Newer
Older
%% The code is written by Behnaz Pirzamanbein, bepi@dtu.dk last version 2020.08.04
%% Transformation
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
samples = {'out_out_CD','out_out_MD','in_in_CD','in_in_MD'};
layer_name = {'outer','inner'};
%% move the mesh between the degree
% go from
% 0dg 2D (points) to 0dg 2D in 180 then 0dg 3D in 180 -> T0 transform then G180 transform
% - - - - then T45 inverse 2D 0dg to 45 space then G45
% - - - - then T90 inverse 2D 0dg to 90 space then G90
% this gives us the representation of 0 degree in 45 90 and 180
load_folder_Reg = 'Results\registration\layer\';
load_folder_layers = 'Results\layer\';
save_folder = 'Results\layer\transfer\0dg_rest\';
if ~exist(save_folder,'dir')
mkdir(save_folder)
end
% if you want to run the measure separately you can use the for loop
%for i = 1:4
sample = samples{i};
disp(['Load Data ',sample])
% registrtaion
ref = load(['Results\registration\tform\reg_tfrom_inner_',sample]);
sz180 = size(ref.dg180_inner);
sz90 = size(ref.dg90_inner);
sz45 = size(ref.dg45_inner);
sz0 = size(ref.dg0_inner);
% T
tform0 = ref.Reg_dg0_inner.Transformation;
tform45 = ref.Reg_dg45_inner.Transformation;
tform90 = ref.Reg_dg90_inner.Transformation;
% location of the mesh (points) in 180 degree;
dg180 = load([load_folder_Reg,'Reg_inner_points_',sample,'_180']);
dg0 = load([load_folder_Reg,'Reg_inner_points_',sample,'_0']);
dg45 = load([load_folder_Reg,'Reg_inner_points_',sample,'_45']);
dg90 = load([load_folder_Reg,'Reg_inner_points_',sample,'_90']);
% meshes in 3D as reference for G transform
inner180 = load([load_folder_layers,'inner_converted_layer_',sample,'_180']); % 3D surface
outer180 = load([load_folder_layers,'outer_converted_layer_',sample,'_180']); % 3D surface
inner90 = load([load_folder_layers,'inner_converted_layer_',sample,'_90']); % 3D surface
outer90 = load([load_folder_layers,'outer_converted_layer_',sample,'_90']); % 3D surface
inner45 = load([load_folder_layers,'inner_converted_layer_',sample,'_45']); % 3D surface
outer45 = load([load_folder_layers,'outer_converted_layer_',sample,'_45']); % 3D surface
inner0 = load([load_folder_layers,'inner_converted_layer_',sample,'_0']); % 3D surface
outer0 = load([load_folder_layers,'outer_converted_layer_',sample,'_0']); % 3D surface
% 2D of 0dg T0 to 2D 180 dg -> 2D of 0 dg in 180 space to 3D of 0 dg in 180 space
[inner_surface_0_180, outer_surface_0_180] = extrapolate_mesh(dg0.points,sz0,inner180,outer180,sz180);% this is equavalnt of reading load('['Results\layer\transfer\',sample,'_transfomred_90to180']')
% to 45
for s = 1:2
[p_0to45(:,1,s), p_0to45(:,2,s)] = transformPointsInverse(tform45, dg0.points(:,1,s), dg0.points(:,2,s));
end
[inner_surface_0_45, outer_surface_0_45] = extrapolate_mesh(p_0to45,sz0,inner45,outer45,sz45);% this is equavalnt of reading load('['Results\layer\transfer\',sample,'_transfomred_90to180']')
% 90
for s = 1:2
[p_0to90(:,1,s), p_0to90(:,2,s)] = transformPointsInverse(tform90, dg0.points(:,1,s), dg0.points(:,2,s));
end
[inner_surface_0_90, outer_surface_0_90] = extrapolate_mesh(p_0to90,sz0,inner90,outer90,sz90);% this is equavalnt of reading load('['Results\layer\transfer\',sample,'_transfomred_90to180']')
if flag_fig
p = 10;
% outer
for s = 1:2
figure
title([sample,' outer 0 to 45,90,180 dg surface: ',s])
surf(outer_surface_0_180(1:p:end,1:p:end,1,s),outer_surface_0_180(1:p:end,1:p:end,2,s),outer_surface_0_180(1:p:end,1:p:end,3,s),...
'EdgeColor','k','FaceColor','none','FaceAlpha',0.6, 'FaceLighting','phong')
hold on
surf(outer_surface_0_45(1:p:end,1:p:end,1,s),outer_surface_0_45(1:p:end,1:p:end,2,s),outer_surface_0_45(1:p:end,1:p:end,3,s),...
