`AFQ.viz.fury_backend`#

Module Contents#

Functions#

`_inline_interact`(scene, inline, interact)	Helper function to reuse across viz functions
`visualize_bundles`(sft[, n_points, bundle_dict, ...])	Visualize bundles in 3D using VTK.
`scene_rotate_forward`(scene)
`create_gif`(figure, file_name[, n_frames, zoom, ...])	Convert a Fury Scene object into a gif
`visualize_roi`(roi[, affine_or_mapping, static_img, ...])	Render a region of interest into a VTK viz as a volume
`visualize_volume`(volume[, x, y, z, figure, flip_axes, ...])	Visualize a volume
`_draw_core`(sls, n_points, figure, bundle_name, ...)
`single_bundle_viz`(indiv_profile, sft, bundle, scalar_name)	Visualize a single bundle in 3D with core bundle and associated profile

Attributes#

viz_logger

AFQ.viz.fury_backend.viz_logger[source]#

AFQ.viz.fury_backend._inline_interact(scene, inline, interact)[source]#: Helper function to reuse across viz functions

AFQ.viz.fury_backend.visualize_bundles(sft, n_points=None, bundle_dict=None, bundle=None, colors=None, color_by_direction=False, opacity=1.0, line_width=2.0, flip_axes=[False, False, False], figure=None, background=(1, 1, 1), interact=False, inline=False, **kwargs)[source]#

Visualize bundles in 3D using VTK. Parameters not described below are extras to conform fury and plotly APIs.

Parameters

sftStateful Tractogram, str: A Stateful Tractogram containing streamline information or a path to a trk file In order to visualize individual bundles, the Stateful Tractogram must contain a bundle key in it’s data_per_streamline which is a list of bundle ‘uid’.
n_pointsint or None: n_points to resample streamlines to before plotting. If None, no resampling is done.
bundle_dictdict, optional: Keys are names of bundles and values are dicts that specify them. Default: bundles are either not identified, or identified only as unique integers in the metadata.
bundlestr or int, optional: The name of a bundle to select from among the keys in bundle_dict or an integer for selection from the sft metadata.
colorsdict or list: If this is a dict, keys are bundle names and values are RGB tuples. If this is a list, each item is an RGB tuple. Defaults to a list with Tableau 20 RGB values if bundle_dict is None, or dict from bundles to Tableau 20 RGB values if bundle_dict is not None.
color_by_directionbool: Whether to color by direction instead of by bundle. Default: False
opacityfloat: Float between 0 and 1 defining the opacity of the bundle. Default: 1.0
backgroundtuple, optional: RGB values for the background. Default: (1, 1, 1), which is white background.
figurefury Scene object, optional: If provided, the visualization will be added to this Scene. Default: Initialize a new Scene.
interactbool: Whether to provide an interactive VTK window for interaction. Default: False
inlinebool: Whether to embed the visualization inline in a notebook. Only works in the notebook context. Default: False.

Returns

Fury Scene object

AFQ.viz.fury_backend.scene_rotate_forward(scene)[source]#

AFQ.viz.fury_backend.create_gif(figure, file_name, n_frames=60, zoom=1, z_offset=0.5, size=(600, 600), rotate_forward=True)[source]#

Convert a Fury Scene object into a gif

Parameters

figure: Fury Scene object: Scene to be converted to a gif
file_name: str: File to save gif to.
n_frames: int, optional: Number of frames in gif. Will be evenly distributed throughout the rotation. Default: 60
zoom: int, optional: How much to magnify the figure in the fig. Default: 1
size: tuple, optional: Size of the gif. Default: (600, 600)
rotate_forward: bool, optional: Whether to rotate the figure forward before converting to a gif. Generally necessary for fury scenes. Default: True

AFQ.viz.fury_backend.visualize_roi(roi, affine_or_mapping=None, static_img=None, roi_affine=None, static_affine=None, reg_template=None, name='ROI', figure=None, color=np.array([1, 0, 0]), flip_axes=None, opacity=1.0, inline=False, interact=False)[source]#

Render a region of interest into a VTK viz as a volume

Parameters

roistr or Nifti1Image: The ROI information
affine_or_mappingndarray, Nifti1Image, or str, optional: An affine transformation or mapping to apply to the ROIs before visualization. Default: no transform.
static_img: str or Nifti1Image, optional: Template to resample roi to. Default: None
roi_affine: ndarray, optional: Default: None
static_affine: ndarray, optional: Default: None
reg_template: str or Nifti1Image, optional: Template to use for registration. Default: None
name: str, optional: Name of ROI for the legend. Default: ‘ROI’
colorndarray, optional: RGB color for ROI. Default: np.array([1, 0, 0])
flip_axesNone: This parameter is to conform fury and plotly APIs.
opacityfloat, optional: Opacity of ROI. Default: 1.0
figurefury Scene object, optional: If provided, the visualization will be added to this Scene. Default: Initialize a new Scene.
interactbool: Whether to provide an interactive VTK window for interaction. Default: False
inlinebool: Whether to embed the visualization inline in a notebook. Only works in the notebook context. Default: False.

Returns

Fury Scene object

AFQ.viz.fury_backend.visualize_volume(volume, x=None, y=None, z=None, figure=None, flip_axes=None, opacity=0.6, inline=True, interact=False)[source]#

Visualize a volume

Parameters

volumendarray or str: 3d volume to visualize.
figurefury Scene object, optional: If provided, the visualization will be added to this Scene. Default: Initialize a new Scene.
flip_axesNone: This parameter is to conform fury and plotly APIs.
opacityfloat, optional: Initial opacity of slices. Default: 0.6
interactbool: Whether to provide an interactive VTK window for interaction. Default: False
inlinebool: Whether to embed the visualization inline in a notebook. Only works in the notebook context. Default: False.

Returns

Fury Scene object

AFQ.viz.fury_backend._draw_core(sls, n_points, figure, bundle_name, indiv_profile, labelled_points, dimensions, flip_axes)[source]#

AFQ.viz.fury_backend.single_bundle_viz(indiv_profile, sft, bundle, scalar_name, bundle_dict=None, flip_axes=[False, False, False], labelled_nodes=[0, -1], figure=None, include_profile=False)[source]#

Visualize a single bundle in 3D with core bundle and associated profile

Parameters

indiv_profilendarray: A numpy array containing a tract profile for this bundle for a scalar.
sftStateful Tractogram, str: A Stateful Tractogram containing streamline information. If bundle is an int, the Stateful Tractogram must contain a bundle key in it’s data_per_streamline which is a list of bundle `’uid’. Otherwise, the entire Stateful Tractogram will be used as the bundle for the visualization.
bundlestr or int: The name of the bundle to be used as the label for the plot, and for selection from the sft metadata.
scalar_namestr: The name of the scalar being used.
bundle_dictdict, optional: This parameter is used if bundle is an int. Keys are names of bundles and values are dicts that specify them. Default: Either the entire sft is treated as a bundle, or identified only as unique integers in the metadata.
flip_axesndarray: Which axes to flip, to orient the image as RAS, which is how we visualize. For example, if the input image is LAS, use [True, False, False]. Default: [False, False, False]
labelled_nodeslist or ndarray: Which nodes to label. -1 indicates the last node. Default: [0, -1]
figurePlotly Figure object, optional: If provided, the visualization will be added to this Figure. Default: Initialize a new Figure.
include_profilebool, optional: Not yet implemented in fury. Default: False

Returns

Fury Figure object

AFQ.viz.fury_backend#

Module Contents#

Functions#

Attributes#

`AFQ.viz.fury_backend`#