Viewing segmentations

It is common to segment raw medical images into different tissues. This jupyter script emulates the JavaScript web page.

import json
import ipywidgets as widgets
from ipyniivue import NiiVue, ShowRender, SliceType

nv = NiiVue(
    back_color=(0.3, 0.3, 0.3, 1),
    show_3d_crosshair=True,
)
nv.set_radiological_convention(False)

nv.load_volumes(
    [
        {"path": "../images/mni152.nii.gz"},
        {"path": "../images/mni152_pveseg.nii.gz", "opacity": 0.5},
    ]
)

nv.opts.multiplanar_show_render = ShowRender.ALWAYS
nv.set_slice_type(SliceType.MULTIPLANAR)
nv.graph.auto_size_multiplanar = True

## Add user interface widgets

background_checkbox = widgets.Checkbox(
    value=True,
    description="Background",
)

mask_checkbox = widgets.Checkbox(
    value=False,
    description="Mask",
)

smooth_checkbox = widgets.Checkbox(
    value=True,
    description="Smooth",
)

opacity_slider = widgets.IntSlider(
    value=127,
    min=1,
    max=255,
    description="Opacity",
)

# Define Event Handlers

def on_opacity_change(change):
    """Adjust the opacity of the second volume."""
    nv.set_opacity(1, change["new"] / 255)


def on_background_checkbox_change(change):
    """Show or hide the background volume."""
    nv.volumes[0].opacity = 1.0 if change["new"] else 0.0


def on_mask_checkbox_change(change):
    """Set is_alpha_clip_dark."""
    nv.opts.is_alpha_clip_dark = change["new"]


def on_smooth_checkbox_change(change):
    """Set interpolation."""
    nv.set_interpolation(not change["new"])


opacity_slider.observe(on_opacity_change, names="value")
background_checkbox.observe(on_background_checkbox_change, names="value")
mask_checkbox.observe(on_mask_checkbox_change, names="value")
smooth_checkbox.observe(on_smooth_checkbox_change, names="value")

# set initial values

on_opacity_change({"new": opacity_slider.value})
on_background_checkbox_change({"new": background_checkbox.value})
on_mask_checkbox_change({"new": mask_checkbox.value})
on_smooth_checkbox_change({"new": smooth_checkbox.value})

## Custom colormap

colormap_textarea = widgets.Textarea(
    value="""{
    "R": [0,   0, 120, 175],
    "G": [0,  90,  60, 185],
    "B": [0, 120,  60, 175],
    "labels": ["air", "CSF", "gray", "white"]
}""",
    description="Custom Colormap (JSON)",
    style={"description_width": "initial"},
    layout=widgets.Layout(width="100%", height="150px"),
)

apply_button = widgets.Button(
    description="Apply Colormap",
)

def on_apply_button_click(b):
    """Apply custom colormap json."""
    json_str = colormap_textarea.value
    try:
        cmap = json.loads(json_str)
        nv.volumes[1].set_colormap_label(cmap)
    except json.JSONDecodeError as e:
        print("Invalid JSON format:", e)


apply_button.on_click(on_apply_button_click)

on_apply_button_click(None)

## Show hover information

location_label = widgets.HTML(" ")


def handle_location_change(data):
    """Update the location label when the crosshair moves."""
    location_label.value = "  " + data["string"]


nv.on_location_change(handle_location_change)

## Display all

controls = widgets.HBox(
    [
        background_checkbox,
        mask_checkbox,
        smooth_checkbox,
        opacity_slider,
    ]
)

script_controls = widgets.VBox(
    [
        colormap_textarea,
        apply_button,
    ]
)

display_widgets = widgets.VBox(
    [
        controls,
        nv,
        location_label,
        script_controls,
    ]
)

display(display_widgets)