def test(opt):
os.environ['CUDA_VISIBLE_DEVICES'] = opt.gpus_str
Dataset = dataset_factory[opt.dataset]
opt = Opts().update_dataset_info_and_set_heads(opt, Dataset)
print(opt)
Logger(opt)
Detector = detector_factory[opt.task]
split = 'val' if not opt.trainval else 'test'
dataset = Dataset(opt, split)
detector = Detector(opt)
results = {}
num_iters = len(dataset)
bar = Bar('{}'.format(opt.exp_id), max=num_iters)
time_stats = ['tot', 'load', 'pre', 'net', 'dec', 'post', 'merge']
avg_time_stats = {t: AverageMeter() for t in time_stats}
for ind in range(num_iters):
img_id = dataset.images[ind]
img_info = dataset.coco.loadImgs(ids=[img_id])[0]
img_path = os.path.join(dataset.img_dir, img_info['file_name'])
if opt.task == 'ddd':
ret = detector.run(img_path, img_info['calib'])
else:
ret = detector.run(img_path)
results[img_id] = ret['results']
Bar.suffix = '[{0}/{1}]|Tot: {total:} |ETA: {eta:} '.format(
ind, num_iters, total=bar.elapsed_td, eta=bar.eta_td)
for t in avg_time_stats:
avg_time_stats[t].update(ret[t])
Bar.suffix = Bar.suffix + '|{} {:.3f} '.format(
t, avg_time_stats[t].avg)
bar.next()
bar.finish()
dataset.run_eval(results, opt.save_dir)
def prefetch_test(opt):
os.environ['CUDA_VISIBLE_DEVICES'] = opt.gpus_str
Dataset = dataset_factory[opt.dataset]
opt = Opts().update_dataset_info_and_set_heads(opt, Dataset)
print(opt)
Logger(opt)
Detector = detector_factory[opt.task]
split = 'val' if not opt.trainval else 'test'
dataset = Dataset(opt, split)
detector = Detector(opt)
data_loader = torch.utils.data.DataLoader(PrefetchDataset(
opt, dataset, detector.pre_process),
batch_size=1,
shuffle=False,
num_workers=1,
pin_memory=True)
results = {}
num_iters = len(dataset)
bar = Bar('{}'.format(opt.exp_id), max=num_iters)
time_stats = ['tot', 'load', 'pre', 'net', 'dec', 'post', 'merge']
avg_time_stats = {t: AverageMeter() for t in time_stats}
for ind, (img_id, pre_processed_images) in enumerate(data_loader):
ret = detector.run(pre_processed_images)
results[img_id.numpy().astype(np.int32)[0]] = ret['results']
Bar.suffix = '[{0}/{1}]|Tot: {total:} |ETA: {eta:} '.format(
ind, num_iters, total=bar.elapsed_td, eta=bar.eta_td)
for t in avg_time_stats:
avg_time_stats[t].update(ret[t])
Bar.suffix = Bar.suffix + '|{} {tm.val:.3f}s ({tm.avg:.3f}s) '.format(
t, tm=avg_time_stats[t])
bar.next()
bar.finish()
dataset.run_eval(results, opt.save_dir)
import cv2
import torch
from tqdm import tqdm
from opts import Opts
from utils.utils import test_time_aug, make_dir, img_predict
def predict():
with tqdm(total=args.n_test, desc=f'Predict', unit='img') as p_bar:
for index, i in enumerate(os.listdir(args.dir_test)):
save_path = os.path.join(args.dir_result, i)
image = cv2.imread(os.path.join(args.dir_test, i))
img_predict(args, image, save_path=save_path)
p_bar.update(1)
if __name__ == '__main__':
args = Opts().init()
args.dir_test = os.path.join(args.dir_data, 'test')
args.n_test = len(os.listdir(args.dir_test))
args.net.load_state_dict(
torch.load(
os.path.join(args.dir_log, f'{args.dataset}_{args.arch}_{args.exp_id}.pth'), map_location=args.device
)
)
if args.tta:
args.net = test_time_aug(args.net, merge_mode='mean')
make_dir(dir_path=args.dir_result)
predict()
print('Plotting Calibration..')
experiments.plot_defer_simulation(X, y, config)
elif config.exp_name == 'toy_regression':
print('Toy regression ..')
experiments.plot_toy_regression(config)
elif config.exp_name == 'clusterwise_ood':
print('Plotting OOD..')
experiments.plot_ood(X, y, config)
elif config.exp_name == 'kl_mode':
print('Plotting KL..')
experiments.plot_kl(X, y, config)
elif config.exp_name == 'show_summary':
print('Showing..')
experiments.show_model_summary(X, y, config)
elif config.exp_name == 'empirical_rule_test':
print('Emprical rule tests..')
experiments.empirical_rule_test(X, y, config)
if __name__ == '__main__':
opts = Opts()
config = opts.parse()
config.verbose = (int)(config.verbose)
main(config)
# python main.py train --datasets_dir datasets --dataset boston --model_dir boston_anc_models_comsplit_10folds --n_folds 3 --build_model anc_ens --verbose 1
def main():
# Parse the options
opts = Opts().parse()
opts.device = torch.device(f'cuda:{opts.gpu[0]}')
print(opts.expID, opts.task)
# Record the start time
time_start = time.time()
# TODO: select the dataset by the options
# Set up dataset
train_loader_unit = PENN_CROP(opts, 'train')
train_loader = tud.DataLoader(train_loader_unit,
batch_size=opts.trainBatch,
shuffle=False,
num_workers=int(opts.num_workers))
val_loader = tud.DataLoader(PENN_CROP(opts, 'val'),
batch_size=1,
shuffle=False,
num_workers=int(opts.num_workers))
# Read number of joints(dim of output) from dataset
opts.nJoints = train_loader_unit.part.shape[1]
# Create the Model, Optimizer and Criterion
if opts.loadModel == 'none':
model = Hourglass2DPrediction(opts).cuda(device=opts.device)
else:
model = torch.load(opts.loadModel).cuda(device=opts.device)
# Set the Criterion and Optimizer
criterion = torch.nn.MSELoss(reduce=False).cuda(device=opts.device)
# opts.nOutput = len(model.outnode.children)
optimizer = torch.optim.RMSprop(model.parameters(),
opts.LR,
alpha=opts.alpha,
eps=opts.epsilon,
weight_decay=opts.weightDecay,
momentum=opts.momentum)
# If TEST, just validate
# TODO: save the validate results to mat or hdf5
if opts.test:
loss_test, pck_test = val(0, opts, val_loader, model, criterion)
print(f"test: | loss_test: {loss_test}| PCK_val: {pck_test}\n")
## TODO: save the predictions for the test
#sio.savemat(os.path.join(opts.saveDir, 'preds.mat'), mdict = {'preds':preds})
return
# NOT TEST, Train and Validate
for epoch in range(1, opts.nEpochs + 1):
## Train the model
loss_train, pck_train = train(epoch, opts, train_loader, model,
criterion, optimizer)
## Show results and elapsed time
time_elapsed = time.time() - time_start
print(
f"epoch: {epoch} | loss_train: {loss_train} | PCK_train: {pck_train} | {time_elapsed//60:.0f}min {time_elapsed%60:.0f}s\n"
)
## Intervals to show eval results
if epoch % opts.valIntervals == 0:
# TODO: Test the validation part
### Validation
loss_val, pck_val = val(epoch, opts, val_loader, model, criterion)
print(
f"epoch: {epoch} | loss_val: {loss_val}| PCK_val: {pck_val}\n")
### Save the model
torch.save(model, os.path.join(opts.save_dir,
f"model_{epoch}.pth"))
### TODO: save the preds for the validation
#sio.savemat(os.path.join(opts.saveDir, f"preds_{epoch}.mat"), mdict={'preds':preds})
# Use the optimizer to adjust learning rate
if epoch % opts.dropLR == 0:
lr = adjust_learning_rate(optimizer, epoch, opts.dropLR, opts.LR)
print(f"Drop LR to {lr}\n")
def generate_B0ECC_SeqFile(iT, tr, te, Npuls, mg, ms, grt, fA, reps, sliceT,
tPre, tPos, tX, tY, tZ, tPlot, tReport,
testPRE_POST, rf_offset, dummy, Ndummies):
# %% ===========================================================================
# %% --- 1 - Instantiation and gradient limits ---
system = Opts(max_grad=mg,
grad_unit='mT/m',
max_slew=ms,
slew_unit='T/m/s',
rf_ringdown_time=20e-6,
rf_dead_time=100e-6,
adc_dead_time=10e-6)
seq = Sequence(system)
# I need to check the manually inputed inverse raster time and the actual value are the same.
i_raster_time = 100000
assert 1 / i_raster_time == seq.grad_raster_time, "Manualy inputed inverse raster time does not match the actual value."
