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dataio_motion.py
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dataio_motion.py
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import torch.utils.data as data
import torch
from os import listdir
from os.path import join
import numpy as np
import nibabel as nib
import glob
import neural_renderer as nr
class TrainDataset(data.Dataset):
def __init__(self, data_path):
super(TrainDataset, self).__init__()
self.data_path = data_path
self.filename = [f for f in sorted(listdir(self.data_path))]
def __getitem__(self, index):
input_sa, input_2ch, input_4ch, contour_sa, contour_2ch, contour_4ch, \
vertex_ed, faces, affine_inv, affine, origin = load_data(self.data_path, self.filename[index], T_num=50)
img_sa_t = input_sa[0]
img_sa_ed = input_sa[1]
img_2ch_t = input_2ch[0]
img_2ch_ed = input_2ch[1]
img_4ch_t = input_4ch[0]
img_4ch_ed = input_4ch[1]
return img_sa_t, img_sa_ed, img_2ch_t, img_2ch_ed, img_4ch_t, img_4ch_ed,\
contour_sa, contour_2ch, contour_4ch, \
vertex_ed, faces, affine_inv, affine, origin
def __len__(self):
return len(self.filename)
class ValDataset(data.Dataset):
def __init__(self, data_path):
super(ValDataset, self).__init__()
self.data_path = data_path
self.filename = [f for f in sorted(listdir(self.data_path))]
def __getitem__(self, index):
input_sa, input_2ch, input_4ch, contour_sa, contour_2ch, contour_4ch, \
vertex_ed, faces, affine_inv, affine, origin = load_data(self.data_path, self.filename[index], T_num=50, rand_frame=20)
img_sa_t = input_sa[0]
img_sa_ed = input_sa[1]
img_2ch_t = input_2ch[0]
img_2ch_ed = input_2ch[1]
img_4ch_t = input_4ch[0]
img_4ch_ed = input_4ch[1]
return img_sa_t, img_sa_ed, img_2ch_t, img_2ch_ed, img_4ch_t, img_4ch_ed,\
contour_sa, contour_2ch, contour_4ch, \
vertex_ed, faces, affine_inv, affine, origin
def __len__(self):
return len(self.filename)
class TestDataset(data.Dataset):
def __init__(self, data_path):
super(TestDataset, self).__init__()
self.data_path = data_path
self.filename = [f for f in sorted(listdir(self.data_path))]
# print (self.filename)
def __getitem__(self, index):
input_sa, input_2ch, input_4ch, contour_sa_es, contour_2ch_es, contour_4ch_es, \
vertex_es, faces, affine_inv, affine, origin = load_data_ES(self.data_path, self.filename[index])
img_sa_es = input_sa[0]
img_sa_ed = input_sa[1]
img_2ch_es = input_2ch[0]
img_2ch_ed = input_2ch[1]
img_4ch_es = input_4ch[0]
img_4ch_ed = input_4ch[1]
return img_sa_es, img_sa_ed, img_2ch_es, img_2ch_ed, img_4ch_es, img_4ch_ed, \
contour_sa_es, contour_2ch_es, contour_4ch_es, vertex_es, faces, affine_inv, affine, origin
def __len__(self):
return len(self.filename)
def get_data(path, fr):
nim = nib.load(path)
image = nim.get_data()[:, :, :, :] # (h, w, slices, frame)
image = np.array(image, dtype='float32')
image_fr = image[..., fr]
image_fr = image_fr[np.newaxis]
image_ed = image[..., 0]
image_ed = image_ed[np.newaxis]
image_bank = np.concatenate((image_fr, image_ed), axis=0)
image_bank = np.transpose(image_bank, (0, 3, 1, 2))
return image_bank
def get_data_ES(path, path_ES):
nim = nib.load(path)
image = nim.get_data()[:, :, :, :] # (h, w, slices, frame)
image = np.array(image, dtype='float32')
nim_ES = nib.load(path_ES)
image_ES = nim_ES.get_data()[:, :, :, :] # (h, w, slices, frame=0)
image_ES = np.array(image_ES, dtype='float32')
image_z_ed = image[..., 0]
image_z_ed = image_z_ed[np.newaxis]
image_z_es = image_ES[..., 0]
image_z_es = image_z_es[np.newaxis]
image_bank = np.concatenate((image_z_es, image_z_ed), axis=0)
image_bank = np.transpose(image_bank, (0, 3, 1, 2))
return image_bank
def load_data(data_path, filename, T_num, rand_frame=None):
# Load images and labels
img_sa_path = join(data_path, filename, 'sa_img.nii.gz') # (H, W, 1, frames)
img_2ch_path = join(data_path, filename, '2ch_img.nii.gz')
img_4ch_path = join(data_path, filename, '4ch_img.nii.gz')
