codebase / stimlib

Commit a2bf1d0853c4497c8a94fec854b7e99892ea5b4f

Authored by David Mayerich
1 parent c8c976a9

general bug fixes and clean compiling and exiting for HSIproc

Showing 10 changed files with 172 additions and 144 deletions   Show diff stats
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stim/envi/binary.h
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... ... @@ -285,7 +285,6 @@ public:
285 285 if(PROGRESS) progress = (double)(i+1) / N * 100;
286 286 }
287 287  
288   - if(PROGRESS) progress = 100;
289 288 return true;
290 289  
291 290  
... ...
stim/envi/bip.h
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... ... @@ -8,8 +8,10 @@
8 8 #include <utility>
9 9  
10 10 //CUDA
11   -#include <cuda_runtime.h>
12   -#include "cublas_v2.h"
  11 +#ifdef CUDA_FOUND
  12 + #include <cuda_runtime.h>
  13 + #include "cublas_v2.h"
  14 +#endif
13 15  
14 16 namespace stim{
15 17  
... ... @@ -31,82 +33,10 @@ protected:
31 33 //std::vector<double> w; //band wavelength
32 34 unsigned long long offset; //header offset
33 35  
34   - /*unsigned long long X(){
35   - return R[1];
36   - }
37   - unsigned long long Y(){
38   - return R[2];
39   - }
40   - unsigned long long Z(){
41   - return R[0];
42   - }*/
43 36 using hsi<T>::w; //use the wavelength array in stim::hsi
44 37 using hsi<T>::nnz;
45 38 using binary<T>::progress;
46   -
47   - /// Call the binary nnz() function for the BIP orientation
48   - //unsigned long long nnz(unsigned char* mask){
49   - // return binary<T>::nnz(mask, X()*Y());
50   - //}
51   -
52   - /// Linear interpolation of a spectral value given the bounding spectral samples
53   - /*T lerp(double w, T low_v, double low_w, T high_v, double high_w){
54   - if(low_w == high_w) return low_v; //if the interval is of zero length, just return one of the bounds
55   - double alpha = (w - low_w) / (high_w - low_w); //calculate the interpolation factor
56   - return (1.0 - alpha) * low_v + alpha * high_v; //interpolate
57   - }
58   -
59   - /// Gets the two band indices surrounding a given wavelength
60   - void band_bounds(double wavelength, unsigned long long& low, unsigned long long& high){
61   - unsigned long long B = Z();
62   - for(high = 0; high < B; high++){
63   - if(w[high] > wavelength) break;
64   - }
65   - low = 0;
66   - if(high > 0)
67   - low = high-1;
68   - }
69   -
70   - /// Get the list of band numbers that bound a list of wavelengths
71   - void band_bounds(std::vector<double> wavelengths,
72   - std::vector<unsigned long long>& low_bands,
73   - std::vector<unsigned long long>& high_bands){
74   -
75   - unsigned long long W = w.size(); //get the number of wavelengths in the list
76   - low_bands.resize(W); //pre-allocate space for the band lists
77   - high_bands.resize(W);
78   -
79   - for(unsigned long long wl = 0; wl < W; wl++){ //for each wavelength
80   - band_bounds(wavelengths[wl], low_bands[wl], high_bands[wl]); //find the low and high bands
81   - }
82   - }
83   -
84   - /// Returns the interpolated in the given spectrum based on the given wavelength
85   -
86   - /// @param s is the spectrum in main memory of length Z()
87   - /// @param wavelength is the wavelength value to interpolate out
88   - T interp_spectrum(T* s, double wavelength){
89   - unsigned long long low, high; //indices for the bands surrounding wavelength
90   - band_bounds(wavelength, low, high); //get the surrounding band indices
91   -
92   - if(high == w.size()) return s[w.size()-1]; //if the high band is above the wavelength range, return the highest wavelength value
93   -
94   - return lerp(wavelength, s[low], w[low], s[high], w[high]);
95   - }