slice_thickness, slice_gap, TR, TE, rf_offset_z = sliceT, 15e-3, tr, te, 0
posAxxis = [slice_thickness + rf_offset, -slice_thickness - rf_offset]
# %% --- 2 - Gradients
G = iT
G_zero = np.zeros(len(iT[:, 0]))
G_pre = np.zeros(math.floor(tPre * i_raster_time))
G_pos = np.zeros(math.floor(tPos * i_raster_time))
# %% --- 3 - Slice Selection
# =========
# Create 90 degree slice selection pulse and gradient
# =========
# RF90
flip90 = fA * pi / 180
rfx, gxRF, gxr = make_sinc_pulse_channel(channel='x',
flip_angle=flip90,
duration=3e-3,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=4,
system=system)
rfy, gyRF, gyr = make_sinc_pulse_channel(channel='y',
flip_angle=flip90,
duration=3e-3,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=4,
system=system)
rfz, gzRF, gzr = make_sinc_pulse(flip_angle=flip90,
duration=3e-3,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=4,
system=system)
# %% --- 4 - ADCs / Readouts
adc_samples = math.floor(len(G) / 4) * 4 - 1
adc_samples_pre = math.floor(len(G_pre) / 4) * 4 - 2
adc_samples_pos = math.floor(len(G_pos) / 4) * 4 - 100
adc = make_adc(num_samples=adc_samples,
duration=adc_samples / i_raster_time,
system=system)
adc_pre = make_adc(num_samples=adc_samples_pre,
duration=adc_samples_pre / i_raster_time,
system=system)
adc_pos = make_adc(num_samples=adc_samples_pos,
duration=adc_samples_pos / i_raster_time,
system=system)
# %% --- 5 - Spoilers
pre_time = 8e-4
n_pre_time = math.ceil(pre_time * i_raster_time)
gx_rephz = make_trapezoid(channel='x',
area=-gxRF.area / 2,
duration=2e-3,
system=system)
gx_spoil = make_trapezoid(channel='x',
area=-gxRF.area / 2,
duration=3 * n_pre_time / i_raster_time,
system=system)
gy_rephz = make_trapezoid(channel='y',
area=-gyRF.area / 2,
duration=2e-3,
system=system)
gy_spoil = make_trapezoid(channel='y',
area=-gyRF.area / 2,
duration=3 * n_pre_time / i_raster_time,
system=system)
gz_rephz = make_trapezoid(channel='z',
area=-gzRF.area / 2,
duration=2e-3,
system=system)
gz_spoil = make_trapezoid(channel='z',
area=-gzRF.area / 2,
duration=3 * n_pre_time / i_raster_time,
system=system)
# double area for all second pulses
gx_spoil_double = make_trapezoid(channel='x',
area=-gxRF.area,
duration=3 * n_pre_time / i_raster_time,
system=system)
gy_spoil_double = make_trapezoid(channel='y',
area=-gyRF.area,
duration=3 * n_pre_time / i_raster_time,
system=system)
gz_spoil_double = make_trapezoid(channel='z',
area=-gzRF.area,
duration=3 * n_pre_time / i_raster_time,
system=system)
aux_gx = make_arbitrary_grad(channel='x',
waveform=np.squeeze(G[:, 0]),
system=system)
aux_gy = make_arbitrary_grad(channel='y',
waveform=np.squeeze(G[:, 0]),
system=system)
aux_gz = make_arbitrary_grad(channel='y',
waveform=np.squeeze(G[:, 0]),
system=system)
# %% --- 6 - Calculate timing/Delays
n_TE = math.ceil(TE * i_raster_time)
n_TR = math.ceil(TR * i_raster_time)
n_dur_adc_pre = math.ceil(calc_duration(adc_pre) * i_raster_time)
n_dur_adc_pos = math.ceil(calc_duration(adc_pos) * i_raster_time)
# for x
# delay pre ADC
n_dur_gx_rephz = math.ceil(calc_duration(gx_rephz) * i_raster_time)
n_dur_rfx = math.ceil(calc_duration(rfx) * i_raster_time)
n_del_preGRS_x = n_TE - (n_dur_gx_rephz + math.ceil(n_dur_rfx / 2)
) # Time before input in points
del_preGRS_x = n_del_preGRS_x / i_raster_time
delay_preGRS_x = make_delay(del_preGRS_x)
# delay pos ADC
n_dur_aux_gx = math.ceil(calc_duration(aux_gx) * i_raster_time)
n_dur_gx_spoil = math.ceil(calc_duration(gx_spoil) * i_raster_time)
n_delTR_x = n_TR - (
n_dur_gx_rephz + math.ceil(n_dur_rfx / 2) + n_dur_adc_pre +
n_dur_aux_gx + n_dur_adc_pos + n_dur_gx_spoil
) # Time after input to the system in points
delTR_x = n_delTR_x / i_raster_time
delayTR_x = make_delay(delTR_x)
# for y
# delay pre ADC
n_dur_gy_rephz = math.ceil(calc_duration(gy_rephz) * i_raster_time)
n_dur_rfy = math.ceil(calc_duration(rfy) * i_raster_time)
n_del_preGRS_y = n_TE - (n_dur_gy_rephz + math.ceil(n_dur_rfy / 2)
) # Time before input in points
del_preGRS_y = n_del_preGRS_y / i_raster_time
delay_preGRS_y = make_delay(del_preGRS_y)
# delay pos ADC
n_dur_aux_gy = math.ceil(calc_duration(aux_gy) * i_raster_time)
n_dur_gy_spoil = math.ceil(calc_duration(gy_spoil) * i_raster_time)
n_delTR_y = n_TR - (n_dur_gy_rephz + math.ceil(n_dur_rfy / 2) +
n_dur_adc_pre + n_dur_aux_gy + n_dur_adc_pos +
n_dur_gy_spoil)
delTR_y = n_delTR_y / i_raster_time
delayTR_y = make_delay(delTR_y)
# for z
# delay pre ADC
n_dur_gz_rephz = math.ceil(calc_duration(gz_rephz) * i_raster_time)
n_dur_rfz = math.ceil(calc_duration(rfz) * i_raster_time)
n_del_preGRS_z = n_TE - (n_dur_gz_rephz + math.ceil(n_dur_rfz / 2)
) # Time before input in points
del_preGRS_z = n_del_preGRS_z / i_raster_time
delay_preGRS_z = make_delay(del_preGRS_z)
# delay pos ADC
n_dur_aux_gz = math.ceil(calc_duration(aux_gz) * i_raster_time)
n_dur_gz_spoil = math.ceil(calc_duration(gx_spoil) * i_raster_time)
n_delTR_z = n_TR - (n_dur_gz_rephz + math.ceil(n_dur_rfz / 2) +
n_dur_adc_pre + n_dur_aux_gz + n_dur_adc_pos +
n_dur_gz_spoil)
delTR_z = n_delTR_z / i_raster_time
delayTR_z = make_delay(delTR_z)
# %% --- 7 - Define sequence for measuring k_trajectory - blocks/Readouts
if dummy:
for nd in range(Ndummies):
# for x and y rf pulse
freq_offset_gx = gxRF.amplitude * posAxxis[0]
rfx.freq_offset = freq_offset_gx
freq_offset_gy = gyRF.amplitude * posAxxis[0]
rfy.freq_offset = freq_offset_gy
# RF90
seq.add_block(rfx, gxRF)
seq.add_block(gx_rephz)
# Delay for spiral
seq.add_block(delay_preGRS_x)
# Read k-space - Imaging Gradient waveforms
gx_zero = make_arbitrary_grad(channel='x',
waveform=np.squeeze(G_zero),
system=system)
seq.add_block(adc, gx_zero)
# Gradients Spoils
seq.add_block(gx_spoil)
# Delay to TR
seq.add_block(delayTR_x)
n_x = 0
if tX:
for ns in range(Npuls):
for r in range(reps):
for s in range(2): # for position of axis
for a in range(2): # for positive or negative gradient
n_x = n_x + 1
# for x rf pulse
freq_offset_gx = gxRF.amplitude * posAxxis[s]
rfx.freq_offset = freq_offset_gx
# RF90
seq.add_block(rfx, gxRF)
seq.add_block(gx_rephz)
# Delay for spiral
seq.add_block(delay_preGRS_x)
# Read - pre GIRF
if testPRE_POST:
gx_pre = make_arbitrary_grad(
channel='x',
waveform=np.squeeze(G_pre),
system=system)
seq.add_block(adc_pre, gx_pre)
# Read k-space - Imaging Gradient waveforms
if a == 1:
# %% --- for x-axis negative gradient --- %% #
gx = make_arbitrary_grad(channel='x',
waveform=np.squeeze(
G[:, ns] * -1),
system=system)
else:
# %% --- for x-axis positive gradient --- %% #
gx = make_arbitrary_grad(channel='x',
waveform=np.squeeze(
G[:, ns]),
system=system)
seq.add_block(adc, gx)
# Read - pos GIRF
if testPRE_POST:
gx_pos = make_arbitrary_grad(
channel='x',
waveform=np.squeeze(G_pos),
system=system)
seq.add_block(adc_pos, gx_pos)
# Gradients Spoils
if (n_x % 2) == 0:
# seq.add_block(gx_spoil,gy_spoil,gz_spoil)
seq.add_block(gx_spoil_double)
# seq.add_block(gy_spoil_double)
else:
# seq.add_block(gx_spoil,gy_spoil,gz_spoil)
seq.add_block(gx_spoil)
# seq.add_block(gy_spoil)
# Delay to TR
seq.add_block(delayTR_x)
n_y = 0
if tY:
for ns in range(Npuls):
for r in range(reps):
