Colormaps

NiiVue provides many colormaps to convert voxel intensity to a color range. Many of these colormaps are designed to be distinctive for individuals with color vision deficiency. This Python demo that replicates the functionality of the colormaps web page.

import json
import ipywidgets as widgets
from IPython.display import display
from ipyniivue import NiiVue

# Create NiiVue instance
nv = NiiVue(back_color=(0.3, 0.3, 0.3, 1))

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

nv.opts.is_colorbar = True

## Controls

# Invert Checkbox
invert_check = widgets.Checkbox(value=False, description="Invert")


def on_invert_change(change):
    """Set colormap invert."""
    nv.volumes[0].colormap_invert = change["new"]


invert_check.observe(on_invert_change, names="value")

# Green Dragging Selection Checkbox
select_check = widgets.Checkbox(value=False, description="Green Dragging Selection")


def on_select_change(change):
    """Set selection box color."""
    if change["new"]:
        nv.set_selection_box_color((0, 1, 0, 0.7))
    else:
        nv.set_selection_box_color((1, 1, 1, 0.5))


select_check.observe(on_select_change, names="value")

# Green Crosshairs Checkbox
cross_check = widgets.Checkbox(value=False, description="Green Crosshairs")


def on_cross_change(change):
    """Set crosshair color."""
    if change["new"]:
        nv.set_crosshair_color((0, 1, 0, 1))
    else:
        nv.set_crosshair_color((1, 0, 0, 1))


cross_check.observe(on_cross_change, names="value")

# Wide Crosshairs Checkbox
wide_check = widgets.Checkbox(value=False, description="Wide Crosshairs")


def on_wide_change(change):
    """Set crosshair width."""
    if change["new"]:
        nv.set_crosshair_width(3)
    else:
        nv.set_crosshair_width(1)


wide_check.observe(on_wide_change, names="value")

# Gamma Slider
gamma_slider = widgets.IntSlider(
    value=100,
    min=10,
    max=400,
    step=10,
    description="Gamma",
    readout=False
)


def on_gamma_change(change):
    """Set gamma."""
    nv.set_gamma(change["new"] * 0.01)


gamma_slider.observe(on_gamma_change, names="value")

# Save Bitmap Button
save_bmp_button = widgets.Button(description="Save Bitmap")


def on_save_bmp_clicked(b):
    """Save scene."""
    nv.save_scene("ScreenShot.png")

save_bmp_button.on_click(on_save_bmp_clicked)

# colormap dropdown

# Dropdown for Colormaps
colormaps = sorted(nv.colormaps())
colormap_dropdown = widgets.Dropdown(
    options=colormaps,
    description="Colormap:",
    value="gray",
)

def on_colormap_change(change):
    """Handle selection in Colormap Dropdown."""
    selected_cmap = change["new"]
    if nv.volumes:
        nv.set_colormap(nv.volumes[0].id, selected_cmap)

# Organize header controls
header_controls = widgets.HBox(
    [
        invert_check,
        select_check,
        cross_check,
        wide_check,
        gamma_slider,
        save_bmp_button
    ]
)


# Custom Colormap TextArea
cmap_textarea = widgets.Textarea(
    value="""{
  "R": [0, 255, 0],
  "G": [0, 0, 255],
  "B": [0, 0, 0],
  "A": [0, 64, 64],
  "I": [0, 85, 255]
}""",
    description="Custom Colormap",
    layout=widgets.Layout(width="60%", height="100px"),
    style={"description_width": "initial"},
)

# Custom Colormap Button
custom_button = widgets.Button(description="Custom")


def on_custom_clicked(b):
    """Add the custom colormap to nv."""
    cmap = json.loads(cmap_textarea.value)
    key = "Custom"
    nv.add_colormap(key, cmap)
    nv.set_colormap(nv.volumes[0].id, key)



custom_button.on_click(on_custom_clicked)
colormap_dropdown.observe(on_colormap_change, names="value")

## Display everything

# Display header controls
display(header_controls)
# Display image
display(nv)
# Display colormap footer
display(widgets.Box([cmap_textarea, custom_button, colormap_dropdown]))