AFQ.viz.fury_backend#

Module Contents#

Functions#

_inline_interact(scene, inline, interact)

Helper function to reuse across viz functions

visualize_bundles(sft, n_points=None, bundle_dict=None, bundle=None, colors=None, shade_by_volume=None, color_by_streamline=None, sbv_lims=[None, None], include_profiles=(None, None), flip_axes=[False, False, False], opacity=1.0, figure=None, background=(1, 1, 1), interact=False, inline=False)

Visualize bundles in 3D using VTK.

scene_rotate_forward(scene)

create_gif(figure, file_name, n_frames=60, zoom=1, z_offset=0.5, size=(600, 600), rotate_forward=True)

Convert a Fury Scene object into a gif

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)

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

visualize_volume(volume, x=None, y=None, z=None, figure=None, flip_axes=None, opacity=0.6, inline=True, interact=False)

Visualize a volume

_draw_core(sls, n_points, figure, bundle_name, indiv_profile, labelled_points, dimensions, flip_axes)

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)

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, shade_by_volume=None, color_by_streamline=None, sbv_lims=[None, None], include_profiles=(None, None), flip_axes=[False, False, False], opacity=1.0, figure=None, background=(1, 1, 1), interact=False, inline=False)[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.

shade_by_volumendarray or str, optional

3d volume use to shade the bundles. If None, no shading is performed. Only works when using the plotly backend. Default: None

sbv_limsndarray

Of the form (lower bound, upper bound). Shading based on shade_by_volume will only differentiate values within these bounds. If lower bound is None, will default to 0. If upper bound is None, will default to the maximum value in shade_by_volume. Default: [None, None]

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