Merge pull request #4 from MREYE-LUMC/examples

Examples

examples/Retinal illumination in pseudophakic eyes with and without Negative Dysphotopsia/Analyze.py

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+"""
+Supplementary materials to the scientific publication:
+
+van Vught L, Que I, Luyten GPM, Beenakker JWM. Effect of anatomical differences and intraocular lens design on Negative
+Dysphotopsia. Journal of Cataract & Refractive Surgery: September 06, 2022. doi: 10.1097/j.jcrs.0000000000001054
+
+These supplementary materials consist of:
+
+-	Eye models with specific anatomical characteristics for patients with Negative Dysphotopsia and for pseudophakic
+controls
+
+-	A python script to automatically determine the retinal illumination in Zemax Optic Studio through the ZOSPy API
+
+
+When using these data/scripts, please cite the above mentioned paper.
+
+The presented code and data are made available for research purposes only, no rights can be derived from them.
+
+These methods has been tested using Zemax Optic Studio version 20.3.2, python version 3.7.5 and ZOSPy version 0.6.0.
+
+Prior to running the script, make sure that the STL files supplied with this script are copied to the OpticStudio
+r'Objects/CAD Files' folder. The exact location (if unknown)  can be obtained by running:
+
+```
+import zospy as zp
+zos = zp.ZOS()
+zos.wakeup()
+zos.create_new_application()
+objdir = zos.Application.ObjectsDir
+zos.Application.CloseApplication()
+```
+"""
+
+import os
+
+import zospy as zp
+
+import matplotlib.pyplot as plt
+from mpl_toolkits.mplot3d import Axes3D
+import numpy as np
+
+
+def set_axes_equal_3d(ax):
+    """Make axes of 3D plot have equal scale so that spheres appear as spheres,
+    cubes as cubes, etc..  This is one possible solution to Matplotlib's
+    ax.set_aspect('equal') and ax.axis('equal') not working for 3D.
+
+    Parameters
+    ----------
+        ax: a matplotlib axis, e.g., as output from plt.gca().
+    """
+
+    x_limits = ax.get_xlim3d()
+    y_limits = ax.get_ylim3d()
+    z_limits = ax.get_zlim3d()
+
+    x_range = abs(x_limits[1] - x_limits[0])
+    x_middle = np.mean(x_limits)
+    y_range = abs(y_limits[1] - y_limits[0])
+    y_middle = np.mean(y_limits)
+    z_range = abs(z_limits[1] - z_limits[0])
+    z_middle = np.mean(z_limits)
+
+    # The plot bounding box is a sphere in the sense of the infinity
+    # norm, hence I call half the max range the plot radius.
+    plot_radius = 0.5*max([x_range, y_range, z_range])
+
+    ax.set_xlim3d([x_middle - plot_radius, x_middle + plot_radius])
+    ax.set_ylim3d([y_middle - plot_radius, y_middle + plot_radius])
+    ax.set_zlim3d([z_middle - plot_radius, z_middle + plot_radius])
+
+
+zos = zp.ZOS()
+zos.wakeup()
+
+# Make sure that Zemax OpticStudio in in `Interactive Extension` mode (Programming > Interactive Extension)
+zos.connect_as_extension()
+
+oss = zos.get_primary_system()
+
+pachy = 0.55
+cornea_irisdist = 3.12
+object_distance = 30  # distance object -> pupil center
+
+results = {}
+for model in ['NegativeDysphotopsia',
+              'PseudophakicControl'
+              ]:
+    fp = os.path.join(os.getcwd(), rf'{model}Model.zmx')
+    oss.load(fp)
+
+    # Get pointers to source and retina objects
+    obj_source = oss.NCE.GetObjectAt(2)
+    obj_retina = oss.NCE.GetObjectAt(14)
+
+    # Set number of rays
+    obj_source.GetCellAt(12).Value = str(1e5)
+
+    first = True  # use this to get position of detectors on first analysis only
+    results[model] = {'Irradiance': {}, 'AbsorbedIrradiance': {}, 'Flux': {}, 'AbsorbedFlux': {}}
+    for angle in range(0, 165, 5):
+        xnew = np.sin(np.deg2rad(angle)) * object_distance
+        znew = np.cos(np.deg2rad(angle)) * object_distance
+        obj_source.XPosition = xnew
+        obj_source.ZPosition = -(znew - pachy - cornea_irisdist)
+        obj_source.TiltAboutY = -angle
+
+        # Trace
+        RayTrace = oss.Tools.OpenNSCRayTrace()
+        RayTrace.NumberOfCores = 8
+        RayTrace.ClearDetectors(0)  # clear the old detector data!
+        RayTrace.ScatterNSCRays = True
+        RayTrace.UsePolarization = False
+        RayTrace.SplitNSCRays = False
+        RayTrace.IgnoreErrors = True
+        RayTrace.RunAndWaitForCompletion()
+        RayTrace.Close()
+
+        # Get data
+        fd = obj_retina.GetFacetedObjectData()
+
+        centroids = []
+        irradiance = []
+        absorbed_irradiance = []
+        flux = []
+        absorbed_flux = []
+
+        for facenum in range(fd.NumberOfFaces):
+            fd.CurrentFace = facenum
+            if first:
+                verts = np.array([list(fd.GetVertex(vertnum, 0, 0, 0)[1:]) for vertnum in range(fd.NumberOfVertices)])
+                centroids.append(verts.mean(axis=0))
+            irradiance.append(fd.Irradiance)
+            absorbed_irradiance.append(fd.AbsorbedIrradiance)
+            flux.append(fd.Flux)
+            absorbed_flux.append(fd.AbsorbedFlux)
+
+        if first:
+            results[model]['Centroids'] = np.array(centroids)
+            first = False  # Make sure centroids are only read in once
+        results[model]['Irradiance'][angle] = np.array(irradiance)
+        results[model]['AbsorbedIrradiance'][angle] = np.array(absorbed_irradiance)
+        results[model]['Flux'][angle] = np.array(flux)
+        results[model]['AbsorbedFlux'][angle] = np.array(absorbed_flux)
+
+# Show results
+cumulative_irr_nd = np.array([results['NegativeDysphotopsia']['Irradiance'][key]
+                              for key in results['NegativeDysphotopsia']['Irradiance'].keys()]).sum(axis=0)
+
+cumulative_irr_co = np.array([results['PseudophakicControl']['Irradiance'][key]
+                              for key in results['PseudophakicControl']['Irradiance'].keys()]).sum(axis=0)
+
+fig = plt.figure()
+ax1 = fig.add_subplot(121, projection=Axes3D.name)
+ax2 = fig.add_subplot(122, projection=Axes3D.name)
+
+vmax = np.max([cumulative_irr_nd.max(), cumulative_irr_co.max()])
+filter_nd = cumulative_irr_nd != 0
+ax1.scatter(*results['NegativeDysphotopsia']['Centroids'][filter_nd].T[np.array([0, 2, 1])],
+            c=cumulative_irr_nd[filter_nd], cmap='Greys_r', vmin=0, vmax=vmax, s=1)
+
+filter_co = cumulative_irr_co != 0
+ax2.scatter(*results['PseudophakicControl']['Centroids'][filter_co].T[np.array([0, 2, 1])],
+            c=cumulative_irr_co[filter_co], cmap='Greys_r', vmin=0, vmax=vmax, s=1)
+
+ax1.set_title('ND')
+ax2.set_title('Control')
+
+set_axes_equal_3d(ax1)
+set_axes_equal_3d(ax2)
+
+ax1.set_xlabel('x')
+ax1.set_ylabel('z')
+ax1.set_zlabel('y')
+
+ax2.set_xlabel('x')
+ax2.set_ylabel('z')
+ax2.set_zlabel('y')
+
+plt.show()

