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Isolate Matching and tracking -> stepD_2DDIC refactoring #2

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johnaoga Apr 5, 2025
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johnaoga Apr 5, 2025
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48 changes: 42 additions & 6 deletions src/dic_param.m
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Original file line number Diff line number Diff line change
@@ -1,21 +1,57 @@
% STEP D, E, F: 2D-DIC, 3D Reconstruction, Deformation analysis

%% Subject and Trial Settings
subject_id = "S09"; % Subject identifier
phase_id = "loading"; % Phase identifier
material_id = 2; % Material identifier
nfcond_set = [5]; % Number of conditions
spddxlcond_set = [0.04, 0.08]; % Speed conditions

% Calibration settings
%% Calibration Settings
calib_folder_set = "2";
ref_trial_id = 5; % Reference trial number

% Reference trial number
ref_trial_id = 5;

% Frame settings
%% Frame Settings
idx_frame_start = 1;
idx_frame_end = 150;
frame_jump = 1;

% Visualization settings
%% Visualization Settings
showvisu = 0; % Boolean for visualization
debug_mode = 0; % Debug mode flag

%% DIC Global Constants
DIC.TRUE_FPS = 50;
DIC.LIMIT_GRAYSCALE = struct(...
'default', 100,...
'early_subjects', 70,...
'threshold', 8 ... % Subject numbers below this use early_subjects value
);

%% DIC Analysis Parameters
DIC.filtering = struct(...
'enabled', true...
);

DIC.ncorr = struct(...
'analysis_direction', 'regular',...
'subset_radius', struct(...
'tracking', 40,...
'matching', 60 ...
),...
'subset_spacing', 10,...
'cutoff', struct(...
'tracking', 1e-5,...
'matching', 1e-5 ...
),...
'solver', struct(...
'max_iterations', 100,...
'num_threads', 1 ...
),...
'strain_analysis', struct(...
'enabled', 1,...
'propagation', 'seed',...
'auto_ref_change', 1,...
'step_ref_change', 10 ...
) ...
);
90 changes: 90 additions & 0 deletions src/lib/dic_matching.m
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Original file line number Diff line number Diff line change
@@ -0,0 +1,90 @@
function [matching_results] = dic_matching(prep_params)
% Get required parameters
base_parameters = prep_params.base_parameters;
step1_2_parameters = prep_params.step1_2_parameters;
cam_data = prep_params.cam_data;

% Define file paths
roifile = prep_params.roifile;

matchingfile = prep_params.matchingfile;

seedfile = prep_params.seedfile;

%% ROI and Seed initialization
% Draw ROI if needed
if ~exist(roifile, 'file')
draw_ref_roi(base_parameters);
end

% Perform matching if needed
if ~exist(matchingfile, 'file')
ncorr_matching2ref(cam_data.first_satur(:,:,1), prep_params, step1_2_parameters);
end

% Load matching results
matching = load(matchingfile);
refmask_REF = matching.reference_save(1).roi.mask;
refmask_trial = matching.current_save(1).roi.mask;
fprintf('--> STEP: ROI loaded and formatted\n');

% Handle seed points
if ~exist(seedfile, 'file')
draw_ref_seed(base_parameters, 'roi', refmask_REF);
end

% Load and map seed points
seed_point = load(seedfile);
ref_seed_point.pw = seed_point.seed_point;
ref_seed_point.sw = map_pixel2subset(ref_seed_point.pw, step1_2_parameters.spacing);

% Map coordinates
U_mapped = matching.data_dic_save.displacements(1).plot_u_ref_formatted/(step1_2_parameters.spacing + 1);
V_mapped = matching.data_dic_save.displacements(1).plot_v_ref_formatted/(step1_2_parameters.spacing + 1);

initial_seed_point_set1.sw = map_pointcoordinate(ref_seed_point.sw, {U_mapped, V_mapped});
initial_seed_point_set1.pw = map_subset2pixel(initial_seed_point_set1.sw, step1_2_parameters.spacing);

fprintf('--> STEP: SEED loaded and formatted\n');

