def test_get_plot(self):
# save a score_list
savedir_base = '.tmp'
exp_dict = {'model':{'name':'mlp', 'n_layers':30},
'dataset':'mnist', 'batch_size':1}
score_list = [{'epoch': 0, 'acc':0.5}, {'epoch': 1, 'acc':0.9}]
hu.save_pkl(os.path.join(savedir_base, hu.hash_dict(exp_dict),
'score_list.pkl'), score_list)
hu.save_json(os.path.join(savedir_base, hu.hash_dict(exp_dict),
'exp_dict.json'), exp_dict)
# check if score_list can be loaded and viewed in pandas
exp_list = hu.get_exp_list(savedir_base=savedir_base)
fig, axis = hr.get_plot(exp_list,
savedir_base=savedir_base,
filterby_list=[({'model':{'name':'mlp'}},
{'style':{'color':'red'}})],
x_metric='epoch',
y_metric='acc')
# fig, axis = hr.get_plot(exp_list,
# savedir_base=savedir_base,
# x_metric='epoch',
# y_metric='acc',
# mode='pretty_plot')
fig, axis = hr.get_plot(exp_list,
savedir_base=savedir_base,
x_metric='epoch',
y_metric='acc',
mode='bar')
fig.savefig(os.path.join('.tmp',
'test.png'))
shutil.rmtree('.tmp')
def test_get_score_lists():
# save a score_list
savedir_base = ".tmp"
exp_dict = {
"model": {
"name": "mlp",
"n_layers": 30
},
"dataset": "mnist",
"batch_size": 1
}
score_list = [{"epoch": 0, "acc": 0.5}, {"epoch": 0, "acc": 0.9}]
hu.save_pkl(
os.path.join(savedir_base, hu.hash_dict(exp_dict), "score_list.pkl"),
score_list)
hu.save_json(
os.path.join(savedir_base, hu.hash_dict(exp_dict), "exp_dict.json"),
exp_dict)
# check if score_list can be loaded and viewed in pandas
exp_list = hu.get_exp_list(savedir_base=savedir_base)
score_lists = hr.get_score_lists(exp_list, savedir_base=savedir_base)
assert score_lists[0][0]["acc"] == 0.5
assert score_lists[0][1]["acc"] == 0.9
shutil.rmtree(savedir_base)
def test_zipdir(self):
# save a score_list
savedir_base = ".tmp"
exp_dict = {
"model": {
"name": "mlp",
"n_layers": 30
},
"dataset": "mnist",
"batch_size": 1
}
score_list = [{"epoch": 0, "acc": 0.5}, {"epoch": 0, "acc": 0.9}]
hu.save_pkl(
os.path.join(savedir_base, hu.hash_dict(exp_dict),
"score_list.pkl"), score_list)
hu.save_json(
os.path.join(savedir_base, hu.hash_dict(exp_dict),
"exp_dict.json"), exp_dict)
# check if score_list can be loaded and viewed in pandas
exp_list = hr.get_exp_list(savedir_base=savedir_base)
score_lists = hr.get_score_lists(exp_list, savedir_base=savedir_base)
assert score_lists[0][0]["acc"] == 0.5
assert score_lists[0][1]["acc"] == 0.9
from haven import haven_dropbox as hd
hd.zipdir([hu.hash_dict(exp_dict) for exp_dict in exp_list],
savedir_base,
src_fname=".tmp/results.zip")
shutil.rmtree(savedir_base)
def test_get_score_df(self):
# save a score_list
savedir_base = '.tmp'
exp_dict = {'model':{'name':'mlp', 'n_layers':30},
'dataset':'mnist', 'batch_size':1}
exp_dict2 = {'model':{'name':'mlp2', 'n_layers':30},
'dataset':'mnist', 'batch_size':1}
score_list = [{'epoch': 0, 'acc':0.5}, {'epoch': 0, 'acc':0.9}]
hu.save_pkl(os.path.join(savedir_base, hu.hash_dict(exp_dict),
'score_list.pkl'), score_list)
hu.save_json(os.path.join(savedir_base, hu.hash_dict(exp_dict),
'exp_dict.json'), exp_dict)
hu.save_json(os.path.join(savedir_base, hu.hash_dict(exp_dict2),
'exp_dict.json'), exp_dict)
# check if score_list can be loaded and viewed in pandas
exp_list = hu.get_exp_list(savedir_base=savedir_base)
score_df = hr.get_score_df(exp_list, savedir_base=savedir_base)
assert(np.array(score_df['dataset'])[0].strip("'") == 'mnist')
shutil.rmtree('.tmp')
def test_get_score_lists(self):
# save a score_list
savedir_base = '.tmp'
exp_dict = {
'model': {
'name': 'mlp',
'n_layers': 30
},
'dataset': 'mnist',
'batch_size': 1
}
score_list = [{'epoch': 0, 'acc': 0.5}, {'epoch': 0, 'acc': 0.9}]
hu.save_pkl(
os.path.join(savedir_base, hu.hash_dict(exp_dict),
'score_list.pkl'), score_list)
hu.save_json(
os.path.join(savedir_base, hu.hash_dict(exp_dict),
'exp_dict.json'), exp_dict)
# check if score_list can be loaded and viewed in pandas
exp_list = hr.get_exp_list(savedir_base=savedir_base)
score_lists = hr.get_score_lists(exp_list, savedir_base=savedir_base)
assert (score_lists[0][0]['acc'] == 0.5)
assert (score_lists[0][1]['acc'] == 0.9)
shutil.rmtree(savedir_base)
def compute_fstar(self, model_func, loss_function, fname):
if os.path.exists(fname):
fstar_list = hu.load_pkl(fname)
else:
fstar_list = np.ones(len(self)) * -1
for i in range(len(self)):
batch = self[i]
images, labels = batch['images'][None].cuda(), batch['labels'][None].cuda()
model = model_func()
opt = torch.optim.Adam(model.parameters())
for j in range(10000):
opt.zero_grad()
closure = lambda : loss_function(model, images, labels, backwards=True)
loss = opt.step(closure).item()
grad_current = sps.get_grad_list(model.parameters())
grad_norm = sps.compute_grad_norm(grad_current)
if np.isnan(loss):
print('nan')
# print(i, loss)
if grad_norm < 1e-6:
break
if j > 0 and abs(loss_old - loss) < 1e-6:
break
loss_old = loss
print("%d/%d - converged:%d - %.6f"% (i, len(self), j, loss))
fstar_list[i] = loss
hu.save_pkl(fname, fstar_list)
self.fstar_list = fstar_list
def __init__(
self,
split,
datadir,
exp_dict,
):
self.exp_dict = exp_dict
self.datadir = datadir
self.split = split
self.n_classes = 5
self.img_path = os.path.join(datadir, 'OpenSourceDCMs')
self.lung_path = os.path.join(datadir, 'LungMasks')
self.tgt_path = os.path.join(datadir, 'InfectionMasks')
self.img_tgt_dict = []
for tgt_name in os.listdir(self.tgt_path):
lung_name = os.path.join(self.lung_path, tgt_name)
scan_id, slice_id = tgt_name.split('_')
slice_id = str(int(slice_id.replace('z', '').replace('.png',
''))).zfill(4)
img_name = [
f for f in os.listdir(
os.path.join(self.img_path, 'DCM' + scan_id))
if 's%s' % slice_id in f
][0]
img_name = os.path.join('DCM' + scan_id, img_name)
self.img_tgt_dict += [{
'img': img_name,
'tgt': tgt_name,
'lung': lung_name
}]
# get label_meta
fname = os.path.join(datadir, 'tmp', 'labels_array.pkl')
if not os.path.exists(fname):
labels_array = np.zeros((len(self.img_tgt_dict), 3))
for i, idict in enumerate(tqdm.tqdm(self.img_tgt_dict)):
img_name, tgt_name = idict['img'], idict['tgt']
mask = np.array(
Image.open(os.path.join(self.tgt_path, tgt_name)))
uniques = np.unique(mask)
if 0 in uniques:
labels_array[i, 0] = 1
if 127 in uniques:
labels_array[i, 1] = 1
if 255 in uniques:
labels_array[i, 2] = 1
hu.save_pkl(fname, labels_array)
labels_array = hu.load_pkl(fname)
# self.np.where(labels_array[:,1:].max(axis=1))
ind_list = np.where(labels_array[:, 1:].max(axis=1))[0]
self.img_tgt_dict = np.array(self.img_tgt_dict)[ind_list]
if split == 'train':
self.img_tgt_dict = self.img_tgt_dict[:300]
elif split == 'val':
self.img_tgt_dict = self.img_tgt_dict[300:]
def test_get_plot():
# save a score_list
savedir_base = ".tmp"
exp_dict = {
"model": {
"name": "mlp",
"n_layers": 30
},
"dataset": "mnist",
"batch_size": 1
}
score_list = [{"epoch": 0, "acc": 0.5}, {"epoch": 1, "acc": 0.9}]
hu.save_pkl(
os.path.join(savedir_base, hu.hash_dict(exp_dict), "score_list.pkl"),
score_list)
hu.save_json(
os.path.join(savedir_base, hu.hash_dict(exp_dict), "exp_dict.json"),
exp_dict)
# check if score_list can be loaded and viewed in pandas
exp_list = hu.get_exp_list(savedir_base=savedir_base)
fig, axis = hr.get_plot(
exp_list,
savedir_base=savedir_base,
filterby_list=[({
"model": {
"name": "mlp"
}
}, {
"style": {
"color": "red"
}
})],
x_metric="epoch",
y_metric="acc",
)
# fig, axis = hr.get_plot(exp_list,
# savedir_base=savedir_base,
# x_metric='epoch',
# y_metric='acc',
# mode='pretty_plot')
fig, axis = hr.get_plot(exp_list,
savedir_base=savedir_base,
x_metric="epoch",
y_metric="acc",
mode="bar")
fig.savefig(os.path.join(".tmp", "test.png"))
shutil.rmtree(".tmp")
def test_get_best_exp_dict(self):
savedir_base = '.tmp'
exp_dict_1 = {'model':{'name':'mlp', 'n_layers':30},
'dataset':'mnist', 'batch_size':1}
score_list = [{'epoch': 0, 'acc':0.5}, {'epoch': 1, 'acc':0.9}]
