hyve

Interactive and static 3D visualisation for functional brain mapping

hyve (hypercoil visualisation engine) is a Python package for interactive and static 3D visualisation of functional brain mapping data. It was originally designed to be used in conjunction with the hypercoil project for differentiable programming in the context of functional brain mapping, but can be used independently.

This system is currently under development, and the API is accordingly subject to sweeping changes without notice. In particular, before using this system, be aware of the major limitations that exist, detailed under the v1.0.0 header here (and soon to be added as issues). Documentation is also extremely sparse, but will be added in the near future. To get a sense of how the package might look and feel when it is more mature, you can take a look at the test cases in the tests directory.

hyve allows for the visualisation of 3D data in a variety of formats, including volumetric data, surface meshes, and 3-dimensional network renderings. It is built using a rudimentary quasi-functional programming paradigm, allowing users to compose new plotting utilities for their data by chaining together functional primitives. The system is designed to be modular and extensible, and can be easily extended to support new data types and visualisation techniques. It is built on top of the pyvista library and therefore uses VTK as its rendering backend. The system is also capable of combining visualisations as panels of a SVG figure.

Installation

hyve can be installed from PyPI using pip:

pip install hyve==0.0.2

The below examples also require installation of the hyve-examples package, which can be installed from PyPI using pip:

pip install hyve-examples

Contributing

Suggestions for improvement and contributions are welcome. Please open an issue or submit a pull request if you have any ideas for how to improve the package. hyve is not feature-complete and is still under active development, so there are many opportunities for improvement. There are also likely to be many bugs, so please open an issue if you encounter any problems.

Basic usage

The following example demonstrates how to use hyve to visualise a 3D surface mesh and create a HTML-based interactive visualisation (built on the trame library) that can be viewed in a web browser:

from hyve_examples import get_null400_cifti
from hyve.flows import plotdef
from hyve.transforms import (
    surf_from_archive,
    surf_scalars_from_cifti,
    parcellate_colormap,
    vertex_to_face,
    plot_to_html,
)

plot_f = plotdef(
    surf_from_archive(),
    surf_scalars_from_cifti('parcellation'),
    parcellate_colormap('parcellation', 'network'),
    vertex_to_face('parcellation'),
    plot_to_html(
        fname_spec=(
            'scalars-{surfscalars}_hemisphere-{hemisphere}_cmap-network'
        ),
    ),
)
plot_f(
    template='fsLR',
    load_mask=True,
    parcellation_cifti=get_null400_cifti(),
    surf_projection=['veryinflated'],
    hemisphere=['left', 'right'],
    window_size=(800, 800),
    output_dir='/tmp',
)

The HTML files generated by this example will be written to /tmp/scalars-parcellation_hemisphere-left_cmap-network_scene.html and /tmp/scalars-parcellation_hemisphere-right_cmap-network_scene.html. These files can be opened in a web browser to view the interactive visualisation.

Note that, unlike many other plotting libraries, hyve does not provide a single function that can be used to generate a plot. Instead, it provides a set of functional primitives that can be chained together to create a custom plotting pipeline using the plotdef function. This allows users to create new plotting utilities by composing primirives. For example, the plot_f function used in the example above is a composition of the surf_from_archive, surf_scalars_from_cifti, parcellate_colormap, vertex_to_face, and plot_to_html functions with a unified base plotter. The plot_f function can be used to generate a plot by passing it a set of keyword arguments that specify the data to be plotted and the visualisation parameters. The plot_f function can also be used to generate a plot from a set of keyword arguments that specify the data to be plotted and the visualisation parameters.

This approach allows users to create new plotting utilities without having to write much new code, but it can be difficult to understand at first.

It's also possible to use hyve to create static visualisations. For example, the following example creates glass brain visualisations of the pain network from Xu et al. (2020) (10.1016/j.neubiorev.2020.01.004).

from hyve_examples import get_pain_thresh_nifti
from hyve.flows import plotdef
from hyve.transforms import (
    surf_from_archive,
    points_scalars_from_nifti,
    plot_to_image,
    save_snapshots,
)


nii = get_pain_thresh_nifti()
plot_f = plotdef(
    surf_from_archive(),
    points_scalars_from_nifti('pain'),
    plot_to_image(),
    save_snapshots(
        fname_spec=(
            'scalars-{pointsscalars}_view-{view}'
        ),
    ),
)
plot_f(
    template='fsaverage',
    surf_projection=('pial',),
    surf_alpha=0.3,
    pain_nifti=nii,
    points_scalars_cmap='magma',
    views=('dorsal', 'left', 'anterior'),
    output_dir='/tmp',
)

