| import torch |
| import torch.nn as nn |
| import numpy as np |
| import nibabel as nib |
| import os |
| def get_boundary(seg, kernel_size): |
| pad_size = int((kernel_size - 1) / 2) |
| m_xy = nn.AvgPool3d((kernel_size, kernel_size, 1), stride=1, padding=(pad_size, pad_size, 0)).cuda() |
| output_xy = m_xy(seg) |
| edge_xy = abs(seg - output_xy) |
| |
| edge_locations = torch.multiply(edge_xy, seg) |
| edge_locations[edge_locations > 0] = 1 |
| edge_mask = edge_locations.squeeze(0) |
|
|
| return edge_mask |
|
|
|
|
| def find_boundary_map(seg, boundary_kernel=3, margin_kernel=7): |
| boundary = get_boundary(seg, kernel_size=boundary_kernel).unsqueeze(0) |
| margin = get_boundary(seg, kernel_size=margin_kernel).unsqueeze(0) - boundary |
| content = seg - margin - boundary |
| return boundary.squeeze(0), margin.squeeze(0), content.squeeze(0) |
|
|
|
|
| def get_points(seg, sample): |
| x = torch.where(seg == 1)[2][sample] |
| y = torch.where(seg == 1)[3][sample] |
| z = torch.where(seg == 1)[4][sample] |
| return x, y, z |
|
|
|
|
| def get_points_location(seg, num=1, use_seed=True, seed=0): |
| """ |
| use this to get anchor points |
| """ |
| l = len(torch.where(seg == 1)[0]) |
| if use_seed: |
| np.random.seed(seed) |
| else: |
| np.random.seed(None) |
| sample = np.random.choice(np.arange(l), num, replace=True) |
| x, y, z = get_points(seg, sample) |
|
|
|
|
| points_dict = {'x_location': x, 'y_location': y, 'z_location': z} |
| return points_dict |
|
|
| if __name__ == '__main__': |
| seg_data = nib.load('./example_label_cropped.nii.gz') |
| seg = seg_data.get_fdata() |
| seg = torch.from_numpy(seg).float().cuda().unsqueeze(0).unsqueeze(0) |
|
|
| boundary, margin, content = find_boundary_map(seg) |
|
|
| points_dict = get_points_location(seg) |
|
|
| boundary = boundary.squeeze(0).squeeze(0).cpu().detach().numpy() |
| margin = margin.squeeze(0).squeeze(0).cpu().detach().numpy() |
| content = content.squeeze(0).squeeze(0).cpu().detach().numpy() |
|
|
| nib.save(nib.Nifti1Image(boundary, seg_data.affine, seg_data.header), os.path.join(os.getcwd(), 'boundary.nii.gz')) |
| nib.save(nib.Nifti1Image(margin, seg_data.affine, seg_data.header), os.path.join(os.getcwd(), 'margin.nii.gz')) |
| nib.save(nib.Nifti1Image(content, seg_data.affine, seg_data.header), os.path.join(os.getcwd(), 'content.nii.gz')) |
| print('points location: {}'.format(points_dict)) |
|
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