Merge pull request #86 from VirtualPhotonics/72-net-polyglot-notebook…

…-and-jupyter-notebook-documentation-and-samples

72 Implement and test script-style use of the VTS

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "dotnet.defaultSolution": "src/Vts.sln"
+}

matlab/vts_wrapper/short_course_monte_carlo_lab.m

@@ -7,7 +7,7 @@
 startup();
 
 % ======================================================================= %
-%% Example 1a: run Monte Carlo simulations for fluence with increasing N photons
+%% Example 01a: run Monte Carlo simulations for fluence with increasing N photons
 clear;
 Nphot=[10, 100, 1000, 10000]; % number of photons launched takes about 1 mins
 
@@ -129,7 +129,8 @@
     save(sprintf('dawSD%d.txt',j),'-ascii','SD');
   end
 end
-%% Example 1b: Compare standard deviation of two absorption methods
+
+%% Example 01b: Compare standard deviation of two absorption methods
 % this cell relies on above cell execution
 f=figure('Position',[scrsz(3)/5 scrsz(4)/5 scrsz(3)/2 scrsz(4)/2]);
 set(f,'Name','Analog relative error - DAW relative error');
@@ -156,7 +157,7 @@
 end
 
 % ======================================================================= %
-%% Example 2: run Monte Carlo simulations accounting for absorption with
+%% Example 02: run Monte Carlo simulations accounting for absorption with
 % analog and continuous absorption weighting with 10,000 photons and compare
 % time and relative error
 

matlab/vts_wrapper/vts_mc_demo.m

@@ -8,7 +8,7 @@
 startup();
 
 % ======================================================================= %
-%% Example 1: run a simple Monte Carlo simulation with 1000 photons
+%% Example 01: run a simple Monte Carlo simulation with 1000 photons
 
 % create a default set of inputs
 si = SimulationInput();
@@ -29,7 +29,7 @@
 set(f,'Name','Reflectance vs Rho for N=1000');
 
 % ======================================================================= %
-%% Example 2: run Monte Carlo simulations for two absorption weighting types 
+%% Example 02: run Monte Carlo simulations for two absorption weighting types 
 % with 1000 photons each and compare computation time
 
 % create a default set of inputs
@@ -49,7 +49,7 @@
 output2 = VtsMonteCarlo.RunSimulation(si);
 
 % ======================================================================= %
-%% Example 3: run a Monte Carlo simulation with a fully-customized input
+%% Example 03: run a Monte Carlo simulation with a fully-customized input
 % (values used here are the class defaults)
 
 % 1) define a source...
@@ -128,7 +128,7 @@
 output = VtsMonteCarlo.RunSimulation(input);
 
 % ======================================================================= %
-%% Example 4: run a list of Monte Carlo simulations
+%% Example 04: run a list of Monte Carlo simulations
 % create a list of two default SimulationInput with different numbers of 
 % photons
 
@@ -156,7 +156,7 @@
 set(f,'Name','Simulation 2 results');
 
 % ======================================================================= %
-% Example 5: run a Monte Carlo simulation with post-processing enabled
+% Example 05: run a Monte Carlo simulation with post-processing enabled
 % First run a simulation, then post-process the generated database and
 % compare on-the-fly results with post-processed results
 si = SimulationInput();
@@ -187,7 +187,7 @@
 legend('on-the-fly','post-processed');
 
 % ======================================================================= %
-% Example 6: run a Monte Carlo simulation with pMC post-processing enabled
+% Example 06: run a Monte Carlo simulation with pMC post-processing enabled
 % First run a simulation, then post-process the generated database CA
 % varying optical properties
 si = SimulationInput();
@@ -260,7 +260,7 @@
 set(f,'Name','Perturbation MC using CAW');
 
 % ======================================================================= %
-% Example 7: run a Monte Carlo simulation with pMC post-processing enabled
+% Example 07: run a Monte Carlo simulation with pMC post-processing enabled
 % Use generated database to solve inverse problem with measured data
 % generated using Nurbs
 % NOTE: convergence to measured data optical properties affected by:
@@ -375,7 +375,7 @@
     abs(measMus-recoveredOPs(2))/measOPs(2)));
 
