0c9bf8ae
 dmayerich
Case-sensitive er...
|
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
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
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
|
#include <fstream>
using namespace std;
#include "interactivemie.h"
#include <QtGui/QApplication>
#include "qtSpectrumDisplay.h"
#include "globals.h"
#include "rtsGUIConsole.h"
#include "PerformanceData.h"
#include <complex>
//#include <direct.h>
PerformanceData PD;
qtSpectrumDisplay* gpSpectrumDisplay;
vector<vector<SpecPair> > RefSpectrum;
vector<SpecPair> SimSpectrum;
vector<SpecPair> EtaK;
vector<SpecPair> EtaN;
int currentSpec = 0;
double nuMin = 800;
double nuMax = 4000;
double dNu = 2;
double aMin = 0;
double aMax = 1;
double scaleI0 = 1.0;
double refSlope = 0.0;
bool dispRefSpec = true;
bool dispSimSpec = true;
bool dispSimK = true;
bool dispMatK = true;
bool dispSimN = true;
bool dispMatN = true;
double dispScaleK = 1.0;
double dispScaleN = 1.0;
SpecType dispSimType = AbsorbanceSpecType;
bool dispNormalize = false;
double dispNormFactor = 1.0;
//material parameters
double radius = 4.0f;
double baseIR = 1.49f;
double cA = 1.0;
//vector<SpecPair> KMaterial;
//vector<SpecPair> NMaterial;
bool applyMaterial = true;
vector<Material> MaterialList;
int currentMaterial = 0;
//optical parameters
double cNAi = 0.0;
double cNAo = 0.6;
double oNAi = 0.0;
double oNAo = 0.6;
OpticsType opticsMode = TransmissionOpticsType;
bool pointDetector = false;
int objectiveSamples = 200;
//fitting parameters
double minMSE = 0.00001;
int maxFitIter = 20;
void TempSimSpectrum()
{
SpecPair temp;
for(int i=800; i<4000; i++)
{
temp.nu = i;
temp.A = sin((double)i/200);
SimSpectrum.push_back(temp);
}
}
void UpdateDisplay(){
gpSpectrumDisplay->updateGL();
}
void LoadMaterial(string fileNameK, string fileNameN, string materialName)
{
Material newMaterial;
newMaterial.name = materialName;
vector<SpecPair> KMaterial = LoadSpectrum(fileNameK.c_str());
vector<SpecPair> NMaterial = LoadSpectrum(fileNameN.c_str());
//make sure that the sizes are the same
if(KMaterial.size() != NMaterial.size()){
cout<<"Error, material properties don't match."<<endl;
exit(1);
}
complex<double> eta;
//int j;
for(unsigned int i=0; i<KMaterial.size(); i++){
newMaterial.nu.push_back(KMaterial[i].nu);
eta = complex<double>(NMaterial[i].A, KMaterial[i].A);
newMaterial.eta.push_back(eta);
}
MaterialList.push_back(newMaterial);
}
void LoadMaterial(string fileNameK, string materialName){
//load the material absorbance
vector<SpecPair> KMaterial = LoadSpectrum(fileNameK.c_str());
vector<SpecPair> NMaterial;
//KMaterial = LoadSpectrum("eta_TolueneK.txt");
//compute the real IR using Kramers Kronig
//copy the absorbance values into a linear array
double* k = (double*)malloc(sizeof(double) * KMaterial.size());
double* n = (double*)malloc(sizeof(double) * KMaterial.size());
for(unsigned int i=0; i<KMaterial.size(); i++)
k[i] = KMaterial[i].A;
//use Kramers Kronig to determine the real part of the index of refraction
cudaKramersKronig(n, k, KMaterial.size(), KMaterial[0].nu, KMaterial.back().nu, baseIR);
SpecPair temp;
for(unsigned int i=0; i<KMaterial.size(); i++)
{
temp.nu = KMaterial[i].nu;
temp.A = n[i];
NMaterial.push_back(temp);
}
//create the material
Material newMaterial;
newMaterial.name = materialName;
complex<double> eta;
for(unsigned int i=0; i<KMaterial.size(); i++){
newMaterial.nu.push_back(KMaterial[i].nu);
eta = complex<double>(NMaterial[i].A, KMaterial[i].A);
newMaterial.eta.push_back(eta);
}
MaterialList.push_back(newMaterial);
}
void FitDisplay(){
double minA = 99999.0;
double maxA = -99999.0;
double k, n;
if(dispSimSpec)