for s in range(2):
for a in range(2):
n_y = n_y + 1
# for x rf pulse
freq_offset_gy = gyRF.amplitude * posAxxis[s]
rfy.freq_offset = freq_offset_gy
# RF90
seq.add_block(rfy, gyRF)
seq.add_block(gy_rephz)
# Delay for spiral
seq.add_block(delay_preGRS_y)
# Read - pre GIRF
if testPRE_POST:
gy_pre = make_arbitrary_grad(
channel='y',
waveform=np.squeeze(G_pre),
system=system)
seq.add_block(adc_pre, gy_pre)
# Read k-space - Imaging Gradient waveforms
if a == 1:
# %% --- for y-axis negative gradient --- %% #
gy = make_arbitrary_grad(channel='y',
waveform=np.squeeze(
G[:, ns] * -1),
system=system)
else:
# %% --- for y-axis positive gradient --- %% #
gy = make_arbitrary_grad(channel='y',
waveform=np.squeeze(
G[:, ns]),
system=system)
seq.add_block(adc, gy)
# Read - pos GIRF
if testPRE_POST:
gy_pos = make_arbitrary_grad(
channel='y',
waveform=np.squeeze(G_pos),
system=system)
seq.add_block(adc_pos, gy_pos)
# Gradients Spoils
if (n_y % 2) == 0:
# seq.add_block(gx_spoil,gy_spoil,gz_spoil)
seq.add_block(gy_spoil_double)
# seq.add_block(gx_spoil_double)
else:
# seq.add_block(gx_spoil,gy_spoil,gz_spoil)
seq.add_block(gy_spoil)
# seq.add_block(gx_spoil)
# Delay to TR
seq.add_block(delayTR_y)
if tZ:
for ns in range(Npuls):
for r in range(reps):
for s in range(2):
for a in range(2):
# for x rf pulse
freq_offset_gz = gzRF.amplitude * posAxxis[s]
rfz.freq_offset = freq_offset_gz
# RF90
seq.add_block(rfz, gz_rephz)
# Delay for spiral
seq.add_block(delay_preGRS_z)
# Read - pre GIRF
if testPRE_POST:
gz_pre = make_arbitrary_grad(
channel='z',
waveform=np.squeeze(G_pre),
system=system)
seq.add_block(adc_pre, gz_pre)
# Read k-space - Imaging Gradient waveforms
if a == 1:
# %% --- for y-axis negative gradient --- %% #
gz = make_arbitrary_grad(channel='z',
waveform=np.squeeze(
G[:, ns] * -1),
system=system)
else:
# %% --- for y-axis positive gradient --- %% #
gz = make_arbitrary_grad(channel='z',
waveform=np.squeeze(
G[:, ns]),
system=system)
seq.add_block(adc, gz)
# Read - pos GIRF
if testPRE_POST:
gz_pos = make_arbitrary_grad(
channel='z',
waveform=np.squeeze(G_pos),
system=system)
seq.add_block(adc_pos, gz_pos)
# Gradients Spoils
seq.add_block(gx_spoil, gy_spoil, gz_spoil)
# seq.add_block(gz_spoil)
# Delay to TR
seq.add_block(delayTR_z)
# %% --- 8 - Plot ADCs, GX, GY, GZ, RFpulse, RFphase
# # plt.figure()
if tPlot:
seq.plot()
if tReport:
print(seq.test_report())
seq.check_timing()
return seq
def main(opt):
torch.manual_seed(opt.seed)
torch.backends.cudnn.benchmark = not opt.not_cuda_benchmark and not opt.test
Dataset = get_dataset(opt.dataset, opt.task)
val_dataset = Dataset(opt, 'val')
opt = Opts().update_dataset_info_and_set_heads(opt, val_dataset)
print(opt)
logger = Logger(opt)
os.environ['CUDA_VISIBLE_DEVICES'] = opt.gpus_str
opt.device = torch.device('cuda' if opt.gpus[0] >= 0 else 'cpu')
print('Creating model...')
model = create_model(opt.arch, opt.heads, opt.head_conv)
optimizer = torch.optim.Adam(model.parameters(), opt.lr)
start_epoch = 0
if opt.load_model != '':
model, optimizer, start_epoch = load_model(
model, opt.load_model, optimizer, opt.resume, opt.lr, opt.lr_step)
print("Model:")
print(model)
print("Total number of parameters: {}".format(count_parameters(model)))
print("Trainable parameters: {}".format(count_parameters(model, trainable=True)))
Trainer = train_factory[opt.task]
trainer = Trainer(opt, model, optimizer)
trainer.set_device(opt.gpus, opt.chunk_sizes, opt.device)
print('Setting up data...')
val_loader = torch.utils.data.DataLoader(
val_dataset,
batch_size=1,
shuffle=False,
num_workers=1,
pin_memory=True
)
if opt.test:
_, preds = trainer.val(0, val_loader)
val_loader.dataset.run_eval(preds, opt.save_dir)
print("{} images failed!".format(len(val_loader.dataset.failed_images)))
print(val_loader.dataset.failed_images)
return
train_loader = torch.utils.data.DataLoader(
Dataset(opt, 'train'),
batch_size=opt.batch_size,
shuffle=True,
num_workers=opt.num_workers,
pin_memory=True,
drop_last=True
)
# Report failed images
failed_images = list(train_loader.dataset.failed_images | val_loader.dataset.failed_images)
if len(failed_images):
print("{} images failed!".format(len(failed_images)))
dump_path = os.path.join(opt.save_dir, 'failed_images.json')
with open(dump_path, 'w') as f:
json.dump(failed_images, f, sort_keys=True, indent=4, separators=(',', ': '))
print("Failed image paths saved in: {}".format(dump_path))
print('Starting training...')
best = 1e10
for epoch in range(start_epoch + 1, opt.num_epochs + 1):
mark = epoch if opt.save_all else 'last'
log_dict_train, _ = trainer.train(epoch, train_loader)
logger.write('epoch: {} |'.format(epoch))
for k, v in log_dict_train.items():
logger.scalar_summary('train_{}'.format(k), v, epoch)
logger.write('{} {:8f} | '.format(k, v))
if opt.val_intervals > 0 and epoch % opt.val_intervals == 0:
save_model(os.path.join(opt.save_dir, 'model_{}.pth'.format(mark)),
epoch, model, optimizer)
with torch.no_grad():
log_dict_val, preds = trainer.val(epoch, val_loader)
for k, v in log_dict_val.items():
logger.scalar_summary('val_{}'.format(k), v, epoch)
logger.write('{} {:8f} | '.format(k, v))
if log_dict_val[opt.metric] < best:
best = log_dict_val[opt.metric]
save_model(os.path.join(opt.save_dir, 'model_best.pth'),
epoch, model)
else:
save_model(os.path.join(opt.save_dir, 'model_last.pth'),
epoch, model, optimizer)
logger.write('\n')
if epoch in opt.lr_step:
save_model(os.path.join(opt.save_dir, 'model_{}.pth'.format(epoch)),
epoch, model, optimizer)
lr = opt.lr * (0.1 ** (opt.lr_step.index(epoch) + 1))
print('Drop LR to', lr)
for param_group in optimizer.param_groups:
param_group['lr'] = lr
logger.close()
logger.write('{} {:8f} | '.format(k, v))
if opt.val_intervals > 0 and epoch % opt.val_intervals == 0:
save_model(os.path.join(opt.save_dir, 'model_{}.pth'.format(mark)),
epoch, model, optimizer)
with torch.no_grad():
log_dict_val, preds = trainer.val(epoch, val_loader)
for k, v in log_dict_val.items():
logger.scalar_summary('val_{}'.format(k), v, epoch)
logger.write('{} {:8f} | '.format(k, v))
if log_dict_val[opt.metric] < best:
best = log_dict_val[opt.metric]
save_model(os.path.join(opt.save_dir, 'model_best.pth'),
epoch, model)
else:
save_model(os.path.join(opt.save_dir, 'model_last.pth'),
epoch, model, optimizer)
logger.write('\n')
if epoch in opt.lr_step:
save_model(os.path.join(opt.save_dir, 'model_{}.pth'.format(epoch)),
epoch, model, optimizer)
lr = opt.lr * (0.1 ** (opt.lr_step.index(epoch) + 1))
print('Drop LR to', lr)
for param_group in optimizer.param_groups:
param_group['lr'] = lr
logger.close()
if __name__ == '__main__':
opt = Opts().parse()
main(opt)
def main():
# Parse the options from parameters
opts = Opts().parse()
## For PyTorch 0.4.1, cuda(device)
opts.device = torch.device(f'cuda:{opts.gpu[0]}')
print(opts.expID, opts.task, os.path.dirname(os.path.realpath(__file__)))
# Load the trained model test
if opts.loadModel != 'none':
model_path = os.path.join(opts.root_dir, opts.loadModel)
model = torch.load(model_path).cuda(device=opts.device)
model.eval()
else:
print('ERROR: No model is loaded!')