hu.save_pkl(os.path.join(savedir_base, hu.hash_dict(exp_dict_1),
'score_list.pkl'), score_list)
exp_dict_2 = {'model':{'name':'mlp', 'n_layers':35},
'dataset':'mnist', 'batch_size':1}
score_list = [{'epoch': 0, 'acc':0.6}, {'epoch': 1, 'acc':1.9}]
hu.save_pkl(os.path.join(savedir_base, hu.hash_dict(exp_dict_2),
'score_list.pkl'), score_list)
best_exp_list = hu.filter_exp_list([exp_dict_1, exp_dict_2], savedir_base=savedir_base,
filterby_list=[({'model.name':'mlp'},
{'best':{'avg_across':'run',
'metric':'acc',
'metric_agg':'max'}}
)])
assert len(best_exp_list) == 1
assert best_exp_list[0]['model']['n_layers'] == 35
best_exp_list = hu.filter_exp_list([exp_dict_1, exp_dict_2], savedir_base=savedir_base,
filterby_list=[({'model.name':'mlp'},
{'best':{'avg_across':'run',
'metric':'acc',
'metric_agg':'min'}}
)])
assert best_exp_list[0]['model']['n_layers'] == 30
# exp 2
exp_dict_2 = {'model':{'name':'mlp2', 'n_layers':30},
'dataset':'mnist', 'batch_size':1, 'run':0}
score_list = [{'epoch': 0, 'acc':1.5}, {'epoch': 1, 'acc':1.8}]
hu.save_pkl(os.path.join(savedir_base, hu.hash_dict(exp_dict_2),
'score_list.pkl'), score_list)
# exp 3
exp_dict_3 = {'model':{'name':'mlp2', 'n_layers':30},
'dataset':'mnist', 'batch_size':1, 'run':1}
score_list = [{'epoch': 0, 'acc':1.5}, {'epoch': 1, 'acc':1.3}]
hu.save_pkl(os.path.join(savedir_base, hu.hash_dict(exp_dict_3),
'score_list.pkl'), score_list)
exp_list = [exp_dict_1, exp_dict_2, exp_dict_3]
best_exp_dict = hu.get_best_exp_dict(exp_list,
savedir_base=savedir_base, metric='acc',
avg_across='run',
metric_agg='max',
)
assert(best_exp_dict['model']['name'] == 'mlp2')
def trainval(exp_dict, savedir, args):
"""
exp_dict: dictionary defining the hyperparameters of the experiment
savedir: the directory where the experiment will be saved
args: arguments passed through the command line
"""
# -- Datasets
train_set = datasets.get_dataset(dataset_name=exp_dict["dataset"],
train_flag=True,
datadir=args.datadir)
val_set = datasets.get_dataset(dataset_name=exp_dict["dataset"],
train_flag=False,
datadir=args.datadir)
# -- Model
model = models.Model(exp_dict, device=torch.device('cuda'))
# -- Train & Val Loop
score_list = []
for e in range(0, 50):
# Compute metrics
score_dict = {"epoch": e}
score_dict["train_loss"] = model.val_on_dataset(
val_set, metric_name='softmax_loss')
score_dict["val_acc"] = model.val_on_dataset(val_set,
metric_name='softmax_acc')
score_list += [score_dict]
# Train model for one epoch
model.train_on_dataset(train_set)
# Visualize
images = model.vis_on_dataset(val_set,
fname=os.path.join(
savedir, 'images', 'results.png'))
# Report & Save
score_df = pd.DataFrame(score_list)
print("\n", score_df.tail(), "\n")
hu.save_pkl(os.path.join(savedir, 'score_list.pkl'), score_list)
hu.torch_save(os.path.join(savedir, 'model.pth'), model.state_dict())
print("Checkpoint Saved: %s" % savedir)
print('Experiment completed et epoch %d' % e)
def save_example_results(savedir_base="results"):
import os
import pandas
import requests
import io
import matplotlib.pyplot as plt
from .. import haven_results as hr
from .. import haven_utils as hu
from PIL import Image
# create hyperparameters
exp_list = [{
"dataset": "mnist",
"model": "mlp",
"lr": lr
} for lr in [1e-1, 1e-2, 1e-3]]
for i, exp_dict in enumerate(exp_list):
# get hash for experiment
exp_id = hu.hash_dict(exp_dict)
# add scores for loss, and accuracy
score_list = []
for e in range(1, 10):
score_list += [{
"epoch": e,
"loss": 1 - e * exp_dict["lr"] * 0.9,
"acc": e * exp_dict["lr"] * 0.1
}]
# save scores and images
hu.save_json(os.path.join(savedir_base, exp_id, "exp_dict.json"),
exp_dict)
hu.save_pkl(os.path.join(savedir_base, exp_id, "score_list.pkl"),
score_list)
url = "https://raw.githubusercontent.com/haven-ai/haven-ai/master/haven/haven_examples/data/%d.png" % (
i + 1)
response = requests.get(url).content
img = plt.imread(io.BytesIO(response), format="JPG")
hu.save_image(os.path.join(savedir_base, exp_id, "images/1.png"),
img[:, :, :3])
def test_get_best_exp_dict(self):
savedir_base = '.tmp'
exp_dict_1 = {'model':{'name':'mlp', 'n_layers':30},
'dataset':'mnist', 'batch_size':1}
score_list = [{'epoch': 0, 'acc':0.5}, {'epoch': 1, 'acc':0.9}]
hu.save_pkl(os.path.join(savedir_base, hu.hash_dict(exp_dict_1),
'score_list.pkl'), score_list)
exp_dict_2 = {'model':{'name':'mlp2', 'n_layers':30},
'dataset':'mnist', 'batch_size':1}
score_list = [{'epoch': 0, 'acc':0.5}, {'epoch': 1, 'acc':1.2}]
hu.save_pkl(os.path.join(savedir_base, hu.hash_dict(exp_dict_2),
'score_list.pkl'), score_list)
exp_list = [exp_dict_1, exp_dict_2]
best_exp_dict = hr.get_best_exp_dict(exp_list, savedir_base=savedir_base, metric='acc', min_or_max='max')
assert(best_exp_dict['model']['name'] == 'mlp2')
def test_get_score_df():
# save a score_list
savedir_base = ".tmp"
exp_dict = {
"model": {
"name": "mlp",
"n_layers": 30
},
"dataset": "mnist",
"batch_size": 1
}
exp_dict2 = {
"model": {
"name": "mlp2",
"n_layers": 30
},
"dataset": "mnist",
"batch_size": 1
}
score_list = [{"epoch": 0, "acc": 0.5}, {"epoch": 0, "acc": 0.9}]
hu.save_pkl(
os.path.join(savedir_base, hu.hash_dict(exp_dict), "score_list.pkl"),
score_list)
hu.save_json(
os.path.join(savedir_base, hu.hash_dict(exp_dict), "exp_dict.json"),
exp_dict)
hu.save_json(
os.path.join(savedir_base, hu.hash_dict(exp_dict2), "exp_dict.json"),
exp_dict)
# check if score_list can be loaded and viewed in pandas
exp_list = hu.get_exp_list(savedir_base=savedir_base)
score_df = hr.get_score_df(exp_list, savedir_base=savedir_base)
assert np.array(score_df["dataset"])[0].strip("'") == "mnist"
shutil.rmtree(".tmp")
def save_example_results(savedir_base='results'):
import os, pandas
import requests, io
import matplotlib.pyplot as plt
from .. import haven_results as hr
from .. import haven_utils as hu
from PIL import Image
# create hyperparameters
exp_list = [{
'dataset': 'mnist',
'model': 'mlp',
'lr': lr
} for lr in [1e-1, 1e-2, 1e-3]]
for i, exp_dict in enumerate(exp_list):
# get hash for experiment
exp_id = hu.hash_dict(exp_dict)
# add scores for loss, and accuracy
score_list = []
for e in range(1, 10):
score_list += [{
'epoch': e,
'loss': 1 - e * exp_dict['lr'] * 0.9,
'acc': e * exp_dict['lr'] * 0.1
}]
# save scores and images
hu.save_json(os.path.join(savedir_base, exp_id, 'exp_dict.json'),
exp_dict)
hu.save_pkl(os.path.join(savedir_base, exp_id, 'score_list.pkl'),
score_list)
url = 'https://raw.githubusercontent.com/haven-ai/haven-ai/master/haven/haven_examples/data/%d.png' % (
i + 1)
response = requests.get(url).content
img = plt.imread(io.BytesIO(response), format='JPG')
hu.save_image(os.path.join(savedir_base, exp_id, 'images/1.png'),
img[:, :, :3])
def trainval(exp_dict, savedir_base, datadir, reset=False, num_workers=0):
# bookkeepting stuff
# ==================
pprint.pprint(exp_dict)
exp_id = hu.hash_dict(exp_dict)
savedir = os.path.join(savedir_base, exp_id)
if reset:
hc.delete_and_backup_experiment(savedir)
os.makedirs(savedir, exist_ok=True)
if not os.path.join(savedir, "exp_dict.json"):
hu.save_json(os.path.join(savedir, "exp_dict.json"), exp_dict)
print("Experiment saved in %s" % savedir)
# BCD train
# ==================
# Ignore the following combinations
if not ut.is_valid_exp(exp_dict):
return
score_list_fname = os.path.join(savedir, 'score_list.pkl')
if os.path.exists(score_list_fname):
score_list = hu.load_pkl(score_list_fname)
else:
score_list = train(dataset_name=exp_dict['dataset']['name'],
loss_name=exp_dict['dataset']['loss'],
block_size=exp_dict['block_size'],
partition_rule=exp_dict['partition'],
selection_rule=exp_dict['selection'],
update_rule=exp_dict['update'],
n_iters=exp_dict['max_iters'],
L1=exp_dict.get('l1', 0),
L2=0,
datasets_path=datadir)
hu.save_pkl(score_list_fname, score_list)
print('Experiment completed.')
