def init(filename=None):
rootLogger = logging.getLogger()
if filename is None:
FileUtils.createDir('./logs')
filename = os.path.abspath(
'./logs/' + datetime.now().strftime('%y-%m-%d_auto') + '.log')
if len(rootLogger.handlers) > 0:
if os.path.exists(filename):
return
for each in rootLogger.handlers:
rootLogger.removeHandler(each)
logFormatter = logging.Formatter(
"%(asctime)s [%(threadName)-12.12s] [%(levelname)-5.5s] %(message)s"
)
rootLogger.level = logging.INFO #level
fileHandler = logging.FileHandler(filename)
fileHandler.setFormatter(logFormatter)
rootLogger.addHandler(fileHandler)
consoleHandler = logging.StreamHandler()
consoleHandler.setFormatter(logFormatter)
rootLogger.addHandler(consoleHandler)
def create_local(args):
try:
if args.name and len(args.name) > 0:
filename = './tasks/' + args.report + '/runs/' + args.name + '/' + args.name + '.csv'
if not os.path.exists(filename):
headers = args.params_report_local
with open(filename, 'w') as outfile:
FileUtils.lock_file(outfile)
outfile.write(','.join(headers) + '\n')
outfile.flush()
os.fsync(outfile)
FileUtils.unlock_file(outfile)
except Exception as e:
logging.error(str(e))
exc_type, exc_value, exc_tb = sys.exc_info()
logging.error(
traceback.format_exception(exc_type, exc_value, exc_tb))
def create(args):
try:
if args.report and len(args.report) > 0:
filename = os.path.join('reports', args.report) + '.csv'
if not os.path.exists(filename):
headers = args.params_report
if not args.params_grid is None:
headers += args.params_grid
with open(filename, 'w') as outfile:
FileUtils.lock_file(outfile)
outfile.write(','.join(headers) + '\n')
outfile.flush()
os.fsync(outfile)
FileUtils.unlock_file(outfile)
except Exception as e:
logging.error(str(e))
exc_type, exc_value, exc_tb = sys.exc_info()
logging.error(
traceback.format_exception(exc_type, exc_value, exc_tb))
def process_dists(idx_start, y_each, y_list, path_embeddings, sample_count,
classes_size, embedding_size, triplet_similarity, mode):
try:
path_emb_json = f'{path_embeddings}/{y_each}.json'
path_emb_mem = f'{path_embeddings}/{y_each}.mmap'
path_dists_mem = f'{path_embeddings}/dists.mmap'
dists_mem = np.memmap(path_dists_mem,
mode='r+',
dtype=np.float16,
shape=(sample_count, classes_size))
emb_json = FileUtils.loadJSON(path_emb_json)
emb_mem = np.memmap(path_emb_mem,
mode='r',
dtype=np.float16,
shape=(emb_json['count'], embedding_size))
path_centroids_mem = f'{path_embeddings}/dists.mmap'
centroids_mem = np.memmap(path_centroids_mem,
mode='r',
dtype=np.float16,
shape=(classes_size, embedding_size))
for idx_y in y_list:
np_class_centroids_tiled = np.tile(centroids_mem[idx_y],
(emb_json['count'], 1))
dists = get_distance(emb_mem, np_class_centroids_tiled,
triplet_similarity, mode).tolist()
dists_mem[idx_start:idx_start + emb_json['count'],
idx_y] = dists[:]
#dists_mem.flush()
except Exception as e:
logging.error(str(e))
exc_type, exc_value, exc_tb = sys.exc_info()
logging.error('\n'.join(
traceback.format_exception(exc_type, exc_value, exc_tb)))
parser.add_argument('-debug_batch_count', default=0, type=int) # 0 = release version
parser.add_argument('-embedding_size', default=32, type=int)
parser.add_argument('-gamma', default=0.0, type=float)
parser.add_argument('-C_0', default=0.0, type=float)
parser.add_argument('-C_n', default=5.0, type=float)
parser.add_argument('-C_interval', default=10000, type=int)
parser.add_argument('-C_start', default=0, type=int)
args, args_other = parser.parse_known_args()
