Initial commit

src/Cxx.md

@@ -1034,6 +1034,8 @@ See [this tutorial](http://www.vtk.org/Wiki/VTK/Tutorials/3DDataTypes) for a bri
 [Follower](/Cxx/Visualization/Follower) | Draw text that stays right side up.
 [FontFile](/Cxx/Visualization/FontFile) | Use an external font.
 [FrogBrain](/Cxx/Visualization/FrogBrain) | The frog’s brain. Model extracted without smoothing (left) and with smoothing (right).
+[FroggieSurface](/Cxx/Visualization/FroggieSurface) | All or some frog tissues are reconstructed from the original segmented data.
+[FroggieView](/Cxx/Visualization/FroggieView) | View all or some frog tissues and adjust the translucency of the tissues.
 [FrogSlice](/Cxx/Visualization/FrogSlice) | Photographic slice of frog (upper left), segmented frog (upper right) and composite of photo and segmentation (bottom). The purple color represents the stomach and the kidneys are yellow.
 [Glyph2D](/Cxx/Filtering/Glyph2D) |
 [Glyph3D](/Cxx/Filtering/Glyph3D) |

src/Cxx/Visualization/CMakeLists.txt

@@ -48,8 +48,10 @@ if(NOT VTK_BINARY_DIR)
   RenderingLOD
   RenderingLabel
   RenderingOpenGL2
+  OPTIONAL_COMPONENTS
+  cli11
+  jsoncpp
   TestingRendering
-  ${optional}
   QUIET
 )
 endif()
@@ -61,6 +63,18 @@ set(KIT_LIBS ${VTK_LIBRARIES})
 
 file(GLOB ALL_FILES *.cxx)
 
+include(${WikiExamples_SOURCE_DIR}/CMake/RequiresCxxVersion.cmake)
+set(CXX_VERSION_MIN "17")
+Requires_Cxx_Version(FroggieSurface ${CXX_VERSION_MIN} ALL_FILES)
+Requires_Cxx_Version(FroggieView ${CXX_VERSION_MIN} ALL_FILES)
+
+include(${WikiExamples_SOURCE_DIR}/CMake/RequiresModule.cmake)
+Requires_Module(FroggieSurface cli11)
+Requires_Module(FroggieView cli11)
+Requires_Module(FroggieSurface jsoncpp)
+Requires_Module(FroggieView jsoncpp)
+
+
 Requires_Module(ExtrudePolyDataAlongLine SplineDrivenImageSlicer)
 #Requires_Module(ShadowsOpenGL RenderingOpenGL)
 #Requires_Setting_Off(StreamLines VTK_LEGACY_REMOVE)
@@ -102,6 +116,8 @@ if (BUILD_TESTING)
     ExtrudePolyDataAlongLine
     FontFile
     FrogBrain
+    FroggieSurface
+    FroggieView
     FrogSlice
     Glyph3DImage
     Glyph3DMapper
@@ -182,6 +198,15 @@ if (BUILD_TESTING)
   add_test(${KIT}-FontFile ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${KIT}CxxTests
     TestFontFile ${DATA}/CopyPaste.ttf)
 
+    if(TARGET FroggieSurface)
+    add_test(${KIT}-FroggieSurface ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${KIT}CxxTests
+    TestFroggieSurface ${DATA}/Frog_mhd.json)
+  endif()
+  if(TARGET FroggieView)
+    add_test(${KIT}-FroggieView ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${KIT}CxxTests
+      TestFroggieView ${DATA}/Frog_vtk.json)
+  endif()
+
   add_test(${KIT}-Glyph3DImage ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${KIT}CxxTests
     TestGlyph3DImage ${DATA}/emote.jpg)
 