return score_list
def trainval(exp_dict, savedir, args):
"""
exp_dict: dictionary defining the hyperparameters of the experiment
savedir: the directory where the experiment will be saved
args: arguments passed through the command line
"""
# set seed
# ==================
seed = 42
np.random.seed(seed)
torch.manual_seed(seed)
if args.use_cuda:
device = 'cuda'
torch.cuda.manual_seed_all(seed)
assert torch.cuda.is_available(
), 'cuda is not, available please run with "-c 0"'
else:
device = 'cpu'
print('Running on device: %s' % device)
# Dataset
# Load val set and train set
val_set = datasets.get_dataset(dataset_name=exp_dict["dataset"],
split="val",
transform=exp_dict.get("transform"),
datadir=args.datadir)
train_set = datasets.get_dataset(dataset_name=exp_dict["dataset"],
split="train",
transform=exp_dict.get("transform"),
datadir=args.datadir)
# Load train loader, val loader, and vis loader
train_loader = DataLoader(train_set,
sampler=RandomSampler(
train_set,
replacement=True,
num_samples=max(min(500, len(train_set)),
len(val_set))),
batch_size=exp_dict["batch_size"])
val_loader = DataLoader(val_set,
shuffle=False,
batch_size=exp_dict["batch_size"])
vis_loader = DataLoader(val_set,
sampler=ut.SubsetSampler(train_set,
indices=[0, 1, 2]),
batch_size=1)
# Create model, opt, wrapper
model_original = models.get_model(exp_dict["model"],
exp_dict=exp_dict).cuda()
opt = torch.optim.Adam(model_original.parameters(),
lr=1e-5,
weight_decay=0.0005)
model = wrappers.get_wrapper(exp_dict["wrapper"],
model=model_original,
opt=opt).cuda()
score_list = []
# Checkpointing
# =============
score_list_path = os.path.join(savedir, "score_list.pkl")
model_path = os.path.join(savedir, "model_state_dict.pth")
opt_path = os.path.join(savedir, "opt_state_dict.pth")
if os.path.exists(score_list_path):
# resume experiment
score_list = hu.load_pkl(score_list_path)
model.load_state_dict(torch.load(model_path))
opt.load_state_dict(torch.load(opt_path))
s_epoch = score_list[-1]["epoch"] + 1
else:
# restart experiment
score_list = []
s_epoch = 0
# Run training and validation
for epoch in range(s_epoch, exp_dict["max_epoch"]):
score_dict = {"epoch": epoch}
# visualize
model.vis_on_loader(vis_loader,
savedir=os.path.join(savedir, "images"))
# validate
score_dict.update(model.val_on_loader(val_loader))
# train
score_dict.update(model.train_on_loader(train_loader))
# Add score_dict to score_list
score_list += [score_dict]
# Report and save
print(pd.DataFrame(score_list).tail())
hu.save_pkl(score_list_path, score_list)
hu.torch_save(model_path, model.state_dict())
hu.torch_save(opt_path, opt.state_dict())
print("Saved in %s" % savedir)
def trainval(exp_dict, savedir_base, datadir, reset=False, num_workers=0):
# bookkeepting stuff
# ==================
savedir = os.path.join(savedir_base, hu.hash_dict(exp_dict))
os.makedirs(savedir, exist_ok=True)
if reset:
hc.delete_and_backup_experiment(savedir)
print("Experiment saved in %s" % savedir)
# Dataset
# ==================
# train set
data_transform = A.Compose(
[
A.Flip(p=0.3),
A.IAAAffine(p=0.3),
A.Rotate(p=0.3),
A.HueSaturationValue(hue_shift_limit=10,
sat_shift_limit=15,
val_shift_limit=10,
p=0.3),
A.GaussianBlur(3, p=0.3),
A.GaussNoise(30, p=0.3)
],
keypoint_params=A.KeypointParams(format='xy'),
additional_targets={
'mask0': 'mask',
'mask1': 'mask',
'mask2': 'mask',
'keypoints0': 'keypoints',
'keypoints1': 'keypoints',
'keypoints2': 'keypoints',
'keypoints3': 'keypoints',
'keypoints4': 'keypoints',
'keypoints5': 'keypoints'
})
# random.seed(20201009)
random_seed = random.randint(0, 20201009)
train_set = HEDataset_Fast(data_dir=datadir,
n_classes=exp_dict["n_classes"],
transform=data_transform,
option="Train",
random_seed=random_seed,
obj_option=exp_dict["obj"],
patch_size=exp_dict["patch_size"],
bkg_option=exp_dict["bkg"])
test_transform = A.Compose([A.Resize(1024, 1024)],
keypoint_params=A.KeypointParams(format='xy'),
additional_targets={
'mask0': 'mask',
'mask1': 'mask'
})
# val set
val_set = HEDataset(data_dir=datadir,
transform=test_transform,
option="Validation")
val_loader = DataLoader(val_set, batch_size=1, num_workers=num_workers)
# test set
test_set = HEDataset(data_dir=datadir,
transform=test_transform,
option="Test")
test_loader = DataLoader(test_set, batch_size=1, num_workers=num_workers)
# Model
# ==================
# torch.manual_seed(20201009)
model = models.get_model(exp_dict['model'],
exp_dict=exp_dict,
train_set=train_set).cuda()
model_path = os.path.join(savedir, "model.pth")
score_list_path = os.path.join(savedir, "score_list.pkl")
if os.path.exists(score_list_path):
# resume experiment
model.load_state_dict(hu.torch_load(model_path))
score_list = hu.load_pkl(score_list_path)
s_epoch = score_list[-1]['epoch'] + 1
else:
# restart experiment
score_list = []
s_epoch = 0
# Train & Val
# ==================
print("Starting experiment at epoch %d" % (s_epoch))
# train_sampler = torch.utils.data.RandomSampler(
# train_set, replacement=True, num_samples=2*len(val_set))
train_loader = DataLoader(train_set,
batch_size=exp_dict["batch_size"],
shuffle=True,
num_workers=num_workers)
for e in range(s_epoch, exp_dict['max_epoch']):
# Validate only at the start of each cycle
score_dict = {}
# Train the model
train_dict = model.train_on_loader(train_loader)
# Validate and Visualize the model
val_dict = model.val_on_loader(val_loader,
savedir_images=os.path.join(
savedir, "images"),
n_images=7)
score_dict.update(val_dict)
# Get new score_dict
score_dict.update(train_dict)
score_dict["epoch"] = len(score_list)
# Add to score_list and save checkpoint
score_list += [score_dict]
# Report & Save
score_df = pd.DataFrame(score_list)
print("\n", score_df.tail(), "\n")
hu.torch_save(model_path, model.get_state_dict())
hu.save_pkl(score_list_path, score_list)
print("Checkpoint Saved: %s" % savedir)
# Save Best Checkpoint
if e == 0 or (score_dict.get("val_score", 0) >
score_df["val_score"][:-1].fillna(0).max()):
hu.save_pkl(os.path.join(savedir, "score_list_best.pkl"),
score_list)
hu.torch_save(os.path.join(savedir, "model_best.pth"),
model.get_state_dict())
print("Saved Best: %s" % savedir)
# if s_epoch==exp_dict['max_epoch']:
# e = s_epoch
model.load_state_dict(
hu.torch_load(os.path.join(savedir, "model_best.pth")))
test_dict = model.test_on_loader(test_loader)
hu.save_pkl(os.path.join(savedir, 'test_iou.pkl'), test_dict)
print('Test IoU:{}'.format(test_dict["test_iou"]))
print('Experiment completed et epoch %d' % e)
def trainval(exp_dict, savedir_base, reset=False):
# bookkeeping
# ---------------
# get experiment directory
exp_id = hu.hash_dict(exp_dict)
savedir = os.path.join(savedir_base, exp_id)
if reset:
# delete and backup experiment
hc.delete_experiment(savedir, backup_flag=True)
# create folder and save the experiment dictionary
os.makedirs(savedir, exist_ok=True)
hu.save_json(os.path.join(savedir, 'exp_dict.json'), exp_dict)
pprint.pprint(exp_dict)
print('Experiment saved in %s' % savedir)
# Dataset
# -----------
# train loader
train_loader = datasets.get_loader(dataset_name=exp_dict['dataset'],
datadir=savedir_base,
split='train')
# val loader
val_loader = datasets.get_loader(dataset_name=exp_dict['dataset'],
datadir=savedir_base,
split='val')
# Model
# -----------
model = models.get_model(model_name=exp_dict['model'])
# Checkpoint
# -----------
model_path = os.path.join(savedir, 'model.pth')
