AFQ.viz.plotly_backend#
Module Contents#
Functions#
|
Helper function to reuse across viz functions |
|
|
|
|
|
|
|
|
|
|
|
Visualize bundles in 3D |
|
Convert a Plotly Figure object into a gif |
|
|
|
Render a region of interest into a volume |
|
|
|
|
|
Visualize a volume |
|
|
|
Visualize a single bundle in 3D with core bundle and associated profile |
Attributes#
- AFQ.viz.plotly_backend._inline_interact(figure, show, show_inline)[source]#
Helper function to reuse across viz functions
- AFQ.viz.plotly_backend._draw_streamlines(figure, sls, dimensions, color, name, cbv=None, cbs=None, sbv_lims=[None, None], flip_axes=[False, False, False], opacity=1.0)[source]#
- AFQ.viz.plotly_backend.visualize_bundles(sft, n_points=None, bundle=None, colors=None, shade_by_volume=None, color_by_streamline=None, n_sls_viz=3600, 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, **kwargs)[source]#
Visualize bundles in 3D
- 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.
- bundlestr, optional
The name of a bundle to select 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 dict from bundles to Tableau 20 RGB values.
- 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
- color_by_streamlinendarray or dict, optional
N by 3 array, where N is the number of streamlines in sft; for each streamline you specify 3 values between 0 and 1 for rgb. If sft has multiple bundles, then use a dict for color_by_streamline, where keys are bundle names and values are n by 3 arrays. Overrides colors for bundles in the keys of the dict if passing a dict, or for all streamlines if using ndarray. Default: None
- n_sls_vizint
Number of streamlines to randomly select if plotting all bundles. Selections will be proportional to the original number of streamlines per bundle. Default: 3600
- 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]
- include_profilesTuple of Pandas Dataframe and string
The first element of the uple is a Pandas Dataframe containing profiles in the standard pyAFQ output format for the bundle(s) being displayed. It will be used to generate a graph of the tract profiles for each bundle, with colors corresponding to the colors on the bundles. The string is the scalar to use from the profile. If these are None, no tract profiles will be graphed. Defualt: (None, 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]
- 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.
- figurePlotly Figure object, optional
If provided, the visualization will be added to this Figure. Default: Initialize a new Figure.
- interactbool
Whether to open the visualization in an interactive window. Default: False
- inlinebool
Whether to embed the interactivevisualization inline in a notebook. Only works in the notebook context. Default: False.
- Returns
- Plotly Figure object
- AFQ.viz.plotly_backend.create_gif(figure, file_name, n_frames=30, zoom=2.5, z_offset=0.5, size=(600, 600))[source]#
Convert a Plotly Figure object into a gif
- Parameters
- figure: Plotly Figure object
Figure 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: float, optional
How much to magnify the figure in the fig. Default: 2.5
- size: tuple, optional
Size of the gif. Default: (600, 600)
- AFQ.viz.plotly_backend.visualize_roi(roi, affine_or_mapping=None, static_img=None, roi_affine=None, static_affine=None, reg_template=None, name='ROI', figure=None, flip_axes=[False, False, False], color=np.array([0.9999, 0, 0]), opacity=1.0, interact=False, inline=False)[source]#
Render a region of interest into 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([0.9999, 0, 0])
- opacityfloat, optional
Opacity of ROI. Default: 1.0
- 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]
- figurePlotly Figure object, optional
If provided, the visualization will be added to this Figure. Default: Initialize a new Figure.
- interactbool
Whether to open the visualization in an interactive window. Default: False
- inlinebool
Whether to embed the interactive visualization inline in a notebook. Only works in the notebook context. Default: False.
- Returns
- Plotly Figure object
- class AFQ.viz.plotly_backend.Axes[source]#
Bases:
enum.IntEnumEnum where members are also (and must be) ints
- AFQ.viz.plotly_backend._draw_slice(figure, axis, volume, opacity=0.3, pos=0.5, colorscale='greys', invert_colorscale=False)[source]#
- AFQ.viz.plotly_backend.visualize_volume(volume, figure=None, x_pos=0.5, y_pos=0.5, z_pos=0.5, interact=False, inline=False, opacity=0.3, colorscale='gray', invert_colorscale=False, flip_axes=[False, False, False])[source]#
Visualize a volume
- Parameters
- volumendarray or str
3d volume to visualize.
- figurePlotly Figure object, optional
If provided, the visualization will be added to this Figure. Default: Initialize a new Figure.
- x_posfloat or None, optional
Where to show Coronal Slice. If None, slice is not shown. Should be a decimal between 0 and 1. Indicatesthe fractional position along the perpendicular axis to the slice. Default: 0.5
- y_posfloat or None, optional
Where to show Sagittal Slice. If None, slice is not shown. Should be a decimal between 0 and 1. Indicatesthe fractional position along the perpendicular axis to the slice. Default: 0.5
- z_posfloat or None, optional
Where to show Axial Slice. If None, slice is not shown. Should be a decimal between 0 and 1. Indicatesthe fractional position along the perpendicular axis to the slice. Default: 0.5
- opacityfloat, optional
Opacity of slices. Default: 1.0
- colorscalestring, optional
Plotly colorscale to use to color slices. Default: “greys”
- invert_colorscalebool, optional
Whether to invert colorscale. Default: False
- 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]
- interactbool
Whether to open the visualization in an interactive window. Default: False
- inlinebool
Whether to embed the interactive visualization inline in a notebook. Only works in the notebook context. Default: False.
- Returns
- Plotly Figure object
- AFQ.viz.plotly_backend._draw_core(sls, n_points, figure, bundle_name, indiv_profile, labelled_points, dimensions, flip_axes)[source]#
- AFQ.viz.plotly_backend.single_bundle_viz(indiv_profile, sft, bundle, scalar_name, 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.
- 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
If true, also plot the tract profile. Default: False
- Returns
- Plotly Figure object