e8eb202f
David Mayerich
added a new ENVI ...
|
1
2
3
4
|
#ifndef STIM_BSQ_H
#define STIM_BSQ_H
#include "../envi/envi_header.h"
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
5
|
#include "../envi/hsi.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>
|
9b2a5d71
David Mayerich
implemented finit...
|
10
|
#include <deque>
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
11
|
#include <chrono>
|
3fc1d461
heziqi
Ziqi added saveBa...
|
12
|
|
77060b79
David Mayerich
started DOxygen d...
|
13
14
|
|
8a86bd56
David Mayerich
changed rts names...
|
15
|
namespace stim{
|
3fc1d461
heziqi
Ziqi added saveBa...
|
16
|
|
77060b79
David Mayerich
started DOxygen d...
|
17
18
19
20
21
22
23
24
|
/**
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...
|
25
26
|
template <typename T>
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
27
|
class bsq: public hsi<T> {
|
3fc1d461
heziqi
Ziqi added saveBa...
|
28
|
|
77060b79
David Mayerich
started DOxygen d...
|
29
|
|
3fc1d461
heziqi
Ziqi added saveBa...
|
30
|
protected:
|
43dec788
David Mayerich
added code for si...
|
31
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
32
33
|
//std::vector<double> w; //band wavelengths
unsigned long long offset;
|
3fc1d461
heziqi
Ziqi added saveBa...
|
34
|
|
724ec347
David Mayerich
simplified the EN...
|
35
36
|
using binary<T>::R;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
37
38
|
using hsi<T>::w; //use the wavelength array in stim::hsi
using hsi<T>::nnz;
|
63fc1df8
David Mayerich
added an inverse ...
|
39
|
using binary<T>::progress;
|
cbce396e
David Mayerich
added support for...
|
40
|
|
3fc1d461
heziqi
Ziqi added saveBa...
|
41
42
|
public:
|
fc712213
David Mayerich
code simplifications
|
43
44
|
using binary<T>::open;
using binary<T>::file;
|
63fc1df8
David Mayerich
added an inverse ...
|
45
|
using binary<T>::read_line_2;
|
724ec347
David Mayerich
simplified the EN...
|
46
|
using binary<T>::read_plane_2;
|
43dec788
David Mayerich
added code for si...
|
47
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
48
|
bsq(){ hsi<T>::init_bsq(); }
|
fc712213
David Mayerich
code simplifications
|
49
|
|
a08c98c3
David Mayerich
finished document...
|
50
|
/// Open a data file for reading using the class interface.
|
77060b79
David Mayerich
started DOxygen d...
|
51
52
53
54
55
56
|
/// @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
|
43dec788
David Mayerich
added code for si...
|
57
|
/// @param wavelengths is an STL vector of size B specifying a numerical label for each band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
58
59
60
61
62
63
|
bool open(std::string filename,
unsigned long long X,
unsigned long long Y,
unsigned long long B,
unsigned long long header_offset,
std::vector<double> wavelengths){
|
3fc1d461
heziqi
Ziqi added saveBa...
|
64
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
65
66
|
//copy the wavelengths to the BSQ file structure
w = wavelengths;
|
6708cc25
heziqi
Ziqi added envi c...
|
67
68
|
//copy the wavelengths to the structure
offset = header_offset;
|
e8eb202f
David Mayerich
added a new ENVI ...
|
69
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
70
|
return open(filename, vec<unsigned long long>(X, Y, B), header_offset);
|
3fc1d461
heziqi
Ziqi added saveBa...
|
71
72
|
}
|
a08c98c3
David Mayerich
finished document...
|
73
|
/// Retrieve a single band (based on index) and stores it in pre-allocated memory.
|
77060b79
David Mayerich
started DOxygen d...
|
74
75
76
|
/// @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.
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
77
|
bool band_index( T * p, unsigned long long page){
|
63fc1df8
David Mayerich
added an inverse ...
|
78
|
return read_plane_2(p, page); //call the binary read_plane function (don't let it update the progress)
|
3fc1d461
heziqi
Ziqi added saveBa...
|
79
80
|
}
|
a08c98c3
David Mayerich
finished document...
|
81
|
/// Retrieve a single band (by numerical label) and stores it in pre-allocated memory.
|
77060b79
David Mayerich
started DOxygen d...
|
82
83
84
|
/// @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.
|
63fc1df8
David Mayerich
added an inverse ...
|
85
86
|
bool band( T * p, double wavelength, bool PROGRESS = false){
if(PROGRESS) progress = 0;
|
ee4dea28
David Mayerich
fixed errors in c...
|
87
|
//if there are no wavelengths in the BSQ file
|
44f44bb5
David Mayerich
fixed a minor bug...
|
88
89
90
91
92
|
if(w.size() == 0){
band_index(p, (unsigned long long)wavelength);
if(PROGRESS) progress = 100;
return true;
}
|
0e48cc9c
heziqi
Ziqi added getBan...
|
93
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
94
95
|
unsigned long long XY = X() * Y(); //calculate the number of pixels in a band
unsigned long long page = 0;
|
517876d6
heziqi
metrics finished ...
|
96
|
|
0e48cc9c
heziqi
Ziqi added getBan...
|
97
|
|
ebe94c9d
David Mayerich
modified comments
|
98
|
//get the two neighboring bands (above and below 'wavelength')
|
0e48cc9c
heziqi
Ziqi added getBan...
|
99
100
|
//if wavelength is smaller than the first one in header file
|
e8eb202f
David Mayerich
added a new ENVI ...
|
101
|
if ( w[page] > wavelength ){
|
0e48cc9c
heziqi
Ziqi added getBan...
|
102
103
104
105
|
band_index(p, page);
return true;
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
106
|
while( w[page] < wavelength )
|
0e48cc9c
heziqi
Ziqi added getBan...
|
107
108
|
{
page++;
|
ebe94c9d
David Mayerich
modified comments
|
109
110
|
//if wavelength is larger than the last wavelength in the header file
// (the wavelength is out of bounds)
|
724ec347
David Mayerich
simplified the EN...
|
111
112
|
if (page == Z()) {
band_index(p, Z()-1); //return the last band
|
0e48cc9c
heziqi
Ziqi added getBan...
|
113
114
115
|
return true;
}
}
|
ebe94c9d
David Mayerich
modified comments
|
116
117
|
//when the page counter points to the first band above 'wavelength'
if ( wavelength < w[page] ){
|
193ff00e
David Mayerich
dealth with preci...
|
118
|
|
ebe94c9d
David Mayerich
modified comments
|
119
|
//do the interpolation
|
517876d6
heziqi
metrics finished ...
|
120
121
|
T * p1;
T * p2;
|
0e48cc9c
heziqi
Ziqi added getBan...
|
122
123
124
125
|
p1=(T*)malloc( XY * sizeof(T)); //memory allocation
p2=(T*)malloc( XY * sizeof(T));
band_index(p1, page - 1);
band_index(p2, page );
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
126
127
128
|
for(unsigned long long i=0; i < XY; i++){
double r = (wavelength - w[page-1]) / (w[page] - w[page-1]);
p[i] = (T)(((double)p2[i] - (double)p1[i]) * r + (double)p1[i]);
|
0e48cc9c
heziqi
Ziqi added getBan...
|
129
|
}
|
517876d6
heziqi
metrics finished ...
|
130
131
|
free(p1);
free(p2);
|
0e48cc9c
heziqi
Ziqi added getBan...
|
132
|
}
|
ebe94c9d
David Mayerich
modified comments
|
133
134
135
|
//if the wavelength is equal to a wavelength in header file
else{
band_index(p, page); //return the band
|
0e48cc9c
heziqi
Ziqi added getBan...
|
136
|
}
|
63fc1df8
David Mayerich
added an inverse ...
|
137
|
if(PROGRESS) progress = 100;
|
0e48cc9c
heziqi
Ziqi added getBan...
|
138
139
140
|
return true;
}
|
724ec347
David Mayerich
simplified the EN...
|
141
|
/// Retrieve a single spectrum (Z-axis line) at a given (x, y) location and stores it in pre-allocated memory.
|
77060b79
David Mayerich
started DOxygen d...
|
142
143
144
145
|
/// @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.