score_list_path = os.path.join(savedir, 'score_list.pkl')
if os.path.exists(score_list_path):
# resume experiment
model.set_state_dict(hu.torch_load(model_path))
score_list = hu.load_pkl(score_list_path)
s_epoch = score_list[-1]['epoch'] + 1
else:
# restart experiment
score_list = []
s_epoch = 0
# Train & Val
# ------------
print('Starting experiment at epoch %d' % (s_epoch))
for e in range(s_epoch, 10):
score_dict = {}
# Train the model
train_dict = model.train_on_loader(train_loader)
# Validate the model
val_dict = model.val_on_loader(val_loader)
# Get metrics
score_dict['train_loss'] = train_dict['train_loss']
score_dict['val_acc'] = val_dict['val_acc']
score_dict['epoch'] = e
# Add to score_list and save checkpoint
score_list += [score_dict]
# Report & Save
score_df = pd.DataFrame(score_list)
print(score_df.tail())
hu.torch_save(model_path, model.get_state_dict())
hu.save_pkl(score_list_path, score_list)
print('Checkpoint Saved: %s' % savedir)
print('experiment completed')
def trainval(exp_dict, savedir_base, datadir_base, reset=False,
num_workers=0, pin_memory=False, ngpu=1, cuda_deterministic=False):
# bookkeeping
# ==================
# get experiment directory
exp_id = hu.hash_dict(exp_dict)
savedir = os.path.join(savedir_base, exp_id)
if reset:
# delete and backup experiment
hc.delete_experiment(savedir, backup_flag=True)
# create folder and save the experiment dictionary
hu.save_json(os.path.join(savedir, 'exp_dict.json'), exp_dict)
pprint.pprint(exp_dict)
print('Experiment saved in %s' % savedir)
if DEVICE.type == "cuda":
if cuda_deterministic:
cudnn.benchmark = False
cudnn.deterministic = True
else:
cudnn.benchmark = True
# Dataset
# ==================
trainset = get_dataset(exp_dict['dataset'], 'train',
exp_dict=exp_dict, datadir_base=datadir_base,
n_samples=exp_dict['dataset_size']['train'],
transform_lvl=exp_dict['dataset']['transform_lvl'],
colorjitter=exp_dict['dataset'].get('colorjitter')
)
valset = get_dataset(exp_dict['dataset'], 'validation',
exp_dict=exp_dict, datadir_base=datadir_base,
n_samples=exp_dict['dataset_size']['train'],
transform_lvl=0,
val_transform=exp_dict['dataset']['val_transform'])
testset = get_dataset(exp_dict['dataset'], 'test',
exp_dict=exp_dict, datadir_base=datadir_base,
n_samples=exp_dict['dataset_size']['test'],
transform_lvl=0,
val_transform=exp_dict['dataset']['val_transform'])
print("Dataset defined.")
# define dataloaders
if exp_dict['dataset']['name'] == 'bach':
testloader = torch.utils.data.DataLoader(testset, batch_size=1,
shuffle=False,
num_workers=num_workers,
pin_memory=pin_memory)
else:
testloader = torch.utils.data.DataLoader(testset, batch_size=exp_dict['batch']['size'],
shuffle=False,
num_workers=num_workers,
pin_memory=pin_memory)
print("Testloader defined.")
# Model
# ==================
model = get_model(exp_dict, trainset, device=DEVICE)
print("Model loaded")
model_path = os.path.join(savedir, 'model.pth')
model_best_path = os.path.join(savedir, 'model_best.pth')
score_list_path = os.path.join(savedir, 'score_list.pkl')
# checkpoint management
if os.path.exists(score_list_path):
# resume experiment
model.load_state_dict(hu.torch_load(model_path))
score_list = hu.load_pkl(score_list_path)
s_epoch = len(score_list)
else:
# restart experiment
score_list = []
s_epoch = 0
# define and log random seed for reproducibility
assert('fixedSeed' in exp_dict)
seed = exp_dict['fixedSeed']
random.seed(seed)
torch.manual_seed(seed)
torch.cuda.manual_seed_all(seed)
np.random.seed(seed)
print("Seed defined.")
# Train & Val
# ==================
print("Starting experiment at epoch %d/%d" % (s_epoch, exp_dict['niter']))
for epoch in range(s_epoch, exp_dict['niter']):
s_time = time.time()
# Sample new train val
trainloader, valloader = get_train_val_dataloader(exp_dict,
trainset, valset,
mixtrainval=exp_dict['mixTrainVal'],
num_workers=num_workers,
pin_memory=pin_memory)
# Train & validate
train_dict = model.train_on_loader(trainloader, valloader, epoch=epoch,
exp_dict=exp_dict)
# Test phase
train_dict_2 = model.test_on_loader(trainloader)
val_dict = model.test_on_loader(valloader)
test_dict = model.test_on_loader(testloader)
# Vis phase
model.vis_on_loader('train', trainset, savedir_images=os.path.join(
savedir, 'images'), epoch=epoch)
score_dict = {}
score_dict["epoch"] = epoch
score_dict["test_acc"] = test_dict['acc']
score_dict["val_acc"] = val_dict['acc']
score_dict["train_acc"] = train_dict_2['acc']
score_dict["train_loss"] = train_dict['loss']
score_dict["time_taken"] = time.time() - s_time
score_dict["netC_lr"] = train_dict['netC_lr']
if exp_dict['model']['netA'] is not None:
if 'transformations_mean' in train_dict:
for i in range(len(train_dict['transformations_mean'])):
score_dict[str(
i) + "_mean"] = train_dict['transformations_mean'][i].item()
if 'transformations_std' in train_dict:
for i in range(len(train_dict['transformations_std'])):
score_dict[str(
i) + "_std"] = train_dict['transformations_std'][i].item()
# Add to score_list and save checkpoint
score_list += [score_dict]
# Report & Save
score_df = pd.DataFrame(score_list)
print("\n", score_df.tail(), "\n")
hu.torch_save(model_path, model.get_state_dict())
hu.save_pkl(score_list_path, score_list)
print("Checkpoint Saved: %s" % savedir)
# Update best score
if epoch == 0 or (score_dict["test_acc"] >= score_df["test_acc"][:-1].max()):
hu.save_pkl(os.path.join(
savedir, "score_list_best.pkl"), score_list)
hu.torch_save(os.path.join(savedir, "model_best.pth"),
model.get_state_dict())
print("Saved Best: %s" % savedir)
print('experiment completed')
def trainval(exp_dict,
savedir_base,
reset=False,
num_workers=0,
run_ssl=False):
# bookkeeping
# ---------------
# get experiment directory
exp_id = hu.hash_dict(exp_dict)
savedir = os.path.join(savedir_base, exp_id)
if reset:
# delete and backup experiment
hc.delete_experiment(savedir, backup_flag=True)
# create folder and save the experiment dictionary
os.makedirs(savedir, exist_ok=True)
hu.save_json(os.path.join(savedir, 'exp_dict.json'), exp_dict)
pprint.pprint(exp_dict)
print('Experiment saved in %s' % savedir)
# load datasets
# ==========================
train_set = datasets.get_dataset(
dataset_name=exp_dict["dataset_train"],
data_root=exp_dict["dataset_train_root"],
split="train",
transform=exp_dict["transform_train"],
classes=exp_dict["classes_train"],
support_size=exp_dict["support_size_train"],
query_size=exp_dict["query_size_train"],
n_iters=exp_dict["train_iters"],
unlabeled_size=exp_dict["unlabeled_size_train"])
val_set = datasets.get_dataset(
dataset_name=exp_dict["dataset_val"],
data_root=exp_dict["dataset_val_root"],
split="val",
transform=exp_dict["transform_val"],
classes=exp_dict["classes_val"],
support_size=exp_dict["support_size_val"],
query_size=exp_dict["query_size_val"],
n_iters=exp_dict["val_iters"],
unlabeled_size=exp_dict["unlabeled_size_val"])
test_set = datasets.get_dataset(
dataset_name=exp_dict["dataset_test"],
data_root=exp_dict["dataset_test_root"],
split="test",
transform=exp_dict["transform_val"],
classes=exp_dict["classes_test"],
support_size=exp_dict["support_size_test"],
query_size=exp_dict["query_size_test"],
n_iters=exp_dict["test_iters"],
unlabeled_size=exp_dict["unlabeled_size_test"])
# get dataloaders
# ==========================
train_loader = torch.utils.data.DataLoader(
