codebase / stimlib

Commit c5da629063f64c2f67ca26e8a87758c2d582997a

Authored by David Mayerich
2 parents 904614c3 fba6e7e3

Merge branch 'master' of git.stim.ee.uh.edu:codebase/stimlib

Showing 3 changed files with 92 additions and 21 deletions   Show diff stats
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stim/gl/gl_spider.h
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... ... @@ -140,7 +140,7 @@ class gl_spider : public virtual gl_texture<T>
140 140 setMatrix(); //create the transformation matrix.
141 141 glCallList(dList+1); //move the templates to p, d, m.
142 142 int best = getCost(ptexbufferID, numSamplesPos); //find min cost.
143   - std::cerr << best << std::endl;
  143 +// std::cerr << best << std::endl;
144 144 stim::vec<float> next( //find next position.
145 145 pV[best][0],
146 146 pV[best][1],
... ...
stim/grids/image_stack.h
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1 1 #ifndef STIM_IMAGE_STACK_H
2 2 #define STIM_IMAGE_STACK_H
3 3  
4   -#include "../parser/wildcards.h"
5   -#include "../parser/filename.h"
6   -#include "../grids/grid.h"
7   -#include "../image/image.h"
  4 +#include <stim/parser/wildcards.h>
  5 +#include <stim/parser/filename.h>
  6 +#include <stim/grids/grid.h>
  7 +#include <stim/image/image.h>
8 8  
9 9 namespace stim{
10 10  
... ... @@ -48,7 +48,7 @@ public:
48 48 }
49 49  
50 50 //load the first image and set all of the image_stack properties
51   - std::cout<<"File to Load: "<<file_list[0].str()<<std::endl;
  51 +// std::cout<<"File to Load: "<<file_list[0].str()<<std::endl;
52 52 stim::image<T> I(file_list[0].str());
53 53  
54 54 //set the image resolution and number of channels
... ... @@ -63,7 +63,7 @@ public:
63 63 //load and copy each image into the grid
64 64 for(unsigned int i = 0; i<R[3]; i++){
65 65  
66   - std::cout<<"File to Load: "<<file_list[i].str()<<std::endl;
  66 +// std::cout<<"File to Load: "<<file_list[i].str()<<std::endl;
67 67 //load the image
68 68 stim::image<T> I(file_list[i].str());
69 69  
... ... @@ -73,8 +73,15 @@ public:
73 73 }
74 74 }
75 75  
76   - ///Saves a single page to an image file
  76 + ///Inserts image I into slot i.
  77 + /// @param stim::image<T> I; image to insert.
  78 + /// @int I, where to place the image.
  79 + void insert_image(stim::image<T> I, int i)
  80 + {
  81 + I.get_interleaved_rgb(&ptr[i *R[0] *R[1] *R[2] ]);
  82 + }
77 83  
  84 + ///Saves a single page to an image file
78 85 /// @param file_name is the name of the image file to be created
79 86 /// @param i is the page to be saved
80 87 void save_image(std::string file_name, unsigned int i){
... ... @@ -83,10 +90,11 @@ public:
83 90 stim::image<T> I;
84 91  
85 92 //retrieve the interlaced data from the image - store it in the grid
86   - I.set_interleaved(&ptr[ i * R[0] * R[1] * R[2] ], R[1], R[2], R[0]);
  93 + I.set_interleaved_rgb(&ptr[ i * R[0] * R[1] * R[2] ], R[1], R[2], R[0]);
87 94  
88 95 I.save(file_name);
89 96 }
  97 +
90 98 ///Sets the dimensions of the image in each direction
91 99 ///Voxel-size.
92 100 /// @param x size in the x direction
... ... @@ -100,8 +108,24 @@ public:
100 108 S[2] = y;
101 109 S[3] = z;
102 110 }
103   - ///Saves the entire stack to a set of images
104 111  
  112 + ///set dimensions of the grid.
  113 + /// @param channels, number of channels in each image.
  114 + /// @param width, number of pixels in width each image.
  115 + /// @param height, number of pixels in height.
  116 + /// @param depth, number of pixels in depth.
  117 + void init(int channels, int width, int height, int depth)
  118 + {
  119 + R.resize(4);
  120 + R[0] = channels;
  121 + R[1] = width;
  122 + R[2] = height;
  123 + R[3] = depth;
  124 +
  125 + ptr = (T*)malloc(sizeof(T) * samples());
  126 + }
  127 +
  128 + ///Saves the entire stack to a set of images
105 129 /// @param file_mask is the mask describing how the file names will be saved (ex. image????.bmp)
106 130 void save_images(std::string file_mask){
107 131  
... ...
stim/image/image.h
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... ... @@ -24,6 +24,8 @@ class image{
24 24 size_t Y() const { return R[2]; }
25 25 size_t C() const { return R[0]; }
26 26  
  27 + size_t bytes(){ return size() * sizeof(T); }
  28 +
27 29 void init(){ //initializes all variables, assumes no memory is allocated
28 30 memset(R, 0, sizeof(size_t) * 3); //set the resolution and number of channels to zero
29 31 img = NULL;
... ... @@ -31,6 +33,8 @@ class image{
31 33  
32 34 void unalloc(){ //frees any resources associated with the image
33 35 if(img) free(img); //if memory has been allocated, free it
  36 + img=NULL;
  37 +
34 38 }
35 39  
36 40  
... ... @@ -40,15 +44,17 @@ class image{
40 44 }
41 45  
42 46 void allocate(){
43   - img = (T*) malloc( sizeof(T) * R[0] * R[1] * R[2] ); //allocate memory
