e8eb202f
David Mayerich
added a new ENVI ...
|
1
2
3
4
|
#ifndef STIM_BIP_H
#define STIM_BIP_H
#include "../envi/envi_header.h"
|
6aa04ba2
David Mayerich
interleave types
|
5
|
#include "../envi/bil.h"
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
6
|
#include "../envi/hsi.h"
|
88c3e636
heziqi
Ziqi added big.h
|
7
8
9
|
#include <cstring>
#include <utility>
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
10
|
//CUDA
|
a2bf1d08
David Mayerich
general bug fixes...
|
11
12
13
14
|
#ifdef CUDA_FOUND
#include <cuda_runtime.h>
#include "cublas_v2.h"
#endif
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
15
|
|
8a86bd56
David Mayerich
changed rts names...
|
16
|
namespace stim{
|
88c3e636
heziqi
Ziqi added big.h
|
17
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
18
19
20
21
22
23
24
25
|
/**
The BIP class represents a 3-dimensional binary file stored using band interleaved by pixel (BIP) image encoding. The binary file is stored
such that Z-X "frames" are stored sequentially to form an image stack along the y-axis. When accessing the data sequentially on disk,
the dimensions read, from fastest to slowest, are Z, X, Y.
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.
*/
|
88c3e636
heziqi
Ziqi added big.h
|
26
27
|
template <typename T>
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
28
|
class bip: public hsi<T> {
|
88c3e636
heziqi
Ziqi added big.h
|
29
30
31
|
protected:
|
6708cc25
heziqi
Ziqi added envi c...
|
32
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
33
34
|
//std::vector<double> w; //band wavelength
unsigned long long offset; //header offset
|
88c3e636
heziqi
Ziqi added big.h
|
35
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
36
37
|
using hsi<T>::w; //use the wavelength array in stim::hsi
using hsi<T>::nnz;
|
63fc1df8
David Mayerich
added an inverse ...
|
38
|
using binary<T>::progress;
|
a2bf1d08
David Mayerich
general bug fixes...
|
39
|
|
88c3e636
heziqi
Ziqi added big.h
|
40
41
42
43
|
public:
using binary<T>::open;
using binary<T>::file;
|
6708cc25
heziqi
Ziqi added envi c...
|
44
|
using binary<T>::R;
|
63fc1df8
David Mayerich
added an inverse ...
|
45
|
using binary<T>::read_line_0;
|
88c3e636
heziqi
Ziqi added big.h
|
46
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
47
48
|
bip(){ hsi<T>::init_bip(); }
|
a23c4132
David Mayerich
Doxygen comments ...
|
49
50
51
52
53
54
55
56
|
/// Open a data file for reading using the class interface.
/// @param filename is the name of the binary file on disk
/// @param X is the number of samples along dimension 1
/// @param Y is the number of samples (lines) along dimension 2
/// @param B is the number of samples (bands) along dimension 3
/// @param header_offset is the number of bytes (if any) in the binary header
/// @param wavelengths is an optional STL vector of size B specifying a numerical label for each band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
57
58
59
60
61
62
|
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){
|
88c3e636
heziqi
Ziqi added big.h
|
63
|
|
6708cc25
heziqi
Ziqi added envi c...
|
64
65
66
67
|
//copy the wavelengths to the BSQ file structure
w = wavelengths;
//copy the offset to the structure
offset = header_offset;
|
88c3e636
heziqi
Ziqi added big.h
|
68
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
69
|
return open(filename, vec<unsigned long long>(B, X, Y), header_offset);
|
88c3e636
heziqi
Ziqi added big.h
|
70
71
72
|
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
73
74
75
76
|
/// Retrieve a single band (based on index) and stores it in pre-allocated memory.
/// @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, bool PROGRESS = false){
|
63fc1df8
David Mayerich
added an inverse ...
|
78
|
return binary<T>::read_plane_0(p, page, PROGRESS);
|
88c3e636
heziqi
Ziqi added big.h
|
79
80
|
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
81
82
83
84
|
/// Retrieve a single band (by numerical label) and stores it in pre-allocated memory.
/// @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
|
bool band( T * p, double wavelength, bool PROGRESS = false){
|
88c3e636
heziqi
Ziqi added big.h
|
86
|
|
ee4dea28
David Mayerich
fixed errors in c...
|
87
88
|
//if there are no wavelengths in the BSQ file
if(w.size() == 0)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
89
|
return band_index(p, (unsigned long long)wavelength, PROGRESS);
|
ee4dea28
David Mayerich
fixed errors in c...
|
90
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
91
|
unsigned long long XY = X() * Y(); //calculate the number of pixels in a band
|
88c3e636
heziqi
Ziqi added big.h
|
92
93
|
unsigned page=0; //bands around the wavelength
|
517876d6
heziqi
metrics finished ...
|
94
|
|
88c3e636
heziqi
Ziqi added big.h
|
95
96
97
98
|
//get the bands numbers around the wavelength
//if wavelength is smaller than the first one in header file
|
6708cc25
heziqi
Ziqi added envi c...
|
99
|
if ( w[page] > wavelength ){
|
63fc1df8
David Mayerich
added an inverse ...
|
100
|
band_index(p, page, PROGRESS);
|
88c3e636
heziqi
Ziqi added big.h
|
101
102
103
|
return true;
}
|
6708cc25
heziqi
Ziqi added envi c...
|
104
|
while( w[page] < wavelength )
|
88c3e636
heziqi
Ziqi added big.h
|
105
106
107
|
{
page++;
//if wavelength is larger than the last wavelength in header file
|
724ec347
David Mayerich
simplified the EN...
|
108
|
if (page == Z()) {
|
63fc1df8
David Mayerich
added an inverse ...
|
109
|
band_index(p, Z()-1, PROGRESS);
|
88c3e636
heziqi
Ziqi added big.h
|
110
111
112
|
return true;
}
}
|
6708cc25
heziqi
Ziqi added envi c...
|
113
|
if ( wavelength < w[page] )
|
88c3e636
heziqi
Ziqi added big.h
|
114
|
{
|
517876d6
heziqi
metrics finished ...
|
115
116
|
T * p1;
T * p2;
|
88c3e636
heziqi
Ziqi added big.h
|
117
118
119
|
p1=(T*)malloc( XY * sizeof(T)); //memory allocation
p2=(T*)malloc( XY * sizeof(T));
band_index(p1, page - 1);
|
63fc1df8
David Mayerich
added an inverse ...
|
120
|
band_index(p2, page, PROGRESS);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
121
|
for(unsigned long long i=0; i < XY; i++){
|
6708cc25
heziqi
Ziqi added envi c...
|
122
|
double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
123
|
p[i] = (T)(((double)p2[i] - (double)p1[i]) * r + (double)p1[i]);
|
88c3e636
heziqi
Ziqi added big.h
|
124
|
}
|
517876d6
heziqi
metrics finished ...
|
125
126
|
free(p1);
free(p2);
|
88c3e636
heziqi
Ziqi added big.h
|
127
128
129
|
}
else //if the wavelength is equal to a wavelength in header file
{
|
63fc1df8
David Mayerich
added an inverse ...
|
130
|
band_index(p, page, PROGRESS);
|
88c3e636
heziqi
Ziqi added big.h
|
131
|
}
|
88c3e636
heziqi
Ziqi added big.h
|
132
133
|
return true;
}
|
724ec347
David Mayerich
simplified the EN...
|
134
135
136
137
138
139
|
/// Retrieve a single spectrum (Z-axis line) at a given (x, y) location and stores it in pre-allocated memory.
/// @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...
|
140
|
bool spectrum(T * p, unsigned long long x, unsigned long long y, bool PROGRESS = false){
|
63fc1df8
David Mayerich
added an inverse ...
|
141
|
return read_line_0(p, x, y, PROGRESS); //read a line in the binary YZ plane (dimension order for BIP is ZXY)
|
724ec347
David Mayerich
simplified the EN...
|
142
143
144
145
146
147
148
149
|
}
/// Retrieves a band of x values from a given xz plane.
