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TimeS_InverseSkel_Sp2.m~
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TimeS_InverseSkel_Sp2.m~
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clear all;
addpath( 'ellipse' );
%% Read Data
sampling_interval = 20;
for i = 2:2
filePath = [ 'ellipse_flow__t_' num2str( i ) '.mat' ];
fileFilledPath = [ 'ellipse_flow__t_' num2str( i ) '_filled.mat' ];
if i == 0
fileSkelDPath = [ 'ellipse_flow__t_' num2str( i ) '_skel_0topo.mat' ];
else
fileSkelDPath = [ 'ellipse_flow__t_' num2str( i ) '_skel_0topo.mat' ];
fileSkelInitPath = [ 'ellipse_flow__t_' num2str( i - 1 ) '_skel_0topo_Updated.mat' ];
fileRadiusInitPath = [ 'ellipse_flow__t_' num2str( i - 1 ) '_radius_Updated.mat' ];
end
% Read Image
% Target Image (Contour)
bwImg = load( filePath );
bwImg = bwImg.ellipseImg_p;
% Target Image (Filled)
bwFilled = load( fileFilledPath );
bwFilled = bwFilled.ellipseF;
% Read Initial Skeleton - Single Line
skelD = load( fileSkelDPath );
skelD = skelD.skelD;
skelIdx = load( fileSkelInitPath );
skelIdx = skelIdx.skelIdx_t;
radiiList = load( fileRadiusInitPath );
radiiList = radiiList.radiiList_t;
skelIdx_t = round( skelIdx );
radiiList_t = radiiList;
% Target Area
object_area = sum( bwFilled(:) );
% Reconstruct Object Surface by Skeleton + Radii Function
estimated_surface = zeros( size( bwImg ) );
for j = 1:size( skelIdx, 1 )
skel_r = round( skelIdx( j, 1 ) );
skel_c = round( skelIdx( j, 2 ) );
radius = radiiList( j );
estimated_surface = MidpointCircle( estimated_surface, radius, skel_r, skel_c, 1 );
end
overlapped_surface = bitand( logical( estimated_surface ), logical( bwFilled ) );
overlapped_area = sum( overlapped_surface(:) );
estimated_area = sum( estimated_surface(:) );
% Image Matching Energy - Inverse Dice Coefficient
energy_estimated = 1 / ( 2 * overlapped_area / ( object_area + estimated_area ) )
% Medial Curve Smoothness/Elasticity Energy (Smoothness Regularization)
[ gradListX, gradList ] = gradient( skelIdx_t );
[ grad2ListX, grad2List ] = gradient( gradList );
gradNorm = gradList .* gradList;
gradNorm = sum( gradNorm, 2 );
gradNorm_prev = mean( sqrt( gradNorm ) );
grad2Norm = grad2List .* grad2List;
grad2Norm_prev = mean( sqrt( sum( grad2Norm, 2 ) ) );
gd_m_step = 0.5;
gd_r_step = 0.5;
gd_alpha = 1000;
gd_r_alpha = 1000;
smooth_eps = 0.00005;
grad2_eps = 50;
energy_smooth_prev = gradNorm_prev + grad2_eps * grad2Norm_prev;
energy_0 = energy_estimated + smooth_eps * ( energy_smooth_prev );
energy_prev = energy_0;
disp( 'Initial Energy' );
disp( energy_prev );
% Interpolation Ratio
interp_ratio = 1;
iter_t = 5;
iter_m_t = 50;
iter_r_t = 50;
EnergyArr_m = zeros( iter_t, iter_m_t );
EnergyArr_r = zeros( iter_t, iter_r_t );
DiceArr_m = zeros( iter_t, iter_m_t );
DiceArr_r = zeros( iter_t, iter_r_t );
visInterp_ratio = 50;
[ recon_org, reconRGB_Org ] = ReconOutputSkel( skelIdx_t, radiiList_t, bwImg, skelD, visInterp_ratio );
imwrite( reconRGB_Org, [ 'ellipse/SingleSkel5/ellipse_flow__t_' num2str( i ) '_singleSkel_Org.png' ] );
for t = 1:iter_t
%{
% Update Medial Curve
for t_m = 1:iter_m_t
gateaux_dev_mc_max = 0;
gateux_dev_mc_sum = 0;
for j = 1:size( skelIdx_t, 1 )
for k = 1:2
skelIdx_temp = skelIdx_t;
skelIdx_temp( j, k ) = skelIdx_t( j, k ) + gd_m_step;
estimated_surface = zeros( size( bwImg ) );
% Interpolate
skelIdx_temp_int_r = interp( skelIdx_temp( :, 1 ), interp_ratio );
skelIdx_temp_int_c = interp( skelIdx_temp( :, 2 ), interp_ratio );
radiiList_t_int = interp( radiiList_t, interp_ratio );
skelIdx_temp_int = [ skelIdx_temp_int_r( 1:(end-interp_ratio+1), 1 ), skelIdx_temp_int_c( 1:(end-interp_ratio+1), 1 ) ];
radiiList_t_int = radiiList_t_int( 1:(end-interp_ratio+1), 1 );