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
146
|
bool spectrum(T * p, unsigned long long x, unsigned long long y, bool PROGRESS = false){
|
63fc1df8
David Mayerich
added an inverse ...
|
147
|
return read_line_2(p, x, y, PROGRESS);
|
3fc1d461
heziqi
Ziqi added saveBa...
|
148
|
}
|
f0d5a769
heziqi
Ziqi changed the ...
|
149
|
|
a08c98c3
David Mayerich
finished document...
|
150
|
/// Retrieve a single pixel and stores it in pre-allocated memory.
|
77060b79
David Mayerich
started DOxygen d...
|
151
152
153
|
/// @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.
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
154
|
bool pixel(T * p, unsigned long long n){
|
bfe9c6db
heziqi
added feature_mat...
|
155
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
156
|
unsigned long long bandnum = X() * Y(); //calculate numbers in one band
|
bfe9c6db
heziqi
added feature_mat...
|
157
158
159
160
161
|
if ( n >= bandnum){ //make sure the pixel number is right
std::cout<<"ERROR: sample or line out of range"<<std::endl;
return false;
}
|
eb5dfb2b
David Mayerich
fixed linux compa...
|
162
|
file.seekg(n * sizeof(T) + binary<T>::header, std::ios::beg); //point to the certain pixel
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
163
|
for (unsigned long long i = 0; i < Z(); i++)
|
bfe9c6db
heziqi
added feature_mat...
|
164
165
166
167
168
|
{
file.read((char *)(p + i), sizeof(T));
file.seekg((bandnum - 1) * sizeof(T), std::ios::cur); //go to the next band
}
|
43dec788
David Mayerich
added code for si...
|
169
|
return true;
|
bfe9c6db
heziqi
added feature_mat...
|
170
171
|
}
|
a08c98c3
David Mayerich
finished document...
|
172
|
/// Perform baseline correction given a list of baseline points and stores the result in a new BSQ file.
|
77060b79
David Mayerich
started DOxygen d...
|
173
174
|
/// @param outname is the name of the output file used to store the resulting baseline-corrected data.
|
43dec788
David Mayerich
added code for si...
|
175
|
/// @param wls is the list of baseline points based on band labels.
|
798cea97
David Mayerich
added progress ba...
|
176
|
bool baseline(std::string outname, std::vector<double> wls, unsigned char* mask = NULL, bool PROGRESS = false )
|
f0d5a769
heziqi
Ziqi changed the ...
|
177
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
178
|
size_t N = wls.size(); //get the number of baseline points
|
31394e2a
heziqi
Ziqi added method...
|
179
|
|
f0d5a769
heziqi
Ziqi changed the ...
|
180
|
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
|
0c748c81
heziqi
Ziqi added save h...
|
181
|
std::string headername = outname + ".hdr"; //the header file name
|
f0d5a769
heziqi
Ziqi changed the ...
|
182
183
|
//simplify image resolution
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
184
185
186
|
unsigned long long B = Z(); //calculate the number of bands
unsigned long long XY = X() * Y(); //calculate the number of pixels in a band
unsigned long long S = XY * sizeof(T); //calculate the number of bytes in a band
|
f0d5a769
heziqi
Ziqi changed the ...
|
187
188
189
|
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...
|
190
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
191
|
unsigned long long control=0;
|
f0d5a769
heziqi
Ziqi changed the ...
|
192
193
194
195
196
197
|
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
|
43dec788
David Mayerich
added code for si...
|
198
199
|
b = (T*)malloc( S );
c = (T*)malloc( S );
|
f0d5a769
heziqi
Ziqi changed the ...
|
200
201
202
203
204
205
206
|
if (a == NULL || b == NULL || c == NULL){
std::cout<<"ERROR: error allocating memory";
exit(1);
}
|
43dec788
David Mayerich
added code for si...
|
207
|
//initialize lownum, highnum, low, high
|
e8eb202f
David Mayerich
added a new ENVI ...
|
208
|
ai=w[0];
|
f0d5a769
heziqi
Ziqi changed the ...
|
209
210
211
|
//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 ...
|
212
|
if(wls[0] != w[0]){
|
43dec788
David Mayerich
added code for si...
|
213
|
bi = wls[control];
|
f0d5a769
heziqi
Ziqi changed the ...
|
214
215
216
217
218
|
memset(a, (char)0, S);
}
//else get the low band
else{
control += 1;
|
e933c14e
David Mayerich
cleaned up the code
|
219
|
band(a, ai);
|
f0d5a769
heziqi
Ziqi changed the ...
|
220
221
222
|
bi = wls[control];
}
//get the high band
|
e933c14e
David Mayerich
cleaned up the code
|
223
|
band(b, bi);
|
f0d5a769
heziqi
Ziqi changed the ...
|
224
|
|
43dec788
David Mayerich
added code for si...
|
225
|
//correct every band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
226
|
for(unsigned long long cii = 0; cii < B; cii++){
|
f0d5a769
heziqi
Ziqi changed the ...
|
227
228
|
//update baseline points, if necessary
|
e8eb202f
David Mayerich
added a new ENVI ...
|
229
|
if( w[cii] >= bi && cii != B - 1) {
|
f0d5a769
heziqi
Ziqi changed the ...
|
230
231
232
233
234
235
236
237
238
|
//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
|
239
|
band(b, bi);
|
f0d5a769
heziqi
Ziqi changed the ...
|
240
241
242
|
}
//if the last BL point on the last band of the file?
|
e8eb202f
David Mayerich
added a new ENVI ...
|
243
|
else if ( wls[control] < w[B - 1]) {
|
f0d5a769
heziqi
Ziqi changed the ...
|
244
245
246
247
248
249
|
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 ...
|
250
|
bi = w[B - 1];
|
f0d5a769
heziqi
Ziqi changed the ...
|
251
252
253
254
255
|
}
}
//get the current band
band_index(c, cii);
|
e8eb202f
David Mayerich
added a new ENVI ...
|
256
|
ci = w[cii];
|
43dec788
David Mayerich
added code for si...
|
257
|
|
f0d5a769
heziqi
Ziqi changed the ...
|
258
|
//perform the baseline correction
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
259
|
for(unsigned long long i=0; i < XY; i++){
|
798cea97
David Mayerich
added progress ba...
|
260
261
262
263
264
265
|
if(mask != NULL && !mask[i]) //if the pixel is excluded by a mask
c[i] = 0; //set the value to zero
else{
double r = (double) (ci - ai) / (double) (bi - ai);
c[i] =(T) ( c[i] - (b[i] - a[i]) * r - a[i] );
}
|
f0d5a769
heziqi
Ziqi changed the ...
|
266
|
}
|
43dec788
David Mayerich
added code for si...
|
267
|
|
f0d5a769
heziqi
Ziqi changed the ...
|
268
|
target.write(reinterpret_cast<const char*>(c), S); //write the corrected data into destination
|
cbce396e
David Mayerich
added support for...
|
269
|
|
63fc1df8
David Mayerich
added an inverse ...
|
270
|
if(PROGRESS)progress = (double)(cii+1) / B * 100;
|
43dec788
David Mayerich
added code for si...
|
271
272
|
}
|
0c748c81
heziqi
Ziqi added save h...
|
273
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
274
|
//header.save(headername); //save the new header file
|
43dec788
David Mayerich
added code for si...
|
275
|
|
f0d5a769
heziqi
Ziqi changed the ...
|
276
277
278
279
|
free(a);
free(b);
free(c);
target.close();
|
cbce396e
David Mayerich
added support for...
|
280
|
|
f0d5a769
heziqi
Ziqi changed the ...