/// @param p is a pointer to pre-allocated memory at least X * sizeof(T) in size
/// @param c is a pointer to an existing XZ plane (size X*Z*sizeof(T))
/// @param wavelength is the wavelength of X values to retrieve
bool read_x_from_xz(T* p, T* c, double wavelength)
|
11f177d5
heziqi
Ziqi added functi...
|
150
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
151
|
unsigned long long B = Z();
|
11f177d5
heziqi
Ziqi added functi...
|
152
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
153
|
unsigned long long page=0; //samples around the wavelength
|
517876d6
heziqi
metrics finished ...
|
154
|
|
11f177d5
heziqi
Ziqi added functi...
|
155
156
157
158
|
//get the bands numbers around the wavelength
//if wavelength is smaller than the first one in header file
|
6708cc25
heziqi
Ziqi added envi c...
|
159
|
if ( w[page] > wavelength ){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
160
|
for(unsigned long long j = 0; j < X(); j++)
|
11f177d5
heziqi
Ziqi added functi...
|
161
162
163
164
165
166
|
{
p[j] = c[j * B];
}
return true;
}
|
6708cc25
heziqi
Ziqi added envi c...
|
167
|
while( w[page] < wavelength )
|
11f177d5
heziqi
Ziqi added functi...
|
168
169
170
171
|
{
page++;
//if wavelength is larger than the last wavelength in header file
if (page == B) {
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
172
|
for(unsigned long long j = 0; j < X(); j++)
|
11f177d5
heziqi
Ziqi added functi...
|
173
174
175
176
177
178
|
{
p[j] = c[(j + 1) * B - 1];
}
return true;
}
}
|
6708cc25
heziqi
Ziqi added envi c...
|
179
|
if ( wavelength < w[page] )
|
11f177d5
heziqi
Ziqi added functi...
|
180
|
{
|
517876d6
heziqi
metrics finished ...
|
181
182
|
T * p1;
T * p2;
|
724ec347
David Mayerich
simplified the EN...
|
183
184
|
p1=(T*)malloc( X() * sizeof(T)); //memory allocation
p2=(T*)malloc( X() * sizeof(T));
|
11f177d5
heziqi
Ziqi added functi...
|
185
|
//band_index(p1, page - 1);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
186
|
for(unsigned long long j = 0; j < X(); j++)
|
11f177d5
heziqi
Ziqi added functi...
|
187
188
189
190
|
{
p1[j] = c[j * B + page - 1];
}
//band_index(p2, page );
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
191
|
for(unsigned long long j = 0; j < X(); j++)
|
11f177d5
heziqi
Ziqi added functi...
|
192
193
194
195
|
{
p2[j] = c[j * B + page];
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
196
|
for(unsigned long long i=0; i < X(); i++){
|
6708cc25
heziqi
Ziqi added envi c...
|
197
|
double r = (double) (wavelength - w[page-1]) / (double) (w[page] - w[page-1]);
|
11f177d5
heziqi
Ziqi added functi...
|
198
199
|
p[i] = (p2[i] - p1[i]) * r + p1[i];
}
|
517876d6
heziqi
metrics finished ...
|
200
201
|
free(p1);
free(p2);
|
11f177d5
heziqi
Ziqi added functi...
|
202
203
204
205
|
}
else //if the wavelength is equal to a wavelength in header file
{
//band_index(p, page);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
206
|
for(unsigned long long j = 0; j < X(); j++)
|
11f177d5
heziqi
Ziqi added functi...
|
207
208
209
210
211
212
213
|
{
p[j] = c[j * B + page];
}
}
return true;
}
|
bfe9c6db
heziqi
added feature_mat...
|
214
|
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
215
|
/// Retrieve a single pixel and store it in a pre-allocated double array.
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
216
217
|
bool pixeld(double* p, unsigned long long n){
unsigned long long bandnum = X() * Y(); //calculate numbers in one band
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
218
219
220
221
|
if ( n >= bandnum){ //make sure the pixel number is right
std::cout<<"ERROR: sample or line out of range"<<std::endl;
return false;
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
222
|
unsigned long long B = Z();
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
223
224
225
226
227
|
T* temp = (T*) malloc(B * sizeof(T)); //allocate space for the raw pixel data
file.seekg(n * B * sizeof(T), std::ios::beg); //point to the certain pixel
file.read((char *)temp, sizeof(T) * B); //read the spectrum from disk to the temp pointer
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
228
|
for(unsigned long long i = 0; i < B; i++) //for each element of the spectrum
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
229
|
p[i] = (double) temp[i]; //cast each element to a double value
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
230
|
return true;
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
231
232
|
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
233
234
235
236
|
/// Retrieve a single pixel and stores it in pre-allocated memory.
/// @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...
|
237
|
bool pixel(T * p, unsigned long long n){
|
bfe9c6db
heziqi
added feature_mat...
|
238
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
239
|
unsigned long long N = X() * Y(); //calculate numbers in one band
|
63fc1df8
David Mayerich
added an inverse ...
|
240
|
if ( n >= N){ //make sure the pixel number is right
|
bfe9c6db
heziqi
added feature_mat...
|
241
242
243
244
|
std::cout<<"ERROR: sample or line out of range"<<std::endl;
return false;
}
|
724ec347
David Mayerich
simplified the EN...
|
245
246
247
|
file.seekg(n * Z() * sizeof(T), std::ios::beg); //point to the certain pixel
file.read((char *)p, sizeof(T) * Z());
return true;
|
bfe9c6db
heziqi
added feature_mat...
|
248
|
}
|
11f177d5
heziqi
Ziqi added functi...
|
249
250
|
//given a Y ,return a ZX slice
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
251
|
bool read_plane_y(T * p, unsigned long long y){
|
724ec347
David Mayerich
simplified the EN...
|
252
|
return binary<T>::read_plane_2(p, y);
|
11f177d5
heziqi
Ziqi added functi...
|
253
254
|
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
255
256
257
258
|
/// Perform baseline correction given a list of baseline points and stores the result in a new BSQ file.
/// @param outname is the name of the output file used to store the resulting baseline-corrected data.
/// @param wls is the list of baseline points based on band labels.
|
798cea97
David Mayerich
added progress ba...
|
259
|
bool baseline(std::string outname, std::vector<double> base_pts, unsigned char* mask = NULL, bool PROGRESS = false){
|
88c3e636
heziqi
Ziqi added big.h
|
260
261
|
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
|
88c3e636
heziqi
Ziqi added big.h
|
262
|
|
63fc1df8
David Mayerich
added an inverse ...
|
263
264
265
266
267
268
269
270
|
unsigned long long N = X() * Y(); //calculate the total number of pixels to be processed
unsigned long long B = Z(); //get the number of bands
T* s = (T*)malloc(sizeof(T) * B); //allocate memory to store a pixel
T* sbc = (T*)malloc(sizeof(T) * B); //allocate memory to store the baseline corrected spectrum
std::vector<T> base_vals; //allocate space for the values at each baseline point
double aw, bw; //surrounding baseline point wavelengths
T av, bv; //surrounding baseline point values
|
63fc1df8
David Mayerich
added an inverse ...
|
271
272
|
unsigned long long ai, bi; //surrounding baseline point band indices
for(unsigned long long n = 0; n < N; n++){ //for each pixel in the image
|
798cea97
David Mayerich
added progress ba...
|
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
|
if(mask != NULL && !mask[n]){ //if the pixel isn't masked
memset(sbc, 0, sizeof(T) * B); //set the baseline corrected spectrum to zero
}
else{
pixel(s, n); //retrieve the spectrum s
base_vals = interp_spectrum(s, base_pts); //get the values at each baseline point
ai = bi = 0;
aw = w[0]; //initialize the current baseline points (assume the spectrum starts at 0)
av = s[0];
bw = base_pts[0];
for(unsigned long long b = 0; b < B; b++){ //for each band in the spectrum
while(bi < base_pts.size() && base_pts[bi] < w[b]) //while the current wavelength is higher than the second baseline point
bi++; //move to the next baseline point
if(bi < base_pts.size()){
bw = base_pts[bi]; //set the wavelength for the upper bound baseline point
bv = base_vals[bi]; //set the value for the upper bound baseline point
}
if(bi == base_pts.size()){ //if we have passed the last baseline point
bw = w[B-1]; //set the outer bound to the last spectral band
bv = s[B-1];
}
if(bi != 0){
ai = bi - 1; //set the lower bound baseline point index
aw = base_pts[ai]; //set the wavelength for the lower bound baseline point
av = base_vals[ai]; //set the value for the lower bound baseline point
}
sbc[b] = s[b] - lerp(w[b], av, aw, bv, bw); //perform the baseline correction and save the new value
|
63fc1df8
David Mayerich
added an inverse ...
|
302
|
}
|
63fc1df8
David Mayerich
added an inverse ...
|
303
|
}
|
88c3e636
heziqi
Ziqi added big.h
|
304
|
|
63fc1df8
David Mayerich
added an inverse ...
|
305
|
if(PROGRESS) progress = (double)(n+1) / N * 100; //set the current progress
|
6708cc25
heziqi
Ziqi added envi c...
|
306
|
|
63fc1df8
David Mayerich
added an inverse ...
|
307
308
|
target.write((char*)sbc, sizeof(T) * B); //write the corrected data into destination
} //end for each pixel
|
88c3e636
heziqi
Ziqi added big.h
|
309
|
|
63fc1df8
David Mayerich
added an inverse ...
|
310
311
|
free(s);
free(sbc);
|
88c3e636
heziqi
Ziqi added big.h
|
312
|
target.close();
|
63fc1df8
David Mayerich
added an inverse ...
|
313
|
|
11f177d5
heziqi
Ziqi added functi...
|
314
315
|
return true;
|
88c3e636
heziqi
Ziqi added big.h
|
316
|
}
|
11f177d5
heziqi
Ziqi added functi...
|
317
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
318
319
320
321
322
|
/// Normalize all spectra based on the value of a single band, storing the result in a new BSQ file.