train_set,
batch_size=exp_dict["batch_size"],
shuffle=True,
num_workers=num_workers,
collate_fn=ut.get_collate(exp_dict["collate_fn"]),
drop_last=True)
val_loader = torch.utils.data.DataLoader(val_set,
batch_size=1,
shuffle=False,
num_workers=num_workers,
collate_fn=lambda x: x,
drop_last=True)
test_loader = torch.utils.data.DataLoader(test_set,
batch_size=1,
shuffle=False,
num_workers=num_workers,
collate_fn=lambda x: x,
drop_last=True)
# create model and trainer
# ==========================
# Create model, opt, wrapper
backbone = backbones.get_backbone(
backbone_name=exp_dict['model']["backbone"], exp_dict=exp_dict)
model = models.get_model(model_name=exp_dict["model"]['name'],
backbone=backbone,
n_classes=exp_dict["n_classes"],
exp_dict=exp_dict)
if run_ssl:
# runs the SSL experiments
score_list_path = os.path.join(savedir, 'score_list.pkl')
if not os.path.exists(score_list_path):
test_dict = model.test_on_loader(test_loader, max_iter=None)
hu.save_pkl(score_list_path, [test_dict])
return
# Checkpoint
# -----------
checkpoint_path = os.path.join(savedir, 'checkpoint.pth')
score_list_path = os.path.join(savedir, 'score_list.pkl')
if os.path.exists(score_list_path):
# resume experiment
model.load_state_dict(hu.torch_load(checkpoint_path))
score_list = hu.load_pkl(score_list_path)
s_epoch = score_list[-1]['epoch'] + 1
else:
# restart experiment
score_list = []
s_epoch = 0
# Run training and validation
for epoch in range(s_epoch, exp_dict["max_epoch"]):
score_dict = {"epoch": epoch}
score_dict.update(model.get_lr())
# train
score_dict.update(model.train_on_loader(train_loader))
# validate
score_dict.update(model.val_on_loader(val_loader))
score_dict.update(model.test_on_loader(test_loader))
# Add score_dict to score_list
score_list += [score_dict]
# Report
score_df = pd.DataFrame(score_list)
print(score_df.tail())
# Save checkpoint
hu.save_pkl(score_list_path, score_list)
hu.torch_save(checkpoint_path, model.get_state_dict())
print("Saved: %s" % savedir)
if "accuracy" in exp_dict["target_loss"]:
is_best = score_dict[exp_dict["target_loss"]] >= score_df[
exp_dict["target_loss"]][:-1].max()
else:
is_best = score_dict[exp_dict["target_loss"]] <= score_df[
exp_dict["target_loss"]][:-1].min()
# Save best checkpoint
if is_best:
hu.save_pkl(os.path.join(savedir, "score_list_best.pkl"),
score_list)
hu.torch_save(os.path.join(savedir, "checkpoint_best.pth"),
model.get_state_dict())
print("Saved Best: %s" % savedir)
# Check for end of training conditions
if model.is_end_of_training():
break
def test(exp_dict,
savedir_base,
datadir,
num_workers=0,
model_path=None,
scan_id=None):
# bookkeepting stuff
# ==================
pprint.pprint(exp_dict)
exp_id = hu.hash_dict(exp_dict)
savedir = os.path.join(savedir_base, exp_id)
os.makedirs(savedir, exist_ok=True)
hu.save_json(os.path.join(savedir, "exp_dict.json"), exp_dict)
print("Experiment saved in %s" % savedir)
# Dataset
# ==================
# val set
test_set = datasets.get_dataset(dataset_dict=exp_dict["dataset"],
split="val",
datadir=datadir,
exp_dict=exp_dict,
dataset_size=exp_dict['dataset_size'])
if str(scan_id) != 'None':
test_set.active_data = test_set.get_scan(scan_id)
test_sampler = torch.utils.data.SequentialSampler(test_set)
test_loader = DataLoader(test_set,
sampler=test_sampler,
batch_size=1,
collate_fn=ut.collate_fn,
num_workers=num_workers)
# Model
# ==================
# chk = torch.load('best_model.ckpt')
model = models.get_model_for_onnx_export(model_dict=exp_dict['model'],
exp_dict=exp_dict,
train_set=test_set).cuda()
epoch = -1
if str(model_path) != 'None':
model_path = model_path
model.load_state_dict(hu.torch_load(model_path))
else:
try:
exp_dict_train = copy.deepcopy(exp_dict)
del exp_dict_train['test_mode']
savedir_train = os.path.join(savedir_base,
hu.hash_dict(exp_dict_train))
model_path = os.path.join(savedir_train, "model_best.pth")
score_list = hu.load_pkl(
os.path.join(savedir_train, 'score_list_best.pkl'))
epoch = score_list[-1]['epoch']
print('Loaded model at epoch %d with score %.3f' % epoch)
model.load_state_dict(hu.torch_load(model_path))
except:
pass
s_time = time.time()
savedir_images = os.path.join(savedir, 'images')
# delete image folder if exists
if os.path.exists(savedir_images):
shutil.rmtree(savedir_images)
os.makedirs(savedir_images, exist_ok=True)
# for i in range(20):
# score_dict = model.train_on_loader(test_loader)
score_dict = model.val_on_loader(test_loader,
savedir_images=savedir_images,
n_images=30000,
save_preds=True)
score_dict['epoch'] = epoch
score_dict["time"] = time.time() - s_time
score_dict["saved_at"] = hu.time_to_montreal()
# save test_score_list
test_path = os.path.join(savedir, "score_list.pkl")
if os.path.exists(test_path):
test_score_list = [
sd for sd in hu.load_pkl(test_path) if sd['epoch'] != epoch
]
else:
test_score_list = []
# append score_dict to last result
test_score_list += [score_dict]
hu.save_pkl(test_path, test_score_list)
print('Final Score is ', str(score_dict["val_score"]) + "\n")
def trainval(exp_dict, savedir_base, datadir, reset=False, num_workers=0):
# bookkeepting stuff
# ==================
pprint.pprint(exp_dict)
exp_id = hu.hash_dict(exp_dict)
savedir = os.path.join(savedir_base, exp_id)
if reset:
hc.delete_and_backup_experiment(savedir)
os.makedirs(savedir, exist_ok=True)
hu.save_json(os.path.join(savedir, "exp_dict.json"), exp_dict)
print("Experiment saved in %s" % savedir)
# set seed
# ==================
seed = 42
np.random.seed(seed)
torch.manual_seed(seed)
torch.cuda.manual_seed_all(seed)
# Dataset
# ==================
# train set
train_set = datasets.get_dataset(dataset_dict=exp_dict["dataset"],
split="train",
datadir=datadir,
exp_dict=exp_dict,
dataset_size=exp_dict['dataset_size'])
# val set
val_set = datasets.get_dataset(dataset_dict=exp_dict["dataset"],
split="val",
datadir=datadir,
exp_dict=exp_dict,
dataset_size=exp_dict['dataset_size'])
# test set
test_set = datasets.get_dataset(dataset_dict=exp_dict["dataset"],
split="test",
datadir=datadir,
exp_dict=exp_dict,
dataset_size=exp_dict['dataset_size'])
# val_sampler = torch.utils.data.SequentialSampler(val_set)
val_loader = DataLoader(
val_set,
# sampler=val_sampler,
batch_size=1,
collate_fn=ut.collate_fn,
num_workers=num_workers)
test_loader = DataLoader(
test_set,
# sampler=val_sampler,
batch_size=1,
collate_fn=ut.collate_fn,
num_workers=num_workers)
# Model
# ==================
model = models.get_model(model_dict=exp_dict['model'],
exp_dict=exp_dict,
train_set=train_set).cuda()
# model.opt = optimizers.get_optim(exp_dict['opt'], model)
model_path = os.path.join(savedir, "model.pth")
score_list_path = os.path.join(savedir, "score_list.pkl")
if os.path.exists(score_list_path):
# resume experiment
model.load_state_dict(hu.torch_load(model_path))
score_list = hu.load_pkl(score_list_path)
s_epoch = score_list[-1]['epoch'] + 1
else:
# restart experiment
score_list = []
s_epoch = 0
# Train & Val
# ==================
print("Starting experiment at epoch %d" % (s_epoch))
model.waiting = 0
model.val_score_best = -np.inf
train_sampler = torch.utils.data.RandomSampler(train_set,
replacement=True,
num_samples=2 *
len(test_set))
train_loader = DataLoader(train_set,
sampler=train_sampler,
collate_fn=ut.collate_fn,
batch_size=exp_dict["batch_size"],
drop_last=True,
num_workers=num_workers)