'EdgeColor','r','FaceColor','none','FaceAlpha',0.6, 'FaceLighting','phong')
surf(outer_surface_0_90(1:p:end,1:p:end,1,s),outer_surface_0_90(1:p:end,1:p:end,2,s),outer_surface_0_90(1:p:end,1:p:end,3,s),...
'EdgeColor','g','FaceColor','none','FaceAlpha',0.6, 'FaceLighting','phong')
surf(outer0.surface_XYZ(1:p:end,1:p:end,1,s),outer0.surface_XYZ(1:p:end,1:p:end,2,s),outer0.surface_XYZ(1:p:end,1:p:end,3,s),...
'EdgeColor','b','FaceColor','none','FaceAlpha',0.6, 'FaceLighting','phong')
saveas(gcf,[save_folder,sample,'_outer_s',int2str(s),'.png'])
% inner
figure
title([sample,' inner 0 to 45,90,180 dg surface: ',s])
surf(inner_surface_0_180(1:p:end,1:p:end,1,s),inner_surface_0_180(1:p:end,1:p:end,2,s),inner_surface_0_180(1:p:end,1:p:end,3,s),...
'EdgeColor','k','FaceColor','none','FaceAlpha',0.6, 'FaceLighting','phong')
hold on
surf(inner_surface_0_45(1:p:end,1:p:end,1,s),inner_surface_0_45(1:p:end,1:p:end,2,s),inner_surface_0_45(1:p:end,1:p:end,3,s),...
'EdgeColor','r','FaceColor','none','FaceAlpha',0.6, 'FaceLighting','phong')
surf(inner_surface_0_90(1:p:end,1:p:end,1,s),inner_surface_0_90(1:p:end,1:p:end,2,s),inner_surface_0_90(1:p:end,1:p:end,3,s),...
'EdgeColor','g','FaceColor','none','FaceAlpha',0.6, 'FaceLighting','phong')
surf(inner0.surface_XYZ(1:p:end,1:p:end,1,s),inner0.surface_XYZ(1:p:end,1:p:end,2,s),inner0.surface_XYZ(1:p:end,1:p:end,3,s),...
'EdgeColor','b','FaceColor','none','FaceAlpha',0.6, 'FaceLighting','phong')
saveas(gcf,[save_folder,sample,'_inner_s',int2str(s),'.png'])
end
end
if flag_save
save([save_folder,sample],'inner0','outer0','inner_surface_0_45', 'outer_surface_0_45','inner_surface_0_90', 'outer_surface_0_90','inner_surface_0_180', 'outer_surface_0_180')
end
clear p_0to45 p_0to90 inner_surface_0_180 outer_surface_0_180 inner_surface_0_45 outer_surface_0_45 inner_surface_0_90 outer_surface_0_90
%end
%% move 90,45,0 dg to 180 dg
load_folder_Reg = 'Results\registration\layer\';
load_folder_layers = 'Results\layer\';
save_folder = 'Results\layer\transfer\all_to_180dg\';
if ~exist(save_folder,'dir')
mkdir(save_folder)
end
% if you want to run the measure separately you can use the for loop
%for i = 1:4
sample = samples{i};
disp(['Load Data ',sample])
% registrtaion
ref = load(['Results\registration\tform\reg_tfrom_inner_',sample]);
% location of the mesh (points); this is same for inner and outer but
% the interpolation value of 180 is different
%dg180 = load(['Results\registration\layer\Reg_inner_points_',sample,'_180']);
dg0 = load([load_folder_Reg,'Reg_inner_points_',sample,'_0']);
dg45 = load([load_folder_Reg,'Reg_inner_points_',sample,'_45']);
dg90 = load([load_folder_Reg,'Reg_inner_points_',sample,'_90']);
%% extrapolate from 2D into 3D --- 90,45,0 dg to 180 dg:
%load(['Results\layer\stitched\smoothed_layers_',sample,'_180'])% smooth 3D surface
inner = load([load_folder_layers,'inner_converted_layer_',sample,'_180']); % 3D surface
outer = load([load_folder_layers,'outer_converted_layer_',sample,'_180']); % 3D surface
%% 90 dg
[inner_surface_90, outer_surface_90] = extrapolate_mesh(dg90.points,size(ref.dg90_inner),inner,outer,size(ref.dg180_inner),0);
%% 45 dg
[inner_surface_45, outer_surface_45] = extrapolate_mesh(dg45.points,size(ref.dg45_inner),inner,outer,size(ref.dg180_inner),0);
%% 0 dg
[inner_surface_0, outer_surface_0] = extrapolate_mesh(dg0.points,size(ref.dg0_inner),inner,outer,size(ref.dg180_inner),0);
%% figure
if flag_fig
figure
s = 1;
p = 10;
title([sample,' inner 0,45,90 to 180 dg'],'Interpreter','none')
surf(inner.surface_XYZ(1:p:end,1:p:end,1,s),inner.surface_XYZ(1:p:end,1:p:end,2,s),inner.surface_XYZ(1:p:end,1:p:end,3,s),...
