codebase / stimlib

Commit 35a7195f62dc2428df5f4b6024956ebdb8713e1b

Authored by David Mayerich
1 parent 1b2858a2

added median spectra to ENVI files, updated mean spectra in interleave formats

Showing 9 changed files with 140 additions and 79 deletions   Show diff stats
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matlab/enviLoadRaw.m
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1 1 %loads an ENVI file without any manipulation (changing orientation)
  2 +% enviLoadRaw(filename, headername)
2 3 function M = enviLoadRaw(filename, headername)
3 4  
4 5 %if a header isn't provided, assume it's just the filename
... ...
matlab/enviSaveRaw.m
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1 1 %saves an ENVI file without any manipulation, assumes (X, Y, S)
  2 +% enviSaveRaw(M, filename, headername)
2 3 function enviSaveRaw(M, filename, headername)
3 4  
4 5 %if a header isn't provided, assume it's just the filename
... ...
stim/cuda/cudatools/error.h
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... ... @@ -11,12 +11,7 @@ using namespace std;
11 11 //handle error macro
12 12 static void HandleError( cudaError_t err, const char *file, int line ) {
13 13 if (err != cudaSuccess) {
14   - //FILE* outfile = fopen("cudaErrorLog.txt", "w");
15   - //fprintf(outfile, "%s in %s at line %d\n", cudaGetErrorString( err ), file, line );
16   - //fclose(outfile);
17 14 printf("%s in %s at line %d\n", cudaGetErrorString( err ), file, line );
18   - //exit( EXIT_FAILURE );
19   -
20 15 }
21 16 }
22 17 #define HANDLE_ERROR( err ) (HandleError( err, __FILE__, __LINE__ ))
... ...
stim/envi/bil.h
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... ... @@ -992,32 +992,35 @@ public:
992 992  
993 993 /// @param p is a pointer to pre-allocated memory of size [B * sizeof(T)] that stores the mean spectrum
994 994 /// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
995   - bool avg_band(double* p, unsigned char* mask = NULL, bool PROGRESS = false){
  995 + bool mean_spectrum(double* m, double* std, unsigned char* mask = NULL, bool PROGRESS = false){
996 996 unsigned long long XZ = X() * Z();
997 997 unsigned long long XY = X() * Y();
998 998 T* temp = (T*)malloc(sizeof(T) * XZ);
999   - for (unsigned long long j = 0; j < Z(); j++){
1000   - p[j] = 0;
1001   - }
  999 + memset(m, 0, Z() * sizeof(double)); //initialize the mean to zero
  1000 + double* e_x2 = (double*)malloc(Z() * sizeof(double)); //allocate space for E[x^2]
  1001 + memset(e_x2, 0, Z() * sizeof(double)); //initialize E[x^2] to zero
1002 1002 //calculate vaild number in a band
1003   - unsigned long long count = 0;
1004   - for (unsigned long long j = 0; j < XY; j++){
1005   - if (mask == NULL || mask[j] != 0){
1006   - count++;
1007   - }
1008   - }
  1003 + size_t count = nnz(mask); //count the number of pixels in the mask
  1004 +
  1005 + double x; //create a register to store the pixel value
1009 1006 for (unsigned long long k = 0; k < Y(); k++){
1010 1007 read_plane_y(temp, k);
1011 1008 unsigned long long kx = k * X();
1012 1009 for (unsigned long long i = 0; i < X(); i++){
1013 1010 if (mask == NULL || mask[kx + i] != 0){
1014 1011 for (unsigned long long j = 0; j < Z(); j++){
1015   - p[j] += temp[j * X() + i] / (double)count;
  1012 + x = temp[j * X() + i];
  1013 + m[j] += x / (double)count;
  1014 + e_x2[j] += x*x / (double)count;
1016 1015 }
1017 1016 }
1018 1017 }
1019 1018 if(PROGRESS) progress = (double)(k+1) / Y() * 100;
1020 1019 }
  1020 +
  1021 + for(size_t i = 0; i < Z(); i++) //calculate the standard deviation
  1022 + std[i] = sqrt(e_x2[i] - m[i] * m[i]);
  1023 +
1021 1024 free(temp);
1022 1025 return true;
1023 1026 }
... ...
