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
|
|
8a86bd56
David Mayerich
changed rts names...
|
11
|
namespace stim{
|
3fc1d461
heziqi
Ziqi added saveBa...
|
12
13
14
15
16
17
18
|
template <typename T>
class bsq: public binary<T> {
protected:
|
e8eb202f
David Mayerich
added a new ENVI ...
|
19
20
21
|
//envi_header header;
std::vector<double> w; //band wavelengths
|
6708cc25
heziqi
Ziqi added envi c...
|
22
|
unsigned int offset;
|
3fc1d461
heziqi
Ziqi added saveBa...
|
23
|
|
3fc1d461
heziqi
Ziqi added saveBa...
|
24
25
|
public:
|
fc712213
David Mayerich
code simplifications
|
26
27
28
|
using binary<T>::open;
using binary<T>::file;
using binary<T>::getSlice;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
29
|
using binary<T>::R;
|
fc712213
David Mayerich
code simplifications
|
30
|
|
e933c14e
David Mayerich
cleaned up the code
|
31
|
//open a file, given the file name and dimensions
|
e8eb202f
David Mayerich
added a new ENVI ...
|
32
|
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...
|
33
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
34
35
|
//copy the wavelengths to the BSQ file structure
w = wavelengths;
|
6708cc25
heziqi
Ziqi added envi c...
|
36
37
|
//copy the wavelengths to the structure
offset = header_offset;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
38
39
|
return open(filename, vec<unsigned int>(X, Y, B), header_offset);
|
3fc1d461
heziqi
Ziqi added saveBa...
|
40
41
42
|
}
|
e933c14e
David Mayerich
cleaned up the code
|
43
|
//retrieve one band (specified by the band index)
|
0e48cc9c
heziqi
Ziqi added getBan...
|
44
|
bool band_index( T * p, unsigned int page){
|
3fc1d461
heziqi
Ziqi added saveBa...
|
45
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
46
|
if (page >= R[2]){ //make sure the bank number is right
|
3fc1d461
heziqi
Ziqi added saveBa...
|
47
48
49
50
|
std::cout<<"ERROR: page out of range"<<std::endl;
return false;
}
|
193ff00e
David Mayerich
dealth with preci...
|
51
|
file.seekg(R[0] * R[1] * page * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
52
53
54
|
file.read((char *)p, sizeof(T) * R[0] * R[1]);
|
3fc1d461
heziqi
Ziqi added saveBa...
|
55
56
57
|
return true;
}
|
e933c14e
David Mayerich
cleaned up the code
|
58
59
|
//retrieve one band (specified by the wavelength)
bool band( T * p, double wavelength){
|
0e48cc9c
heziqi
Ziqi added getBan...
|
60
|
|
ee4dea28
David Mayerich
fixed errors in c...
|
61
62
63
|
//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...
|
64
|
|
ee4dea28
David Mayerich
fixed errors in c...
|
65
|
unsigned int XY = R[0] * R[1]; //calculate the number of pixels in a band
|
ebe94c9d
David Mayerich
modified comments
|
66
|
unsigned page = 0;
|
517876d6
heziqi
metrics finished ...
|
67
|
|
0e48cc9c
heziqi
Ziqi added getBan...
|
68
|
|
ebe94c9d
David Mayerich
modified comments
|
69
|
//get the two neighboring bands (above and below 'wavelength')
|
0e48cc9c
heziqi
Ziqi added getBan...
|
70
71
|
//if wavelength is smaller than the first one in header file
|
e8eb202f
David Mayerich
added a new ENVI ...
|
72
|
if ( w[page] > wavelength ){
|
0e48cc9c
heziqi
Ziqi added getBan...
|
73
74
75
76
|
band_index(p, page);
return true;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
77
|
while( w[page] < wavelength )
|
0e48cc9c
heziqi
Ziqi added getBan...
|
78
79
|
{
page++;
|
ebe94c9d
David Mayerich
modified comments
|
80
81
|
//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 ...