|
281
282
|
return true;
}
|
089d9c81
heziqi
Ziqi added normal...
|
283
|
|
a08c98c3
David Mayerich
finished document...
|
284
|
/// 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...
|
285
286
287
288
|
/// @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.
|
c30dd3e6
David Mayerich
added vector norm...
|
289
|
bool ratio(std::string outname, double w, unsigned char* mask = NULL, bool PROGRESS = false)
|
089d9c81
heziqi
Ziqi added normal...
|
290
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
291
292
293
|
unsigned long long B = Z(); //calculate the number of bands
unsigned long long XY = X() * Y(); //calculate the number of pixels in a band
unsigned long long S = XY * sizeof(T); //calculate the number of bytes in a band
|
089d9c81
heziqi
Ziqi added normal...
|
294
295
296
297
298
299
300
301
|
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
|
43dec788
David Mayerich
added code for si...
|
302
|
c = (T*)malloc( S );
|
089d9c81
heziqi
Ziqi added normal...
|
303
|
|
e933c14e
David Mayerich
cleaned up the code
|
304
|
band(b, w); //get the certain band into memory
|
089d9c81
heziqi
Ziqi added normal...
|
305
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
306
|
for(unsigned long long j = 0; j < B; j++)
|
089d9c81
heziqi
Ziqi added normal...
|
307
308
|
{
band_index(c, j); //get the current band into memory
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
309
|
for(unsigned long long i = 0; i < XY; i++)
|
089d9c81
heziqi
Ziqi added normal...
|
310
|
{
|
798cea97
David Mayerich
added progress ba...
|
311
|
if(mask != NULL && !mask[i])
|
93503ec6
David Mayerich
allowed masking d...
|
312
313
314
|
c[i] = (T)0.0;
else
c[i] = c[i] / b[i];
|
089d9c81
heziqi
Ziqi added normal...
|
315
316
|
}
target.write(reinterpret_cast<const char*>(c), S); //write normalized data into destination
|
cbce396e
David Mayerich
added support for...
|
317
|
|
63fc1df8
David Mayerich
added an inverse ...
|
318
|
if(PROGRESS) progress = (double)(j+1) / B * 100;
|
089d9c81
heziqi
Ziqi added normal...
|
319
320
|
}
|
43dec788
David Mayerich
added code for si...
|
321
|
|
cbce396e
David Mayerich
added support for...
|
322
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
323
|
//header.save(headername); //save the new header file
|
43dec788
David Mayerich
added code for si...
|
324
|
|
089d9c81
heziqi
Ziqi added normal...
|
325
326
327
|
free(b);
free(c);
target.close();
|
089d9c81
heziqi
Ziqi added normal...
|
328
329
|
return true;
}
|
43dec788
David Mayerich
added code for si...
|
330
|
|
c30dd3e6
David Mayerich
added vector norm...
|
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
|
void normalize(std::string outfile, unsigned char* mask = NULL, bool PROGRESS = false){
size_t B = Z(); //calculate the number of bands
size_t XY = X() * Y(); //calculate the number of pixels in a band
size_t XYb = XY * sizeof(T); //calculate the size of a band in bytes
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file
file.seekg(0, std::ios::beg); //move the pointer to the current file to the beginning
T* len = (T*)malloc(XYb); //allocate space to store the vector length
memset(len, 0, XYb); //initialize the vector length to zero (0)
T* band = (T*) malloc(XYb); //allocate space to store a band image
for(size_t b = 0; b < B; b++){
file.read((char*)band, XYb);
for(size_t xy = 0; xy < XY; xy++){
if(mask == NULL || mask[xy]){
len[xy] += pow(band[xy], 2); //sum the squared value for each pixel value in the band
}
}
if(PROGRESS) progress = (double) (b+1) / (double)B * 50;
}
for(size_t xy = 0; xy < XY; xy++){ //for each pixel, calculate the square root
if(mask == NULL || mask[xy]){
len[xy] += pow(band[xy], 2); //sum the squared value for each pixel value in the band
}
}
file.seekg(0, std::ios::beg); //move the pointer to the current file to the beginning
for(size_t b = 0; b < B; b++){
file.read((char*)band, XYb);
for(size_t xy = 0; xy < XY; xy++){
if(mask == NULL || mask[xy]){
band[xy] /= len[xy]; //divide the band by the vector length
}
}
out.write((char*)band, XYb);
if(PROGRESS) progress = (double) (b+1) / (double)B * 50 + 50;
}
}
|
a08c98c3
David Mayerich
finished document...
|
372
|
/// Convert the current BSQ file to a BIL file with the specified file name.
|
77060b79
David Mayerich
started DOxygen d...
|
373
374
|
/// @param outname is the name of the output BIL file to be saved to disk.
|
63fc1df8
David Mayerich
added an inverse ...
|
375
|
bool bil(std::string outname, bool PROGRESS = false)
|
c25e7d0d
heziqi
speed of bip.base...
|
376
377
|
{
//simplify image resolution
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
378
|
unsigned long long jump = (Y() - 1) * X() * sizeof(T);
|
43dec788
David Mayerich
added code for si...
|
379
|
|
c25e7d0d
heziqi
speed of bip.base...
|
380
381
|
std::ofstream target(outname.c_str(), std::ios::binary);
std::string headername = outname + ".hdr";
|
43dec788
David Mayerich
added code for si...
|
382
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
383
|
unsigned long long L = X();
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
384
|
T* line = (T*)malloc(sizeof(T) * L);
|
cbce396e
David Mayerich
added support for...
|
385
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
386
|
for ( unsigned long long y = 0; y < Y(); y++) //for each y position
|
c25e7d0d
heziqi
speed of bip.base...
|
387
|
{
|
cbce396e
David Mayerich
added support for...
|
388
|
file.seekg(y * X() * sizeof(T), std::ios::beg); //seek to the beginning of the xz slice
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
389
|
for ( unsigned long long z = 0; z < Z(); z++ ) //for each band
|
c25e7d0d
heziqi
speed of bip.base...
|
390
|
{
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
391
392
|
file.read((char *)line, sizeof(T) * X()); //read a line
target.write((char*)line, sizeof(T) * X()); //write the line to the output file
|
cbce396e
David Mayerich
added support for...
|
393
|
file.seekg(jump, std::ios::cur); //seek to the next band
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
394
|
if(PROGRESS) progress = (double)((y+1) * Z() + z + 1) / (Z() * Y()) * 100; //update the progress counter
|
43dec788
David Mayerich
added code for si...
|
395
|
}
|
c25e7d0d
heziqi
speed of bip.base...
|
396
|
}
|
3150c537
David Mayerich
added further pro...
|
397
|
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
398
|
free(line);
|
c25e7d0d
heziqi
speed of bip.base...
|
399
|
target.close();
|
3150c537
David Mayerich
added further pro...
|
400
|
|
c25e7d0d
heziqi
speed of bip.base...
|
401
402
|
return true;
}
|
20c212c0
heziqi
Ziqi added functi...
|
403
|
|
a08c98c3
David Mayerich
finished document...
|
404
|
/// 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...
|
405
406
407
408
409
410
411
|
/// @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...
|
412
413
|
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
414
|
unsigned long long XY = X() * Y();
|
20c212c0
heziqi
Ziqi added functi...
|
415
416
417
418
|
band(result, wavelength); //get band
//perform the baseline correction
double r = (double) (wavelength - lb) / (double) (rb - lb);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
419
|
for(unsigned long long i=0; i < XY; i++){
|
20c212c0
heziqi
Ziqi added functi...
|
420
421
422
423
|
result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
|
517876d6
heziqi
metrics finished ...
|
424
|
|
a08c98c3
David Mayerich
finished document...
|
425
|
/// 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...
|
426
427
428
429
430
|
/// @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...
|
431
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
432
433
434
|
T* lp;
T* rp;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
435
436
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
70407ea9
heziqi
Ziqi completed he...