stim/envi/bip.h
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... ... @@ -954,26 +954,31 @@ public:
954 954  
955 955 /// @param p is a pointer to pre-allocated memory of size [B * sizeof(T)] that stores the mean spectrum
956 956 /// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
957   - bool avg_band(double* p, unsigned char* mask = NULL, bool PROGRESS = false){
  957 + bool mean_spectrum(double* m, double* std, unsigned char* mask = NULL, bool PROGRESS = false){
958 958 unsigned long long XY = X() * Y(); //calculate the total number of pixels in the HSI
959 959 T* temp = (T*)malloc(sizeof(T) * Z()); //allocate space for the current spectrum to be read
960   - memset(p, 0, sizeof(double) * Z()); //initialize the average spectrum to zero (0)
961   - //for (unsigned j = 0; j < Z(); j++){
962   - // p[j] = 0;
963   - //}
  960 + memset(m, 0, Z() * sizeof(double)); //set the mean spectrum to zero
  961 + double* e_x2 = (double*)malloc(Z() * sizeof(double)); //allocate space for E[x^2]
  962 + memset(e_x2, 0, Z() * sizeof(double)); //set all values for E[x^2] to zero
964 963  
965 964 unsigned long long count = nnz(mask); //calculate the number of masked pixels
966   -
  965 + double x;
967 966 for (unsigned long long i = 0; i < XY; i++){ //for each pixel in the HSI
968 967 if (mask == NULL || mask[i] != 0){ //if the pixel is masked
969 968 pixel(temp, i); //get the spectrum
970 969 for (unsigned long long j = 0; j < Z(); j++){ //for each spectral component
971   - p[j] += (double)temp[j] / (double)count; //add the weighted value to the average
  970 + x = temp[j];
  971 + m[j] += x / (double)count; //add the weighted value to the average
  972 + e_x2[j] += x*x / (double)count;
972 973 }
973 974 }
974 975 if(PROGRESS) progress = (double)(i+1) / XY * 100; //increment the progress
975 976 }
976 977  
  978 + //calculate the standard deviation
  979 + for(size_t i = 0; i < Z(); i++)
  980 + std[i] = sqrt(e_x2[i] - m[i] * m[i]);
  981 +
977 982 free(temp);
978 983 return true;
979 984 }
... ...
stim/envi/bsq.h
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... ... @@ -561,12 +561,12 @@ public:
561 561 free(src[1]);
562 562 free(dst[0]);
563 563 free(dst[1]);
564   - //if(VERBOSE){
  564 + if(VERBOSE){
565 565 std::cout<<"total time to execute bsq::bip(): "<<t_total<<" ms"<<std::endl;
566 566 std::cout<<" total time spent processing: "<<pt_total<<" ms"<<std::endl;
567 567 std::cout<<" total time spent reading: "<<rt_total<<" ms"<<std::endl;
568 568 std::cout<<" total time spent writing: "<<wt_total<<" ms"<<std::endl;
569   - //}
  569 + }
570 570 return true; //return true
571 571 }
572 572  
... ... @@ -1120,27 +1120,61 @@ public:
1120 1120  
1121 1121 /// @param p is a pointer to pre-allocated memory of size [B * sizeof(T)] that stores the mean spectrum
1122 1122 /// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
1123   - bool avg_band(double* p, unsigned char* mask = NULL, bool PROGRESS = false){
  1123 + bool mean_spectrum(double* m, double* std, unsigned char* mask = NULL, bool PROGRESS = false){
1124 1124 unsigned long long XY = X() * Y();
1125   - unsigned long long count = 0; //count will store the number of masked pixels