for j2 = 1:size( skelIdx_temp_int, 1 )
skel_r = round( skelIdx_temp_int( j2, 1 ) );
skel_c = round( skelIdx_temp_int( j2, 2 ) );
radius = round( radiiList_t_int( j2 ) );
try
estimated_surface = MidpointCircle( estimated_surface, radius, skel_r, skel_c, 1 );
catch
dkdkslslsl = 0;
end
end
[ gradListX, gradList ] = gradient( skelIdx_temp );
[ grad2ListX, grad2List ] = gradient( gradList );
gradNorm_temp = gradList .* gradList;
gradNorm_temp = mean( sqrt( sum( gradNorm_temp, 2 ) ) );
grad2Norm_temp = grad2List .* grad2List;
grad2Norm_temp = mean( sqrt( sum( grad2Norm_temp, 2 ) ) );
overlapped_surface = bitand( logical( estimated_surface ), logical( bwFilled ) );
overlapped_area = sum( overlapped_surface(:) );
estimated_area = sum( estimated_surface(:) );
energy_i_t = 1 / ( 2 * overlapped_area / ( object_area + estimated_area ) );
energy_s_t = gradNorm_temp + grad2_eps * grad2Norm_temp;
energy_estimated = ( energy_i_t + smooth_eps * energy_s_t ); % / energy_0;
gateaux_dev = ( energy_estimated - energy_prev ) / gd_m_step;
gateux_dev_mc_sum = gateux_dev_mc_sum + abs( gateaux_dev );
if abs( gateaux_dev ) > gateaux_dev_mc_max
gateaux_dev_mc_max = abs( gateaux_dev );
end
skelIdx_t( j, k ) = skelIdx_t( j, k ) - ( gd_alpha * gateaux_dev );
energy_prev = energy_estimated;
end
end
EnergyArr_m( t, t_m ) = energy_estimated;
DiceArr_m( t, t_m ) = 1.0 / energy_i_t ;
disp( 'Medial Curve Update : i ' );
disp( [ 'Estimated Energy at Iter - ' num2str( t_m ) ' : ' num2str( energy_estimated ) ] );
disp( [ 'Energy Overlapped - ' num2str( energy_i_t ) ] );
disp( [ 'Dice Coeff - ' num2str( 1.0 / energy_i_t ) ] );
disp( [ 'Energy Curve Smoothness - ' num2str( energy_s_t ) ] );
disp( [ 'Mean Gateaux Derivative : ' num2str( gateux_dev_mc_sum / ( 2 * size( skelIdx_t, 1 ) ) ) ] );
disp( [ 'Max Gateaux Derivative : ' num2str( gateaux_dev_mc_max ) ] );
if gateaux_dev_mc_max < 0.000005
disp( 'Optimization Terminated : dE/dm < threshold' );
break;
end
end
skelIdx_t( :, 1 ) = smooth( skelIdx_t( :, 1 ), 3 );
skelIdx_t( :, 2 ) = smooth( skelIdx_t( :, 2 ), 3 );
dev_m = gateux_dev_mc_sum / ( 2 * size( skelIdx_t, 1 ) );
disp( '====================================================================' );
disp( '====================================================================' );
disp( 'Medial Curve Update' );
disp( [ 'Estimated Energy at Iter - ' num2str( t ) ' : ' num2str( energy_estimated ) ] );
disp( [ 'Energy Overlapped - ' num2str( energy_i_t ) ] );
disp( [ 'Dice Coeff - ' num2str( 1.0 / energy_i_t ) ] );
disp( [ 'Energy Curve Smoothness - ' num2str( energy_s_t ) ] );
disp( [ 'Mean Gateaux Derivative : ' num2str( gateux_dev_mc_sum / ( 2 * size( skelIdx_t, 1 ) ) ) ] );
disp( [ 'Max Gateaux Derivative : ' num2str( gateaux_dev_mc_max ) ] );
disp( '====================================================================' );
disp( '====================================================================' );
visInterp_ratio = 50;
[ recon_mc, reconRGB_mc ] = ReconOutputSkel( skelIdx_t, radiiList_t, bwImg, skelD, visInterp_ratio );
imwrite( reconRGB_mc, [ 'ellipse/SingleSkel5/ellipse_flow__t_' num2str( i ) '_singleSkel_MC' num2str( t ) '.png' ] );
%}
% Update Radial Function
% Medial Curve Regularization does not change but included for energy
% normalization
[ gradListX, gradList_r ] = gradient( skelIdx_t );
[ grad2ListX, grad2List_r ] = gradient( gradList_r );
gradNorm_r = gradList_r .* gradList_r;
gradNorm_r = mean( sqrt( sum( gradNorm_r, 2 ) ) );
grad2Norm_r = grad2List_r .* grad2List_r;
grad2Norm_r = mean( sqrt( sum( grad2Norm_r, 2 ) ) );
energy_s_t_r = gradNorm_r + grad2_eps * grad2Norm_r;
energy_s_t = energy_s_t_r;
for t_r = 1:iter_r_t
gateux_dev_r_sum = 0;