96   -
97   - /// Returns the interpolated value corresponding to the given list of wavelengths
98   - std::vector<T> interp_spectrum(T* s, std::vector<double> wavelengths){
99   -
100   - unsigned long long N = wavelengths.size(); //get the number of wavelength measurements
101   -
102   - std::vector<T> v; //allocate space for the resulting values
103   - v.resize(wavelengths.size());
104   - for(unsigned long long n = 0; n < N; n++){ //for each measurement
105   - v[n] = interp_spectrum(s, wavelengths[n]); //interpolate the measurement
106   - }
107   - return v;
108   - }*/
109   -
  39 +
110 40 public:
111 41  
112 42 using binary<T>::open;
... ... @@ -199,7 +129,6 @@ public:
199 129 {
200 130 band_index(p, page, PROGRESS);
201 131 }
202   -
203 132 return true;
204 133 }
205 134  
... ... @@ -899,7 +828,7 @@ public:
899 828 return true;
900 829 }
901 830  
902   - bool unsift(std::string outfile, unsigned char* mask, unsigned long long samples, unsigned long long lines){
  831 + bool unsift(std::string outfile, unsigned char* mask, unsigned long long samples, unsigned long long lines, bool PROGRESS = false){
903 832  
904 833 // open an output stream
905 834 std::ofstream target(outfile.c_str(), std::ios::binary);
... ... @@ -938,7 +867,7 @@ public:
938 867 target.write((char *)spectrum, B * sizeof(T));
939 868 }
940 869  
941   - progress = (double)x / XY * 100;
  870 + if(PROGRESS) progress = (double)(x + 1) / XY * 100;
942 871  
943 872 }
944 873  
... ... @@ -946,7 +875,7 @@ public:
946 875 target.close();
947 876 free(spectrum);
948 877  
949   - progress = 100;
  878 + //progress = 100;
950 879  
951 880 return true;
952 881  
... ...
stim/envi/bsq.h
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... ... @@ -765,13 +765,7 @@ public:
765 765 unsigned long long L = XY * sizeof(T); //size of XY plane (in bytes)
766 766  
767 767 //calculate the number of pixels in the mask
768   - unsigned long long P = 0;
769   - if(mask == NULL) P = XY;
770   - else{
771   - for(unsigned long long xy = 0; xy < XY; xy++){
772   - if(mask[xy] != 0) P++;
773   - }
774   - }
  768 + //unsigned long long P = nnz(mask);
775 769  
776 770 T* band_image = (T*) malloc( XY * sizeof(T)); //allocate space for a single band
777 771  
... ... @@ -784,7 +778,9 @@ public:
784 778 if(mask == NULL || mask[xy] != 0){ //if the pixel is valid
785 779 matrix[i*Z() + b] = band_image[xy]; //copy it to the appropriate point in the values[] array
786 780 i++;
  781 + //std::cout<<i<<std::endl;
787 782 }
  783 +
788 784 }
789 785 }
790 786  
... ... @@ -828,7 +824,7 @@ public:
828 824 }
829 825  
830 826 /// Generates a spectral image from a matrix of spectral values in lexicographic order and a mask
831   - bool unsift(std::string outfile, unsigned char* p, unsigned long long samples, unsigned long long lines){
  827 + bool unsift(std::string outfile, unsigned char* p, unsigned long long samples, unsigned long long lines, bool PROGRESS = false){
832 828  
833 829 //create a binary output stream
834 830 std::ofstream target(outfile.c_str(), std::ios::binary);
... ... @@ -870,7 +866,7 @@ public:
870 866 i++;
871 867 }
872 868 //std::cout<<xi<<"/"<<XY<<", "<<b<<"/"<<B<<std::endl;
873   - progress = (double)(b * XY + xi) / (B * XY) * 100;
  869 + if(PROGRESS) progress = (double)((b + 1) * XY + xi + 1) / (B * XY) * 100;
874 870 }
875 871 //std::cout<<b*XY<<"/"<<B*XY<<" "<<B<<"-"<<XY<<std::endl;
876 872 //write the band image to disk
... ... @@ -878,7 +874,7 @@ public:
878 874 }
879 875  
880 876 //std::cout<<"unsifted"<<std::endl;
881   - progress = 100;
  877 + //progress = 100;
882 878  
883 879 return true;
884 880 }
... ...
