def test(data, folder, e):
label_col = list(data.columns)
result = data
model = AE()
model.load_state_dict(
torch.load(f'{folder}/ep{e}data_aug.pth', map_location='cpu'))
model.eval()
dataset = AEDataset(data)
dataloader = DataLoader(dataset=dataset, batch_size=128, shuffle=False)
for inputs in tqdm(dataloader):
outputs = model(inputs.float(), 'cpu')
for i in range(len(outputs)):
tmp = outputs[i].detach().numpy()
tmp = pd.DataFrame([tmp], columns=label_col)
result = pd.concat([result, tmp], ignore_index=True)
result.to_csv(f'{folder}/data_augment.csv',
mode='a',
header=True,
index=False)
return result
for i, data in enumerate(test_loader):
x_test = data.x.to(device)
if i == 3:
break
x_test2 = x_test[1, :, :].reshape(1, 5023, 3).float()
meshdata.save_mesh('x2.ply', x_test2.reshape((tensor_x02.size()[1], 3)).cpu())
# =============================================================================
checkpoint = torch.load(
"out/interpolation_exp/checkpoints/checkpoint_300_64.pt")
model.load_state_dict(checkpoint['model_state_dict'])
optimizer.load_state_dict(checkpoint['optimizer_state_dict'])
## The output as follows:
model.eval() #turn off model weights inconsistence behavior
with torch.no_grad(
): #turn off graident to update wieghts https://stackoverflow.com/questions/60018578/what-does-model-eval-do-in-pytorch
pred = model(x_test2)
### save pred in .ply to visulize it
vertices = pred.reshape((pred.size()[1], 3)).float() #*self.std + self.mean
meshdata.save_mesh('pred2.ply', vertices.cpu())
# encode a mesh
z = model.encoder(x_test2)
print("z values:", z)
# decode
def train():
from benchmark import calc_fid, extract_feature_from_generator_fn, load_patched_inception_v3, real_image_loader, image_generator, image_generator_perm
import lpips
from config import IM_SIZE_GAN, BATCH_SIZE_GAN, NFC, NBR_CLS, DATALOADER_WORKERS, EPOCH_GAN, ITERATION_AE, GAN_CKECKPOINT
from config import SAVE_IMAGE_INTERVAL, SAVE_MODEL_INTERVAL, LOG_INTERVAL, SAVE_FOLDER, TRIAL_NAME, DATA_NAME, MULTI_GPU
from config import FID_INTERVAL, FID_BATCH_NBR, PRETRAINED_AE_PATH
from config import data_root_colorful, data_root_sketch_1, data_root_sketch_2, data_root_sketch_3
real_features = None
inception = load_patched_inception_v3().cuda()
inception.eval()
percept = lpips.PerceptualLoss(model='net-lin', net='vgg', use_gpu=True)
saved_image_folder = saved_model_folder = None
log_file_path = None
if saved_image_folder is None:
saved_image_folder, saved_model_folder = make_folders(
SAVE_FOLDER, 'GAN_' + TRIAL_NAME)
log_file_path = saved_image_folder + '/../gan_log.txt'
log_file = open(log_file_path, 'w')
log_file.close()
dataset = PairedMultiDataset(data_root_colorful,
data_root_sketch_1,
data_root_sketch_2,
data_root_sketch_3,
im_size=IM_SIZE_GAN,
rand_crop=True)
print('the dataset contains %d images.' % len(dataset))