|
437
438
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
439
|
|
70407ea9
heziqi
Ziqi completed he...
|
440
|
band(lp, lb);
|
43dec788
David Mayerich
added code for si...
|
441
|
band(rp, rb);
|
20c212c0
heziqi
Ziqi added functi...
|
442
443
444
|
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
heziqi
metrics finished ...
|
445
446
|
free(lp);
free(rp);
|
20c212c0
heziqi
Ziqi added functi...
|
447
448
449
|
return true;
}
|
c359422d
heziqi
Ziqi added functi...
|
450
|
|
a08c98c3
David Mayerich
finished document...
|
451
|
/// 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...
|
452
453
454
455
456
457
|
/// @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...
|
458
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
459
460
461
462
463
|
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...
|
464
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
465
466
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
20c212c0
heziqi
Ziqi added functi...
|
467
468
469
470
471
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
472
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
473
|
//find the wavelength position in the whole band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
474
475
476
|
unsigned long long n = w.size();
unsigned long long ai = 0; //left bound position
unsigned long long bi = n - 1; //right bound position
|
20c212c0
heziqi
Ziqi added functi...
|
477
478
479
480
481
482
483
484
|
//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);
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
485
|
//to make sure right bound is bigger than left bound
|
20c212c0
heziqi
Ziqi added functi...
|
486
487
488
489
490
|
else if(lb > rb){
std::cout<<"ERROR: right bound should be bigger than left bound"<<std::endl;
exit(1);
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
491
492
|
//find the indices of the left and right baseline points
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
493
494
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
495
|
while (rab <= w[bi]){
|
20c212c0
heziqi
Ziqi added functi...
|
496
497
498
|
bi--;
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
499
|
band(lp, lb); //get the band images for the left and right baseline points
|
20c212c0
heziqi
Ziqi added functi...
|
500
501
|
band(rp, rb);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
502
503
504
505
506
507
508
|
// calculate the average value of the indexed region
memset(result, 0, S); //initialize the integral to zero (0)
//integrate the region between the specified bands and the closest indexed band
// this integrates the "tails" of the spectrum that lie outside the main indexed region
baseline_band(lb, rb, lp, rp, rab, cur2); //calculate the image for the right-most band in the integral
baseline_band(lb, rb, lp, rp, w[bi], cur); //calculate the image for the right-most indexed band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
509
510
|
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((rab - w[bi]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
511
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
512
513
|
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
514
515
|
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((w[ai] - lab) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
516
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
517
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
518
|
//integrate the main indexed region
|
20c212c0
heziqi
Ziqi added functi...
|
519
|
ai++;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
520
|
for(unsigned long long i = ai; i <= bi ;i++) //for each band in the integral
|
20c212c0
heziqi
Ziqi added functi...
|
521
|
{
|
ba51ae6a
David Mayerich
fixed metric calc...
|
522
523
|
baseline_band(lb, rb, lp, rp, w[ai], cur2); //get the baselined band
for(unsigned long long j = 0; j < XY; j++){ //for each pixel in that band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
524
|
result[j] += (T)((w[ai] - w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
525
526
527
|
}
std::swap(cur,cur2); //swap the band pointers
}
|
70407ea9
heziqi
Ziqi completed he...
|
528
|
|
517876d6
heziqi
metrics finished ...
|
529
530
531
532
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
533
534
535
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
536
|
/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
|
77060b79
David Mayerich
started DOxygen d...
|
537
538
539
540
541
542
543
544
|
/// @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
|
ba51ae6a
David Mayerich
fixed metric calc...
|
545
|
bool ph_to_ph(T* result, double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, unsigned char* mask = NULL){
|
20c212c0
heziqi
Ziqi added functi...
|
546
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
547
548
549
550
|
size_t XYbytes = X() * Y() * sizeof(T); //calculate the size of the band image (in bytes)
T* p1 = (T*)malloc(XYbytes); //allocate space for both bands in the ratio
T* p2 = (T*)malloc(XYbytes);
|
43dec788
David Mayerich
added code for si...
|
551
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
552
|
memset(result, 0, XYbytes); //initialize the ratio to zero
|
70407ea9
heziqi
Ziqi completed he...
|
553
554
555
556
|
//get the two peak band
height(lb1, rb1, pos1, p1);
height(lb2, rb2, pos2, p2);
//calculate the ratio in result
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
557
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
558
|
if(mask == NULL || mask[i]){
|
70407ea9
heziqi
Ziqi completed he...
|
559
|
result[i] = p1[i] / p2[i];
|
ba51ae6a
David Mayerich
fixed metric calc...
|
560
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
561
|
}
|
517876d6
heziqi
metrics finished ...
|
562
563
564
|
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
565
|
return true;
|
70407ea9
heziqi
Ziqi completed he...
|
566
|
}
|
43dec788
David Mayerich
added code for si...
|
567
|
|
a08c98c3
David Mayerich
finished document...
|
568
|
/// Compute the ratio between a peak area and peak height.
|
77060b79
David Mayerich
started DOxygen d...
|
569
570
571
572
573
574
575
576
|
/// @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
|
ba51ae6a
David Mayerich
fixed metric calc...
|
577
578
|
bool pa_to_ph(T* result, double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double pos, unsigned char* mask = NULL){
|
43dec788
David Mayerich
added code for si...
|
579
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
580
581
582
|
size_t bytes = X() * Y() * sizeof(T);
T* p1 = (T*)malloc(bytes); //allocate space for both ratio components
T* p2 = (T*)malloc(bytes);
|
43dec788
David Mayerich
added code for si...
|
583
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
584
|
memset(result, 0, bytes); //initialize the ratio to zero
|
70407ea9
heziqi
Ziqi completed he...
|
585
586
587
588
|
//get the area and the peak band
area(lb1, rb1, lab1, rab1, p1);
height(lb2, rb2, pos, p2);
//calculate the ratio in result
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
589
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
590
|
if(mask == NULL || mask[i])
|
70407ea9
heziqi
Ziqi completed he...
|
591
592
|
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
593
594
595
|
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
596
597
598
|
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
599
|
/// Compute the ratio between two peak areas.
|
0722eb39
David Mayerich
further updates t...
|
600
601
602
603
604
605
606
607
|
/// @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)
|
43dec788
David Mayerich
added code for si...
|
608
|
/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
|
0722eb39
David Mayerich
further updates t...
|
609
|
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
610
611
|
bool pa_to_pa(T* result, double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double lab2, double rab2, unsigned char* mask = NULL){
|
43dec788
David Mayerich
added code for si...
|
612
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
613
614
615
|
size_t bytes = X() * Y() * sizeof(T);
T* p1 = (T*)malloc(bytes); //allocate space for each of the operands
T* p2 = (T*)malloc(bytes);
|
43dec788
David Mayerich
added code for si...
|
616
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
617
|
memset(result, 0, bytes); //initialize the ratio result to zero (0)
|
70407ea9
heziqi
Ziqi completed he...
|
618
619
620
621
|
//get the area and the peak band
area(lb1, rb1, lab1, rab1, p1);
area(lb2, rb2, lab2, rab2, p2);
//calculate the ratio in result
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
622
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
623
624
|
if(mask == NULL || mask[i]) //if the pixel is masked
result[i] = p1[i] / p2[i]; //calculate the ratio
|
70407ea9
heziqi
Ziqi completed he...
|
625
|
}
|
517876d6
heziqi
metrics finished ...
|
626
627
628
|
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
629
630
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
631
|
|
ba51ae6a
David Mayerich
fixed metric calc...
|
632
|
/// Compute the definite integral of a baseline corrected peak weighted by the corresponding wavelength
|
0722eb39
David Mayerich
further updates t...
|
633
634
635
636
637
638
|
/// @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 ...
|
639
640
641
642
643
644
|
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
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
645
646
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
517876d6
heziqi
metrics finished ...
|
647
648
649
650
651
652
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
517876d6
heziqi
metrics finished ...