path_sequence = f'./results/{args.sequence_name}'
args.run_name += ('-' + datetime.utcnow().strftime(f'%y-%m-%d--%H-%M-%S'))
path_run = f'./results/{args.sequence_name}/{args.run_name}'
FileUtils.createDir(path_run)
path_artifacts = f'./artifacts/{args.sequence_name}/{args.run_name}'
FileUtils.createDir(path_artifacts)
FileUtils.writeJSON(f'{path_run}/args.json', args.__dict__)
CsvUtils2.create_global(path_sequence)
CsvUtils2.create_local(path_sequence, args.run_name)
summary_writer = tensorboard_utils.CustomSummaryWriter(
logdir=path_run
)
rootLogger = logging.getLogger()
logFormatter = logging.Formatter("%(asctime)s [%(process)d] [%(thread)d] [%(levelname)s] %(message)s")
rootLogger.level = logging.INFO #level
default=False,
type=lambda x: (str(x).lower() == 'true'))
args, args_other = parser.parse_known_args()
args = ArgsUtils.add_other_args(args, args_other)
args_other_names = ArgsUtils.extract_other_args_names(args_other)
if args.is_restricted_cpu:
from cgroups import Cgroup # pip install cgroups
# sudo /home/ubuntu/anaconda3/bin/user_cgroups ubuntu
# sudo /home/evalds/.conda/envs/conda_env/bin/user_cgroups evalds
# add all testable parameters to final report header
args.params_report += args_other_names
FileUtils.createDir('./reports')
FileUtils.createDir('./tasks')
FileUtils.createDir('./tasks/' + args.report)
logging_utils = LoggingUtils(filename=os.path.join('reports', args.report +
'.txt'))
ArgsUtils.log_args(args, 'taskgen.py', logging_utils)
task_settings = {'id': 0, 'repeat_id': 0}
tasks_settings_path = os.path.join('tasks', 'tasks.json')
if os.path.exists(tasks_settings_path):
with open(tasks_settings_path, 'r') as outfile:
tasks_settings_loaded = json.load(outfile)
for key in tasks_settings_loaded:
task_settings[key] = tasks_settings_loaded[key]
'score_best',
'loss',
'loss_dqn',
'loss_inverse',
'loss_forward',
'cosine_distance'
]
if not args.params_report is None:
for it in reversed(args.params_report):
if not it in tmp:
tmp.insert(0, it)
args.params_report = tmp
args.params_report_local = args.params_report
FileUtils.createDir('./tasks/' + args.report)
run_path = './tasks/' + args.report + '/runs/' + args.name
if os.path.exists(run_path):
shutil.rmtree(run_path, ignore_errors=True)
time.sleep(3)
while os.path.exists(run_path):
pass
FileUtils.createDir(run_path)
logging_utils = LoggingUtils(filename=os.path.join(run_path, 'log.txt'))
is_logged_cnorm = False
ArgsUtils.log_args(args, 'main.py', logging_utils)
CsvUtils.create_local(args)
parser.add_argument('-hpc_mem',
help='HPC - override mem GB',
default=0,
type=int)
parser.add_argument('-is_hpc',
help='is HPC qsub tasks or local tasks',
default=True,
type=lambda x: (str(x).lower() == 'true'))
parser.add_argument('-hpc_queue', help='hpc queue', default='batch', type=str)
args, args_other = parser.parse_known_args()
FileUtils.createDir('./reports')
FileUtils.createDir('./tasks')
#FileUtils.createDir('./tasks/' + args.report)
if args.is_hpc:
FileUtils.createDir(os.path.expanduser('~') + '/tmp')
logging_utils = LoggingUtils(name=os.path.join('reports', args.report +
'.txt'))
task_settings = {'id': 0, 'repeat_id': 0}
hpc_settings_path = os.path.join('tasks', 'tasks.json')
if os.path.exists(hpc_settings_path):
with open(hpc_settings_path, 'r') as outfile:
hpc_settings_loaded = json.load(outfile)
def add_hparams(path_sequence, run_name, args_dict, metrics_dict, global_step):
try:
path_local_csv = f'{path_sequence}/{run_name}.csv'