  47 + unalloc();
  48 + img = (T*) malloc( bytes() ); //allocate memory
  49 + memset(img, 0, bytes());
44 50 }
45 51  
46 52 void allocate(size_t x, size_t y, size_t c){ //allocate memory based on the resolution
  53 + unalloc();
47 54 R[0] = c; R[1] = x; R[2] = y; //set the resolution
48 55 allocate(); //allocate memory
49 56 }
50 57  
51   - size_t bytes(){ return size() * sizeof(T); }
52 58  
53 59 size_t idx(size_t x, size_t y, size_t c = 0){
54 60 return y * C() * X() + x * C() + c;
... ... @@ -90,24 +96,27 @@ public:
90 96  
91 97 /// Constructor with a filename - loads the specified file
92 98 image(std::string filename){ //constructor initialize the image with an image file
  99 + init();
93 100 load(filename);
94 101 }
95 102  
96 103 /// Create a new image from scratch given a number of samples and channels
97 104 image(size_t x, size_t y = 1, size_t c = 1){
  105 + init();
98 106 allocate(x, y, c);
99 107 }
100 108  
101 109 /// Create a new image with the data given in 'data'
102 110 image(T* data, size_t x, size_t y, size_t c = 1){
  111 + init();
103 112 allocate(x, y, c);
104 113 memcpy(img, data, bytes());
105 114 }
106 115  
107 116 /// Copy constructor - duplicates an image object
108 117 image(const stim::image<T>& I){
  118 + init();
109 119 allocate(I.X(), I.Y(), I.C());
110   - //allocate(I.R[1], I.R[2], I.R[0]);
111 120 memcpy(img, I.img, bytes());
112 121 }
113 122  
... ... @@ -133,11 +142,18 @@ public:
133 142 exit(1);
134 143 }
135 144 allocate(cvImage.cols, cvImage.rows, cvImage.channels()); //allocate space for the image
136   - T* cv_ptr = (T*)cvImage.data;
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
  145 + T* cv_ptr = (T*) cvImage.data;
  146 + if(C() == 1)
  147 + {
  148 + //if this is a single-color image, just copy the data
  149 + memcpy(img, cv_ptr, bytes());
  150 + }
  151 + if(C() == 3)
  152 + { //if this is a 3-color image, OpenCV uses BGR interleaving
140 153 set_interleaved_bgr(cv_ptr, X(), Y());
  154 + }
  155 +
  156 + cvImage.release();
141 157 }
142 158  
143 159 //save a file
... ... @@ -151,16 +167,18 @@ public:
151 167 get_interleaved_bgr(buffer);
152 168 cv::Mat cvImage((int)Y(), (int)X(), cv_type(), buffer);
153 169 cv::imwrite(filename, cvImage);
  170 + cvImage.release();
  171 + free(buffer);
154 172 }
155 173  
156 174 //create an image from an interleaved buffer
157   - void set_interleaved_rgb(T* buffer, size_t width, size_t height){
158   - allocate(width, height, 3);
  175 + void set_interleaved_rgb(T* buffer, size_t width, size_t height, size_t channels = 3){
  176 + allocate(width, height, channels);
159 177 memcpy(img, buffer, bytes());
160 178 }
161 179  
162   - void set_interleaved_bgr(T* buffer, size_t width, size_t height){
163   - allocate(width, height, 3);
  180 + void set_interleaved_bgr(T* buffer, size_t width, size_t height, size_t channels = 3){
  181 + allocate(width, height, channels);
164 182 for(size_t c = 0; c < C(); c++){ //copy directly
165 183 for(size_t y = 0; y < Y(); y++){
166 184 for(size_t x = 0; x < X(); x++){
... ... @@ -340,6 +358,34 @@ public:
340 358  
341 359 return r; //return the inverted image
342 360 }
  361 +
  362 + /// Invert an image by calculating I1 = alpha - I0, where alpha is the maximum image value
  363 + image<T> invert(){
  364 + size_t N = size(); //calculate the total number of values in the image
  365 + image<T> r(X(), Y(), C()); //allocate space for the resulting image
  366 + T white_val = maxv();
  367 + for(size_t n = 0; n < N; n++)
  368 + r.img[n] = white_val - img[n]; //perform the inversion
  369 +
  370 + return r; //return the inverted image
  371 + }
  372 +
  373 + ///crops the image from x1 to x0 and y1 to y0 and returns a new (smaller) image.
  374 + image<T> crop(int x0, int x1, int y0, int y1)
  375 + {
  376 +
  377 + image<T> ret(x1-x0, y1-y0, C());
  378 + int newWidth = x1-x0;
  379 + int destidx, srcidx;
  380 + ///for each row, cut what amount of data from the original and put it into the new copy.
  381 + for(int i = 0; i < (y1-y0); i++)
  382 + {
  383 + destidx = i*newWidth*C(); ///destination index one per each row
  384 + srcidx = ((i+(y0))*X()+x0)*C(); ///source index, one per each row.
  385 + memcpy(&ret.img[destidx], &img[srcidx], sizeof(T)*newWidth*C());
  386 + }
  387 + return ret;
  388 + }
343 389  
344 390 image<T> srgb2lab(){
345 391 std::cout<<"ERROR stim::image::srgb2lab - function has been broken, re-implement."<<std::endl;
... ... @@ -358,6 +404,7 @@ public:
358 404 exit(1);
359 405 }
360 406  
  407 +
361 408 // leila's code for non_interleaving data in 3D
362 409 //create an data set from an interleaved buffer
363 410 void set_interleaved3(T* buffer, size_t width, size_t height, size_t depth, size_t channels = 3){
... ...