/// @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...
|
323
|
bool ratio(std::string outname, double w, unsigned char* mask = NULL, bool PROGRESS = false)
|
88c3e636
heziqi
Ziqi added big.h
|
324
|
{
|
88c3e636
heziqi
Ziqi added big.h
|
325
|
std::ofstream target(outname.c_str(), std::ios::binary); //open the target binary file
|
63fc1df8
David Mayerich
added an inverse ...
|
326
327
328
329
330
331
332
|
std::string headername = outname + ".hdr"; //the header file name
unsigned long long N = X() * Y(); //calculate the total number of pixels to be processed
unsigned long long B = Z(); //get the number of bands
T* s = (T*)malloc(sizeof(T) * B); //allocate memory to store a pixel
T nv; //stores the value of the normalized band
for(unsigned long long n = 0; n < N; n++){ //for each pixel in the image
|
798cea97
David Mayerich
added progress ba...
|
333
|
if(mask != NULL && !mask[n]) //if the normalization band is below threshold
|
63fc1df8
David Mayerich
added an inverse ...
|
334
335
|
memset(s, 0, sizeof(T) * B); //set the output to zero
else{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
336
337
338
339
|
pixel(s, n); //retrieve the spectrum s
nv = interp_spectrum(s, w); //find the value of the normalization band
for(unsigned long long b = 0; b < B; b++) //for each band in the spectrum
|
63fc1df8
David Mayerich
added an inverse ...
|
340
|
s[b] /= nv; //divide by the normalization value
|
88c3e636
heziqi
Ziqi added big.h
|
341
|
}
|
63fc1df8
David Mayerich
added an inverse ...
|
342
343
|
if(PROGRESS) progress = (double)(n+1) / N * 100; //set the current progress
|
6708cc25
heziqi
Ziqi added envi c...
|
344
|
|
63fc1df8
David Mayerich
added an inverse ...
|
345
346
|
target.write((char*)s, sizeof(T) * B); //write the corrected data into destination
} //end for each pixel
|
88c3e636
heziqi
Ziqi added big.h
|
347
|
|
63fc1df8
David Mayerich
added an inverse ...
|
348
|
free(s);
|
88c3e636
heziqi
Ziqi added big.h
|
349
|
target.close();
|
88c3e636
heziqi
Ziqi added big.h
|
350
351
|
return true;
}
|
c30dd3e6
David Mayerich
added vector norm...
|
352
353
|
void normalize(std::string outfile, unsigned char* mask = NULL, bool PROGRESS = false){}
|
88c3e636
heziqi
Ziqi added big.h
|
354
|
|
f6169dea
heziqi
Ziqi completed bi...
|
355
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
356
357
358
|
/// Convert the current BIP file to a BIL file with the specified file name.
/// @param outname is the name of the output BIL file to be saved to disk.
|
63fc1df8
David Mayerich
added an inverse ...
|
359
|
bool bil(std::string outname, bool PROGRESS = false)
|
11f177d5
heziqi
Ziqi added functi...
|
360
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
361
|
unsigned long long S = X() * Z() * sizeof(T); //calculate the number of bytes in a ZX slice
|
11f177d5
heziqi
Ziqi added functi...
|
362
363
|
std::ofstream target(outname.c_str(), std::ios::binary);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
364
|
//std::string headername = outname + ".hdr";
|
11f177d5
heziqi
Ziqi added functi...
|
365
|
|
f6169dea
heziqi
Ziqi completed bi...
|
366
|
T * p; //pointer to the current ZX slice for bip file
|
11f177d5
heziqi
Ziqi added functi...
|
367
|
p = (T*)malloc(S);
|
f6169dea
heziqi
Ziqi completed bi...
|
368
369
|
T * q; //pointer to the current XZ slice for bil file
q = (T*)malloc(S);
|
11f177d5
heziqi
Ziqi added functi...
|
370
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
371
|
for ( unsigned long long i = 0; i < Y(); i++)
|
11f177d5
heziqi
Ziqi added functi...
|
372
|
{
|
724ec347
David Mayerich
simplified the EN...
|
373
|
read_plane_y(p, i);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
374
|
for ( unsigned long long k = 0; k < Z(); k++)
|
f6169dea
heziqi
Ziqi completed bi...
|
375
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
376
377
|
unsigned long long ks = k * X();
for ( unsigned long long j = 0; j < X(); j++)
|
724ec347
David Mayerich
simplified the EN...
|
378
|
q[ks + j] = p[k + j * Z()];
|
cbce396e
David Mayerich
added support for...
|
379
|
|
63fc1df8
David Mayerich
added an inverse ...
|
380
|
if(PROGRESS) progress = (double)(i * Z() + k+1) / (Y() * Z()) * 100;
|
f6169dea
heziqi
Ziqi completed bi...
|
381
382
|
}
target.write(reinterpret_cast<const char*>(q), S); //write a band data into target file
|
11f177d5
heziqi
Ziqi added functi...
|
383
|
}
|
f6169dea
heziqi
Ziqi completed bi...
|
384
|
|
11f177d5
heziqi
Ziqi added functi...
|
385
|
free(p);
|
f6169dea
heziqi
Ziqi completed bi...
|
386
|
free(q);
|
11f177d5
heziqi
Ziqi added functi...
|
387
388
389
|
target.close();
return true;
}
|
88c3e636
heziqi
Ziqi added big.h
|
390
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
391
392
393
394
395
396
397
398
|
/// Return a baseline corrected band given two adjacent baseline points and their bands. The result is stored in a pre-allocated array.
/// @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...
|
399
400
|
bool baseline_band(double lb, double rb, T* lp, T* rp, double wavelength, T* result){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
401
|
unsigned long long XY = X() * Y();
|
20c212c0
heziqi
Ziqi added functi...
|
402
403
404
405
|
band(result, wavelength); //get band
//perform the baseline correction
double r = (double) (wavelength - lb) / (double) (rb - lb);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
406
|
for(unsigned long long i=0; i < XY; i++){
|
20c212c0
heziqi
Ziqi added functi...
|
407
408
409
410
|
result[i] =(T) (result[i] - (rp[i] - lp[i]) * r - lp[i] );
}
return true;
}
|
517876d6
heziqi
metrics finished ...
|
411
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
412
413
414
415
416
417
|
/// Return a baseline corrected band given two adjacent baseline points. The result is stored in a pre-allocated array.
/// @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...
|
418
|
bool height(double lb, double rb, double bandwavelength, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
419
420
421
|
T* lp;
T* rp;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
422
423
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
70407ea9
heziqi
Ziqi completed he...
|
424
425
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
426
|
|
70407ea9
heziqi
Ziqi completed he...
|
427
|
band(lp, lb);
|
20c212c0
heziqi
Ziqi added functi...
|
428
429
430
431
|
band(rp, rb);
baseline_band(lb, rb, lp, rp, bandwavelength, result);
|
517876d6
heziqi
metrics finished ...
|
432
433
|
free(lp);
free(rp);
|
20c212c0
heziqi
Ziqi added functi...
|
434
435
436
|
return true;
}
|
c359422d
heziqi
Ziqi added functi...
|
437
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
438
439
440
441
442
443
444
|
/// Calculate the area under the spectrum between two specified points and stores the result in a pre-allocated array.
