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bgeorge
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May 15, 2019
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,71 +1,68 @@ | ||
| % bg_unwrapping | ||
| % Make sure we've got the files loaded | ||
| addpath(genpath(pwd)); | ||
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| data_select = 'data1'; | ||
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| % Load some data | ||
| % This will in theory be from CERR | ||
| tic | ||
| disp('Doing setup') | ||
| UNWRAPPING_DATA = struct; | ||
| START_POIs = getXYZD(25,1,planC); | ||
| FINISH_POIs = getXYZD(26,1,planC); | ||
| UNWRAPPING_DATA.as_points.START_POIs = START_POIs(:,1:3); | ||
| UNWRAPPING_DATA.as_points.FINISH_POIs = FINISH_POIs(:,1:3); | ||
| [UNWRAPPING_DATA.as_points.point_cloudD,~] = getXYZD(2,1,planC); | ||
| %UNWRAPPING_DATA.as_points.START_POIs = test_startPOI(data_select); | ||
| %UNWRAPPING_DATA.as_points.FINISH_POIs = test_endPOI(data_select); | ||
| %UNWRAPPING_DATA.as_points.point_cloudD = test_structXYZD(data_select); | ||
| UNWRAPPING_DATA.as_points.point_cloud = UNWRAPPING_DATA.as_points.point_cloudD(:,1:3); | ||
| UNWRAPPING_DATA.as_points.unwrap_centre = (max(UNWRAPPING_DATA.as_points.point_cloud) + min(UNWRAPPING_DATA.as_points.point_cloud))/2; | ||
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| % Remove this later | ||
| %UNWRAPPING_DATA.as_points.point_cloudD(:,4) = sqrt(sum((UNWRAPPING_DATA.as_points.point_cloudD(:,1:3) - UNWRAPPING_DATA.as_points.unwrap_centre).^2,2)); | ||
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| % Set some options | ||
| UNWRAPPING_DATA.options.SLICES = 30; | ||
| UNWRAPPING_DATA.options.RAYS = 30; | ||
| UNWRAPPING_DATA.voxelise_size_x = 100; | ||
| UNWRAPPING_DATA.voxelise_size_y = 100; | ||
| UNWRAPPING_DATA.voxelise_size_z = 100; | ||
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| % Do some data conversion to a voxelised labelmap | ||
| % This is necessary for the shortest path algorithm | ||
| UNWRAPPING_DATA = cloud_to_labelmap(UNWRAPPING_DATA); | ||
| UNWRAPPING_DATA = pois_to_labelmap(UNWRAPPING_DATA); | ||
| toc | ||
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| % Find the shortest path | ||
| % Uses 'curve extraction' module | ||
| tic | ||
| disp('Finding shortest path') | ||
| UNWRAPPING_DATA = complex_3D_bg(UNWRAPPING_DATA); | ||
| % Convert the voxel indices to points in 3D space | ||
| UNWRAPPING_DATA = shortest_as_points(UNWRAPPING_DATA); | ||
| toc | ||
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||
| % The the correct sized curve | ||
| % NB: Always need an extra point at hte start and the end | ||
| % Might think about ignoring the first and last 'n' points to avoid | ||
| % issues at the edge | ||
| [UNWRAPPING_DATA.as_points.full_path,~,~] = interparc(UNWRAPPING_DATA.options.SLICES+2,UNWRAPPING_DATA.as_points.shortest_path(:,1),UNWRAPPING_DATA.as_points.shortest_path(:,2),UNWRAPPING_DATA.as_points.shortest_path(:,3)); | ||
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| % There is where the magic happens! | ||
| % Do the ray_tracing algorithm to find the intersection from each central | ||
| % point to the surface | ||
| % This also deals with finding the rays from each point | ||
| tic | ||
| disp('Ray tracing') | ||
| UNWRAPPING_DATA = ray_trace(UNWRAPPING_DATA); | ||
| toc | ||
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||
| % Find the dose at each surface point and form into flattened DSM | ||