path_global_csv = f'{path_sequence}/sequence-{os.path.basename(path_sequence)}.csv'
args_dict = copy.copy(args_dict)
metrics_dict = copy.copy(metrics_dict)
for each_dict in [args_dict, metrics_dict]:
for key in list(each_dict.keys()):
if not isinstance(each_dict[key], float) and \
not isinstance(each_dict[key], int) and \
not isinstance(each_dict[key], str) and \
not isinstance(each_dict[key], np.float) and \
not isinstance(each_dict[key], np.int) and \
not isinstance(each_dict[key], np.float32):
del each_dict[key]
for path_csv in [path_local_csv, path_global_csv]:
if os.path.exists(path_csv):
with open(path_csv, 'r+') as outfile:
FileUtils.lock_file(outfile)
lines_all = outfile.readlines()
lines_all = [it.replace('\n', '').split(',') for it in lines_all if ',' in it]
if len(lines_all) == 0 or len(lines_all[0]) < 2:
headers = ['step'] + list(args_dict.keys()) + list(metrics_dict.keys())
headers = [str(it).replace(',', '_') for it in headers]
lines_all.append(headers)
values = [global_step] + list(args_dict.values()) + list(metrics_dict.values())
values = [str(it).replace(',', '_') for it in values]
if path_csv == path_local_csv:
lines_all.append(values)
else:
# global
existing_line_idx = -1
args_values = list(args_dict.values())
args_values = [str(it).replace(',', '_') for it in args_values]
for idx_line, line in enumerate(lines_all):
if len(line) > 1:
is_match = True
for idx_arg in range(len(args_values)):
if line[idx_arg + 1] != args_values[idx_arg]:
is_match = False
break
if is_match:
existing_line_idx = idx_line
break
if existing_line_idx >= 0:
lines_all[existing_line_idx] = values
else:
lines_all.append(values)
outfile.truncate(0)
outfile.seek(0)
outfile.flush()
rows = [','.join(it) for it in lines_all]
rows = [it for it in rows if len(it.replace('\n', '').strip()) > 0]
outfile.write('\n'.join(rows).strip())
outfile.flush()
os.fsync(outfile)
FileUtils.unlock_file(outfile)
except Exception as e:
logging.exception(e)
# /simpsons/test.mmap
# /simpsons/test.json
parser.add_argument('-path_output',
default='/Users/evalds/Downloads/simpsons_x/',
type=str)
# scale and squeeze images to this size
parser.add_argument('-size_img', default=128, type=int)
parser.add_argument('-thread_max', default=10, type=int)
parser.add_argument('-test_split', default=0.2, type=float)
args, args_other = parser.parse_known_args()
FileUtils.createDir(args.path_output)
logging_utils = LoggingUtils(
f"{args.path_output}/simpsons-{datetime.now().strftime('%y-%m-%d_%H-%M-%S')}.log"
)
class_names = []
last_class_name = None
mmap_shape = [0, 3, args.size_img, args.size_img]
logging_utils.info(
f'move test samples into train to change from classification to re-identification task'
)
paths_files = FileUtils.listSubFiles(args.path_input_test)
for path_file in paths_files:
args_other_names = ArgsUtils.extract_other_args_names(args_other)
if len(args.datasource_include_test_class_ids) > 0:
args.datasource_include_test_class_ids = ' '.join(
args.datasource_include_test_class_ids)
if len(args.datasource_exclude_train_class_ids) > 0:
args.datasource_exclude_train_class_ids = ' '.join(
args.datasource_exclude_train_class_ids)
if args.hpc_queue == 'inf':
args.hpc_gpu_max_queue = 0 # for old ones disable GPU
# add all testable parameters to final report header
args.params_report += args_other_names
FileUtils.createDir('./reports')
FileUtils.createDir('./tasks')
FileUtils.createDir('./tasks/' + args.report)
if args.is_hpc:
FileUtils.createDir(os.path.expanduser('~') + '/tmp')