/// @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...
|
445
|
bool area(double lb, double rb, double lab, double rab, T* result){
|
20c212c0
heziqi
Ziqi added functi...
|
446
447
448
449
450
|
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...
|
451
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
452
453
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
20c212c0
heziqi
Ziqi added functi...
|
454
455
456
457
458
|
lp = (T*) malloc(S); //memory allocation
rp = (T*) malloc(S);
cur = (T*) malloc(S);
cur2 = (T*) malloc(S);
|
20c212c0
heziqi
Ziqi added functi...
|
459
460
461
462
|
memset(result, (char)0, S);
//find the wavelenght position in the whole band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
463
464
465
|
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...
|
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
|
//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...
|
481
|
while (lab >= w[ai]){
|
20c212c0
heziqi
Ziqi added functi...
|
482
483
|
ai++;
}
|
70407ea9
heziqi
Ziqi completed he...
|
484
|
while (rab <= w[bi]){
|
20c212c0
heziqi
Ziqi added functi...
|
485
486
487
488
489
490
491
|
bi--;
}
band(lp, lb);
band(rp, rb);
//calculate the beginning and the ending part
|
70407ea9
heziqi
Ziqi completed he...
|
492
493
|
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...
|
494
495
|
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...
|
496
|
}
|
70407ea9
heziqi
Ziqi completed he...
|
497
498
|
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...
|
499
500
|
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...
|
501
|
}
|
517876d6
heziqi
metrics finished ...
|
502
|
|
20c212c0
heziqi
Ziqi added functi...
|
503
504
|
//calculate the area
ai++;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
505
|
for(unsigned long long i = ai; i <= bi ;i++)
|
20c212c0
heziqi
Ziqi added functi...
|
506
507
|
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
508
|
for(unsigned long long j = 0; j < XY; j++)
|
20c212c0
heziqi
Ziqi added functi...
|
509
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
510
|
result[j] += (T)((w[ai] - w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 2.0);
|
20c212c0
heziqi
Ziqi added functi...
|
511
512
513
|
}
std::swap(cur,cur2); //swap the band pointers
}
|
70407ea9
heziqi
Ziqi completed he...
|
514
|
|
517876d6
heziqi
metrics finished ...
|
515
516
517
518
|
free(lp);
free(rp);
free(cur);
free(cur2);
|
20c212c0
heziqi
Ziqi added functi...
|
519
520
521
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
522
523
524
525
526
527
528
529
530
|
/// Compute the ratio of two baseline-corrected peaks. The result is stored in a pre-allocated array.
/// @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...
|
531
|
bool ph_to_ph(T* result, double lb1, double rb1, double pos1, double lb2, double rb2, double pos2, unsigned char* mask = NULL){
|
70407ea9
heziqi
Ziqi completed he...
|
532
|
|
724ec347
David Mayerich
simplified the EN...
|
533
534
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
535
536
537
538
539
|
//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...
|
540
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
541
542
543
544
545
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
546
547
548
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
549
550
551
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
552
553
554
555
556
557
558
559
560
|
/// Compute the ratio between a peak area and peak height.
/// @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...
|
561
562
|
bool pa_to_ph(T* result, double lb1, double rb1, double lab1, double rab1,
double lb2, double rb2, double pos, unsigned char* mask = NULL){
|
70407ea9
heziqi
Ziqi completed he...
|
563
|
|
724ec347
David Mayerich
simplified the EN...
|
564
565
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
566
567
568
569
570
|
//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...
|
571
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
572
573
574
575
576
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
577
578
579
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
580
581
582
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
583
584
585
586
587
588
589
590
591
592
593
|
/// Compute the ratio between two peak areas.
/// @param lb1 is the label value for the left baseline point for the first peak (numerator)
/// @param rb1 is the label value for the right baseline point for the first peak (numerator)
/// @param lab1 is the label value for the left bound (start of the integration) of the first peak (numerator)
/// @param rab1 is the label value for the right bound (end of the integration) of the first peak (numerator)
/// @param lb2 is the label value for the left baseline point for the second peak (denominator)
/// @param rb2 is the label value for the right baseline point for the second peak (denominator)
/// @param lab2 is the label value for the left bound (start of the integration) of the second peak (denominator)
/// @param rab2 is the label value for the right bound (end of the integration) of the second peak (denominator)
/// @param result is a pointer to a pre-allocated array at least X * Y * sizeof(T) in size
|
ba51ae6a
David Mayerich
fixed metric calc...
|
594
595
|
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){
|
70407ea9
heziqi
Ziqi completed he...
|
596
|
|
724ec347
David Mayerich
simplified the EN...
|
597
598
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
70407ea9
heziqi
Ziqi completed he...
|
599
600
601
602
603
|
//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...
|
604
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
70407ea9
heziqi
Ziqi completed he...
|
605
606
607
608
609
|
if(p1[i] == 0 && p2[i] ==0)
result[i] = 1;
else
result[i] = p1[i] / p2[i];
}
|
517876d6
heziqi
metrics finished ...
|
610
611
612
|
free(p1);
free(p2);
|
70407ea9
heziqi
Ziqi completed he...
|
613
614
|
return true;
}
|
517876d6
heziqi
metrics finished ...
|
615
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
616
617
618
619
620
621
622
|
/// Compute the definite integral of a baseline corrected peak.
/// @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 ...
|
623
624
625
626
627
628
|
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...
|
629
630
|
unsigned long long XY = X() * Y();
unsigned long long S = XY * sizeof(T);
|
517876d6
heziqi
metrics finished ...
|
631
632
633
634
635
636
637
638
639
|
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
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
640
641
642
|
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 ...
|
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
|
//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);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
669
670
|
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 ...
|
671
672
673
|
}
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...
|
674
675
|
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 ...
|
676
677
678
679
|
}
//calculate f(x) times x
ai++;
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
680
|
for(unsigned long long i = ai; i <= bi ;i++)
|
517876d6
heziqi
metrics finished ...
|
681
682
|
{
baseline_band(lb, rb, lp, rp, w[ai], cur2);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
683
|
for(unsigned long long j = 0; j < XY; j++)
|
517876d6
heziqi
metrics finished ...
|
684
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
685
|
result[j] += (T)((w[ai] - w[ai-1]) * (w[ai] + w[ai-1]) * ((double)cur[j] + (double)cur2[j]) / 4.0);
|
517876d6
heziqi
metrics finished ...
|
686
687
688
689
690
691
692
693
694
695
696
|
}
std::swap(cur,cur2); //swap the band pointers
}
free(lp);
free(rp);
free(cur);
free(cur2);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
697
698
699
700
701
702
703
|
/// Compute the centroid of a baseline corrected peak.
/// @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...
|
704
|
bool centroid(T* result, double lb, double rb, double lab, double rab, unsigned char* mask = NULL){
|
724ec347
David Mayerich
simplified the EN...
|
705
706
|
T* p1 = (T*)malloc(X() * Y() * sizeof(T));
T* p2 = (T*)malloc(X() * Y() * sizeof(T));
|
517876d6
heziqi
metrics finished ...
|
707
708
709
710
711
|
//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...
|
712
|
for(unsigned long long i = 0; i < X() * Y(); i++){
|
ba51ae6a
David Mayerich
fixed metric calc...
|
713
|
if(mask == NULL || mask[i])
|
517876d6
heziqi
metrics finished ...
|
714
715
716
717
718
719
720
721
|
result[i] = p1[i] / p2[i];
}
free(p1);
free(p2);
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
722
723
724
725
726
727
728
|
/// Create a mask based on a given band and threshold value.
/// 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...
|
729
|
bool build_mask(unsigned char* mask, double mask_band, double threshold, bool PROGRESS = false){
|
4a6f666c
heziqi
Added mask method
|
730
|
|
724ec347
David Mayerich
simplified the EN...
|
731
|
T* temp = (T*)malloc(X() * Y() * sizeof(T)); //allocate memory for the certain band
|
798cea97
David Mayerich
added progress ba...
|
732
|
band(temp, mask_band, PROGRESS);
|
4a6f666c
heziqi
Added mask method
|
733
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
734
|
for (unsigned long long i = 0; i < X() * Y();i++) {
|
798cea97
David Mayerich
added progress ba...
|
735
|
if (temp[i] < threshold)
|
ba51ae6a
David Mayerich
fixed metric calc...
|
736
|
mask[i] = 0;
|
798cea97
David Mayerich
added progress ba...
|
737
|
else
|
ba51ae6a
David Mayerich
fixed metric calc...
|
738
|
mask[i] = 255;
|
4a6f666c
heziqi
Added mask method
|
739
740
|
}
|
517876d6
heziqi
metrics finished ...
|
741
|
free(temp);
|
4a6f666c
heziqi
Added mask method
|
742
743
744
745
|
return true;
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
746
747
748
749
|
/// Apply a mask file to the BSQ image, setting all values outside the mask to zero.
