e8eb202f
David Mayerich
added a new ENVI ...
|
1
2
3
4
|
#ifndef STIM_BSQ_H
#define STIM_BSQ_H
#include "../envi/envi_header.h"
|
3fc1d461
heziqi
Ziqi added saveBa...
|
5
|
#include "../envi/binary.h"
|
e8eb202f
David Mayerich
added a new ENVI ...
|
6
|
#include "../envi/bil.h"
|
fc712213
David Mayerich
code simplifications
|
7
8
|
#include <cstring>
#include <utility>
|
e8eb202f
David Mayerich
added a new ENVI ...
|
9
|
#include <vector>
|
3fc1d461
heziqi
Ziqi added saveBa...
|
10
|
|
77060b79
David Mayerich
started DOxygen d...
|
11
12
|
|
8a86bd56
David Mayerich
changed rts names...
|
13
|
namespace stim{
|
3fc1d461
heziqi
Ziqi added saveBa...
|
14
|
|
77060b79
David Mayerich
started DOxygen d...
|
15
16
17
18
19
20
21
22
|
/**
The BIP class represents a 3-dimensional binary file stored using band sequential (BSQ) image encoding. The binary file is stored
such that X-Y "frames" are stored sequentially to form an image stack along the z-axis. When accessing the data sequentially on disk,
the dimensions read, from fastest to slowest, are X, Y, Z.
This class is optimized for data streaming, and therefore supports extremely large (terabyte-scale) files. Data is loaded from disk
on request. Functions used to access data are written to support efficient reading.
*/
|
3fc1d461
heziqi
Ziqi added saveBa...
|
23
24
25
26
|
template <typename T>
class bsq: public binary<T> {
|
77060b79
David Mayerich
started DOxygen d...
|
27
|
|
3fc1d461
heziqi
Ziqi added saveBa...
|
28
29
|
protected:
|
e8eb202f
David Mayerich
added a new ENVI ...
|
30
|
std::vector<double> w; //band wavelengths
|
6708cc25
heziqi
Ziqi added envi c...
|
31
|
unsigned int offset;
|
3fc1d461
heziqi
Ziqi added saveBa...
|
32
|
|
3fc1d461
heziqi
Ziqi added saveBa...
|
33
34
|
public:
|
fc712213
David Mayerich
code simplifications
|
35
36
|
using binary<T>::open;
using binary<T>::file;
|
32504c2c
David Mayerich
fixed some functi...
|
37
|
//using binary<T>::getSlice;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
38
|
using binary<T>::R;
|
fc712213
David Mayerich
code simplifications
|
39
|
|
a08c98c3
David Mayerich
finished document...
|
40
|
/// Open a data file for reading using the class interface.
|
77060b79
David Mayerich
started DOxygen d...
|
41
42
43
44
45
46
47
|
/// @param filename is the name of the binary file on disk
/// @param X is the number of samples along dimension 1
/// @param Y is the number of samples (lines) along dimension 2
/// @param B is the number of samples (bands) along dimension 3
/// @param header_offset is the number of bytes (if any) in the binary header
/// @param wavelengths is an optional STL vector of size B specifying a numerical label for each band
|
e8eb202f
David Mayerich
added a new ENVI ...
|
48
|
bool open(std::string filename, unsigned int X, unsigned int Y, unsigned int B, unsigned int header_offset, std::vector<double> wavelengths){
|
3fc1d461
heziqi
Ziqi added saveBa...
|
49
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
50
51
|
//copy the wavelengths to the BSQ file structure
w = wavelengths;
|
6708cc25
heziqi
Ziqi added envi c...
|
52
53
|
//copy the wavelengths to the structure
offset = header_offset;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
54
55
|
return open(filename, vec<unsigned int>(X, Y, B), header_offset);
|
3fc1d461
heziqi
Ziqi added saveBa...
|
56
57
58
|
}
|
a08c98c3
David Mayerich
finished document...
|
59
|
/// Retrieve a single band (based on index) and stores it in pre-allocated memory.
|
77060b79
David Mayerich
started DOxygen d...
|
60
61
62
|
/// @param p is a pointer to an allocated region of memory at least X * Y * sizeof(T) in size.
/// @param page <= B is the integer number of the band to be copied.
|
0e48cc9c
heziqi
Ziqi added getBan...
|
63
|
bool band_index( T * p, unsigned int page){
|
3fc1d461
heziqi
Ziqi added saveBa...
|
64
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
65
|
if (page >= R[2]){ //make sure the bank number is right
|
3fc1d461
heziqi
Ziqi added saveBa...
|
66
67
68
|
std::cout<<"ERROR: page out of range"<<std::endl;
return false;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
69
|
//move the file pointer to the start of the page on disk
|
193ff00e
David Mayerich
dealth with preci...
|
70
|
file.seekg(R[0] * R[1] * page * sizeof(T));
|
a23c4132
David Mayerich
Doxygen comments ...
|
71
|
//read the page from disk
|
70407ea9
heziqi
Ziqi completed he...
|
72
73
|
file.read((char *)p, sizeof(T) * R[0] * R[1]);
|
3fc1d461
heziqi
Ziqi added saveBa...
|
74
75
76
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
77
|
/// Retrieve a single band (by numerical label) and stores it in pre-allocated memory.
|
77060b79
David Mayerich
started DOxygen d...
|
78
79
80
|
/// @param p is a pointer to an allocated region of memory at least X * Y * sizeof(T) in size.
