vis module¶

Classes and functions to deal with the visualisation of the AmpObjects. These include wrappers for vtk and Qt Copyright: Joshua Steer 2020, Joshua.Steer@soton.ac.uk

class ampActor(CMap=None, bands=128)

Bases: sphinx.ext.autodoc.importer._MockObject

A wrapper around the classic vtkActor that makes it easier to transfer data from the ampObject

addSlices(slices)

Adds slices into the AmpActor which can then be rendered

Parameters:	slices (array_like) – The values in the z-axis of which to make the slices

setCMap(CMap, bands=128)

Sets the colormap used to display scalar values

Parameters:	CMap (array_like) – The base colors used to define the color map bands (int, default 128) – The number of contour bands to divide up the color map

setColor(color=[1.0, 1.0, 1.0])

Sets the color of the ampActor

Parameters:	color (array_like, default [1.0, 1.0, 1.0]) – The RGB values as floats of the ampActor colour between [0, 1]

setFaces(faces, deep=0)

Sets the faces of the ampActor

Parameters:	faces (ndarray) – The numpy array specifying the faces, or connectivity index based upon the vertex array deep (int, default 0) – If 1, the numpy array will be deep-copied to the ampActor

setNorm(norm=None, deep=0)

Sets or calculates the vertex normals

Parameters:	norm (ndarray, default None) – The numpy array specifying the face normals. If None, the inbuilt vtk method will be used to calculate the normals deep (int, default 0) – If 1, the numpy array will be deep-copied to the ampActor

setOpacity(opacity=1.0)

Sets the opacity of the ampActor

Parameters:	opacity (float, default 1.0) – Opacity value between [0 1]

setScalarRange(sRange)

Sets the scalar range on the ampActor

Parameters:	sRange (array_like) – Specifies the lower and upper bound of the scalar range to display

setShading(shading=True)

Sets whether shading is used on the ampActor

Parameters:	shading (boolean, default True) – If True, shading is used in the display of the ampActor

setValues(values, deep=0)

Set the values of the ampActor

Parameters:	values (ndarray) – Scalar data attached to each vertex deep (int, default 0) – If 1, the numpy array will be deep-copied to the ampActor

setVert(vert, deep=0)

Set the vertices of the ampActor

Parameters:	vert (ndarray) – The numpy array specifying the vertices deep (int, default 0) – If 1, the numpy array will be deep-copied to the ampActor

class qtVtkWindow

Bases: sphinx.ext.autodoc.importer._MockObject

This provides the interface between Qt and the vtkRenWin

class visMixin

Bases: object

Set of visualisation methods that are contained within the AmpActor

addActor(CMap=None, bands=128, sRange=[0, 8]): Creates an ampActor based upon the ampObject

createCMap(cmap=None, n=50)

Function to generate a linear colormap for the AmpObj based upon base colours

cmap: array_like: The rgb float values of the base colors used to generate the colormap
n: int, default 50: The number of bands that form the colormap

display()

Function to display the ampActor within in an interactable vtkRenWin window

Returns:	win – The generated vtkRenWin
Return type:	vtkRenWin

genIm(size=[512, 512], views=[[0, -1, 0]], background=[1.0, 1.0, 1.0], projection=True, shading=True, mag=10, out='im', fh='test.tiff', zoom=1.0, az=0, el=0, crop=False, cam=None)

Creates a temporary off screen vtkRenWin which is then either returned as a numpy array or saved as a .png file

Parameters:	out (str: default 'im') – If ‘im’ the the image will be returned as an array, if ‘fh’ the image will be saved as .png image size (array_like, default [512, 512]) – The width and height of the vtkRenWin to create views (array_like, default [[0, -1, 0],]) – The camera view set for each viewport, the length of this also sets the number of viewports background (array_like, default [1, 1, 1]) – The RGB values as floats of the background colour between [0, 1] projection (boolean, default True) – If true, then perspective will be used as the projection for the camera shading (boolean, default True) – If true, shading will be used on the ampActor mag (int, default 10) – The magnification for saving the image fh (str) – The file handle used if out =’fh’
Returns:	im – The array representation of the image if out = ‘im’
Return type:	ndarray

class vtkRenWin

Bases: sphinx.ext.autodoc.importer._MockObject

This class inherits from the vtkRenderWindow and wraps extra functions on top

This window can be either be used on it’s own, or embedded within a Qt Window

Pick_point(loc): This receives coordinates in the GUI where user has picked, converts it to mesh coordinates using vtkCellPicker, and places a sphere at picked location as a visual aid. Also places a label at the point in the render window. TO-DO: Add functionality so user can type the label in, rather than have it read ‘Mid Patella’ every time

addAxes(actors, viewport=0, color=[1.0, 1.0, 1.0], font=None)

Add 3D axes to the vtk window

Parameters:	actors (list) – List of ampActors, this is used to determine the necessary limits of the axes viewport (int, default 0) – The index of the viewport add the axes into color (array_like) – The RGB values as floats of the axes line and text colour between [0, 1]

addTriad(actors, viewport=0, color=[1.0, 1.0, 1.0], font=None)

Add 3D axes to the vtk window

Parameters:	actors (list) – List of ampActors, this is used to determine the necessary limits of the axes viewport (int, default 0) – The index of the viewport add the axes into color (array_like) – The RGB values as floats of the axes line and text colour between [0, 1]

delMarker(): removes the sphere marker and label from the renderer

getImage()

Return an array representation of the image

Returns:	im – The array representation of the image
Return type:	ndarray

getScreenshot(fname, mag=10)

Generate a screenshot of the window and save to a png file

Parameters:	fname (str) – The file handle to save the image to mag (int, default 10) – The magnificaiton of the image, this will scale the resolution of the saved image by this face

mark(x, y, z): mark the picked point with a sphere

renderActors(actors, viewport=0, zoom=1.0)

Given a list of ampActors, this function removes those which are not in the new list, and adds in the new ones

Parameters:	actors (list of ampActors) – A list of actors to be displayed in the render window viewport (int, default 0) – The viewport index to render the actor within zoom (float, default 1.0) – The zoom magnitude of the camera

setBackground(color=[0.1, 0.2, 0.4])

Set the background colour of the renderer

Parameters:	color (array_like) – The RGB values as floats of the background colour between [0, 1]

setProjection(perspective=False, viewport=0)

Set the projection of the camera to either parallel or perspective

Parameters:	perspective (boolean, default False) – If true, then perspective will be used as the projection for the camera viewport (int, default 0) – The index of the viewport to set the projection of the camera in

setScalarBar(actor, viewport=0, title='')

Set the scalar bar within the window based upon a look-up table defined within an actor

Parameters:	actor (ampActor) – The actor from which the lut is read from, the actor must have the attribute actor.lut viewport (int, default 0) – The viewport index to render the scalar bar within title (str) – The accompanying title for the scalar bar
Returns:	A vtkScalarBarActor attribute to the vtkRenWin
Return type:	scalar_bar

setView(view=[0, -1, 0], viewport=0)

Function to set the camera view within the specified viewport

Parameters:	view (array_like, default [0, -1, 0]) – The view of the vtk camera viewport (int, default 0) – The index of the viewport to set the camera view

setnumViewports(n)

Function to set multiple viewports within the vtkWindow

Parameters:	n (int) – number of viewports required