'EdgeColor','none','FaceColor','r','FaceAlpha',0.2, 'FaceLighting','phong')
hold on
surf(inner_surface_45(1:p:end,1:p:end,1,s),inner_surface_45(1:p:end,1:p:end,2,s),inner_surface_45(1:p:end,1:p:end,3,s),...
'EdgeColor','none','FaceColor','r','FaceAlpha',0.4, 'FaceLighting','phong')
surf(inner_surface_90(1:p:end,1:p:end,1,s),inner_surface_90(1:p:end,1:p:end,2,s),inner_surface_90(1:p:end,1:p:end,3,s),...
'EdgeColor','none','FaceColor','g','FaceAlpha',0.4, 'FaceLighting','phong')
surf(inner_surface_0(1:p:end,1:p:end,1,s),inner_surface_0(1:p:end,1:p:end,2,s),inner_surface_0(1:p:end,1:p:end,3,s),...
'EdgeColor','none','FaceColor','b','FaceAlpha',0.4, 'FaceLighting','phong')
saveas(gcf,[save_folder,sample,'_inner_allto180.png'])
figure
title([sample,' outer 0,45,90 to 180 dg'],'Interpreter','none')
surf(outer.surface_XYZ(1:p:end,1:p:end,1,s),outer.surface_XYZ(1:p:end,1:p:end,2,s),outer.surface_XYZ(1:p:end,1:p:end,3,s),...
'EdgeColor','none','FaceColor','k','FaceAlpha',0.2, 'FaceLighting','phong')
hold on
surf(outer_surface_45(1:p:end,1:p:end,1,s),outer_surface_45(1:p:end,1:p:end,2,s),outer_surface_45(1:p:end,1:p:end,3,s),...
'EdgeColor','none','FaceColor','r','FaceAlpha',0.4, 'FaceLighting','phong')
surf(outer_surface_90(1:p:end,1:p:end,1,s),outer_surface_90(1:p:end,1:p:end,2,s),outer_surface_90(1:p:end,1:p:end,3,s),...
'EdgeColor','none','FaceColor','g','FaceAlpha',0.4, 'FaceLighting','phong')
surf(outer_surface_0(1:p:end,1:p:end,1,s),outer_surface_0(1:p:end,1:p:end,2,s),outer_surface_0(1:p:end,1:p:end,3,s),...
'EdgeColor','none','FaceColor','b','FaceAlpha',0.4, 'FaceLighting','phong')
saveas(gcf,[save_folder,sample,'_outer_allto180.png'])
end
%% save the mesh
if flag_save
save([save_folder,sample,'_transfomred_90to180'],'inner_surface_90', 'outer_surface_90')
save([save_folder,sample,'_transfomred_45to180'],'inner_surface_45', 'outer_surface_45')
save([save_folder,sample,'_transfomred_0to180'],'inner_surface_0', 'outer_surface_0')
end
%end
%% move all the bend to the concave part for inner
load_folder_layers = 'Results\layer\transfer\0dg_rest\';
save_folder = 'Results\layer\transfer\align_0dg_rest\';
if ~exist(save_folder,'dir')
mkdir(save_folder)
end
% if you want to run the measure separately you can use the for loop
%for i = 1
sample = samples{i};
disp(['Load Data ',sample])
load([load_folder_layers,sample])
sz0 = size(outer0.surface_XYZ);
p = 10;
for s = 1:2
% move dg 180,90,45 to the most concave part
% 180 dg
X180 = outer_surface_0_180(:,:,1,s);
Y180 = outer_surface_0_180(:,:,2,s);
Z180 = outer_surface_0_180(:,:,3,s);
mY180 = min(Y180,[],'all');
indmY180 = find(Y180 == mY180);
mY180X = X180(indmY180);
mY180Z = Z180(indmY180);
mX180 = min(X180,[],'all');
MX180 = max(X180,[],'all');
rX0 = (mY180X - mX180)/(MX180-mX180);