|
653
|
//find the wavelenght position in the whole band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
654
655
656
|
unsigned long long n = w.size();
unsigned long long ai = 0; //left bound position
unsigned long long bi = n - 1; //right bound position
|
517876d6
heziqi
metrics finished ...
|
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
|
//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);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
680
681
|
memset(result, (char)0, S); //initialize the integral to zero (0)
|
517876d6
heziqi
metrics finished ...
|
682
683
684
|
//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);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
685
686
|
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((rab - w[bi]) * (rab + w[bi]) * ((double)cur[j] + (double)cur2[j]) / 4.0);
|
517876d6
heziqi
metrics finished ...
|
687
688
689
|
}
baseline_band(lb, rb, lp, rp, lab, cur2); //beginnning part
baseline_band(lb, rb, lp, rp, w[ai], cur);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
690
691
|
for(unsigned long long j = 0; j < XY; j++){
result[j] += (T)((w[ai] - lab) * (w[ai] + lab) * ((double)cur[j] + (double)cur2[j]) / 4.0);
|
517876d6
heziqi
metrics finished ...
|
692
693
694
695
|
}
//calculate f(x) times x
ai++;
|
ba51ae6a
David Mayerich
fixed metric calc...
|
696
|
for(unsigned long long i = ai; i <= bi ;i++){
|
517876d6
heziqi
metrics finished ...
|
697
|
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
ba51ae6a
David Mayerich
fixed metric calc...
|
698
699
700
|
for(unsigned long long j = 0; j < XY; j++){
T v = (T)((w[ai] - w[ai-1]) * (w[ai] + w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 4.0);
result[j] += v;
|
517876d6
heziqi
metrics finished ...
|
701
702
703
704
705
706
707
708
709
710
711
|
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
712
|
/// Compute the centroid of a baseline corrected peak.
|
ba51ae6a
David Mayerich
fixed metric calc...
|
713
|
/// Note that the values for the centroid can be outside of [lab, rab] if the spectrum goes negative.
|
0722eb39
David Mayerich
further updates t...
|
714
715
716
717
718
719
|
/// @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
|
ba51ae6a
David Mayerich
fixed metric calc...
|
720
721
722
|
bool centroid(T* result, double lb, double rb, double lab, double rab, unsigned char* mask = NULL){
size_t bytes = X() * Y() * sizeof(T); //calculate the number of bytes in a band image
T* p1 = (T*)malloc(X() * Y() * sizeof(T)); //allocate space for both operands
|
43dec788
David Mayerich
added code for si...
|
723
724
|
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
ba51ae6a
David Mayerich
fixed metric calc...
|
725
|
memset(result, 0, bytes); //initialize the ratio result to zero (0)
|
517876d6
heziqi
metrics finished ...
|
726
727
728
729
|
//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
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
730
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
731
|
if(mask == NULL || mask[i]){
|
517876d6
heziqi
metrics finished ...
|
732
|
result[i] = p1[i] / p2[i];
|
ba51ae6a
David Mayerich
fixed metric calc...
|
733
|
}
|
517876d6
heziqi
metrics finished ...
|
734
735
736
737
|
}
free(p1);
free(p2);
|
43dec788
David Mayerich
added code for si...
|
738
|
return true;
|
517876d6
heziqi
metrics finished ...
|
739
740
|
}
|
a08c98c3
David Mayerich
finished document...
|
741
|
/// Create a mask based on a given band and threshold value.
|
0722eb39
David Mayerich
further updates t...
|
742
743
744
745
746
747
|
/// 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
|
ba51ae6a
David Mayerich
fixed metric calc...
|
748
|
bool build_mask(unsigned char* mask, double mask_band, double threshold, bool PROGRESS = false){
|
4a6f666c
heziqi
Added mask method
|
749
|
|
724ec347
David Mayerich
simplified the EN...
|
750
|
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
|
4a6f666c
heziqi
Added mask method
|
751
752
|
band(temp, mask_band);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
753
|
for (unsigned long long i = 0; i < X() * Y(); i++) {
|
798cea97
David Mayerich
added progress ba...
|
754
|
if (temp[i] < threshold)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
755
|
mask[i] = 0;
|
798cea97
David Mayerich
added progress ba...
|
756
|
else
|
ba51ae6a
David Mayerich
fixed metric calc...
|
757
|
mask[i] = 255;
|
798cea97
David Mayerich
added progress ba...
|
758
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
759
|
if(PROGRESS) progress = (double) (i+1) / (X() * Y()) * 100;
|
4a6f666c
heziqi
Added mask method
|
760
761
|
}
|
517876d6
heziqi
metrics finished ...
|
762
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
763
764
765
|
return true;
}
|
740f8cd2
heziqi
added apply_mask
|
766
|
|
a08c98c3
David Mayerich
finished document...
|
767
|
/// Apply a mask file to the BSQ image, setting all values outside the mask to zero.
|
0722eb39
David Mayerich
further updates t...
|
768
769
770
|
/// @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.
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
771
|
bool apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
740f8cd2
heziqi
added apply_mask
|
772
773
774
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
775
776
|
unsigned long long XY = X() * Y(); //calculate number of a band
unsigned long long L = XY * sizeof(T);
|
740f8cd2
heziqi
added apply_mask
|
777
778
779
|
T * temp = (T*)malloc(L);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
780
|
for (unsigned long long i = 0; i < Z(); i++) //for each spectral bin
|
740f8cd2
heziqi
added apply_mask
|
781
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
782
|
band_index(temp, i); //get the specified band (by index)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
783
|
for ( unsigned long long j = 0; j < XY; j++) // for each pixel
|
740f8cd2
heziqi
added apply_mask
|
784
|
{
|
e843658b
Brad Deutsch
Previous push did...
|
785
786
|
if(p[j] == 0){ //if the mask is 0 at that pixel
temp[j] = 0; //set temp to zero
|
740f8cd2
heziqi
added apply_mask
|
787
788
789
790
791
|
}
else{
continue;
}
}
|
e843658b
Brad Deutsch
Previous push did...
|
792
|
target.write(reinterpret_cast<const char*>(temp), L); //write the XY slice at that band to disk
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
793
|
if(PROGRESS) progress = (double)(i + 1) / (double)Z() * 100;
|
740f8cd2
heziqi
added apply_mask
|
794
795
796
797
798
799
|
}
target.close();
free(temp);
return true;
}
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
800
801
802
803
804
805
|
/// Copies all spectra corresponding to nonzero values of a mask into a pre-allocated matrix of size (B x P)
/// where P is the number of masked pixels and B is the number of bands. The allocated memory can be accessed
/// using the following indexing: i = p*B + b
/// @param matrix is the destination for the pixel data
/// @param mask is the mask
bool sift(T* matrix, unsigned char* mask){
|
43dec788
David Mayerich
added code for si...
|
806
807
|
unsigned long long XY = X() * Y(); //Number of XY pixels
unsigned long long L = XY * sizeof(T); //size of XY plane (in bytes)
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
808
809
|
//calculate the number of pixels in the mask
|
a2bf1d08
David Mayerich
general bug fixes...
|
810
|
//unsigned long long P = nnz(mask);
|
eb5dfb2b
David Mayerich
fixed linux compa...
|
811
|
|
3d0b6243
David Mayerich
fixed hsiproc bug...
|
812
813
814
815
816
817
818
819
820
821
822
|
T* band_image = (T*) malloc( XY * sizeof(T)); //allocate space for a single band
unsigned long long i; //pixel index into the sifted array
for(unsigned long long b = 0; b < Z(); b++){ //for each band in the data set
band_index(band_image, b); //retrieve an image of that band
i = 0;
for(unsigned long long xy = 0; xy < XY; xy++){
if(mask == NULL || mask[xy] != 0){ //if the pixel is valid
matrix[i*Z() + b] = band_image[xy]; //copy it to the appropriate point in the values[] array
i++;
|
a2bf1d08
David Mayerich
general bug fixes...