stim/envi/envi.h
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... ... @@ -214,7 +214,7 @@ public:
214 214 /// @param band is the band label to be output
215 215 /// @param threshold is a threshold value specified such that normalization will only be done to values in the band > threshold (preventing division by small numbers)
216 216 bool normalize(std::string outfile, double band, unsigned char* mask = NULL, bool PROGRESS = false){
217   -
  217 + header.save(outfile + ".hdr");
218 218 if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
219 219 if(header.data_type ==envi_header::float32)
220 220 return ((bsq<float>*)file)->normalize(outfile, band, mask, PROGRESS);
... ... @@ -355,17 +355,17 @@ public:
355 355 /// @param outfile is the file name for the converted output
356 356 /// @param interleave is the interleave format for the destination file
357 357 bool convert(std::string outfile, stim::envi_header::interleaveType interleave, bool PROGRESS = false){
358   -
  358 +
359 359 if(header.interleave == envi_header::BSQ){ //if the infile is bsq file
360 360  
361   - if(header.data_type ==envi_header::float32){ //if the data type of infile is float
  361 + if(header.data_type ==envi_header::float32){ //ERROR
362 362 if(interleave == envi_header::BSQ){
363 363 std::cout<<"ERROR: is already BSQ file"<<std::endl;
364 364 exit(1);
365 365 }
366   - else if(interleave == envi_header::BIL) //if the target file is bil file
367   - return ((bsq<float>*)file)->bil(outfile, PROGRESS);
368   - else if(interleave == envi_header::BIP){ //if the target file is bip file
  366 + else if(interleave == envi_header::BIL) //convert BSQ -> BIL
  367 + ((bsq<float>*)file)->bil(outfile, PROGRESS);
  368 + else if(interleave == envi_header::BIP){ //ERROR
369 369 std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
370 370 //return ((bsq<float>*)file)->bip(outfile, PROGRESS);
371 371 exit(1);
... ... @@ -373,13 +373,13 @@ public:
373 373 }
374 374  
375 375 else if(header.data_type == envi_header::float64){ //if the data type is float
376   - if(interleave == envi_header::BSQ){
  376 + if(interleave == envi_header::BSQ){ //ERROR
377 377 std::cout<<"ERROR: is already BSQ file"<<std::endl;
378 378 exit(1);
379 379 }
380   - else if(interleave == envi_header::BIL)
381   - return ((bsq<double>*)file)->bil(outfile, PROGRESS);
382   - else if(interleave == envi_header::BIP){ //if the target file is bip file
  380 + else if(interleave == envi_header::BIL) //convert BSQ -> BIL
  381 + ((bsq<double>*)file)->bil(outfile, PROGRESS);
  382 + else if(interleave == envi_header::BIP){ //ERROR
383 383 std::cout<<"ERROR: conversion from BSQ to BIP isn't practical; use BSQ->BIL->BIP instead"<<std::endl;
384 384 //return ((bsq<float>*)file)->bip(outfile, PROGRESS);
385 385 exit(1);
... ... @@ -394,26 +394,26 @@ public:
394 394  
395 395 else if(header.interleave == envi_header::BIL){
396 396  
397   - if(header.data_type ==envi_header::float32){ //if the data type of infile is float
  397 + if(header.data_type ==envi_header::float32){ //ERROR
398 398 if(interleave == envi_header::BIL){
399 399 std::cout<<"ERROR: is already BIL file"<<std::endl;
400 400 exit(1);
401 401 }
402   - else if(interleave == envi_header::BSQ) //if the target file is bsq file
403   - return ((bil<float>*)file)->bsq(outfile, PROGRESS);
404   - else if(interleave == envi_header::BIP) //if the target file is bip file
405   - return ((bil<float>*)file)->bip(outfile, PROGRESS);
  402 + else if(interleave == envi_header::BSQ) //BIL -> BSQ
  403 + ((bil<float>*)file)->bsq(outfile, PROGRESS);