|
82
|
if (page == R[2]) {
|
ebe94c9d
David Mayerich
modified comments
|
83
|
band_index(p, R[2]-1); //return the last band
|
0e48cc9c
heziqi
Ziqi added getBan...
|
84
85
86
|
return true;
}
}
|
ebe94c9d
David Mayerich
modified comments
|
87
88
|
//when the page counter points to the first band above 'wavelength'
if ( wavelength < w[page] ){
|
193ff00e
David Mayerich
dealth with preci...
|
89
|
|
ebe94c9d
David Mayerich
modified comments
|
90
|
//do the interpolation
|
517876d6
heziqi
metrics finished ...
|
91
92
|
T * p1;
T * p2;
|
0e48cc9c
heziqi
Ziqi added getBan...
|
93
94
95
96
97
|
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 ...
|
98
|
double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
|
0e48cc9c
heziqi
Ziqi added getBan...
|
99
100
|
p[i] = (p2[i] - p1[i]) * r + p1[i];
}
|
517876d6
heziqi
metrics finished ...
|
101
102
|
free(p1);
free(p2);
|
0e48cc9c
heziqi
Ziqi added getBan...
|
103
|
}
|
ebe94c9d
David Mayerich
modified comments
|
104
105
106
|
//if the wavelength is equal to a wavelength in header file
else{
band_index(p, page); //return the band
|
0e48cc9c
heziqi
Ziqi added getBan...
|
107
108
|
}
|
0e48cc9c
heziqi
Ziqi added getBan...
|
109
110
111
|
return true;
}
|
3fc1d461
heziqi
Ziqi added saveBa...
|
112
|
//save one pixel of the file into the memory, and return the pointer
|
e933c14e
David Mayerich
cleaned up the code
|
113
|
bool spectrum(T * p, unsigned x, unsigned y){
|
3fc1d461
heziqi
Ziqi added saveBa...
|
114
115
116
|
unsigned int i;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
117
|
if ( x >= R[0] || y >= R[1]){ //make sure the sample and line number is right
|
3fc1d461
heziqi
Ziqi added saveBa...
|
118
119
120
121
|
std::cout<<"ERROR: sample or line out of range"<<std::endl;
return false;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
122
|
file.seekg((x + y * R[0]) * sizeof(T), std::ios::beg); //point to the certain sample and line
|
bfe9c6db
heziqi
added feature_mat...
|
123
|
for (i = 0; i < R[2]; i++)
|
3fc1d461
heziqi
Ziqi added saveBa...
|
124
125
|
{
file.read((char *)(p + i), sizeof(T));
|
e8eb202f
David Mayerich
added a new ENVI ...
|
126
|
file.seekg((R[1] * R[0] - 1) * sizeof(T), std::ios::cur); //go to the next band
|
3fc1d461
heziqi
Ziqi added saveBa...
|
127
128
|
}
|
3fc1d461
heziqi
Ziqi added saveBa...
|
129
130
|
return true;
}
|
f0d5a769
heziqi
Ziqi changed the ...
|
131
|
|
bfe9c6db
heziqi
added feature_mat...
|
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
|
//save one pixel into memory
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;
}
|
f0d5a769
heziqi
Ziqi changed the ...
|
151
152
153
154
155
|
//baseline correction and save it into file
bool baseline(std::string outname, std::vector<double> wls )
{
unsigned N = wls.size(); //get the number of baseline points
|
31394e2a
heziqi
Ziqi added method...
|
156
|
|
f0d5a769
heziqi
Ziqi changed the ...
|
157
|
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
|
0c748c81
heziqi
Ziqi added save h...
|
158
|
std::string headername = outname + ".hdr"; //the header file name
|
f0d5a769
heziqi
Ziqi changed the ...
|
159
160
|
//simplify image resolution
|
e8eb202f
David Mayerich
added a new ENVI ...
|
161
162
|
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 ...
|
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
|
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
// unsigned aii, bii; //stores the two baseline points number surrounding the current band
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 ...
