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Done with shape comparison
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@albusdemens
albusdemens committed Sep 17, 2017
1 parent 4843741 commit 28080c5
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4 changes: 2 additions & 2 deletions recon3d.py
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Original file line number Diff line number Diff line change
Expand Up @@ -136,8 +136,8 @@ def reconstruct_part(self, ista, isto, x_rot, acc_proj):

dety_size = np.shape(self.fullarray)[3]
detz_size = np.shape(self.fullarray)[4]
detz_center = (dety_size - 0.) / 2
dety_center = int(x_rot[0])
detz_center = int(x_rot[0])
dety_center = (dety_size - 0.) / 2
lens = len(slow)
lenm = len(med)
lenf = len(fast)
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293 changes: 149 additions & 144 deletions vol3D.m
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Original file line number Diff line number Diff line change
Expand Up @@ -9,47 +9,95 @@
Summed_img = readNPY('/u/data/alcer/DFXRM_rec/Rec_test_2/summed_data_astra.npy');
V = readNPY('/u/data/alcer/DFXRM_rec/Rec_test_2/grain_ang.npy');

%for i = [1 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 130 135 140 145 150 155 160]
for i = 160%1:5:160
for i = [1 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 130 135 140 145 150 155 160]
proj_number = i;
compare_shapes(proj_number, V, Summed_img);
disp(i);
[P_05, P_07, P_09] = compare_shapes(proj_number, V);

P_05 = flipud(rot90(imresize(P_05(1:100, 1:100),3)));
P_07 = flipud(rot90(imresize(P_07(1:100, 1:100),3)));
P_09 = flipud(rot90(imresize(P_09(1:100, 1:100),3)));

P_05_bin = zeros(size(P_05));
P_07_bin = zeros(size(P_07));
P_09_bin = zeros(size(P_09));

for ii = 1:size(P_05,1)
for jj = 1:size(P_05,2)
if P_05(ii,jj) > 0
P_05_bin(ii,jj) = 1;
end
if P_07(ii,jj) > 0
P_07_bin(ii,jj) = 1;
end
if P_09(ii,jj) > 0
P_09_bin(ii,jj) = 1;
end
end
end

% Fill holes in the binary images
P_05_bin = imfill(P_05_bin);
P_07_bin = imfill(P_07_bin);
P_09_bin = imfill(P_09_bin);

% Find perimeter of binary images
Per_05 = bwperim(P_05_bin);
Per_07 = bwperim(P_07_bin);
Per_09 = bwperim(P_09_bin);

% Select the summed intensities image corresponding to the considered
% angle
Sum = squeeze(Summed_img(:,proj_number,:));

overlay1 = flipud(imoverlay(imoverlay(imoverlay(Sum, Per_05, [.3 1 .3]), Per_07, [.3 1 .3]), Per_09, [.3 1 .3]));

F = figure;
subplot(1,3,1);
h = pcolor(Sum); shading flat; hold on;
subplot(1,3,2);
h = pcolor(P_05); shading flat; hold on;
subplot(1,3,3);
imshow(overlay1);
address_F = sprintf('Shape_comp/Shape_comp%03i.png', proj_number);
saveas(F, address_F, 'png');
close;
end

function compare_shapes(alpha, V, Summed_img)
% For a given completeness value, and a given rotation angle, this function
% calculates the shape of the diffraction signal collected by the detector,
% and the border of the shape
function [Proj_final_05, Proj_final_07, Proj_final_09] = compare_shapes(alpha, V)

% Select volume corresponding to a certain completeness
V_th_low = zeros(size(V,1), size(V,2), size(V,1));
V_th_up = zeros(size(V,1), size(V,2), size(V,1));
% Select volume corresponding to the lower completeness value considered (0.5)
V_th= zeros(size(V,1), size(V,2), size(V,1));
for ii =1:size(V,1)
for jj = 1:size(V,2)
for kk = 1:size(V,3)
if V(ii,jj,kk,3) > 0.5
V_th_low(ii,jj,kk) = V(ii,jj,kk,3);
end
if V(ii,jj,kk,3) > 0.9
V_th_up(ii,jj,kk) = V(ii,jj,kk,3);
V_th(ii,jj,kk) = V(ii,jj,kk,3);
end
end
end
end