%% Perform matching analysis
tic;
step1_2_parameters.initial_seed = initial_seed_point_set1.pw;

siz = size(cam_data.first);
input1 = cam_data.first_satur(:,:,1);
input2 = zeros(siz(1), siz(2), 2, 'uint8');
input2(:,:,1) = cam_data.second_satur(:,:,1);
input2(:,:,2) = cam_data.first_satur(:,:,1);

[h12, file_logic] = ncorr_dic_rewrited('cam_number', [cam_data.cam_1, cam_data.cam_2],...
'cam_data_ref', input1,...
'cam_data_cur', input2,...
'mask', refmask_trial,...
'automatic_process', base_parameters.automatic_process,...
'step_param', step1_2_parameters,...
'base_param', base_parameters);

% Get results for next step
refmask_trial_matched = h12.current(1).roi.mask;
U_mapped = h12.data_dic.displacements(1).plot_u_ref_formatted/(step1_2_parameters.spacing + 1);
V_mapped = h12.data_dic.displacements(1).plot_v_ref_formatted/(step1_2_parameters.spacing + 1);

initial_seed_point_set2.sw = map_pointcoordinate(initial_seed_point_set1.sw, {U_mapped, V_mapped});
initial_seed_point_set2.pw = map_subset2pixel(initial_seed_point_set2.sw, step1_2_parameters.spacing);

if ~file_logic
close(h12.handles_gui.figure);
end
clear('h12');

elapsedTime = toc;
fprintf("--> STEP: Ncorr matching 1-2 done in %1.1fs\n", elapsedTime);

%% Prepare output structure
matching_results = struct(...
'refmask_trial', refmask_trial,...
'refmask_trial_matched', refmask_trial_matched,...
'initial_seed_point_set1', initial_seed_point_set1,...
'initial_seed_point_set2', initial_seed_point_set2);
end
239 changes: 239 additions & 0 deletions src/lib/dic_preparation.m
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Original file line number Diff line number Diff line change
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function [prep_params] = dic_preparation(varargin)
%% Parse input arguments
p = inputParser;
p.addParameter('baseDataPath',[]);
p.addParameter('baseResultPath',[]);
p.addParameter('subject',[]);
p.addParameter('material',[]);
p.addParameter('trial',[]);
p.addParameter('stereopair',[]);
p.addParameter('phase',[]);
p.addParameter('jump',[]);
p.addParameter('idxstart_set',[]);
p.addParameter('idxend_set',[]);
p.addParameter('showvisu',0);
p.addParameter('savedata',1);
p.addParameter('reftrial_setmanual',[]);
p.addParameter('param_filt_im',[25 300]);
p.addParameter('automatic_process', true);

p.parse(varargin{:});
base_parameters = struct(...
'baseDataPath', p.Results.baseDataPath,...
'baseResultPath', p.Results.baseResultPath,...
'subject', p.Results.subject,...
'material', p.Results.material,...
'trial', p.Results.trial,...
'stereopair', p.Results.stereopair,...
'phase', p.Results.phase,...
'jump', p.Results.jump,...
'idxstart_set', p.Results.idxstart_set,...
'idxend_set', p.Results.idxend_set,...
'automatic_process', p.Results.automatic_process, ...
'reftrial_setmanual', p.Results.reftrial_setmanual, ...
'param_filt_im', p.Results.param_filt_im, ...
'savedata', p.Results.savedata, ...
'showvisu', p.Results.showvisu ...
);


%% Load DIC parameters
dic_param;

%% Get subject-specific grayscale limit
subject_number = str2double(cell2mat(regexp(base_parameters.subject, '\d+', 'match')));
if subject_number < DIC.LIMIT_GRAYSCALE.threshold
LIMIT_GRAYSCALE = DIC.LIMIT_GRAYSCALE.early_subjects;
else
LIMIT_GRAYSCALE = DIC.LIMIT_GRAYSCALE.default;
end

% Get DIC parameters
TRUE_FPS = DIC.TRUE_FPS;
im_filter_mode = DIC.filtering.enabled;

