World Space Viewer

Voxel-based images can be oriented differently from world space. NiiVue lets you display images either in their native image space or reoriented to world space. Because world space views require interpolation, they may introduce artifacts due to the lack of a one-to-one mapping between voxels and pixels. This example demonstrates world space navigation and explores the effects of different orientation settings.

This notebook emulated the world space web page.

import ipywidgets as widgets
from IPython.display import display, Javascript
from ipyniivue import DragMode, NiiVue

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

nv.set_slice_mm(True)
nv.set_radiological_convention(False)
nv.set_slice_type(nv.opts.slice_type.MULTIPLANAR)

nv.load_volumes(
    [
        {
            "path": "../images/FLAIR.nii.gz",
            "colormap": "gray",
            "opacity": 1.0,
            "visible": True,
        }
    ]
)

## Create Interactive Controls

# LR checkbox (Radiological convention)
lr_checkbox = widgets.Checkbox(
    value=False,
    description="LR",
    tooltip="Toggle between radiological and neurological convention",
)

# nose checkbox (Sagittal nose direction)
nose_checkbox = widgets.Checkbox(
    value=False, description="Nose", tooltip="Toggle sagittal nose direction"
)

# world checkbox (World space vs voxel space)
world_checkbox = widgets.Checkbox(
    value=True,
    description="World",
    tooltip="Toggle between world space (mm) and voxel space",
)

# drag mode dropdown
drag_dropdown = widgets.Dropdown(
    options=[
        ("contrast", DragMode.CONTRAST),
        ("measurement", DragMode.MEASUREMENT),
        ("pan/zoom", DragMode.PAN),
        ("none", DragMode.NONE),
    ],
    value=DragMode.CONTRAST,
    description="Drag mode:",
)

## Event Handlers

def on_lr_change(change):
    """Handle radiological convention checkbox changes."""
    nv.set_radiological_convention(change["new"])


def on_nose_change(change):
    """Handle nose direction checkbox changes."""
    nv.opts.sagittal_nose_left = change["new"]


def on_world_change(change):
    """Handle world space checkbox changes."""
    nv.set_slice_mm(change["new"])


def on_drag_mode_change(change):
    """Handle drag mode dropdown changes."""
    nv.opts.drag_mode = change["new"]


lr_checkbox.observe(on_lr_change, names="value")
nose_checkbox.observe(on_nose_change, names="value")
world_checkbox.observe(on_world_change, names="value")
drag_dropdown.observe(on_drag_mode_change, names="value")

## Display voxels and controls

controls = widgets.HBox([lr_checkbox, nose_checkbox, world_checkbox, drag_dropdown])

display(widgets.VBox([controls, nv]))

# ---- JavaScript to disable JupyterLab right-click menu inside this widget ----
display(Javascript("""
setTimeout(() => {
    document.querySelectorAll('canvas').forEach(c => {
        c.addEventListener('contextmenu', event => {
            event.preventDefault();
            event.stopPropagation();
            return false;
        }, true);
    });
}, 1000);
"""))

/home/runner/work/ipyniivue/ipyniivue/src/ipyniivue/widget.py:1327: UserWarning: Ignored unsupported kwargs in Volume: ['visible']
  volume_objects.append(Volume(**item))