return
# Read the input image, pass input to gpu
if opts.img == 'None':
val_dataset = PENN_CROP(opts, 'val')
val_loader = tud.DataLoader(val_dataset,
batch_size=1,
shuffle=False,
num_workers=int(opts.num_workers))
opts.nJoints = val_dataset.nJoints
opts.skeleton = val_dataset.skeleton
for i, gt in enumerate(val_loader):
# Test Visualizer, Input and get_preds
if i == 0:
input, label = gt['input'], gt['label']
gtpts, center, scale, proj = gt['gtpts'], gt['center'], gt[
'scale'], gt['proj']
input_var = input[:, 0, ].float().cuda(device=opts.device,
non_blocking=True)
# output = label
output = model(input_var)
# Test Loss, Err and Acc(PCK)
Loss, Err, Acc = AverageMeter(), AverageMeter(), AverageMeter()
ref = get_ref(opts.dataset, scale)
for j in range(opts.preSeqLen):
pred = get_preds(output[:, j, ].cpu().float())
pred = original_coordinate(pred, center[:, ], scale,
opts.outputRes)
err, ne = error(pred, gtpts[:, j, ], ref)
acc, na = accuracy(pred, gtpts[:, j, ], ref)
# assert ne == na, "ne must be the same as na"
Err.update(err)
Acc.update(acc)
print(j, f"{Err.val:.6f}", Acc.val)
print('all', f"{Err.avg:.6f}", Acc.avg)
# Visualizer Object
## Initialize
v = Visualizer(opts.nJoints, opts.skeleton, opts.outputRes)
# ## Add input image
# v.add_img(input[0,0,].transpose(2, 0).numpy().astype(np.uint8))
# ## Get the predicted joints
# predJoints = get_preds(output[:, 0, ])
# # ## Add joints and skeleton to the figure
# v.add_2d_joints_skeleton(predJoints, (0, 0, 255))
# Transform heatmap to show
hm_img = output[0, 0, ].cpu().detach().numpy()
v.add_hm(hm_img)
## Show image
v.show_img(pause=True)
break
else:
print('NOT ready for the raw input outside the dataset')
img = cv2.imread(opts.img)
input = torch.from_numpy(img.tramspose(2, 0, 1)).float() / 256.
input = input.view(1, input.size(0), input.size(1), input.size(2))
input_var = torch.autograd.variable(input).float().cuda(
device=opts.device)
output = model(input_var)
predJoints = get_preds(output[-2].data.cpu().numpy())[0] * 4
def generate_SeqFile_Spiral(gx,
gy,
tr,
n_shots,
mg,
ms,
fA,
n_slices,
reps,
st,
tPlot,
tReport,
rf_offset=0):
#%% ===========================================================================
# --- 1 - Instantiation and gradient limits ---
system = Opts(max_grad=mg,
grad_unit='mT/m',
max_slew=ms,
slew_unit='T/m/s',
rf_ringdown_time=20e-6,
rf_dead_time=100e-6,
adc_dead_time=10e-6)
seq = Sequence(system)
# I need to check the manually inputed inverse raster time and the actual value are the same.
i_raster_time = 100000
assert 1 / i_raster_time == seq.grad_raster_time, "Manualy inputed inverse raster time does not match the actual value."
slice_thickness, slice_gap, TE, TR = st, 15e-3, 5e-3, tr
delta_z = n_slices * slice_thickness
z = np.linspace((-delta_z / 2), (delta_z / 2), n_slices) + rf_offset
#%% --- 2 - Gradients
# scl = 1.05
# gx = gx/(scl*np.max(gx)/(max_grad*42576000e-3));
# gy = gy/(scl*np.max(gy)/(max_grad*42576000e-3));
G = gx + 1J * gy
#%% --- 3 - Slice Selection
# =========
# Create 90 degree slice selection pulse and gradient
# =========
# RF90
flip90 = fA * pi / 180
rf, gz, gzr = make_sinc_pulse(flip_angle=flip90,
duration=3e-3,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=4,
system=system)
# RF180
#%% --- 4 - ADCs / Readouts
adc_samples = math.floor(len(G) / 4) * 4 - 4
adc = make_adc(num_samples=adc_samples,
duration=adc_samples / i_raster_time,
system=system)
#%% --- 5 - Spoilers
pre_time = 8e-4
n_pre_time = math.ceil(pre_time * i_raster_time)
gz_rephz = make_trapezoid(channel='z',
area=-gz.area / 2,
duration=1e-3,
system=system)
gz_spoil = make_trapezoid(channel='z',
area=-gz.area / 2,
duration=3 * n_pre_time / i_raster_time,
system=system)
aux_gx = make_arbitrary_grad(channel='x',
waveform=np.squeeze(np.real(G[:, 0])),
system=system)
# Make the spiral in Gx and Gy finish in zero - I use pre_time because I know for sure it's long enough.
# Furthermore, this is after readout and TR is supposed to be long.
spoil_time = [0, calc_duration(gz_spoil)]
gxAmplitud_Spoil = [np.real(G[-1][0]), 0]
gyAmplitud_Spoil = [np.imag(G[-1][0]), 0]
gx_spoil = make_extended_trapezoid(channel='x',
times=spoil_time,
amplitudes=gxAmplitud_Spoil,
system=system)
gy_spoil = make_extended_trapezoid(channel='y',
times=spoil_time,
amplitudes=gyAmplitud_Spoil,
system=system)
# # =========
# # Prephase and Rephase
# # =========
# phase_areas = (np.arange(Ny) - (Ny / 2)) * delta_k
# kwargs_for_gy_pre = {"channel": 'y', "system": system, "area": phase_areas[-1], "duration": 2e-3}
# gy_pre = maketrapezoid(kwargs_for_gy_pre)
#
# kwargs_for_gxpre = {"channel": 'x', "system": system, "area": -gx.area / 2, "duration": 2e-3}
# gx_pre = maketrapezoid(kwargs_for_gxpre)
#
# kwargs_for_gz_reph = {"channel": 'z', "system": system, "area": -gz.area / 2, "duration": 2e-3}
# gz_reph = maketrapezoid(kwargs_for_gz_reph)
#%% --- 6 - Calculate timing/Delays
n_TE = math.ceil(TE * i_raster_time)
n_dur_gz_rephz = math.ceil(calc_duration(gz_rephz) * i_raster_time)
n_dur_rf = math.ceil(calc_duration(rf) * i_raster_time)
n_del_preGRS = n_TE - (n_dur_gz_rephz + math.ceil(n_dur_rf / 2)
) # Time before input in points
del_preGRS = n_del_preGRS / i_raster_time
delay_preGRS = make_delay(del_preGRS)
n_TR = math.ceil(TR * i_raster_time)
n_dur_aux_gx = math.ceil(calc_duration(aux_gx) * i_raster_time)
n_dur_gz_spoil = math.ceil(calc_duration(gz_spoil) * i_raster_time)
n_delTR = n_TR - (n_dur_gz_rephz + n_dur_rf - n_dur_aux_gx - n_dur_gz_spoil
) # Time after input to the system in points
delTR = n_delTR / i_raster_time
delayTR = make_delay(delTR)
#%% --- 7 - Define sequence blocks/Readouts + Create '.seq' file
for r in range(reps):
for s in range(n_slices):
for ns in range(n_shots):
freq_offset = gz.amplitude * z[s]
rf.freq_offset = freq_offset
# RF90
seq.add_block(rf, gz)
seq.add_block(gz_rephz)
# Delay for spiral
seq.add_block(delay_preGRS)
# if (r % 2 == 0):
# Read k-space - Imaging Gradient waveforms
gx = make_arbitrary_grad(channel='x',
waveform=np.squeeze(np.real(G[:,
ns])),
system=system)
gy = make_arbitrary_grad(channel='y',
waveform=np.squeeze(np.imag(G[:,
ns])),
system=system)
seq.add_block(gx, gy, adc)
# Gradients Spoils
seq.add_block(gz_spoil, gx_spoil, gy_spoil)
# seq.add_block(gz_spoil)
# else: # to allow measure phase with no gradient
# # Read k-space - Imaging Gradient waveforms
# seq.add_block(adc)
#
# # Gradients Spoils
# seq.add_block(gz_spoil)
# Delay to TR
seq.add_block(delayTR)
# %% --- 8 - Plot ADCs, GX, GY, GZ, RFpulse, RFphase
# # plt.figure()
if tPlot:
seq.plot()
if tReport:
print(seq.test_report())
seq.check_timing()
return seq
def generate_SeqFile_SpiralDiffusion(gx, gy, tr, n_shots, mg, ms, fA, n_slices,
reps, st, tPlot, tReport, b_values,
n_dirs, fov, Nx):
#%% --- 1 - Create new Sequence Object + Parameters
seq = Sequence()
# =========
# Parameters
# =========
i_raster_time = 100000
assert 1 / i_raster_time == seq.grad_raster_time, "Manualy inputed inverse raster time does not match the actual value."