for e in range(s_epoch, exp_dict['max_epoch']):
# Validate only at the start of each cycle
score_dict = {}
test_dict = model.val_on_loader(test_loader,
savedir_images=os.path.join(
savedir, "images"),
n_images=3)
# Train the model
train_dict = model.train_on_loader(train_loader)
# Validate the model
val_dict = model.val_on_loader(val_loader)
score_dict["val_score"] = val_dict["val_score"]
# Get new score_dict
score_dict.update(train_dict)
score_dict["epoch"] = e
score_dict["waiting"] = model.waiting
model.waiting += 1
# Add to score_list and save checkpoint
score_list += [score_dict]
# Save Best Checkpoint
score_df = pd.DataFrame(score_list)
if score_dict["val_score"] >= model.val_score_best:
test_dict = model.val_on_loader(test_loader,
savedir_images=os.path.join(
savedir, "images"),
n_images=3)
score_dict.update(test_dict)
hu.save_pkl(os.path.join(savedir, "score_list_best.pkl"),
score_list)
# score_df.to_csv(os.path.join(savedir, "score_best_df.csv"))
hu.torch_save(os.path.join(savedir, "model_best.pth"),
model.get_state_dict())
model.waiting = 0
model.val_score_best = score_dict["val_score"]
print("Saved Best: %s" % savedir)
# Report & Save
score_df = pd.DataFrame(score_list)
# score_df.to_csv(os.path.join(savedir, "score_df.csv"))
print("\n", score_df.tail(), "\n")
hu.torch_save(model_path, model.get_state_dict())
hu.save_pkl(score_list_path, score_list)
print("Checkpoint Saved: %s" % savedir)
if model.waiting > 100:
break
print('Experiment completed et epoch %d' % e)
def trainval(exp_dict, savedir_base, reset=False):
# bookkeeping
# ---------------
# get experiment directory
exp_id = hu.hash_dict(exp_dict)
savedir = os.path.join(savedir_base, exp_id)
if reset:
# delete and backup experiment
hc.delete_experiment(savedir, backup_flag=True)
# create folder and save the experiment dictionary
os.makedirs(savedir, exist_ok=True)
hu.save_json(os.path.join(savedir, 'exp_dict.json'), exp_dict)
pprint.pprint(exp_dict)
print('Experiment saved in %s' % savedir)
# set seed
# ---------------
seed = 42 + exp_dict['runs']
np.random.seed(seed)
torch.manual_seed(seed)
torch.cuda.manual_seed_all(seed)
# Dataset
# -----------
# train loader
train_set = datasets.get_dataset(dataset_name=exp_dict["dataset"],
train_flag=True,
datadir=savedir_base,
exp_dict=exp_dict)
train_loader = torch.utils.data.DataLoader(
train_set,
drop_last=True,
shuffle=True,
batch_size=exp_dict["batch_size"])
# val set
val_set = datasets.get_dataset(dataset_name=exp_dict["dataset"],
train_flag=False,
datadir=savedir_base,
exp_dict=exp_dict)
# Model
# -----------
model = models.get_model(exp_dict["model"], train_set=train_set).cuda()
# Choose loss and metric function
loss_function = metrics.get_metric_function(exp_dict["loss_func"])
# Compute fstar
# -------------
if exp_dict['opt'].get('fstar_flag'):
ut.compute_fstar(train_set, loss_function, savedir_base, exp_dict)
# Load Optimizer
n_batches_per_epoch = len(train_set) / float(exp_dict["batch_size"])
opt = optimizers.get_optimizer(opt_dict=exp_dict["opt"],
params=model.parameters(),
n_batches_per_epoch=n_batches_per_epoch)
# Checkpoint
# -----------
model_path = os.path.join(savedir, 'model.pth')
score_list_path = os.path.join(savedir, 'score_list.pkl')
opt_path = os.path.join(savedir, 'opt_state_dict.pth')
if os.path.exists(score_list_path):
# resume experiment
score_list = hu.load_pkl(score_list_path)
model.load_state_dict(torch.load(model_path))
opt.load_state_dict(torch.load(opt_path))
s_epoch = score_list[-1]['epoch'] + 1
else:
# restart experiment
score_list = []
s_epoch = 0
# Train & Val
# ------------
print('Starting experiment at epoch %d/%d' %
(s_epoch, exp_dict['max_epoch']))
for e in range(s_epoch, exp_dict['max_epoch']):
# Set seed
seed = e + exp_dict['runs']
np.random.seed(seed)
torch.manual_seed(seed)
torch.cuda.manual_seed_all(seed)
score_dict = {}
# Compute train loss over train set
score_dict["train_loss"] = metrics.compute_metric_on_dataset(
model, train_set, metric_name=exp_dict["loss_func"])
# Compute val acc over val set
score_dict["val_acc"] = metrics.compute_metric_on_dataset(
model, val_set, metric_name=exp_dict["acc_func"])
# Train over train loader
model.train()
print("%d - Training model with %s..." % (e, exp_dict["loss_func"]))
# train and validate
s_time = time.time()
for batch in tqdm.tqdm(train_loader):
images, labels = batch["images"].cuda(), batch["labels"].cuda()
opt.zero_grad()
# closure
def closure():
return loss_function(model, images, labels, backwards=True)
opt.step(closure)
e_time = time.time()
# Record metrics
score_dict["epoch"] = e
score_dict["step_size"] = opt.state["step_size"]
score_dict["step_size_avg"] = opt.state["step_size_avg"]
score_dict["n_forwards"] = opt.state["n_forwards"]
score_dict["n_backwards"] = opt.state["n_backwards"]
score_dict["grad_norm"] = opt.state["grad_norm"]
score_dict["batch_size"] = train_loader.batch_size
score_dict["train_epoch_time"] = e_time - s_time
score_list += [score_dict]
# Report and save
print(pd.DataFrame(score_list).tail())
hu.save_pkl(score_list_path, score_list)
hu.torch_save(model_path, model.state_dict())
hu.torch_save(opt_path, opt.state_dict())
print("Saved: %s" % savedir)
print('Experiment completed')
def trainval(exp_dict, savedir_base, datadir_base, reset=False):
# bookkeeping stuff
# ==================
pprint.pprint(exp_dict)
exp_id = hu.hash_dict(exp_dict)
savedir = os.path.join(savedir_base, exp_id)
if reset:
hc.delete_and_backup_experiment(savedir)
os.makedirs(savedir, exist_ok=True)
hu.save_json(os.path.join(savedir, "exp_dict.json"), exp_dict)
print("Experiment saved in %s" % savedir)
# Dataset
# ==================
# load train and acrtive set
train_set = datasets.get_dataset(dataset_name=exp_dict["dataset"],
split="train",
datadir_base=datadir_base,
exp_dict=exp_dict)
active_set = ActiveLearningDataset(train_set, random_state=42)
# val set
val_set = datasets.get_dataset(dataset_name=exp_dict["dataset"],
split="val",
datadir_base=datadir_base,
exp_dict=exp_dict)
val_loader = DataLoader(val_set, batch_size=exp_dict["batch_size"])
# Model
# ==================
model = models.get_model(model_name=exp_dict['model']['name'],
exp_dict=exp_dict).cuda()
model_path = os.path.join(savedir, "model.pth")
score_list_path = os.path.join(savedir, "score_list.pkl")
if os.path.exists(score_list_path):
# resume experiment
model.set_state_dict(hu.torch_load(model_path))
active_set.load_state_dict(
hu.load_pkl(os.path.join(savedir, "active_set.pkl")))
score_list = hu.load_pkl(score_list_path)
inner_s_epoch = score_list[-1]['inner_epoch'] + 1
s_cycle = score_list[-1]['cycle']
else:
# restart experiment
score_list = []
inner_s_epoch = 0
s_cycle = 0
# Train & Val
# ==================
print("Starting experiment at cycle %d epoch %d" %
(s_cycle, inner_s_epoch))
for c in range(s_cycle, exp_dict['max_cycle']):
# Set seed
np.random.seed(c)
torch.manual_seed(c)
torch.cuda.manual_seed_all(c)
if inner_s_epoch == 0:
active_set.label_next_batch(model)
hu.save_pkl(os.path.join(savedir, "active_set.pkl"),
active_set.state_dict())
train_loader = DataLoader(active_set,
sampler=samplers.get_sampler(
exp_dict['sampler']['train'],
active_set),
batch_size=exp_dict["batch_size"])
# Visualize the model
model.vis_on_loader(vis_loader,
savedir=os.path.join(savedir, "images"))
for e in range(inner_s_epoch, exp_dict['max_epoch']):
