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Frog

vtk-examples/Python/Visualization/Frog


Description

Frog organs along with a translucent skin can be viewed.

The dataset is derived from a frog. This data was prepared at Lawrence Berkeley National Laboratories and is included with their permission. The data was acquired by physically slicing the frog and photographing the slices. The original segmented data is in the form of tissue masks with one file per tissue. There are 136 slices per tissue and 15 different tissues. Each slice is 470 by 500 pixels.

This example uses the vtkPolyData file for the skin and files that are generated from the tissue masks. You add tissues by specifying a list of tissue names. Note that the skin is rendered as being translucent so that you can see the internal organs.

The code uses a general way of specifying transformations that can permute image and other geometric data in order to maintain proper orientation regardless of the acquisition order. See the class SliceOrder.

Info

FrogReconstruction for an example detailing a general method for reconstructing from the original data.

Info

By specifying the tissues and other parameters, as outlined in the code, you can generate the following figures: Figure 12-9a, Figure 12-9b, Figure 12-9c, and Figure 12-9d in Chapter 12 of the VTK Textbook.

Question

If you have a question about this example, please use the VTK Discourse Forum

Code

Frog.py

#!/usr/bin/env python

from pathlib import Path

import vtk


def get_program_parameters(argv):
    import argparse
    description = 'Display the frog organs along with a translucent skin.'
    epilogue = '''
To specify all the tissues at once:
 blood brain duodenum eye_retna eye_white heart ileum kidney l_intestine liver lung nerve skeleton spleen stomach skin

You can leave out brainbin, it is the brain with no gaussian smoothing.

Here are the parameters used to get the views in the VTK Textbook:
Fig12-9a:
 blood brain duodenum eye_retna eye_white heart ileum kidney l_intestine liver lung nerve skeleton spleen stomach skin -a
Fig12-9b:
 blood brain duodenum eye_retna eye_white heart ileum kidney l_intestine liver lung nerve skeleton spleen stomach -a
Fig12-9c:
 brain duodenum eye_retna eye_white heart ileum kidney l_intestine liver lung nerve spleen stomach -c
Fig12-9c:
 brain duodenum eye_retna eye_white heart ileum kidney l_intestine liver lung nerve spleen stomach -d
    '''
    parser = argparse.ArgumentParser(description=description, epilog=epilogue,
                                     formatter_class=argparse.RawDescriptionHelpFormatter)

    group = parser.add_mutually_exclusive_group()
    group.add_argument('-a', action='store_const', dest='view', const='a',
                       help='The view corresponds to Figs 12-9a and 12-9b in the VTK Textbook')
    group.add_argument('-c', action='store_const', dest='view', const='c',
                       help='The view corresponds to Figs 12-9c in the VTK Textbook')
    group.add_argument('-d', action='store_const', dest='view', const='d',
                       help='The view corresponds to Figs 12-9d in the VTK Textbook')
    parser.set_defaults(type=None)

    parser.add_argument('data_folder', help='The path to the files: frog.mhd and frogtissue.mhd.')
    parser.add_argument('tissues', nargs='+', help='List of one or more tissues.')
    args = parser.parse_args()
    return args.data_folder, args.tissues, args.view


def main(data_folder, tissues, view):
    colors = vtk.vtkNamedColors()

    # Setup render window, renderer, and interactor.
    renderer = vtk.vtkRenderer()
    render_window = vtk.vtkRenderWindow()
    render_window.AddRenderer(renderer)
    render_window_interactor = vtk.vtkRenderWindowInteractor()
    render_window_interactor.SetRenderWindow(render_window)