% Get Ncorr parameters
analysis_direction = DIC.ncorr.analysis_direction;
subset_radius_ncorr_tracking = DIC.ncorr.subset_radius.tracking;
subset_radius_ncorr_matching = DIC.ncorr.subset_radius.matching;
subset_spacing = DIC.ncorr.subset_spacing;
cutoff_tracking = DIC.ncorr.cutoff.tracking;
cutoff_matching = DIC.ncorr.cutoff.matching;
number_iteration_solver = DIC.ncorr.solver.max_iterations;
number_threads = DIC.ncorr.solver.num_threads;
high_strain_analysis = DIC.ncorr.strain_analysis.enabled;
seed_propagation = DIC.ncorr.strain_analysis.propagation;
auto_ref_change = DIC.ncorr.strain_analysis.auto_ref_change;
step_ref_change = DIC.ncorr.strain_analysis.step_ref_change;

%% Setup paths and load protocol
outputPath = fullfile(base_parameters.baseResultPath, base_parameters.subject, ...
base_parameters.material, base_parameters.trial, base_parameters.phase);
if ~exist(outputPath, 'dir')
mkdir(outputPath);
end

% load protocol
protocolPath = fullfile(fullfile(base_parameters.baseDataPath, "rawdata", ...
base_parameters.subject, "speckles", base_parameters.material, "protocol", sprintf('*.mat')));
S = dir(protocolPath);
if isempty(S)
error('Error: Protocol not found.');
end
p = load(fullfile(S.folder, S.name));
protocol = p.cond;

dircond = protocol.table(:,strcmp(protocol.titles,'dir'));
nfcond = cell2mat(protocol.table(:,strcmp(protocol.titles,'nf')));
spdcond = cell2mat(protocol.table(:,strcmp(protocol.titles,'spd')));
repcond = cell2mat(protocol.table(:,strcmp(protocol.titles,'rep')));

% reference trial determination
if (strcmp(base_parameters.phase,"loading") || nfcond(str2double(base_parameters.trial)) == 1)
reftrial = sprintf("%03d",find(nfcond == 1 & strcmp(dircond,"Ubnf"),1));
elseif strcmp(base_parameters.phase,"slide1") && nfcond(str2double(base_parameters.trial)) == 5
reftrial = sprintf("%03d",find(nfcond == 5 & strcmp(dircond,"Ubnf"),1));
else
error('Error: no ref trial assigned');
end

if ~isempty(base_parameters.reftrial_setmanual)
reftrial = base_parameters.reftrial_setmanual;
end

%% Read and process images
tic;
[cam_first_raw, cam_second_raw, cam_1, cam_2] = import_vid(base_parameters.baseDataPath,...
'subject', base_parameters.subject,...
'material', base_parameters.material,...
'trial', base_parameters.trial,...
'stereopair', base_parameters.stereopair,...
'phase', base_parameters.phase,...
'idxstart_set', base_parameters.idxstart_set,...
'idxend_set', base_parameters.idxend_set,...
'framejump', base_parameters.jump);
elapsedTime = toc;
fprintf("reading done in %1.1fs\n", elapsedTime);

% Process phase-specific data
if strcmp(base_parameters.phase, "slide1")
cam_first_raw = cam_first_raw(:,:,1:end/2+5);
cam_second_raw = cam_second_raw(:,:,1:end/2+5);
end

% Image saturation
cam_first_satur = satur(cam_first_raw, 'level', LIMIT_GRAYSCALE);
cam_second_satur = satur(cam_second_raw, 'level', LIMIT_GRAYSCALE);

% Image filtering
if im_filter_mode
[cam_first, gsboundaries] = filter_like_ben(cam_first_satur, 'paramfilt', base_parameters.param_filt_im);
cam_second = filter_like_ben(cam_second_satur, 'gsbound', gsboundaries, 'paramfilt', base_parameters.param_filt_im);
fprintf('--> STEP: filtering done\n');
else
cam_first = cam_first_raw;
cam_second = cam_second_raw;
fprintf('--> STEP: raw data used\n');
end