% Save calculated volumes
%savevtk(V_th_low, '/u/data/alcer/DFXRM_rec/Rec_test_2/V_th_low.vtk');
%savevtk(V_th_up, '/u/data/alcer/DFXRM_rec/Rec_test_2/V_th_up.vtk');
%savevtk(V_th, '/u/data/alcer/DFXRM_rec/Rec_test_2/V_th.vtk');

% Rotation angle
alpha1 = alpha*1.12;
alpha1 = alpha*1.125;

C_tot = sum(sum(sum(V_th_low)));
C_tot = sum(sum(sum(V_th)));
% Calculate centre of mass of V_th_up, weighted by completeness
X_CM = 0; Y_CM = 0; Z_CM = 0;
for ii = 1:size(V,1)
for jj = 1:size(V,2)
for kk = 1:size(V,3)
if V_th_low(ii,jj,kk) > 0.5
X_CM = X_CM + ii*V_th_low(ii,jj,kk);
Y_CM = Y_CM + jj*V_th_low(ii,jj,kk);
Z_CM = Z_CM + kk*V_th_low(ii,jj,kk);
% Set a threshold to accept a voxel
if V_th(ii,jj,kk) > 0.5
X_CM = X_CM + ii*V_th(ii,jj,kk);
Y_CM = Y_CM + jj*V_th(ii,jj,kk);
Z_CM = Z_CM + kk*V_th(ii,jj,kk);
end
end
end
Expand All @@ -61,14 +109,13 @@ function compare_shapes(alpha, V, Summed_img)
% sample along Z
Sum_Z = zeros(size(V,1), size(V,2));
% Project all values along Z
Sum_Z = sum(V_th_low,3);
Sum_Z = sum(V_th,3);

% Plot binarized projection along Z, together with CM
%figure;
%Sum_Z(CM(1), CM(2)) = 100;
%h = pcolor(Sum_Z); shading flat;
Sum_Z(int8(CM(1)), int8(CM(2))) = 100;

% Find radius of the circle containing the binarized proj of the volume
% Find radius of the circle containing the entire XY projection
count_dist = zeros(nnz(Sum_Z), 2);
cc = 0;
for ii = 1:size(V,1)
Expand All @@ -83,48 +130,46 @@ function compare_shapes(alpha, V, Summed_img)
% Find radius containg all values
R = max(count_dist(:,2));

% Translate the projection, so that the CM is at the image center
Circle_container = zeros(int8(2*R) + 4, int8(2*R) + 4);
Dx = abs(int8(R) - CM(1));
Dy = abs(int8(R) - CM(2));
for ii = 3:size(V,1) + 2
for jj = 3:size(V,2) + 2
Circle_container(ii + Dx, jj + Dy) = Sum_Z(ii-2, jj-2);
Dx = abs(int8((size(Circle_container,1)/2) - CM(1)));
Dy = abs(int8((size(Circle_container,2)/2) - CM(2)));
Dz = abs(int8(size(V,3)/2 - CM(3)));
for ii = 1:size(V,1)
for jj = 1:size(V,2)
Circle_container(ii + Dx, jj + Dy) = Sum_Z(ii, jj);
end
end

% Plot circle containing grain, and projected image before and after
% padding
% figure;
X_CM_circ = 0; Y_CM_circ = 0;
for aa = 1:size(Circle_container, 1)
for bb = 1:size(Circle_container, 2)
X_CM_circ = X_CM_circ + aa*Circle_container(aa,bb);
Y_CM_circ = Y_CM_circ + bb*Circle_container(aa,bb);
end
end
C_tot_circ = sum(sum(sum(V_th)));
CM_circ = [X_CM_circ, Y_CM_circ] / C_tot_circ;

% Plot projection before and after translation
% figure;
% subplot(1,2,1);
% h = pcolor(Sum_Z); shading flat;
% hold on;
% th = 0:pi/50:2*pi;
% xunit = R * cos(th) + CM(2);
% yunit = R * sin(th) + CM(1);
% plot(xunit, yunit);
% hold on;
% scatter(CM(2), CM(1), 'o', 'MarkerFaceColor', 'b');
% title('Before padding');
% h = pcolor(Sum_Z); shading flat; hold on;
% scatter(CM(2), CM(1));
% subplot(1,2,2);
% h = pcolor(Circle_container); shading flat;
% hold on;
% th = 0:pi/50:2*pi;
% xunit = R * cos(th) + R + 3;
% yunit = R * sin(th) + R + 3;
% plot(xunit, yunit);
% hold on;
% scatter(CM(2) + Dy + 2, CM(1) + Dx + 2, 'o', 'MarkerFaceColor', 'b');
% title('After padding');
% h = pcolor(Circle_container); shading flat; hold on;
% scatter(CM_circ(2), CM_circ(1));