|
823
|
//std::cout<<i<<std::endl;
|
43dec788
David Mayerich
added code for si...
|
824
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
825
|
|
43dec788
David Mayerich
added code for si...
|
826
827
|
}
}
|
eb5dfb2b
David Mayerich
fixed linux compa...
|
828
|
|
43dec788
David Mayerich
added code for si...
|
829
830
|
return true;
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
831
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
832
|
/// Saves to disk only those spectra corresponding to mask values != 0
|
43dec788
David Mayerich
added code for si...
|
833
834
|
/// @param outfile is the name of the sifted ENVI file to be written to disk
/// @param unsigned char* p is the mask file used for sifting
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
835
|
bool sift(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
e843658b
Brad Deutsch
Previous push did...
|
836
837
|
std::ofstream target(outfile.c_str(), std::ios::binary);
// open a band (XY plane)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
838
839
|
unsigned long long XY = X() * Y(); //Number of XY pixels
unsigned long long L = XY * sizeof(T); //size of XY pixels
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
840
|
unsigned long long B = Z();
|
e843658b
Brad Deutsch
Previous push did...
|
841
842
843
844
|
T * temp = (T*)malloc(L); //allocate memory for a band
T * temp_vox = (T*)malloc(sizeof(T)); //allocate memory for one voxel
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
845
|
for (unsigned long long i = 0; i < B; i++) //for each spectral bin
|
e843658b
Brad Deutsch
Previous push did...
|
846
847
|
{
band_index(temp, i); //get the specified band (XY sheet by index)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
848
|
for (unsigned long long j = 0; j < XY; j++) // for each pixel
|
e843658b
Brad Deutsch
Previous push did...
|
849
850
851
852
853
854
855
|
{
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;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
856
|
}
|
e843658b
Brad Deutsch
Previous push did...
|
857
|
}
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
858
|
if(PROGRESS) progress = (double)(i+1)/ B * 100;
|
e843658b
Brad Deutsch
Previous push did...
|
859
860
861
|
}
target.close();
free(temp);
|
3150c537
David Mayerich
added further pro...
|
862
|
|
63fc1df8
David Mayerich
added an inverse ...
|
863
|
progress = 100;
|
3150c537
David Mayerich
added further pro...
|
864
|
|
e843658b
Brad Deutsch
Previous push did...
|
865
866
867
|
return true;
}
|
2fcab4f0
David Mayerich
added unsifting f...
|
868
|
/// Generates a spectral image from a matrix of spectral values in lexicographic order and a mask
|
a2bf1d08
David Mayerich
general bug fixes...
|
869
|
bool unsift(std::string outfile, unsigned char* p, unsigned long long samples, unsigned long long lines, bool PROGRESS = false){
|
2fcab4f0
David Mayerich
added unsifting f...
|
870
871
872
873
874
875
876
877
878
879
880
881
882
|
//create a binary output stream
std::ofstream target(outfile.c_str(), std::ios::binary);
//make sure that there's only one line
if(Y() != 1){
std::cout<<"ERROR in stim::bsq::sift() - number of lines does not equal 1"<<std::endl;
return false;
}
std::cout<<"started sifting"<<std::endl;
//get the number of pixels and bands in the input image
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
883
884
885
|
unsigned long long P = X(); //Number of pixels
unsigned long long B = Z(); //number of bands
unsigned long long XY = samples * lines; //total number of pixels in an unsifted image
|
2fcab4f0
David Mayerich
added unsifting f...
|
886
887
888
889
890
891
892
893
|
// allocate memory for a sifted band
T * sifted = (T*)malloc(P * sizeof(T)); //allocate memory for a band
//allocate memory for an unsifted band image
T* unsifted = (T*) malloc(XY * sizeof(T));
//for each band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
894
|
for(unsigned long long b = 0; b < B; b++){
|
2fcab4f0
David Mayerich
added unsifting f...
|
895
896
|
//set the unsifted index value to zero
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
897
|
unsigned long long i = 0;
|
2fcab4f0
David Mayerich
added unsifting f...
|
898
899
900
901
902
|
//retrieve the sifted band (masked pixels only)
band_index(sifted, b);
//for each pixel in the final image (treat it as a 1D image)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
903
|
for(unsigned long long xi = 0; xi < XY; xi++){
|
2fcab4f0
David Mayerich
added unsifting f...
|
904
905
906
907
908
909
|
if( p[xi] == 0 )
unsifted[xi] = 0;
else{
unsifted[xi] = sifted[i];
i++;
}
|
3150c537
David Mayerich
added further pro...
|
910
|
//std::cout<<xi<<"/"<<XY<<", "<<b<<"/"<<B<<std::endl;
|
a2bf1d08
David Mayerich
general bug fixes...
|
911
|
if(PROGRESS) progress = (double)((b + 1) * XY + xi + 1) / (B * XY) * 100;
|
2fcab4f0
David Mayerich
added unsifting f...
|
912
|
}
|
3150c537
David Mayerich
added further pro...
|
913
|
//std::cout<<b*XY<<"/"<<B*XY<<" "<<B<<"-"<<XY<<std::endl;
|
2fcab4f0
David Mayerich
added unsifting f...
|
914
915
916
917
|
//write the band image to disk
target.write(reinterpret_cast<const char*>(unsifted), sizeof(T) * XY);
}
|
3150c537
David Mayerich
added further pro...
|
918
|
//std::cout<<"unsifted"<<std::endl;
|
a2bf1d08
David Mayerich
general bug fixes...
|
919
|
//progress = 100;
|
3150c537
David Mayerich
added further pro...
|
920
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
921
922
923
|
return true;
}
|
e843658b
Brad Deutsch
Previous push did...
|
924
|
|
a08c98c3
David Mayerich
finished document...
|
925
|
/// Calculate the mean band value (average along B) at each pixel location.
|
0722eb39
David Mayerich
further updates t...
|
926
927
|
/// @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...
|
928
|
bool band_avg(T* p){
|
724ec347
David Mayerich
simplified the EN...
|
929
|
unsigned long long XY = X() * Y();
|
a43c4fe1
heziqi
Added crop in env...
|
930
931
932
|
T* temp = (T*)malloc(sizeof(T) * XY);
//initialize p
band_index(p, 0);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
933
|
for (unsigned long long j = 0; j < XY; j++){
|
724ec347
David Mayerich
simplified the EN...
|
934
|
p[j] /= (T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
935
936
|
}
//get every band and add them all
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
937
|
for (unsigned long long i = 1; i < Z(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
938
|
band_index(temp, i);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
939
|
for (unsigned long long j = 0; j < XY; j++){
|
724ec347
David Mayerich
simplified the EN...
|
940
|
p[j] += temp[j]/(T)Z();
|
a43c4fe1
heziqi
Added crop in env...
|
941
942
943
944
945
946
|
}
}
free(temp);
return true;
}
|
a08c98c3
David Mayerich
finished document...
|
947
948
949
950
|
/// 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
|
63fc1df8
David Mayerich
added an inverse ...
|
951
|
bool avg_band(double* p, unsigned char* mask = NULL, bool PROGRESS = false){
|
724ec347
David Mayerich
simplified the EN...
|
952
|
unsigned long long XY = X() * Y();
|
2aa68315
David Mayerich
major bug fixes f...
|
953
|
unsigned long long count = 0; //count will store the number of masked pixels
|
a43c4fe1
heziqi
Added crop in env...
|
954
|
T* temp = (T*)malloc(sizeof(T) * XY);
|
a08c98c3
David Mayerich
finished document...
|
955
|
//calculate this loop counts the number of true pixels in the mask
|
a43c4fe1
heziqi
Added crop in env...
|
956
|
for (unsigned j = 0; j < XY; j++){
|
2aa68315
David Mayerich
major bug fixes f...
|
957
|
if (mask == NULL || mask[j] != 0){
|
a43c4fe1
heziqi
Added crop in env...