/// @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...
|
750
|
bool apply_mask(std::string outfile, unsigned char* p, bool PROGRESS = false){
|
740f8cd2
heziqi
added apply_mask
|
751
752
753
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
754
755
|
unsigned long long ZX = Z() * X(); //calculate the number of values in a page (XZ in BIP)
unsigned long long L = ZX * sizeof(T); //calculate the number of bytes in a page
|
740f8cd2
heziqi
added apply_mask
|
756
|
|
1a55a328
David Mayerich
Added comments fo...
|
757
|
T * temp = (T*)malloc(L); //allocate space for that page
|
740f8cd2
heziqi
added apply_mask
|
758
|
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
759
|
for (unsigned long long i = 0; i < Y(); i++) //for each page (Y in BIP)
|
740f8cd2
heziqi
added apply_mask
|
760
|
{
|
724ec347
David Mayerich
simplified the EN...
|
761
|
read_plane_y(temp, i); //load that page (it's pointed to by temp)
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
762
|
for ( unsigned long long j = 0; j < X(); j++) //for each X value
|
740f8cd2
heziqi
added apply_mask
|
763
|
{
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
764
|
for (unsigned long long k = 0; k < Z(); k++) //for each B value (band)
|
740f8cd2
heziqi
added apply_mask
|
765
|
{
|
724ec347
David Mayerich
simplified the EN...
|
766
767
|
if (p[i * X() + j] == 0) //if the mask value is zero
temp[j * Z() + k] = 0; //set the pixel value to zero
|
1a55a328
David Mayerich
Added comments fo...
|
768
|
else //otherwise just continue
|
740f8cd2
heziqi
added apply_mask
|
769
770
771
|
continue;
}
}
|
1a55a328
David Mayerich
Added comments fo...
|
772
|
target.write(reinterpret_cast<const char*>(temp), L); //write the edited band data into target file
|
6a46c8ff
David Mayerich
fixed bugs in app...
|
773
|
if(PROGRESS) progress = (double)(i+1) / (double)Y() * 100;
|
740f8cd2
heziqi
added apply_mask
|
774
|
}
|
1a55a328
David Mayerich
Added comments fo...
|
775
776
777
|
target.close(); //close the target file
free(temp); //free allocated memory
return true; //return true
|
740f8cd2
heziqi
added apply_mask
|
778
779
|
}
|
ba51ae6a
David Mayerich
fixed metric calc...
|
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
|
/// 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){
size_t Bbytes = sizeof(T) * Z();
size_t XY = X() * Y();
T* band = (T*) malloc( Bbytes ); //allocate space for a line
file.seekg(0, std::ios::beg); //seek to the beginning of the file
size_t p = 0; //create counter variables
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
if(mask[xy]){ //if the current pixel is masked
file.read( (char*)band, Bbytes ); //read the current line
for(size_t b = 0; b < Z(); b++){ //copy each band value to the sifted matrix
size_t i = p * Z() + b; //calculate the index in the sifted matrix
matrix[i] = band[b]; //store the current value in the line at the correct matrix location
}
p++; //increment the pixel pointer
}
else
file.seekg(Bbytes, std::ios::cur); //otherwise skip this band
}
return true;
}
|
e843658b
Brad Deutsch
Previous push did...
|
807
|
|
2fcab4f0
David Mayerich
added unsifting f...
|
808
|
/// Saves to disk only those spectra corresponding to mask values != 0
|
c1078e19
David Mayerich
HSIproc bug fixes...
|
809
|
bool sift(std::string outfile, unsigned char* mask, bool PROGRESS = false){
|
8550e94f
David Mayerich
added sifting and...
|
810
811
812
813
814
|
//reset the file pointer to the beginning of the file
file.seekg(0, std::ios::beg);
// open an output stream
|
e843658b
Brad Deutsch
Previous push did...
|
815
816
|
std::ofstream target(outfile.c_str(), std::ios::binary);
|
8550e94f
David Mayerich
added sifting and...
|
817
|
//allocate space for a single spectrum
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
818
|
unsigned long long B = Z();
|
8550e94f
David Mayerich
added sifting and...
|
819
|
T* spectrum = (T*) malloc(B * sizeof(T));
|
e843658b
Brad Deutsch
Previous push did...
|
820
|
|
8550e94f
David Mayerich
added sifting and...
|
821
|
//calculate the number of pixels in a band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
822
|
unsigned long long XY = X() * Y();
|
e843658b
Brad Deutsch
Previous push did...
|
823
|
|
8550e94f
David Mayerich
added sifting and...
|
824
|
//for each pixel
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
825
826
|
unsigned long long skip = 0; //number of spectra to skip
for(unsigned long long x = 0; x < XY; x++){
|
8550e94f
David Mayerich
added sifting and...
|
827
828
829
830
831
|
//if the current pixel isn't masked
if( mask[x] == 0){
//increment the number of skipped pixels
skip++;
|
e843658b
Brad Deutsch
Previous push did...
|
832
|
}
|
8550e94f
David Mayerich
added sifting and...
|
833
834
835
836
837
838
839
840
841
842
843
844
845
846
|
//if the current pixel is masked
else{
//skip the intermediate pixels
file.seekg(skip * B * sizeof(T), std::ios::cur);
//set the skip value to zero
skip = 0;
//read this pixel into memory
file.read((char *)spectrum, B * sizeof(T));
//write this pixel out
target.write((char *)spectrum, B * sizeof(T));
|
8550e94f
David Mayerich
added sifting and...
|
847
|
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
848
|
if(PROGRESS) progress = (double) (x+1) / XY * 100;
|
8550e94f
David Mayerich
added sifting and...
|
849
|
|
e843658b
Brad Deutsch
Previous push did...
|
850
|
}
|
8550e94f
David Mayerich
added sifting and...
|
851
852
|
//close the output file
|
e843658b
Brad Deutsch
Previous push did...
|
853
|
target.close();
|
8550e94f
David Mayerich
added sifting and...
|
854
|
free(spectrum);
|
cbce396e
David Mayerich
added support for...
|
855
|
|
cbce396e
David Mayerich
added support for...
|
856
|
return true;
|
8550e94f
David Mayerich
added sifting and...
|
857
858
|
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
859
|
bool unsift(std::string outfile, unsigned char* mask, unsigned long long samples, unsigned long long lines, bool PROGRESS = false){
|
8550e94f
David Mayerich
added sifting and...
|
860
861
862
863
864
865
866
867
|
// open an output stream
std::ofstream target(outfile.c_str(), std::ios::binary);
//reset the file pointer to the beginning of the file
file.seekg(0, std::ios::beg);
//allocate space for a single spectrum
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
868
|
unsigned long long B = Z();
|
8550e94f
David Mayerich
added sifting and...
|
869
870
871
872
873
874
875
|
T* spectrum = (T*) malloc(B * sizeof(T));
//allocate space for a spectrum of zeros
T* zeros = (T*) malloc(B * sizeof(T));
memset(zeros, 0, B * sizeof(T));
//calculate the number of pixels in a band
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
876
|
unsigned long long XY = samples * lines;
|
8550e94f
David Mayerich
added sifting and...
|
877
878
|
//for each pixel
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
879
880
|
unsigned long long skip = 0; //number of spectra to skip
for(unsigned long long x = 0; x < XY; x++){
|
8550e94f
David Mayerich
added sifting and...
|
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
|
//if the current pixel isn't masked
if( mask[x] == 0){
//write a bunch of zeros
target.write((char *)zeros, B * sizeof(T));
}
//if the current pixel is masked
else{
//read a pixel into memory
file.read((char *)spectrum, B * sizeof(T));
//write this pixel out
target.write((char *)spectrum, B * sizeof(T));
}
|
a2bf1d08
David Mayerich
general bug fixes...
|
898
|
if(PROGRESS) progress = (double)(x + 1) / XY * 100;
|
3150c537
David Mayerich
added further pro...
|
899
|
|
8550e94f
David Mayerich
added sifting and...
|
900
901
902
903
904
905
|
}
//close the output file
target.close();
free(spectrum);
|
a2bf1d08
David Mayerich
general bug fixes...
|
906
|
//progress = 100;
|
3150c537
David Mayerich
added further pro...
|
907
|
|
e843658b
Brad Deutsch
Previous push did...