src/Cxx/Visualization/FroggieSurface.md

+### Description
+
+Frog organs along with a translucent skin are reconstructed from the original segmented data.
+
+By default the frog is oriented so that we look down on the dorsal (posterior) surface and the superior surface faces the top of the screen. The frog is rendered with the skin being translucent so that you can see the internal organs.
+
+In the lower left of the image there is a prop assembly with labelled XYZ axes and a cube labelled with anatomical orientations:
+
+- **Sagittal plane**
+  - L - left
+  - R - right
+- **Coronal plane**
+  - A - anterior
+  - P - posterior
+- **Transverse plane**
+  - S - superior  
+  - I - inferior
+
+This prop assembly can be moved and resized.
+
+Individual tissues can be specified by using the "**-t**" option e.g. "**-t skin skeleton**".
+
+We use vtkFlyingEdges3D to take the 3D structured point set and generate the iso-surfaces. However, if desired, you can specify vtkMarchingCubes instead, use the option "**-m**".
+
+The parameters used to generate the example image are loaded from a JSON file containing the data needed to access and generate the actors for each tissue along with other supplementary data such as the data file names. This means that the user need only load this one file in order to generate the data for rendering. This file is called:
+
+``` text
+<DATA>/Frog_mhd.json
+```
+
+Where `<DATA>` is the path to `?vtk-?examples/src/Testing/Data`.
+
+For information about the parameters in the JSON file, please see [Frog_mhd_format](../../Documentation/Frog_mhd_format.md).
+
+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**.
+
+The dataset was prepared at the 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.
+
+To accommodate the volume readers in VTK, the mask files were processed and combined into one vtkMetaImageReader file, called 'frogtissue.mhd'. Integer numbers 1-15 are used to represent the 15 tissues. A similar process was done for the frog skin with the result being stored in a file called 'frog.mhd'.
+
+
+!!! info
+    Mutually exclusive options "***-a, -b, -c, -d**" are provided to let you generate approximations to the following figures: [Figure 12-9a](../../../VTKBook/12Chapter12/#Figure%2012-9a), [Figure 12-9b](../../../VTKBook/12Chapter12/#Figure%2012-9b), [Figure 12-9c](../../../VTKBook/12Chapter12/#Figure%2012-9c), and [Figure 12-9d](../../../VTKBook/12Chapter12/#Figure%2012-9d) in [Chapter 12](../../../VTKBook/12Chapter12) of the [VTK Textbook](../../../VTKBook/01Chapter1).

src/Cxx/Visualization/FroggieView.md

+### Description
+
+Frog organs along with a translucent skin are reconstructed from the original segmented data.
+
+By default the frog is oriented so that we look down on the dorsal (posterior) surface and the superior surface faces the top of the screen. The frog is rendered with the skin being translucent so that you can see the internal organs.
+
+In the lower left of the image there is a prop assembly with labelled XYZ axes and a cube labelled with anatomical orientations:
+
+- **Sagittal plane**
+  - L - left
+  - R - right
+- **Coronal plane**
+  - A - anterior
+  - P - posterior
+- **Transverse plane**
+  - S - superior  
+  - I - inferior
+
+This prop assembly can be moved and resized.
+
+The opacity of eaxh tissue is controlled by a slider, additionally you can turn all the sliders on or off by pressing the "**n**" key.
+
+If the option "**-n**" is selected, no sliders will displayed.
+
+Individual tissues can be specified by using the "**-t**" option e.g. "**-t skin skeleton**".
+
+The parameters used to generate the example image are loaded from a JSON file containing the data needed to access and generate the actors for each tissue along with other supplementary data such as the data file names. This means that the user need only load this one file in order to generate the data for rendering. This file is called:
+
+``` text
+<DATA>/Frog_vtk.json
+```
+
+Where `<DATA>` is the path to `?vtk-?examples/src/Testing/Data`.
+
+For information about the parameters in the JSON file, please see [Frog_vtk_format](../../Documentation/Frog_vtk_format.md).
+
+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**.
+
+The dataset was prepared at the Lawrence Berkeley National Laboratories. It 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 `*.vtk` tissue files. These were pre-processed using the original data so that loading is much faster.
+
+!!! info
+    Mutually exclusive options "***-a -b -c -d**" are provided to let you generate approximations to the following figures: [Figure 12-9a](../../../VTKBook/12Chapter12/#Figure%2012-9a), [Figure 12-9b](../../../VTKBook/12Chapter12/#Figure%2012-9b), [Figure 12-9c](../../../VTKBook/12Chapter12/#Figure%2012-9c), and [Figure 12-9d](../../../VTKBook/12Chapter12/#Figure%2012-9d) in [Chapter 12](../../../VTKBook/12Chapter12) of the [VTK Textbook](../../../VTKBook/01Chapter1).