logging_utils = LoggingUtils(filename=os.path.join('reports', args.report +
'.txt'))
ArgsUtils.log_args(args, 'taskgen.py', logging_utils)
task_settings = {'id': 0, 'repeat_id': 0}
hpc_settings_path = os.path.join('tasks', 'tasks.json')
if os.path.exists(hpc_settings_path):
with open(hpc_settings_path, 'r') as outfile:
hpc_settings_loaded = json.load(outfile)
for key in hpc_settings_loaded:
def __init__(self, args, is_test_data):
super().__init__()
self.args = args
self.is_test_data = is_test_data
path_data = f'{self.args.path_data}/{self.args.datasource_type}'
FileUtils.createDir(path_data)
if not os.path.exists(
f'{self.args.path_data}/{self.args.datasource_type}/lock'):
with open(
f'{self.args.path_data}/{self.args.datasource_type}/lock',
'w') as fp_download_lock:
fp_download_lock.write('')
time.sleep(1.0)
with open(f'{self.args.path_data}/{self.args.datasource_type}/lock',
'r+') as fp_download_lock:
FileUtils.lock_file(fp_download_lock)
transform_colors = torchvision.transforms.ToTensor()
if self.args.datasource_is_grayscale:
transform_colors = torchvision.transforms.Compose([
torchvision.transforms.Grayscale(),
torchvision.transforms.ToTensor()
])
if self.args.datasource_type == 'fassion_mnist':
self.dataset = torchvision.datasets.FashionMNIST(
path_data,
download=True,
train=not is_test_data,
transform=torchvision.transforms.ToTensor())
elif self.args.datasource_type == 'mnist':
self.dataset = torchvision.datasets.MNIST(
path_data,
download=True,
train=not is_test_data,
transform=torchvision.transforms.ToTensor())
elif self.args.datasource_type == 'cifar_10':
self.dataset = torchvision.datasets.CIFAR10(
path_data,
download=True,
train=not is_test_data,
transform=transform_colors)
elif self.args.datasource_type == 'cifar_100':
self.dataset = torchvision.datasets.CIFAR100(
path_data,
download=True,
train=not is_test_data,
transform=transform_colors)
elif self.args.datasource_type == 'emnist': # extended mnist https://arxiv.org/pdf/1702.05373.pdf
self.dataset = torchvision.datasets.EMNIST(
path_data,
download=True,
split='balanced',
train=not is_test_data,
transform=torchvision.transforms.Compose([
lambda img: torchvision.transforms.functional.rotate(
img, -90), lambda img: torchvision.transforms.
functional.hflip(img),
torchvision.transforms.ToTensor()
]))
FileUtils.unlock_file(fp_download_lock)
self.classes = np.arange(np.array(self.dataset.targets).max() +
1).tolist()
groups = [{'samples': [], 'counter': 0} for _ in self.classes]
for img, label_idx in self.dataset:
groups[int(label_idx)]['samples'].append(img)
args.input_size = img.size(1) # channels, w, h
args.input_features = img.size(0)
if not is_test_data:
ids = [
int(it) for it in self.args.datasource_exclude_train_class_ids
]
ids = sorted(ids, reverse=True)
for remove_id in ids:
del self.classes[remove_id]
del groups[remove_id]
else:
if len(self.args.datasource_include_test_class_ids):
ids = set(self.classes) - set([
int(it)
for it in self.args.datasource_include_test_class_ids
])
ids = list(ids)
ids = sorted(ids, reverse=True)
for remove_id in ids:
del self.classes[remove_id]
del groups[remove_id]
self.classes = np.array(self.classes, dtype=np.int)
self.size_samples = 0
for idx, group in enumerate(groups):
samples = group['samples']
self.size_samples += len(samples)
self.groups = groups
# for debugging purposes
# DEBUGGING
if self.args.datasource_size_samples > 0:
logging.info(
f'debugging: reduced data size {self.args.datasource_size_samples}'
)
