Feature/16 rename and reorganize the demos in the repo

forward-solvers/readme.txt

@@ -0,0 +1 @@
+This folder will contain the Forward Solver demos.

inverse-solutions/readme.txt

@@ -0,0 +1 @@
+This folder will contain the Inverse Solution demos.

scripting/libraries/readme.txt → libraries/readme.txt

@@ -1 +1 @@
-The VTS libraries should be copied into this folder. Get the latest VTS library (VTS.dll) and its dependencies from the releases section of this repository https://github.com/VirtualPhotonics/Vts.Scripting.Python/releases
+The VTS libraries should be copied into this folder. Get the latest VTS library (VTS.dll) and its dependencies from the releases section of this repository https://github.com/VirtualPhotonics/Vts.Scripting.Python/releases

scripting/monte_carlo/demo_02_DAW_vs_CAW.ipynb → monte-carlo/daw_vs_caw.ipynb

@@ -27,7 +27,7 @@
     "#Import the Operating System so we can access the files for the VTS library\n",
     "import os\n",
     "current_directory = os.getcwd()\n",
-    "library_directory = current_directory.replace(\"monte_carlo\", \"libraries\")\n",
+    "library_directory = current_directory.replace(\"monte-carlo\", \"libraries\")\n",
     "vts_path = os.path.join(library_directory, \"Vts.dll\")"
    ]
   },
@@ -72,7 +72,6 @@
     "clr.AddReference(vts_path)\n",
     "import numpy as np\n",
     "import plotly.graph_objects as go\n",
-    "import plotly.express as px\n",
     "from Vts import *\n",
     "from Vts.Common import *\n",
     "from Vts.Extensions import *\n",

monte-carlo/r-of-rho-impulse-beam.py

@@ -0,0 +1,111 @@
+# This is an example of python code using VTS to plot R(rho) using MCCL
+#
+# Import the Operating System so we can access the files for the VTS library
+from pythonnet import load
+load('coreclr')
+import clr
+import os
+file = '../libraries/Vts.dll'
+print('Does this filepath exist?', os.path.isfile(file))
+clr.AddReference(os.path.abspath(file))
+
+print('Import numpy')
+import numpy as np
+print('Import pyplot')
+import matplotlib.pyplot as plt
+print('Import Vts')
+from Vts import *
+from Vts.Common import *
+from Vts.Extensions import *
+from Vts.Modeling.Optimizers import *
+from Vts.Modeling.ForwardSolvers import *
+from Vts.SpectralMapping import *
+from Vts.Factories import *
+from Vts.MonteCarlo import *
+from Vts.MonteCarlo.Sources import *
+from Vts.MonteCarlo.Tissues import *
+from Vts.MonteCarlo.Detectors import *
+from Vts.MonteCarlo.Factories import *
+from Vts.MonteCarlo.PhotonData import *
+from Vts.MonteCarlo.PostProcessing import *
+print('Import System')
+from System import Array, Double
+
+# SimulationInput defines the simulation. I think the default is collimated point source illumination normal to the surface.
+simulationInput = SimulationInput()
+simulationInput.N = 10000
+
+# We add four detectors. One to monitor the reflected excitance as a function of radius, and three to monitor the overall reflection and transmission.
+# add detectors to Simulation object
+detectors = Array.CreateInstance(IDetectorInput, 4)
+
+detectors[0] = ROfRhoDetectorInput()
+detectors[0].Rho = DoubleRange(start=0, stop=5, number=401)
+detectors[1] = RDiffuseDetectorInput()
+detectors[2] = RSpecularDetectorInput()
+detectors[3] = TDiffuseDetectorInput()
+
+simulationInput.DetectorInputs = detectors
+
+# This is an index matched sample that has scattering of 0.99/mm and absorption of 0.01/mm. It is 10mm thick.
+d = 10       # mm
+mua = 0.01   # mm⁻¹
+musp = 0.99  # mm⁻¹
+g = 0        # scattering anisotropy
+n = 1        # matched index of refraction
+
+regions = Array.CreateInstance(ITissueRegion, 3)
+
+regions[0] = LayerTissueRegion(zRange=DoubleRange(Double.NegativeInfinity, 0.0), op=OpticalProperties(mua=0.0, musp=1E-10, g=1.0, n=1.0))
+regions[1] = LayerTissueRegion(zRange=DoubleRange(0.0, d), op=OpticalProperties(mua=mua, musp=musp, g=g, n=n))
+regions[2] = LayerTissueRegion(zRange=DoubleRange(d, Double.PositiveInfinity), op=OpticalProperties(0.0, 1E-10, 1.0, 1.0))
+
+simulationInput.TissueInput = MultiLayerTissueInput(regions)
+
+# create the simulation
+simulation = MonteCarloSimulation(simulationInput)
+
+# run the simulation
+simulationOutput = simulation.Run()
+
+# extract the data
+rDiffuse = Array.CreateInstance(RDiffuseDetector, 1)
+rDiffuse[0] = simulationOutput.ResultsDictionary["RDiffuse"]
+
+tDiffuse = Array.CreateInstance(TDiffuseDetector, 1)
+tDiffuse[0] = simulationOutput.ResultsDictionary["TDiffuse"]
+
+rSpecular = Array.CreateInstance(RSpecularDetector, 1)
+rSpecular[0] = simulationOutput.ResultsDictionary["RSpecular"]
+
+print("specular R = %.5f" % rSpecular[0].Mean)
+print(" diffuse R = %.5f" % rDiffuse[0].Mean)
+print(" diffuse T = %.5f" % tDiffuse[0].Mean)
+
+# plot the results using Pyplot
+detectorResults = Array.CreateInstance(ROfRhoDetector, 1)
+detectorResults[0] = simulationOutput.ResultsDictionary["ROfRho"]
+
+reflectance = np.array([r for r in detectorResults[0].Mean])
+edges = np.array([mp for mp in detectorResults[0].Rho])[:-1]
+
+plt.figure(figsize=(8,4.5))
+plt.plot(edges, reflectance, 'ob', markersize=2)
+plt.plot(-edges, reflectance, 'ob', markersize=2)
+plt.xlabel('ρ [mm]')
+plt.ylabel('R(ρ) [W/mm²]')
+plt.title('1 W Impulse Beam')
+
+text_args = {
+    'ha': 'left',  # Horizontal alignment
+    'va': 'top',   # Vertical alignment
+    'transform': plt.gca().transAxes,  # Coordinate system transformation
+    'fontsize': 9  # Font size
+}
+
+plt.text(0.8, 0.95, 'n=%.3f' % n, **text_args)
+plt.text(0.8, 0.90, r'$\mu_a$=%.2f mm⁻¹' % mua, **text_args)
+plt.text(0.8, 0.85, r"${\mu_s}'$=%.2f mm⁻¹" % musp, **text_args)
+plt.text(0.8, 0.80, 'g=%.2f' % g, **text_args)
+plt.text(0.8, 0.75, 'd=%.1f mm' % d, **text_args)
+plt.show()