IM_x_th_low = zeros(size(Circle_container,1), size(Circle_container,2));
IM_x_th_up = zeros(size(Circle_container,1), size(Circle_container,2));

% Iterate for each layer
Cylinder_container = zeros(size(Circle_container,1), size(Circle_container, 2), size(V,3));
% Iterate for each layer. Z translation to make CM at the center of the
% projected image
Cylinder_container = zeros(size(Circle_container,1), size(Circle_container, 2), size(V,3) + Dz);
for ii = 3:size(V,1) + 2
for jj = 3:size(V,2) + 2
for kk = 1:size(V,3)
Cylinder_container(ii + Dx,jj + Dy, kk) = V_th_low(ii-2, jj-2, kk);
for kk = 3:size(V,3) + 2
Cylinder_container(ii + Dx,jj + Dy, kk + Dz) = V_th(ii-2, jj-2, kk - 2);
end
end
end
Expand All @@ -150,116 +195,76 @@ function compare_shapes(alpha, V, Summed_img)
end
end

savevtk(Rot_Z, '/u/data/alcer/DFXRM_rec/Rec_test_2/Rot_Z.vtk');
savevtk(Rot_Y, '/u/data/alcer/DFXRM_rec/Rec_test_2/Rot_Y.vtk');

% Find CM in Rot_Y (to check that it's approx. at the center of the volume)
X_CM_rot = 0; Y_CM_rot = 0; Z_CM_rot = 0;
C_tot_rot = sum(sum(sum(Rot_Y)));
for ii = 1:size(Rot_Y,1)
for jj = 1:size(Rot_Y,2)
for kk = 1:size(Rot_Y,3)
if Rot_Y(ii,jj,kk) == 0
Rot_Y(ii,jj,kk) = nan;
if Rot_Y(ii,jj,kk) > 0
X_CM_rot = X_CM_rot + ii*Rot_Y(ii,jj,kk);
Y_CM_rot = Y_CM_rot + jj*Rot_Y(ii,jj,kk);
Z_CM_rot = Z_CM_rot + kk*Rot_Y(ii,jj,kk);
end
end
end
end
CM_rot = [X_CM_rot, Y_CM_rot, Z_CM_rot] / C_tot_rot;

% Sum the rotated volume along the X axis
X_sum_05 = zeros(size(Rot_Y,2), size(Rot_Y,3));
X_sum_05 = squeeze(sum(Rot_Y, 1));

% Resize the image, so that it matches the original size
Proj_final_05 = zeros(size(Sum_Z));
frame_x = int8((size(Rot_Y,2) - size(Proj_final_05,1))/2);
frame_y = int8((size(Rot_Y,3) - size(Proj_final_05,2))/2);
for aa = 1:size(Proj_final_05, 1)
for bb = 1:size(Proj_final_05, 2)
Proj_final_05(aa, bb) = X_sum_05(aa + frame_x, bb + frame_y);
end
end

for ii = 1:size(Rot_Z,1)
for jj = 1:size(Rot_Z,2)
for kk = 1:size(Rot_Z,3)
if Rot_Z(ii,jj,kk) == 0
Rot_Z(ii,jj,kk) = nan;
% We also want to project the volumes corresponding to C = 0.7 and C = 0.9
Rot_Y_07 = zeros(size(Rot_Y));
Rot_Y_09 = zeros(size(Rot_Y));
for ii = 1:size(Rot_Y,1)
for jj = 1:size(Rot_Y,2)
for kk = 1:size(Rot_Y,3)
if Rot_Y(ii,jj,kk) > 0.7
Rot_Y_07(ii,jj,kk) = Rot_Y(ii,jj,kk);
end
if Rot_Y(ii,jj,kk) > 0.9
Rot_Y_09(ii,jj,kk) = Rot_Y(ii,jj,kk);
end
end
end
end

[x,y,z] = meshgrid(1:size(Rot_Y,1),1:size(Rot_Y,2),1:size(Rot_Y,3));
figure; scatter3(x(:),y(:),z(:),5,Rot_Y(:));
xlabel('X'); ylabel('Y');

