AFQ.viz.fury_backend#
Attributes#
Functions#
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Helper function to reuse across viz functions |
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Visualize bundles in 3D using VTK. |
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Convert a Fury Scene object into a gif |
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Render a region of interest into a VTK viz as a volume |
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Visualize a volume |
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Visualize a single bundle in 3D with core bundle and associated profile |
Module Contents#
- AFQ.viz.fury_backend._inline_interact(scene, inline, interact)[source]#
Helper function to reuse across viz functions
- AFQ.viz.fury_backend.visualize_bundles(seg_sft, img=None, n_points=None, bundle=None, colors=None, color_by_direction=False, opacity=1.0, line_width=2.0, flip_axes=None, 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:
- seg_sftSegmentedSFT, str
A SegmentedSFT containing streamline information or a path to a segmented trk file.
- imgNifti1Image, optional
Image to register streamlines to. Default: None
- n_pointsint or None
n_points to resample streamlines to before plotting. If None, no resampling is done.
- 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.create_gif(figure, file_name, n_frames=36, az_ang=-10, size=(600, 600))[source]#
Convert a Fury Scene object into a gif
Make a video from a Fury Show Manager.
- Parameters:
- figureFury Scene object
The Fury Scene object to render.
- file_namestr
The name of the output file.
- n_framesint
The number of frames to render. Default: 36
- az_angfloat
The angle to rotate the camera around the z-axis for each frame, in degrees. Default: -10
- sizetuple
The size of the output gif, in pixels. Default: (600, 600)
- AFQ.viz.fury_backend.visualize_roi(roi, resample_to=None, name='ROI', figure=None, color=None, 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
- resample_toNifti1Image, optional
If not None, the ROI will be resampled to the space of this image. 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, seg_sft, bundle, scalar_name, img=None, flip_axes=None, labelled_nodes=None, 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.
- seg_sftSegmentedSFT, str
A SegmentedSFT containing streamline information or a path to a segmented trk file.
- 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.
- imgNifti1Image, optional
Image to register streamlines to. Default: None
- 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