Commit e9bddc57f2e79c9c378049499775a4be385b4101
1 parent
912d9073
added band cropping for BSQ files
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5 changed files
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60 additions
and
24 deletions
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stim/envi/bil.h
@@ -1005,7 +1005,12 @@ public: | @@ -1005,7 +1005,12 @@ public: | ||
1005 | /// @param y0 is the lower-left y pixel coordinate to be included in the cropped image | 1005 | /// @param y0 is the lower-left y pixel coordinate to be included in the cropped image |
1006 | /// @param x1 is the upper-right x pixel coordinate to be included in the cropped image | 1006 | /// @param x1 is the upper-right x pixel coordinate to be included in the cropped image |
1007 | /// @param y1 is the upper-right y pixel coordinate to be included in the cropped image | 1007 | /// @param y1 is the upper-right y pixel coordinate to be included in the cropped image |
1008 | - bool crop(std::string outfile, unsigned x0, unsigned y0, unsigned x1, unsigned y1){ | 1008 | + bool crop(std::string outfile, unsigned long long x0, |
1009 | + unsigned long long y0, | ||
1010 | + unsigned long long x1, | ||
1011 | + unsigned long long y1, | ||
1012 | + unsigned long long b0, | ||
1013 | + unsigned long long b1){ | ||
1009 | 1014 | ||
1010 | //calculate the new number of samples and lines | 1015 | //calculate the new number of samples and lines |
1011 | unsigned long long sam = x1 - x0; //samples | 1016 | unsigned long long sam = x1 - x0; //samples |
stim/envi/bip.h
@@ -1061,7 +1061,12 @@ public: | @@ -1061,7 +1061,12 @@ public: | ||
1061 | /// @param y0 is the lower-left y pixel coordinate to be included in the cropped image | 1061 | /// @param y0 is the lower-left y pixel coordinate to be included in the cropped image |
1062 | /// @param x1 is the upper-right x pixel coordinate to be included in the cropped image | 1062 | /// @param x1 is the upper-right x pixel coordinate to be included in the cropped image |
1063 | /// @param y1 is the upper-right y pixel coordinate to be included in the cropped image | 1063 | /// @param y1 is the upper-right y pixel coordinate to be included in the cropped image |
1064 | - bool crop(std::string outfile, unsigned x0, unsigned y0, unsigned x1, unsigned y1){ | 1064 | + bool crop(std::string outfile, unsigned long long x0, |
1065 | + unsigned long long y0, | ||
1066 | + unsigned long long x1, | ||
1067 | + unsigned long long y1, | ||
1068 | + unsigned long long b0, | ||
1069 | + unsigned long long b1){ | ||
1065 | 1070 | ||
1066 | //calculate the new number of samples and lines | 1071 | //calculate the new number of samples and lines |
1067 | unsigned long long sam = x1 - x0; //samples | 1072 | unsigned long long sam = x1 - x0; //samples |
stim/envi/bsq.h
@@ -968,27 +968,45 @@ public: | @@ -968,27 +968,45 @@ public: | ||
968 | /// @param y0 is the lower-left y pixel coordinate to be included in the cropped image | 968 | /// @param y0 is the lower-left y pixel coordinate to be included in the cropped image |
969 | /// @param x1 is the upper-right x pixel coordinate to be included in the cropped image | 969 | /// @param x1 is the upper-right x pixel coordinate to be included in the cropped image |
970 | /// @param y1 is the upper-right y pixel coordinate to be included in the cropped image | 970 | /// @param y1 is the upper-right y pixel coordinate to be included in the cropped image |
971 | - bool crop(std::string outfile, unsigned x0, unsigned y0, unsigned x1, unsigned y1){ | ||
972 | - | ||
973 | - //calculate the new number of samples and lines | ||
974 | - unsigned long long sam = x1 - x0; //samples | ||