%% Create parameter structures for DIC analysis
step1_parameters = struct(...
'type', analysis_direction,...
'radius', subset_radius_ncorr_tracking,...
'spacing', subset_spacing,...
'cutoff_diffnorm', cutoff_tracking,...
'cutoff_iteration', number_iteration_solver,...
'total_threads', number_threads,...
'stepanalysis_params', struct(...
'enabled', high_strain_analysis,...
'type', seed_propagation,...
'auto', auto_ref_change,...
'step', step_ref_change));

step1_2_parameters = struct(...
'type', analysis_direction,...
'radius', subset_radius_ncorr_matching,...
'spacing', subset_spacing,...
'cutoff_diffnorm', cutoff_matching,...
'cutoff_iteration', number_iteration_solver,...
'total_threads', number_threads,...
'stepanalysis_params', struct(...
'enabled', high_strain_analysis,...
'type', seed_propagation,...
'auto', auto_ref_change,...
'step', step_ref_change));

%% Save frame information
idxframe = base_parameters.idxstart_set:base_parameters.jump:base_parameters.idxend_set;
actual_fps_meas = TRUE_FPS/base_parameters.jump;

savefileName = fullfile(outputPath, sprintf('dic_info_data_target_pair%d.mat', base_parameters.stereopair));
save(savefileName, 'actual_fps_meas', 'idxframe');

%% Prepare tracking configurations
tracking_configs = {
struct(...
'cam_number', cam_1,...
'ref_data', cam_first(:,:,1),...
'cur_data', cam_first(:,:,1:end),...
'step_number', 1 ...
), ...
struct(...
'cam_number', cam_2,...
'ref_data', cam_second(:,:,1),...
'cur_data', cam_second(:,:,2:end),...
'step_number', 2 ...
)
};

%% Prepare output structure
roifile = fullfile(base_parameters.baseResultPath, base_parameters.subject, ...
base_parameters.material, sprintf("REF_MASK_%s_%s_pair%s.mat", ...
reftrial, base_parameters.phase, base_parameters.stereopair+""));

matchingfile = fullfile(outputPath, ...
sprintf("MATCHING2%s_pair%s.mat", reftrial, base_parameters.stereopair+""));

seedfile = fullfile(base_parameters.baseResultPath, base_parameters.subject, ...
base_parameters.material, sprintf("REF_SEED_%s_%s_pair%s.mat", ...
reftrial, base_parameters.phase, base_parameters.stereopair+""));

prep_params = struct(...
'base_parameters', base_parameters,...
'step1_parameters', step1_parameters,...
'step1_2_parameters', step1_2_parameters,...
'outputPath', outputPath,...
'reftrial', reftrial,...
'cam_data', struct(...
'first_raw', cam_first_raw,...
'second_raw', cam_second_raw,...
'first', cam_first,...
'second', cam_second,...
'first_satur', cam_first_satur,...
'second_satur', cam_second_satur,...
'cam_1', cam_1,...
'cam_2', cam_2),...
'tracking_configs', tracking_configs,...
'LIMIT_GRAYSCALE', LIMIT_GRAYSCALE,...
'actual_fps_meas', actual_fps_meas,...
'idxframe', idxframe, ...
'roifile', roifile, ...
'matchingfile', matchingfile, ...
'seedfile', seedfile ...
);

% Print summary
fprintf("Trial information summary '%s' %s %s %s\n > Dir: %s\n > Force: %dN\n > Spd: %dmm/s\n > Rep: %d\n > REFtrial: '%s'\n > NbrFr: %d\n > Frame : %s\n > Actual FPS : %d\n",...
base_parameters.trial,...
base_parameters.phase,...
base_parameters.material,...
base_parameters.subject,...
dircond{str2double(base_parameters.trial)},...
nfcond(str2double(base_parameters.trial)),...
spdcond(str2double(base_parameters.trial)),...
repcond(str2double(base_parameters.trial)),...
reftrial,...
size(cam_first,3),...
mat2str(idxframe),...
actual_fps_meas);
end
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