  404 + else if(interleave == envi_header::BIP) //BIL -> BIP
  405 + ((bil<float>*)file)->bip(outfile, PROGRESS);
406 406 }
407 407  
408   - else if(header.data_type == envi_header::float64){ //if the data type is float
409   - if(interleave == envi_header::BIL){
  408 + else if(header.data_type == envi_header::float64){
  409 + if(interleave == envi_header::BIL){ //ERROR
410 410 std::cout<<"ERROR: is already BIL file"<<std::endl;
411 411 exit(1);
412 412 }
413   - else if(interleave == envi_header::BSQ)
414   - return ((bil<double>*)file)->bsq(outfile, PROGRESS);
415   - else if(interleave == envi_header::BIP)
416   - return ((bil<double>*)file)->bip(outfile, PROGRESS);
  413 + else if(interleave == envi_header::BSQ) //BIL -> BSQ
  414 + ((bil<double>*)file)->bsq(outfile, PROGRESS);
  415 + else if(interleave == envi_header::BIP) //BIL -> BIP
  416 + ((bil<double>*)file)->bip(outfile, PROGRESS);
417 417 }
418 418  
419 419 else{
... ... @@ -424,28 +424,28 @@ public:
424 424  
425 425 else if(header.interleave == envi_header::BIP){
426 426  
427   - if(header.data_type ==envi_header::float32){ //if the data type of infile is float
428   - if(interleave == envi_header::BIP){
  427 + if(header.data_type ==envi_header::float32){
  428 + if(interleave == envi_header::BIP){ //ERROR
429 429 std::cout<<"ERROR: is already BIP file"<<std::endl;
430 430 exit(1);
431 431 }
432   - else if(interleave == envi_header::BIL) //if the target file is bil file
433   - return ((bip<float>*)file)->bil(outfile, PROGRESS);
434   - else if(interleave == envi_header::BSQ){ //if the target file is bip file
  432 + else if(interleave == envi_header::BIL) //BIP -> BIL
  433 + ((bip<float>*)file)->bil(outfile, PROGRESS);
  434 + else if(interleave == envi_header::BSQ){ //ERROR
435 435 std::cout<<"ERROR: conversion from BIP to BSQ isn't practical; use BIP->BIL->BSQ instead"<<std::endl;
436 436 //return ((bsq<float>*)file)->bip(outfile, PROGRESS);
437 437 exit(1);
438 438 }
439 439 }
440 440  
441   - else if(header.data_type == envi_header::float64){ //if the data type is float
442   - if(interleave == envi_header::BIP){
  441 + else if(header.data_type == envi_header::float64){
  442 + if(interleave == envi_header::BIP){ //ERROR
443 443 std::cout<<"ERROR: is already BIP file"<<std::endl;
444 444 exit(1);
445 445 }
446   - else if(interleave == envi_header::BIL) //if the target file is bil file
447   - return ((bip<double>*)file)->bil(outfile, PROGRESS);
448   - else if(interleave == envi_header::BSQ){ //if the target file is bip file
  446 + else if(interleave == envi_header::BIL) //BIP -> BIL
  447 + ((bip<double>*)file)->bil(outfile, PROGRESS);
  448 + else if(interleave == envi_header::BSQ){ //ERROR
449 449 std::cout<<"ERROR: conversion from BIP to BSQ isn't practical; use BIP->BIL->BSQ instead"<<std::endl;
450 450 //return ((bsq<float>*)file)->bip(outfile, PROGRESS);
451 451 exit(1);
... ... @@ -462,7 +462,11 @@ public:
462 462 std::cout<<"ERROR: unidentified interleave type"<<std::endl;
463 463 exit(1);
464 464 }
465   - return false;
  465 + stim::envi_header h = header;
  466 + h.interleave = interleave;
  467 + h.save(outfile + ".hdr");
  468 +
  469 + return true;
466 470  
467 471 }
468 472  
... ... @@ -509,7 +513,7 @@ public:
509 513 /// @param p is memory of size X*Y containing the mask (0 = false, all other values are true)
510 514 bool apply_mask(std::string outfile, unsigned char* p)
511 515 {
512   -
  516 + header.save(outfile + ".hdr");
513 517 if (header.interleave == envi_header::BSQ){ //if the infile is bsq file
514 518 if (header.data_type == envi_header::float32)