contour_sa_path = join(data_path, filename, 'contour_sa.npy') # (H, W, 9, frames)
contour_2ch_path = join(data_path, filename, 'contour_2ch.npy') # (H, W, 1, frames)
contour_4ch_path = join(data_path, filename, 'contour_4ch.npy')# (H, W, 1, frames)
vertices_path = join(data_path, filename, 'pred_vertices_ED_new.npy')
faces_path = join(data_path, filename, 'faces_init_myo_ED.npy')
affine_path = join(data_path, filename, 'affine.npz')
origin_path = join(data_path, filename, 'origin.npz')
# generate random index for t and z dimension
if rand_frame is not None:
rand_t = rand_frame
else:
rand_t = np.random.randint(0, T_num)
image_sa_bank = get_data(img_sa_path, rand_t)
image_2ch_bank = get_data(img_2ch_path, rand_t)
image_4ch_bank = get_data(img_4ch_path, rand_t)
contour_sa = np.transpose(np.load(contour_sa_path)[:,:,:,rand_t], (2,0,1)) # [H,W,slices,frame]
contour_2ch = np.load(contour_2ch_path)[:,:, 0, rand_t] # [H,W,1, frame]
contour_4ch = np.load(contour_4ch_path)[:,:, 0, rand_t] # [H,W,1, frame]
# load mesh
vertex_ed = np.load(vertices_path)
faces = np.load(faces_path)
# load affine
aff_sa_inv = np.load(affine_path)['sainv']
aff_2ch_inv = np.load(affine_path)['la2chinv']
aff_4ch_inv = np.load(affine_path)['la4chinv']
affine_inv = np.stack((aff_sa_inv, aff_2ch_inv, aff_4ch_inv), 0)
aff_sa = np.load(affine_path)['sa']
aff_2ch = np.load(affine_path)['la2ch']
aff_4ch = np.load(affine_path)['la4ch']
affine = np.stack((aff_sa, aff_2ch, aff_4ch), 0)
# load origin
origin_sa = np.load(origin_path)['sa']
origin_2ch = np.load(origin_path)['la2ch']
origin_4ch = np.load(origin_path)['la4ch']
origin = np.stack((origin_sa, origin_2ch, origin_4ch), 0)
return image_sa_bank, image_2ch_bank, image_4ch_bank, contour_sa, contour_2ch, contour_4ch, \
vertex_ed, faces, affine_inv, affine, origin
def load_data_ES(data_path, filename):
# Load images and labels
img_sa_path = join(data_path, filename, 'sa_img.nii.gz')
img_2ch_path = join(data_path, filename, '2ch_img.nii.gz')
img_4ch_path = join(data_path, filename, '4ch_img.nii.gz')
img_sa_ES_path = join(data_path, filename, 'sa_ES_img.nii.gz')
img_2ch_ES_path = join(data_path, filename, '2ch_ES_img.nii.gz')
img_4ch_ES_path = join(data_path, filename, '4ch_ES_img.nii.gz')
contour_sa_path = join(data_path, filename, 'contour_sa_es.npy')
contour_2ch_path = join(data_path, filename, 'contour_2ch_es.npy')
contour_4ch_path = join(data_path, filename, 'contour_4ch_es.npy')
vertices_path = join(data_path, filename, 'pred_vertices_ED_new.npy')
faces_path = join(data_path, filename, 'faces_init_myo_ED.npy')
affine_path = join(data_path, filename, 'affine.npz')
origin_path = join(data_path, filename, 'origin.npz')
# load obj
vertex_ed = np.load(vertices_path)
faces = np.load(faces_path)
# load affine
aff_sa_inv = np.load(affine_path)['sainv']
aff_2ch_inv = np.load(affine_path)['la2chinv']
aff_4ch_inv = np.load(affine_path)['la4chinv']
affine_inv = np.stack((aff_sa_inv, aff_2ch_inv, aff_4ch_inv), 0)
aff_sa = np.load(affine_path)['sa']
aff_2ch = np.load(affine_path)['la2ch']
aff_4ch = np.load(affine_path)['la4ch']
affine = np.stack((aff_sa, aff_2ch, aff_4ch), 0)
# load origin
origin_sa = np.load(origin_path)['sa']
origin_2ch = np.load(origin_path)['la2ch']
origin_4ch = np.load(origin_path)['la4ch']
origin = np.stack((origin_sa, origin_2ch, origin_4ch), 0)
image_sa_ES_bank = get_data_ES(img_sa_path, img_sa_ES_path)
image_2ch_ES_bank = get_data_ES(img_2ch_path, img_2ch_ES_path)
image_4ch_ES_bank = get_data_ES(img_4ch_path, img_4ch_ES_path)
contour_sa_es = np.transpose(np.load(contour_sa_path)[:, :, :, 0], (2, 0, 1)) # [H,W,slices,frame]
contour_2ch_es = np.load(contour_2ch_path)[:, :, 0, 0] # [H,W,frame]
contour_4ch_es = np.load(contour_4ch_path)[:, :, 0, 0] # [H,W,frame]
return image_sa_ES_bank, image_2ch_ES_bank, image_4ch_ES_bank, \
contour_sa_es, contour_2ch_es, contour_4ch_es, vertex_ed, faces, affine_inv, affine, origin