close all clear addpath(genpath('../Functions')) %% Defaults Data_path = '..\..\..\..\..\..\LINX FP08.001\Activity 7 - bending - visualizations and tiff stacks\mat_file\'; samples = {'out_out_CD','out_out_MD','in_in_CD','in_in_MD'}; degree = {'0','45','90','180'}; layer_name = {'outer','inner'}; %% extract poitns for the pipeline clc flag_points = 0; % 1 if no point has been extracted and first time use of the code if flag_points for i = 1 sample = samples{i}; for j = 1:4 dg = degree{j}; %% load data load([Data_path,'Processed_',sample,'_',dg]) %% use the pre_processing to extract the points PointSelection end end end clearvars -except Data_path samples degree layer_name %% layer segmentation and investigation clc answer = questdlg('Do you want to enhance the contrast? ','Contrast:','No','Yes','No'); for i = 1 sample = samples{i}; for j = 1:4 %% load data dg = degree{j}; fprintf('Load Data %s %s \n',sample,dg) load([Data_path,'Processed_',sample,'_',dg]) %% use the pre_processing to extract the points % detect the layers layer_name = {'outer','inner'}; for l = 1:length(layer_name) flag_layer = layer_name{l}; disp(['Layer Detection ',flag_layer]) load(['Results\point\',flag_layer,'_points_',sample,'_',dg]) Delta_LU = [3, 7]; if any(strcmp(dg,'0') | strcmp(dg,'45')) range = 15:-1:-15; else switch flag_layer case 'inner' range = 30:-1:-35; case 'outer' range = 20:-1:-20; end end LayerDetection end %% measure disp('Measure ...') PrepMeasure %% registration disp('Registration ...') PrepRegistration end end %% visualize the measure for i = 1%:4 Measure end close all %% apply the registration for i = 1%:4 Registration end close all %% apply the alignment and transformation for i = 1%:4 Transformation end close all %% convert the meshes for i = 1%:4 Export2inp end close all