self.size_samples = self.args.datasource_size_samples
logging.info(
f'{self.args.datasource_type} {"test" if is_test_data else "train"}: classes: {len(groups)} total triplets: {self.size_samples}'
)
if not is_test_data:
self.args.datasource_classes_train = len(
groups) # override class count
if self.args.batch_size % self.args.triplet_positives != 0 or self.args.batch_size <= self.args.triplet_positives:
logging.error(
f'batch does not accommodate triplet_positives {self.args.batch_size} {self.args.triplet_positives}'
)
exit()
self.reshuffle()
def add_results(args, state):
try:
if args.report and len(args.report) > 0:
filename = os.path.join('reports', args.report) + '.csv'
if not os.path.exists(filename):
if not os.path.exists('./reports'):
os.mkdir('./reports')
with open(filename, 'w') as outfile:
FileUtils.lock_file(outfile)
outfile.write(','.join(args.params_report) + '\n')
outfile.flush()
os.fsync(outfile)
FileUtils.unlock_file(outfile)
lines_all = []
with open(filename, 'r+') as outfile:
FileUtils.lock_file(outfile)
raw_lines = outfile.readlines()
if len(raw_lines) > 0:
header_line = raw_lines[0].strip()
headers = header_line.split(',')
else:
headers = args.params_report
lines_all.append(headers)
for line in raw_lines:
line = line.strip()
if len(line) > 0 and ',' in line:
parts = line.split(',')
lines_all.append(parts)
line_new = []
for key in headers:
#! gather from state
if key in state:
line_new.append(str(state[key]))
# ! gather also from args
elif key in vars(args):
line_new.append(str(getattr(args, key)))
# ! if not found empty
else:
line_new.append('')
# look for existing line to override
part_idx_id = headers.index('id')
is_exist = False
try:
for idx_line in range(1, len(lines_all)):
parts = lines_all[idx_line]
part_id = parts[part_idx_id]
if str(args.id) == part_id.strip():
lines_all[idx_line] = line_new
is_exist = True
break
except Exception as e:
logging.error(str(e))
exc_type, exc_value, exc_tb = sys.exc_info()
logging.error(
traceback.format_exception(exc_type, exc_value,
exc_tb))
if not is_exist:
lines_all.append(line_new)
outfile.truncate(0)
outfile.seek(0)
outfile.flush()
rows = [','.join(it) for it in lines_all]
outfile.write('\n'.join(rows))
outfile.flush()
os.fsync(outfile)
FileUtils.unlock_file(outfile)
except Exception as e:
logging.error(str(e))
exc_type, exc_value, exc_tb = sys.exc_info()
logging.error(
traceback.format_exception(exc_type, exc_value, exc_tb))
def calculate_accuracy(
path_embeddings,
meter_acc: tnt.meter.ClassErrorMeter,
meter_auc: tnt.meter.AUCMeter,
type='range',
norm='l2',
triplet_similarity='cos',
mode='cpu',
embedding_size=None,
class_max_dist=None, # precomputed
class_centroids=None,
y_list=None, #precumputed
sample_count=None, #precomputed
paths_embs_idx_path_pairs=None): # precomputed
paths_embs = FileUtils.listSubFiles(path_embeddings)
# calculate centroids first
if class_max_dist is None:
class_centroids = {}
class_max_dist = {}
y_list = []
paths_embs_idx_path_pairs = []
sample_count = 0
for path_emb in paths_embs:
if path_emb.endswith('.json'):
y_each = int(os.path.basename(path_emb).split('.')[0])
path_emb_json = f'{path_embeddings}/{y_each}.json'
path_emb_mem = f'{path_embeddings}/{y_each}.mmap'
emb_json = FileUtils.loadJSON(path_emb_json)
emb_mem = np.memmap(path_emb_mem,
mode='r',
dtype=np.float16,
shape=(emb_json['count'], embedding_size))
paths_embs_idx_path_pairs.append((sample_count, y_each))
sample_count += emb_json['count']
y_list += (np.ones(
(emb_json['count'], ), dtype=np.int) * y_each).tolist()
