def __call__(self, data):
if isinstance(data, list):
data = [self._process(d) for d in tq(data)]
data = list(itertools.chain(*data)) # 2d list needs to be flatten
else:
data = self._process(data)
return data
def download_file(url: str, path: str, verbose: bool = False) -> None:
"""
Download file with progressbar
Usage:
download_file('http://web4host.net/5MB.zip')
"""
if not os.path.exists(path):
os.makedirs(path)
local_filename = os.path.join(path, url.split('/')[-1])
r = requests.get(url, stream=True)
file_size = int(r.headers['Content-Length']) if 'Content-Length' in r.headers else 0
chunk_size = 1024
num_bars = int(file_size / chunk_size)
if verbose:
print(dict(file_size=file_size))
print(dict(num_bars=num_bars))
if not os.path.exists(local_filename):
with open(local_filename, 'wb') as fp:
for chunk in tq(
r.iter_content(chunk_size=chunk_size),
total=num_bars,
unit='KB',
desc=local_filename,
leave=True # progressbar stays
):
fp.write(chunk) # type: ignore
if '.zip' in local_filename:
if os.path.exists(local_filename):
with zipfile.ZipFile(local_filename, 'r') as zip_ref:
zip_ref.extractall(path)
def _process_filenames(self, filenames):
data_raw_list = []
data_list = []
categories_ids = [self.category_ids[cat] for cat in self.categories]
cat_idx = {categories_ids[i]: i for i in range(len(categories_ids))}
has_pre_transform = self.pre_transform is not None
id_scan = -1
for name in tq(filenames):
cat = name.split(osp.sep)[0]
if cat not in categories_ids:
continue
id_scan += 1
data = read_txt_array(osp.join(self.raw_dir, name))
pos = data[:, :3]
x = data[:, 3:6]
y = data[:, -1].type(torch.long)
category = torch.ones(x.shape[0], dtype=torch.long) * cat_idx[cat]
id_scan_tensor = torch.from_numpy(np.asarray([id_scan])).clone()
data = Data(pos=pos,
x=x,
y=y,
category=category,
id_scan=id_scan_tensor)
data = SaveOriginalPosId()(data)
if self.pre_filter is not None and not self.pre_filter(data):
continue
data_raw_list.append(data.clone() if has_pre_transform else data)
if has_pre_transform:
data = self.pre_transform(data)
data_list.append(data)
if not has_pre_transform:
return [], data_raw_list
return data_raw_list, data_list
def generate(size, **kwargs):
generator = DataGenerator.from_robbins_dataset(
diamlims=kwargs["diamlims"],
ellipse_limit=kwargs["ellipse_limit"],
arc_lims=kwargs["arc_lims"],
axis_threshold=kwargs["axis_threshold"],
fov=kwargs["fov"],
resolution=kwargs["resolution"],
filled=kwargs["filled"],
mask_thickness=kwargs["mask_thickness"],
instancing=kwargs["instancing"])
date_dataset = np.empty((size, 3), int)
images_dataset = np.empty((size, 1, *generator.resolution), np.float32)
if kwargs["instancing"]:
masks_dataset = np.empty((size, 1, *generator.resolution), np.int16)
else:
masks_dataset = np.empty((size, 1, *generator.resolution), np.bool_)
position_dataset = np.empty((size, 3, 1), np.float64)
attitude_dataset = np.empty((size, 3, 3), np.float64)
sol_incidence_dataset = np.empty((size, 1), np.float16)
A_craters = []
for i in tq(range(size), desc="Creating dataset"):
date = dt.date(2021, np.random.randint(1, 12), 1)
generator.set_random_position()
generator.scene_time = date
date_dataset[i] = np.array((date.year, date.month, date.day))
while not (kwargs["min_sol_incidence"] <=
generator.solar_incidence_angle <=
kwargs["max_sol_incidence"]):
generator.set_random_position() # Generate random position
position_dataset[i] = generator.position
sol_incidence_dataset[i] = generator.solar_incidence_angle
generator.point_nadir()
if kwargs["randomized_orientation"]:
# Rotations are incremental (order matters)
generator.rotate('roll', np.random.randint(0, 360))
generator.rotate('pitch', np.random.randint(-30, 30))
generator.rotate('yaw', np.random.randint(-30, 30))
attitude_dataset[i] = generator.attitude
image, mask = generator.image_mask_pair()
masks_dataset[i] = mask[None, None, ...]
images_dataset[i] = image[None, None, ...]