    tm = create_tissue_map()
    path = Path(data_folder)
    color_lut = create_frog_lut(colors)
    res = ['Using the following tissues:']
    for tissue in tissues:
        source = None
        if path.is_dir():
            source = path.joinpath(tissue).with_suffix('.vtk')
            if not source.is_file():
                s = 'The file: {:s} does not exist.'.format(str(source))
                print(s)
                continue
        actor = create_frog_actor(str(source), tissue, tm[tissue][1])
        actor.GetProperty().SetOpacity(tm[tissue][2])
        actor.GetProperty().SetDiffuseColor(color_lut.GetTableValue(tm[tissue][0])[:3])
        actor.GetProperty().SetSpecular(0.2)
        actor.GetProperty().SetSpecularPower(10)
        renderer.AddActor(actor)
        res.append('{:>11s}, label: {:2d}'.format(tissue, tm[tissue][0]))

    if len(res) > 1:
        print('\n'.join(res))

    render_window.SetSize(640, 640)
    render_window.SetWindowName('Frog')

    renderer.SetBackground(colors.GetColor3d('LightSteelBlue'))

    # Initial view (looking down on the dorsal surface).
    renderer.GetActiveCamera().Roll(-90)
    renderer.ResetCamera()

    #  Final view
    if view:
        if view == 'a':
            # Figs 12-9a and 12-9b in the VTK Textbook
            camera = renderer.GetActiveCamera()
            camera.SetPosition(-599.880035, 548.906952, 313.670289)
            camera.SetFocalPoint(-8.376500, 40.691664, -156.007163)
            camera.SetViewUp(0.294699, -0.440638, 0.847933)
            camera.SetDistance(910.360434)
            camera.SetClippingRange(231.699387, 1758.550290)
        elif view == 'c':
            # Figs 12-9c in the VTK Textbook
            camera = renderer.GetActiveCamera()
            camera.SetPosition(-206.616664, 182.524078, 87.589931)
            camera.SetFocalPoint(-5.721571, -0.074326, -97.940837)
            camera.SetViewUp(0.300335, -0.496855, 0.814208)
            camera.SetDistance(328.820135)
            camera.SetClippingRange(0.810268, 810.268454)
        elif view == 'd':
            # Fig 12-9d in the VTK Textbook
            camera = renderer.GetActiveCamera()
            camera.SetPosition(-40.912047, -65.274764, 588.508700)
            camera.SetFocalPoint(-10.418979, 17.700133, -158.643842)
            camera.SetViewUp(0.741687, -0.669297, -0.044059)
            camera.SetDistance(752.363995)
            camera.SetClippingRange(444.653021, 997.508259)

    render_window.Render()

    axes = vtk.vtkAxesActor()

    widget = vtk.vtkOrientationMarkerWidget()
    rgba = [0.0, 0.0, 0.0, 0.0]
    colors.GetColor("Carrot", rgba)
    widget.SetOutlineColor(rgba[0], rgba[1], rgba[2])
    widget.SetOrientationMarker(axes)
    widget.SetInteractor(render_window_interactor)
    widget.SetViewport(0.0, 0.0, 0.2, 0.2)
    widget.SetEnabled(1)
    widget.InteractiveOn()

    render_window_interactor.Start()


def create_frog_actor(file_name, tissue, transform):
    so = SliceOrder()

    reader = vtk.vtkPolyDataReader()
    reader.SetFileName(file_name)
    reader.Update()

    trans = so.get(transform)
    if tissue == 'brainbin':
        trans.Scale(1, -1, 1)
        trans.RotateZ(180)
    tf = vtk.vtkTransformPolyDataFilter()
    tf.SetInputConnection(reader.GetOutputPort())
    tf.SetTransform(trans)
    tf.SetInputConnection(reader.GetOutputPort())

    normals = vtk.vtkPolyDataNormals()
    normals.SetInputConnection(tf.GetOutputPort())
    normals.SetFeatureAngle(60.0)

    mapper = vtk.vtkPolyDataMapper()
    mapper.SetInputConnection(normals.GetOutputPort())

    actor = vtk.vtkActor()
    actor.SetMapper(mapper)

    return actor


class SliceOrder:
    """
    These transformations permute image and other geometric data to maintain proper
     orientation regardless of the acquisition order. After applying these transforms with
    vtkTransformFilter, a view up of 0,-1,0 will result in the body part
    facing the viewer.
    NOTE: some transformations have a -1 scale factor for one of the components.
          To ensure proper polygon orientation and normal direction, you must
          apply the vtkPolyDataNormals filter.