975 | - unsigned long long lin = y1 - y0; //lines | ||
976 | - unsigned long long L = sam * lin * sizeof(T); | ||
977 | - //get specified band and save | 971 | + bool crop(std::string outfile, unsigned long long x0, |
972 | + unsigned long long y0, | ||
973 | + unsigned long long x1, | ||
974 | + unsigned long long y1, | ||
975 | + unsigned long long b0, | ||
976 | + unsigned long long b1){ | ||
977 | + | ||
978 | + //calculate the new number of samples, lines, and bands | ||
979 | + unsigned long long samples = x1 - x0; | ||
980 | + unsigned long long lines = y1 - y0; | ||
981 | + unsigned long long bands = b1 - b0; | ||
982 | + | ||
983 | + //calculate the size of a single band | ||
984 | + unsigned long long L = samples * lines * sizeof(T); | ||
985 | + | ||
986 | + //allocate space for a single band | ||
978 | T* temp = (T*)malloc(L); | 987 | T* temp = (T*)malloc(L); |
988 | + | ||
989 | + //create an output stream to store the output file | ||
979 | std::ofstream out(outfile.c_str(), std::ios::binary); | 990 | std::ofstream out(outfile.c_str(), std::ios::binary); |
980 | - unsigned long long jumpb = X() * (Y() - lin) * sizeof(T); //jump pointer to the next band | ||
981 | - unsigned long long jumpl = (X() - sam) * sizeof(T); //jump pointer to the next line | ||
982 | - //get start | ||
983 | - file.seekg((y0 * X() + x0) * sizeof(T), std::ios::beg); | ||
984 | - for (unsigned z = 0; z < Z(); z++) | 991 | + |
992 | + //calculate the distance required to jump from the end of one band to the beginning of another | ||
993 | + unsigned long long jumpb = X() * (Y() - lines) * sizeof(T); | ||
994 | + | ||
995 | + //calculate the distance required to jump from the end of one line to the beginning of another | ||
996 | + unsigned long long jumpl = (X() - samples) * sizeof(T); | ||
997 | + | ||
998 | + //seek to the start of the cropped region in the input file | ||
999 | + file.seekg( (b0 * X() * Y() + y0 * X() + x0) * sizeof(T), std::ios::beg); | ||
1000 | + | ||
1001 | + //for each band | ||
1002 | + for (unsigned long long z = b0; z < b1; z++) | ||
985 | { | 1003 | { |
986 | - for (unsigned j = 0; j < lin; j++) | 1004 | + for (unsigned y = 0; y < lines; y++) |
987 | { | 1005 | { |
988 | - file.read((char *)(temp + j * sam), sizeof(T) * sam); | 1006 | + file.read((char *)(temp + y * samples), sizeof(T) * samples); |
989 | file.seekg(jumpl, std::ios::cur); //go to the next band | 1007 | file.seekg(jumpl, std::ios::cur); //go to the next band |
990 | 1008 | ||
991 | - thread_data = (double)(z * lin + j) / (Z() * lin) * 100; | 1009 | + thread_data = (double)(z * lines + y) / (Z() * lines) * 100; |
992 | } | 1010 | } |
993 | out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file | 1011 | out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file |
994 | file.seekg(jumpb, std::ios::cur); | 1012 | file.seekg(jumpb, std::ios::cur); |
stim/envi/envi.h
@@ -1022,13 +1022,13 @@ public: | @@ -1022,13 +1022,13 @@ public: | ||
1022 | /// @param y0 is the lower-left y pixel coordinate to be included in the cropped image | 1022 | /// @param y0 is the lower-left y pixel coordinate to be included in the cropped image |
1023 | /// @param x1 is the upper-right x pixel coordinate to be included in the cropped image | 1023 | /// @param x1 is the upper-right x pixel coordinate to be included in the cropped image |
1024 | /// @param y1 is the upper-right y pixel coordinate to be included in the cropped image | 1024 | /// @param y1 is the upper-right y pixel coordinate to be included in the cropped image |
1025 | - bool crop(std::string outfile,unsigned x0, unsigned y0, unsigned x1, unsigned y1){ | 1025 | + bool crop(std::string outfile,unsigned x0, unsigned y0, unsigned x1, unsigned y1, unsigned b0, unsigned b1){ |