if kwargs["save_craters"]:
A_craters.append(generator.craters_in_image())
return images_dataset, masks_dataset, position_dataset, attitude_dataset, date_dataset, sol_incidence_dataset, A_craters
def sample_chains(susceptible,
initial_infected,
model,
daily_ri_values,
num_chains=1000,
n_workers=None,
pool=None,
deterministic=False,
show_progress=False):
if n_workers is not None and n_workers > 1 and pool is None:
pool = initialize_pool(n_workers, np.random.SeedSequence())
pbar = None
if show_progress:
try:
from tqdm.auto import tqdm as tq
pbar = tq(total=num_chains)
except:
warnings.warn(
"Could not load tqdm to show progress, please install it to use the option show_progress"
)
simulations = np.zeros(shape=(num_chains, len(daily_ri_values),
len(STATE_NAMES)))
if pool is None:
it = (simulation(susceptible,
initial_infected,
model,
daily_ri_values,
deterministic=deterministic)
for _ in range(num_chains))
else:
it = pool.imap_unordered(
_fn_simulation,
[(susceptible, initial_infected, model.parameters, daily_ri_values,
model.alphas, model.betas, deterministic)
for _ in range(num_chains)])
for i, (st, _) in enumerate(it):
simulations[i, :, :] = st
if pbar is not None:
pbar.update()
if pbar is not None:
pbar.close()
if pool is not None:
pool.terminate()
return simulations
def download_data(url: str,
path: str = "data/",
verbose: bool = False) -> None:
"""
Download file with progressbar
# Code taken from: https://gist.github.com/ruxi/5d6803c116ec1130d484a4ab8c00c603
# __author__ = "github.com/ruxi"
# __license__ = "MIT"
Usage:
download_file('http://web4host.net/5MB.zip')
"""
if url == "NEED_TO_BE_CREATED":
raise NotImplementedError
if not os.path.exists(path):
os.makedirs(path)
local_filename = os.path.join(path, url.split('/')[-1])
r = requests.get(url, stream=True, verify=False)
file_size = int(
r.headers['Content-Length']) if 'Content-Length' in r.headers else 0
chunk_size = 1024
num_bars = int(file_size / chunk_size)
if verbose:
print(dict(file_size=file_size))
print(dict(num_bars=num_bars))
if not os.path.exists(local_filename):
with open(local_filename, 'wb') as fp:
for chunk in tq(
r.iter_content(chunk_size=chunk_size),
total=num_bars,
unit='KB',
desc=local_filename,
leave=True # progressbar stays
):
fp.write(chunk) # type: ignore
if '.zip' in local_filename:
if os.path.exists(local_filename):
with zipfile.ZipFile(local_filename, 'r') as zip_ref:
zip_ref.extractall(path)
def process_filenames(self, filenames):
data_list = []
categories_ids = [self.category_ids[cat] for cat in self.categories]
cat_idx = {categories_ids[i]: i for i in range(len(categories_ids))}
for name in tq(filenames):
cat = name.split(osp.sep)[0]
if cat not in categories_ids:
continue
data = read_txt_array(osp.join(self.raw_dir, name))
pos = data[:, :3]
x = data[:, 3:6]
y = data[:, -1].type(torch.long)
category = torch.ones(x.shape[0], dtype=torch.long) * cat_idx[cat]
data = Data(pos=pos, x=x, y=y, category=category)
if self.pre_filter is not None and not self.pre_filter(data):
continue
if self.pre_transform is not None:
data = self.pre_transform(data)
data_list.append(data)
return data_list
def download_file(url: str, path: str, verbose: bool = False) -> None:
"""
Download file with progressbar
Usage:
download_file('http://web4host.net/5MB.zip')
"""
if not os.path.exists(path):
os.makedirs(path)
local_filename = os.path.join(path, url.split('/')[-1])
if not os.path.exists(local_filename):
r = requests.get(url, stream=True)
file_size = int(r.headers.get('Content-Length', 0))
chunk = 1
chunk_size = 1024
num_bars = int(file_size / chunk_size)
if verbose:
logging.info(f'file size: {file_size}\n# bars: {num_bars}')
with open(local_filename, 'wb') as fp:
for chunk in tq(
r.iter_content(chunk_size=chunk_size),
total=num_bars,
unit='KB',
desc=local_filename,
leave=True # progressbar stays
):
fp.write(chunk) # type: ignore
if '.zip' in local_filename:
if os.path.exists(local_filename):
with zipfile.ZipFile(local_filename, 'r') as zip_ref:
zip_ref.extractall(path)
elif '.tar.gz' in local_filename:
if os.path.exists(local_filename):