    Naming (the nomenclature is medical):
    si - superior to inferior (top to bottom)
    is - inferior to superior (bottom to top)
    ap - anterior to posterior (front to back)
    pa - posterior to anterior (back to front)
    lr - left to right
    rl - right to left
    """

    def __init__(self):
        self.si_mat = vtk.vtkMatrix4x4()
        self.si_mat.Zero()
        self.si_mat.SetElement(0, 0, 1)
        self.si_mat.SetElement(1, 2, 1)
        self.si_mat.SetElement(2, 1, -1)
        self.si_mat.SetElement(3, 3, 1)

        self.is_mat = vtk.vtkMatrix4x4()
        self.is_mat.Zero()
        self.is_mat.SetElement(0, 0, 1)
        self.is_mat.SetElement(1, 2, -1)
        self.is_mat.SetElement(2, 1, -1)
        self.is_mat.SetElement(3, 3, 1)

        self.lr_mat = vtk.vtkMatrix4x4()
        self.lr_mat.Zero()
        self.lr_mat.SetElement(0, 2, -1)
        self.lr_mat.SetElement(1, 1, -1)
        self.lr_mat.SetElement(2, 0, 1)
        self.lr_mat.SetElement(3, 3, 1)

        self.rl_mat = vtk.vtkMatrix4x4()
        self.rl_mat.Zero()
        self.rl_mat.SetElement(0, 2, 1)
        self.rl_mat.SetElement(1, 1, -1)
        self.rl_mat.SetElement(2, 0, 1)
        self.rl_mat.SetElement(3, 3, 1)

        """
        The previous transforms assume radiological views of the slices (viewed from the feet). other
        modalities such as physical sectioning may view from the head. These transforms modify the original
        with a 180° rotation about y
        """

        self.hf_mat = vtk.vtkMatrix4x4()
        self.hf_mat.Zero()
        self.hf_mat.SetElement(0, 0, -1)
        self.hf_mat.SetElement(1, 1, 1)
        self.hf_mat.SetElement(2, 2, -1)
        self.hf_mat.SetElement(3, 3, 1)

    def s_i(self):
        t = vtk.vtkTransform()
        t.SetMatrix(self.si_mat)
        return t

    def i_s(self):
        t = vtk.vtkTransform()
        t.SetMatrix(self.is_mat)
        return t

    @staticmethod
    def a_p():
        t = vtk.vtkTransform()
        return t.Scale(1, -1, 1)

    @staticmethod
    def p_a():
        t = vtk.vtkTransform()
        return t.Scale(1, -1, -1)

    def l_r(self):
        t = vtk.vtkTransform()
        t.SetMatrix(self.lr_mat)
        t.Update()
        return t

    def r_l(self):
        t = vtk.vtkTransform()
        t.SetMatrix(self.lr_mat)
        return t

    def h_f(self):
        t = vtk.vtkTransform()
        t.SetMatrix(self.hf_mat)
        return t

    def hf_si(self):
        t = vtk.vtkTransform()
        t.Concatenate(self.hf_mat)
        t.Concatenate(self.si_mat)
        return t

    def hf_is(self):
        t = vtk.vtkTransform()
        t.Concatenate(self.hf_mat)
        t.Concatenate(self.is_mat)
        return t

    def hf_ap(self):
        t = vtk.vtkTransform()
        t.Concatenate(self.hf_mat)
        t.Scale(1, -1, 1)
        return t

    def hf_pa(self):
        t = vtk.vtkTransform()
        t.Concatenate(self.hf_mat)
        t.Scale(1, -1, -1)
        return t

    def hf_lr(self):
        t = vtk.vtkTransform()
        t.Concatenate(self.hf_mat)
        t.Concatenate(self.lr_mat)
        return t

    def hf_rl(self):
        t = vtk.vtkTransform()
        t.Concatenate(self.hf_mat)
        t.Concatenate(self.rl_mat)
        return t

    def get(self, order):
        """
        Returns the vtkTransform corresponding to the slice order.