# =========
# Code parameters
# =========
fatsat_enable = 0 # Fat saturation
kplot = 0
# =========
# Acquisition Parameters
# =========
TR = tr # Spin-Echo parameters - TR in [s]
n_TR = math.ceil(
TR * i_raster_time) # Spin-Echo parameters - number of points TR
bvalue = b_values # b-value [s/mm2]
nbvals = np.shape(bvalue)[0] # b-value parameters
ndirs = n_dirs # b-value parameters
Ny = Nx
slice_thickness = st # Acquisition Parameters in [m]
Nshots = n_shots
# =========
# Gradient Scaling
# =========
gscl = np.zeros(nbvals + 1)
gscl[1:] = np.sqrt(bvalue / np.max(bvalue))
gdir, nb0s = difunc.get_dirs(ndirs)
# =========
# Create system
# =========
system = Opts(max_grad=mg,
grad_unit='mT/m',
max_slew=ms,
slew_unit='T/m/s',
rf_ringdown_time=20e-6,
rf_dead_time=100e-6,
adc_dead_time=10e-6)
#%% --- 2 - Fat saturation
if fatsat_enable:
fatsat_str = "_fatsat"
b0 = 1.494
sat_ppm = -3.45
sat_freq = sat_ppm * 1e-6 * b0 * system.gamma
rf_fs, _, _ = make_gauss_pulse(flip_angle=110 * math.pi / 180,
system=system,
duration=8e-3,
bandwidth=abs(sat_freq),
freq_offset=sat_freq)
gz_fs = make_trapezoid(channel='z',
system=system,
delay=calc_duration(rf_fs),
area=1 / 1e-4)
else:
fatsat_str = ""
#%% --- 3 - Slice Selection
# =========
# Create 90 degree slice selection pulse and gradient
# =========
flip90 = fA * pi / 180
rf, gz, _ = make_sinc_pulse(flip_angle=flip90,
system=system,
duration=3e-3,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=4)
# =========
# Refocusing pulse with spoiling gradients
# =========
rf180, gz180, _ = make_sinc_pulse(flip_angle=math.pi,
system=system,
duration=5e-3,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=4)
rf180.phase_offset = math.pi / 2
gz_spoil = make_trapezoid(channel='z',
system=system,
area=6 / slice_thickness,
duration=3e-3)
#%% --- 4 - Gradients
# =========
# Spiral trajectory
# =========
G = gx + 1J * gy
#%% --- 5 - ADCs / Readouts
delta_k = 1 / fov
adc_samples = math.floor(
len(G) / 4
) * 4 - 2 # Apparently, on Siemens the number of samples needs to be divisible by 4...
adc = make_adc(num_samples=adc_samples,
system=system,
duration=adc_samples / i_raster_time)
# =========
# Pre-phasing gradients
# =========
pre_time = 1e-3
n_pre_time = math.ceil(pre_time * i_raster_time)
gz_reph = make_trapezoid(channel='z',
system=system,
area=-gz.area / 2,
duration=pre_time)
#%% --- 6 - Obtain TE and diffusion-weighting gradient waveform
# For S&T monopolar waveforms
# From an initial TE, check we satisfy all constraints -> otherwise increase TE.
# Once all constraints are okay -> check b-value, if it is lower than the target one -> increase TE
# Looks time-inefficient but it is fast enough to make it user-friendly.
# TODO: Re-scale the waveform to the exact b-value because increasing the TE might produce slightly higher ones.
# Calculate some times constant throughout the process
# We need to compute the exact time sequence. For the normal SE-MONO-EPI sequence micro second differences
# are not important, however, if we wanna import external gradients the allocated time for them needs to
# be the same, and thus exact timing is mandatory. With this in mind, we establish the following rounding rules:
# Duration of RFs + spoiling, and EPI time to the center of the k-space is always math.ceil().
# The time(gy) refers to the number of blips, thus we substract 0.5 since the number of lines is always even.
# The time(gx) refers to the time needed to read each line of the k-space. Thus, if Ny is even, it would take half of the lines plus another half.
n_duration_center = 0 # The spiral starts right in 0 -- or ADC_dead_time??
rf_center_with_delay = rf.delay + calc_rf_center(rf)[0]
n_rf90r = math.ceil((calc_duration(gz) - rf_center_with_delay + pre_time) /
seq.grad_raster_time)
n_rf180r = math.ceil((calc_duration(rf180) + 2 * calc_duration(gz_spoil)) /
2 / seq.grad_raster_time)
n_rf180l = math.floor(
(calc_duration(rf180) + 2 * calc_duration(gz_spoil)) / 2 /
seq.grad_raster_time)
# =========
# Find minimum TE considering the readout times.
# =========
n_TE = math.ceil(20e-3 / seq.grad_raster_time)
n_delay_te1 = -1
while n_delay_te1 <= 0:
n_TE = n_TE + 2
n_tINV = math.floor(n_TE / 2)
n_delay_te1 = n_tINV - n_rf90r - n_rf180l
# =========
# Find minimum TE for the target b-value
# =========
bvalue_tmp = 0
while bvalue_tmp < np.max(bvalue):
n_TE = n_TE + 2
n_tINV = math.floor(n_TE / 2)
n_delay_te1 = n_tINV - n_rf90r - n_rf180l
delay_te1 = n_delay_te1 / i_raster_time
n_delay_te2 = n_tINV - n_rf180r - n_duration_center
delay_te2 = n_delay_te2 / i_raster_time
# Waveform Ramp time
n_gdiff_rt = math.ceil(system.max_grad / system.max_slew /
seq.grad_raster_time)
# Select the shortest available time
n_gdiff_delta = min(n_delay_te1, n_delay_te2)
n_gdiff_Delta = n_delay_te1 + 2 * math.ceil(
calc_duration(gz_spoil) / seq.grad_raster_time) + math.ceil(
calc_duration(gz180) / seq.grad_raster_time)
gdiff = make_trapezoid(channel='x',
system=system,
amplitude=system.max_grad,
duration=n_gdiff_delta / i_raster_time)
# delta only corresponds to the rectangle.
n_gdiff_delta = n_gdiff_delta - 2 * n_gdiff_rt
bv = difunc.calc_bval(system.max_grad, n_gdiff_delta / i_raster_time,
n_gdiff_Delta / i_raster_time,
n_gdiff_rt / i_raster_time)
bvalue_tmp = bv * 1e-6
# =========
# Show final TE and b-values:
# =========
print("TE:", round(n_TE / i_raster_time * 1e3, 2), "ms")
for bv in range(1, nbvals + 1):
print(
round(
difunc.calc_bval(system.max_grad * gscl[bv], n_gdiff_delta /
i_raster_time, n_gdiff_Delta / i_raster_time,
n_gdiff_rt / i_raster_time) * 1e-6, 2),
"s/mm2")
TE = n_TE / i_raster_time
TR = n_TR / i_raster_time
#%% --- 7 - Crusher gradients
gx_crush = make_trapezoid(channel='x',
area=2 * Nx * delta_k,
system=system)
gz_crush = make_trapezoid(channel='z',
area=4 / slice_thickness,
system=system)
# TR delay - Takes everything into account
# Distance between the center of the RF90s must be TR
# The n_pre_time here is the time used to drive the Gx, and Gy spiral gradients to zero.
n_spiral_time = adc_samples
n_tr_per_slice = math.ceil(TR / n_slices * i_raster_time)
if fatsat_enable:
n_tr_delay = n_tr_per_slice - (n_TE - n_duration_center + n_spiral_time) \
- math.ceil(rf_center_with_delay * i_raster_time) \
- n_pre_time \
- math.ceil(calc_duration(gx_crush, gz_crush) * i_raster_time) \
- math.ceil(calc_duration(rf_fs, gz_fs) * i_raster_time)
else:
n_tr_delay = n_tr_per_slice - (n_TE - n_duration_center + n_spiral_time) \
- math.ceil(rf_center_with_delay * i_raster_time) \
- n_pre_time \
- math.ceil(calc_duration(gx_crush, gz_crush) * i_raster_time)
tr_delay = n_tr_delay / i_raster_time
#%% --- 8 - Checks
# =========
# Check TR delay time
# =========
assert n_tr_delay > 0, "Such parameter configuration needs longer TR."
# =========
# Delay time,
# =========
# Time between the gradient and the RF180. This time might be zero some times, although it is not normal.
if n_delay_te1 > n_delay_te2:
n_gap_te1 = n_delay_te1 - n_delay_te2
gap_te1 = n_gap_te1 / i_raster_time
gap_te2 = 0
else:
n_gap_te2 = n_delay_te2 - n_delay_te1
gap_te2 = n_gap_te2 / i_raster_time
gap_te1 = 0
#%% --- 9 - b-zero acquisition
for r in range(reps):
for d in range(nb0s):
for nshot in range(Nshots):
for s in range(n_slices):
# Fat saturation
if fatsat_enable:
seq.add_block(rf_fs, gz_fs)
# RF90
rf.freq_offset = gz.amplitude * slice_thickness * (
s - (n_slices - 1) / 2)
seq.add_block(rf, gz)
seq.add_block(gz_reph)
# Delay for RF180
seq.add_block(make_delay(delay_te1))
# RF180
seq.add_block(gz_spoil)
rf180.freq_offset = gz180.amplitude * slice_thickness * (
s - (n_slices - 1) / 2)
seq.add_block(rf180, gz180)
seq.add_block(gz_spoil)
# Delay for spiral
seq.add_block(make_delay(delay_te2))
# Read k-space
# Imaging Gradient waveforms
gx = make_arbitrary_grad(channel='x',
waveform=np.squeeze(
G[:, nshot].real),
system=system)
gy = make_arbitrary_grad(channel='y',
waveform=np.squeeze(
G[:, nshot].imag),
system=system)
seq.add_block(gx, gy, adc)