src/Documentation/Frog_mhd_format.md

+# Frog MHD Format
+
+The following keys are recognised:
+
+## Keys
+
+- **title**: A title.
+- **files**: A vector/list of paths to the *.mhd files needed.
+- **tissues**
+  - **colors**: A map/dict of tissue names and colors.
+- **figures**
+  - **fig12-9b**: The vector/list of tissues needed for figure 12-9b.
+  - **fig12-9cd**: The vector/list of tissues needed for figure 12-9c and 12-9d.
+- **tissue_parameters**: The required parameters for each tissue are specified here.
+  - **parameter types**: A map/dict of tissue parameters of each tissue parameter and its type. Essential for C++ code.
+  - **default**>: The default tissue parameters, a map/dict of tissue parameters and values.
+  - <**tissue name**>: The map/dict of tissue parameters and values for each tissue.

src/Documentation/Frog_vtk_format.md

+# Frog VTK Format
+
+The following keys are recognised:
+
+## Keys
+
+- **title**: A title.
+- **files**: A vector/list of paths to the *.vtk files needed.
+- **tissues**
+  - **names**: A vector/list of the tissue names.
+  - **indices**: A map/dict of tissue names and index.
+  - **colors**: A map/dict of tissue names and colors.
+  - **orientation**: A map/dict of tissue names and orientation.
+  - **opacity**: A map/dict of tissue names and opacity.
+- **figures**
+  - **fig12-9b**: The vector/list of tissues needed for figure 12-9b.
+  - **fig12-9cd**: The vector/list of tissues needed for figure 12-9c and 12-9d.

src/Python.md

@@ -548,10 +548,9 @@ See [this tutorial](http://www.vtk.org/Wiki/VTK/Tutorials/3DDataTypes) for a bri
 [ElevationBandsWithGlyphs](/Python/Visualization/ElevationBandsWithGlyphs) | Demonstrates the coloring of a surface by partitioning the elevation into bands and using arrows to display the normals on the surface.
 [ExponentialCosine](/Python/VisualizationAlgorithms/ExponentialCosine) | Carpet plots. Visualization of an exponential cosine function. Function values are indicated by surface displacement. Colors indicate derivative values.
 [FlyingHeadSlice](/Python/VisualizationAlgorithms/FlyingHeadSlice) | Flying edges used to generate contour lines.
-[Frog](/Python/Visualization/Frog) | View frog organs through a translucent skin. Used to generate the illustrations in the VTK TextBook.
-[FrogBrain](/Python/Visualization/FrogBrain) | The frog’s brain. Model extracted without smoothing (left) and with smoothing (right).
-[FrogDemo](/Python/Visualization/FrogDemo) | View all or some frog tissues and adjust the translucency of the tissues.
-[FrogReconstruction](/Python/Visualization/FrogReconstruction) | Frog organs along with a translucent skin are reconstructed from the original segmented data.
+[FrogBrain](/Python/Visualization/FrogBrain) | The frog's brain. Model extracted without smoothing (left) and with smoothing (right).
+[FroggieSurface](/Python/Visualization/FroggieSurface) | All or some frog tissues are reconstructed from the original segmented data.
+[FroggieView](/Python/Visualization/FroggieView) | View all or some frog tissues and adjust the translucency of the tissues.
 [FrogSlice](/Python/Visualization/FrogSlice) | Photographic slice of frog (upper left), segmented frog (upper right) and composite of photo and segmentation (bottom). The purple color represents the stomach and the kidneys are yellow.
 [GlyphTable](/Python/Visualization/GlyphTable) | Vary the shapes of glyphed points using a glyph table
 [Hanoi](/Python/Visualization/Hanoi) | Towers of Hanoi.