        :param order: The slice order
        :return: The vtkTransform to use
        """
        if order == 'si':
            return self.s_i()
        elif order == 'is':
            return self.i_s()
        elif order == 'ap':
            return self.a_p()
        elif order == 'pa':
            return self.p_a()
        elif order == 'lr':
            return self.l_r()
        elif order == 'rl':
            return self.r_l()
        elif order == 'hf':
            return self.h_f()
        elif order == 'hfsi':
            return self.hf_si()
        elif order == 'hfis':
            return self.hf_is()
        elif order == 'hfap':
            return self.hf_ap()
        elif order == 'hfpa':
            return self.hf_pa()
        elif order == 'hflr':
            return self.hf_lr()
        elif order == 'hfrl':
            return self.hf_rl()
        else:
            s = 'No such transform "{:s}" exists.'.format(order)
            raise Exception(s)


def create_frog_lut(colors):
    lut = vtk.vtkLookupTable()
    lut.SetNumberOfColors(16)
    lut.SetTableRange(0, 15)
    lut.Build()

    lut.SetTableValue(0, colors.GetColor4d('LimeGreen'))  # skin
    lut.SetTableValue(1, colors.GetColor4d('salmon'))  # blood
    lut.SetTableValue(2, colors.GetColor4d('beige'))  # brain
    lut.SetTableValue(3, colors.GetColor4d('orange'))  # duodenum
    lut.SetTableValue(4, colors.GetColor4d('misty_rose'))  # eye_retina
    lut.SetTableValue(5, colors.GetColor4d('white'))  # eye_white
    lut.SetTableValue(6, colors.GetColor4d('tomato'))  # heart
    lut.SetTableValue(7, colors.GetColor4d('raspberry'))  # ileum
    lut.SetTableValue(8, colors.GetColor4d('banana'))  # kidney
    lut.SetTableValue(9, colors.GetColor4d('peru'))  # l_intestine
    lut.SetTableValue(10, colors.GetColor4d('pink'))  # liver
    lut.SetTableValue(11, colors.GetColor4d('powder_blue'))  # lung
    lut.SetTableValue(12, colors.GetColor4d('carrot'))  # nerve
    lut.SetTableValue(13, colors.GetColor4d('wheat'))  # skeleton
    lut.SetTableValue(14, colors.GetColor4d('violet'))  # spleen
    lut.SetTableValue(15, colors.GetColor4d('plum'))  # stomach

    return lut


def create_tissue_map():
    tiss = dict()
    # key: name of the tissue
    # value: [lut_index, transform, opacity]
    tiss['skin'] = [0, 'hfsi', 0.4]
    tiss['blood'] = [1, 'is', 1.0]
    tiss['brain'] = [2, 'is', 1.0]
    tiss['brainbin'] = [2, 'is', 1.0]
    tiss['duodenum'] = [3, 'is', 1.0]
    tiss['eye_retna'] = [4, 'is', 1.0]
    tiss['eye_white'] = [5, 'is', 1.0]
    tiss['heart'] = [6, 'is', 1.0]
    tiss['ileum'] = [7, 'is', 1.0]
    tiss['kidney'] = [8, 'is', 1.0]
    tiss['l_intestine'] = [9, 'is', 1.0]
    tiss['liver'] = [10, 'is', 1.0]
    tiss['lung'] = [11, 'is', 1.0]
    tiss['nerve'] = [12, 'is', 1.0]
    tiss['skeleton'] = [13, 'is', 1.0]
    tiss['spleen'] = [14, 'is', 1.0]
    tiss['stomach'] = [15, 'is', 1.0]
    return tiss


if __name__ == '__main__':
    import sys

    data_folder, tissues, view = get_program_parameters(sys.argv)
    main(data_folder, tissues, view)