515 519 return ((bsq<float>*)file)->apply_mask(outfile, p);
... ... @@ -630,7 +634,7 @@ public:
630 634 return false;
631 635 }
632 636  
633   - bool unsift(std::string outfile, unsigned char* mask, unsigned long long samples, unsigned long long lines){
  637 + bool unsift(std::string outfile, unsigned char* mask, unsigned long long samples, unsigned long long lines, bool PROGRESS = false){
634 638  
635 639 //create a new header
636 640 envi_header new_header = header;
... ... @@ -643,9 +647,9 @@ public:
643 647  
644 648 if (header.interleave == envi_header::BSQ){ //if the infile is bsq file
645 649 if (header.data_type == envi_header::float32)
646   - return ((bsq<float>*)file)->unsift(outfile, mask, samples, lines);
  650 + return ((bsq<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
647 651 else if (header.data_type == envi_header::float64)
648   - return ((bsq<double>*)file)->unsift(outfile, mask, samples, lines);
  652 + return ((bsq<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
649 653 else
650 654 std::cout << "ERROR: unidentified data type" << std::endl;
651 655 }
... ... @@ -658,9 +662,9 @@ public:
658 662 else if (header.interleave == envi_header::BIP){ //if the infile is bip file
659 663  
660 664 if (header.data_type == envi_header::float32)
661   - return ((bip<float>*)file)->unsift(outfile, mask, samples, lines);
  665 + return ((bip<float>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
662 666 else if (header.data_type == envi_header::float64)
663   - return ((bip<double>*)file)->unsift(outfile, mask, samples, lines);
  667 + return ((bip<double>*)file)->unsift(outfile, mask, samples, lines, PROGRESS);
664 668 else
665 669 std::cout << "ERROR: unidentified data type" << std::endl;
666 670 }
... ...
stim/envi/envi_header.h
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... ... @@ -411,6 +411,26 @@ struct envi_header
411 411 }
412 412  
413 413 }
  414 +
  415 + /// Convert an interleave type to a string
  416 + static std::string interleave_str(interleaveType t){
  417 + switch(t){
  418 + case stim::envi_header::BSQ:
  419 + return std::string("BSQ");
  420 + case stim::envi_header::BIL:
  421 + return std::string("BIL");
  422 + case stim::envi_header::BIP:
  423 + return std::string("BIP");
  424 + default:
  425 + std::cout<<"ERROR in stim::envi_header::typestr() - unrecognized type"<<std::endl;
  426 + exit(1);
  427 + }
  428 + }
  429 +
  430 + /// Convert the current interleave type to a string
  431 + std::string interleave_str(){
  432 + return interleave_str(interleave);
  433 + }
414 434 }; //end EnviHeader
415 435 }
416 436 #endif
... ...
stim/envi/hsi.h
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... ... @@ -102,6 +102,17 @@ protected:
102 102 }
103 103 return v;
104 104 }
  105 +
  106 + /// Returns the 1D on-disk index of a specified pixel location and band
  107 + size_t idx(size_t x, size_t y, size_t b){
  108 + size_t c[3]; //generate a coefficient list
  109 +
  110 + c[O[0]] = x; //assign the coordinates based on the coefficient order
  111 + c[O[1]] = y;
  112 + c[O[2]] = b;
  113 +
  114 + return c[2] * R[0] * R[1] + c[1] * R[0] + c[0]; //calculate and return the index (trust me this works)
  115 + }
105 116 };
106 117  
107 118 } //end namespace STIM
... ...
stim/image/image.h
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... ... @@ -5,6 +5,7 @@
5 5 #include <opencv2/highgui/highgui.hpp>
6 6 #include <vector>
7 7 #include <iostream>
  8 +#include <limits>
8 9  
9 10 namespace stim{
10 11 /// This static class provides the STIM interface for loading, saving, and storing 2D images.