|
958
959
960
|
count++;
}
}
|
724ec347
David Mayerich
simplified the EN...
|
961
|
//this loops goes through each band in B (Z())
|
a08c98c3
David Mayerich
finished document...
|
962
|
// masked (or valid) pixels from that band are averaged and the average is stored in p
|
2aa68315
David Mayerich
major bug fixes f...
|
963
|
for (unsigned long long i = 0; i < Z(); i++){
|
a43c4fe1
heziqi
Added crop in env...
|
964
|
p[i] = 0;
|
a08c98c3
David Mayerich
finished document...
|
965
|
band_index(temp, i); //get the band image and store it in temp
|
2aa68315
David Mayerich
major bug fixes f...
|
966
967
968
|
for (unsigned long long j = 0; j < XY; j++){ //loop through temp, averaging valid pixels
if (mask == NULL || mask[j] != 0){
p[i] += (double)temp[j] / (double)count;
|
43dec788
David Mayerich
added code for si...
|
969
|
}
|
a43c4fe1
heziqi
Added crop in env...
|
970
|
}
|
63fc1df8
David Mayerich
added an inverse ...
|
971
|
if(PROGRESS) progress = (double)(i+1) / Z() * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
972
973
974
975
|
}
free(temp);
return true;
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
976
|
|
a08c98c3
David Mayerich
finished document...
|
977
978
979
980
981
982
983
|
/// 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
|
e9bddc57
David Mayerich
added band croppi...
|
984
985
986
987
988
|
bool crop(std::string outfile, unsigned long long x0,
unsigned long long y0,
unsigned long long x1,
unsigned long long y1,
unsigned long long b0,
|
63fc1df8
David Mayerich
added an inverse ...
|
989
990
|
unsigned long long b1,
bool PROGRESS = false){
|
e9bddc57
David Mayerich
added band croppi...
|
991
992
993
994
995
996
997
998
999
1000
|
//calculate the new number of samples, lines, and bands
unsigned long long samples = x1 - x0;
unsigned long long lines = y1 - y0;
unsigned long long bands = b1 - b0;
//calculate the size of a single band
unsigned long long L = samples * lines * sizeof(T);
//allocate space for a single band
|
a43c4fe1
heziqi
Added crop in env...
|
1001
|
T* temp = (T*)malloc(L);
|
e9bddc57
David Mayerich
added band croppi...
|
1002
1003
|
//create an output stream to store the output file
|
a43c4fe1
heziqi
Added crop in env...
|
1004
|
std::ofstream out(outfile.c_str(), std::ios::binary);
|
e9bddc57
David Mayerich
added band croppi...
|
1005
1006
1007
1008
1009
1010
1011
1012
1013
1014
1015
1016
|
//calculate the distance required to jump from the end of one band to the beginning of another
unsigned long long jumpb = X() * (Y() - lines) * sizeof(T);
//calculate the distance required to jump from the end of one line to the beginning of another
unsigned long long jumpl = (X() - samples) * sizeof(T);
//seek to the start of the cropped region in the input file
file.seekg( (b0 * X() * Y() + y0 * X() + x0) * sizeof(T), std::ios::beg);
//for each band
for (unsigned long long z = b0; z < b1; z++)
|
a43c4fe1
heziqi
Added crop in env...
|
1017
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1018
|
for (unsigned long long y = 0; y < lines; y++)
|
a43c4fe1
heziqi
Added crop in env...
|
1019
|
{
|
e9bddc57
David Mayerich
added band croppi...
|
1020
|
file.read((char *)(temp + y * samples), sizeof(T) * samples);
|
43dec788
David Mayerich
added code for si...
|
1021
|
file.seekg(jumpl, std::ios::cur); //go to the next band
|
3150c537
David Mayerich
added further pro...
|
1022
|
|
63fc1df8
David Mayerich
added an inverse ...
|
1023
|
if(PROGRESS) progress = (double)((z+1) * lines + y + 1) / ((b1 - b0) * lines) * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1024
|
}
|
43dec788
David Mayerich
added code for si...
|
1025
|
out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
|
a43c4fe1
heziqi
Added crop in env...
|
1026
1027
1028
|
file.seekg(jumpb, std::ios::cur);
}
free(temp);
|
3150c537
David Mayerich
added further pro...
|
1029
|
|
a43c4fe1
heziqi
Added crop in env...
|
1030
1031
|
return true;
}
|
0df38ff3
heziqi
fixed head detached
|
1032
|
|
dc8eb8aa
David Mayerich
added band trimmi...
|
1033
1034
1035
1036
1037
1038
1039
1040
1041
1042
1043
1044
1045
1046
1047
1048
1049
1050
1051
1052
1053
1054
1055
1056
1057
1058
1059
1060
1061
|
/// Remove a list of bands from the ENVI file
/// @param outfile is the file name for the output hyperspectral image (with trimmed bands)
/// @param b is an array of bands to be eliminated
void trim(std::string outfile, std::vector<size_t> band_array, bool PROGRESS = false){
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
file.seekg(0, std::ios::beg); //move to the beginning of the input file
size_t XY = X() * Y(); //calculate the number of elements in a band
size_t XYb = XY * sizeof(T); //calculate the number of bytes in a band
T* temp = (T*)malloc(XYb); //allocate space to store a band
size_t i = 0; //store the first index into the band array
for(size_t b = 0; b < Z(); b++){ //for each band
if(b != band_array[i]){ //if this band is not trimmed
file.read((char*)temp, XYb); //read the band
out.write((char*)temp, XYb); //output the band
}
else{
file.seekg(XYb, std::ios::cur); //otherwise, skip the band
i++;
}
if(PROGRESS) progress = (double)(b+1) / (double) Z() * 100;
}
free(temp); //free the scratch space for the band
}
|
2ce6954b
David Mayerich
added the ability...
|
1062
1063
1064
1065
1066
1067
1068
1069
1070
1071
1072
1073
1074
1075
1076
1077
1078
1079
1080
1081
1082
1083
1084
1085
1086
1087
1088
1089
1090
1091
1092
1093
1094
1095
1096
1097
1098
1099
1100
1101
1102
1103
|
/// Combine two BSQ images along the Y axis
/// @param outfile is the combined file to be output
/// @param infile is the input file stream for the image to combine with this one
/// @param Sx is the size of the second image along X
/// @param Sy is the size of the second image along Y
/// @param offset is a shift (negative or positive) in the combined image to the left or right
void combine(std::string outfile, bsq<T>* C, long long xp, long long yp, bool PROGRESS = false){
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
file.seekg(0, std::ios::beg); //move to the beginning of both files
C->file.seekg(0, std::ios::beg);
size_t S[2]; //size of the output band image
size_t p0[2]; //position of the current image in the output
size_t p1[2]; //position of the source image in the output
hsi<T>::calc_combined_size(xp, yp, C->X(), C->Y(), S[0], S[1], p0[0], p0[1], p1[0], p1[1]); //calculate the image placement parameters
size_t line_bytes = X() * sizeof(T);
size_t band_bytes = X() * Y() * sizeof(T);
T* cur = (T*)malloc(X() * Y() * sizeof(T)); //allocate space for a band of the current image
size_t line_src_bytes = C->X() * sizeof(T);
size_t band_src_bytes = C->X() * C->Y() * sizeof(T);
T* src = (T*)malloc(C->X() * C->Y() * sizeof(T)); //allocate space for a band of the source image
size_t line_dst_bytes = S[0] * sizeof(T);
size_t band_dst_bytes = S[0] * S[1] * sizeof(T);
T* dst = (T*)malloc(band_dst_bytes); //allocate space for a band of the destination image
memset(dst, 0, band_dst_bytes); //set all values to zero (0) in the destination image
for(size_t b = 0; b < Z(); b++){ //for each band in both images
file.read((char*)cur, band_bytes); //read a band from the current image
C->file.read((char*)src, band_src_bytes); //read a band from the source image
for(size_t y = 0; y < Y(); y++)
memcpy( &dst[ (p0[1]+y) * S[0] + p0[0] ], &cur[ y * X() ], line_bytes); //copy the line from the current to the destination image
//memset( &dst[ (p0[1]+y) * S[0] + p0[0] ], 0, line_dst_bytes);
for(size_t y = 0; y < C->Y(); y++)
memcpy( &dst[ (p1[1]+y) * S[0] + p1[0] ], &src[ y * C->X() ], line_src_bytes); //copy the line from the source to the destination image
out.write((char*)dst, band_dst_bytes); //write the combined image to an output file
if(PROGRESS) progress = (double)(b + 1) / (double) Z() * 100;
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1104
1105
1106
1107
1108
1109
1110
1111
1112
1113
1114
|
out.close();
}
/// Convolve the given band range with a kernel specified by a vector of coefficients.