src/Python/Visualization/Frog.md

-### 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](../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](../../../VTKBook/12Chapter12/#Figure%2012-9a), [Figure 12-9b](../../../VTKBook/12Chapter12/#Figure%2012-9b), [Figure 12-9c](../../../VTKBook/12Chapter12/#Figure%2012-9c), and [Figure 12-9d](../../../VTKBook/12Chapter12/#Figure%2012-9d) in [Chapter 12](../../../VTKBook/12Chapter12) of the [VTK Textbook](../../../VTKBook/01Chapter1).

src/Python/Visualization/Frog.py

-#!/usr/bin/env python
-
-from pathlib import Path
-
-# noinspection PyUnresolvedReferences
-import vtkmodules.vtkInteractionStyle
-# noinspection PyUnresolvedReferences
-import vtkmodules.vtkRenderingOpenGL2
-from vtkmodules.vtkCommonColor import vtkNamedColors
-from vtkmodules.vtkCommonCore import vtkLookupTable
-from vtkmodules.vtkCommonMath import vtkMatrix4x4
-from vtkmodules.vtkCommonTransforms import vtkTransform
-from vtkmodules.vtkFiltersCore import vtkPolyDataNormals
-from vtkmodules.vtkFiltersGeneral import vtkTransformPolyDataFilter
-from vtkmodules.vtkIOLegacy import vtkPolyDataReader
-from vtkmodules.vtkInteractionWidgets import vtkOrientationMarkerWidget
-from vtkmodules.vtkRenderingAnnotation import vtkAxesActor
-from vtkmodules.vtkRenderingCore import (
-    vtkActor,
-    vtkPolyDataMapper,
-    vtkRenderWindow,
-    vtkRenderWindowInteractor,
-    vtkRenderer
-)
-
-
-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 = vtkNamedColors()
-
-    # Setup render window, renderer, and interactor.
-    renderer = vtkRenderer()
-    render_window = vtkRenderWindow()
-    render_window.AddRenderer(renderer)
-    render_window_interactor = 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 = vtkAxesActor()
-
-    widget = 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 = vtkPolyDataReader()
-    reader.SetFileName(file_name)
-    reader.Update()
-
-    trans = so.get(transform)
-    if tissue == 'brainbin':
-        trans.Scale(1, -1, 1)
-        trans.RotateZ(180)
-    tf = vtkTransformPolyDataFilter()
-    tf.SetInputConnection(reader.GetOutputPort())
-    tf.SetTransform(trans)
-    tf.SetInputConnection(reader.GetOutputPort())
-
-    normals = vtkPolyDataNormals()
-    normals.SetInputConnection(tf.GetOutputPort())
-    normals.SetFeatureAngle(60.0)
-
-    mapper = vtkPolyDataMapper()
-    mapper.SetInputConnection(normals.GetOutputPort())
-
-    actor = 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 = 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 = 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 = 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 = 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 = 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 = vtkTransform()
-        t.SetMatrix(self.si_mat)
-        return t
-
-    def i_s(self):
-        t = vtkTransform()
-        t.SetMatrix(self.is_mat)
-        return t
-
-    @staticmethod
-    def a_p():
-        t = vtkTransform()
-        return t.Scale(1, -1, 1)
-
-    @staticmethod
-    def p_a():
-        t = vtkTransform()
-        return t.Scale(1, -1, -1)
-
-    def l_r(self):
-        t = vtkTransform()
-        t.SetMatrix(self.lr_mat)
-        t.Update()
-        return t
-
-    def r_l(self):
-        t = vtkTransform()
-        t.SetMatrix(self.lr_mat)
-        return t
-
-    def h_f(self):
-        t = vtkTransform()
-        t.SetMatrix(self.hf_mat)
-        return t
-
-    def hf_si(self):
-        t = vtkTransform()
-        t.Concatenate(self.hf_mat)
-        t.Concatenate(self.si_mat)
-        return t
-
-    def hf_is(self):
-        t = vtkTransform()
-        t.Concatenate(self.hf_mat)
-        t.Concatenate(self.is_mat)
-        return t
-
-    def hf_ap(self):
-        t = vtkTransform()
-        t.Concatenate(self.hf_mat)
-        t.Scale(1, -1, 1)
-        return t
-
-    def hf_pa(self):
-        t = vtkTransform()
-        t.Concatenate(self.hf_mat)
-        t.Scale(1, -1, -1)
-        return t
-
-    def hf_lr(self):
-        t = vtkTransform()
-        t.Concatenate(self.hf_mat)
-        t.Concatenate(self.lr_mat)
-        return t
-
-    def hf_rl(self):
-        t = 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 = 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)

src/Python/Visualization/FrogDemo.md

-### Description
-
-View all or some frog tissues and adjust the translucency of the tissues.
-
-Sliders are provided in the right-hand window to to control the opacity of the individual tissues.
-
-This example extends [Frog](../Frog) by providing user control over opacity.