# Make the spiral finish in zero - I use pre_time because I know for sure it's long enough.
# Furthermore, this is after readout and TR is supposed to be long.
amp_x = [G[:, nshot].real[-1], 0]
amp_y = [G[:, nshot].imag[-1], 0]
gx_to_zero = make_extended_trapezoid(channel='x',
amplitudes=amp_x,
times=[0, pre_time],
system=system)
gy_to_zero = make_extended_trapezoid(channel='y',
amplitudes=amp_y,
times=[0, pre_time],
system=system)
seq.add_block(gx_to_zero, gy_to_zero)
seq.add_block(gx_crush, gz_crush)
# Wait TR
if tr_delay > 0:
seq.add_block(make_delay(tr_delay))
#%% --- 9 - DWI acquisition
for r in range(reps):
for bv in range(1, nbvals + 1):
for d in range(ndirs):
for nshot in range(Nshots):
for s in range(n_slices):
# Fat saturation
if fatsat_enable:
seq.add_block(rf_fs, gz_fs)
# RF90
rf.freq_offset = gz.amplitude * slice_thickness * (
s - (n_slices - 1) / 2)
seq.add_block(rf, gz)
seq.add_block(gz_reph)
# Diffusion-weighting gradient
gdiffx = make_trapezoid(channel='x',
system=system,
amplitude=system.max_grad *
gscl[bv] * gdir[d, 0],
duration=calc_duration(gdiff))
gdiffy = make_trapezoid(channel='y',
system=system,
amplitude=system.max_grad *
gscl[bv] * gdir[d, 1],
duration=calc_duration(gdiff))
gdiffz = make_trapezoid(channel='z',
system=system,
amplitude=system.max_grad *
gscl[bv] * gdir[d, 2],
duration=calc_duration(gdiff))
seq.add_block(gdiffx, gdiffy, gdiffz)
# Delay for RF180
seq.add_block(make_delay(gap_te1))
# RF180
seq.add_block(gz_spoil)
rf180.freq_offset = gz180.amplitude * slice_thickness * (
s - (n_slices - 1) / 2)
seq.add_block(rf180, gz180)
seq.add_block(gz_spoil)
# Diffusion-weighting gradient
seq.add_block(gdiffx, gdiffy, gdiffz)
# Delay for spiral
seq.add_block(make_delay(gap_te2))
# Read k-space
# Imaging Gradient waveforms
gx = make_arbitrary_grad(channel='x',
waveform=np.squeeze(
G[:, nshot].real),
system=system)
gy = make_arbitrary_grad(channel='y',
waveform=np.squeeze(
G[:, nshot].imag),
system=system)
seq.add_block(gx, gy, adc)
# Make the spiral finish in zero - I use pre_time because I know for sure it's long enough.
# Furthermore, this is after readout and TR is supposed to be long.
amp_x = [G[:, nshot].real[-1], 0]
amp_y = [G[:, nshot].imag[-1], 0]
gx_to_zero = make_extended_trapezoid(
channel='x',
amplitudes=amp_x,
times=[0, pre_time],
system=system)
gy_to_zero = make_extended_trapezoid(
channel='y',
amplitudes=amp_y,
times=[0, pre_time],
system=system)
seq.add_block(gx_to_zero, gy_to_zero)
seq.add_block(gx_crush, gz_crush)
# Wait TR
if tr_delay > 0:
seq.add_block(make_delay(tr_delay))
if tPlot:
seq.plot()
if tReport:
print(seq.test_report())
seq.check_timing()
return seq, TE, TR, fatsat_str
def generate_SeqFile_EPIDiffusion(FOV, nx, ny, ns, mg, ms, reps, st, tr, fA,
b_values, n_dirs, partialFourier, tPlot,
tReport):
#%% --- 1 - Create new Sequence Object + Parameters
seq = Sequence()
# =========
# Parameters
# =========
i_raster_time = 100000
assert 1 / i_raster_time == seq.grad_raster_time, "Manualy inputed inverse raster time does not match the actual value."
# =========
# Code parameters
# =========
fatsat_enable = 0 # Fat saturation
kplot = 0
# =========
# Acquisition Parameters
# =========
fov = FOV
Nx = nx
Ny = ny
n_slices = ns
TR = tr # Spin-Echo parameters - TR in [s]
n_TR = math.ceil(
TR * i_raster_time) # Spin-Echo parameters - number of points TR
bvalue = b_values # b-value [s/mm2]
nbvals = np.shape(bvalue)[0] # b-value parameters
ndirs = n_dirs # b-value parameters
slice_thickness = st # Acquisition Parameters in [m]
# =========
# Partial Fourier
# =========
pF = partialFourier
Nyeff = int(pF * Ny) # Number of Ny samples acquired
if pF is not 1:
pF_str = "_" + str(pF) + "pF"
else:
pF_str = ""
# =========
# Gradient Scaling
# =========
gscl = np.zeros(nbvals + 1)
gscl[1:] = np.sqrt(bvalue / np.max(bvalue))
gdir, nb0s = difunc.get_dirs(ndirs)
# =========
# Create system
# =========
system = Opts(max_grad=mg,
grad_unit='mT/m',
max_slew=ms,
slew_unit='T/m/s',
rf_ringdown_time=20e-6,
rf_dead_time=100e-6,
adc_dead_time=10e-6)
#%% --- 2 - Fat saturation
if fatsat_enable:
fatsat_str = "_fatsat"
b0 = 1.494
sat_ppm = -3.45
sat_freq = sat_ppm * 1e-6 * b0 * system.gamma
rf_fs, _, _ = make_gauss_pulse(flip_angle=110 * math.pi / 180,
system=system,
duration=8e-3,
bandwidth=abs(sat_freq),
freq_offset=sat_freq)
gz_fs = make_trapezoid(channel='z',
system=system,
delay=calc_duration(rf_fs),
area=1 / 1e-4)
else:
fatsat_str = ""
#%% --- 3 - Slice Selection
# =========
# Create 90 degree slice selection pulse and gradient
# =========
flip90 = fA * pi / 180
rf, gz, _ = make_sinc_pulse(flip_angle=flip90,
system=system,
duration=3e-3,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=4)
# =========
# Refocusing pulse with spoiling gradients
# =========
rf180, gz180, _ = make_sinc_pulse(flip_angle=math.pi,
system=system,
duration=5e-3,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=4)
rf180.phase_offset = math.pi / 2
gz_spoil = make_trapezoid(channel='z',
system=system,
area=6 / slice_thickness,
duration=3e-3)
#%% --- 4 - Define other gradients and ADC events
delta_k = 1 / fov
k_width = Nx * delta_k
dwell_time = seq.grad_raster_time # Full receiver bandwith
readout_time = Nx * dwell_time # T_acq (acquisition time)
flat_time = math.ceil(
readout_time / seq.grad_raster_time) * seq.grad_raster_time
gx = make_trapezoid(channel='x',
system=system,
amplitude=k_width / readout_time,
flat_time=flat_time)
adc = make_adc(num_samples=Nx,
duration=readout_time,
delay=gx.rise_time + flat_time / 2 -
(readout_time - dwell_time) / 2)
# =========
# Pre-phasing gradients
# =========
pre_time = 1e-3
gx_pre = make_trapezoid(channel='x',
system=system,
area=-gx.area / 2,
duration=pre_time)
gz_reph = make_trapezoid(channel='z',
system=system,
area=-gz.area / 2,
duration=pre_time)
gy_pre = make_trapezoid(
channel='y',
system=system,
area=-(Ny / 2 - 0.5 - (Ny - Nyeff)) * delta_k,
duration=pre_time
) # Es -0.5 y no +0.5 porque hay que pensar en areas, no en rayas!
# =========
# Phase blip in shortest possible time
# =========
gy = make_trapezoid(channel='y', system=system, area=delta_k)
dur = math.ceil(
calc_duration(gy) / seq.grad_raster_time) * seq.grad_raster_time
#%% --- 5 - Obtain TE and diffusion-weighting gradient waveform
# =========
# Calculate some times constant throughout the process
# =========
duration_center = math.ceil(
(calc_duration(gx) * (Ny / 2 + 0.5 -
(Ny - Nyeff)) + calc_duration(gy) *
(Ny / 2 - 0.5 -
(Ny - Nyeff))) / seq.grad_raster_time) * seq.grad_raster_time
rf_center_with_delay = rf.delay + calc_rf_center(rf)[0]
rf180_center_with_delay = rf180.delay + calc_rf_center(rf180)[0]
# =========
# Find minimum TE considering the readout times.
# =========
TE = 40e-3 # [s]
delay_te2 = -1
while delay_te2 <= 0:
TE = TE + 0.02e-3 # [ms]
delay_te2 = math.ceil((TE / 2 - calc_duration(rf180) + rf180_center_with_delay - calc_duration(gz_spoil) - \
calc_duration(gx_pre,
gy_pre) - duration_center) / seq.grad_raster_time) * seq.grad_raster_time
# =========
# Find minimum TE for the target b-value
# =========
bvalue_tmp = 0
while bvalue_tmp < np.max(bvalue):
TE = TE + 2 * seq.grad_raster_time # [ms]
delay_te1 = math.ceil((TE / 2 - calc_duration(gz) + rf_center_with_delay - pre_time - calc_duration(gz_spoil) - \
rf180_center_with_delay) / seq.grad_raster_time) * seq.grad_raster_time
delay_te2 = math.ceil((TE / 2 - calc_duration(rf180) + rf180_center_with_delay - calc_duration(gz_spoil) - \
calc_duration(gx_pre,
gy_pre) - duration_center) / seq.grad_raster_time) * seq.grad_raster_time
# Waveform Ramp time
gdiff_rt = math.ceil(system.max_grad / system.max_slew /
seq.grad_raster_time) * seq.grad_raster_time
# Select the shortest available time
gdiff_delta = min(delay_te1, delay_te2)
gdiff_Delta = math.ceil(
(delay_te1 + 2 * calc_duration(gz_spoil) + calc_duration(gz180)) /
seq.grad_raster_time) * seq.grad_raster_time
gdiff = make_trapezoid(channel='x',
system=system,
amplitude=system.max_grad,
duration=gdiff_delta)