/// @param wavelength is a floating point value (usually a wavelength in spectral data) used as a label for the band to be copied.
|
e933c14e
David Mayerich
cleaned up the code
|
81
|
bool band( T * p, double wavelength){
|
0e48cc9c
heziqi
Ziqi added getBan...
|
82
|
|
ee4dea28
David Mayerich
fixed errors in c...
|
83
84
85
|
//if there are no wavelengths in the BSQ file
if(w.size() == 0)
return band_index(p, (unsigned int)wavelength);
|
0e48cc9c
heziqi
Ziqi added getBan...
|
86
|
|
ee4dea28
David Mayerich
fixed errors in c...
|
87
|
unsigned int XY = R[0] * R[1]; //calculate the number of pixels in a band
|
ebe94c9d
David Mayerich
modified comments
|
88
|
unsigned page = 0;
|
517876d6
heziqi
metrics finished ...
|
89
|
|
0e48cc9c
heziqi
Ziqi added getBan...
|
90
|
|
ebe94c9d
David Mayerich
modified comments
|
91
|
//get the two neighboring bands (above and below 'wavelength')
|
0e48cc9c
heziqi
Ziqi added getBan...
|
92
93
|
//if wavelength is smaller than the first one in header file
|
e8eb202f
David Mayerich
added a new ENVI ...
|
94
|
if ( w[page] > wavelength ){
|
0e48cc9c
heziqi
Ziqi added getBan...
|
95
96
97
98
|
band_index(p, page);
return true;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
99
|
while( w[page] < wavelength )
|
0e48cc9c
heziqi
Ziqi added getBan...
|
100
101
|
{
page++;
|
ebe94c9d
David Mayerich
modified comments
|
102
103
|
//if wavelength is larger than the last wavelength in the header file
// (the wavelength is out of bounds)
|
e8eb202f
David Mayerich
added a new ENVI ...
|
104
|
if (page == R[2]) {
|
ebe94c9d
David Mayerich
modified comments
|
105
|
band_index(p, R[2]-1); //return the last band
|
0e48cc9c
heziqi
Ziqi added getBan...
|
106
107
108
|
return true;
}
}
|
ebe94c9d
David Mayerich
modified comments
|
109
110
|
//when the page counter points to the first band above 'wavelength'
if ( wavelength < w[page] ){
|
193ff00e
David Mayerich
dealth with preci...
|
111
|
|
ebe94c9d
David Mayerich
modified comments
|
112
|
//do the interpolation
|
517876d6
heziqi
metrics finished ...
|
113
114
|
T * p1;
T * p2;
|
0e48cc9c
heziqi
Ziqi added getBan...
|
115
116
117
118
119
|
p1=(T*)malloc( XY * sizeof(T)); //memory allocation
p2=(T*)malloc( XY * sizeof(T));
band_index(p1, page - 1);
band_index(p2, page );
for(unsigned i=0; i < XY; i++){
|
e8eb202f
David Mayerich
added a new ENVI ...
|
120
|
double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
|
0e48cc9c
heziqi
Ziqi added getBan...
|
121
122
|
p[i] = (p2[i] - p1[i]) * r + p1[i];
}
|
517876d6
heziqi
metrics finished ...
|
123
124
|
free(p1);
free(p2);
|
0e48cc9c
heziqi
Ziqi added getBan...
|
125
|
}
|
ebe94c9d
David Mayerich
modified comments
|
126
127
128
|
//if the wavelength is equal to a wavelength in header file
else{
band_index(p, page); //return the band
|
0e48cc9c
heziqi
Ziqi added getBan...
|
129
130
|
}
|
0e48cc9c
heziqi
Ziqi added getBan...
|
131
132
133
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
134
|
/// Retrieve a single spectrum (B-axis line) at a given (x, y) location and stores it in pre-allocated memory.
|
77060b79
David Mayerich
started DOxygen d...
|
135
136
137
138
|
/// @param p is a pointer to pre-allocated memory at least B * sizeof(T) in size.
/// @param x is the x-coordinate (dimension 1) of the spectrum.
/// @param y is the y-coordinate (dimension 2) of the spectrum.
|
e933c14e
David Mayerich
cleaned up the code
|
139
|
bool spectrum(T * p, unsigned x, unsigned y){
|
3fc1d461
heziqi
Ziqi added saveBa...
|
140
141
142
|
unsigned int i;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
143
|
if ( x >= R[0] || y >= R[1]){ //make sure the sample and line number is right
|
3fc1d461
heziqi
Ziqi added saveBa...
|
144
145
146
147
|
std::cout<<"ERROR: sample or line out of range"<<std::endl;
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
148
|
file.seekg((x + y * R[0]) * sizeof(T), std::ios::beg); //point to the certain sample and line
|
bfe9c6db
heziqi
added feature_mat...
|
149
|
for (i = 0; i < R[2]; i++)
|
3fc1d461
heziqi
Ziqi added saveBa...
|
150
151
|
{
file.read((char *)(p + i), sizeof(T));
|
e8eb202f
David Mayerich
added a new ENVI ...
|
152
|
file.seekg((R[1] * R[0] - 1) * sizeof(T), std::ios::cur); //go to the next band
|
3fc1d461
heziqi
Ziqi added saveBa...
|
153
154
|
}
|
3fc1d461
heziqi
Ziqi added saveBa...
|
155
156
|
return true;
}
|
f0d5a769
heziqi
Ziqi changed the ...
|
157
|
|
a08c98c3
David Mayerich
finished document...
|
158
|
/// Retrieve a single pixel and stores it in pre-allocated memory.
|
77060b79
David Mayerich
started DOxygen d...
|
159
160
161
|
/// @param p is a pointer to pre-allocated memory at least sizeof(T) in size.