gateaux_dev_r_max = 0;
for j = 1:size( radiiList_t, 1 )
radiiList_temp = radiiList_t;
radiiList_temp( j ) = radiiList_t( j ) + gd_r_step;
estimated_surface = zeros( size( bwImg ) );
skelIdx_t_int_r = interp( skelIdx_t( :, 1 ), interp_ratio );
skelIdx_t_int_c = interp( skelIdx_t( :, 2 ), interp_ratio );
radiiList_temp_int = interp( radiiList_temp, interp_ratio );
skelIdx_t_int = [ skelIdx_t_int_r( 1:(end-interp_ratio+1), 1 ), skelIdx_t_int_c( 1:(end-interp_ratio+1), 1 ) ];
radiiList_temp_int = radiiList_temp_int( 1:(end-interp_ratio+1), 1 );
for j2 = 1:size( skelIdx_t_int, 1 )
skel_r = round( skelIdx_t_int( j2, 1 ) );
skel_c = round( skelIdx_t_int( j2, 2 ) );
radius = round( radiiList_temp_int( j2 ) );
estimated_surface = MidpointCircle( estimated_surface, radius, skel_r, skel_c, 1 );
end
overlapped_surface = bitand( logical( estimated_surface ), logical( bwFilled ) );
overlapped_area = sum( overlapped_surface(:) );
estimated_area = sum( estimated_surface(:) );
energy_i_t = 1 / ( 2 * overlapped_area / ( object_area + estimated_area ) );
energy_estimated = ( energy_i_t + smooth_eps * energy_s_t_r );
gateaux_dev = ( energy_estimated - energy_prev ) / gd_r_step;
gateux_dev_r_sum = gateux_dev_r_sum + abs( gateaux_dev );
if abs( gateaux_dev ) > gateaux_dev_r_max
gateaux_dev_r_max = abs( gateaux_dev );
end
radiiList_t( j ) = radiiList_t( j ) - ( gd_r_alpha * gateaux_dev );
energy_prev = energy_estimated;
end
dev_r = gateux_dev_r_sum / size( radiiList_t, 1 );
disp( 'Radius Update: i' );
disp( [ 'Estimated Energy at Iter - ' num2str( t_r ) ' : ' num2str( energy_estimated ) ] );
disp( [ 'Energy Overlapped - ' num2str( energy_i_t ) ] );
disp( [ 'Dice Coeff - ' num2str( 1.0 / energy_i_t ) ] );
disp( [ 'Energy Curve Smoothness - ' num2str( energy_s_t_r ) ] );
disp( [ 'Mean Gateaux Derivative : ' num2str( dev_r ) ] );
disp( [ 'Max Gateaux Derivative : ' num2str( gateaux_dev_r_max ) ] );
EnergyArr_r( t, t_r ) = energy_estimated;
DiceArr_r( t, t_r ) = 1.0 / energy_i_t ;
if gateaux_dev_r_max < 0.000005
disp( 'Optimization Terminated : dE/dr < threshold' );
break;
end
end
disp( '=============================================================================' );
disp( '=============================================================================' );
disp( 'Radius Update' );
disp( [ 'Estimated Energy at Iter - ' num2str( t ) ' : ' num2str( energy_estimated ) ] );
disp( [ 'Energy Overlapped - ' num2str( energy_i_t ) ] );
disp( [ 'Dice Coeff - ' num2str( 1.0 / energy_i_t ) ] );
disp( [ 'Energy Curve Smoothness - ' num2str( energy_s_t ) ] );
disp( [ 'Mean Gateaux Derivative : ' num2str( dev_r ) ] );
disp( [ 'Max Gateaux Derivative : ' num2str( gateaux_dev_r_max ) ] );
disp( '====================================================================' );
disp( '====================================================================' );
visInterp_ratio = 50;
[ recon_r, reconRGB_r ] = ReconOutputSkel( skelIdx_t, radiiList_t, bwImg, skelD, visInterp_ratio );
imwrite( reconRGB_r, [ 'ellipse/SingleSkel5/ellipse_flow__t_' num2str( i ) '_singleSkel_R' num2str( t ) '.png' ] );
end
%% Save Updated Skel and Radius
fileSkelResultPath = [ 'ellipse_flow__t_' num2str( i ) '_skel_0topo_Updated.mat' ];
fileRadiusResultPath = [ 'ellipse_flow__t_' num2str( i ) '_radius_Updated.mat' ];
save( fileSkelResultPath, 'skelIdx_t' );
save( fileRadiusResultPath, 'radiiList_t' );
%% Reconstruction
% Reconstruct Object Surface by Skeleton + Radii Function
visInterp_ratio = 50;
[ recon, reconRGB ] = ReconOutputSkel( skelIdx_t, radiiList_t, bwImg, skelD, visInterp_ratio );
imwrite( reconRGB, [ 'ellipse/SingleSkel5/ellipse_flow__t_' num2str( i ) '_singleSkel.png' ] );
%}
end