c9aba18a
Laila Saadatifard
ivote3 on the GPU...
|
1
|
#include <iostream>
|
46820b25
Laila Saadatifard
create an obj fil...
|
2
|
#include <string>
|
c9aba18a
Laila Saadatifard
ivote3 on the GPU...
|
3
|
#include <fstream>
|
c9aba18a
Laila Saadatifard
ivote3 on the GPU...
|
4
5
6
7
|
#include <cuda_runtime.h>
#include <stim/math/vector.h>
#include <stim/parser/arguments.h>
#include <stim/parser/filename.h>
|
c9aba18a
Laila Saadatifard
ivote3 on the GPU...
|
8
|
#include <stim/visualization/colormap.h>
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
9
|
#include <stim/image/image.h>
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
10
|
#include <stim/math/constants.h>
|
c9aba18a
Laila Saadatifard
ivote3 on the GPU...
|
11
|
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
12
13
14
15
16
17
18
19
|
stim::arglist args;
int iter;
unsigned int rmax;
unsigned int nlmax;
float t;
float sigma;
float phi;
size_t x, y, z;
|
1f55a874
Laila Saadatifard
upload the fixed ...
|
20
|
|
a744d027
Laila Saadatifard
upload the ivote3...
|
21
|
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
22
|
void ivote3(float* img, float std[], float phi, float d_phi, unsigned int r[], int iter, float t, unsigned int conn[],
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
23
|
unsigned int x, unsigned int y, unsigned int z);
|
46820b25
Laila Saadatifard
create an obj fil...
|
24
|
void lmax(float* center, float* vote, float t1, unsigned int conn[], unsigned int x, unsigned int y, unsigned int z);
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
25
26
27
28
29
30
31
32
33
34
35
|
void invert_data(float* cpuI, unsigned int x, unsigned int y, unsigned int z){
for(int ix = 0; ix < x; ix++){
for (int iy = 0; iy < y; iy++){
for (int iz = 0; iz < z; iz++){
int idx = iz * x * y + iy * x + ix;
cpuI[idx] = 255 - cpuI[idx];
}
}
}
}
|
94d437dd
Laila Saadatifard
ivote3 code compi...
|
36
|
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
37
|
|
94d437dd
Laila Saadatifard
ivote3 code compi...
|
38
|
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
39
40
41
42
43
44
45
46
|
void advertise() {
std::cout << std::endl << std::endl;
std::cout << "=========================================================================" << std::endl;
std::cout << "Thank you for using the ivote3 segmentation tool!" << std::endl;
std::cout << "Scalable Tissue Imaging and Modeling (STIM) Lab, University of Houston" << std::endl;
std::cout << "Developers: Laila Saadatifard and David Mayerich" << std::endl;
std::cout << "Source: https://git.stim.ee.uh.edu/segmentation/ivote3" << std::endl;
std::cout << "=========================================================================" << std::endl << std::endl;
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
47
|
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
48
|
}
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
49
|
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
50
|
void init_args(int argc, char* argv[]) {
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
51
52
53
54
55
56
57
58
59
60
|
#ifdef _WIN32
args.set_ansi(false);
#endif
//add arduments
args.add("help", "prints this help");
args.add("x", "size of the dataset along X axis", "positive value");
args.add("y", "size of the dataset along Y axis", "positive value");
args.add("z", "size of the dataset along Z axis", "positive value");
args.add("t", "threshold value for the final result", "positive valu");
|
94d437dd
Laila Saadatifard
ivote3 code compi...
|
61
|
args.add("invert", "to invert the input data set", "string");
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
62
63
64
65
66
|
args.add("rmax", "maximum possible radius of the cells in the input image", "10", "[positive value]");
args.add("phi", "starting angle for the vote region (in degrees)", "25.0", "0 <= phi < 180");
args.add("iter", "number of iterations for voting", "8", "i > 0");
args.add("sigma", "the gaussian blur standard deviation", "5", "s >=0 (s = 0, no blurring)");
args.add("conn", "the number of connected neighbors for calculating the local maxima", "5", "[positive value]");
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
67
68
69
70
|
//parse the command line arguments.
args.parse(argc, argv);
//display the help text if requested
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
71
72
73
74
75
76
77
78
|
if (args["help"].is_set()) {
advertise();
std::cout << std::endl << "usage: ivote input_image output_list --option [A B C ...]" << std::endl;
std::cout << std::endl << std::endl
<< "examples: ivote blue.bmp list.txt " << std::endl;
std::cout << std::endl << std::endl;
std::cout << args.str() << std::endl;
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
79
80
81
82
|
exit(1);
}
//if the input and output files aren't specified, throw an error and exit
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
83
84
|
if (args.nargs() < 3) {
std::cout << "ERROR: three files must be specified for segmentation, enter ivote --help for options." << std::endl << std::endl;
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
85
86
87
|
exit(1);
}
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
88
89
90
91
92
93
94
95
96
97
98
99
100
|
//set the x, y, z.