src/Python/Visualization/FrogDemo.py

-#!/usr/bin/env python
-
-from pathlib import Path
-
-# noinspection PyUnresolvedReferences
-import vtkmodules.vtkInteractionStyle
-# noinspection PyUnresolvedReferences
-import vtkmodules.vtkRenderingOpenGL2
-from vtkmodules.vtkCommonColor import vtkNamedColors
-from vtkmodules.vtkCommonCore import (
-    vtkCommand,
-    vtkLookupTable
-)
-from vtkmodules.vtkCommonMath import vtkMatrix4x4
-from vtkmodules.vtkCommonTransforms import vtkTransform
-from vtkmodules.vtkFiltersCore import vtkPolyDataNormals
-from vtkmodules.vtkFiltersGeneral import vtkTransformPolyDataFilter
-from vtkmodules.vtkIOLegacy import vtkPolyDataReader
-from vtkmodules.vtkInteractionWidgets import (
-    vtkOrientationMarkerWidget,
-    vtkSliderRepresentation2D,
-    vtkSliderWidget
-)
-from vtkmodules.vtkRenderingAnnotation import vtkAxesActor
-from vtkmodules.vtkRenderingCore import (
-    vtkActor,
-    vtkPolyDataMapper,
-    vtkRenderWindow,
-    vtkRenderWindowInteractor,
-    vtkRenderer
-)
-
-
-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 = vtkNamedColors()
-
-    # Setup render window, renderers, and interactor.
-    # ren_1 is for the frog rendering, ren_2 is for the slider rendering.
-    ren_1 = vtkRenderer()
-    ren_2 = vtkRenderer()
-    render_window = vtkRenderWindow()
-    render_window.AddRenderer(ren_1)
-    render_window.AddRenderer(ren_2)
-    ren_1.SetViewport(0.0, 0.0, 0.7, 1.0)
-    ren_2.SetViewport(0.7, 0.0, 1, 1)
-    render_window_interactor = vtkRenderWindowInteractor()
-    render_window_interactor.SetRenderWindow(render_window)
-
-    tm = create_tissue_map()
-    path = Path(data_folder)
-    lut = create_frog_lut(colors)
-    sliders = dict()
-    step_size = 1.0 / 17
-    pos_y = 0.05
-
-    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(lut.GetTableValue(tm[tissue][0])[:3])
-        actor.GetProperty().SetSpecular(0.2)
-        actor.GetProperty().SetSpecularPower(10)
-        ren_1.AddActor(actor)
-        res.append('{:>11s}, label: {:2d}'.format(tissue, tm[tissue][0]))
-
-        slider_properties = SliderProperties()
-        slider_properties.value_initial = tm[tissue][2]
-        slider_properties.title = tissue
-        # Screen coordinates
-        slider_properties.p1 = [0.05, pos_y]
-        slider_properties.p2 = [0.25, pos_y]
-        pos_y += step_size
-        cb = SliderCB(actor.GetProperty())
-
-        slider_widget = make_slider_widget(slider_properties, colors, lut, tm[tissue][0])
-        slider_widget.SetInteractor(render_window_interactor)
-        slider_widget.SetAnimationModeToAnimate()
-        slider_widget.EnabledOn()
-        slider_widget.SetCurrentRenderer(ren_2)
-        slider_widget.AddObserver(vtkCommand.InteractionEvent, cb)
-        sliders[tissue] = slider_widget
-
-    if len(res) > 1:
-        print('\n'.join(res))
-
-    render_window.SetSize(800, 600)
-    render_window.SetWindowName('FrogDemo')
-
-    ren_1.SetBackground(colors.GetColor3d('LightSteelBlue'))
-    ren_2.SetBackground(colors.GetColor3d('MidnightBlue'))
-
-    # Initial view (looking down on the dorsal surface).
-    ren_1.GetActiveCamera().Roll(-90)
-    ren_1.ResetCamera()
-
-    #  Final view
-    if view:
-        if view == 'a':
-            # Figs 12-9a and 12-9b in the VTK Textbook
-            camera = ren_1.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 = ren_1.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 = ren_1.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 = vtkAxesActor()
-
-    widget = 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 = vtkPolyDataReader()
-    reader.SetFileName(file_name)
-    reader.Update()
-
-    trans = so.get(transform)
-    if tissue == 'brainbin':
-        trans.Scale(1, -1, 1)
-        trans.RotateZ(180)
-    tf = vtkTransformPolyDataFilter()
-    tf.SetInputConnection(reader.GetOutputPort())
-    tf.SetTransform(trans)
-    tf.SetInputConnection(reader.GetOutputPort())
-
-    normals = vtkPolyDataNormals()
-    normals.SetInputConnection(tf.GetOutputPort())
-    normals.SetFeatureAngle(60.0)
-
-    mapper = vtkPolyDataMapper()
-    mapper.SetInputConnection(normals.GetOutputPort())
-
-    actor = 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 = 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 = 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 = 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 = 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 = 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 = vtkTransform()