# delta only corresponds to the rectangle.
gdiff_delta = math.ceil((gdiff_delta - 2 * gdiff_rt) /
seq.grad_raster_time) * seq.grad_raster_time
bv = difunc.calc_bval(system.max_grad, gdiff_delta, gdiff_Delta,
gdiff_rt)
bvalue_tmp = bv * 1e-6
# =========
# Show final TE and b-values:
# =========
print("TE:", round(TE * 1e3, 2), "ms")
for bv in range(1, nbvals + 1):
print(
round(
difunc.calc_bval(system.max_grad * gscl[bv], gdiff_delta,
gdiff_Delta, gdiff_rt) * 1e-6, 2), "s/mm2")
# =========
# Crusher gradients
# =========
gx_crush = make_trapezoid(channel='x',
area=2 * Nx * delta_k,
system=system)
gz_crush = make_trapezoid(channel='z',
area=4 / slice_thickness,
system=system)
#%% --- 6 - Delays
# =========
# TR delay - Takes everything into account
# EPI reading time:
# Distance between the center of the RF90s must be TR
# =========
EPI_time = calc_duration(gx) * Nyeff + calc_duration(gy) * (Nyeff - 1)
if fatsat_enable:
tr_delay = math.floor(
(TR - (TE - duration_center + EPI_time) - rf_center_with_delay - calc_duration(gx_crush, gz_crush) \
- calc_duration(rf_fs, gz_fs)) \
/ seq.grad_raster_time) * seq.grad_raster_time
else:
tr_delay = math.floor(
(TR - (TE - duration_center + EPI_time) - rf_center_with_delay - calc_duration(gx_crush, gz_crush)) \
/ seq.grad_raster_time) * seq.grad_raster_time
# =========
# Check TR delay time
# =========
assert tr_delay > 0, "Such parameter configuration needs longer TR."
# =========
# Delay time
# =========
# =========
# Time between the gradient and the RF180. This time might be zero some times, although it is not normal.
# =========
gap_te1 = math.ceil((delay_te1 - calc_duration(gdiff)) /
seq.grad_raster_time) * seq.grad_raster_time
# =========
# Time between the gradient and the locate k-space gradients.
# =========
gap_te2 = math.ceil((delay_te2 - calc_duration(gdiff)) /
seq.grad_raster_time) * seq.grad_raster_time
#%% --- 9 - b-zero acquisition
for d in range(nb0s):
for s in range(n_slices):
# Fat saturation
if fatsat_enable:
seq.add_block(rf_fs, gz_fs)
# RF90
rf.freq_offset = gz.amplitude * slice_thickness * (
s - (n_slices - 1) / 2)
seq.add_block(rf, gz)
seq.add_block(gz_reph)
# Delay for RF180
seq.add_block(make_delay(delay_te1))
# RF180
seq.add_block(gz_spoil)
rf180.freq_offset = gz180.amplitude * slice_thickness * (
s - (n_slices - 1) / 2)
seq.add_block(rf180, gz180)
seq.add_block(gz_spoil)
# Delay for EPI
seq.add_block(make_delay(delay_te2))
# Locate k-space
seq.add_block(gx_pre, gy_pre)
for i in range(Nyeff):
seq.add_block(gx, adc) # Read one line of k-space
if i is not Nyeff - 1:
seq.add_block(gy) # Phase blip
gx.amplitude = -gx.amplitude # Reverse polarity of read gradient
seq.add_block(gx_crush, gz_crush)
# Wait TR
if tr_delay > 0:
seq.add_block(make_delay(tr_delay))
#%% --- 10 - DWI acquisition
for bv in range(1, nbvals + 1):
for d in range(ndirs):
for s in range(n_slices):
# Fat saturation
if fatsat_enable:
seq.add_block(rf_fs, gz_fs)
# RF90
rf.freq_offset = gz.amplitude * slice_thickness * (
s - (n_slices - 1) / 2)
seq.add_block(rf, gz)
seq.add_block(gz_reph)
# Diffusion-weighting gradient
gdiffx = make_trapezoid(channel='x',
system=system,
amplitude=system.max_grad * gscl[bv] *
gdir[d, 0],
duration=calc_duration(gdiff))
gdiffy = make_trapezoid(channel='y',
system=system,
amplitude=system.max_grad * gscl[bv] *
gdir[d, 1],
duration=calc_duration(gdiff))
gdiffz = make_trapezoid(channel='z',
system=system,
amplitude=system.max_grad * gscl[bv] *
gdir[d, 2],
duration=calc_duration(gdiff))
seq.add_block(gdiffx, gdiffy, gdiffz)
# Delay for RF180
seq.add_block(make_delay(gap_te1))
# RF180
seq.add_block(gz_spoil)
rf180.freq_offset = gz180.amplitude * slice_thickness * (
s - (n_slices - 1) / 2)
seq.add_block(rf180, gz180)
seq.add_block(gz_spoil)
# Diffusion-weighting gradient
seq.add_block(gdiffx, gdiffy, gdiffz)
# Delay for EPI
seq.add_block(make_delay(gap_te2))
# Locate k-space
seq.add_block(gx_pre, gy_pre)
for i in range(Nyeff):
seq.add_block(gx, adc) # Read one line of k-space
if i is not Nyeff - 1:
seq.add_block(gy) # Phase blip
gx.amplitude = -gx.amplitude # Reverse polarity of read gradient
seq.add_block(gx_crush, gz_crush)
# Wait TR
if tr_delay > 0:
seq.add_block(make_delay(tr_delay))
if tPlot:
seq.plot()
if tReport:
print(seq.test_report())
seq.check_timing()
return seq, TE, TR, fatsat_str
def generate_GIRF_SeqFile(iT, tr, te, Npuls, mg, ms, grt, fA, n_slices, reps,
sliceT, tPre, tPos, tX, tY, tPlot, tReport,
rf_offset, testPRE_POST, dummy):
# %% ===========================================================================
# %% --- 1 - Instantiation and gradient limits ---
system = Opts(max_grad=mg,
grad_unit='mT/m',
max_slew=ms,
slew_unit='T/m/s',
rf_ringdown_time=20e-6,
rf_dead_time=100e-6,
adc_dead_time=10e-6)
seq = Sequence(system)
# I need to check the manually inputed inverse raster time and the actual value are the same.
i_raster_time = 100000
assert 1 / i_raster_time == seq.grad_raster_time, "Manualy inputed inverse raster time does not match the actual value."
slice_thickness, slice_gap, TR, TE, rf_offset_z = sliceT, 15e-3, tr, te, 0
delta_z = n_slices * slice_thickness
z = np.linspace((-delta_z / 2), (delta_z / 2), n_slices) + rf_offset_z
x = np.linspace((-delta_z / 2), (delta_z / 2), n_slices) + rf_offset
y = np.linspace((-delta_z / 2), (delta_z / 2), n_slices) + rf_offset
# %% --- 2 - Gradients
G = iT
G_zero = np.zeros(len(iT[:, 0]))
G_pre = np.zeros(math.floor(tPre * i_raster_time))
G_pos = np.zeros(math.floor(tPos * i_raster_time))
# %% --- 3 - Slice Selection
# =========
# Create 90 degree slice selection pulse and gradient
# =========
# RF90
flip90 = fA * pi / 180
rf, gz, gzr = make_sinc_pulse(flip_angle=flip90,
duration=3e-3,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=4,
system=system)
rfx, gxRF, gxr = make_sinc_pulse_channel(channel='x',
flip_angle=flip90,
duration=3e-3,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=4,
system=system)
rfy, gyRF, gyr = make_sinc_pulse_channel(channel='y',
flip_angle=flip90,
duration=3e-3,
slice_thickness=slice_thickness,
apodization=0.5,
time_bw_product=4,
system=system)
# %% --- 4 - ADCs / Readouts
# timeStart = -5e-3
# timeEnd = 63e-3
# n_timeStart = math.ceil(timeStart * i_raster_time)
# n_timeEnd = math.ceil(timeEnd * i_raster_time)
# adc_samples = n_timeEnd - n_timeStart
adc_samples = math.floor(len(G) / 4) * 4 - 1
adc_samples_pre = math.floor(len(G_pre) / 4) * 4 - 2
adc_samples_pos = math.floor(len(G_pos) / 4) * 4 - 100
adc = make_adc(num_samples=adc_samples,
duration=adc_samples / i_raster_time,
system=system)
adc_pre = make_adc(num_samples=adc_samples_pre,
duration=adc_samples_pre / i_raster_time,
system=system)
adc_pos = make_adc(num_samples=adc_samples_pos,
duration=adc_samples_pos / i_raster_time,
system=system)
# %% --- 5 - Spoilers
pre_time = 8e-4
n_pre_time = math.ceil(pre_time * i_raster_time)
gz_rephz = make_trapezoid(channel='z',
area=-gz.area / 2,
duration=2e-3,
system=system)
gz_spoil = make_trapezoid(channel='z',
area=-gz.area / 2,
duration=3 * n_pre_time / i_raster_time,
system=system)
gx_rephz = make_trapezoid(channel='x',