|
185
|
ai=w[0];
|
f0d5a769
heziqi
Ziqi changed the ...
|
186
187
188
|
//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 ...
|
189
|
if(wls[0] != w[0]){
|
f0d5a769
heziqi
Ziqi changed the ...
|
190
191
192
193
194
195
|
bi = wls[control];
memset(a, (char)0, S);
}
//else get the low band
else{
control += 1;
|
e933c14e
David Mayerich
cleaned up the code
|
196
|
band(a, ai);
|
f0d5a769
heziqi
Ziqi changed the ...
|
197
198
199
|
bi = wls[control];
}
//get the high band
|
e933c14e
David Mayerich
cleaned up the code
|
200
|
band(b, bi);
|
f0d5a769
heziqi
Ziqi changed the ...
|
201
202
203
204
205
|
//correct every band
for(unsigned cii = 0; cii < B; cii++){
//update baseline points, if necessary
|
e8eb202f
David Mayerich
added a new ENVI ...
|
206
|
if( w[cii] >= bi && cii != B - 1) {
|
f0d5a769
heziqi
Ziqi changed the ...
|
207
208
209
210
211
212
213
214
215
|
//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
|
216
|
band(b, bi);
|
f0d5a769
heziqi
Ziqi changed the ...
|
217
218
219
|
}
//if the last BL point on the last band of the file?
|
e8eb202f
David Mayerich
added a new ENVI ...
|
220
|
else if ( wls[control] < w[B - 1]) {
|
f0d5a769
heziqi
Ziqi changed the ...
|
221
222
223
224
225
226
|
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 ...
|
227
|
bi = w[B - 1];
|
f0d5a769
heziqi
Ziqi changed the ...
|
228
229
230
231
232
|
}
}
//get the current band
band_index(c, cii);
|
e8eb202f
David Mayerich
added a new ENVI ...
|
233
|
ci = w[cii];
|
f0d5a769
heziqi
Ziqi changed the ...
|
234
235
236
237
|
//perform the baseline correction
for(unsigned i=0; i < XY; i++){
double r = (double) (ci - ai) / (double) (bi - ai);
|
92e4cf05
heziqi
include file fixed
|
238
|
c[i] =(T) ( c[i] - (b[i] - a[i]) * r - a[i] );
|
f0d5a769
heziqi
Ziqi changed the ...
|
239
240
241
242
243
|
}
target.write(reinterpret_cast<const char*>(c), S); //write the corrected data into destination
}
|
0c748c81
heziqi
Ziqi added save h...
|
244
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
245
|
//header.save(headername); //save the new header file
|
f0d5a769
heziqi
Ziqi changed the ...
|
246
247
248
249
250
251
252
|
free(a);
free(b);
free(c);
target.close();
return true;
}
|
089d9c81
heziqi
Ziqi added normal...
|
253
254
|
// normalize the BSQ file
|
e933c14e
David Mayerich
cleaned up the code
|
255
|
bool normalize(std::string outname, double w)
|
089d9c81
heziqi
Ziqi added normal...
|
256
|
{
|
e8eb202f
David Mayerich
added a new ENVI ...
|
257
258
|
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...
|
259
260
261
262
263
264
265
266
267
268
269
|
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
|
270
|
band(b, w); //get the certain band into memory
|
089d9c81
heziqi
Ziqi added normal...
|
271
272
273
274
275
276
277
278
279
280
281
|
for(unsigned j = 0; j < B; j++)
{
band_index(c, j); //get the current band into memory
for(unsigned i = 0; i < XY; i++)
{
c[i] = c[i] / b[i];
}
target.write(reinterpret_cast<const char*>(c), S); //write normalized data into destination
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
282
|
//header.save(headername); //save the new header file
|
089d9c81
heziqi
Ziqi added normal...
|
283
284
285
286
287
288
|
free(b);
free(c);
target.close();
return true;
}
|
f0d5a769
heziqi
Ziqi changed the ...