  1125 + unsigned long long count = nnz(mask); //count will store the number of masked pixels
1126 1126 T* temp = (T*)malloc(sizeof(T) * XY);
1127   - //calculate this loop counts the number of true pixels in the mask
1128   - for (unsigned j = 0; j < XY; j++){
1129   - if (mask == NULL || mask[j] != 0){
1130   - count++;
1131   - }
1132   - }
  1127 +
1133 1128 //this loops goes through each band in B (Z())
1134 1129 // masked (or valid) pixels from that band are averaged and the average is stored in p
  1130 + double e_x; //stores E[x]^2
  1131 + double e_x2; //stores E[x^2]
  1132 + double x;
1135 1133 for (unsigned long long i = 0; i < Z(); i++){
1136   - p[i] = 0;
  1134 + e_x = 0;
  1135 + e_x2 = 0;
1137 1136 band_index(temp, i); //get the band image and store it in temp
1138 1137 for (unsigned long long j = 0; j < XY; j++){ //loop through temp, averaging valid pixels
1139 1138 if (mask == NULL || mask[j] != 0){
1140   - p[i] += (double)temp[j] / (double)count;
  1139 + x = (double)temp[j];
  1140 + e_x += x / (double)count; //sum the expected value of x
  1141 + e_x2 += (x * x) / (double)count; //sum the expected value of x^2
  1142 + }
  1143 + }
  1144 + m[i] = e_x; //store the mean
  1145 + std[i] = sqrt(e_x2 - e_x * e_x); //calculate the standard deviation
  1146 + if(PROGRESS) progress = (double)(i+1) / Z() * 100; //update the progress counter
  1147 + }
  1148 + free(temp);
  1149 + return true;
  1150 + }
  1151 +
  1152 + /// Calculate the median value for all masked (or valid) pixels in a band and returns the median spectrum
  1153 +
  1154 + /// @param p is a pointer to pre-allocated memory of size [B * sizeof(T)] that stores the mean spectrum
  1155 + /// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
  1156 + bool median_spectrum(double* m, unsigned char* mask = NULL, bool PROGRESS = false){
  1157 + size_t XY = X() * Y();
  1158 + size_t count = nnz(mask); //count will store the number of masked pixels
  1159 + T* temp = (T*)malloc(sizeof(T) * XY);
  1160 +
  1161 + std::vector<T> band_values(count); //create an STD vector of band values
  1162 +
  1163 + //this loops goes through each band in B (Z())
  1164 + // masked (or valid) pixels from that band are averaged and the average is stored in p
  1165 + size_t k;
  1166 + for (size_t i = 0; i < Z(); i++){ //for each band
  1167 + band_index(temp, i); //get the band image and store it in temp
  1168 + k = 0; //initialize the band_value index to zero
  1169 + for (size_t j = 0; j < XY; j++){ //loop through temp, averaging valid pixels
  1170 + if (mask == NULL || mask[j] != 0){
  1171 + band_values[k] = temp[j]; //store the value in the band_values array
  1172 + k++; //increment the band_values index
1141 1173 }
1142 1174 }
1143   - if(PROGRESS) progress = (double)(i+1) / Z() * 100;
  1175 + std::sort(band_values.begin(), band_values.end()); //sort all of the values in the band
  1176 + m[i] = band_values[ count/2 ]; //store the center value in the array
  1177 + if(PROGRESS) progress = (double)(i+1) / Z() * 100; //update the progress counter
1144 1178 }
1145 1179 free(temp);
1146 1180 return true;
... ...
