NIFTIVisualizer Documentation

The NIFTIVisualizer class in the PYCAD library provides a user-friendly approach to visualize one or multiple NIfTI files using the vedo and vtk libraries. With this class, users can conveniently visualize volumetric data in NIfTI format without dealing with the intricacies of plotting and colormap configurations.

Introduction

NIFTIVisualizer is designed for those who require a simple method to visualize NIfTI files, especially in the context of medical imaging. This documentation delves into the class structure, its methods, and standard use cases.

Class Definition

class NIFTIVisualizer:

Initialization

def __init__(self, path_to_files, bg=(1,1,1), mesh_colors=None):

• path_to_files: List of paths to NIfTI files or a single path as a string.
• bg (optional): Background color defined as a tuple of RGB values. Default is white (1,1,1).
• mesh_colors (optional): List of colormap names for each volume. If not given, random colormaps are generated.

Public Methods

def visualize(self):

• Loads and visualizes the NIfTI volumes using the specified or generated colormaps.

Example Usage

Single NIfTI File

from pycad.visualization import NIFTIVisualizer

visualizer = NIFTIVisualizer("./data/sample1.nii")
visualizer.visualize()

Multiple NIfTI Files with Custom Colors

paths = ["./data/sample1.nii", "./data/sample2.nii.gz"]
colors = ['viridis', 'inferno']
visualizer = NIFTIVisualizer(paths, mesh_colors=colors)
visualizer.visualize()

Notes

• The class only accepts paths ending with .nii or .nii.gz. Any other file type will raise a ValueError.
• The number of provided colormaps should match the number of NIfTI file paths. If not, a ValueError will be thrown.
• A wide range of colormaps is available, including 'viridis', 'inferno', 'magma', and many more. If not specified, random colormaps are chosen for each NIfTI file.