VTKTest/ome_tiff.cpp at main · RoomOfAnalysis/VTKTest · 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
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
#include <vtkNew.h>
#include <vtkSmartPointer.h>
#include <vtkImageData.h>
#include <vtkOMETIFFReader.h>
#include <vtkImageViewer2.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkInteractorStyleImage.h>
#include <vtkRenderWindow.h>

#include <vtkCornerAnnotation.h>
#include <vtkTextProperty.h>
#include <vtkCallbackCommand.h>
#include <vtkRenderer.h>
#include <vtkObjectFactory.h>
#include <vtkImageHistogramStatistics.h>
#include <vtkImageMapToWindowLevelColors.h>

#include <vtkInformation.h>

#include <filesystem>
#include <sstream>
#include <iostream>

class myInteractorStyler final: public vtkInteractorStyleImage
{
public:
    static myInteractorStyler* New();

    vtkTypeMacro(myInteractorStyler, vtkInteractorStyleImage);

    void setImageViewer(vtkImageViewer2* imageViewer, int slice_no = 0)
    {
        m_viewer = imageViewer;
        m_slice_min = imageViewer->GetSliceMin();
        m_slice_max = imageViewer->GetSliceMax();
        m_slice = slice_no <= 0 ? (m_slice_min + m_slice_max) / 2 : slice_no;
        m_viewer->SetSlice(m_slice);

        if (!m_text)
        {
            m_text = vtkSmartPointer<vtkCornerAnnotation>::New();
            m_text->GetTextProperty()->SetColor(1.0, 0.72, 0.0);
            m_viewer->GetRenderer()->AddViewProp(m_text);
        }
        ShowSliceText();
    }

protected:
    void OnMouseWheelForward() override { moveSliceForward(); }

    void OnMouseWheelBackward() override { moveSliceBackward(); }

    void OnChar() override
    {
        if (Interactor->GetKeyCode() == 'x')
            m_viewer->SetSliceOrientationToYZ();
        else if (Interactor->GetKeyCode() == 'y')
            m_viewer->SetSliceOrientationToXZ();
        else if (Interactor->GetKeyCode() == 'z')
            m_viewer->SetSliceOrientationToXY();
    }

private:
    void moveSliceForward()
    {
        if (m_slice < m_slice_max)
        {
            m_slice += 1;

            m_viewer->SetSlice(m_slice);
            ShowSliceText();
        }
    }

    void moveSliceBackward()
    {
        if (m_slice > m_slice_min)
        {
            m_slice -= 1;

            m_viewer->SetSlice(m_slice);
            ShowSliceText();
        }
    }

    void ShowSliceText()
    {
        std::stringstream ss;
        ss << m_slice << " / " << m_slice_max;
        m_text->SetText(vtkCornerAnnotation::LowerRight, ss.str().c_str());
    }

private:
    vtkImageViewer2* m_viewer;
    int m_slice;
    int m_slice_min;
    int m_slice_max;
    vtkSmartPointer<vtkCornerAnnotation> m_text = nullptr;
};
vtkStandardNewMacro(myInteractorStyler);

int main(int argc, char* argv[])
{
    if (argc != 2)
    {
        std::cerr << "1) .ome.tiff file path" << std::endl;
        return EXIT_FAILURE;
    }

    std::filesystem::path path{argv[1]};

    vtkNew<vtkOMETIFFReader> reader;
    if (!reader->CanReadFile(path.string().c_str()))
    {
        std::cerr << "ERROR: vtkOMETIFFReader cannot read the provided file: " << path << std::endl;
        return EXIT_FAILURE;
    }
    reader->SetFileName(path.string().c_str());
    reader->Update();
    auto img_data = reader->GetOutput();

    std::cout << img_data->GetScalarTypeAsString() << std::endl;

    //img_data->PrintSelf(std::cout, vtkIndent{});
    // according to https://github.com/Kitware/VTK/blob/master/IO/Image/vtkOMETIFFReader.cxx
    // vtk only reads the following XML fields...
    //omeinternals.IsValid = true;
    //omeinternals.SizeX = pixelsXML.attribute("SizeX").as_int(0);
    //omeinternals.SizeY = pixelsXML.attribute("SizeY").as_int(0);
    //omeinternals.SizeZ = pixelsXML.attribute("SizeZ").as_int(1);
    //omeinternals.SizeC = pixelsXML.attribute("SizeC").as_int(1);
    //omeinternals.SizeT = pixelsXML.attribute("SizeT").as_int(1);
    //omeinternals.TimeIncrement = pixelsXML.attribute("TimeIncrement").as_double(1.0);
    //omeinternals.PhysicalSize[0] = pixelsXML.attribute("PhysicalSizeX").as_double(1.0);
    //omeinternals.PhysicalSize[1] = pixelsXML.attribute("PhysicalSizeY").as_double(1.0);
    //omeinternals.PhysicalSize[2] = pixelsXML.attribute("PhysicalSizeZ").as_double(1.0);
    //omeinternals.PhysicalSizeUnit[0] = pixelsXML.attribute("PhysicalSizeXUnit").as_string();
    //omeinternals.PhysicalSizeUnit[1] = pixelsXML.attribute("PhysicalSizeYUnit").as_string();
    //omeinternals.PhysicalSizeUnit[2] = pixelsXML.attribute("PhysicalSizeZUnit").as_string();

    img_data->GetInformation()->Print(std::cout);

    vtkNew<vtkImageViewer2> viewer;
    viewer->SetInputData(img_data);
    viewer->SetSliceOrientationToXY();

    vtkNew<vtkRenderWindowInteractor> interactor;
    vtkNew<myInteractorStyler> style;
    style->setImageViewer(viewer);
    viewer->SetupInteractor(interactor); // this line should be put before the next line... otherwise the style not work
    interactor->SetInteractorStyle(style);
    viewer->GetRenderWindow()->SetWindowName("ome tiff viewer");
    viewer->GetRenderWindow()->SetSize(500, 500);
    viewer->Render();
    interactor->Start();

    return 0;
}