# Validate only at the start of each cycle
score_dict = {}
if e == 0:
score_dict.update(model.val_on_loader(val_loader))
# Train the model
score_dict.update(model.train_on_loader(train_loader))
# Validate the model
score_dict["epoch"] = len(score_list)
score_dict["inner_epoch"] = e
score_dict["cycle"] = c
score_dict['n_ratio'] = active_set.n_labelled_ratio
score_dict["n_train"] = len(train_loader.dataset)
score_dict["n_pool"] = len(train_loader.dataset.pool)
# Add to score_list and save checkpoint
score_list += [score_dict]
# Report & Save
score_df = pd.DataFrame(score_list)
print("\n", score_df.tail(), "\n")
hu.torch_save(model_path, model.get_state_dict())
hu.save_pkl(score_list_path, score_list)
print("Checkpoint Saved: %s" % savedir)
inner_s_epoch = 0
def trainval(exp_dict, savedir_base, data_root, reset=False, tensorboard=True):
# bookkeeping
# ---------------
# get experiment directory
exp_id = hu.hash_dict(exp_dict)
savedir = os.path.join(savedir_base, exp_id)
np.random.seed(exp_dict["seed"])
torch.manual_seed(exp_dict["seed"])
if reset:
# delete and backup experiment
hc.delete_experiment(savedir, backup_flag=True)
writer = tensorboardX.SummaryWriter(savedir) \
if tensorboard == 1 else None
# create folder and save the experiment dictionary
os.makedirs(savedir, exist_ok=True)
hu.save_json(os.path.join(savedir, "exp_dict.json"), exp_dict)
pprint.pprint(exp_dict)
print("Experiment saved in %s" % savedir)
# Dataset
# -----------
train_dataset, val_dataset = get_dataset(['train', 'val'], data_root,
exp_dict)
# val_dataset = get_dataset('val', exp_dict)
# train and val loader
if exp_dict["episodic"] == False:
train_loader = DataLoader(train_dataset,
batch_size=exp_dict['batch_size'],
shuffle=True,
num_workers=args.num_workers)
val_loader = DataLoader(val_dataset,
batch_size=exp_dict['batch_size'],
shuffle=True,
num_workers=args.num_workers)
else: # to support episodes TODO: move inside each model
from datasets.episodic_dataset import EpisodicDataLoader
train_loader = EpisodicDataLoader(train_dataset,
batch_size=exp_dict['batch_size'],
shuffle=True,
collate_fn=lambda x: x,
num_workers=args.num_workers)
val_loader = EpisodicDataLoader(val_dataset,
batch_size=exp_dict['batch_size'],
shuffle=True,
collate_fn=lambda x: x,
num_workers=args.num_workers)
# Model
# -----------
model = get_model(exp_dict,
labelset=train_dataset.raw_labelset,
writer=writer)
print("Model with:",
sum(p.numel() for p in model.parameters() if p.requires_grad),
"parameters")
# Checkpoint
# -----------
model_path = os.path.join(savedir, "model.pth")
score_list_path = os.path.join(savedir, "score_list.pkl")
if os.path.exists(score_list_path):
# resume experiment
model.set_state_dict(hu.torch_load(model_path))
score_list = hu.load_pkl(score_list_path)
s_epoch = score_list[-1]['epoch'] + 1
else:
# restart experiment
score_list = []
s_epoch = 0
# Train & Val
# ------------
print("Starting experiment at epoch %d" % (s_epoch))
for e in range(s_epoch, exp_dict['max_epoch']):
score_dict = {}
# Train the model
score_dict.update(model.train_on_loader(e, train_loader))
# Validate the model
score_dict.update(model.val_on_loader(e, val_loader))
score_dict["epoch"] = e
if tensorboard:
for key, value in score_dict.items():
writer.add_scalar(key, value, e)
writer.flush()
# Visualize the model
# model.vis_on_loader(vis_loader, savedir=savedir+"/images/")
# Add to score_list and save checkpoint
score_list += [score_dict]
# Report & Save
score_df = pd.DataFrame(score_list)
print("\n", score_df.tail())
hu.torch_save(model_path, model.get_state_dict())
hu.save_pkl(score_list_path, score_list)
print("Checkpoint Saved: %s" % savedir)
# if model.is_end():
# print("Early stopping")
# break
print('experiment completed')
# Cleanup
if tensorboard == 1:
writer.close()
def get_dataset(dataset_name, train_flag, datadir, exp_dict):
if dataset_name == "mnist":
dataset = torchvision.datasets.MNIST(datadir, train=train_flag,
download=True,
transform=torchvision.transforms.Compose([
torchvision.transforms.ToTensor(),
torchvision.transforms.Normalize(
(0.5,), (0.5,))
]))
if dataset_name == "cifar10":
if train_flag:
transform_function = transforms.Compose([
transforms.RandomCrop(32, padding=4),
transforms.RandomHorizontalFlip(),
transforms.ToTensor(),
transforms.Normalize((0.4914, 0.4822, 0.4465),
(0.2023, 0.1994, 0.2010)),
])
else:
transform_function = transforms.Compose([
transforms.ToTensor(),
transforms.Normalize((0.4914, 0.4822, 0.4465), (0.2023, 0.1994, 0.2010)),
])
dataset = torchvision.datasets.CIFAR10(
root=datadir,
train=train_flag,
download=True,
transform=transform_function)
if dataset_name == "cifar100":
if train_flag:
transform_function = transforms.Compose([
transforms.RandomCrop(32, padding=4),
transforms.RandomHorizontalFlip(),
transforms.ToTensor(),
transforms.Normalize((0.4914, 0.4822, 0.4465),
(0.2023, 0.1994, 0.2010)),
])
else:
transform_function = transforms.Compose([
transforms.ToTensor(),
transforms.Normalize((0.4914, 0.4822, 0.4465), (0.2023, 0.1994, 0.2010)),
])
dataset = torchvision.datasets.CIFAR100(
root=datadir,
train=train_flag,
download=True,
transform=transform_function)
if dataset_name in ['syn']:
bias = 1;
scaling = 10;
sparsity = 10;
solutionSparsity = 0.1;
n = 1000
p = 100
A = np.random.randn(n,p)+bias;
A = A.dot(np.diag(scaling* np.random.randn(p)))
A = A * (np.random.rand(n,p) < (sparsity*np.log(n)/n));
w = np.random.randn(p) * (np.random.rand(p) < solutionSparsity);
b = np.sign(A.dot(w));
b = b * np.sign(np.random.rand(n)-0.1);
labels = np.unique(b)
A = A / np.linalg.norm(A, axis=1)[:, None].clip(min=1e-6)
A = A * 2
b[b==labels[0]] = 0
b[b==labels[1]] = 1
dataset = torch.utils.data.TensorDataset(torch.FloatTensor(A), torch.FloatTensor(b))
return DatasetWrapper(dataset)
if dataset_name in ['mushrooms', 'w8a', 'rcv1', 'ijcnn']:
sigma_dict = {"mushrooms": 0.5,
"w8a":20.0,
"rcv1":0.25 ,
"ijcnn":0.05}
X, y = load_libsvm(dataset_name, data_dir=datadir)
labels = np.unique(y)
y[y==labels[0]] = 0
y[y==labels[1]] = 1
# splits used in experiments
splits = train_test_split(X, y, test_size=0.2, shuffle=True, random_state=9513451)
X_train, X_test, Y_train, Y_test = splits
if train_flag:
# fname_rbf = "%s/rbf_%s_%s_train.pkl" % (datadir, dataset_name, sigma_dict[dataset_name])
fname_rbf = "%s/rbf_%s_%s_train.npy" % (datadir, dataset_name, sigma_dict[dataset_name])
if os.path.exists(fname_rbf):
k_train_X = np.load(fname_rbf)
else:
k_train_X = rbf_kernel(X_train, X_train, sigma_dict[dataset_name])
np.save(fname_rbf, k_train_X)
print('%s saved' % fname_rbf)
X_train = k_train_X
X_train = torch.FloatTensor(X_train)
Y_train = torch.FloatTensor(Y_train)
dataset = torch.utils.data.TensorDataset(X_train, Y_train)
else:
fname_rbf = "%s/rbf_%s_%s_test.npy" % (datadir, dataset_name, sigma_dict[dataset_name])
if os.path.exists(fname_rbf):
k_test_X = np.load(fname_rbf)
else:
k_test_X = rbf_kernel(X_test, X_train, sigma_dict[dataset_name])
# hu.save_pkl(fname_rbf, k_test_X)
np.save(fname_rbf, k_test_X)
print('%s saved' % fname_rbf)
X_test = k_test_X
X_test = torch.FloatTensor(X_test)
Y_test = torch.FloatTensor(Y_test)
dataset = torch.utils.data.TensorDataset(X_test, Y_test)
if dataset_name == "matrix_fac":
fname = datadir + 'matrix_fac.pkl'
if not os.path.exists(fname):
data = generate_synthetic_matrix_factorization_data()
