t) { return (t==GetTypeAsString<T>()); }
119 template<> bool IsSameType<char>(std::string t);
120 template<> bool IsSameType<signed char>(std::string t);
121 template<> bool IsSameType<unsigned char>(std::string t);
122 template<> bool IsSameType<unsigned short>(std::string t);
124 //--------------------------------------------------------------------
126 std::string CreateListOfTypes(bool last=true) {
127 return GetTypeAsString<T1>();
130 template<class T1, class T2>
131 std::string CreateListOfTypes(bool last=true) {
132 if (last) return CreateListOfTypes<T1>()+" and "+CreateListOfTypes<T2>();
133 else return CreateListOfTypes<T1>()+", "+CreateListOfTypes<T2>();
136 template<class T1, class T2, class T3>
137 std::string CreateListOfTypes(bool last=true) {
138 if (last) return CreateListOfTypes<T1,T2>(false)+" and "+CreateListOfTypes<T3>();
139 else return CreateListOfTypes<T1,T2>(false)+", "+CreateListOfTypes<T3>();
142 template<class T1, class T2, class T3, class T4>
143 std::string CreateListOfTypes(bool last=true) {
144 if (last) return CreateListOfTypes<T1,T2,T3>(false)+" and "+CreateListOfTypes<T4>();
145 else return CreateListOfTypes<T1,T2,T3>(false)+", "+CreateListOfTypes<T4>();
148 template<class T1, class T2, class T3, class T4, class T5>
149 std::string CreateListOfTypes(bool last=true) {
150 if (last) return CreateListOfTypes<T1,T2,T3,T4>(false)+" and "+CreateListOfTypes<T5>();
151 else return CreateListOfTypes<T1,T2,T3,T4>(false)+", "+CreateListOfTypes<T5>();
154 template<class T1, class T2, class T3, class T4, class T5, class T6>
155 std::string CreateListOfTypes(bool last=true) {
156 if (last) return CreateListOfTypes<T1,T2,T3,T4,T5>(false)+" and "+CreateListOfTypes<T6>();
157 else return CreateListOfTypes<T1,T2,T3,T4,T5>(false)+", "+CreateListOfTypes<T6>();
160 template<class T1, class T2, class T3, class T4, class T5, class T6, class T7>
161 std::string CreateListOfTypes(bool last=true) {
162 if (last) return CreateListOfTypes<T1,T2,T3,T4,T5,T6>(false)+" and "+CreateListOfTypes<T7>();
163 else return CreateListOfTypes<T1,T2,T3,T4,T5,T6>(false)+", "+CreateListOfTypes<T7>();
166 template<class T1, class T2, class T3, class T4, class T5, class T6, class T7, class T8>
167 std::string CreateListOfTypes(bool last=true) {
168 if (last) return CreateListOfTypes<T1,T2,T3,T4,T5,T6,T7>(false)+" and "+CreateListOfTypes<T8>();
169 else return CreateListOfTypes<T1,T2,T3,T4,T5,T6,T7>(false)+", "+CreateListOfTypes<T8>();
171 //--------------------------------------------------------------------
173 //--------------------------------------------------------------------
174 void FindAndReplace(std::string & line, const std::string & tofind, const std::string & replacement);
175 void FindAndReplace(std::string & line, const std::vector<std::string> & tofind, const std::vector<std::string> & toreplace);
176 void FindAndReplace(std::ifstream & in, const std::vector<std::string> & tofind, const std::vector<std::string> & toreplace, std::ofstream & out);
177 //--------------------------------------------------------------------
179 //--------------------------------------------------------------------
180 double ComputeEuclideanDistanceFromPointToPlane(const itk::ContinuousIndex<double, 3> point,
181 const itk::ContinuousIndex<double, 3> pointInPlane,
182 const itk::ContinuousIndex<double, 3> normalPlane);
184 //--------------------------------------------------------------------
185 // Open a File for reading/writing
186 void openFileForReading(std::ifstream & is, const std::string & filename);
187 void openFileForWriting(std::ofstream & os, const std::string & filename);
189 //--------------------------------------------------------------------
190 void readDoubleFromFile(const std::string & filename, std::vector<double> & list);
192 //--------------------------------------------------------------------
193 double cotan(double i);
194 double invcotan(double i);
196 //--------------------------------------------------------------------
197 void disableStdCerr();
198 void enableStdCerr();
200 //--------------------------------------------------------------------
201 template<class ImageType>
202 void CloneImage(const typename ImageType::Pointer & input, typename ImageType::Pointer & output);
204 #include "clitkCommon.txx"
208 #endif /* end #define CLITKCOMMON_H */