/// @param n is an integer index to the pixel using linear array indexing.
|
bfe9c6db
heziqi
added feature_mat...
|
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
|
bool pixel(T * p, unsigned n){
unsigned bandnum = R[0] * R[1]; //calculate numbers in one band
if ( n >= bandnum){ //make sure the pixel number is right
std::cout<<"ERROR: sample or line out of range"<<std::endl;
return false;
}
file.seekg(n * sizeof(T), std::ios::beg); //point to the certain pixel
for (unsigned i = 0; i < R[2]; i++)
{
file.read((char *)(p + i), sizeof(T));
file.seekg((bandnum - 1) * sizeof(T), std::ios::cur); //go to the next band
}
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
180
|
/// Perform baseline correction given a list of baseline points and stores the result in a new BSQ file.
|
77060b79
David Mayerich
started DOxygen d...
|
181
182
183
|
/// @param outname is the name of the output file used to store the resulting baseline-corrected data.
/// @param wls is the list of baseline points based on band labels.
|
f0d5a769
heziqi
Ziqi changed the ...
|
184
185
186
|
bool baseline(std::string outname, std::vector<double> wls )
{
unsigned N = wls.size(); //get the number of baseline points
|
31394e2a
heziqi
Ziqi added method...
|
187
|
|
f0d5a769
heziqi
Ziqi changed the ...
|
188
|
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
|
0c748c81
heziqi
Ziqi added save h...
|
189
|
std::string headername = outname + ".hdr"; //the header file name
|
f0d5a769
heziqi
Ziqi changed the ...
|
190
191
|
//simplify image resolution
|
e8eb202f
David Mayerich
added a new ENVI ...
|
192
193
|
unsigned int B = R[2]; //calculate the number of bands
unsigned int XY = R[0] * R[1]; //calculate the number of pixels in a band
|
f0d5a769
heziqi
Ziqi changed the ...
|
194
195
196
197
|
unsigned int S = XY * sizeof(T); //calculate the number of bytes in a band
double ai, bi; //stores the two baseline points wavelength surrounding the current band
double ci; //stores the current band's wavelength
|
77060b79
David Mayerich
started DOxygen d...
|
198
|
|
f0d5a769
heziqi
Ziqi changed the ...
|
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
|
unsigned control=0;
T * a; //pointers to the high and low band images
T * b;
T * c; //pointer to the current image
a = (T*)malloc( S ); //memory allocation
b = (T*)malloc( S );
c = (T*)malloc( S );
if (a == NULL || b == NULL || c == NULL){
std::cout<<"ERROR: error allocating memory";
exit(1);
}
//initialize lownum, highnum, low, high
|
e8eb202f
David Mayerich
added a new ENVI ...
|
216
|
ai=w[0];
|
f0d5a769
heziqi
Ziqi changed the ...
|
217
218
219
|
//if no baseline point is specified at band 0,
//set the baseline point at band 0 to 0
|
e8eb202f
David Mayerich
added a new ENVI ...
|
220
|
if(wls[0] != w[0]){
|
f0d5a769
heziqi
Ziqi changed the ...
|
221
222
223
224
225
226
|
bi = wls[control];
memset(a, (char)0, S);
}
//else get the low band
else{
control += 1;
|
e933c14e
David Mayerich
cleaned up the code
|
227
|
band(a, ai);
|
f0d5a769
heziqi
Ziqi changed the ...
|
228
229
230
|
bi = wls[control];
}
//get the high band
|
e933c14e
David Mayerich
cleaned up the code
|
231
|
band(b, bi);
|
f0d5a769
heziqi
Ziqi changed the ...
|
232
233
234
235
236
|
//correct every band
for(unsigned cii = 0; cii < B; cii++){
//update baseline points, if necessary
|
e8eb202f
David Mayerich
added a new ENVI ...
|
237
|
if( w[cii] >= bi && cii != B - 1) {
|
f0d5a769
heziqi
Ziqi changed the ...
|
238
239
240
241
242
243
244
245
246
|
//if the high band is now on the last BL point?
if (control != N-1) {
control++; //increment the index
std::swap(a, b); //swap the baseline band pointers
ai = bi;
bi = wls[control];
|
e933c14e
David Mayerich
cleaned up the code
|
247
|
band(b, bi);
|
f0d5a769
heziqi
Ziqi changed the ...
|
248
249
250
|
}
//if the last BL point on the last band of the file?
|
e8eb202f
David Mayerich
added a new ENVI ...
|
251
|
else if ( wls[control] < w[B - 1]) {
|
f0d5a769
heziqi
Ziqi changed the ...
|
252
253
254
255
256
257
|
std::swap(a, b); //swap the baseline band pointers
memset(b, (char)0, S); //clear the high band
ai = bi;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
258
|
bi = w[B - 1];
|
f0d5a769
heziqi
Ziqi changed the ...
|
259
260
261
262
263
|
}
}
//get the current band
band_index(c, cii);
|
e8eb202f
David Mayerich
added a new ENVI ...
|
264
|
ci = w[cii];
|
f0d5a769
heziqi
Ziqi changed the ...
|
265
266
267
268
|
//perform the baseline correction
for(unsigned i=0; i < XY; i++){
double r = (double) (ci - ai) / (double) (bi - ai);
|
92e4cf05
heziqi
include file fixed
|
269
|
c[i] =(T) ( c[i] - (b[i] - a[i]) * r - a[i] );
|
f0d5a769
heziqi
Ziqi changed the ...
|
270
271
272
273
274
|
}
target.write(reinterpret_cast<const char*>(c), S); //write the corrected data into destination
}
|
0c748c81
heziqi
Ziqi added save h...
|
275
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
276
|
//header.save(headername); //save the new header file
|
f0d5a769
heziqi
Ziqi changed the ...
|
277
278
279
280
281
282
283
|
free(a);
free(b);
free(c);
target.close();
return true;
}
|
089d9c81
heziqi
Ziqi added normal...
|
284
|
|
a08c98c3
David Mayerich
finished document...
|
285
|
/// Normalize all spectra based on the value of a single band, storing the result in a new BSQ file.
|
77060b79
David Mayerich
started DOxygen d...
|
286
287
288
289
|
/// @param outname is the name of the output file used to store the resulting baseline-corrected data.