with tarfile.open(local_filename, 'r') as tar_ref:
tar_ref.extractall(path)
def process(self):
if not os.path.exists(self.pre_processed_path):
train_areas = [f for f in self.folders if str(self.test_area) not in f]
test_areas = [f for f in self.folders if str(self.test_area) in f]
train_files = [
(f, room_name, osp.join(self.raw_dir, f, room_name))
for f in train_areas
for room_name in os.listdir(osp.join(self.raw_dir, f))
if os.path.isdir(osp.join(self.raw_dir, f, room_name))
]
test_files = [
(f, room_name, osp.join(self.raw_dir, f, room_name))
for f in test_areas
for room_name in os.listdir(osp.join(self.raw_dir, f))
if os.path.isdir(osp.join(self.raw_dir, f, room_name))
]
# Gather data per area
data_list = [[] for _ in range(6)]
for (area, room_name, file_path) in tq(train_files + test_files):
area_num = int(area[-1]) - 1
if self.debug:
read_s3dis_format(file_path, room_name, label_out=True, verbose=self.verbose, debug=self.debug)
continue
else:
xyz, rgb, room_labels, room_object_indices = read_s3dis_format(
file_path, room_name, label_out=True, verbose=self.verbose, debug=self.debug
)
rgb_norm = rgb.float() / 255.0
data = Data(pos=xyz, y=room_labels, rgb=rgb_norm)
if room_name in VALIDATION_ROOMS:
data.validation_set = True
else:
data.validation_set = False
if self.keep_instance:
data.room_object_indices = room_object_indices
if self.pre_filter is not None and not self.pre_filter(data):
continue
data_list[area_num].append(data)
raw_areas = cT.PointCloudFusion()(data_list)
for i, area in enumerate(raw_areas):
torch.save(area, self.raw_areas_paths[i])
for area_datas in data_list:
# Apply pre_transform
if self.pre_transform is not None:
for data in area_datas:
data = self.pre_transform(data)
torch.save(data_list, self.pre_processed_path)
else:
data_list = torch.load(self.pre_processed_path)
if self.debug:
return
train_data_list = {}
val_data_list = {}
trainval_data_list = {}
for i in range(6):
if i != self.test_area - 1:
train_data_list[i] = []
val_data_list[i] = []
for data in data_list[i]:
validation_set = data.validation_set
del data.validation_set
if validation_set:
val_data_list[i].append(data)
else:
train_data_list[i].append(data)
trainval_data_list[i] = val_data_list[i] + train_data_list[i]
train_data_list = list(train_data_list.values())
val_data_list = list(val_data_list.values())
trainval_data_list = list(trainval_data_list.values())
test_data_list = data_list[self.test_area - 1]
if self.pre_collate_transform:
log.info("pre_collate_transform ...")
log.info(self.pre_collate_transform)
train_data_list = self.pre_collate_transform(train_data_list)
val_data_list = self.pre_collate_transform(val_data_list)
test_data_list = self.pre_collate_transform(test_data_list)
trainval_data_list = self.pre_collate_transform(trainval_data_list)
self._save_data(train_data_list, val_data_list, test_data_list, trainval_data_list)
num_workers=2)
#confusion matrix
conf_mat = np.zeros((len(LABELS), len(LABELS)))
outputs = []
y_trues = []
# SVM, RF, NB and HGB
y_trues_sota = []
y_preds_svm = []
y_preds_rf = []
y_preds_nb = []
y_preds_hgb = []
for idx, (image, y_true, _) in tq(enumerate(test_loader),
total=len(test_loader)):
if sota:
# apply SVM, RF, NB and HGB methods
features = s2_to_ndvifdi(image.squeeze(0).numpy())
y_trues_sota.append(y_true.squeeze(0))
# svm
y_pred_svm = clf_svm.predict(features.reshape(2, -1).T).reshape(
128, 128)
y_preds_svm.append(y_pred_svm)
# rf
y_pred_rf = clf_rf.predict(features.reshape(2, -1).T).reshape(
128, 128)
y_preds_rf.append(y_pred_rf)
def download_data(url: str,
path: str = "data/",
verbose: bool = False) -> None:
"""Download file with progressbar.
# Code adapted from: https://gist.github.com/ruxi/5d6803c116ec1130d484a4ab8c00c603
# __author__ = "github.com/ruxi"
# __license__ = "MIT"
Examples
________
.. doctest::
>>> import os
>>> from flash.core.data.utils import download_data
>>> download_data("https://pl-flash-data.s3.amazonaws.com/titanic.zip", "./data")
>>> os.listdir("./data") # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
[...]