/// @param outfile is an already open stream to the output file
/// @param C is an array of coefficients
/// @param start is the band to start processing (the first coefficient starts here)
/// @param nbands is the number of bands to process
/// @param center is the index for the center coefficient for the kernel (used to set the wavelengths in the output file)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1115
|
void convolve(std::ofstream& out, std::vector<double> C, size_t start, size_t end, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1116
1117
1118
1119
1120
1121
1122
1123
1124
1125
1126
1127
1128
1129
1130
1131
1132
1133
1134
1135
|
size_t nbands = end - start + 1;
size_t XY = X() * Y(); //calculate the number of values in a band
size_t XYb = XY * sizeof(T); //calculate the size of a band (frame) in bytes
file.seekg(XYb * start, std::ios::beg); //move to the beginning of the 'start' band
size_t nframes = C.size(); //get the number of bands that the kernel spans
std::deque<T*> frame(nframes, NULL); //create an array to store pointers to each frame
for(size_t f = 0; f < nframes; f++){ //for each frame
frame[f] = (T*)malloc(XYb); //allocate space for the frame
file.read((char*)frame[f], XYb); //load the frame
}
T* outband = (T*)malloc(XYb); //allocate space for the output band
//Implementation: In order to minimize reads from secondary storage, each band is only loaded once into the 'frame' deque.
// When a new band is loaded, the last band is popped, a new frame is copied to the pointer, and it is
// re-inserted into the deque.
for(size_t b = 0; b < nbands; b++){ //for each band
memset(outband, 0, XYb); //set the output band to zero (0)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1136
1137
1138
1139
1140
1141
1142
1143
|
size_t c, xy;
double coeff;
for(c = 0; c < nframes; c++){ //for each frame (corresponding to each coefficient)
coeff = C[c];
for(xy = 0; xy < XY; xy++){ //for each pixel
if(mask == NULL || mask[xy]){
outband[xy] += (T)(coeff * frame[c][xy]); //calculate the contribution of the current frame (scaled by the corresponding coefficient)
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1144
1145
1146
1147
1148
1149
1150
1151
1152
1153
1154
1155
1156
1157
1158
1159
|
}
}
out.write((char*)outband, XYb); //output the band
file.read((char*)frame[0], XYb); //read the next band
frame.push_back(frame.front()); //put the first element in the back
frame.pop_front(); //pop the first element
if(PROGRESS) progress = (double)(b+1) / (double)nbands * 100;
}
}
/// Performs a single convolution and saves it to an output file
/// @param outfile is the convolved file to be output
/// @param C is an array of coefficients
/// @param start is the band to start processing (the first coefficient starts here)
/// @param nbands is the number of bands to process
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1160
|
void convolve(std::string outfile, std::vector<double> C, size_t start, size_t end, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1161
|
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1162
|
convolve(out, C, start, end, mask, PROGRESS); //start the convolution
|
9b2a5d71
David Mayerich
implemented finit...
|
1163
1164
1165
1166
1167
1168
1169
1170
1171
|
out.close();
}
/// Performs a set of convolutions and chains the results together in a single file
/// @param outfile is the convolved file to be output
/// @param C is an array containing an array of coefficients for each kernel
/// @param start is the list of start bands for each kernel
/// @param end is the list of end bands for each kernel
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1172
|
void convolve(std::string outfile, std::vector< std::vector<double> > C, std::vector<size_t> start, std::vector<size_t> end, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1173
1174
1175
1176
1177
1178
|
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
size_t K = C.size(); //get the number of kernels
for(size_t k = 0; k < K; k++){
size_t b0 = start[k]; //calculate the range of the convolution
size_t b1 = end[k];
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1179
|
convolve(out, C[k], b0, b1, mask, PROGRESS); //perform the convolution with the current kernel in the given range
|
9b2a5d71
David Mayerich
implemented finit...
|
1180
1181
1182
1183
1184
1185
|
}
out.close();
}
/// Approximate the spectral derivative of the image
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1186
|
void deriv(std::string outfile, size_t d, size_t order, const std::vector<double> w = std::vector<double>(), unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1187
1188
1189
1190
1191
1192
1193
1194
1195
1196
1197
1198
1199
1200
1201
1202
1203
1204
1205
1206
1207
1208
1209
1210
1211
1212
1213
1214
1215
1216
1217
1218
1219
1220
1221
1222
1223
1224
|
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
size_t XY = X() * Y(); //calculate the number of values in a band
size_t XYb = XY * sizeof(T); //calculate the size of a band (frame) in bytes
size_t B = Z();
file.seekg(0, std::ios::beg); //move to the beginning of the file
size_t N = order + d; //approximating a derivative requires order + d samples
std::deque<T*> frame(N, NULL); //create an array to store pointers to each frame
for(size_t f = 0; f < N; f++){ //for each frame
frame[f] = (T*)malloc(XYb); //allocate space for the frame
file.read((char*)frame[f], XYb); //load the frame
}
T* outband = (T*)malloc(XYb); //allocate space for the output band
//Implementation: In order to minimize reads from secondary storage, each band is only loaded once into the 'frame' deque.
// When a new band is loaded, the last band is popped, a new frame is copied to the pointer, and it is
// re-inserted into the deque.
size_t mid = (size_t)(N / 2); //calculate the mid point of the kernel
size_t iw; //index to the first wavelength used to evaluate the derivative at this band
for(size_t b = 0; b < B; b++){ //for each band
if(b < mid) //calculate the first wavelength used to evaluate the derivative at this band
iw = 0;
else if(b > B - (N - mid + 1))
iw = B - N;
else{
iw = b - mid;
file.read((char*)frame[0], XYb); //read the next band
frame.push_back(frame.front()); //put the first element in the back
frame.pop_front(); //pop the first element
}
std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + N); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[b], w_pts, d); //get the optimal sample weights
memset(outband, 0, XYb); //set the output band to zero (0)
for(size_t c = 0; c < N; c++){ //for each frame (corresponding to each coefficient)
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1225
1226
1227
|
if(mask == NULL || mask[xy]){
outband[xy] += (T)(C[c] * frame[c][xy]); //calculate the contribution of the current frame (scaled by the corresponding coefficient)
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1228
1229
1230
1231
1232
|
}
}
out.write((char*)outband, XYb); //output the band
if(PROGRESS) progress = (double)(b+1) / (double)B * 100;
}
|
2ce6954b
David Mayerich
added the ability...
|
1233
1234
1235
|
}
|
740f8cd2
heziqi
added apply_mask
|
1236
|
|
a08c98c3
David Mayerich
finished document...
|
1237
|
/// Close the file.
|
f6169dea
heziqi
Ziqi completed bi...
|
1238
1239
1240
1241
|
bool close(){
file.close();
return true;
}
|
31394e2a
heziqi
Ziqi added method...
|
1242
|
|
3fc1d461
heziqi
Ziqi added saveBa...
|
1243
1244
|
};
}
|
31394e2a
heziqi
Ziqi added method...
|
1245
|
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1246
|
#endif
|
43dec788
David Mayerich
added code for si...
|
|
|