 % ======================================================================= %
-% Example 8: run a Monte Carlo simulation and verify results with
+% Example 08: run a Monte Carlo simulation and verify results with
 % those in unit tests in Visual Studio
 % spell out all input to ensure same settings as in unit test
 si = SimulationInput();
@@ -422,8 +422,9 @@
     (abs(d3.Mean(1,1)-95.492965855)<0.000000001))
   disp('unit tests pass');
 end
+
 % ======================================================================= %
-%% Example 9: run a Monte Carlo simulation for transmittance tallies with 1000 photons
+%% Example 09: run a Monte Carlo simulation for transmittance tallies with 1000 photons
 
 % create a default set of inputs
 si = SimulationInput();
@@ -463,6 +464,7 @@
 f = figure; plot(d2.Fx, abs(d2.Mean)); ylabel('T(fx) [unitless]'); xlabel('Fx (mm^-^1)');
 title('Transmittance vs fx for N=1000');
 set(f,'Name','Transmittance vs Fx for N=1000');
+
 % ======================================================================= %
 %% Example 10: run R(fx) detector results
 

matlab/vts_wrapper/vts_solver_demo.m

@@ -8,7 +8,7 @@
 
 startup();
 
-%% Example ROfRhoAndFt
+%% Example 01: ROfRhoAndFt
 % Evaluate reflectance as a function of rho and temporal-frequency with one 
 % set of optical properites.
 
@@ -41,7 +41,7 @@
 xlabel('f_t');
 set(f,'Name','Reflectance as a function of Rho and Temporal-frequency');
 
-%% Example ROfFxAndFt
+%% Example 02: ROfFxAndFt
 % Evaluate reflectance as a function of spatial- and temporal- frequencies 
 % with one set of optical properites.
 
@@ -68,7 +68,7 @@
 xlabel('f_t');
 set(f,'Name','Reflectance as a function of Spatial- and Temporal- frequencies');
 
-%% Example FluenceOfRhoAndZ
+%% Example 03: FluenceOfRhoAndZ
 % Evaluate fluence as a function of rho and z using optical properties from 
 % a list of chromophore absorbers with their concentrations and a power law 
 % scatterer for a range of wavelengths.
@@ -105,11 +105,11 @@
 f = figure; imagesc(wv,zs,log(squeeze(test(:,1,:))));
 ylabel('z [mm]');
 xlabel('wavelength, \lambda [nm]');
-title('Fluence of \lambda and z and \rho=0.1 mm'); 
-set(f,'Name','Fluence as a function of Rho and z');
+title('Fluence of \lambda and z at \rho=0.1 mm'); 
+set(f,'Name','Fluence as a function of lambda and z');
 
 
-%% Example FluenceOfRhoAndZAndFt
+%% Example 04: FluenceOfRhoAndZAndFt
 % Evaluate fluence as a function of rho and z using one set of optical 
 % properties and a distributed gaussian source SDA solver type.
 
@@ -148,7 +148,7 @@
 ylabel('z [mm]')
 set(f,'Name','Modulation of fluence (AC/DC) of Rho and z and ft (ft=1GHz)');
 
-%% Example PHDOfRhoAndZ
+%% Example 05: PHDOfRhoAndZ
 % Evaluate Photon Hitting Density in cylindrical coordinates
 % using one set of optical properties and a distributed gaussian source SDA
 % solver type.
@@ -167,7 +167,7 @@
 ylabel('z [mm]')
 set(f,'Name','PHD of Rho and z');
 
-%% Example FluenceOfRhoAndZTwoLayer
+%% Example 06: FluenceOfRhoAndZTwoLayer
 % Evaluate fluence in cylindrical coordinates for a two
 % layer tissue with specified source-detector separation and top layer thickness
 % using two sets of optical properties.
@@ -185,7 +185,7 @@
 ylabel('z [mm]');
 set(f,'Name','Fluence of Rho and z - Two Layer');
 
-%% Example PHDOfRhoAndZTwoLayer
+%% Example 07: PHDOfRhoAndZTwoLayer
 % Evaluate Photon Hitting Density in cylindrical coordinates for a two
 % layer tissue with specified source-detector separation and top layer thickness
 % using two sets of optical properties.
@@ -204,7 +204,7 @@
 ylabel('z [mm]');
 set(f,'Name','PHD of Rho and z - Two Layer');
 
-%% Example AbsorbedEnergyOfRhoAndZ
+%% Example 08: AbsorbedEnergyOfRhoAndZ
 % Evaluate Absorbed Energy of rho and z using one set of optical properties 
 % and a point source SDA solver type.
 
