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Interactive and static 3D visualisation for functional brain mapping

Project description

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. 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(
                content='GM density',
                bounding_box_height=192,
                font_size_multiplier=0.2,
                font_color='#cccccc',
                priority=-1,
            ),
        ),
    },
    load_mask=True,
    hemisphere=['left', 'right', None],
    views={
        'left': ('medial', 'lateral'),
        'right': ('medial', 'lateral'),
        'both': ('dorsal', 'ventral', 'anterior', 'posterior'),
    },
    output_dir='/tmp',
    window_size=(600, 500),
)

Feature roadmap

Among others, the following significant features are planned for future releases:

  • More 3D visual primitives, including contours, reconstructed regional surfaces, and voxel block volumes.
  • Support for grouping semantics in figure parameterisations, allowing users to specify that certain parameters should be applied to multiple elements at once according to shared metadata (e.g., same hemisphere), or that the same layout should be applied groupwise in a single figure (e.g., to visualise multiple parcellations or surface projections).
  • Joining the outputs from multiple calls to the core plotting automapper into a single figure.
  • Floating plot elements that are not anchored to a specific panel, and whose parameters can be defined in relation to a plot page, plot group, or plot panel. This feature could be used to add inset plots, colorbars, and legends to a figure.
  • More interactive pyvista widgets, for instance to allow users to slice volumes or to select a subset of nodes or edges to highlight in a plot.
  • Control over lighting, texture, material, etc. of 3D scenes and objects.
  • Transformations for adding panel and plot elements.
  • Postprocessing of snapshots (with the option to filter by metadata), e.g., background removal, cropping, and resizing.
  • Additional SVG plot elements, including text, drop shadows, and shapes.
  • Additional cameras, for instance close-up views of specific regions of interest.
  • Injection of vector plots generated by other libraries, such as matplotlib, into hyve figures. Injection of raster and vector graphic files as elements in hyve figures.
  • Self-documenting parameterisation of plot definitions.

If there is another feature you would like to see in hyve, please open an issue to let us know! We are also interested in hearing which of the above features would be most useful to you, so that we can prioritise our development efforts accordingly. Finally, if you would like to contribute to the development of hyve, please open an issue or pull request on GitHub. We will add a more detailed guide for contributions in the near future.

Alternative options

While hyve is designed to be modular and extensible, some users might prefer a library with a more stable and intuitive API, or one that uses a backend that is simpler to install. If you are looking for a more user-friendly alternative, you might consider the following more mature libraries:

  • netplotbrain: A Python library that supports many of the same kinds of plots, but is more user-friendly and uses matplotlib as its visualisation backend.
  • surfplot: A lightweight VTK-based package (using the brainspaces library) that provides a user-friendly interface and produces simple and high-quality figures out of the box.
  • pysurfer: A Python library for visualising and manipulating surface-based neuroimaging data that is built on top of VTK (using the mayavi library) and provides a tksurfer-like user experience.
  • brainnetviewer: A MATLAB-based package that provides a GUI for visualising brain networks and surface-based neuroimaging data. A top-quality library that is widely used in the community, but it is built on a proprietary platform and is not easily extensible.

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