hu.save_pkl(fname, data)
A, y = hu.load_pkl(fname)
X_train, X_test, y_train, y_test = train_test_split(A, y, test_size=0.2, random_state=9513451)
training_set = torch.utils.data.TensorDataset(torch.tensor(X_train, dtype=torch.float), torch.tensor(y_train, dtype=torch.float))
test_set = torch.utils.data.TensorDataset(torch.tensor(X_test, dtype=torch.float), torch.tensor(y_test, dtype=torch.float))
if train_flag:
dataset = training_set
else:
dataset = test_set
return DatasetWrapper(dataset)
def test_get_result_manager(self):
# save a score_list
savedir_base = '.tmp_plots'
if os.path.exists(savedir_base):
shutil.rmtree(savedir_base)
exp_dict = {'model':{'name':'mlp', 'n_layers':30},
'dataset':'mnist', 'batch_size':1}
score_list = [{'epoch': 0, 'acc':0.5}, {'epoch': 1, 'acc':0.9}]
hu.save_pkl(os.path.join(savedir_base, hu.hash_dict(exp_dict),
'score_list.pkl'), score_list)
hu.save_json(os.path.join(savedir_base, hu.hash_dict(exp_dict),
'exp_dict.json'), exp_dict)
exp_dict = {'model':{'name':'mlp', 'n_layers':30},
'dataset':'cifar10', 'batch_size':1}
score_list = [{'epoch': 0, 'acc':0.25}, {'epoch': 1, 'acc':1.24}, {'epoch': 2, 'acc':1.5}]
hu.save_pkl(os.path.join(savedir_base, hu.hash_dict(exp_dict),
'score_list.pkl'), score_list)
hu.save_json(os.path.join(savedir_base, hu.hash_dict(exp_dict),
'exp_dict.json'), exp_dict)
exp_dict = {'model':{'name':'lenet', 'n_layers':30},
'dataset':'cifar10', 'batch_size':1}
score_list = [{'epoch': 0, 'acc':0.35}, {'epoch': 1, 'acc':1.2}, {'epoch': 2, 'acc':1.3}]
hu.save_pkl(os.path.join(savedir_base, hu.hash_dict(exp_dict),
'score_list.pkl'), score_list)
hu.save_json(os.path.join(savedir_base, hu.hash_dict(exp_dict),
'exp_dict.json'), exp_dict)
exp_dict = {'model':{'name':'lenet', 'n_layers':30},
'dataset':'cifar10', 'batch_size':5}
score_list = [{'epoch': 0, 'acc':0.15}, {'epoch': 1, 'acc':1.21}, {'epoch': 2, 'acc':1.7}]
hu.save_pkl(os.path.join(savedir_base, hu.hash_dict(exp_dict),
'score_list.pkl'), score_list)
hu.save_json(os.path.join(savedir_base, hu.hash_dict(exp_dict),
'exp_dict.json'), exp_dict)
rm = hr.ResultManager(savedir_base=savedir_base)
# assert(len(rm.exp_groups) == 2)
# for exp_list in rm.exp_groups:
# assert(exp_list[0]['dataset'] in ['mnist', 'cifar10'])
rm.get_exp_list_df()
rm.get_score_df(avg_across='dataset')
rm.get_score_df(avg_across='dataset', add_prefix=True)
rm.get_score_df()
rm.get_score_lists()
rm.get_images()
table = rm.get_score_table()
table = rm.get_exp_table()
fig_list = rm.get_plot(x_metric='epoch', y_metric='acc', title_list=['dataset'], legend_list=['model'])
for i, fig in enumerate(fig_list):
fig.savefig(os.path.join(savedir_base, '%d.png' % i))
order = 'groups_by_metrics'
fig_list = rm.get_plot_all(order=order, x_metric='epoch', y_metric_list=['acc', 'epoch'], title_list=['dataset'],
legend_list=['model'],
groupby_list=['dataset'],
log_metric_list=['acc'],
map_title_list=[{'mnist':'MNIST'}, {'cifar10':'CIFAR-10'}],
map_xlabel_list=[{'epoch':'EPOCHS'}],
map_ylabel_list=[{'acc':'Score'}],
ylim_list=[[(0.5, 0.8),(0.5, 0.8)],
[(0.5, 0.8),(0.5, 0.8)]])
for i, fig in enumerate(fig_list):
fig.savefig(os.path.join(savedir_base, '%s_%d.png' % (order, i)))
order = 'metrics_by_groups'
fig_list = rm.get_plot_all(order=order, x_metric='epoch', y_metric_list=['acc', 'epoch'], title_list=['dataset'],
legend_list=['model'], avg_across='batch_size')
for i, fig in enumerate(fig_list):
fig.savefig(os.path.join(savedir_base, '%s_%d.png' % (order, i)))
def trainval(exp_dict, savedir_base, reset=False):
# bookkeeping
# ---------------
# get experiment directory
exp_id = hu.hash_dict(exp_dict)
savedir = os.path.join(savedir_base, exp_id)
if reset:
# delete and backup experiment
hc.delete_experiment(savedir, backup_flag=True)
# create folder and save the experiment dictionary
os.makedirs(savedir, exist_ok=True)
hu.save_json(os.path.join(savedir, "exp_dict.json"), exp_dict)
print(exp_dict)
print("Experiment saved in %s" % savedir)
# Set Seed
# -------
seed = exp_dict.get('seed')
np.random.seed(seed)
torch.manual_seed(seed)
# Dataset
# -----------
train_dataset = get_dataset('train', exp_dict['dataset'])
val_dataset = get_dataset('test', exp_dict['dataset'])
# train and val loader
train_loader = DataLoader(
train_dataset,
batch_size=exp_dict['batch_size'],
shuffle=True,
collate_fn=lambda x: x
if exp_dict['batch_size'] == 1 else default_collate,
# to handle episodes
num_workers=args.num_workers)
val_loader = DataLoader(
val_dataset,
batch_size=exp_dict['batch_size'],
collate_fn=lambda x: x
if exp_dict['batch_size'] == 1 else default_collate,
shuffle=True,
num_workers=args.num_workers)
# Model
# -----------
model = get_model(exp_dict)
# Checkpoint
# -----------
model_path = os.path.join(savedir, "model.pth")
score_list_path = os.path.join(savedir, "score_list.pkl")
if os.path.exists(score_list_path):
# resume experiment
model.set_state_dict(hu.torch_load(model_path))
score_list = hu.load_pkl(score_list_path)
s_epoch = score_list[-1]['epoch'] + 1
else:
# restart experiment
score_list = []
s_epoch = 0
# Train & Val
# ------------
print("Starting experiment at epoch %d" % (s_epoch))
for e in range(s_epoch, exp_dict['max_epoch']):
score_dict = {}
# Train the model
score_dict.update(model.train_on_loader(train_loader))
# Validate the model
savepath = os.path.join(savedir_base, exp_dict['dataset']['name'])
score_dict.update(model.val_on_loader(val_loader, savedir=savepath))
model.on_train_end(savedir=savedir, epoch=e)
score_dict["epoch"] = e
# Visualize the model
# model.vis_on_loader(vis_loader, savedir=savedir+"/images/")
# Add to score_list and save checkpoint
score_list += [score_dict]
# Report & Save
score_df = pd.DataFrame(score_list)
print("\n", score_df.tail())
hu.torch_save(model_path, model.get_state_dict())
hu.save_pkl(score_list_path, score_list)
print("Checkpoint Saved: %s" % savedir)
print('experiment completed')
val_dict_dfc.rename(columns={
'test_score': 'mIoU',
'test_class0': 'IoU class 0',
'test_class1': 'IoU class 1',
'test_mae': 'MAE',
'test_game': 'GAME'
},
inplace=True)
val_dict_lst.append(val_dict_dfc)
val_dict_df = pd.concat(val_dict_lst, axis=0)
val_dict_df.to_csv(os.path.join(
'/mnt/public/predictions/habitat/',
"%s_habitat_score_df.csv" % hash_id),
index=False)
val_dict_df.to_latex(os.path.join(
'/mnt/public/predictions/habitat/',
"%s_habitat_score_df.tex" % hash_id),
index=False,
caption=hash_dct[hash_id],
label=hash_dct[hash_id])
hu.save_pkl(fname, val_dict)
val_dict['model'] = exp_dict['model']
score_list += [val_dict]
print(pd.DataFrame(score_list))
# score_df = pd.DataFrame(score_list)
# score_df.to_csv(os.path.join('/mnt/public/predictions/habitat/', "habitat_score_df.csv"))
# score_df.to_latex(os.path.join('/mnt/public/predictions/habitat/', "habitat_score_df.tex"))
if __name__ == "__main__":
savedir_base = ".tmp"
exp_dict = {
"model": {
"name": "mlp",
"n_layers": 30
},
"dataset": "mnist",
"batch_size": 1
}
score_list = [{"epoch": 4, "acc": 0.5}, {"epoch": 6, "acc": 0.9}]
hu.save_pkl(
os.path.join(savedir_base, hu.hash_dict(exp_dict), "score_list.pkl"),
score_list)
hu.save_json(
os.path.join(savedir_base, hu.hash_dict(exp_dict), "exp_dict.json"),
exp_dict)
exp_dict = {
"model": {
"name": "mlp2",
"n_layers": 35
},
"dataset": "mnist",
"batch_size": 1
}
score_list = [{"epoch": 2, "acc": 0.1}, {"epoch": 6, "acc": 0.3}]