class_centroids[y_each] = np.average(emb_mem, axis=0)
if norm == 'l2':
class_centroids[y_each] = normalize_vec(
class_centroids[y_each])
np_class_centroids_tiled = np.tile(class_centroids[y_each],
(len(emb_mem), 1))
list_dists = get_distance(np_class_centroids_tiled, emb_mem,
triplet_similarity, mode).tolist()
list_dists = sorted(list_dists, reverse=False)
list_dists = list_dists[:max(
2, int(len(list_dists) * 0.9)
)] # drop 10 top percent embeddings as they could contain noise
class_max_dist[y_each] = list_dists[
-1] # last largest distance
classes_size = int(np.max(y_list)) + 1
# store distance matrix as memmap for optimization
path_dists_mem = f'{path_embeddings}/dists.mmap'
is_exist_dists_mem = os.path.exists(path_dists_mem)
dists_mem = np.memmap(path_dists_mem,
mode='r+' if is_exist_dists_mem else 'w+',
dtype=np.float16,
shape=(sample_count, classes_size))
#dists_mem.flush()
path_centroids_mem = f'{path_embeddings}/dists.mmap'
is_exist_centroids_mem = os.path.exists(path_centroids_mem)
centroids_mem = np.memmap(path_centroids_mem,
mode='r+' if is_exist_centroids_mem else 'w+',
dtype=np.float16,
shape=(classes_size, embedding_size))
for key, value in class_centroids.items():
centroids_mem[key] = value
#centroids_mem.flush()
if not is_exist_dists_mem:
Parallel(n_jobs=multiprocessing.cpu_count() * 2, backend='threading')(
delayed(process_dists)(idx_start, y_each, y_list, path_embeddings,
sample_count, classes_size, embedding_size,
triplet_similarity, mode)
for idx_start, y_each in paths_embs_idx_path_pairs)
dists_mem = np.memmap(path_dists_mem,
mode='r',
dtype=np.float16,
shape=(sample_count, classes_size))
# iterate through precomputed distances to add to data to meters for mem optimization
chunk_size = 1024
for idx_chunk_start in range(sample_count // chunk_size + 1):
idx_chunk_end = min(sample_count, idx_chunk_start + chunk_size)
chunk_each_size = idx_chunk_end - idx_chunk_start
if chunk_each_size == 0:
break
if type == 'range':
predicted = np.zeros((chunk_each_size, classes_size),
dtype=np.float)
else:
predicted = np.ones(
(chunk_each_size, classes_size), dtype=np.float) * 1e9
target = np.zeros((chunk_each_size, classes_size), dtype=np.float)
for idx_y in class_max_dist.keys():
max_dist = class_max_dist[idx_y]
for idx_class in range(chunk_each_size):
target[idx_class, y_list[idx_chunk_start + idx_class]] = 1.0
dists = dists_mem[idx_chunk_start:idx_chunk_end]
if type == 'range':
for idx_emb, dist in enumerate(dists):
if max_dist > dist[idx_y]:
predicted[idx_emb, idx_y] += 1.0
else:
predicted[:, idx_y] = np.minimum(
predicted[:, idx_y], dists[:, idx_y]
) # store for each class closest embedding with distance value
if type == 'range':
predicted = predicted / (np.sum(predicted, axis=1, keepdims=True) +
1e-18)
else:
# TODO softmax/hardmax based accuracy
idx_class = np.argmin(
predicted, axis=1) # for each sample select closest distance
predicted = np.zeros_like(predicted) # init probabilities vector
predicted[
np.arange(predicted.shape[0]),
idx_class] = 1.0 # for each sample set prob 100% by columns
y_chunk = np.array(y_list[idx_chunk_start:idx_chunk_end])
meter_acc.add(predicted, y_chunk)
# AssertionError: targets should be binary (0, 1)
idxes_classes = np.argmax(predicted, axis=1)
target_tp = np.array(np.equal(y_chunk, idxes_classes), dtype=np.int)
meter_auc.add(np.max(predicted, axis=1), target_tp)
return class_max_dist, class_centroids, y_list, sample_count, paths_embs_idx_path_pairs