dataloader = iter(
DataLoader(dataset,
BATCH_SIZE_GAN,
sampler=InfiniteSamplerWrapper(dataset),
num_workers=DATALOADER_WORKERS,
pin_memory=True))
from datasets import ImageFolder
from datasets import trans_maker_augment as trans_maker
dataset_rgb = ImageFolder(data_root_colorful, trans_maker(512))
dataset_skt = ImageFolder(data_root_sketch_3, trans_maker(512))
net_ae = AE(nfc=NFC, nbr_cls=NBR_CLS)
if PRETRAINED_AE_PATH is None:
PRETRAINED_AE_PATH = 'train_results/' + 'AE_' + TRIAL_NAME + '/models/%d.pth' % ITERATION_AE
else:
from config import PRETRAINED_AE_ITER
PRETRAINED_AE_PATH = PRETRAINED_AE_PATH + '/models/%d.pth' % PRETRAINED_AE_ITER
net_ae.load_state_dicts(PRETRAINED_AE_PATH)
net_ae.cuda()
net_ae.eval()
RefineGenerator = None
if DATA_NAME == 'celeba':
from models import RefineGenerator_face as RefineGenerator
elif DATA_NAME == 'art' or DATA_NAME == 'shoe':
from models import RefineGenerator_art as RefineGenerator
net_ig = RefineGenerator(nfc=NFC, im_size=IM_SIZE_GAN).cuda()
net_id = Discriminator(nc=3).cuda(
) # we use the patch_gan, so the im_size for D should be 512 even if training image size is 1024
if MULTI_GPU:
net_ae = nn.DataParallel(net_ae)
net_ig = nn.DataParallel(net_ig)
net_id = nn.DataParallel(net_id)
net_ig_ema = copy_G_params(net_ig)
opt_ig = optim.Adam(net_ig.parameters(), lr=2e-4, betas=(0.5, 0.999))
opt_id = optim.Adam(net_id.parameters(), lr=2e-4, betas=(0.5, 0.999))
if GAN_CKECKPOINT is not None:
ckpt = torch.load(GAN_CKECKPOINT)
net_ig.load_state_dict(ckpt['ig'])
net_id.load_state_dict(ckpt['id'])
net_ig_ema = ckpt['ig_ema']
opt_ig.load_state_dict(ckpt['opt_ig'])
opt_id.load_state_dict(ckpt['opt_id'])
## create a log file
losses_g_img = AverageMeter()
losses_d_img = AverageMeter()
losses_mse = AverageMeter()
losses_rec_s = AverageMeter()
losses_rec_ae = AverageMeter()
fixed_skt = fixed_rgb = fixed_perm = None
fid = [[0, 0]]
for epoch in range(EPOCH_GAN):
for iteration in tqdm(range(10000)):
rgb_img, skt_img_1, skt_img_2, skt_img_3 = next(dataloader)
rgb_img = rgb_img.cuda()
rd = random.randint(0, 3)
if rd == 0:
skt_img = skt_img_1.cuda()
elif rd == 1:
skt_img = skt_img_2.cuda()
else:
skt_img = skt_img_3.cuda()
if iteration == 0:
fixed_skt = skt_img_3[:8].clone().cuda()
fixed_rgb = rgb_img[:8].clone()
fixed_perm = true_randperm(fixed_rgb.shape[0], 'cuda')
### 1. train D
gimg_ae, style_feats = net_ae(skt_img, rgb_img)
g_image = net_ig(gimg_ae, style_feats)
pred_r = net_id(rgb_img)
pred_f = net_id(g_image.detach())
loss_d = d_hinge_loss(pred_r, pred_f)
net_id.zero_grad()
loss_d.backward()
opt_id.step()
loss_rec_ae = F.mse_loss(gimg_ae, rgb_img) + F.l1_loss(
gimg_ae, rgb_img)
losses_rec_ae.update(loss_rec_ae.item(), BATCH_SIZE_GAN)
### 2. train G
pred_g = net_id(g_image)
loss_g = g_hinge_loss(pred_g)
if DATA_NAME == 'shoe':