/// @param w is the label specifying the band that the hyperspectral image will be normalized to.
/// @param t is a threshold specified such that a spectrum with a value at w less than t is set to zero. Setting this threshold allows the user to limit division by extremely small numbers.
|
93503ec6
David Mayerich
allowed masking d...
|
290
|
bool normalize(std::string outname, double w, double t = 0.0)
|
089d9c81
heziqi
Ziqi added normal...
|
291
|
{
|
e8eb202f
David Mayerich
added a new ENVI ...
|
292
293
|
unsigned int B = R[2]; //calculate the number of bands
unsigned int XY = R[0] * R[1]; //calculate the number of pixels in a band
|
089d9c81
heziqi
Ziqi added normal...
|
294
295
296
297
298
299
300
301
302
303
304
|
unsigned int S = XY * sizeof(T); //calculate the number of bytes in a band
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
std::string headername = outname + ".hdr"; //the header file name
T * b; //pointers to the certain wavelength band
T * c; //pointer to the current image
b = (T*)malloc( S ); //memory allocation
c = (T*)malloc( S );
|
e933c14e
David Mayerich
cleaned up the code
|
305
|
band(b, w); //get the certain band into memory
|
089d9c81
heziqi
Ziqi added normal...
|
306
307
308
309
310
311
|
for(unsigned j = 0; j < B; j++)
{
band_index(c, j); //get the current band into memory
for(unsigned i = 0; i < XY; i++)
{
|
93503ec6
David Mayerich
allowed masking d...
|
312
313
314
315
|
if(b[i] < t)
c[i] = (T)0.0;
else
c[i] = c[i] / b[i];
|
089d9c81
heziqi
Ziqi added normal...
|
316
317
318
319
|
}
target.write(reinterpret_cast<const char*>(c), S); //write normalized data into destination
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
320
|
//header.save(headername); //save the new header file
|
089d9c81
heziqi
Ziqi added normal...
|
321
322
323
324
325
326
|
free(b);
free(c);
target.close();
return true;
}
|
f0d5a769
heziqi
Ziqi changed the ...
|
327
|
|
a08c98c3
David Mayerich
finished document...
|
328
|
/// Convert the current BSQ file to a BIP file with the specified file name.
|
77060b79
David Mayerich
started DOxygen d...
|
329
330
|
/// @param outname is the name of the output BIP file to be saved to disk.
|
421219ba
heziqi
Ziqi added bip.h ...
|
331
332
|
bool bip(std::string outname)
{
|
f6169dea
heziqi
Ziqi completed bi...
|
333
334
335
336
337
|
std::string temp = outname + "_temp";
std::string headtemp = temp + ".hdr";
//first creat a temporary bil file and convert bsq file to bil file
bil(temp);
|
8a86bd56
David Mayerich
changed rts names...
|
338
|
stim::bil<T> n;
|
e933c14e
David Mayerich
cleaned up the code
|
339
|
if(n.open(temp, R[0], R[1], R[2], offset, w)==false){ //open infile
|
f6169dea
heziqi
Ziqi completed bi...
|
340
341
|
std::cout<<"ERROR: unable to open input file"<<std::endl;
exit(1);
|
421219ba
heziqi
Ziqi added bip.h ...
|
342
|
}
|
f6169dea
heziqi
Ziqi completed bi...
|
343
344
345
346
347
|
//then convert bil file to bip file
n.bip(outname);
n.close();
remove(temp.c_str());
remove(headtemp.c_str());
|
421219ba
heziqi
Ziqi added bip.h ...
|
348
349
|
return true;
}
|
c25e7d0d
heziqi
speed of bip.base...
|
350
|
|
a08c98c3
David Mayerich
finished document...
|
351
|
/// Convert the current BSQ file to a BIL file with the specified file name.
|
77060b79
David Mayerich
started DOxygen d...
|
352
353
|
/// @param outname is the name of the output BIL file to be saved to disk.
|
c25e7d0d
heziqi
speed of bip.base...
|
354
355
356
|
bool bil(std::string outname)
{
//simplify image resolution
|
6708cc25
heziqi
Ziqi added envi c...
|
357
|
unsigned int L = R[0] * R[2] * sizeof(T); //calculate the number of bytes of a ZX slice
|
e8eb202f
David Mayerich
added a new ENVI ...
|
358
|
unsigned int jump = (R[1] - 1) * R[0] * sizeof(T);
|
c25e7d0d
heziqi
speed of bip.base...
|
359
360
361
362
363
364
365
|
std::ofstream target(outname.c_str(), std::ios::binary);
std::string headername = outname + ".hdr";
T * p; //pointer to the current spectrum
p = (T*)malloc(L);
|
e8eb202f
David Mayerich
added a new ENVI ...