1026 | 1026 | ||
1027 | if (header.interleave == envi_header::BSQ){ | 1027 | if (header.interleave == envi_header::BSQ){ |
1028 | if (header.data_type == envi_header::float32) | 1028 | if (header.data_type == envi_header::float32) |
1029 | - return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1); | 1029 | + return ((bsq<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1); |
1030 | else if (header.data_type == envi_header::float64) | 1030 | else if (header.data_type == envi_header::float64) |
1031 | - return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1); | 1031 | + return ((bsq<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1); |
1032 | else{ | 1032 | else{ |
1033 | std::cout << "ERROR: unidentified data type" << std::endl; | 1033 | std::cout << "ERROR: unidentified data type" << std::endl; |
1034 | exit(1); | 1034 | exit(1); |
@@ -1036,9 +1036,9 @@ public: | @@ -1036,9 +1036,9 @@ public: | ||
1036 | } | 1036 | } |
1037 | else if (header.interleave == envi_header::BIL){ | 1037 | else if (header.interleave == envi_header::BIL){ |
1038 | if (header.data_type == envi_header::float32) | 1038 | if (header.data_type == envi_header::float32) |
1039 | - return ((bil<float>*)file)->crop(outfile, x0, y0, x1, y1); | 1039 | + return ((bil<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1); |
1040 | else if (header.data_type == envi_header::float64) | 1040 | else if (header.data_type == envi_header::float64) |
1041 | - return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1); | 1041 | + return ((bil<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1); |
1042 | else{ | 1042 | else{ |
1043 | std::cout << "ERROR: unidentified data type" << std::endl; | 1043 | std::cout << "ERROR: unidentified data type" << std::endl; |
1044 | exit(1); | 1044 | exit(1); |
@@ -1046,9 +1046,9 @@ public: | @@ -1046,9 +1046,9 @@ public: | ||
1046 | } | 1046 | } |
1047 | else if (header.interleave == envi_header::BIP){ | 1047 | else if (header.interleave == envi_header::BIP){ |
1048 | if (header.data_type == envi_header::float32) | 1048 | if (header.data_type == envi_header::float32) |
1049 | - return ((bip<float>*)file)->crop(outfile, x0, y0, x1, y1); | 1049 | + return ((bip<float>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1); |
1050 | else if (header.data_type == envi_header::float64) | 1050 | else if (header.data_type == envi_header::float64) |
1051 | - return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1); | 1051 | + return ((bip<double>*)file)->crop(outfile, x0, y0, x1, y1, b0, b1); |
1052 | else{ | 1052 | else{ |
1053 | std::cout << "ERROR: unidentified data type" << std::endl; | 1053 | std::cout << "ERROR: unidentified data type" << std::endl; |
1054 | exit(1); | 1054 | exit(1); |
stim/parser/arguments.h
@@ -479,6 +479,14 @@ namespace stim{ | @@ -479,6 +479,14 @@ namespace stim{ | ||
479 | return args.size(); | 479 | return args.size(); |
480 | } | 480 | } |
481 | 481 | ||
482 | + /// Returns the number of options that are set | ||
483 | + unsigned int nopts(){ | ||
484 | + unsigned int n = 0; //initialize the counter for the number of options | ||
485 | + for(unsigned int i = 0; i < opts.size(); i++) //go through each option | ||
486 | + if(opts[i].is_set()) n++; //if a value is specified, increment the counter | ||
487 | + return n; | ||
488 | + } | ||
489 | + | ||
482 | ///Returns the name of an argument, given its index | 490 | ///Returns the name of an argument, given its index |
483 | 491 | ||
484 | /// @param a is the index of the requested argument | 492 | /// @param a is the index of the requested argument |