loss_mse = 10 * (F.l1_loss(g_image, rgb_img) +
F.mse_loss(g_image, rgb_img))
else:
loss_mse = 10 * percept(
F.adaptive_avg_pool2d(g_image, output_size=256),
F.adaptive_avg_pool2d(rgb_img, output_size=256)).sum()
losses_mse.update(loss_mse.item() / BATCH_SIZE_GAN, BATCH_SIZE_GAN)
loss_all = loss_g + loss_mse
if DATA_NAME == 'shoe':
### the grey image reconstruction
perm = true_randperm(BATCH_SIZE_GAN)
img_ae_perm, style_feats_perm = net_ae(skt_img, rgb_img[perm])
gimg_grey = net_ig(img_ae_perm, style_feats_perm)
gimg_grey = gimg_grey.mean(dim=1, keepdim=True)
real_grey = rgb_img.mean(dim=1, keepdim=True)
loss_rec_grey = F.mse_loss(gimg_grey, real_grey)
loss_all += 10 * loss_rec_grey
net_ig.zero_grad()
loss_all.backward()
opt_ig.step()
for p, avg_p in zip(net_ig.parameters(), net_ig_ema):
avg_p.mul_(0.999).add_(p.data, alpha=0.001)
### 3. logging
losses_g_img.update(pred_g.mean().item(), BATCH_SIZE_GAN)
losses_d_img.update(pred_r.mean().item(), BATCH_SIZE_GAN)
if iteration % SAVE_IMAGE_INTERVAL == 0: #show the current images
with torch.no_grad():
backup_para_g = copy_G_params(net_ig)
load_params(net_ig, net_ig_ema)
gimg_ae, style_feats = net_ae(fixed_skt, fixed_rgb)
gmatch = net_ig(gimg_ae, style_feats)
gimg_ae_perm, style_feats = net_ae(fixed_skt,
fixed_rgb[fixed_perm])
gmismatch = net_ig(gimg_ae_perm, style_feats)
gimg = torch.cat([
F.interpolate(fixed_rgb, IM_SIZE_GAN),
F.interpolate(fixed_skt.repeat(1, 3, 1, 1),
IM_SIZE_GAN), gmatch,
F.interpolate(gimg_ae, IM_SIZE_GAN), gmismatch,
F.interpolate(gimg_ae_perm, IM_SIZE_GAN)
])
vutils.save_image(
gimg,
f'{saved_image_folder}/img_iter_{epoch}_{iteration}.jpg',
normalize=True,
range=(-1, 1))
del gimg
make_matrix(
dataset_rgb, dataset_skt, net_ae, net_ig, 5,
f'{saved_image_folder}/img_iter_{epoch}_{iteration}_matrix.jpg'
)
load_params(net_ig, backup_para_g)
if iteration % LOG_INTERVAL == 0:
log_msg = 'Iter: [{0}/{1}] G: {losses_g_img.avg:.4f} D: {losses_d_img.avg:.4f} MSE: {losses_mse.avg:.4f} Rec: {losses_rec_s.avg:.5f} FID: {fid:.4f}'.format(
epoch,
iteration,
losses_g_img=losses_g_img,
losses_d_img=losses_d_img,
losses_mse=losses_mse,
losses_rec_s=losses_rec_s,
fid=fid[-1][0])
print(log_msg)
print('%.5f' % (losses_rec_ae.avg))
if log_file_path is not None:
log_file = open(log_file_path, 'a')
log_file.write(log_msg + '\n')
log_file.close()
losses_g_img.reset()
losses_d_img.reset()
losses_mse.reset()
losses_rec_s.reset()
losses_rec_ae.reset()
if iteration % SAVE_MODEL_INTERVAL == 0 or iteration + 1 == 10000:
print('Saving history model')
torch.save(
{
'ig': net_ig.state_dict(),
'id': net_id.state_dict(),
'ae': net_ae.state_dict(),
'ig_ema': net_ig_ema,
'opt_ig': opt_ig.state_dict(),
'opt_id': opt_id.state_dict(),
}, '%s/%d.pth' % (saved_model_folder, epoch))
if iteration % FID_INTERVAL == 0 and iteration > 1:
print("calculating FID ...")