|
366
|
for ( unsigned i = 0; i < R[1]; i++)
|
c25e7d0d
heziqi
speed of bip.base...
|
367
|
{
|
e8eb202f
David Mayerich
added a new ENVI ...
|
368
369
|
file.seekg(R[0] * i * sizeof(T), std::ios::beg);
for ( unsigned j = 0; j < R[2]; j++ )
|
c25e7d0d
heziqi
speed of bip.base...
|
370
|
{
|
e8eb202f
David Mayerich
added a new ENVI ...
|
371
|
file.read((char *)(p + j * R[0]), sizeof(T) * R[0]);
|
c25e7d0d
heziqi
speed of bip.base...
|
372
373
374
375
|
file.seekg(jump, std::ios::cur); //go to the next band
}
target.write(reinterpret_cast<const char*>(p), L); //write XZ slice data into target file
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
376
377
|
//header.interleave = rts::envi_header::BIL; //change the type of file in header file
//header.save(headername);
|
c25e7d0d
heziqi
speed of bip.base...
|
378
379
380
381
382
|
free(p);
target.close();
return true;
}
|
20c212c0
heziqi
Ziqi added functi...
|
383
|
|
a08c98c3
David Mayerich
finished document...
|
384
|
/// Return a baseline corrected band given two adjacent baseline points and their bands. The result is stored in a pre-allocated array.
|
77060b79
David Mayerich
started DOxygen d...
|
385
386
387
388
389
390
391
|
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lp is a pointer to an array holding the band image for the left baseline point
/// @param rp is a pointer to an array holding the band image for the right baseline point
/// @param wavelength is the label value for the requested baseline-corrected band
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size.
|
20c212c0
heziqi
Ziqi added functi...
|
392
393
394
395
396
397
398
399
400
401
402
403
|
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
unsigned XY = R[0] * R[1];
band(result, wavelength); //get band
//perform the baseline correction
double r = (double) (wavelength - lb) / (double) (rb - lb);
for(unsigned i=0; i < XY; i++){
result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
|
517876d6
heziqi
metrics finished ...
|
404
|
|
a08c98c3
David Mayerich
finished document...
|
405
|
/// Return a baseline corrected band given two adjacent baseline points. The result is stored in a pre-allocated array.
|
77060b79
David Mayerich
started DOxygen d...
|
406
407
408
409
410
|
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param bandwavelength is the label value for the desired baseline-corrected band
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size.
|
70407ea9
heziqi
Ziqi completed he...
|
411
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
412
413
414
|
T* lp;
T* rp;
|
70407ea9
heziqi
Ziqi completed he...
|
415
416
417
418
|
unsigned XY = R[0] * R[1];
unsigned S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
419
|
|
70407ea9
heziqi
Ziqi completed he...
|
420
|
band(lp, lb);
|
20c212c0
heziqi
Ziqi added functi...
|
421
422
423
424
|
band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
heziqi
metrics finished ...
|
425
426
|
free(lp);
free(rp);
|
20c212c0
heziqi
Ziqi added functi...
|
427
428
429
|
return true;
}
|
c359422d
heziqi
Ziqi added functi...
|
430
|
|
a08c98c3
David Mayerich
finished document...
|
431
|
/// Calculate the area under the spectrum between two specified points and stores the result in a pre-allocated array.
|
77060b79
David Mayerich
started DOxygen d...
|
432
433
434
435
436
437
|
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lab is the label value for the left bound (start of the integration)
/// @param rab is the label value for the right bound (end of the integration)
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
70407ea9
heziqi
Ziqi completed he...
|
438
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
439
440
441
442
443
|
T* lp; //left band pointer
T* rp; //right band pointer
T* cur; //current band 1
T* cur2; //current band 2
|
20c212c0
heziqi
Ziqi added functi...
|
444
445
446
447
448
449
450
451
|
unsigned XY = R[0] * R[1];
unsigned S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
|
memset(result, (char)0, S);
//find the wavelenght position in the whole band
unsigned int n = w.size();
unsigned int ai = 0; //left bound position
unsigned int bi = n - 1; //right bound position
//to make sure the left and the right bound are in the bandwidth
if (lb < w[0] || rb < w[0] || lb > w[n-1] || rb >w[n-1]){
std::cout<<"ERROR: left bound or right bound out of bandwidth"<<std::endl;
exit(1);
}
//to make sure rigth bound is bigger than left bound
else if(lb > rb){
std::cout<<"ERROR: right bound should be bigger than left bound"<<std::endl;
exit(1);
}
//get the position of lb and rb
|
70407ea9
heziqi
Ziqi completed he...
|
474
|
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
475
476
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
477
|
while (rab <= w[bi]){
|
20c212c0
heziqi
Ziqi added functi...
|
478
479
480
481
482
483
484
|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
70407ea9
heziqi
Ziqi completed he...
|
485
486
|
baseline_band(lb, rb, lp, rp, rab, cur2); //ending part
baseline_band(lb, rb, lp, rp, w[bi], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
487
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
heziqi
Ziqi completed he...
|
488
|
result[j] += (rab - w[bi]) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
heziqi
Ziqi added functi...
|
489
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
490
491
|
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
492
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
heziqi
Ziqi completed he...
|
493
|
result[j] += (w[ai] - lab) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
heziqi
Ziqi added functi...
|
494
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
495
|
|
20c212c0
heziqi
Ziqi added functi...