|
289
|
|
421219ba
heziqi
Ziqi added bip.h ...
|
290
291
292
|
//convert BSQ file to BIP file and save it
bool bip(std::string outname)
{
|
f6169dea
heziqi
Ziqi completed bi...
|
293
294
295
296
297
|
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...
|
298
|
stim::bil<T> n;
|
e933c14e
David Mayerich
cleaned up the code
|
299
|
if(n.open(temp, R[0], R[1], R[2], offset, w)==false){ //open infile
|
f6169dea
heziqi
Ziqi completed bi...
|
300
301
|
std::cout<<"ERROR: unable to open input file"<<std::endl;
exit(1);
|
421219ba
heziqi
Ziqi added bip.h ...
|
302
|
}
|
f6169dea
heziqi
Ziqi completed bi...
|
303
304
305
306
307
|
//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 ...
|
308
309
|
return true;
}
|
c25e7d0d
heziqi
speed of bip.base...
|
310
311
312
313
314
|
//convert BSQ file to BIL file and save it
bool bil(std::string outname)
{
//simplify image resolution
|
6708cc25
heziqi
Ziqi added envi c...
|
315
|
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 ...
|
316
|
unsigned int jump = (R[1] - 1) * R[0] * sizeof(T);
|
c25e7d0d
heziqi
speed of bip.base...
|
317
318
319
320
321
322
323
|
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 ...
|
324
|
for ( unsigned i = 0; i < R[1]; i++)
|
c25e7d0d
heziqi
speed of bip.base...
|
325
|
{
|
e8eb202f
David Mayerich
added a new ENVI ...
|
326
327
|
file.seekg(R[0] * i * sizeof(T), std::ios::beg);
for ( unsigned j = 0; j < R[2]; j++ )
|
c25e7d0d
heziqi
speed of bip.base...
|
328
|
{
|
e8eb202f
David Mayerich
added a new ENVI ...
|
329
|
file.read((char *)(p + j * R[0]), sizeof(T) * R[0]);
|
c25e7d0d
heziqi
speed of bip.base...
|
330
331
332
333
|
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 ...
|
334
335
|
//header.interleave = rts::envi_header::BIL; //change the type of file in header file
//header.save(headername);
|
c25e7d0d
heziqi
speed of bip.base...
|
336
337
338
339
340
|
free(p);
target.close();
return true;
}
|
20c212c0
heziqi
Ziqi added functi...
|
341
342
343
344
345
346
347
348
349
350
351
352
353
354
|
//providing the left and the right bound data, return baseline-corrected band height
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 ...
|
355
|
|
20c212c0
heziqi
Ziqi added functi...
|
356
|
//providing the left and the right bound wavelength, return baseline-corrected band height
|
70407ea9
heziqi
Ziqi completed he...
|
357
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
358
359
360
|
T* lp;
T* rp;
|
70407ea9
heziqi
Ziqi completed he...
|
361
362
363
364
|
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...
|
365
|
|
70407ea9
heziqi
Ziqi completed he...
|
366
|
band(lp, lb);
|
20c212c0
heziqi
Ziqi added functi...
|
367
368
369
370
|
band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
heziqi
metrics finished ...
|
371
372
|
free(lp);
free(rp);
|
20c212c0
heziqi
Ziqi added functi...
|
373
374
375
|
return true;
}
|
c359422d
heziqi
Ziqi added functi...
|
376
|
|
20c212c0
heziqi
Ziqi added functi...
|
377
|
//calculate the area between two bound point(including baseline correction)
|
70407ea9
heziqi
Ziqi completed he...
|
378
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
379
380
381
382
383
|
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...
|
384
385
386
387
388
389
390
391
|
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...
|
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
|
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...
|
414
|
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
415
416
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
417
|
while (rab <= w[bi]){
|
20c212c0
heziqi
Ziqi added functi...
|
418
419
420
421
422
423
424
|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
70407ea9
heziqi
Ziqi completed he...