And the below code demonstrates how to use hyve to create a static PNG image of a BrainNetViewer-like scene of a 3D brain network embedded in a surface mesh:

import numpy as np
import pandas as pd

from hyve_examples import (
    get_schaefer400_synthetic_conmat,
    get_schaefer400_cifti,
)
from hyve.flows import plotdef
from hyve.flows import add_network_data
from hyve.transforms import (
    surf_from_archive,
    surf_scalars_from_cifti,
    parcellate_colormap,
    add_node_variable,
    add_edge_variable,
    plot_to_image,
    save_snapshots,
    node_coor_from_parcels,
    build_network,
    add_network_overlay,
)

# Get a parcellation and the corresponding connectivity matrix
parcellation = get_schaefer400_cifti()
cov = pd.read_csv(
    get_schaefer400_synthetic_conmat(), sep='\t', header=None
).values

# Select some nodes and edges to be highlighted
vis_nodes_edge_selection = np.zeros(400, dtype=bool)
vis_nodes_edge_selection[0:5] = True
vis_nodes_edge_selection[200:205] = True

# Define a plotting function
plot_f = plotdef(
    surf_from_archive(),
    surf_scalars_from_cifti('parcellation', plot=False),
    add_network_data(
        add_node_variable('vis'),
        add_edge_variable(
            'vis_conn',
            threshold=10,
            topk_threshold_nodewise=True,
            absolute=True,
            incident_node_selection=vis_nodes_edge_selection,
            emit_degree=True,
        ),
        add_edge_variable(
            'vis_internal_conn',
            absolute=True,
            connected_node_selection=vis_nodes_edge_selection,
        ),
    ),
    node_coor_from_parcels('parcellation'),
    build_network('vis'),
    parcellate_colormap('parcellation', 'network', target='node'),
    plot_to_image(),
    save_snapshots(
        fname_spec=(
            'network-schaefer400_view-{view}'
        ),
    ),
)

# Generate a plot
plot_f(
    template='fsLR',
    surf_projection='inflated',
    surf_alpha=0.2,
    parcellation_cifti=parcellation,
    node_radius='vis_conn_degree',
    node_color='index',
    edge_color='vis_conn_sgn',
    edge_radius='vis_conn_val',
    vis_nodal=vis_nodes_edge_selection.astype(int),
    vis_conn_adjacency=cov,
    vis_internal_conn_adjacency=cov,
    views=('dorsal', 'left', 'posterior'),
    output_dir='/tmp',
)

Here is another, more involved example, this time demonstrating how to use hyve to create a static SVG figure:

import templateflow.api as tflow
from hyve.elements import TextBuilder
from hyve_examples import get_null400_cifti
from hyve.flows import plotdef
from hyve.transforms import (
    surf_from_archive,
    surf_scalars_from_nifti,
    add_surface_overlay,
    save_grid,
    plot_to_image,
)

# Annotate the panels of the figure so that the figure builder knows
# where to place different elements. Note that we'll need a layout with
# 9 panels, so we'll be creating a 3x3 grid of images when we parameterise
# the plot definition below.
annotations = {
    0: dict(
        hemisphere='left',
        view='lateral',
    ),
    1: dict(view='anterior'),
    2: dict(
        hemisphere='right',
        view='lateral',
    ),
    3: dict(view='dorsal'),
    4: dict(elements=['title', 'scalar_bar']),
    5: dict(view='ventral'),
    6: dict(
        hemisphere='left',
        view='medial',
    ),
    7: dict(view='posterior'),
    8: dict(
        hemisphere='right',
        view='medial',
    ),
}

# Define a plotting function
plot_f = plotdef(
    surf_from_archive(),
    add_surface_overlay(
        'GM Density',
        surf_scalars_from_nifti(
            'GM Density', template='fsaverage', plot=True
        ),
    ),
    plot_to_image(),
    save_grid(
        n_cols=3, n_rows=3, padding=10,
        canvas_size=(1800, 1500),
        canvas_color=(0, 0, 0),
        fname_spec='scalars-gmdensity_view-all_page-{page}',
        scalar_bar_action='collect',
        annotations=annotations,
    ),
)

# Generate a plot
plot_f(
    template='fsaverage',
    gm_density_nifti=tflow.get(
        template='MNI152NLin2009cAsym',
        suffix='probseg',
        label='GM',
        resolution=2
    ),
    gm_density_clim=(0.2, 0.9),
    gm_density_below_color=None,
    gm_density_scalar_bar_style={
        'name': None,
        'orientation': 'h',
    },
    surf_projection=('pial',),
    # This won't be the recommended way to add a title in the future.
    elements={
        'title': (
            TextBuilder(