fid_batch_images = FID_BATCH_NBR
if real_features is None:
if os.path.exists('%s_fid_feats.npy' % (DATA_NAME)):
real_features = pickle.load(
open('%s_fid_feats.npy' % (DATA_NAME), 'rb'))
else:
real_features = extract_feature_from_generator_fn(
real_image_loader(dataloader,
n_batches=fid_batch_images),
inception)
real_mean = np.mean(real_features, 0)
real_cov = np.cov(real_features, rowvar=False)
pickle.dump(
{
'feats': real_features,
'mean': real_mean,
'cov': real_cov
}, open('%s_fid_feats.npy' % (DATA_NAME), 'wb'))
real_features = pickle.load(
open('%s_fid_feats.npy' % (DATA_NAME), 'rb'))
sample_features = extract_feature_from_generator_fn(
image_generator(dataset,
net_ae,
net_ig,
n_batches=fid_batch_images),
inception,
total=fid_batch_images)
cur_fid = calc_fid(sample_features,
real_mean=real_features['mean'],
real_cov=real_features['cov'])
sample_features_perm = extract_feature_from_generator_fn(
image_generator_perm(dataset,
net_ae,
net_ig,
n_batches=fid_batch_images),
inception,
total=fid_batch_images)
cur_fid_perm = calc_fid(sample_features_perm,
real_mean=real_features['mean'],
real_cov=real_features['cov'])
fid.append([cur_fid, cur_fid_perm])
print('fid:', fid)
if log_file_path is not None:
log_file = open(log_file_path, 'a')
log_msg = 'fid: %.5f, %.5f' % (fid[-1][0], fid[-1][1])
log_file.write(log_msg + '\n')
log_file.close()
device = 'cuda'
from models import AE, RefineGenerator_art, RefineGenerator_face
net_ae = AE()
net_ae.style_encoder.reset_cls()
net_ig = RefineGenerator_face()
ckpt = torch.load('./models/16.pth')
net_ae.load_state_dict(ckpt['ae'])
net_ig.load_state_dict(ckpt['ig'])
net_ae.to(device)
net_ig.to(device)
net_ae.eval()
#net_ig.eval()
data_root_colorful = './data/rgb/'
#data_root_colorful = '/media/bingchen/database/images/celebaMask/CelebA_1024'
data_root_sketch = './data/skt/'
#data_root_sketch = './data/face_skt/'
BATCH_SIZE = 3
IM_SIZE = 512
DATALOADER_WORKERS = 8
dataset_rgb = ImageFolder(data_root_colorful, trans_maker(512))
dataloader_rgb = iter(DataLoader(dataset_rgb, BATCH_SIZE, shuffle=True))
from tierpsy.helper.params import read_microns_per_pixel
from tierpsy.analysis.ske_create.helperIterROI import getROIfromInd
#load model
model_dir_root = '/data/ajaver/onedrive/classify_strains/logs/worm_autoencoder'
dnames = glob.glob(os.path.join(model_dir_root, 'AE_L64*'))
d = dnames[0]
embedding_size = int(d.split('AE_L')[-1].partition('_')[0])
model_path = os.path.join(d, 'checkpoint.pth.tar')
print(embedding_size)
model = AE(embedding_size)
checkpoint = torch.load(model_path, map_location=lambda storage, loc: storage)
model.load_state_dict(checkpoint['state_dict'])
model.eval()
#%%
mask_file = '/data/ajaver/onedrive/aggregation/N2_1_Ch1_29062017_182108_comp3.hdf5'
feat_file = mask_file.replace('.hdf5', '_featuresN.hdf5')
w_ind = 264
ini_f = 1947
microns_per_pixel = read_microns_per_pixel(feat_file)
with pd.HDFStore(feat_file, 'r') as fid:
trajectories_data = fid['/trajectories_data']
skel_data = trajectories_data[(trajectories_data['skeleton_id'] >= 0)]
skel_g = skel_data.groupby('worm_index_joined')
