I'm using Python 3.7.7.
I'm trying to load a lot of NIFTI images using SimplyITK and Numpy from the [BraTS 2019 dataset].
This is the code I use to load the images into a numpy array.
import SimpleITK as sitk def read_nifti_images(images_full_path): """ Read nifti files from a gziped file. Read nifti files from a gziped file using SimpleITK library. Parameters: images_full_path (string): Full path to gziped file including file name. Returns: SimpleITK.SimpleITK.Image, numpy array: images read as image, images read as numpy array """ # Reads images using SimpleITK. images = sitk.ReadImage(images_full_path) # Get a numpy array from a SimpleITK Image. images_array = sitk.GetArrayFromImage(images) # More info about SimpleITK images: http://simpleitk.github.io/SimpleITK-Notebooks/01_Image_Basics.html return images, images_array
This code works fine with smallest dataset but here I'm trying to load 518 nii.gz files with 155 images each file.
To run the code I'm using PyCharm latest version on a Windows 7.
How do you do it to train with all the images if all of them can't be in memory because memory limits?