deprecated / bimsim

Commit b6179de6d7efffaef298858c1a56f9079f21a89a

Authored by dmayerich
1 parent 967e46a1

added scripts for spectral simulation

Showing 5 changed files with 132 additions and 72 deletions   Show diff stats
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defaults.h
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... ... @@ -75,10 +75,10 @@
75 75  
76 76 #define DEFAULT_INTENSITY_FILE "testappend"
77 77 #define DEFAULT_TRANSMITTANCE_FILE ""
78   -#define DEFAULT_ABSORBANCE_FILE ""
  78 +#define DEFAULT_ABSORBANCE_FILE "out_a"
79 79 #define DEFAULT_NEAR_FILE "out_n.bmp"
80 80 #define DEFAULT_FAR_FILE "out_f.bmp"
81   -#define DEFAULT_EXTENDED_SOURCE ""
  81 +#define DEFAULT_EXTENDED_SOURCE "einstein_small.jpg"
82 82 #define DEFAULT_FIELD_TYPE "magnitude"
83 83 #define DEFAULT_FORMAT fileoutStruct::formatImage
84 84 #define DEFAULT_COLORMAP "brewer"
... ...
fileout.cu
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... ... @@ -113,7 +113,12 @@ void fileoutStruct::saveDetector(microscopeStruct* scope)
113 113 scalarslice I = scope->getIntensity();
114 114  
115 115 if(is_binary(intFile))
116   - I.toEnvi(intFile, scope->nf.lambda, append);
  116 + {
  117 + if(wavenumber)
  118 + I.toEnvi(intFile, 10000.0f/scope->nf.lambda, append);
  119 + else
  120 + I.toEnvi(intFile, scope->nf.lambda, append);
  121 + }
117 122 else
118 123 I.toImage(intFile);
119 124 }
... ... @@ -123,7 +128,12 @@ void fileoutStruct::saveDetector(microscopeStruct* scope)
123 128 scalarslice I = scope->getAbsorbance();
124 129  
125 130 if(is_binary(absFile))
126   - I.toEnvi(absFile, scope->nf.lambda, append);
  131 + {
  132 + if(wavenumber)
  133 + I.toEnvi(absFile, 10000.0f/scope->nf.lambda, append);
  134 + else
  135 + I.toEnvi(absFile, scope->nf.lambda, append);
  136 + }
127 137 else
128 138 I.toImage(absFile);
129 139 }
... ... @@ -133,7 +143,12 @@ void fileoutStruct::saveDetector(microscopeStruct* scope)
133 143 scalarslice I = scope->getTransmittance();
134 144  
135 145 if(is_binary(transFile))
136   - I.toEnvi(transFile, scope->nf.lambda, append);
  146 + {
  147 + if(wavenumber)
  148 + I.toEnvi(transFile, 10000.0f/scope->nf.lambda, append);
  149 + else
  150 + I.toEnvi(transFile, scope->nf.lambda, append);
  151 + }
137 152 else
138 153 I.toImage(transFile);
139 154 }
... ...
fileout.h
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... ... @@ -28,13 +28,15 @@ struct fileoutStruct{
28 28  
29 29 field_type field;
30 30  
  31 + //flag for output in wavenumber
  32 + bool wavenumber;
  33 +
31 34 //image_source source;
32 35  
33 36 //color map info
34 37 rts::colormap::colormapType colormap;
35 38 ptype colorMax;
36 39  
37   -
38 40 void Save(microscopeStruct* scope);
39 41 void Simulate(microscopeStruct* scope);
40 42  
... ... @@ -42,9 +44,10 @@ struct fileoutStruct{
42 44 bool is_binary(std::string filename);
43 45 void saveNearField(nearfieldStruct* nf);
44 46 void saveFarField(microscopeStruct* scope);
45   - void saveDetector(microscopeStruct* scope);
46   -
  47 + void saveDetector(microscopeStruct* scope);
47 48  
48 49 };
49 50  
  51 +
  52 +
50 53 #endif
... ...