|
908
|
return true;
|
8550e94f
David Mayerich
added sifting and...
|
909
910
|
|
e843658b
Brad Deutsch
Previous push did...
|
911
912
|
}
|
a23c4132
David Mayerich
Doxygen comments ...
|
913
914
915
916
|
/// 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 ...
|
917
|
bool avg_band(double* p, unsigned char* mask = NULL, bool PROGRESS = false){
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
918
919
920
921
922
923
924
925
926
927
928
929
930
931
|
unsigned long long XY = X() * Y(); //calculate the total number of pixels in the HSI
T* temp = (T*)malloc(sizeof(T) * Z()); //allocate space for the current spectrum to be read
memset(p, 0, sizeof(double) * Z()); //initialize the average spectrum to zero (0)
//for (unsigned j = 0; j < Z(); j++){
// p[j] = 0;
//}
unsigned long long count = nnz(mask); //calculate the number of masked pixels
for (unsigned long long i = 0; i < XY; i++){ //for each pixel in the HSI
if (mask == NULL || mask[i] != 0){ //if the pixel is masked
pixel(temp, i); //get the spectrum
for (unsigned long long j = 0; j < Z(); j++){ //for each spectral component
p[j] += (double)temp[j] / (double)count; //add the weighted value to the average
|
a43c4fe1
heziqi
Added crop in env...
|
932
933
|
}
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
934
|
if(PROGRESS) progress = (double)(i+1) / XY * 100; //increment the progress
|
a43c4fe1
heziqi
Added crop in env...
|
935
|
}
|
2aa68315
David Mayerich
major bug fixes f...
|
936
|
|
a43c4fe1
heziqi
Added crop in env...
|
937
|
free(temp);
|
a43c4fe1
heziqi
Added crop in env...
|
938
939
|
return true;
}
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
940
941
|
#ifdef CUDA_FOUND
/// Calculate the covariance matrix for masked pixels using cuBLAS
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
942
|
/// Note that cuBLAS only supports integer-sized arrays, so there may be issues with large spectra
|
63fc1df8
David Mayerich
added an inverse ...
|
943
|
bool co_matrix_cublas(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
944
945
946
947
948
|
cudaError_t cudaStat;
cublasStatus_t stat;
cublasHandle_t handle;
|
63fc1df8
David Mayerich
added an inverse ...
|
949
|
progress = 0; //initialize the progress to zero (0)
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
950
951
952
953
954
955
956
957
958
959
960
|
unsigned long long XY = X() * Y(); //calculate the number of elements in a band image
unsigned long long B = Z(); //calculate the number of spectral elements
double* s = (double*)malloc(sizeof(double) * B); //allocate space for the spectrum that will be pulled from the file
double* s_dev; //declare a device pointer that will store the spectrum on the GPU
double* A_dev; //declare a device pointer that will store the covariance matrix on the GPU
double* avg_dev; //declare a device pointer that will store the average spectrum
cudaStat = cudaMalloc(&s_dev, B * sizeof(double)); //allocate space on the CUDA device for the spectrum
cudaStat = cudaMalloc(&A_dev, B * B * sizeof(double)); //allocate space on the CUDA device for the covariance matrix
cudaStat = cudaMemset(A_dev, 0, B * B * sizeof(double)); //initialize the covariance matrix to zero (0)
cudaStat = cudaMalloc(&avg_dev, B * sizeof(double)); //allocate space on the CUDA device for the average spectrum
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
961
|
stat = cublasSetVector((int)B, sizeof(double), avg, 1, avg_dev, 1); //copy the average spectrum to the CUDA device
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
962
963
964
965
966
967
968
969
970
971
|
double ger_alpha = 1.0/(double)XY; //scale the outer product by the inverse of the number of samples (mean outer product)
double axpy_alpha = -1; //multiplication factor for the average spectrum (in order to perform a subtraction)
stat = cublasCreate(&handle); //create a cuBLAS instance
if (stat != CUBLAS_STATUS_SUCCESS) { //test the cuBLAS instance to make sure it is valid
printf ("CUBLAS initialization failed\n");
return EXIT_FAILURE;
}
for (unsigned long long xy = 0; xy < XY; xy++){ //for each pixel
|
5a5359da
David Mayerich
fixed - allows th...
|
972
973
|
if (mask == NULL || mask[xy] != 0){
pixeld(s, xy); //retreive the spectrum at the current xy pixel location
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
974
975
976
|
stat = cublasSetVector((int)B, sizeof(double), s, 1, s_dev, 1); //copy the spectrum from the host to the device
stat = cublasDaxpy(handle, (int)B, &axpy_alpha, avg_dev, 1, s_dev, 1); //subtract the average spectrum
stat = cublasDsyr(handle, CUBLAS_FILL_MODE_UPPER, (int)B, &ger_alpha, s_dev, 1, A_dev, (int)B); //calculate the covariance matrix (symmetric outer product)
|
5a5359da
David Mayerich
fixed - allows th...
|
977
|
}
|
63fc1df8
David Mayerich
added an inverse ...
|
978
|
if(PROGRESS) progress = (double)(xy+1) / XY * 100; //record the current progress
|
5a5359da
David Mayerich
fixed - allows th...
|
979
|
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
980
981
|
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
982
|
cublasGetMatrix((int)B, (int)B, sizeof(double), A_dev, (int)B, co, (int)B); //copy the result from the GPU to the CPU
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
983
984
985
986
987
|
cudaFree(A_dev); //clean up allocated device memory
cudaFree(s_dev);
cudaFree(avg_dev);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
988
989
|
for(unsigned long long i = 0; i < B; i++){ //copy the upper triangular portion to the lower triangular portion
for(unsigned long long j = i+1; j < B; j++){
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
990
991
992
993
|
co[B * i + j] = co[B * j + i];
}
}
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
994
995
996
|
return true;
}
#endif
|
a23c4132
David Mayerich
Doxygen comments ...
|
997
|
|
2aa68315
David Mayerich
major bug fixes f...
|
998
|
/// Calculate the covariance matrix for all masked pixels in the image with 64-bit floating point precision.
|
a23c4132
David Mayerich
Doxygen comments ...
|
999
1000
1001
1002
|
/// @param co is a pointer to pre-allocated memory of size [B * B] that stores the resulting covariance matrix
/// @param avg is a pointer to memory of size B that stores the average spectrum
/// @param mask is a pointer to memory of size [X * Y] that stores the mask value at each pixel location
|
63fc1df8
David Mayerich
added an inverse ...
|
1003
|
bool co_matrix(double* co, double* avg, unsigned char *mask, bool PROGRESS = false){
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1004
1005
|
#ifdef CUDA_FOUND
|
b37665a9
David Mayerich
cuBLAS won't run ...
|
1006
1007
1008
1009
1010
1011
|
int dev_count;
cudaGetDeviceCount(&dev_count); //get the number of CUDA devices
cudaDeviceProp prop;
cudaGetDeviceProperties(&prop, 0); //get the property of the first device
if(dev_count > 0 && prop.major != 9999) //if the first device is not an emulator
return co_matrix_cublas(co, avg, mask, PROGRESS); //use cuBLAS to calculate the covariance matrix
|
c6f526c2
David Mayerich
added cuBLAS supp...
|
1012
|
#endif
|
63fc1df8
David Mayerich
added an inverse ...
|
1013
|
progress = 0;
|
a43c4fe1
heziqi
Added crop in env...
|
1014
|
//memory allocation
|
2aa68315
David Mayerich
major bug fixes f...
|
1015
1016
|
unsigned long long XY = X() * Y();
unsigned long long B = Z();
|
a43c4fe1
heziqi
Added crop in env...
|
1017
|
T* temp = (T*)malloc(sizeof(T) * B);
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1018
1019
|
unsigned long long count = nnz(mask); //count the number of masked pixels
|
63fc1df8
David Mayerich
added an inverse ...
|
1020
|
|
2aa68315
David Mayerich
major bug fixes f...
|
1021
1022
1023
1024
|
//initialize covariance matrix
memset(co, 0, B * B * sizeof(double));
//calculate covariance matrix
|
2aa68315
David Mayerich
major bug fixes f...
