Lung-Nodule-Analysis/helper.py at master · Mahmoud-Da/Lung-Nodule-Analysis · GitHub

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"""
This script contains helper methods
"""


import numpy as np
import SimpleITK as sitk

import config

# Helper function to resample an image to a new spacing


def resample_image(itk_image, new_spacing=config.TARGET_SPACING, is_label=False):
    original_spacing = itk_image.GetSpacing()
    original_size = itk_image.GetSize()

    new_size = [
        int(round(osz * ospc / nspc))
        for osz, ospc, nspc in zip(original_size, original_spacing, new_spacing)
    ]

    resample = sitk.ResampleImageFilter()
    resample.SetOutputSpacing(new_spacing)
    resample.SetSize(new_size)
    resample.SetOutputDirection(itk_image.GetDirection())
    resample.SetOutputOrigin(itk_image.GetOrigin())
    resample.SetTransform(sitk.Transform())
    resample.SetDefaultPixelValue(itk_image.GetPixelIDValue())

    if is_label:
        resample.SetInterpolator(sitk.sitkNearestNeighbor)
    else:
        resample.SetInterpolator(sitk.sitkLinear)

    return resample.Execute(itk_image)

# Helper function to normalize HU values


def normalize_hu(image_array):
    # Clip HU values
    image_array = np.clip(image_array, config.HU_MIN, config.HU_MAX)
    # Normalize to [0, 1]
    image_array = (image_array - config.HU_MIN) / \
        (config.HU_MAX - config.HU_MIN)
    return image_array.astype(np.float32)