| disp('Create DSM') | ||
| tic | ||
| UNWRAPPING_DATA = create_dsm(UNWRAPPING_DATA); | ||
| toc | ||
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| % A nice new plot! | ||
| disp('Plotting') | ||
| UNWRAPPING_DATA = better_plotting(flipud(UNWRAPPING_DATA)); | ||
| function UNWRAPPING_DATA = bg_unwrapping(UNWRAPPING_DATA) | ||
| % bg_unwrapping | ||
| % Make sure we've got the files loaded | ||
| addpath(genpath(pwd)); | ||
|
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||
| if ~exist('UNWRAPPING_DATA','var') || isempty(UNWRAPPING_DATA) | ||
| % Load some data | ||
| data_select = 'data1'; | ||
| UNWRAPPING_DATA = struct; | ||
| UNWRAPPING_DATA.as_points.START_POIs = test_startPOI(data_select); | ||
| UNWRAPPING_DATA.as_points.FINISH_POIs = test_endPOI(data_select); | ||
| UNWRAPPING_DATA.as_points.point_cloudD = test_structXYZD(data_select); | ||
| UNWRAPPING_DATA.as_points.point_cloud = UNWRAPPING_DATA.as_points.point_cloudD(:,1:3); | ||
| UNWRAPPING_DATA.as_points.unwrap_centre = (max(UNWRAPPING_DATA.as_points.point_cloud) + min(UNWRAPPING_DATA.as_points.point_cloud))/2; | ||
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||
| % Set some options | ||
| UNWRAPPING_DATA.options.SLICES = 30; | ||
| UNWRAPPING_DATA.options.RAYS = 30; | ||
| UNWRAPPING_DATA.voxelise_size_x = 100; | ||
| UNWRAPPING_DATA.voxelise_size_y = 100; | ||
| UNWRAPPING_DATA.voxelise_size_z = 100; | ||
| else | ||
| % Assume that UNWRAPPING_DATA is initialised | ||
| end | ||
|
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||
| % Do some data conversion to a voxelised labelmap | ||
| % This is necessary for the shortest path algorithm | ||
| tic | ||
| disp('Data conversion') | ||
| UNWRAPPING_DATA = cloud_to_labelmap(UNWRAPPING_DATA); | ||
| UNWRAPPING_DATA = pois_to_labelmap(UNWRAPPING_DATA); | ||
| toc | ||
|
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||
| % Find the shortest path | ||
| % Uses 'curve extraction' module | ||
| tic | ||
| disp('Finding shortest path') | ||
| UNWRAPPING_DATA = complex_3D_bg(UNWRAPPING_DATA); | ||
| % Convert the voxel indices to points in 3D space | ||
| UNWRAPPING_DATA = shortest_as_points(UNWRAPPING_DATA); | ||
| toc | ||
|
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||
| % The the correct sized curve | ||
| % NB: Always need an extra point at hte start and the end | ||
| % Might think about ignoring the first and last 'n' points to avoid | ||
| % issues at the edge | ||
| [UNWRAPPING_DATA.as_points.full_path,~,~] = interparc(UNWRAPPING_DATA.options.SLICES+2,UNWRAPPING_DATA.as_points.shortest_path(:,1),UNWRAPPING_DATA.as_points.shortest_path(:,2),UNWRAPPING_DATA.as_points.shortest_path(:,3)); | ||
|
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||
| % There is where the magic happens! | ||
| % Do the ray_tracing algorithm to find the intersection from each central | ||
| % point to the surface | ||
| % This also deals with finding the rays from each point | ||
| tic | ||
| disp('Ray tracing') | ||
| UNWRAPPING_DATA = ray_trace(UNWRAPPING_DATA); | ||
| toc | ||
|
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||
| % Find the dose at each surface point and form into flattened DSM | ||
| disp('Create DSM') | ||
| tic | ||
| UNWRAPPING_DATA = create_dsm(UNWRAPPING_DATA); | ||
| toc | ||
|
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||
| % A nice new plot! | ||
| disp('Plotting') | ||
| figure | ||
| UNWRAPPING_DATA = better_plotting(flipud(UNWRAPPING_DATA)); | ||
| end |