nX180 = X180;
nY180 = Y180 - mY180;
nZ180 = Z180;
aligned_outer_dg180(:,:,:,s) = cat(3,nX180,nY180,nZ180);
% same translation on inner
X180_inner = inner_surface_0_180(:,:,1,s);
Y180_inner = inner_surface_0_180(:,:,2,s);
Z180_inner = inner_surface_0_180(:,:,3,s);
nX180_inner = X180_inner;
nY180_inner = Y180_inner - mY180;
nZ180_inner = Z180_inner;
aligned_inner_dg180(:,:,:,s) = cat(3,nX180_inner,nY180_inner,nZ180_inner);
% 45 dg
X45 = outer_surface_0_45(:,:,1,s);
Y45 = outer_surface_0_45(:,:,2,s);
Z45 = outer_surface_0_45(:,:,3,s);
mY45 = min(Y45,[],'all');
indmY45 = find(Y45 == mY45);
mY45X = X45(indmY45);
mY45Z = Z45(indmY45);
nX45 = X45 - (mY45X - mY180X);
nY45 = Y45 - mY45;
nZ45 = Z45;
aligned_outer_dg45(:,:,:,s) = cat(3,nX45,nY45,nZ45);
% same translation on inner
X45_inner = inner_surface_0_45(:,:,1,s);
Y45_inner = inner_surface_0_45(:,:,2,s);
Z45_inner = inner_surface_0_45(:,:,3,s);
nX45_inner = X45_inner - (mY45X - mY180X);
nY45_inner = Y45_inner - mY45;
nZ45_inner = Z45_inner;
aligned_inner_dg45(:,:,:,s) = cat(3,nX45_inner,nY45_inner,nZ45_inner);
% 90 dg
X90 = outer_surface_0_90(:,:,1,s);
Y90 = outer_surface_0_90(:,:,2,s);
Z90 = outer_surface_0_90(:,:,3,s);
mY90 = min(Y90,[],'all');
indmY90 = find(Y90 == mY90);
mY90X = X90(indmY90);
mY90Z = Z90(indmY90);
nX90 = X90 - (mY90X - mY180X);
nY90 = Y90 - mY90;
nZ90 = Z90;
aligned_outer_dg90(:,:,:,s) = cat(3,nX90,nY90,nZ90);
% same translation on inner
X90_inner = inner_surface_0_90(:,:,1,s);
Y90_inner = inner_surface_0_90(:,:,2,s);
Z90_inner = inner_surface_0_90(:,:,3,s);
nX90_inner = X90_inner - (mY90X - mY180X);
nY90_inner = Y90_inner - mY90;
nZ90_inner = Z90_inner;
aligned_inner_dg90(:,:,:,s) = cat(3,nX90_inner,nY90_inner,nZ90_inner);
% 0 dg
% since there is no concavity we move it according to the ratio of
% the lenght on each side of the curve
X0 = outer0.surface_XYZ(:,:,1,s);
Y0 = outer0.surface_XYZ(:,:,2,s);
Z0 = outer0.surface_XYZ(:,:,3,s);
mY0 = min(Y0,[],'all');
mX0 = min(X0,[],'all');
lX = max(X0,[],'all') - mX0;
indmX0 = find(X0 < lX*rX0);
mX0Y180X = X0(indmX0(end)) - mY180X;
nX0 = X0 - (mX0Y180X - mX0);
nY0 = Y0 - ( mY0);
nZ0 = Z0;
aligned_outer_dg0(:,:,:,s) = cat(3,nX0,nY0,nZ0);
% inner
X0_inner = inner0.surface_XYZ(:,:,1,s);
Y0_inner = inner0.surface_XYZ(:,:,2,s);
Z0_inner = inner0.surface_XYZ(:,:,3,s);
nX0_inner = X0_inner - (mX0Y180X - mX0);
nY0_inner = Y0_inner - ( mY0);
nZ0_inner = Z0_inner;
aligned_inner_dg0(:,:,:,s) = cat(3,nX0_inner,nY0_inner,nZ0_inner);
if flag_fig
% illustration
figure(1)
subplot(122)
title('aligned')
hold on
surf(nX0(1:p:end,1:p:end),nY0(1:p:end,1:p:end),nZ0(1:p:end,1:p:end),...
'EdgeColor','b','FaceColor','none','FaceAlpha',0.4, 'FaceLighting','phong')
surf(nX45(1:p:end,1:p:end),nY45(1:p:end,1:p:end),nZ45(1:p:end,1:p:end),...
