2D Segmentation

[tk6684]

I am trying to develop segmentation for CT scan of head. I have my own data for images and labels/masks in two separate folders. An example of data that I have is attached. The 2D segmentation tutorial is based on synthetic data (https://github.com/Project-MONAI/tutorials/blob/main/2d_segmentation/torch/unet_training_array.py). How do I modify the code to fit my data? Thanks!

[KumoLiu]

Hi @tk6684, you could replace the part about generating synthetic data with the example I showed below(need to change the data path).

tutorials/2d_segmentation/torch/unet_training_array.py

Lines 43 to 50 in 56ba738

	print(f"generating synthetic data to {tempdir} (this may take a while)")
	for i in range(40):
	im, seg = create_test_image_2d(128, 128, num_seg_classes=1)
	Image.fromarray((im * 255).astype("uint8")).save(os.path.join(tempdir, f"img{i:d}.png"))
	Image.fromarray((seg * 255).astype("uint8")).save(os.path.join(tempdir, f"seg{i:d}.png"))
	images = sorted(glob(os.path.join(tempdir, "img*.png")))
	segs = sorted(glob(os.path.join(tempdir, "seg*.png")))

# "img*.png" means all the image files start with 'img' and end with 'png'. You could update it based on your data.
images = sorted(glob(os.path.join(images_root_dir, "img*.png")))
# "seg*.png" means all the label files start with 'seg' and end with 'png'. 
segs = sorted(glob(os.path.join(segs_root_dir, "seg*.png")))

Hope it can help you, thanks!

[tk6684]

Thanks for the suggestion @KumoLiu . I am however having issue with the path itself. When I put the path for example- r'"C:\Users\tapan\OneDrive\Desktop\2D img", I am always getting an error that file not recognized or no permission.

If you want to collaborate on the project, I will be happy to. You can reach me at tapan.kavi@gmail.com

[KumoLiu]

Hi @tk6684, there appears to be a single egg quotation in the path you provided; perhaps this is the root of the problem. Alternatively, if you share the entire error message, maybe I could help find more possible reasons. Thanks!

[tk6684]

@KumoLiu
this is the error I get-
AttributeError: 'str' object has no attribute 'read'
If this is the path to the folder on my laptop- C:\Users\tapan\OneDrive\Desktop\2D img, how would you put it in the code you provided above. Thanks!

[KumoLiu]

Something like this?

images_root_dir = r"C:\Users\tapan\OneDrive\Desktop\2D img"
images = sorted(glob(os.path.join(images_root_dir, "img*.png")))