-        t.SetMatrix(self.si_mat)
-        return t
-
-    def i_s(self):
-        t = vtkTransform()
-        t.SetMatrix(self.is_mat)
-        return t
-
-    @staticmethod
-    def a_p():
-        t = vtkTransform()
-        return t.Scale(1, -1, 1)
-
-    @staticmethod
-    def p_a():
-        t = vtkTransform()
-        return t.Scale(1, -1, -1)
-
-    def l_r(self):
-        t = vtkTransform()
-        t.SetMatrix(self.lr_mat)
-        t.Update()
-        return t
-
-    def r_l(self):
-        t = vtkTransform()
-        t.SetMatrix(self.lr_mat)
-        return t
-
-    def h_f(self):
-        t = vtkTransform()
-        t.SetMatrix(self.hf_mat)
-        return t
-
-    def hf_si(self):
-        t = vtkTransform()
-        t.Concatenate(self.hf_mat)
-        t.Concatenate(self.si_mat)
-        return t
-
-    def hf_is(self):
-        t = vtkTransform()
-        t.Concatenate(self.hf_mat)
-        t.Concatenate(self.is_mat)
-        return t
-
-    def hf_ap(self):
-        t = vtkTransform()
-        t.Concatenate(self.hf_mat)
-        t.Scale(1, -1, 1)
-        return t
-
-    def hf_pa(self):
-        t = vtkTransform()
-        t.Concatenate(self.hf_mat)
-        t.Scale(1, -1, -1)
-        return t
-
-    def hf_lr(self):
-        t = vtkTransform()
-        t.Concatenate(self.hf_mat)
-        t.Concatenate(self.lr_mat)
-        return t
-
-    def hf_rl(self):
-        t = 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 = 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
-
-
-class SliderProperties:
-    tube_width = 0.008
-    slider_length = 0.008
-    title_height = 0.01
-    label_height = 0.01
-
-    value_minimum = 0.0
-    value_maximum = 1.0
-    value_initial = 1.0
-
-    p1 = [0.1, 0.1]
-    p2 = [0.3, 0.1]
-
-    title = None
-
-    title_color = 'MistyRose'
-    value_color = 'Cyan'
-    slider_color = 'Coral'
-    selected_color = 'Lime'
-    bar_color = 'Yellow'
-    bar_ends_color = 'Gold'
-
-
-def make_slider_widget(properties, colors, lut, idx):
-    slider = vtkSliderRepresentation2D()
-
-    slider.SetMinimumValue(properties.value_minimum)
-    slider.SetMaximumValue(properties.value_maximum)
-    slider.SetValue(properties.value_initial)
-    slider.SetTitleText(properties.title)
-
-    slider.GetPoint1Coordinate().SetCoordinateSystemToNormalizedDisplay()
-    slider.GetPoint1Coordinate().SetValue(properties.p1[0], properties.p1[1])
-    slider.GetPoint2Coordinate().SetCoordinateSystemToNormalizedDisplay()
-    slider.GetPoint2Coordinate().SetValue(properties.p2[0], properties.p2[1])
-
-    slider.SetTubeWidth(properties.tube_width)
-    slider.SetSliderLength(properties.slider_length)
-    slider.SetTitleHeight(properties.title_height)
-    slider.SetLabelHeight(properties.label_height)
-
-    # Set the color properties
-    # Change the color of the bar.
-    slider.GetTubeProperty().SetColor(colors.GetColor3d(properties.bar_color))
-    # Change the color of the ends of the bar.
-    slider.GetCapProperty().SetColor(colors.GetColor3d(properties.bar_ends_color))
-    # Change the color of the knob that slides.
-    slider.GetSliderProperty().SetColor(colors.GetColor3d(properties.slider_color))
-    # Change the color of the knob when the mouse is held on it.
-    slider.GetSelectedProperty().SetColor(colors.GetColor3d(properties.selected_color))
-    # Change the color of the text displaying the value.
-    slider.GetLabelProperty().SetColor(colors.GetColor3d(properties.value_color))
-    # Change the color of the text indicating what the slider controls
-    if idx in range(0, 16):
-        slider.GetTitleProperty().SetColor(lut.GetTableValue(idx)[:3])
-        slider.GetTitleProperty().ShadowOff()
-    else:
-        slider.GetTitleProperty().SetColor(colors.GetColor3d(properties.title_color))
-
-    slider_widget = vtkSliderWidget()
-    slider_widget.SetRepresentation(slider)
-
-    return slider_widget
-
-
-class SliderCB:
-    def __init__(self, actor_property):
-        self.actorProperty = actor_property
-
-    def __call__(self, caller, ev):
-        slider_widget = caller
-        value = slider_widget.GetRepresentation().GetValue()
-        self.actorProperty.SetOpacity(value)
-
-
-if __name__ == '__main__':
-    import sys
-
-    data_folder, tissues, view = get_program_parameters(sys.argv)
-    main(data_folder, tissues, view)