'EdgeColor','r','FaceColor','none','FaceAlpha',0.4, 'FaceLighting','phong')
surf(nX90(1:p:end,1:p:end),nY90(1:p:end,1:p:end),nZ90(1:p:end,1:p:end),...
'EdgeColor','g','FaceColor','none','FaceAlpha',0.4, 'FaceLighting','phong')
surf(nX180(1:p:end,1:p:end),nY180(1:p:end,1:p:end),nZ180(1:p:end,1:p:end),...
'EdgeColor','k','FaceColor','none','FaceAlpha',0.4, 'FaceLighting','phong')
% inner
surf(nX0_inner(1:p:end,1:p:end),nY0_inner(1:p:end,1:p:end),nZ0_inner(1:p:end,1:p:end),...
'EdgeColor','b','FaceColor','none','FaceAlpha',0.4, 'FaceLighting','phong')
surf(nX45_inner(1:p:end,1:p:end),nY45_inner(1:p:end,1:p:end),nZ45_inner(1:p:end,1:p:end),...
'EdgeColor','r','FaceColor','none','FaceAlpha',0.4, 'FaceLighting','phong')
surf(nX90_inner(1:p:end,1:p:end),nY90_inner(1:p:end,1:p:end),nZ90_inner(1:p:end,1:p:end),...
'EdgeColor','g','FaceColor','none','FaceAlpha',0.4, 'FaceLighting','phong')
surf(nX180_inner(1:p:end,1:p:end),nY180_inner(1:p:end,1:p:end),nZ180_inner(1:p:end,1:p:end),...
'EdgeColor','k','FaceColor','none','FaceAlpha',0.4, 'FaceLighting','phong')
axis image
view(0,90)
hold off
% before transformation
subplot(121)
title('original')
hold on
surf(X0(1:p:end,1:p:end),Y0(1:p:end,1:p:end),Z0(1:p:end,1:p:end),...
'EdgeColor','none','FaceColor','b','FaceAlpha',0.2, 'FaceLighting','phong')
surf(X45(1:p:end,1:p:end),Y45(1:p:end,1:p:end),Z45(1:p:end,1:p:end),...
'EdgeColor','none','FaceColor','r','FaceAlpha',0.2, 'FaceLighting','phong')
surf(X90(1:p:end,1:p:end),Y90(1:p:end,1:p:end),Z90(1:p:end,1:p:end),...
'EdgeColor','none','FaceColor','g','FaceAlpha',0.2, 'FaceLighting','phong')
surf(X180(1:p:end,1:p:end),Y180(1:p:end,1:p:end),Z180(1:p:end,1:p:end),...
'EdgeColor','none','FaceColor','k','FaceAlpha',0.2, 'FaceLighting','phong')
% inner
surf(X0_inner(1:p:end,1:p:end),Y0_inner(1:p:end,1:p:end),Z0_inner(1:p:end,1:p:end),...
'EdgeColor','none','FaceColor','b','FaceAlpha',0.2, 'FaceLighting','phong')
surf(X45_inner(1:p:end,1:p:end),Y45_inner(1:p:end,1:p:end),Z45_inner(1:p:end,1:p:end),...
'EdgeColor','none','FaceColor','r','FaceAlpha',0.2, 'FaceLighting','phong')
surf(X90_inner(1:p:end,1:p:end),Y90_inner(1:p:end,1:p:end),Z90_inner(1:p:end,1:p:end),...
'EdgeColor','none','FaceColor','g','FaceAlpha',0.2, 'FaceLighting','phong')
surf(X180_inner(1:p:end,1:p:end),Y180_inner(1:p:end,1:p:end),Z180_inner(1:p:end,1:p:end),...
'EdgeColor','none','FaceColor','k','FaceAlpha',0.2, 'FaceLighting','phong')
view(0,90)
axis image
hold off
end
end
if flag_fig
legend('0 dg','45 dg','90 dg','180 dg')
suptitle_modified(sample,'none')
saveas(gcf,[save_folder,sample,'_aligned.png'])
end
if flag_save
save([save_folder,sample,'_aligned'],'aligned_outer_dg0','aligned_inner_dg0','aligned_outer_dg45','aligned_inner_dg45','aligned_outer_dg90','aligned_inner_dg90','aligned_outer_dg180','aligned_inner_dg180')
end
clear aligned_outer_dg0 aligned_inner_dg0 aligned_outer_dg45 aligned_inner_dg45 aligned_outer_dg90 aligned_inner_dg90 aligned_outer_dg180 aligned_inner_dg180
%end