[x,y,z] = meshgrid(1:size(Rot_Z,1),1:size(Rot_Z,2),1:size(Rot_Z,3));
figure; scatter3(x(:),y(:),z(:),5,Rot_Z(:));
xlabel('X'); ylabel('Y');
% Sum the rotated volume along the X axis
X_sum_07 = zeros(size(Rot_Y,2), size(Rot_Y,3));
X_sum_07 = squeeze(sum(Rot_Y_07, 1));


% Sum along X, alpha = 0 case
X_sum = zeros(size(Rot_Y,2), size(Rot_Y,3));
X_sum_bin = zeros(size(Rot_Y,2), size(Rot_Y,3));
X_sum = sum(Rot_Y, 3);
X_sum_09 = zeros(size(Rot_Y,2), size(Rot_Y,3));
X_sum_09 = squeeze(sum(Rot_Y_09, 1));

for ii = 1:size(X_sum,1)
for jj = 1:size(X_sum,2)
if X_sum(ii, jj) > 0
X_sum_bin(ii,jj) = 1;
end
% Resize the image, so that it matches the original size
Proj_final_07 = zeros(size(Sum_Z));
frame_x = int8((size(Rot_Y,2) - size(Proj_final_07,1))/2);
frame_y = int8((size(Rot_Y,3) - size(Proj_final_07,2))/2);
for aa = 1:size(Proj_final_07, 1)
for bb = 1:size(Proj_final_07, 2)
Proj_final_07(aa, bb) = X_sum_07(aa + frame_x, bb + frame_y);
end
end

figure;
subplot(1,2,1);
h = pcolor(X_sum); shading flat;
subplot(1,2,2);
h = pcolor(X_sum_bin); shading flat;

%P_os = bwperim(X_sum_bin);

% Frame IM_x_th_low


%overlay1 = flipud(imoverlay(IM_x_th_low, P_os, [.3 1 .3]));
%figure; imshow(overlay1);

IM_x_th_low = rot90(rot90(rot90(IM_x_th_low)));
IM_x_th_up = rot90(rot90(rot90(IM_x_th_up)));

% Find perimeter of the projected data and compare with experimental data
% (summed for a certain projection)
IM_x_bin_low = zeros(size(V,1)-1, size(V,2)-1);
IM_x_bin_up = zeros(size(V,1)-1, size(V,2)-1);

for ii = 1:size(V,1)-1
for jj = 1:size(V,2)-1
if IM_x_th_low(ii,jj) > 0
IM_x_bin_low(ii,jj) = 1;
end
if IM_x_th_up(ii,jj) > 0
IM_x_bin_up(ii,jj) = 1;
end
Proj_final_09 = zeros(size(Sum_Z));
frame_x = int8((size(Rot_Y,2) - size(Proj_final_09,1))/2);
frame_y = int8((size(Rot_Y,3) - size(Proj_final_09,2))/2);
for aa = 1:size(Proj_final_09, 1)
for bb = 1:size(Proj_final_09, 2)
Proj_final_09(aa, bb) = X_sum_09(aa + frame_x, bb + frame_y);
end
end

IM_x_th_low_r = imresize(IM_x_th_low, 3);
IM_x_bin_low_r = imresize(IM_x_bin_low, 3);

IM_x_th_up_r = imresize(IM_x_th_up, 3);
IM_x_bin_up_r = imresize(IM_x_bin_up, 3);

P1 = bwperim(IM_x_bin_low_r);
P3 = bwperim(IM_x_bin_up_r);

S1 = squeeze(Summed_img(:,alpha,:));
S2 = squeeze(Summed_img(:,80,:));

%figure; imagesc(S1);

overlay1 = flipud(imoverlay(imoverlay(S1, P1, [.3 1 .3]), P3, [.3 1 .3]));
%imshow(overlay1);

fig = figure;
title(sprintf('Projection %03i', alpha));
subplot(1,3,1);
h = pcolor(S1); shading flat;
%title('Sum of diffraction images','fontsize',18);
subplot(1,3,2);
h = pcolor(IM_x_th_low_r); shading flat;
%title('Projected reconstruction','fontsize',18);
subplot(1,3,3);
imshow(overlay1);
%title('Perimeter overlay','fontsize',18);
print(fig, sprintf('Shape_comp%03i', alpha), '-dpdf');
close;

%figure; imagesc(rot90(IM_x_shape));
%figure; imagesc(rot90(IM_y_shape));

end

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