|
496
497
498
499
500
501
502
503
504
505
506
|
//calculate the area
ai++;
for(unsigned i = ai; i <= bi ;i++)
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
for(unsigned j = 0; j < XY; j++)
{
result[j] += (w[ai] - w[ai-1]) * (cur[j] + cur2[j]) / 2.0;
}
std::swap(cur,cur2); //swap the band pointers
}
|
70407ea9
heziqi
Ziqi completed he...
|
507
|
|
517876d6
heziqi
metrics finished ...
|
508
509
510
511
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
512
513
514
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
515
|
/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
|
77060b79
David Mayerich
started DOxygen d...
|
516
517
518
519
520
521
522
523
|
/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
/// @param pos1 is the label value for the first peak (numerator) position
/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
/// @param pos2 is the label value for the second peak (denominator) position
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
70407ea9
heziqi
Ziqi completed he...
|
524
|
bool ph_to_ph(double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, T * result){
|
20c212c0
heziqi
Ziqi added functi...
|
525
|
|
70407ea9
heziqi
Ziqi completed he...
|
526
527
528
529
530
531
532
533
534
535
536
537
538
|
T* p1 = (T*)malloc(R[0] * R[1] * sizeof(T));
T* p2 = (T*)malloc(R[0] * R[1] * sizeof(T));
//get the two peak band
height(lb1, rb1, pos1, p1);
height(lb2, rb2, pos2, p2);
//calculate the ratio in result
for(unsigned i = 0; i < R[0] * R[1]; i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
539
540
541
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
542
543
544
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
545
|
/// Compute the ratio between a peak area and peak height.
|
77060b79
David Mayerich
started DOxygen d...
|
546
547
548
549
550
551
552
553
|
/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
/// @param pos1 is the label value for the first peak (numerator) position
/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
/// @param pos2 is the label value for the second peak (denominator) position
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
70407ea9
heziqi
Ziqi completed he...
|
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
|
bool pa_to_ph(double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double pos, T* result){
T* p1 = (T*)malloc(R[0] * R[1] * sizeof(T));
T* p2 = (T*)malloc(R[0] * R[1] * sizeof(T));
//get the area and the peak band
area(lb1, rb1, lab1, rab1, p1);
height(lb2, rb2, pos, p2);
//calculate the ratio in result
for(unsigned i = 0; i < R[0] * R[1]; i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
570
571
572
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
573
574
575
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
576
|
/// Compute the ratio between two peak areas.
|
0722eb39
David Mayerich
further updates t...
|
577
578
579
580
581
582
583
584
585
586
|
/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
/// @param lab1 is the label value for the left bound (start of the integration) of the first peak (numerator)
/// @param rab1 is the label value for the right bound (end of the integration) of the first peak (numerator)
/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
/// @param lab2 is the label value for the left bound (start of the integration) of the second peak (denominator)
/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
70407ea9
heziqi
Ziqi completed he...
|
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
|
bool pa_to_pa(double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double lab2, double rab2, T* result){
T* p1 = (T*)malloc(R[0] * R[1] * sizeof(T));
T* p2 = (T*)malloc(R[0] * R[1] * sizeof(T));
//get the area and the peak band
area(lb1, rb1, lab1, rab1, p1);
area(lb2, rb2, lab2, rab2, p2);
//calculate the ratio in result
for(unsigned i = 0; i < R[0] * R[1]; i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
603
604
605
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
606
607
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
608
|
|
a08c98c3
David Mayerich
finished document...
|
609
|
/// Compute the definite integral of a baseline corrected peak.
|
0722eb39
David Mayerich
further updates t...
|
610
611
612
613
614
615
|
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lab is the label for the start of the definite integral
/// @param rab is the label for the end of the definite integral
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
517876d6
heziqi
metrics finished ...
|
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
|
bool x_area(double lb, double rb, double lab, double rab, T* result){
T* lp; //left band pointer
T* rp; //right band pointer
T* cur; //current band 1
T* cur2; //current band 2
unsigned XY = R[0] * R[1];
unsigned S = XY * sizeof(T);
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
memset(result, (char)0, S);
//find the wavelenght position in the whole band
unsigned int n = w.size();
unsigned int ai = 0; //left bound position
unsigned int bi = n - 1; //right bound position
//to make sure the left and the right bound are in the bandwidth
if (lb < w[0] || rb < w[0] || lb > w[n-1] || rb >w[n-1]){
std::cout<<"ERROR: left bound or right bound out of bandwidth"<<std::endl;
exit(1);
}
//to make sure rigth bound is bigger than left bound
else if(lb > rb){
std::cout<<"ERROR: right bound should be bigger than left bound"<<std::endl;
exit(1);
}
//get the position of lb and rb
while (lab >= w[ai]){
ai++;
}
while (rab <= w[bi]){
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
baseline_band(lb, rb, lp, rp, rab, cur2); //ending part
baseline_band(lb, rb, lp, rp, w[bi], cur);
for(unsigned j = 0; j < XY; j++){
result[j] += (rab - w[bi]) * (rab + w[bi]) * (cur[j] + cur2[j]) / 4.0;
}
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
for(unsigned j = 0; j < XY; j++){
result[j] += (w[ai] - lab) * (w[ai] + lab) * (cur[j] + cur2[j]) / 4.0;
}
//calculate f(x) times x
ai++;
for(unsigned i = ai; i <= bi ;i++)
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
for(unsigned j = 0; j < XY; j++)
{
result[j] += (w[ai] - w[ai-1]) * (w[ai] + w[ai-1]) * (cur[j] + cur2[j]) / 4.0;
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
690
|
/// Compute the centroid of a baseline corrected peak.
|
0722eb39
David Mayerich
further updates t...
