Introduction
The NiftiToPngConverter class is designed to convert medical images from the NIFTI format to PNG images. This class is a part of the pycad library and can be particularly useful in preprocessing steps for machine learning models that use medical images.
Important: Before performing the conversion, please check the values of max_v and min_v to properly window the Hounsfield Units. For more information, consult this video.
Installation
To use this class, make sure to import it as follows:
from pycad.converters import NiftiToPngConverterUsage
Initialize the NiftiToPngConverter class with optional parameters for the Hounsfield window (max_v and min_v).
converter = NiftiToPngConverter(max_v=200, min_v=-200)Methods
__init__(max_v=200, min_v=-200)
Initializes the converter object.
max_v: The maximum Hounsfield Unit for windowing. Default is 200.min_v: The minimum Hounsfield Unit for windowing. Default is -200.
prepare_image(image_data, data_type='vol')
Prepares the image data for conversion. This function normalizes the images based on the provided Hounsfield window.
image_data: The image data in numpy array form.data_type: Either ‘vol’ for volume or ‘seg’ for segmentation.
convert_nifti_to_png(in_dir, out_dir, data_type)
Converts a single NIFTI file into PNG images. Images are saved in the specified output directory.
in_dir: The directory containing the input NIFTI file.out_dir: The directory to save the output PNG files.data_type: Either ‘vol’ for volume or ‘seg’ for segmentation.
convert_nifti_to_png_dir(in_dir, out_dir, data_type)
Converts multiple NIFTI files in a directory into PNG images.
in_dir: The directory containing the input NIFTI files.out_dir: The directory to save the output PNG files.data_type: Either ‘vol’ for volume or ‘seg’ for segmentation.
run(in_dir_vol=None, in_dir_seg=None, out_dir=None)
The main function to perform the conversion for both volumes and segmentations.
in_dir_vol: The directory containing the volume NIFTI files.in_dir_seg: The directory containing the segmentation NIFTI files.out_dir: The directory to save the output PNG files.
Examples
Example 1: Converting a Single NIFTI File
# Initialize the converter
converter = NiftiToPngConverter(max_v=200, min_v=-200)
# Convert a single NIFTI file to PNG
converter.convert_nifti_to_png('path/to/nifti/file', 'path/to/output/dir', 'vol')Example 2: Converting Multiple NIFTI Files
# Initialize the converter
converter = NiftiToPngConverter(max_v=200, min_v=-200)
# Convert multiple NIFTI files to PNG
converter.convert_nifti_to_png_dir('path/to/nifti/directory', 'path/to/output/dir', 'vol')