|
1025
1026
1027
1028
1029
1030
1031
1032
1033
1034
1035
1036
1037
|
double* co_half = (double*) malloc(B * B * sizeof(double)); //allocate space for a higher-precision intermediate matrix
double* temp_precise = (double*) malloc(B * sizeof(double));
memset(co_half, 0, B * B * sizeof(double)); //initialize the high-precision matrix with zeros
unsigned long long idx; //stores i*B to speed indexing
for (unsigned long long xy = 0; xy < XY; xy++){
if (mask == NULL || mask[xy] != 0){
pixel(temp, xy); //retreive the spectrum at the current xy pixel location
for(unsigned long long b = 0; b < B; b++) //subtract the mean from this spectrum and increase the precision
temp_precise[b] = (double)temp[b] - (double)avg[b];
idx = 0;
for (unsigned long long b0 = 0; b0 < B; b0++){ //for each band
for (unsigned long long b1 = b0; b1 < B; b1++)
co_half[idx++] += temp_precise[b0] * temp_precise[b1];
|
a43c4fe1
heziqi
Added crop in env...
|
1038
1039
|
}
}
|
63fc1df8
David Mayerich
added an inverse ...
|
1040
|
if(PROGRESS) progress = (double)(xy+1) / XY * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1041
|
}
|
2aa68315
David Mayerich
major bug fixes f...
|
1042
1043
1044
1045
|
idx = 0;
for (unsigned long long i = 0; i < B; i++){ //copy the precision matrix to both halves of the output matrix
for (unsigned long long j = i; j < B; j++){
co[j * B + i] = co[i * B + j] = co_half[idx++] / (double) count;
|
a43c4fe1
heziqi
Added crop in env...
|
1046
1047
1048
|
}
}
|
a43c4fe1
heziqi
Added crop in env...
|
1049
|
free(temp);
|
2aa68315
David Mayerich
major bug fixes f...
|
1050
|
free(temp_precise);
|
a43c4fe1
heziqi
Added crop in env...
|
1051
1052
1053
|
return true;
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1054
|
bool project(std::string outfile, double* center, double* basis, unsigned long long M, unsigned char* mask = NULL, bool PROGRESS = false){
|
63fc1df8
David Mayerich
added an inverse ...
|
1055
1056
|
std::ofstream target(outfile.c_str(), std::ios::binary); //open the target binary file
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1057
|
//std::string headername = outfile + ".hdr"; //the header file name
|
63fc1df8
David Mayerich
added an inverse ...
|
1058
1059
1060
1061
1062
1063
1064
1065
1066
|
//memory allocation
unsigned long long XY = X() * Y();
unsigned long long B = Z();
T* s = (T*)malloc(sizeof(T) * B); //allocate space for the spectrum
T* rs = (T*)malloc(sizeof(T) * M); //allocate space for the projected spectrum
double* bv; //pointer to the current projection vector
for(unsigned long long xy = 0; xy < XY; xy++){ //for each spectrum in the image
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1067
1068
1069
1070
1071
1072
1073
1074
|
memset(rs, 0, sizeof(T) * M);
if(mask == NULL || mask[xy]){
pixel(s, xy); //load the spectrum
for(unsigned long long m = 0; m < M; m++){ //for each basis vector
bv = &basis[m * B]; //assign 'bv' to the beginning of the basis vector
for(unsigned long long b = 0; b < B; b++){ //for each band
rs[m] += (T)(((double)s[b] - center[b]) * bv[b]); //center the spectrum and perform the projection
}
|
63fc1df8
David Mayerich
added an inverse ...
|
1075
1076
|
}
}
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1077
|
|
63fc1df8
David Mayerich
added an inverse ...
|
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
1104
1105
1106
1107
|
target.write(reinterpret_cast<const char*>(rs), sizeof(T) * M); //write the projected vector
if(PROGRESS) progress = (double)(xy+1) / XY * 100;
}
free(s); //free temporary storage arrays
free(rs);
target.close(); //close the output file
return true;
}
bool inverse(std::string outfile, double* center, double* basis, unsigned long long B, unsigned long long C = 0, bool PROGRESS = false){
std::ofstream target(outfile.c_str(), std::ios::binary); //open the target binary file
std::string headername = outfile + ".hdr"; //the header file name
//memory allocation
unsigned long long XY = X() * Y();
if(C == 0) C = Z(); //if no coefficient number is given, assume all are used
C = std::min<unsigned long long>(C, Z()); //set the number of coefficients (the user can specify fewer)
T* coeff = (T*)malloc(sizeof(T) * Z()); //allocate space for the coefficients
T* s = (T*)malloc(sizeof(T) * B); //allocate space for the spectrum
double* bv; //pointer to the current projection vector
for(unsigned long long xy = 0; xy < XY; xy++){ //for each pixel in the image (expressed as a set of coefficients)
pixel(coeff, xy); //load the coefficients
memset(s, 0, sizeof(T) * B); //initialize the spectrum to zero (0)
for(unsigned long long c = 0; c < C; c++){ //for each basis vector coefficient
bv = &basis[c * B]; //assign 'bv' to the beginning of the basis vector
for(unsigned long long b = 0; b < B; b++){ //for each component of the basis vector
|
9d3ba0b1
David Mayerich
added stim::hsi a...
|
1108
|
s[b] += (T)((double)coeff[c] * bv[b] + center[b]); //calculate the contribution of each element of the basis vector in the final spectrum
|
63fc1df8
David Mayerich
added an inverse ...
|
1109
1110
1111
1112
1113
1114
1115
1116
1117
1118
1119
1120
1121
1122
|
}
}
target.write(reinterpret_cast<const char*>(s), sizeof(T) * B); //write the projected vector
if(PROGRESS) progress = (double)(xy+1) / XY * 100;
}
free(coeff); //free temporary storage arrays
free(s);
target.close(); //close the output file
return true;
}
|
0df38ff3
heziqi
fixed head detached
|
1123
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
1124
1125
1126
1127
1128
1129
1130
|
/// 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...
|
1131
1132
1133
1134
1135
|
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 ...
|
1136
1137
|
unsigned long long b1,
bool PROGRESS = false){
|
a43c4fe1
heziqi
Added crop in env...
|
1138
|
|
3033b886
David Mayerich
implemented spect...
|
1139
1140
1141
1142
1143
1144
1145
1146
1147
1148
1149
|
//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 length of one cropped spectrum
unsigned long long L = bands * sizeof(T);
//unsigned long long L = Z() * sizeof(T);
//allocate space for the spectrum
|
a43c4fe1
heziqi
Added crop in env...
|
1150
|
T* temp = (T*)malloc(L);
|
3033b886
David Mayerich
implemented spect...
|
1151
1152
|
//open an output file for binary writing
|
a43c4fe1
heziqi
Added crop in env...
|
1153
|
std::ofstream out(outfile.c_str(), std::ios::binary);
|
3033b886
David Mayerich
implemented spect...
|
1154
1155
1156
1157
1158
1159
1160
1161
1162
1163
1164
1165
1166
1167
1168
|
//seek to the first pixel in the cropped image
file.seekg( (y0 * X() * Z() + x0 * Z() + b0) * sizeof(T), std::ios::beg);
//distance between sample spectra in the same line
unsigned long long jump_sample = ( (Z() - b1) + b0 ) * sizeof(T);
//distance between sample spectra in adjacent lines
unsigned long long jump_line = (X() - x1) * Z() * sizeof(T);
//unsigned long long sp = y0 * X() + x0; //start pixel
//for each pixel in the image
for (unsigned y = 0; y < lines; y++)
|
a43c4fe1
heziqi
Added crop in env...
|
1169
|
{
|
3033b886
David Mayerich
implemented spect...
|
1170
|
for (unsigned x = 0; x < samples; x++)
|
a43c4fe1
heziqi
Added crop in env...
|
1171
|
{
|
3033b886
David Mayerich
implemented spect...
|
1172
1173
1174
|
//read the cropped spectral region
file.read( (char*) temp, L );
//pixel(temp, sp + x + y * X());
|
a43c4fe1
heziqi
Added crop in env...
|
1175
|
out.write(reinterpret_cast<const char*>(temp), L); //write slice data into target file
|
3150c537
David Mayerich
added further pro...
|
1176
|
|
3033b886
David Mayerich
implemented spect...
|
1177
1178
|
file.seekg(jump_sample, std::ios::cur);
|
63fc1df8
David Mayerich
added an inverse ...
|
1179
|
if(PROGRESS) progress = (double)((y+1) * samples + x + 1) / (lines * samples) * 100;
|
a43c4fe1
heziqi
Added crop in env...
|
1180
|
}
|
3033b886
David Mayerich
implemented spect...
|
1181
1182
|
file.seekg(jump_line, std::ios::cur);
|
a43c4fe1
heziqi
Added crop in env...