examples/Retinal illumination in pseudophakic eyes with and without Negative Dysphotopsia/README.md

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+# Example: Retinal illumination in pseudophakic eyes with and without Negative Dysphotopsia
+
+This example shows how to determine peripheral retinal illumination in models of the (pseudophakic) human eye using ZOSPy. The analysis presented in the *Analyze.py* script is a basic example of the analyses perfomed for the scientific paper [Effect of anatomical differences and intraocular lens design on Negative Dysphotopsia](https://doi.org/10.1097/j.jcrs.0000000000001054). The required eye models and STL files are kindly provided by the authors.
+
+## Warranty and liability
+The presented code and data are made available for research purposes only. There is no warranty and rights can not be 
+derived from them, as is also stated in the general license of this repository.
+
+## Citation
+Please cite the following research when using this example or the data provided with this example:
+
+van Vught L, Que I, Luyten GPM and Beenakker JWM.
+_Effect of anatomical differences and intraocular lens design on Negative Dysphotopsia._
+JCRS: Sep 06, 2022.<br>
+[doi: [10.1097/j.jcrs.0000000000001054](https://doi.org/10.1097/j.jcrs.0000000000001054) ] [[JCRS](https://journals.lww.com/jcrs/Abstract/9900/Effect_of_anatomical_differences_and_intraocular.107.aspx)]