stim/envi/envi.h
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... ... @@ -1380,12 +1380,12 @@ public:
1380 1380  
1381 1381 /// @param p is a pointer to pre-allocated memory of size [B * sizeof(T)] that stores the mean spectrum
1382 1382 /// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
1383   - bool avg_band(double * p, unsigned char* mask, bool PROGRESS = false){
  1383 + bool mean_spectrum(double * p, double* std, unsigned char* mask, bool PROGRESS = false){
1384 1384 if (header.interleave == envi_header::BSQ){
1385 1385 if (header.data_type == envi_header::float32)
1386   - return ((bsq<float>*)file)->avg_band(p, mask, PROGRESS);
  1386 + return ((bsq<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
1387 1387 else if (header.data_type == envi_header::float64)
1388   - return ((bsq<double>*)file)->avg_band(p, mask, PROGRESS);
  1388 + return ((bsq<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
1389 1389 else{
1390 1390 std::cout << "ERROR: unidentified data type" << std::endl;
1391 1391 exit(1);
... ... @@ -1393,9 +1393,9 @@ public:
1393 1393 }
1394 1394 else if (header.interleave == envi_header::BIL){
1395 1395 if (header.data_type == envi_header::float32)
1396   - return ((bil<float>*)file)->avg_band(p, mask, PROGRESS);
  1396 + return ((bil<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
1397 1397 else if (header.data_type == envi_header::float64)
1398   - return ((bil<double>*)file)->avg_band(p, mask, PROGRESS);
  1398 + return ((bil<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
1399 1399 else{
1400 1400 std::cout << "ERROR: unidentified data type" << std::endl;
1401 1401 exit(1);
... ... @@ -1403,9 +1403,9 @@ public:
1403 1403 }
1404 1404 else if (header.interleave == envi_header::BIP){
1405 1405 if (header.data_type == envi_header::float32)
1406   - return ((bip<float>*)file)->avg_band(p, mask, PROGRESS);
  1406 + return ((bip<float>*)file)->mean_spectrum(p, std, mask, PROGRESS);
1407 1407 else if (header.data_type == envi_header::float64)
1408   - return ((bip<double>*)file)->avg_band(p, mask, PROGRESS);
  1408 + return ((bip<double>*)file)->mean_spectrum(p, std, mask, PROGRESS);
1409 1409 else{
1410 1410 std::cout << "ERROR: unidentified data type" << std::endl;
1411 1411 exit(1);
... ... @@ -1414,6 +1414,28 @@ public:
1414 1414 return false;
1415 1415 }
1416 1416  
  1417 + /// Calculate the mean value for all masked (or valid) pixels in a band and returns the average spectrum
  1418 +
  1419 + /// @param p is a pointer to pre-allocated memory of size [B * sizeof(T)] that stores the mean spectrum
  1420 + /// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
  1421 + bool median_spectrum(double* m, unsigned char* mask, bool PROGRESS = false){
  1422 + if (header.interleave == envi_header::BSQ){
  1423 + if (header.data_type == envi_header::float32)
  1424 + return ((bsq<float>*)file)->median_spectrum(m, mask, PROGRESS);
  1425 + else if (header.data_type == envi_header::float64)
  1426 + return ((bsq<double>*)file)->median_spectrum(m, mask, PROGRESS);
  1427 + else{
  1428 + std::cout << "ERROR: unidentified data type" << std::endl;
  1429 + exit(1);
  1430 + }
  1431 + }
  1432 + else{
  1433 + std::cout<<"ERROR: median calculation is only supported for BSQ interleave types. Convert to process."<<std::endl;
  1434 + exit(1);
  1435 + }
  1436 + return false;
  1437 + }
  1438 +
1417 1439 /// Calculate the covariance matrix for all masked pixels in the image.
1418 1440  
1419 1441 /// @param co is a pointer to pre-allocated memory of size [B * B] that stores the resulting covariance matrix
... ...
stim/gl/gl_spider.h
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... ... @@ -473,7 +473,7 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
473 473 glEndList(); ///finilize the display list.
474 474 #ifdef DEBUG
475 475 for(int i = 0; i < numSamplesPos; i++)
476   - std::cout << pV[i] << std::endl;
  476 + std::cout << pV[i].str() << std::endl;
477 477 #endif
478 478 }
479 479  
... ... @@ -1145,8 +1145,8 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
1145 1145 out[3] = temp[2];
1146 1146 }
1147 1147 #ifdef DEBUG
1148   - std::cout << "out is " << out << std::endl;
1149   - std::cout << "when rotating from " << from << " to " << dir << std::endl;
  1148 + std::cout << "out is " << out.str() << std::endl;
  1149 + std::cout << "when rotating from " << from.str() << " to " << dir.str() << std::endl;
1150 1150 #endif
1151 1151 return out;
1152 1152 }
... ... @@ -1531,7 +1531,7 @@ class gl_spider // : public virtual gl_texture&lt;T&gt;
1531 1531 setMagnitude(curSeedMag);
1532 1532  
1533 1533 #ifdef DEBUG
1534   - std::cout << "The new seed " << curSeed << curSeedVec << curSeedMag << std::endl;
  1534 + std::cout << "The new seed " << curSeed.str() << curSeedVec.str() << curSeedMag << std::endl;
1535 1535 #endif
1536 1536  
1537 1537 // Bind(direction_texID, direction_buffID, numSamples, n_pixels);
... ...