@@ -225,7 +225,7 @@
 ylabel('z [mm]');
 set(f,'Name','Absorbed Energy of Rho and z');
 
-%% Example ROfRho
+%% Example 09: ROfRho
 % Evaluate reflectance as a function of rho with three sets
 % of optical properites.
 
@@ -242,7 +242,7 @@
 ylabel('R(\rho)');
 xlabel('\rho');
 
-%% Example ROfRhoAndT
+%% Example 10: ROfRhoAndTime
 % Evaluate reflectance of rho and t at one s-d separation and 
 % two sets of optical properites.
 
@@ -259,7 +259,7 @@
 ylabel('R(t)');
 xlabel('Time, t [ns]');
 
-%% Example ROfFxAndT 
+%% Example 11: ROfFxAndTime
 % Evaluate reflectance as a function of spacial-frequency and t using one 
 % set of optical properites.
 
@@ -291,7 +291,7 @@
 end
 legend(l2, 'FontSize', 12);
 
-%% Example ROfFx (single set of optical properties)
+%% Example 12: ROfFx (single set of optical properties)
 % Evaluate reflectance as a function of spacial-frequency with a single set 
 % of optical properties.
 
@@ -304,7 +304,7 @@
 ylabel('R(f_x)');
 xlabel('Spatial frequency, f_x [mm^-^1]');
 
-%% Example ROfFx (multiple sets of optical properties)
+%% Example 13: ROfFx (multiple sets of optical properties)
 % Evaluate reflectance as a function of spacial-frequency
 % with multiple sets of optical properties, varying mua linearly.
 
@@ -323,8 +323,7 @@
 ylabel('R(f_x)');
 xlabel('Spatial frequency, f_x [mm^-^1]');
 
-
-%% Example ROfFx (multiple optical properties, varying mua as a function of wavelength, mus' as intralipid scatterer)
+%% Example 14: ROfFx (multiple optical properties, varying mua as a function of wavelength, mus' as intralipid scatterer)
 % Evaluate reflectance as a function of spacial-frequency with multiple 
 % sets of optical properties, varying mua as a function of wavelength.
 
@@ -343,14 +342,14 @@
 
 % % or 
 scatterer.Type = 'Intralipid';
-scatterer.vol_frac =  0.5;
+scatterer.vol_frac =  0.01;
 
 % % or 
 % scatterer.Type = 'Mie';
 % scatterer.radius =  0.5;
 % scatterer.n =       1.4;
 % scatterer.nMedium = 1.0;
-% scatterer.vol_frac = 0.5;
+% scatterer.vol_frac = 0.001;
 
 op = VtsSpectroscopy.GetOP(absorbers, scatterer, wv);
 
@@ -384,7 +383,8 @@
 xlabel('Wavelength, \lambda [nm]');
 options = [{'Location', 'NorthWest'}; {'FontSize', 12}; {'Box', 'on'}];
 PlotHelper.CreateLegend(fx, 'f_x = ', 'mm^-^1', options);
-%% Example ROfFx (multiple optical properties, varying mua as a function of wavelength, mus' as mie scatterer)
+
+%% Example 15: ROfFx (multiple optical properties, varying mua as a function of wavelength, mus' as mie scatterer)
 % Evaluate reflectance as a function of spacial-frequency with multiple 
 % sets of optical properties, varying mua as a function of wavelength.
 