"""
# Disable warning about making an insecure request
urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning)
if not os.path.exists(path):
os.makedirs(path)
local_filename = os.path.join(path, url.split("/")[-1])
r = requests.get(url, stream=True, verify=False)
file_size = int(
r.headers["Content-Length"]) if "Content-Length" in r.headers else 0
chunk_size = 1024
num_bars = int(file_size / chunk_size)
if verbose:
print(dict(file_size=file_size))
print(dict(num_bars=num_bars))
if not os.path.exists(local_filename):
with open(local_filename, "wb") as fp:
for chunk in tq(
r.iter_content(chunk_size=chunk_size),
total=num_bars,
unit="KB",
desc=local_filename,
leave=True, # progressbar stays
):
fp.write(chunk) # type: ignore
def extract_tarfile(file_path: str, extract_path: str, mode: str):
if os.path.exists(file_path):
with tarfile.open(file_path, mode=mode) as tar_ref:
for member in tar_ref.getmembers():
try:
tar_ref.extract(member,
path=extract_path,
set_attrs=False)
except PermissionError:
raise PermissionError(
f"Could not extract tar file {file_path}")
if ".zip" in local_filename:
if os.path.exists(local_filename):
with zipfile.ZipFile(local_filename, "r") as zip_ref:
zip_ref.extractall(path)
elif local_filename.endswith(".tar.gz") or local_filename.endswith(".tgz"):
extract_tarfile(local_filename, path, "r:gz")
elif local_filename.endswith(".tar.bz2") or local_filename.endswith(
".tbz"):
extract_tarfile(local_filename, path, "r:bz2")
train_loss_list = []
valid_loss_list = []
dice_score_list = []
lr_rate_list = []
valid_loss_min = np.Inf # track change in validation loss
for epoch in range(1, n_epochs+1):
# keep track of training and validation loss
train_loss = 0.0
valid_loss = 0.0
dice_score = 0.0
###################
# train the model #
###################
model.train()
bar = tq(train_loader, postfix={"train_loss":0.0})
for data, target in bar:
# move tensors to GPU if CUDA is available
if train_on_gpu:
data, target = data.cuda(), target.cuda()
# clear the gradients of all optimized variables
optimizer.zero_grad()
# forward pass: compute predicted outputs by passing inputs to the model
output = model(data)
# calculate the batch loss
loss = criterion(output, target)
#print(loss)
# backward pass: compute gradient of the loss with respect to model parameters
loss.backward()
# perform a single optimization step (parameter update)
optimizer.step()
def performance_metrics(self, iou_threshold=0.5, confidence_thresholds=None, distance_threshold=None):
if confidence_thresholds is None:
confidence_thresholds = torch.arange(start=0.05, end=0.99, step=0.05).to(self.device)
loader = DataLoader(self.ds, batch_size=32, shuffle=True, num_workers=0, collate_fn=collate_fn)
bar = tq(loader, desc=f"Testing",
postfix={
"IoU": 0.,
"GA_distance": 0.,
"precision": 0.,
"recall": 0.,
"f1_score": 0.