... ... @@ -19,9 +20,9 @@ class image{
19 20 T* img; //pointer to the image data (assumes RGB for loading/saving)
20 21 size_t R[3];
21 22  
22   - size_t X(){ return R[1]; }
23   - size_t Y(){ return R[2]; }
24   - size_t C(){ return R[0]; }
  23 + size_t X() const { return R[1]; }
  24 + size_t Y() const { return R[2]; }
  25 + size_t C() const { return R[0]; }
25 26  
26 27 void init(){ //initializes all variables, assumes no memory is allocated
27 28 memset(R, 0, sizeof(size_t) * 3); //set the resolution and number of channels to zero
... ... @@ -67,40 +68,87 @@ class image{
67 68 exit(1);
68 69 }
69 70  
  71 + /// Returns the value for "white" based on the dynamic range (assumes white is 1.0 for floating point images)
  72 + T white(){
  73 + if(std::is_same<T, unsigned char>::value) return UCHAR_MAX;
  74 + if(std::is_same<T, unsigned short>::value) return SHRT_MAX;
  75 + if(std::is_same<T, unsigned>::value) return UINT_MAX;
  76 + if(std::is_same<T, unsigned long>::value) return ULONG_MAX;
  77 + if(std::is_same<T, unsigned long long>::value) return ULLONG_MAX;
  78 + if(std::is_same<T, float>::value) return 1.0f;
  79 + if(std::is_same<T, double>::value) return 1.0;
  80 +
  81 + std::cout<<"ERROR in stim::image::white - no white value known for this data type"<<std::endl;
  82 +
  83 + }
  84 +
70 85  
71 86 public:
72 87  
73   - //default constructor
  88 + /// Default constructor - creates an empty image object
74 89 image(){ init(); } //initialize all variables to zero, don't allocate any memory
75 90  
  91 + /// Constructor with a filename - loads the specified file
76 92 image(std::string filename){ //constructor initialize the image with an image file
77 93 load(filename);
78 94 }
79 95  
80 96 /// Create a new image from scratch given a number of samples and channels
81 97 image(size_t x, size_t y = 1, size_t c = 1){
82   - img = (T*) malloc( sizeof(T) * x * y * c );
  98 + allocate(x, y, c);
83 99 }
84 100  
  101 + /// Create a new image with the data given in 'data'
85 102 image(T* data, size_t x, size_t y, size_t c = 1){
86 103 allocate(x, y, c);
87 104 memcpy(img, data, bytes());
88 105 }
89 106  
  107 + /// Copy constructor - duplicates an image object
  108 + image(const stim::image<T>& I){
  109 + allocate(I.X(), I.Y(), I.C());
  110 + //allocate(I.R[1], I.R[2], I.R[0]);
  111 + memcpy(img, I.img, bytes());
  112 + }
  113 +
  114 + /// Destructor - clear memory
  115 + ~image(){
  116 + free(img);
  117 + }
  118 +
  119 + stim::image<T> operator=(const stim::image<T>& I){
  120 + if(&I == this) //handle self-assignment
  121 + return *this;
  122 + allocate(I.X(), I.Y(), I.C());
  123 + memcpy(img, I.img, bytes());
  124 + return *this;
  125 + }
  126 +
90 127 /// Load an image from a file
91 128 void load(std::string filename){
92 129  
93 130 cv::Mat cvImage = cv::imread(filename, CV_LOAD_IMAGE_UNCHANGED); //use OpenCV to open the image file
  131 + if(!cvImage.data){
  132 + std::cout<<"ERROR stim::image::load() - unable to find image "<<filename<<std::endl;
  133 + exit(1);
  134 + }
94 135 allocate(cvImage.cols, cvImage.rows, cvImage.channels()); //allocate space for the image
95 136 T* cv_ptr = (T*)cvImage.data;
96   - set_interleaved_bgr(cv_ptr, X(), Y());
  137 + if(C() == 1) //if this is a single-color image, just copy the data
  138 + memcpy(img, cv_ptr, bytes());
  139 + if(C() == 3) //if this is a 3-color image, OpenCV uses BGR interleaving
  140 + set_interleaved_bgr(cv_ptr, X(), Y());
97 141 }
98 142  
99 143 //save a file
100 144 void save(std::string filename){
101 145 //OpenCV uses an interleaved format, so convert first and then output
102 146 T* buffer = (T*) malloc(bytes());
103   - data_interleaved_bgr(buffer);
  147 +
  148 + if(C() == 1)
  149 + memcpy(buffer, img, bytes());
  150 + else if(C() == 3)
  151 + data_interleaved_bgr(buffer);
104 152 cv::Mat cvImage((int)Y(), (int)X(), cv_type(), buffer);
105 153 cv::imwrite(filename, cvImage);
106 154 }
... ... @@ -137,7 +185,7 @@ public:
137 185 image<T> channel(size_t c){
138 186  
139 187 //create a new image
140   - image<T> r(R[0], R[1], 1);
  188 + image<T> r(X(), Y(), 1);
141 189  
142 190 for(size_t x = 0; x < X(); x++){
143 191 for(size_t y = 0; y < Y(); y++){
... ... @@ -266,6 +314,16 @@ public:
266 314 return max;
267 315 }
268 316  
  317 + /// Invert an image by calculating I1 = alpha - I0, where alpha is the maximum image value
  318 + image<T> invert(T white_val){
  319 + size_t N = size(); //calculate the total number of values in the image
  320 + image<T> r(X(), Y(), C()); //allocate space for the resulting image
  321 + for(size_t n = 0; n < N; n++)
  322 + r.img[n] = white_val - img[n]; //perform the inversion
  323 +
  324 + return r; //return the inverted image
  325 + }
  326 +
269 327 image<T> srgb2lab(){
270 328 std::cout<<"ERROR stim::image::srgb2lab - function has been broken, re-implement."<<std::endl;
271 329 exit(1);
... ...
