admmOpticalFlow/stackCardiacImages.m at master · ndwork/admmOpticalFlow · GitHub

1
2
3
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

function stackCardiacImages
  close all; clear;

  %-- Parameters
  datacase = 10;
  nStack = 3;
  maxNData = 7;
  bound = 1.2;

  [x,eta,rho] = loadData( datacase );
  [nRows,nCols,nSlices,nData] = size(x);
  nData = min([nData,maxNData]);


  %mask = loadMask( [nRows,nCols,nSlices], datacase );

  nStack = min([nStack,nData]);

  midData = ceil(nData/2);
  midSlice = ceil(nSlices/2);
  flow = struct( 'du', zeros(nRows,nCols,nSlices), ...
                 'dv', zeros(nRows,nCols,nSlices), ...
                 'dw', zeros(nRows,nCols,nSlices)  );
  flows = cell(nData-1,1);

  parfor i=1:nData-1
    disp([ 'Working on i=', num2str(i), ' of ', num2str(nData-1) ]);
    flows{i} = flow;

    data1 = squeeze( x(:,:,:,i) );
    data2 = squeeze( x(:,:,:,i+1) );

    if exist('mask','var')
      maskedIndxs = find( mask>0 & data2~=0 );
      scales = data1(maskedIndxs) ./ data2(maskedIndxs);
      data2 = data2 .* median( scales );
      [du,dv,dw] = opticalFlow3D( data1, data2, eta, rho, mask );
    else
      maskedIndxs = find( data2~=0 );
      scales = data1(maskedIndxs) ./ data2(maskedIndxs);
      data2 = data2 .* median( scales );
      %[du,dv,dw] = opticalFlow3D( data1, data2, eta, rho );
      [du,dv,dw] = boundedOpticalFlow3D( data1, data2, eta, rho, bound );
    end
    flows{i}.du = du;
    flows{i}.dv = dv;
    flows{i}.dw = dw;
  end

save( 'stackState.mat' );
%load 'stackState_1dn3.mat';   % eta=1d-3
%load 'stackState_5dn4.mat';   % eta=5d-4
%load 'stackState_1d10scaleByN.mat';


  % Make a stack
  if mod(nStack,2)==0, error('nStack must be odd'); end;
  nHalfStack = floor( nStack / 2 );
  stack = x(:,:,:,midData);
  simpleStack = x(:,:,:,midData);
figure;
%subplot(1,2,1);  imshow( imresize( x(:,:,midPage,midData), 3), [] );
%subplot(1,2,2);
imshow( imresize( x(:,:,midSlice,midData), 3), [] );
title(num2str(midData), 'FontSize', 20);
  for i=1:nHalfStack
    fIndx = midData + i;
    bIndx = midData - i;

    if i==1
      fFlows = flows{fIndx-1};
      bFlows = flows{bIndx};
      bFlows.du = -bFlows.du;
      bFlows.dv = -bFlows.dv;
      bFlows.dw = -bFlows.dw;
    else
      fFlows.du = fFlows.du + flows{fIndx-1}.du;
      fFlows.dv = fFlows.dv + flows{fIndx-1}.dv;
      fFlows.dw = fFlows.dw + flows{fIndx-1}.dw;
      bFlows.du = bFlows.du - flows{bIndx}.du;
      bFlows.dv = bFlows.dv - flows{bIndx}.dv;
      bFlows.dw = bFlows.dw - flows{bIndx}.dw;
    end

    fInterpd = ofInterp3D( x(:,:,:,fIndx), fFlows.du, fFlows.dv, fFlows.dw );
    bInterpd = ofInterp3D( x(:,:,:,bIndx), bFlows.du, bFlows.dv, bFlows.dw );

figure; imshow( imresize( squeeze(x(125,:,:,fIndx)), 3), [] );
title([num2str(fIndx), ' - Orig'], 'FontSize', 20);
figure; imshow( imresize( squeeze(fInterpd(125,:,:)), 3), [] );
title(num2str(fIndx), 'FontSize', 20);
figure; imshow( imresize( squeeze(x(125,:,:,midData)), 3), [] );
title('Mid Data', 'Fontsize', 20);
figure; imshow( imresize( squeeze(x(125,:,:,bIndx)), 3), [] );
title([num2str(bIndx), ' - Orig'], 'FontSize', 20);
figure; imshow( imresize( squeeze(bInterpd(125,:,:)), 3), [] );
title(num2str(bIndx), 'FontSize', 20);

magFFlows = sqrt( fFlows.du.^2 + fFlows.dv.^2 + fFlows.dw.^2 );
figure;  imshow( imresize( magFFlows(:,:,midSlice), 3), [] );
title(num2str(fIndx), 'FontSize', 20);
magBFlows = sqrt( bFlows.du.^2 + bFlows.dv.^2 + bFlows.dw.^2 );
figure;  imshow( imresize( magBFlows(:,:,midSlice), 3), [] );
title(num2str(bIndx), 'FontSize', 20);

    stack = stack + fInterpd;
    stack = stack + bInterpd;

    simpleStack = simpleStack + x(:,:,:,fIndx);
    simpleStack = simpleStack + x(:,:,:,bIndx);
  end

  figure;  imshow( imresize( abs(x(:,:,midSlice,midData)), 3), [] );
  title('Single Image', 'FontSize', 20);
  figure;  imshow( imresize( abs(simpleStack(:,:,midSlice)), 3), [] );
  title('Simple Stack', 'FontSize', 20);
  figure;  imshow( imresize( abs(stack(:,:,midSlice)), 3), [] );
  title('OF Stacked Image', 'FontSize', 20);

  figure;  imshow( imresize( abs(squeeze(x(125,:,:,midData+1)))', 3), [] );
  title('Single Image-Mid-1', 'FontSize', 20);
  figure;  imshow( imresize( abs(squeeze(x(125,:,:,midData)))', 3), [] );
  title('Single Image-Mid', 'FontSize', 20);
  figure;  imshow( imresize( abs(squeeze(x(125,:,:,midData-1)))', 3), [] );
  title('Single Image-Mid+1', 'FontSize', 20);
  figure;  imshow( imresize( abs(squeeze(simpleStack(125,:,:)))', 3), [] );
  title('Simple Stack', 'FontSize', 20);
  figure;  imshow( imresize( abs(squeeze(stack(125,:,:)))', 3), [] );
  title('OF Stacked Image', 'FontSize', 20);

  midCol = ceil(nCols/2);
  figure;  imshow( imresize( abs(squeeze(x(:,125,:,midData)))', 3), [] );
  title('Single Image', 'FontSize', 20);
  figure;  imshow( imresize( abs(squeeze(simpleStack(:,125,:)))', 3), [] );
  title('Simple Stack', 'FontSize', 20);
  figure;  imshow( imresize( abs(squeeze(stack(:,125,:)))', 3), [] );
  title('OF Stacked Image', 'FontSize', 20);

  %saveAllSlices( stack, 1 );

end