options.h
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... ... @@ -138,14 +138,14 @@ static void loadMaterials(po::variables_map vm)
138 138  
139 139 for(int i=0; i<matVec.size(); i+=2)
140 140 {
141   - rts::material<ptype> newM(vm["lambda"].as<ptype>(), matVec[i], matVec[i+1]);
  141 + rts::material<ptype> newM(SCOPE->nf.lambda, matVec[i], matVec[i+1]);
142 142 SCOPE->nf.mVector.push_back(newM);
143 143 }
144 144 }
145 145 else
146 146 {
147 147 //add the command line material as the default (material 0)
148   - rts::material<ptype> newM(vm["lambda"].as<ptype>(), vm["n"].as<ptype>(), vm["k"].as<ptype>());
  148 + rts::material<ptype> newM(SCOPE->nf.lambda, vm["n"].as<ptype>(), vm["k"].as<ptype>());
149 149 SCOPE->nf.mVector.push_back(newM);
150 150 }
151 151  
... ... @@ -178,7 +178,7 @@ static void loadNearfieldParams(po::variables_map vm)
178 178 SCOPE->nf.planeWave = planeWave;
179 179  
180 180 //get the wavelength
181   - SCOPE->nf.lambda = vm["lambda"].as<ptype>();
  181 + //SCOPE->nf.lambda = vm["lambda"].as<ptype>();
182 182  
183 183 //get the incident field amplitude
184 184 SCOPE->nf.A = vm["amplitude"].as<ptype>();
... ... @@ -328,6 +328,7 @@ static void SetOptions(po::options_description &amp;desc)
328 328 ("material-file,M", po::value< vector<string> >()->multitoken(), "material file:\n [lambda n k]")
329 329 ("materials", po::value< vector<ptype> >()->multitoken(), "materials specified using n, k pairs:\n ex. --materials n1 k1 n2 k2\n (if used --n and --k are ignored)")
330 330 ("lambda,l", po::value<ptype>()->default_value(DEFAULT_LAMBDA), "incident wavelength")
  331 + ("nu", po::value<ptype>(), "incident frequency (in cm^-1)\n(if specified, lambda is ignored)")
331 332 ("theta,t", po::value<ptype>()->default_value(DEFAULT_K_THETA), "light direction (polar coords)")
332 333 ("phi,p", po::value<ptype>()->default_value(DEFAULT_K_PHI))
333 334 ("fx", po::value<ptype>()->default_value(DEFAULT_FOCUS_X), "incident focal point")
... ... @@ -374,6 +375,20 @@ static void LoadParameters(int argc, char *argv[])
374 375 exit(1);
375 376 }
376 377  
  378 + //load the wavelength
  379 + if(vm.count("nu"))
  380 + {
  381 + //wavelength is given in wavenumber - transform and flag
  382 + SCOPE->nf.lambda = 10000/vm["nu"].as<ptype>();
  383 + gFileOut.wavenumber = true;
  384 + }
  385 + //otherwise we are using lambda = wavelength
  386 + else
  387 + {
  388 + SCOPE->nf.lambda = vm["lambda"].as<ptype>();
  389 + gFileOut.wavenumber = false;
  390 + }
  391 +
377 392 //load spheres
378 393 loadSpheres(vm);
379 394  
... ...