@@ -403,14 +403,14 @@
 
 % % or 
 % scatterer.Type = 'Intralipid';
-% scatterer.vol_frac =  0.5;
+% scatterer.vol_frac =  0.01;
 
 % % or 
 scatterer.Type = 'Mie';
 scatterer.radius =  0.5;
 scatterer.n =       1.4;
 scatterer.nMedium = 1.0;
-scatterer.vol_frac = 0.5;
+scatterer.vol_frac = 0.001;
 
 op = VtsSpectroscopy.GetOP(absorbers, scatterer, wv);
 
@@ -445,7 +445,7 @@
 options = [{'Location', 'NorthWest'}; {'FontSize', 12}; {'Box', 'on'}];
 PlotHelper.CreateLegend(fx, 'f_x = ', 'mm^-^1', options);
 
-%% Example ROfFx
+%% Example 16: ROfFx
 % Call planar reflectance with multiple sets of optical
 % properties, varying the scattering prefactor as a function of wavelength.
 
@@ -478,7 +478,7 @@
 options = [{'Location', 'NorthWest'}; {'FontSize', 12}; {'Box', 'on'}];
 PlotHelper.CreateLegend(A, '\mu_s''(1000nm) = ', 'mm^-^1', options);
 
-%% Example ROfRho (multiple wavelengths, multiple rho)
+%% Example 17: ROfRho (multiple wavelengths, multiple rho)
 % Call reflectance varying the wavelength.
 
 VtsSolvers.SetSolverType('PointSourceSDA');
@@ -508,7 +508,7 @@
 xlabel('Wavelength, \lambda [nm]');
 options = [{'Location', 'NorthEast'}; {'FontSize', 12}; {'Box', 'on'}];
 PlotHelper.CreateLegend(rho,'\rho = ', 'mm',options);
-%% Example ROfRho (inverse solution for chromophore concentrations for multiple wavelengths, single rho)
+%% Example 18: ROfRho (inverse solution for chromophore concentrations for multiple wavelengths, single rho)
 
 rho = 1;  % source-detector separation in mm
 wv = 400:50:1000;
@@ -571,7 +571,8 @@
     (measData-recovered)*(measData-recovered)'));
 disp(sprintf('error =   [%5.3f %5.3f %5.3f]',abs(measData(1)-recovered(1))/measData(1),...
     abs(measData(2)-recovered(2))/measData(2),abs(measData(3)-recovered(3))/measData(3)));
-%% Example ROfRho for a two-layer tissue (multiple optical properties and rhos)
+
+%% Example 19: ROfRho for a two-layer tissue (multiple optical properties and rhos)
 clear op
 topLayerThickness = 2;  % units: mm
 
@@ -592,7 +593,8 @@
 title('2-Layer Reflectance vs \rho for various top Layer OPs'); 
 ylabel('R(\rho)');
 xlabel('\rho');
-%% Example ROfFx for a two-layer tissue (multiple optical properties and fxs)
+
+%% Example 20: ROfFx for a two-layer tissue (multiple optical properties and fxs)
 clear op
 topLayerThickness = 2;  % units: mm
 
@@ -605,15 +607,16 @@
 
 fx = 0:0.01:0.5; % range of spatial frequencies in 1/mm
 test = VtsSolvers.ROfFxTwoLayer(op, topLayerThickness, fx);
-f = figure; semilogy(fx, test);
+f = figure; plot(fx, test);
 set(f,'Name','2-Layer Reflectance vs Fx for various top Layer Optical Properties');
 % create the legend with just the mua value from the top layer optical properties
 options = [{'FontSize', 12}; {'Location', 'NorthEast'}];
 PlotHelper.CreateLegend(op(:,1), 'top \mu_a: ', 'mm^-^1', options);
 title('2-Layer Reflectance vs fx for various top Layer OPs'); 
 ylabel('R(fx)');
 xlabel('fx');
-%% Example ROfRhoAndTime for a two-layer tissue (multiple optical properties and times)
+
+%% Example 21: ROfRhoAndTime for a two-layer tissue (multiple optical properties and times)
 clear op
 topLayerThickness = 2;  % units: mm
 % 
@@ -662,7 +665,7 @@
 ylabel('R(t)');
 xlabel('Time, t [ns]');
 
-%% Example ROfRhoAndFt for a two-layer tissue (multiple optical properties and fts)
+%% Example 22: ROfRhoAndFt for a two-layer tissue (multiple optical properties and fts)
 % Evaluate reflectance as a function of rho and temporal-frequency with one 
 % set of optical properites.
 clear op

src/Vts.Scripting.Test/GlobalUsings.cs

@@ -0,0 +1 @@
+global using NUnit.Framework;