Mesh mosaics

A mosaic is a custom collection of perspectives for the same scene. With ipyniivue, you use the set_slice_mosaic_string to define each tile for a lightbox view. Note that the load_meshes() command is asynchronous, so we need to use the on_mesh_loaded() to set the mosaic string after the mesh is available.

This Jupyter notebook mirrors the mesh mosaic web page.

Note Atlas slider will require upgrade to NiiVue 0.66

import ipywidgets as widgets
from ipyniivue import NiiVue, SliceType

nv = NiiVue(
    show_3d_crosshair=True,
    back_color=(1, 1, 1, 1),
)

nv.set_slice_type(SliceType.RENDER)
nv.opts.is_colorbar = True
nv.opts.show_legend = False

mesh_layers = [
    {
        "path": "../images/lh.curv",
        "colormap": "gray",
        "cal_min": 0.49,
        "cal_max": 0.51,
        "opacity": 0.5,
    },
    {
        "path": "../images/boggle.lh.annot",
        "opacity": 0.01,
    },
    {
        "path": "../images/boggle.lh.annot",
        "opacity": 0.01,
    },
]

nv.load_meshes(
    [
        {
            "path": "../images/lh.pial",
            "layers": mesh_layers,
        },
    ]
)

kCurvLayer = 0
kAtlasLayer = 1
kStatLayer = 2

@nv.on_mesh_loaded
def on_mesh_loaded(mesh):
    nv.meshes[0].layers[kStatLayer].cal_min = 2.3
    nv.meshes[0].layers[kStatLayer].cal_max = 5
    nv.meshes[0].layers[kStatLayer].colormap = 'warm'
    nv.meshes[0].layers[kStatLayer].colormap_negative = 'winter'
    nv.meshes[0].layers[kStatLayer].atlas_values = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, -3, 0, 0, 0, 0, 0, 0, 0, -5, 0, 0, 7, 0, 0, 4, 7, 0, 0, 0, 0, 0, 0, 0]    
    nv.set_mesh_shader(nv.meshes[0].id, "Rim")
    nv.meshes[0].layers[kCurvLayer].colorbar_visible = False
    nv.meshes[0].layers[kAtlasLayer].colorbar_visible = False
    nv.opts.slice_mosaic_string = "A R 0 R -0 S R 0 R -0 C R 0 R -0" 

nv.set_clip_plane(-0.1, 270, 0)

## User interface widgets

curv_slider = widgets.IntSlider(
    value=50,
    min=1,
    max=99,
    description="Curvature",
    readout=False
)

def on_curv_change(change):
    """Set curve transparency."""
    nv.set_mesh_layer_property(
        mesh_id=nv.meshes[0].id,
        layer_index=kCurvLayer,
        attribute="opacity",
        value=change["new"] * 0.01,
    )

curv_slider.observe(on_curv_change, names="value")

atlas_slider = widgets.IntSlider(
    value=1,
    min=1,
    max=99,
    description="Atlas",
    readout=False
)

def on_atlas_change(change):
    """Set atlas transparency."""
    nv.set_mesh_layer_property(
        mesh_id=nv.meshes[0].id,
        layer_index=kAtlasLayer,
        attribute="opacity",
        value=change["new"] * 0.01,
    )

atlas_slider.observe(on_atlas_change, names="value")

stat_slider = widgets.IntSlider(
    value=1,
    min=1,
    max=99,
    description="Stats",
    readout=False
)

def on_stat_change(change):
    """Set stat transparency."""
    nv.set_mesh_layer_property(
        mesh_id=nv.meshes[0].id,
        layer_index=kStatLayer,
        attribute="opacity",
        value=change["new"] * 0.01,
    )

stat_slider.observe(on_stat_change, names="value")

border_options = ["Dark border", "Transparent border", "No border", "Opaque border"]
border_dropdown = widgets.Dropdown(
    options=border_options,
    value="No border",
    description="Border",
)

def on_border_change(change):
    """Set mesh border style."""
    value_name = change["new"]

    # Default borderValue for "No border"
    borderValue = 0.0

    if value_name == "Dark border":
        borderValue = -0.01  # MRIcroGL convention: negative = dark border
    elif value_name == "Transparent border":
        borderValue = 0.01   # small positive = transparent border
    elif value_name == "Opaque border":
        borderValue = 1.0    # fully opaque border
    # else "No border" → 0.0

    # Apply to the mesh layer (assuming kAtlasLayer is defined elsewhere)
    nv.set_mesh_layer_property(nv.meshes[0].id, kAtlasLayer, "outline_border", borderValue)
    

border_dropdown.observe(on_border_change, names="value")

widgets.VBox(
    [
        widgets.HBox([curv_slider, stat_slider, border_dropdown]),
        nv,
    ]
)