stim/parser/arguments.h
  Show/Hide comments   View file @a2bf1d0
... ... @@ -82,7 +82,7 @@ namespace stim{
82 82 }
83 83  
84 84 //return the value of a text option
85   - std::string as_string(unsigned int n = 0)
  85 + std::string as_string(size_t n = 0)
86 86 {
87 87 if(!flag)
88 88 {
... ... @@ -97,7 +97,7 @@ namespace stim{
97 97 }
98 98  
99 99 //return the value of a floating point option
100   - float as_float(unsigned int n = 0)
  100 + float as_float(size_t n = 0)
101 101 {
102 102 if(!flag)
103 103 {
... ... @@ -116,7 +116,7 @@ namespace stim{
116 116 }
117 117  
118 118 //return the value of an integer option
119   - int as_int(unsigned int n = 0)
  119 + int as_int(size_t n = 0)
120 120 {
121 121 if(!flag)
122 122 {
... ...
stim/parser/filename.h
  Show/Hide comments   View file @a2bf1d0
... ... @@ -299,9 +299,9 @@ public:
299 299 stim::filename result = *this; //initialize the result filename to the current filename
300 300 size_t loc = result.prefix.find('*'); //find a wild card in the string
301 301 if(loc == std::string::npos) //if a wildcard isn't found
302   - return result; //return the original string
303   -
304   - result.prefix.replace(loc, 1, str); //replace the wildcard with the string
  302 + result.prefix += str; //append the value to the prefix
  303 + else
  304 + result.prefix.replace(loc, 1, str); //replace the wildcard with the string
305 305 return result; //return the result
306 306 }
307 307  
... ...
stim/visualization/colormap.h
  Show/Hide comments   View file @a2bf1d0
... ... @@ -3,6 +3,12 @@
3 3  
4 4 #include <string>
5 5 #include <stdlib.h>
  6 +#include <cmath>
  7 +
  8 +#ifdef _WIN32
  9 + #include <float.h>
  10 +#endif
  11 +
6 12 #ifdef __CUDACC__
7 13 #include <stim/cuda/cudatools/error.h>
8 14 #endif
... ... @@ -226,8 +232,13 @@ static void cpuApplyBrewer(T* cpuSource, unsigned char* cpuDest, size_t N, T min
226 232 a = (cpuSource[i] - minVal) / (maxVal - minVal);
227 233 else
228 234 a = 0.5;
229   - if(a < 0) a = 0;
230   - if(a > 1) a = 1;
  235 +#ifdef _WIN32
  236 + if(!_finite(a)) a = 1; //deal with infinite and NaN values (return maximum in all cases)
  237 +#else
  238 + if(!std::isfinite(a)) a = 1;
  239 +#endif
  240 + else if(a < 0) a = 0;
  241 + else if(a > 1) a = 1;
231 242  
232 243 float c = a * (float)(BREWER_CTRL_PTS-1);
233 244 int ptLow = (int)c;
... ...