ADDED INTERNAL LAMBDA FN THRESHOLD

Rounds slight variations above and below 0-1 range to limits
fuzhiqin0413 · Jan 8, 2022 · 5170b8f · 5170b8f
1 parent 9c9579c
commit 5170b8f
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Showing 4 changed files with 19 additions and 11 deletions.
diff --git a/create_2d_cone_slice.m b/create_2d_cone_slice.m
@@ -9,7 +9,7 @@
     voxScale = voxSize/newVoxSize; % Scale up factor on image for FDTD
 
 writeImage = 0;
-    fileNameBase = 'Cone_EC'; %'Cylinder' 'Cone_EC' 'Cone_CinC' 'Cone_CinC_EC'
+    fileNameBase = 'Cone'; %'Cylinder' 'Cone_EC' 'Cone_CinC' 'Cone_CinC_EC'
 
 % targetFolder = '/Users/gavintaylor/Desktop/AnalysisImages';    
 targetFolder = '/Users/gavintaylor/Documents/Company/Client Projects/Cones MPI/AnalysisVolumes/2 Micron';    
@@ -43,7 +43,7 @@
 
 % Note, these don't automatically adjust the filename
 displayProfiles.CinC = 0; 
-displayProfiles.EpicorneaCone = 1;
+displayProfiles.EpicorneaCone = 0;
 
 %Can be from 1 - 4, can also be equal
 interconeOnLeft = NaN;
@@ -60,7 +60,7 @@
 if ~makeLabels
     outerValue = 1.33;
     innerValue = 1.34;
-    coneValue = 'radialTop'; %1.52 'cylinder', 'radialTop', 'radialBase', 'linear' 'both'
+    coneValue = 'radialBase'; %1.52 'cylinder', 'radialTop', 'radialBase', 'linear' 'both'
     outerCorneaValue = 1.5;
     epicorneaValue = 1.53;
     interconeValue = -1; %1.47; -1; 

diff --git a/graded_RI_trace_and_test.m b/graded_RI_trace_and_test.m
@@ -139,7 +139,7 @@
 scaleBarsOnRayDiagram = 1;
 acceptanceUsingReceptor = 1;
 
-testPlot = 1;
+testPlot = 0;
 testPlotSurface = 0;
 
 loopLim = 10000;
@@ -1025,7 +1025,7 @@
 
 timePerAngle = zeros(length(incidenceAngle),1);
 
-for aAngle = 8; 1:length(incidenceAngle);
+for aAngle = 1:length(incidenceAngle);
 
     tic
 
@@ -1074,7 +1074,7 @@
        periodSpotsArray = zeros(3, numPeriods, nOrigins);
     end
 
-    for iOrigin = 2102; 1:nOrigins;
+    for iOrigin = 1:nOrigins;
 
         tempTime = toc;
         [aAngle iOrigin round(tempTime/60)]
@@ -2611,14 +2611,21 @@
 %         lambda = norm(intersectPoints(nearestInd,:)-x0)/norm(x1-x0);
         lambda = nearestDist/norm(x1-x0);
 
+        % Seem to need a threshold here as well...
+        if lambda > 1 && lambda < 1 + 1e-9
+            lambda = 1;
+        elseif lambda < 0 && lambda > -1e-9
+            lambda = 0;
+        end
+
     else
        % points are equal, set to zero to break
        lambda = 0;
 %        warning('Query points are equal in lambda')
     end
 
     if lambda > 1
-        [lambda inpolyhedron(surface, x1, 'tol', 0, 'flipNormals',true) ...
+        [lambda inpolyhedron(surface, x0, 'tol', 0, 'flipNormals',true) ...
             inpolyhedron(surface, x1, 'tol', 0, 'flipNormals',true) norm(x1-x0) min(abs(intersectDistance))]
 
         error('Large lambda step, intersect was triggered too early, check threshold in intersection function')

diff --git a/plot_cone_data.m b/plot_cone_data.m
@@ -43,7 +43,7 @@
 
 exposedConeInds = find(coneProfileZ*voxelSize > coneTipZ - exposedHeight/1000);
 
-for aAngle = 1:length(incidenceAngle);
+for aAngle = 1:5; 1:length(incidenceAngle);
 
     rayPathArray = rayPathCells{aAngle}; 
     finalIntersect = finalIntersectCells{aAngle};

diff --git a/runConditionsBatch.m b/runConditionsBatch.m
@@ -6,16 +6,17 @@
 
 % metaFile = 'Cone_1000_nm_Cone_0_SD_GRIN_both.mat'; graded_RI_trace_and_test
 % metaFile = 'Cone_1000_nm_Cone_0_SD_GRIN_cylinder.mat'; graded_RI_trace_and_test
-% metaFile = 'Cylinder_1000_nm_Cone_0_SD_GRIN_cylinder.mat'; graded_RI_trace_and_test
+%%% REDO %%% metaFile = 'Cylinder_1000_nm_Cone_0_SD_GRIN_cylinder.mat'; graded_RI_trace_and_test
 % metaFile = 'Cone_1000_nm_Cone_0_SD_GRIN_linear.mat'; graded_RI_trace_and_test
 % metaFile = 'Cone_1000_nm_Cone_0_SD_GRIN_radialTop.mat'; graded_RI_trace_and_test
+metaFile = 'Cone_1000_nm_Cone_0_SD_GRIN_radialBase.mat'; graded_RI_trace_and_test
 % metaFile = 'Cone_1000_nm_Cone_0_SD_GRIN_radialTop_TipCorrection.mat'; graded_RI_trace_and_test
 
 % internal structures
 dataFolder = '/Users/gavintaylor/Documents/Company/Client Projects/Cones MPI/AnalysisVolumes/2 micron/Extra internal structures/Radial RI/';
 
-metaFile = 'Cone_CinC_1000_nm_Cone_0_SD_GRIN_radialTop.mat'; graded_RI_trace_and_test
-metaFile = 'Cone_CinC_EC_1000_nm_Cone_0_SD_GRIN_radialTop.mat'; graded_RI_trace_and_test
+% metaFile = 'Cone_CinC_1000_nm_Cone_0_SD_GRIN_radialTop.mat'; graded_RI_trace_and_test
+% metaFile = 'Cone_CinC_EC_1000_nm_Cone_0_SD_GRIN_radialTop.mat'; graded_RI_trace_and_test
 metaFile = 'Cone_EC_1000_nm_Cone_0_SD_GRIN_radialTop.mat'; graded_RI_trace_and_test
 
 % % Uniform