area=-gxRF.area / 2,
duration=2e-3,
system=system)
gx_spoil = make_trapezoid(channel='x',
area=-gxRF.area / 2,
duration=3 * n_pre_time / i_raster_time,
system=system)
gy_rephz = make_trapezoid(channel='y',
area=-gyRF.area / 2,
duration=2e-3,
system=system)
gy_spoil = make_trapezoid(channel='y',
area=-gyRF.area / 2,
duration=3 * n_pre_time / i_raster_time,
system=system)
aux_gx = make_arbitrary_grad(channel='x',
waveform=np.squeeze(G[:, 0]),
system=system)
aux_gy = make_arbitrary_grad(channel='y',
waveform=np.squeeze(G[:, 0]),
system=system)
# %% --- 6 - Calculate timing/Delays
# for z
# delay pre ADC
n_TE = math.ceil(TE * i_raster_time)
n_dur_gz_rephz = math.ceil(calc_duration(gz_rephz) * i_raster_time)
n_dur_rf = math.ceil(calc_duration(rf) * i_raster_time)
n_del_preGRS = n_TE - (n_dur_gz_rephz + math.ceil(n_dur_rf / 2)
) # Time before input in points
del_preGRS = n_del_preGRS / i_raster_time
delay_preGRS = make_delay(del_preGRS)
# delay pos ADC
n_TR = math.ceil(TR * i_raster_time)
n_dur_aux_gx = math.ceil(calc_duration(aux_gx) * i_raster_time)
n_dur_adc = math.ceil(calc_duration(adc) * i_raster_time)
n_dur_gz_spoil = math.ceil(calc_duration(gx_spoil) * i_raster_time)
n_delTR = n_TR - (n_dur_gz_rephz + n_dur_rf + n_dur_aux_gx + n_dur_gz_spoil
) # Time after input to the system in points
# n_delTR = n_TR - (n_TE + n_dur_adc + n_dur_gz_spoil) # Time after input to the system in points
delTR = n_delTR / i_raster_time
delayTR = make_delay(delTR)
# for x
# delay pre ADC
n_TE = math.ceil(TE * i_raster_time)
n_dur_gx_rephz = math.ceil(calc_duration(gx_rephz) * i_raster_time)
n_dur_rfx = math.ceil(calc_duration(rfx) * i_raster_time)
n_del_preGRS_x = n_TE - (n_dur_gx_rephz + math.ceil(n_dur_rfx / 2)
) # Time before input in points
del_preGRS_x = n_del_preGRS_x / i_raster_time
delay_preGRS_x = make_delay(del_preGRS_x)
# delay pos ADC
n_TR = math.ceil(TR * i_raster_time)
n_dur_gx_spoil = math.ceil(calc_duration(gx_spoil) * i_raster_time)
n_dur_adc_pre = math.ceil(calc_duration(adc_pre) * i_raster_time)
n_dur_adc_pos = math.ceil(calc_duration(adc_pos) * i_raster_time)
n_delTR_x = n_TR - (
n_dur_gx_rephz + math.ceil(n_dur_rfx / 2) + n_dur_adc_pre +
n_dur_aux_gx + n_dur_adc_pos + n_dur_gx_spoil
) # Time after input to the system in points
# n_delTR_x = n_TR - (n_TE + n_dur_adc + n_dur_gx_spoil) # Time after input to the system in points
delTR_x = n_delTR_x / i_raster_time
delayTR_x = make_delay(delTR_x)
# for y
# delay pre ADC
n_TE = math.ceil(TE * i_raster_time)
n_dur_gy_rephz = math.ceil(calc_duration(gy_rephz) * i_raster_time)
n_dur_rfy = math.ceil(calc_duration(rfy) * i_raster_time)
n_del_preGRS_y = n_TE - (n_dur_gy_rephz + math.ceil(n_dur_rfy / 2)
) # Time before input in points
del_preGRS_y = n_del_preGRS_y / i_raster_time
delay_preGRS_y = make_delay(del_preGRS_y)
# delay pos ADC
n_TR = math.ceil(TR * i_raster_time)
n_dur_aux_gy = math.ceil(calc_duration(aux_gy) * i_raster_time)
n_dur_gy_spoil = math.ceil(calc_duration(gy_spoil) * i_raster_time)
n_delTR_y = n_TR - (n_dur_gy_rephz + math.ceil(n_dur_rfy / 2) +
n_dur_adc_pre + n_dur_aux_gy + n_dur_adc_pos +
n_dur_gy_spoil)
# n_delTR_y = n_TR - (n_TE + n_dur_adc + n_dur_gy_spoil) # Time after input to the system in points
delTR_y = n_delTR_y / i_raster_time
delayTR_y = make_delay(delTR_y)
# %% --- 7 - Define sequence for measuring k_trajectory - blocks/Readouts
if dummy:
# for x and y rf pulse
freq_offset_gx = gxRF.amplitude * x[0]
rfx.freq_offset = freq_offset_gx
freq_offset_gy = gyRF.amplitude * y[0]
rfy.freq_offset = freq_offset_gy
# RF90
seq.add_block(rfx, gxRF)
seq.add_block(gx_rephz)
# Delay for spiral
seq.add_block(delay_preGRS_x)
# Read k-space - Imaging Gradient waveforms
gx_zero = make_arbitrary_grad(channel='x',
waveform=np.squeeze(G_zero),
system=system)
seq.add_block(adc, gx_zero)
# Gradients Spoils
seq.add_block(gx_spoil)
# Delay to TR
seq.add_block(delayTR_x)
if tX:
for ns in range(Npuls):
for r in range(reps):
for s in range(n_slices):
# for x and y rf pulse
freq_offset_gx = gxRF.amplitude * x[s]
rfx.freq_offset = freq_offset_gx
freq_offset_gy = gyRF.amplitude * y[s]
rfy.freq_offset = freq_offset_gy
# %% --- for x-axis no gradient --- %% #
# RF90
seq.add_block(rfx, gxRF)
seq.add_block(gx_rephz)
# Delay for spiral
seq.add_block(delay_preGRS_x)
# Read - pre GIRF
if testPRE_POST:
gx_pre = make_arbitrary_grad(
channel='x',
waveform=np.squeeze(G_pre),
system=system)
seq.add_block(adc_pre, gx_pre)
# Read k-space - Imaging Gradient waveforms
gx_zero = make_arbitrary_grad(channel='x',
waveform=np.squeeze(G_zero),
system=system)
seq.add_block(adc, gx_zero)
# Read - pos GIRF
if testPRE_POST:
gx_pos = make_arbitrary_grad(
channel='x',
waveform=np.squeeze(G_pos),
system=system)
seq.add_block(adc_pos, gx_pos)
# Gradients Spoils
seq.add_block(gx_spoil)
# Delay to TR
seq.add_block(delayTR_x)
# %% --- for x-axis w/ gradient --- %% #
# RF90
seq.add_block(rfx, gxRF)
seq.add_block(gx_rephz)
# Delay for spiral
seq.add_block(delay_preGRS_x)
# Read - pre GIRF
if testPRE_POST:
gx_pre = make_arbitrary_grad(
channel='x',
waveform=np.squeeze(G_pre),
system=system)
seq.add_block(adc_pre, gx_pre)
# Read k-space - Imaging Gradient waveforms
gx = make_arbitrary_grad(channel='x',
waveform=np.squeeze(G[:, ns]),
system=system)
seq.add_block(gx, adc)
# Read - pos GIRF
if testPRE_POST:
gx_pos = make_arbitrary_grad(
channel='x',
waveform=np.squeeze(G_pos),
system=system)
seq.add_block(adc_pos, gx_pos)
# Gradients Spoils
seq.add_block(gx_spoil)
# Delay to TR
seq.add_block(delayTR_x)
if tY:
for ns in range(Npuls):
for r in range(reps):
for s in range(n_slices):
# %% --- for y-axis no gradient --- %% #
seq.add_block(rfy, gyRF)
seq.add_block(gy_rephz)
# Delay for spiral
seq.add_block(delay_preGRS_y)
# Read - pre GIRF
if testPRE_POST:
gy_pre = make_arbitrary_grad(
channel='y',
waveform=np.squeeze(G_pre),
system=system)
seq.add_block(adc_pre, gy_pre)
# Read k-space - Imaging Gradient waveforms
gy_zero = make_arbitrary_grad(channel='y',
waveform=np.squeeze(G_zero),
system=system)
seq.add_block(gy_zero, adc)
# Read - pos GIRF
if testPRE_POST:
gy_pos = make_arbitrary_grad(
channel='y',
waveform=np.squeeze(G_pos),
system=system)
seq.add_block(adc_pos, gy_pos)
# Gradients Spoils
seq.add_block(gy_spoil)
# Delay to TR
seq.add_block(delayTR_y)
# %% --- for y-axis w/ gradient --- %% #
# RF90
seq.add_block(rfy, gyRF)
seq.add_block(gy_rephz)
# Delay for spiral
seq.add_block(delay_preGRS_y)
# Read - pre GIRF
if testPRE_POST:
gy_pre = make_arbitrary_grad(
channel='y',
waveform=np.squeeze(G_pre),
system=system)
seq.add_block(adc_pre, gy_pre)
# Read k-space - Imaging Gradient waveforms
gy = make_arbitrary_grad(channel='y',
waveform=np.squeeze(G[:, ns]),
system=system)
seq.add_block(gy, adc)
# Read - pos GIRF
if testPRE_POST:
gy_pos = make_arbitrary_grad(
channel='y',
waveform=np.squeeze(G_pos),
system=system)
seq.add_block(adc_pos, gy_pos)
# Gradients Spoils
seq.add_block(gy_spoil)
# Delay to TR
seq.add_block(delayTR_y)
# %% --- 8 - Plot ADCs, GX, GY, GZ, RFpulse, RFphase
# # plt.figure()
if tPlot:
seq.plot()
if tReport:
print(seq.test_report())
seq.check_timing()
return seq