stim/math/vector.h
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... ... @@ -74,11 +74,11 @@ struct vec : public std::vector&lt;T&gt;
74 74 at(i) = other[i];
75 75 }
76 76 }
77   -
  77 +
78 78 // vec( vec3<T>& other){
79 79 // resize(3); //resize the current vector to match the copy
80 80 // for(size_t i=0; i<3; i++){ //copy each element
81   -// at(i) = other[i];
  81 +// at(i) = other[i];
82 82 // }
83 83 // }
84 84  
... ... @@ -139,16 +139,16 @@ struct vec : public std::vector&lt;T&gt;
139 139  
140 140 }
141 141  
142   -
143   - vec<T> cyl2cart() const
144   - {
145   - vec<T> cyl;
146   - cyl.push_back(at(0)*std::sin(at(1)));
147   - cyl.push_back(at(0)*std::cos(at(1)));
148   - cyl.push_back(at(2));
149   - return(cyl);
150   -
151   - }
  142 +
  143 + vec<T> cyl2cart() const
  144 + {
  145 + vec<T> cyl;
  146 + cyl.push_back(at(0)*std::sin(at(1)));
  147 + cyl.push_back(at(0)*std::cos(at(1)));
  148 + cyl.push_back(at(2));
  149 + return(cyl);
  150 +
  151 + }
152 152 /// Convert the vector from cartesian to spherical coordinates (x, y, z -> r, theta, phi where theta = [0, 2*pi])
153 153 vec<T> cart2sph() const
154 154 {
... ... @@ -335,16 +335,16 @@ struct vec : public std::vector&lt;T&gt;
335 335 return *this;
336 336 }
337 337  
338   - /// Cast to a vec3
339   - operator stim::vec3<T>(){
340   - stim::vec3<T> r;
341   - size_t N = std::min<size_t>(size(), 3);
342   - for(size_t i = 0; i < N; i++)
343   - r[i] = at(i);
344   - return r;
345   - }
346   -
347   -
  338 + /// Cast to a vec3
  339 + operator stim::vec3<T>(){
  340 + stim::vec3<T> r;
  341 + size_t N = min(size(), (size_t)3);
  342 + for(size_t i = 0; i < N; i++)
  343 + r[i] = at(i);
  344 + return r;
  345 + }
  346 +
  347 +
348 348 /// Casting and assignment
349 349 template<typename Y>
350 350 vec<T> & operator=(vec<Y> rhs){
... ... @@ -355,16 +355,16 @@ struct vec : public std::vector&lt;T&gt;
355 355 at(i) = rhs[i];
356 356 return *this;
357 357 }
358   -
359   - /// Assign a vec = vec3
360   - template<typename Y>
361   - vec<T> & operator=(vec3<Y> rhs)
362   - {
363   - resize(3);
364   - for(size_t i=0; i<3; i++)
365   - at(i) = rhs[i];
366   - return *this;
367   - }
  358 +
  359 + /// Assign a vec = vec3
  360 + template<typename Y>
  361 + vec<T> & operator=(vec3<Y> rhs)
  362 + {
  363 + resize(3);
  364 + for(size_t i=0; i<3; i++)
  365 + at(i) = rhs[i];
  366 + return *this;
  367 + }
368 368  
369 369 /// Unary minus (returns the negative of the vector)
370 370 vec<T> operator-() const{
... ...