|
691
692
693
694
695
696
|
/// @param lb is the label value for the left baseline point
/// @param rb is the label value for the right baseline point
/// @param lab is the label for the start of the peak
/// @param rab is the label for the end of the peak
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
517876d6
heziqi
metrics finished ...
|
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
|
bool cpoint(double lb, double rb, double lab, double rab, T* result){
T* p1 = (T*)malloc(R[0] * R[1] * sizeof(T));
T* p2 = (T*)malloc(R[0] * R[1] * sizeof(T));
//get the area and the peak band
x_area(lb, rb, lab, rab, p1);
area(lb, rb, lab, rab, p2);
//calculate the ratio in result
for(unsigned i = 0; i < R[0] * R[1]; i++){
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
717
|
/// Create a mask based on a given band and threshold value.
|
0722eb39
David Mayerich
further updates t...
|
718
719
720
721
722
723
|
/// All pixels in the
/// specified band greater than the threshold are true and all pixels less than the threshold are false.
/// @param mask_band is the band used to specify the mask
/// @param threshold is the threshold used to determine if the mask value is true or false
/// @param p is a pointer to a pre-allocated array at least X * Y in size
|
f4c5d71b
David Mayerich
started working w...
|
724
|
bool build_mask(double mask_band, double threshold, unsigned char* p = NULL){
|
4a6f666c
heziqi
Added mask method
|
725
726
727
728
729
730
731
732
733
734
735
|
T* temp = (T*)malloc(R[0] * R[1] * sizeof(T)); //allocate memory for the certain band
band(temp, mask_band);
for (unsigned int i = 0; i < R[0] * R[1]; i++) {
if (temp[i] < threshold)
p[i] = 0;
else
p[i] = 255;
}
|
517876d6
heziqi
metrics finished ...
|
736
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
737
738
739
|
return true;
}
|
740f8cd2
heziqi
added apply_mask
|
740
|
|
a08c98c3
David Mayerich
finished document...
|
741
|
/// Apply a mask file to the BSQ image, setting all values outside the mask to zero.
|
0722eb39
David Mayerich
further updates t...
|
742
743
744
|
/// @param outfile is the name of the masked output file
/// @param p is a pointer to memory of size X * Y, where p(i) = 0 for pixels that will be set to zero.
|
740f8cd2
heziqi
added apply_mask
|
745
746
747
748
749
750
751
752
753
|
bool apply_mask(std::string outfile, unsigned char* p){
std::ofstream target(outfile.c_str(), std::ios::binary);
unsigned XY = R[0] * R[1]; //calculate number of a band
unsigned L = XY * sizeof(T);
T * temp = (T*)malloc(L);
|
e843658b
Brad Deutsch
Previous push did...
|
754
|
for (unsigned i = 0; i < R[2]; i++) //for each spectral bin
|
740f8cd2
heziqi
added apply_mask
|
755
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
756
757
|
band_index(temp, i); //get the specified band (by index)
for ( unsigned j = 0; j < XY; j++) // for each pixel
|
740f8cd2
heziqi
added apply_mask
|
758
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
759
760
|
if(p[j] == 0){ //if the mask is 0 at that pixel
temp[j] = 0; //set temp to zero
|
740f8cd2
heziqi
added apply_mask
|
761
762
763
764
765
|
}
else{
continue;
}
}
|
e843658b
Brad Deutsch
Previous push did...
|
766
|
target.write(reinterpret_cast<const char*>(temp), L); //write the XY slice at that band to disk
|
740f8cd2
heziqi
added apply_mask
|
767
768
769
770
771
772
|
}
target.close();
free(temp);
return true;
}
|
e843658b
Brad Deutsch
Previous push did...
|
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
|
///Saves to disk only those spectra corresponding to mask values != 0
bool sift_mask(std::string outfile, unsigned char* p){
std::ofstream target(outfile.c_str(), std::ios::binary);
// open a band (XY plane)
unsigned XY = R[0] * R[1]; //Number of XY pixels
unsigned L = XY * sizeof(T); //size of XY pixels
T * temp = (T*)malloc(L); //allocate memory for a band
T * temp_vox = (T*)malloc(sizeof(T)); //allocate memory for one voxel
for (unsigned i = 0; i < R[2]; i++) //for each spectral bin
{
band_index(temp, i); //get the specified band (XY sheet by index)
for (unsigned j = 0; j < XY; j++) // for each pixel
{
if (p[j] != 0){ //if the mask is != 0 at that pixel
temp_vox[0] = temp[j];
target.write(reinterpret_cast<const char*>(temp_vox), sizeof(T)); //write the XY slice at that band to disk
}
else{
continue;
}
}
}
target.close();
free(temp);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
803
|
/// Calculate the mean band value (average along B) at each pixel location.
|
0722eb39
David Mayerich
further updates t...
|
804
805
|
/// @param p is a pointer to memory of size X * Y * sizeof(T) that will store the band averages.
|
a43c4fe1
heziqi
Added crop in env...
|
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
|
bool band_avg(T* p){
unsigned long long XY = R[0] * R[1];
T* temp = (T*)malloc(sizeof(T) * XY);
//initialize p
band_index(p, 0);
for (unsigned j = 0; j < XY; j++){
p[j] /= (T)R[2];
}
//get every band and add them all
for (unsigned i = 1; i < R[2]; i++){
band_index(temp, i);
for (unsigned j = 0; j < XY; j++){
p[j] += temp[j]/(T)R[2];
}
}
free(temp);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
825
826
827
828
|
/// Calculate the mean value for all masked (or valid) pixels in a band and returns the average spectrum
/// @param p is a pointer to pre-allocated memory of size [B * sizeof(T)] that stores the mean spectrum
/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
|
a43c4fe1
heziqi
Added crop in env...