specimage.py
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1   -#!/usr/bin/python3
2   -import subprocess
3   -
4   -command = "bimsim"
5   -
6   -#images
7   -intImage = "out_i.bmp"
8   -absImage = "out_a"
9   -#detector specs
10   -dsize = 208
11   -dsample = 6.5
12   -res = int(dsize / dsample)
13   -sampling = 4
14   -#incident field
15   -#nu = 800
16   -source = "central.bmp"
17   -order = 100
18   -#sphere
19   -x = 0
20   -y = 0
21   -z = 0
22   -a = 5
23   -#spectral samples
24   -nuStart = 800
25   -nuStop = 4000
26   -nuStep = 10
27   -iters = int((nuStop - nuStart) / nuStep)
28   -
29   -
30   -#set the position of the image plane
31   -command += " -u " + str(-dsize/2)
32   -command += " -v " + str(-dsize/2)
33   -command += " -w " + str(a)
34   -command += " -U " + str(dsize/2)
35   -command += " -V " + str(dsize/2)
36   -command += " -W " + str(a)
37   -command += " --plane-norm-x " + str(0)
38   -command += " --plane-norm-y " + str(0)
39   -command += " --plane-norm-z " + str(1)
40   -command += " -R " + str(res)
41   -command += " --supersample " + str(sampling)
42   -command += " -X " + source
43   -command += " --field-order " + str(order)
44   -command += " -I " + intImage
45   -command += " -A " + absImage
46   -command += " --append"
47   -command += " -x " + str(x)
48   -command += " -y " + str(y)
49   -command += " -z " + str(z)
50   -command += " -r " + str(a)
51   -
52   -for inu in range(0, iters):
53   - print("Iteration # " + str(inu + 1) + "/" + str(iters))
54   - nu = nuStart + inu * nuStep
55   - lam = 10000.0/nu
56   -
57   - runcommand = command + " -l " + str(lam)
58   - print(runcommand)
59   - subprocess.call(runcommand, shell=True)
60   -
61   -#print("Hello world!")
62 1 \ No newline at end of file
  2 +#!/usr/bin/python3
  3 +
  4 +
  5 +import subprocess, sys
  6 +
  7 +nuStart = 800
  8 +nuStop = 4000
  9 +nuStep = 10
  10 +
  11 +if len(sys.argv) > 1:
  12 + nuStart = sys.argv[1]
  13 +if len(sys.argv) > 2:
  14 + nuStop = sys.argv[2]
  15 +if len(sys.argv) > 3:
  16 + nuStep = sys.argv[3]
  17 +
  18 +command = "bimsim"
  19 +
  20 +#images
  21 +intImage = "out_i.bmp"
  22 +absImage = "out_a"
  23 +#detector specs
  24 +dsize = 208
  25 +dsample = 1
  26 +res = int(dsize / dsample)
  27 +sampling = 1
  28 +padding = 1
  29 +#incident field
  30 +source = ""
  31 +order = 100
  32 +mc = 400
  33 +#sphere
  34 +x = 0
  35 +y = 0
  36 +z = 0
  37 +a = 5
  38 +n = 1.4
  39 +k = 0.0
  40 +#spectral samples
  41 +iters = int((nuStop - nuStart) / nuStep) + 1
  42 +#optics
  43 +NAin = 0.2
  44 +NAout = 0.5
  45 +
  46 +
  47 +#set the position of the image plane
  48 +command += " -u " + str(-dsize/2)
  49 +command += " -v " + str(-dsize/2)
  50 +command += " -w " + str(a)
  51 +command += " -U " + str(dsize/2)
  52 +command += " -V " + str(dsize/2)
  53 +command += " -W " + str(a)
  54 +command += " --plane-norm-x " + str(0)
  55 +command += " --plane-norm-y " + str(0)
  56 +command += " --plane-norm-z " + str(1)
  57 +command += " -R " + str(res)
  58 +command += " --supersample " + str(sampling)
  59 +
  60 +if source != "":
  61 + command += " -X " + source
  62 +command += " --field-order " + str(order)
  63 +command += " -d " + str(padding)
  64 +command += " -s " + str(mc)
  65 +command += " -I " + intImage
  66 +command += " -A " + absImage
  67 +command += " --append"
  68 +#sphere
  69 +command += " -x " + str(x)
  70 +command += " -y " + str(y)
  71 +command += " -z " + str(z)
  72 +command += " -r " + str(a)
  73 +command += " -n " + str(n)
  74 +command += " -k " + str(k)
  75 +#set the optics
  76 +command += " -c " + str(NAin)
  77 +command += " -C " + str(NAout)
  78 +command += " -o " + str(NAin)
  79 +command += " -O " + str(NAout)
  80 +
  81 +for inu in range(0, iters):
  82 + print("Iteration # " + str(inu + 1) + "/" + str(iters))
  83 + nu = nuStart + inu * nuStep
  84 +
  85 + runcommand = command + " --nu " + str(nu)
  86 + print(runcommand)
  87 + subprocess.call(runcommand, shell=True)
  88 +
  89 +#print("Hello world!")
... ...