|
425
426
|
baseline_band(lb, rb, lp, rp, rab, cur2); //ending part
baseline_band(lb, rb, lp, rp, w[bi], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
427
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
heziqi
Ziqi completed he...
|
428
|
result[j] += (rab - w[bi]) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
heziqi
Ziqi added functi...
|
429
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
430
431
|
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
20c212c0
heziqi
Ziqi added functi...
|
432
|
for(unsigned j = 0; j < XY; j++){
|
70407ea9
heziqi
Ziqi completed he...
|
433
|
result[j] += (w[ai] - lab) * (cur[j] + cur2[j]) / 2.0;
|
20c212c0
heziqi
Ziqi added functi...
|
434
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
435
|
|
20c212c0
heziqi
Ziqi added functi...
|
436
437
438
439
440
441
442
443
444
445
446
|
//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...
|
447
|
|
517876d6
heziqi
metrics finished ...
|
448
449
450
451
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
452
453
454
|
return true;
}
|
70407ea9
heziqi
Ziqi completed he...
|
455
456
|
//peak height ratio
bool ph_to_ph(double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, T * result){
|
20c212c0
heziqi
Ziqi added functi...
|
457
|
|
70407ea9
heziqi
Ziqi completed he...
|
458
459
460
461
462
463
464
465
466
467
468
469
470
|
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 ...
|
471
472
473
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
|
return true;
}
//peak are to peak height ratio
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 ...
|
494
495
496
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
|
return true;
}
//peak area to peak area ratio
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 ...
|
517
518
519
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
520
521
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
|
//x * f(x)
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;
}
//centroid point
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;
}
|
4a6f666c
heziqi
Added mask method
|
619
|
//create mask file
|
f4c5d71b
David Mayerich
started working w...
|
620
|
bool build_mask(double mask_band, double threshold, unsigned char* p = NULL){
|
4a6f666c
heziqi
Added mask method
|
621
622
623
624
625
626
627
628
629
630
631
|
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 ...
|
632
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
633
634
635
|
return true;
}
|
740f8cd2
heziqi
added apply_mask
|
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
|
//apply mask
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);
for (unsigned i = 0; i < R[2]; i++)
{
band_index(temp, i);
for ( unsigned j = 0; j < XY; j++)
{
if(p[j] == 0){
temp[j] = 0;
}
else{
continue;
}
}
target.write(reinterpret_cast<const char*>(temp), L); //write a band data into target file
}
target.close();
free(temp);
return true;
}
|
a43c4fe1
heziqi
Added crop in env...
|
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
|
//calculate the average band
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;
}
//calculate the average number of every band
bool avg_band(T*p, unsigned char* mask){
unsigned long long XY = R[0] * R[1];
unsigned count = 0; //number of vaild pixel in a band
T* temp = (T*)malloc(sizeof(T) * XY);
//calculate valid pixel number
for (unsigned j = 0; j < XY; j++){
if (mask[j] != 0){
count++;
}
}
//calculate average of a band
for (unsigned i = 0; i < R[2]; i++){
p[i] = 0;
band_index(temp, i);
for (unsigned j = 0; j < XY; j++){
if (mask[j] != 0){
p[i] += temp[j] / (T)count;
}
}
}
free(temp);
return true;
}
//calculate correlated matrix
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
|
747
|
|
a43c4fe1
heziqi
Added crop in env...
|
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
|
//crop specified area the of the original file
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
|
776
|
|
740f8cd2
heziqi
added apply_mask
|
777
|
|
f6169dea
heziqi
Ziqi completed bi...
|
778
779
780
781
782
|
//close the file
bool close(){
file.close();
return true;
}
|
31394e2a
heziqi
Ziqi added method...
|
783
|
|
3fc1d461
heziqi
Ziqi added saveBa...
|
784
785
|
};
}
|
31394e2a
heziqi
Ziqi added method...
|
786
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
787
788
|
#endif
|
fc712213
David Mayerich
code simplifications
|
789
|
|