})
precision = torch.zeros((len(loader), loader.batch_size, len(confidence_thresholds)), device=self.device)
recall = torch.zeros((len(loader), loader.batch_size, len(confidence_thresholds)), device=self.device)
f1 = torch.zeros((len(loader), loader.batch_size, len(confidence_thresholds)), device=self.device)
iou = torch.zeros((len(loader), loader.batch_size, len(confidence_thresholds)), device=self.device)
dist = torch.zeros((len(loader), loader.batch_size, len(confidence_thresholds)), device=self.device)
for batch, (images, targets_all) in enumerate(bar):
images = list(image.to(self.device) for image in images)
targets_all = [{k: v.to(self.device) for k, v in t.items()} for t in targets_all]
pred_all = self._model(images)
for i, (pred, targets) in enumerate(zip(pred_all, targets_all)):
for j, confidence_threshold in enumerate(confidence_thresholds):
precision[batch, i, j], recall[batch, i, j], f1[batch, i, j], \
iou[batch, i, j], dist[batch, i, j] = detection_metrics(pred,
targets,
iou_threshold=iou_threshold,
confidence_threshold=confidence_threshold,
distance_threshold=distance_threshold)
postfix = dict(
IoU=iou[batch].mean().item(),
GA_distance=dist[batch].mean().item(),
precision=precision[batch].mean().item(),
recall=recall[batch].mean().item(),
f1_score=f1[batch].mean().item()
)
bar.set_postfix(ordered_dict=postfix)
del images, targets_all
precision_out = torch.zeros(len(confidence_thresholds))
recall_out = torch.zeros(len(confidence_thresholds))
f1_out = torch.zeros(len(confidence_thresholds))
iou_out = torch.zeros(len(confidence_thresholds))
dist_out = torch.zeros(len(confidence_thresholds))
for i in range(len(confidence_thresholds)):
precision_out[i], recall_out[i], f1_out[i], iou_out[i], dist_out[i] = map(
lambda x: x[..., i][x[..., i] > 0.].mean(),
(precision, recall, f1, iou, dist)
)
precision, recall, f1, iou, dist = map(lambda x: x.mean((0, 1)), (precision, recall, f1, iou, dist))
return precision, recall, f1, iou, dist, confidence_thresholds
def train(self, train_loader, valid_loader,
optimizer, scheduler, valid_score_fn,
n_epochs, train_on_gpu=False, verbose=False, rst_path=None):
"""
:param train_loader:
:param valid_loader:
:param optimizer:
:param scheduler:
:param valid_score_fn:
:param n_epochs:
:param train_on_gpu:
:param verbose:
:param rst_path: a string.
Path to the folder where the error and the best model should be stored.
:return:
"""
if train_on_gpu:
self.model.cuda()
train_loss_list, valid_loss_list, dice_score_list = [], [], []
lr_rate_list = []
valid_loss_min = np.Inf
for epoch in range(1, n_epochs + 1):
# keep track of training and validation loss
train_loss = 0.0
valid_loss = 0.0
dice_score = 0.0
###################
# train the model #
###################
self.model.train()
bar = tq(train_loader, postfix={"train_loss": 0.0})
for data, target in bar:
# move tensors to GPU if CUDA is available
if train_on_gpu:
data, target = data.cuda(), target.cuda()
optimizer.zero_grad()
# forward pass: compute predicted outputs by passing inputs to the model
output = self.model(data)
# calculate the batch loss
loss = self.criterion(output, target)
# backward pass: compute gradient of the loss with respect to model parameters
loss.backward()
# perform a single optimization step (parameter update)
optimizer.step()
train_loss += loss.item() * data.size(0)
# print("Loss item: {}, data_size:{}".format(loss.item(), data.size(0)))
bar.set_postfix(ordered_dict={"train_loss": loss.item()})
######################
# validate the model #
######################
self.model.eval()
del data, target
with torch.no_grad():
bar = tq(valid_loader, postfix={"valid_loss": 0.0, "dice_score": 0.0})
for data, target in bar:
# move tensors to GPU if CUDA is available
if train_on_gpu:
data, target = data.cuda(), target.cuda()
output = self.model(data)
loss = self.criterion(output, target)
# update average validation loss
valid_loss += loss.item() * data.size(0)
dice_cof = valid_score_fn(output.cpu(), target.cpu()).item()
dice_score += dice_cof * data.size(0)
bar.set_postfix(ordered_dict={"valid_loss": loss.item(), "dice_score": dice_cof})
# calculate average losses
train_loss = train_loss / len(train_loader.dataset)
valid_loss = valid_loss / len(valid_loader.dataset)
dice_score = dice_score / len(valid_loader.dataset)
train_loss_list.append(train_loss)
valid_loss_list.append(valid_loss)
dice_score_list.append(dice_score)
lr_rate_list.append([param_group['lr'] for param_group in optimizer.param_groups])
# print training/validation statistics
print('Epoch: {} Training Loss: {:.6f} Validation Loss: {:.6f} Dice Score: {:.6f}'.format(
epoch, train_loss, valid_loss, dice_score))
if rst_path is not None:
with open(join(rst_path, 'training_rst.txt'), 'w') as frst:
frst.write(str(train_loss_list) + '\n')
frst.write(str(valid_loss_list) + '\n')
frst.write(str(dice_score_list) + '\n')
# save model if validation loss has decreased
if valid_loss <= valid_loss_min:
print('Validation loss decreased ({:.6f} --> {:.6f}). Saving model ...'.format(
valid_loss_min,
valid_loss))
torch.save(self.model.state_dict(), join(rst_path, 'model_cifar.pt'))
valid_loss_min = valid_loss
scheduler.step(valid_loss)
return train_loss_list, valid_loss_list, dice_score_list, lr_rate_list