src/Python/Visualization/FrogReconstruction.md

-### Description
-
-Frog organs along with a translucent skin are reconstructed from the original segmented data.
-
-vtkFlyingEdges3D is used by default to take the 3D structured point set and generate the iso-surface. However if desired, you can specify vtkMarchingCubes instead.
-
-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.
-
-To accommodate the volume readers we have in VTK, we processed the mask files and combined them all into one vtkMetaImageReader *.mhd* file. Integer numbers 1–15 to represent the 15 tissues. A similar process was done for the frog skin.
-
-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
-    By specifying the tissues and other parameters, as outlined in the code, you can generate approximations to the following figures: [Figure 12-9a](../../../VTKBook/12Chapter12/#Figure%2012-9a), [Figure 12-9b](../../../VTKBook/12Chapter12/#Figure%2012-9b), [Figure 12-9c](../../../VTKBook/12Chapter12/#Figure%2012-9c), and [Figure 12-9d](../../../VTKBook/12Chapter12/#Figure%2012-9d) in [Chapter 12](../../../VTKBook/12Chapter12) of the [VTK Textbook](../../../VTKBook/01Chapter1).

src/Python/Visualization/FroggieSurface.md

+### Description
+
+Frog organs along with a translucent skin are reconstructed from the original segmented data.
+
+By default the frog is oriented so that we look down on the dorsal (posterior) surface and the superior surface faces the top of the screen. The frog is rendered with the skin being translucent so that you can see the internal organs.
+
+In the lower left of the image there is a prop assembly with labelled XYZ axes and a cube labelled with anatomical orientations:
+
+- **Sagittal plane**
+  - L - left
+  - R - right
+- **Coronal plane**
+  - A - anterior
+  - P - posterior
+- **Transverse plane**
+  - S - superior  
+  - I - inferior
+
+This prop assembly can be moved and resized.
+
+Individual tissues can be specified by using the "**-t**" option e.g. "**-t skin skeleton**".
+
+We use vtkFlyingEdges3D to take the 3D structured point set and generate the iso-surfaces. However, if desired, you can specify vtkMarchingCubes instead, use the option "**-m**".
+
+The parameters used to generate the example image are loaded from a JSON file containing the data needed to access and generate the actors for each tissue along with other supplementary data such as the data file names. This means that the user need only load this one file in order to generate the data for rendering. This file is called:
+
+``` text
+<DATA>/Frog_mhd.json
+```
+
+Where `<DATA>` is the path to `?vtk-?examples/src/Testing/Data`.
+
+For information about the parameters in the JSON file, please see [Frog_mhd_format](../../Documentation/Frog_mhd_format.md).
+
+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**.
+
+The dataset was prepared at the 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.
+