x = (size_t)args["x"].as_int();
y = (size_t)args["y"].as_int();
z = (size_t)args["z"].as_int();
iter = args["iter"].as_int();
rmax = (unsigned int)args["rmax"].as_int();
nlmax = (unsigned int)args["conn"].as_int();
t = args["t"].as_float();
sigma = args["sigma"].as_float();
phi = (float)args["phi"].as_float() * (float)stim::PI / 180;
}
int main(int argc, char** argv){
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
101
|
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
102
|
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
103
104
105
106
107
108
109
110
111
112
113
114
|
cudaDeviceProp prop;
int count;
cudaGetDeviceCount(&count);
for (int i=0; i<count; i++){
cudaGetDeviceProperties(&prop, i);
printf("current device ID: %d\n", i);
printf("device name: %s\n", prop.name);
printf("total global mem: %lu\n", prop.totalGlobalMem);
printf("shared memory per block: %lu\n", prop.sharedMemPerBlock);
}
init_args(argc, argv);
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
115
|
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
116
117
118
|
unsigned int r[3] = { rmax , rmax, rmax};
float sigma3[3] = { sigma, sigma, sigma};
|
94d437dd
Laila Saadatifard
ivote3 code compi...
|
119
|
unsigned int conn[3] = { nlmax, nlmax, nlmax};
|
94d437dd
Laila Saadatifard
ivote3 code compi...
|
120
|
float d_phi = phi/(iter+2);
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
121
|
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
122
|
size_t bytes = x*y*z*sizeof(float);
|
c9aba18a
Laila Saadatifard
ivote3 on the GPU...
|
123
|
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
124
|
//allocate space on the cpu for the input data
|
c9aba18a
Laila Saadatifard
ivote3 on the GPU...
|
125
126
|
float* cpuI = (float*) malloc(bytes);
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
127
|
//load the input file into the cpuI
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
128
|
std::ifstream nissl(args.arg(0), std::ios::in | std::ios::binary);
|
c9aba18a
Laila Saadatifard
ivote3 on the GPU...
|
129
130
|
nissl.read((char*)cpuI, bytes);
nissl.close();
|
94d437dd
Laila Saadatifard
ivote3 code compi...
|
131
132
|
if(args["invert"].is_set())
invert_data(cpuI, x, y, z);
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
133
134
|
//write a new file from the cpuI.
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
135
|
std::ofstream original("0-inv-128.vol", std::ofstream::out | std::ofstream::binary);
|
c9aba18a
Laila Saadatifard
ivote3 on the GPU...
|
136
137
|
original.write((char*)cpuI, bytes);
original.close();
|
c9aba18a
Laila Saadatifard
ivote3 on the GPU...
|
138
|
|
a744d027
Laila Saadatifard
upload the ivote3...
|
139
|
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
140
141
142
143
144
|
ivote3(cpuI, sigma3, phi, d_phi, r, iter, t, conn, x, y, z); // call the ivote function
std::ofstream fvote("0-vote8.vol", std::ofstream::out | std::ofstream::binary);
fvote.write((char*)cpuI, bytes);
fvote.close();
|
a744d027
Laila Saadatifard
upload the ivote3...
|
145
|
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
146
147
148
|
//allocate space on the cpu for the output result
float* cpu_out = (float*)malloc(bytes * 3);
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
149
|
//write the output file.
|
a744d027
Laila Saadatifard
upload the ivote3...
|
150
151
|
//for (int t0=0; t0<=5000; t0+=100){
// float t1 = t0;
|
46820b25
Laila Saadatifard
create an obj fil...
|
152
153
154
|
int t0 = t;
lmax(cpu_out, cpuI, t, conn, x, y, z);
//std::ofstream fo("shared2D-v8/" + OutName.str(), std::ofstream::out | std::ofstream::binary);
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
155
|
std::ofstream fo( args.arg(1), std::ofstream::out | std::ofstream::binary);
|
46820b25
Laila Saadatifard
create an obj fil...
|
156
157
|
fo.write((char*)cpu_out, bytes);
fo.close();
|
c9aba18a
Laila Saadatifard
ivote3 on the GPU...
|
158
|
|
94d437dd
Laila Saadatifard
ivote3 code compi...
|
159
|
// creat a file for saving the list centers
|
46820b25
Laila Saadatifard
create an obj fil...
|
160
|
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
161
|
std::ofstream list(args.arg(2));
|
3f0e43ce
Laila Saadatifard
compute the local...
|
162
163
164
165
166
167
168
169
170
171
172
|
// set the number of detected cells to zero.
int nod = 0;
if (list.is_open()){
for (int iz=0; iz<z; iz++){
for (int iy=0; iy<y; iy++){
for (int ix=0; ix<x; ix++){
int idx = iz * x * y + iy * x + ix;
if (cpu_out[idx]>0){
nod++;
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
173
|
list << ix << " " << iy << " "<< iz << " " << cpu_out[idx] << '\n' ;
|
3f0e43ce
Laila Saadatifard
compute the local...
|
174
175
176
177
178
|
}
}
}
}
|
2558ee86
Laila Saadatifard
updating ivote3 t...
|
179
|
|
3f0e43ce
Laila Saadatifard
compute the local...
|
180
181
182
183
|
list.close();
}
|
a744d027
Laila Saadatifard
upload the ivote3...
|
184
|
//}
|
f12505fb
Laila Saadatifard
upload the ivote ...
|
185
|
cudaDeviceReset();
|
c9aba18a
Laila Saadatifard
ivote3 on the GPU...
|
186
|
|
c9aba18a
Laila Saadatifard
ivote3 on the GPU...
|
187
|
}
|