|
1183
1184
|
}
free(temp);
|
3150c537
David Mayerich
added further pro...
|
1185
|
|
a43c4fe1
heziqi
Added crop in env...
|
1186
1187
1188
|
return true;
}
|
dc8eb8aa
David Mayerich
added band trimmi...
|
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
|
/// 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 B = Z(); //calculate the number of elements in a spectrum
size_t Bdst = Z() - band_array.size(); //calculate the number of elements in an output spectrum
size_t Bb = B * sizeof(T); //calculate the number of bytes in a spectrum
size_t XY = X() * Y(); //calculate the number of pixels in the image
T* src = (T*)malloc(Bb); //allocate space to store an input spectrum
T* dst = (T*)malloc(Bdst * sizeof(T)); //allocate space to store an output spectrum
size_t i; //index into the band array
size_t bdst; //index into the output array
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
i = 0;
bdst = 0;
file.read((char*)src, Bb); //read a spectrum
for(size_t b = 0; b < B; b++){ //for each band
if(b != band_array[i]){ //if the band isn't trimmed
dst[bdst] = src[b]; //copy the band value to the output spectrum
bdst++;
}
else i++; //otherwise increment i
}
out.write((char*)dst, Bdst * sizeof(T)); //write the output spectrum
if(PROGRESS) progress = (double)(xy + 1) / (double) XY * 100;
}
free(src);
free(dst);
}
|
2ce6954b
David Mayerich
added the ability...
|
1225
1226
1227
1228
1229
1230
1231
1232
1233
1234
1235
1236
1237
1238
1239
1240
1241
1242
1243
1244
1245
1246
1247
1248
1249
1250
1251
1252
1253
1254
1255
1256
1257
1258
1259
|
/// Combine two BIP 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, bip<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 spec_bytes = Z() * sizeof(T); //calculate the number of bytes in a spectrum
T* spec = (T*)malloc(spec_bytes); //allocate space for a spectrum
for(size_t y = 0; y < S[1]; y++){ //for each pixel in the destination image
for(size_t x = 0; x < S[0]; x++){
if(x >= p0[0] && x < p0[0] + X() && y >= p0[1] && y < p0[1] + Y()) //if this pixel is in the current image
file.read((char*)spec, spec_bytes);
else if(x >= p1[0] && x < p1[0] + C->X() && y >= p1[1] && y < p1[1] + C->Y()) //if this pixel is in the source image
C->file.read((char*)spec, spec_bytes);
else
memset(spec, 0, spec_bytes);
out.write((char*)spec, spec_bytes); //write to the output file
}
if(PROGRESS) progress = (double)( (y+1) * S[0] + 1) / (double) (S[0] * S[1]) * 100;
}
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1260
1261
1262
1263
1264
1265
1266
1267
|
/// 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...
|
1268
|
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...
|
1269
1270
1271
1272
1273
1274
1275
1276
1277
1278
1279
1280
1281
1282
1283
1284
1285
|
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
size_t N = end - start + 1; //number of bands in the output spectrum
size_t Nb = N * sizeof(T); //size of the output spectrum in bytes
size_t B = Z(); //calculate the number of values in a spectrum
size_t Bb = B * sizeof(T); //calculate the size of a spectrum in bytes
file.seekg(0, std::ios::beg); //move to the beginning of the input file
size_t nC = C.size(); //get the number of bands that the kernel spans
T* inspec = (T*)malloc(Bb); //allocate space for the input spectrum
T* outspec = (T*)malloc(Nb); //allocate space for the output spectrum
size_t XY = X() * Y(); //number of pixels in the image
for(size_t xy = 0; xy < XY; xy++){ //for each pixel
file.read((char*)inspec, Bb); //read an input spectrum
memset(outspec, 0, Nb); //set the output spectrum to zero (0)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1286
1287
1288
1289
1290
|
if(mask == NULL || mask[xy]){
for(size_t b = 0; b < N; b++){ //for each component of the spectrum
for(size_t c = 0; c < nC; c++){ //for each coefficient in the kernel
outspec[b] += (T)(inspec[b + start + c] * C[c]); //perform the sum/multiply part of the convolution
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1291
1292
1293
1294
1295
1296
1297
|
}
}
out.write((char*)outspec, Nb); //output the band
if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
}
}
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1298
|
void deriv(std::string outfile, size_t d, size_t order, const std::vector<double> w, unsigned char* mask = NULL, bool PROGRESS = false){
|
9b2a5d71
David Mayerich
implemented finit...
|
1299
1300
1301
1302
1303
1304
1305
1306
1307
1308
1309
1310
1311
1312
1313
1314
1315
1316
1317
1318
1319
1320
1321
1322
|
std::ofstream out(outfile.c_str(), std::ios::binary); //open the output file for writing
size_t B = Z(); //calculate the number of values in a spectrum
size_t Bb = B * sizeof(T); //calculate the size of a spectrum in bytes
bool UNIFORM = true;
double ds = w[1] - w[0]; //initialize ds
for(size_t b = 1; b < B; b++) //test to see if the spectral spacing is uniform (if it is, convolution is much faster)
if(w[b] - w[b-1] != ds) UNIFORM = false;
size_t nC = order + d; //approximating a derivative requires order + d samples
file.seekg(0, std::ios::beg); //move to the beginning of the input file
T* inspec = (T*)malloc(Bb); //allocate space for the input spectrum
T* outspec = (T*)malloc(Bb); //allocate space for the output spectrum
size_t XY = X() * Y(); //number of pixels in the image
size_t mid = (size_t)(nC / 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 xy = 0; xy < XY; xy++){ //for each pixel
file.read((char*)inspec, Bb); //read an input spectrum
memset(outspec, 0, Bb); //set the output spectrum to zero (0)
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1323
1324
1325
|
if(mask == NULL || mask[xy]){
iw = 0;
for(size_t b = 0; b < mid; b++){ //for each component of the spectrum
|
9b2a5d71
David Mayerich
implemented finit...
|
1326
1327
|
std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + nC); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[b], w_pts, d); //get the optimal sample weights
|
9d77bbd9
David Mayerich
updates for HSIvi...
|
1328
1329
1330
1331
1332
1333
1334
1335
1336
1337
1338
1339
1340
1341
1342
1343
1344
1345
1346
1347
|
for(size_t c = 0; c < nC; c++) //for each coefficient in the kernel
outspec[b] += (T)(inspec[iw + c] * C[c]); //perform the sum/multiply part of the convolution
}
std::vector<double> w_pts(w.begin(), w.begin() + nC); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[0], w_pts, d); //get the optimal sample weights
for(size_t b = mid; b <= B - (nC - mid); b++){
iw = b - mid;
if(!UNIFORM){ //if the spacing is non-uniform, we have to re-calculate these points every iteration
std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + nC); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[b], w_pts, d); //get the optimal sample weights
}
for(size_t c = 0; c < nC; c++) //for each coefficient in the kernel
outspec[b] += (T)(inspec[iw + c] * C[c]); //perform the sum/multiply part of the convolution
}
iw = B - nC;
for(size_t b = B - (nC - mid) + 1; b < B; b++){
std::vector<double> w_pts(w.begin() + iw, w.begin() + iw + nC); //get the wavelengths corresponding to each sample
std::vector<double> C = diff_coefficients(w[b], w_pts, d); //get the optimal sample weights
for(size_t c = 0; c < nC; c++) //for each coefficient in the kernel
outspec[b] += (T)(inspec[iw + c] * C[c]); //perform the sum/multiply part of the convolution
|
9b2a5d71
David Mayerich
implemented finit...
|
1348
|
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1349
|
}
|
9b2a5d71
David Mayerich
implemented finit...
|
1350
1351
1352
1353
1354
|
out.write((char*)outspec, Bb); //output the band
if(PROGRESS) progress = (double)(xy+1) / (double)XY * 100;
}
}
|
dc8eb8aa
David Mayerich
added band trimmi...
|
1355
|
|
0df38ff3
heziqi
fixed head detached
|
1356
|
|
a23c4132
David Mayerich
Doxygen comments ...
|
1357
|
/// Close the file.
|
f6169dea
heziqi
Ziqi completed bi...
|
1358
1359
1360
1361
1362
|
bool close(){
file.close();
return true;
}
|
88c3e636
heziqi
Ziqi added big.h
|
1363
|
};
|
6aa04ba2
David Mayerich
interleave types
|
1364
|
}
|
e8eb202f
David Mayerich
added a new ENVI ...
|
1365
1366
|
#endif
|