for(unsigned int i=0; i<SimSpectrum.size(); i++)
{
if(SimSpectrum[i].A < minA)
minA = SimSpectrum[i].A;
if(SimSpectrum[i].A > maxA)
maxA = SimSpectrum[i].A;
}
if(dispRefSpec && RefSpectrum.size() > 0)
for(unsigned int i=0; i<RefSpectrum[currentSpec].size(); i++)
{
if(RefSpectrum[currentSpec][i].A < minA)
minA = RefSpectrum[currentSpec][i].A;
if(RefSpectrum[currentSpec][i].A > maxA)
maxA = RefSpectrum[currentSpec][i].A;
}
if(dispMatK)
for(unsigned int i=0; i<EtaK.size(); i++)
{
k = MaterialList[currentMaterial].eta[i].imag() * dispScaleK;
if(k < minA)
minA = k;
if(k > maxA)
maxA = k;
}
if(dispSimK)
for(unsigned int i=0; i<EtaK.size(); i++)
{
k = EtaK[i].A * dispScaleK;
if(k < minA)
minA = k;
if(EtaK[i].A > maxA)
maxA = k;
}
if(dispMatN)
for(unsigned int i=0; i<EtaN.size(); i++)
{
n = (MaterialList[currentMaterial].eta[i].real() - baseIR) * dispScaleN;
if(n < minA)
minA = n;
if(n > maxA)
maxA = n;
}
if(dispSimN)
for(unsigned int i=0; i<EtaN.size(); i++)
{
n = (EtaN[i].A - baseIR) * dispScaleN;
if(n < minA)
minA = n;
if(n > maxA)
maxA = n;
}
aMin = minA;
aMax = maxA;
UpdateDisplay();
}
void ChangeAbsorbance(){
//compute the real part of the index of refraction
//copy the absorbance values into a linear array
int nSamples = MaterialList[currentMaterial].eta.size();
double startNu = MaterialList[currentMaterial].nu.front();
double endNu = MaterialList[currentMaterial].nu.back();
double* k = (double*)malloc(sizeof(double) * nSamples);
double* n = (double*)malloc(sizeof(double) * nSamples);
for(int i=0; i<nSamples; i++)
k[i] = MaterialList[currentMaterial].eta[i].imag() * cA;
//NMaterial.clear();
EtaK.clear();
EtaN.clear();
//use Kramers Kronig to determine the real part of the index of refraction
cudaKramersKronig(n, k, nSamples, startNu, endNu, baseIR);
//copy the real part of the index of refraction into the vector
SpecPair temp;
//load the imaginary IR from the absorbance data
double nu;
for(int i=0; i<nSamples; i++){
nu = MaterialList[currentMaterial].nu[i];
if(nu >= nuMin && nu <= nuMax){
temp.nu = nu;
temp.A = k[i];
EtaK.push_back(temp);
//temp.A = NMaterial[i].A;
temp.A = n[i];
EtaN.push_back(temp);
}
}
free(k);
free(n);
}
void SetMaterial()
{
EtaK.clear();
EtaN.clear();
int nSamples = MaterialList[currentMaterial].eta.size();
double nu;
SpecPair temp;
//initialize the current nuMin and nuMax values
nuMin = MaterialList[currentMaterial].nu[0];
nuMax = nuMin;
for(int i=0; i<nSamples; i++){
nu = MaterialList[currentMaterial].nu[i];
//if(nu >= nuMin && nu <= nuMax){
//update the min and max values for display
if(nu < nuMin) nuMin = nu;
if(nu > nuMax) nuMax = nu;
temp.nu = nu;
temp.A = MaterialList[currentMaterial].eta[i].imag();
EtaK.push_back(temp);
temp.A = MaterialList[currentMaterial].eta[i].real();
EtaN.push_back(temp);
}
cA = 1.0;
}
int main(int argc, char *argv[])
{
//load the default project file (any previous optical settings)
LoadState();
//load the default materials
LoadMaterial("eta_TolueneK.txt", "eta_TolueneN.txt", "Toluene");
LoadMaterial("kPMMA.txt", "PMMA");
//LoadMaterial("../../../../data/materials/rtsSU8_k.txt", "../../../../data/materials/rtsSU8_n.txt", "SU8");
SetMaterial();
//compute the analytical solution for the Mie scattered spectrum
SimulateSpectrum();
QApplication a(argc, argv);
InteractiveMie w;
w.show();
w.move(0, 0);
QRect frame = w.frameGeometry();
QRect inside = w.geometry();
//activate a console for output
RedirectIOToConsole(0, frame.height(), frame.width());
gpSpectrumDisplay = new qtSpectrumDisplay();
gpSpectrumDisplay->move(frame.width(), 0);
gpSpectrumDisplay->resize(2*inside.height(), inside.height());
gpSpectrumDisplay->show();
//refresh the UI
w.refreshUI();
return a.exec();
}
|