monte-carlo/r-of-rho.py

@@ -0,0 +1,65 @@
+# This is an example of python code using VTS to plot R(rho) using MCCL
+#
+# Import the Operating System so we can access the files for the VTS library
+from pythonnet import load
+load('coreclr')
+import clr
+import os
+file = '../libraries/Vts.dll'
+print('Does this filepath exist?', os.path.isfile(file))
+clr.AddReference(os.path.abspath(file))
+
+print('Import numpy')
+import numpy as np
+print('Import plotly.graph')
+import plotly.graph_objects as go
+print('Import Vts')
+from Vts import *
+from Vts.Common import *
+from Vts.Extensions import *
+from Vts.Modeling.Optimizers import *
+from Vts.Modeling.ForwardSolvers import *
+from Vts.SpectralMapping import *
+from Vts.Factories import *
+from Vts.MonteCarlo import *
+from Vts.MonteCarlo.Sources import *
+from Vts.MonteCarlo.Tissues import *
+from Vts.MonteCarlo.Detectors import *
+from Vts.MonteCarlo.Factories import *
+from Vts.MonteCarlo.PhotonData import *
+from Vts.MonteCarlo.PostProcessing import *
+print('Import System')
+from System import Array
+# Setup the values for the simulations and plot results
+# create a SimulationInput object to define the simulation
+detectorRange = DoubleRange(start=0, stop=40, number=201)
+detectorInput = ROfRhoDetectorInput()
+detectorInput.Rho = detectorRange
+detectorInput.Name = "ROfRho"
+detectors = Array.CreateInstance(IDetectorInput,1)
+detectors[0] = detectorInput
+
+simulationInput = SimulationInput()
+simulationInput.N = 1000
+simulationInput.DetectorInputs = detectors
+
+# create the simulation
+simulation = MonteCarloSimulation(simulationInput)
+
+# run the simulation
+simulationOutput = simulation.Run()
+
+# plot the results using Plotly
+detectorResults = Array.CreateInstance(ROfRhoDetector,1)
+detectorResults[0] = simulationOutput.ResultsDictionary["ROfRho"]
+logReflectance = [r for r in detectorResults[0].Mean]
+detectorMidpoints = [mp for mp in detectorRange]
+
+xLabel = "ρ [mm]"
+yLabel = "log(R(ρ)) [mm-2]"
+
+chart = go.Figure()
+chart.add_trace(go.Scatter(x=detectorMidpoints, y=logReflectance, mode='markers'))
+chart.update_layout( title="log(R(ρ)) [mm-2]", xaxis_title=xLabel, yaxis_title=yLabel)
+chart.update_yaxes(type="log")
+chart.show(renderer="browser")

scripting/monte_carlo/demo_01_r_of_rho_simple.ipynb → monte-carlo/r_of_rho.ipynb

@@ -25,7 +25,7 @@
     "#Import the Operating System so we can access the files for the VTS library\n",
     "import os\n",
     "current_directory = os.getcwd()\n",
-    "library_directory = current_directory.replace(\"monte_carlo\", \"libraries\")\n",
+    "library_directory = current_directory.replace(\"monte-carlo\", \"libraries\")\n",
     "vts_path = os.path.join(library_directory, \"Vts.dll\")"
    ]
   },
@@ -66,7 +66,6 @@
     "clr.AddReference(vts_path)\n",
     "import numpy as np\n",
     "import plotly.graph_objects as go\n",
-    "import plotly.express as px\n",
     "from Vts import *\n",
     "from Vts.Common import *\n",
     "from Vts.Extensions import *\n",

scripting/monte_carlo/vts-trial.ipynb → monte-carlo/r_of_rho_impulse_beam.ipynb

@@ -37,7 +37,7 @@
     "#Import the Operating System so we can get the file path for the Vts library\n",
     "import os\n",
     "current_directory = os.getcwd()\n",
-    "library_directory = current_directory.replace(\"monte_carlo\", \"libraries\")\n",
+    "library_directory = current_directory.replace(\"monte-carlo\", \"libraries\")\n",
     "vts_path = os.path.join(library_directory, \"Vts.dll\")\n",
     "clr.AddReference(vts_path)"
    ]
@@ -260,7 +260,7 @@
    "source": [
     "Which should produce  \n",
     "\n",
-    "<img src='example.svg'>"
+    "<img src='r_of_rho_impulse_beam.svg'>"
    ]
   }
  ],