Using Colormaps

Colormaps play a crucial role in data visualization by mapping image values to display colors. NiiVue offers a range of built-in colormaps and supports user-defined custom maps. Many of the included schemes are designed to be perceptually uniform and robust to common variations in human color vision. The following are examples of popular colormaps viridis, batlow, cubehelix, bone and hot.

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Setting an Initial Colormap

When loading volumes, you can specify the initial colormap for each volume directly in the configuration object.

// Assuming 'nv' is your initialized Niivue instance (e.g., const nv = new Niivue();)
// Ensure nv is attached to a canvas element.

const volumeList = [
  {
    url: "/images/mni152.nii.gz", // Replace with your image path
    colormap: "gray", // Set the initial colormap here ('gray' is the default)
    opacity: 1,
    visible: true,
  },
  // You can add more volumes with different initial colormaps
];

await nv.loadVolumes(volumeList);

Listing Available Colormaps

Niivue comes with several predefined colormaps. You can retrieve a list of their names using the colormaps() method.

// Assuming 'nv' is your Niivue instance

const availableColormaps = nv.colormaps();
console.log(availableColormaps);
// Example Output: ['gray', 'warm', 'cool', 'plasma', 'viridis', 'inferno', ...]

// You can use this list to populate UI elements like dropdowns or buttons.

Changing the Colormap

After a volume is loaded, you can dynamically change its colormap using the setColormap method. You need the ID of the volume you want to modify. Often, for the first loaded volume, this is nv.volumes[0].id. NiiVue sets the ID to a unique value when it is loaded so you don't have to manage this.

// Assuming 'nv' is your Niivue instance and at least one volume is loaded

const firstVolumeId = nv.volumes[0].id;

// Change the colormap of the first volume to 'viridis'
nv.setColormap(firstVolumeId, 'viridis');

// Change it to another map, e.g., 'plasma'
// nv.setColormap(firstVolumeId, 'plasma');

Inverting a Colormap

You can invert the current colormap applied to a volume. This reverses the mapping, so low intensities map to colors previously used for high intensities, and vice-versa.

// Assuming 'nv' is your Niivue instance and at least one volume is loaded

// Get the first volume
const volume = nv.volumes[0];

// Set the inversion status (true to invert, false for normal)
volume.colormapInvert = true;

// Important: You must call updateGLVolume() to apply the change visually
nv.updateGLVolume();

// To revert back:
// volume.colormapInvert = false;
// nv.updateGLVolume();

Adjusting Gamma

While not strictly a colormap change, the gamma setting adjusts the intensity mapping curve, affecting the brightness and contrast, which interacts significantly with how the colormap appears. A gamma value greater than 1 makes the image brighter, while less than 1 makes it darker.

// Assuming 'nv' is your Niivue instance

nv.setGamma(1.5); // Makes the image brighter

// Set gamma to make the image darker
// nv.setGamma(0.7);

// Reset to default
// nv.setGamma(1.0);

Note: Unlike colormapInvert, changes via setGamma update the view automatically

Defining and Using Custom Colormaps

You can create your own colormaps by defining an object with specific properties: R, G, B (arrays of red, green, blue values from 0-255), A (alpha/opacity values from 0-255), and I (intensity values defining the control points for the mapping).

// Assuming 'nv' is your Niivue instance and at least one volume is loaded

// 1. Define the custom colormap structure
const myCustomCmap = {
 R: [0, 255, 0],   // Red channel values at control points
 G: [0, 0, 255],   // Green channel values at control points
 B: [0, 0, 0],     // Blue channel values at control points
 A: [0, 128, 255], // Alpha values
 I: [0, 127, 255], // Intensity values corresponding to R,G,B,A points
};

// 2. Add the colormap to Niivue with a unique name
nv.addColormap('MyCustomMap', myCustomCmap);

// 3. Apply the custom colormap like any other colormap
const firstVolumeId = nv.volumes[0].id;
nv.setColormap(firstVolumeId, 'MyCustomMap');

// You can also apply it directly after adding:
// nv.volumes[0].colormap = 'MyCustomMap';
// nv.updateGLVolume(); // Requires manual update if set this way

Displaying the Colorbar

It's often helpful to display a colorbar alongside the image to show the current colormap and its corresponding data range. You can enable this in the Niivue options.

// Option 1: Set when creating the Niivue instance
const nv = new Niivue({ isColorbar: true });

// Option 2: Set after creating the instance
const nv = new Niivue();
nv.opts.isColorbar = true; // or false
nv.drawScene() // to see the changes.