Added files for natural image and 3-circle model examples in the tuto…

…rial.
appliedtopology · Mar 13, 2015 · b3199ca · b3199ca
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diff --git a/reports/javaplex_tutorial/lazyOpticalDct-k15.png b/reports/javaplex_tutorial/lazyOpticalDct-k15.png
diff --git a/reports/javaplex_tutorial/lazyOpticalDct-k300.png b/reports/javaplex_tutorial/lazyOpticalDct-k300.png
diff --git a/reports/javaplex_tutorial/nk15c30.png b/reports/javaplex_tutorial/nk15c30.png
diff --git a/reports/javaplex_tutorial/nk300c30.png b/reports/javaplex_tutorial/nk300c30.png
diff --git a/reports/javaplex_tutorial/threeCircle.eps b/reports/javaplex_tutorial/threeCircle.eps
diff --git a/reports/javaplex_tutorial/threeCircle.pdf b/reports/javaplex_tutorial/threeCircle.pdf
diff --git a/src/matlab/for_distribution/tutorial_examples/optical_image_example.m b/src/matlab/for_distribution/tutorial_examples/optical_image_example.m
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+% This shows the optical image patch example - Section 6
+
+clc; clear; close all;
+
+% k = 300
+load pointsOpticalDct_k300.mat
+size(pointsOpticalDct_k300)
+
+max_dimension = 3;
+num_landmark_points = 50;
+nu = 1;
+num_divisions = 500;
+
+% create a sequential maxmin landmark selector
+landmark_selector = api.Plex4.createMaxMinSelector(pointsOpticalDct_k300, num_landmark_points);
+R = landmark_selector.getMaxDistanceFromPointsToLandmarks()
+max_filtration_value = R / 4;
+
+% create a lazy witness stream
+stream = streams.impl.LazyWitnessStream(landmark_selector.getUnderlyingMetricSpace(), landmark_selector, max_dimension, max_filtration_value, nu, num_divisions);
+stream.finalizeStream()
+
+% print out the size of the stream
+num_simplices = stream.getSize()
+
+% get persistence algorithm over Z/2Z
+persistence = api.Plex4.getModularSimplicialAlgorithm(max_dimension, 2);
+
+% compute the intervals
+intervals = persistence.computeIntervals(stream);
+
+% create the barcode plots
+options.filename = 'lazyOpticalDct-k300';
+options.max_filtration_value = max_filtration_value;
+options.max_dimension = max_dimension - 1;
+plot_barcodes(intervals, options);
+
+% plot a projection of the dataset onto the first two DCT basis vectors
+figure
+scatter(pointsOpticalDct_k300(:,1), pointsOpticalDct_k300(:,2), '.')
+axis square
+
+% k = 15
+load pointsOpticalDct_k15.mat
+size(pointsOpticalDct_k15)
+
+max_dimension = 3;
+num_landmark_points = 50;
+nu = 1;
+num_divisions = 500;
+
+% create a sequential maxmin landmark selector
+landmark_selector = api.Plex4.createMaxMinSelector(pointsOpticalDct_k15, num_landmark_points);
+R = landmark_selector.getMaxDistanceFromPointsToLandmarks()
+max_filtration_value = R / 4;
+
+% create a lazy witness stream
+stream = streams.impl.LazyWitnessStream(landmark_selector.getUnderlyingMetricSpace(), landmark_selector, max_dimension, max_filtration_value, nu, num_divisions);
+stream.finalizeStream()
+
+% print out the size of the stream
+num_simplices = stream.getSize()
+
+% get persistence algorithm over Z/2Z
+persistence = api.Plex4.getModularSimplicialAlgorithm(max_dimension, 2);
+
+% compute the intervals
+intervals = persistence.computeIntervals(stream);
+
+% create the barcode plots
+options.filename = 'lazyOpticalDct-k15';
+options.max_filtration_value = max_filtration_value;
+options.max_dimension = max_dimension - 1;
+plot_barcodes(intervals, options);
+
+% plot a projection of the dataset onto the first two DCT basis vectors
+figure
+scatter(pointsOpticalDct_k15(:,1), pointsOpticalDct_k15(:,2), '.')
+axis square
diff --git a/src/matlab/for_distribution/tutorial_examples/pointsOpticalDct_k15.mat b/src/matlab/for_distribution/tutorial_examples/pointsOpticalDct_k15.mat
diff --git a/src/matlab/for_distribution/tutorial_examples/pointsOpticalDct_k300.mat b/src/matlab/for_distribution/tutorial_examples/pointsOpticalDct_k300.mat
diff --git a/src/matlab/for_distribution/tutorial_examples/range_image_example.m b/src/matlab/for_distribution/tutorial_examples/range_image_example.m
@@ -0,0 +1,44 @@
+% This shows the range image patch example - Section 6
+
+clc; clear; close all;
+
+load pointsRange.mat
+size(pointsRange)
+
+max_dimension = 3;
+num_landmark_points = 50;
+nu = 1;
+num_divisions = 500;
+
+% create a sequential maxmin landmark selector
+landmark_selector = api.Plex4.createMaxMinSelector(pointsRange, num_landmark_points);
+R = landmark_selector.getMaxDistanceFromPointsToLandmarks()
+max_filtration_value = R / 3;
+
+% create a lazy witness stream
+stream = streams.impl.LazyWitnessStream(landmark_selector.getUnderlyingMetricSpace(), landmark_selector, max_dimension, max_filtration_value, nu, num_divisions);
+stream.finalizeStream()
+
+% print out the size of the stream - will be quite large since the complex
+% construction is very sensitive to the maximum filtration value
+num_simplices = stream.getSize()
+
+% get persistence algorithm over Z/2Z
+persistence = api.Plex4.getModularSimplicialAlgorithm(max_dimension, 2);
+
+% compute the intervals
+intervals = persistence.computeIntervals(stream);
+
+% create the barcode plots
+options.filename = 'lazyRange';
+options.max_filtration_value = max_filtration_value;
+options.max_dimension = max_dimension - 1;
+plot_barcodes(intervals, options);
+
+%% DCT
+
+pointsRangeDct = pointsRange * dct(5);
+
+figure;
+scatter(pointsRangeDct(:,1), pointsRangeDct(:,5), '.')
+axis square