+To accommodate the volume readers in VTK, the mask files were processed and combined into one vtkMetaImageReader file, called 'frogtissue.mhd'. Integer numbers 1-15 are used to represent the 15 tissues. A similar process was done for the frog skin with the result being stored in a file called 'frog.mhd'.
+
+
+!!! info
+    Mutually exclusive options "***-a, -b, -c, -d**" are provided to let you generate approximations to the following figures: [Figure 12-9a](../../../VTKBook/12Chapter12/#Figure%2012-9a), [Figure 12-9b](../../../VTKBook/12Chapter12/#Figure%2012-9b), [Figure 12-9c](../../../VTKBook/12Chapter12/#Figure%2012-9c), and [Figure 12-9d](../../../VTKBook/12Chapter12/#Figure%2012-9d) in [Chapter 12](../../../VTKBook/12Chapter12) of the [VTK Textbook](../../../VTKBook/01Chapter1).

src/Python/Visualization/FroggieView.md

+### Description
+
+Frog organs along with a translucent skin are reconstructed from the original segmented data.
+
+By default the frog is oriented so that we look down on the dorsal (posterior) surface and the superior surface faces the top of the screen. The frog is rendered with the skin being translucent so that you can see the internal organs.
+
+In the lower left of the image there is a prop assembly with labelled XYZ axes and a cube labelled with anatomical orientations:
+
+- **Sagittal plane**
+  - L - left
+  - R - right
+- **Coronal plane**
+  - A - anterior
+  - P - posterior
+- **Transverse plane**
+  - S - superior  
+  - I - inferior
+
+This prop assembly can be moved and resized.
+
+The opacity of eaxh tissue is controlled by a slider, additionally you can turn all the sliders on or off by pressing the "**n**" key.
+
+If the option "**-n**" is selected, no sliders will displayed.
+
+Individual tissues can be specified by using the "**-t**" option e.g. "**-t skin skeleton**".
+
+The parameters used to generate the example image are loaded from a JSON file containing the data needed to access and generate the actors for each tissue along with other supplementary data such as the data file names. This means that the user need only load this one file in order to generate the data for rendering. This file is called:
+
+``` text
+<DATA>/Frog_vtk.json
+```
+
+Where `<DATA>` is the path to `?vtk-?examples/src/Testing/Data`.
+
+For information about the parameters in the JSON file, please see [Frog_vtk_format](../../Documentation/Frog_vtk_format.md).
+
+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**.
+
+The dataset was prepared at the Lawrence Berkeley National Laboratories. It 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 `*.vtk` tissue files. These were pre-processed using the original data so that loading is much faster.
+
+!!! info
+    Mutually exclusive options "***-a -b -c -d**" are provided to let you generate approximations to the following figures: [Figure 12-9a](../../../VTKBook/12Chapter12/#Figure%2012-9a), [Figure 12-9b](../../../VTKBook/12Chapter12/#Figure%2012-9b), [Figure 12-9c](../../../VTKBook/12Chapter12/#Figure%2012-9c), and [Figure 12-9d](../../../VTKBook/12Chapter12/#Figure%2012-9d) in [Chapter 12](../../../VTKBook/12Chapter12) of the [VTK Textbook](../../../VTKBook/01Chapter1).