|
829
830
|
bool avg_band(T*p, unsigned char* mask){
unsigned long long XY = R[0] * R[1];
|
a08c98c3
David Mayerich
finished document...
|
831
|
unsigned count = 0; //count will store the number of masked pixels
|
a43c4fe1
heziqi
Added crop in env...
|
832
|
T* temp = (T*)malloc(sizeof(T) * XY);
|
a08c98c3
David Mayerich
finished document...
|
833
|
//calculate this loop counts the number of true pixels in the mask
|
a43c4fe1
heziqi
Added crop in env...
|
834
835
836
837
838
|
for (unsigned j = 0; j < XY; j++){
if (mask[j] != 0){
count++;
}
}
|
a08c98c3
David Mayerich
finished document...
|
839
840
|
//this loops goes through each band in B (R[2])
// masked (or valid) pixels from that band are averaged and the average is stored in p
|
a43c4fe1
heziqi
Added crop in env...
|
841
842
|
for (unsigned i = 0; i < R[2]; i++){
p[i] = 0;
|
a08c98c3
David Mayerich
finished document...
|
843
844
|
band_index(temp, i); //get the band image and store it in temp
for (unsigned j = 0; j < XY; j++){ //loop through temp, averaging valid pixels
|
a43c4fe1
heziqi
Added crop in env...
|
845
846
847
848
849
850
851
852
853
|
if (mask[j] != 0){
p[i] += temp[j] / (T)count;
}
}
}
free(temp);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
854
855
856
857
858
|
/// Calculate the covariance matrix for all masked pixels in the image.
/// @param co is a pointer to pre-allocated memory of size [B * B] that stores the resulting covariance matrix
/// @param avg is a pointer to memory of size B that stores the average spectrum
/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
|
a43c4fe1
heziqi
Added crop in env...
|
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
|
bool co_matrix(T* co, T* avg, unsigned char *mask){
//memory allocation
unsigned long long xy = R[0] * R[1];
unsigned int B = R[2];
T* bandi = (T*)malloc(sizeof(T) * xy);
T* bandj = (T*)malloc(sizeof(T) * xy);
//count vaild pixels in a band
unsigned count = 0;
for (unsigned j = 0; j < xy; j++){
if (mask[j] != 0){
count++;
}
}
//calculate correlation coefficient matrix
for (unsigned i = 0; i < B; i++)
{
band_index(bandi, i);
for (unsigned j = i; j < B; j++){
band_index(bandj, j);
T numerator = 0; //to calculate element in correlation coefficient matrix, numerator part
//calculate the R(i,j) in correlation coeffient matrix
for (unsigned k = 0; k < xy; k++){
if (mask[k] != 0){
numerator += (bandi[k] - avg[i]) * (bandj[k] - avg[j]) / count;
}
}
co[i*B + j] = numerator;
co[j*B + i] = numerator; //because correlated matrix is a symmetric matrix
}
}
free(bandi);
free(bandj);
return true;
}
|
0df38ff3
heziqi
fixed head detached
|
894
|
|
a43c4fe1
heziqi
Added crop in env...
|
895
|
|
a08c98c3
David Mayerich
finished document...
|
896
897
898
899
900
901
902
|
/// Crop a region of the image and save it to a new file.
/// @param outfile is the file name for the new cropped image
/// @param x0 is the lower-left x pixel coordinate to be included in the cropped image
/// @param y0 is the lower-left y pixel coordinate to be included in the cropped image
/// @param x1 is the upper-right x pixel coordinate to be included in the cropped image
/// @param y1 is the upper-right y pixel coordinate to be included in the cropped image
|
a43c4fe1
heziqi
Added crop in env...
|
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
|
bool crop(std::string outfile, unsigned x0, unsigned y0, unsigned x1, unsigned y1){
//calculate the new number of samples and lines
unsigned long long sam = x1 - x0; //samples
unsigned long long lin = y1 - y0; //lines
unsigned long long L = sam * lin * sizeof(T);
//get specified band and save
T* temp = (T*)malloc(L);
std::ofstream out(outfile.c_str(), std::ios::binary);
unsigned long long jumpb = R[0] * (R[1] - lin) * sizeof(T); //jump pointer to the next band
unsigned long long jumpl = (R[0] - sam) * sizeof(T); //jump pointer to the next line
//get start
file.seekg((y0 * R[0] + x0) * sizeof(T), std::ios::beg);
for (unsigned i = 0; i < R[2]; i++)
{
for (unsigned j = 0; j < lin; j++)
{
file.read((char *)(temp + j * sam), sizeof(T) * sam);
file.seekg(jumpl, std::ios::cur); //go to the next band
}
out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
file.seekg(jumpb, std::ios::cur);
}
free(temp);
return true;
}
|
0df38ff3
heziqi
fixed head detached
|
929
|
|
740f8cd2
heziqi
added apply_mask
|
930
|
|
a08c98c3
David Mayerich
finished document...
|
931
|
/// Close the file.
|
f6169dea
heziqi
Ziqi completed bi...
|
932
933
934
935
|
bool close(){
file.close();
return true;
}
|
31394e2a
heziqi
Ziqi added method...
|
936
|
|
3fc1d461
heziqi
Ziqi added saveBa...
|
937
938
|
};
}
|
31394e2a
heziqi
Ziqi added method...
|
939
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
940
941
|
#endif
|
fc712213
David Mayerich
code simplifications
|
942
|
|