import pdb
import math
import os
from os.path import join as j_
import pickle
import pandas as pd
import datetime
import torch
import numpy as np
import torch.nn as nn
from torch.utils.data import DataLoader, sampler
import torch.optim as optim
import logging
from transformers import (get_constant_schedule_with_warmup,
get_linear_schedule_with_warmup,
get_cosine_schedule_with_warmup)
import re
def get_current_time():
now = datetime.datetime.now()
year = now.year % 100 # convert to 2-digit year
month = now.month
day = now.day
hour = now.hour
minute = now.minute
second = now.second
return f"{year:02d}-{month:02d}-{day:02d}-{hour:02d}-{minute:02d}-{second:02d}"
def extract_patching_info(s):
match = re.search(r"extracted_mag(\d+)x_patch(\d+)_fp", s)
mag, patch_size = -1, -1
if match:
mag = int(match.group(1))
patch_size = int(match.group(2))
return mag, patch_size
def parse_model_name(model_name, ckpt=None, inference_prec=None):
# 'extracted-vit_base_patch16_224.ibot.mgb100m20X_bs1024_cropadjust_opnorm_wd0.04_0012_fp16'
# get inference precision
if inference_prec is None:
inference_prec = 'fp32'
if model_name.endswith('_fp16'):
inference_prec = 'fp16'
model_name = model_name[:-len('_fp16')]
model_name = model_name.replace('extracted-', '')
parsed = model_name.split('.', maxsplit=2)
enc = model_name
algo = ''
exp = ''
if len(parsed) >= 3:
enc = parsed[0]
algo = parsed[1]
exp = '.'.join(parsed[2:])
# get ckpt
if ckpt is None:
exp_parsed = exp.split('.')
ckpt = exp_parsed[-1].split('_')[-1]
if ckpt.isnumeric():
ckpt = int(ckpt)
exp = '.'.join(exp_parsed[:-1]) + '_'.join(exp_parsed[-1].split('_')[:-1])
else:
ckpt = -1
else:
if str(ckpt).isnumeric():
ckpt = int(ckpt)
else:
ckpt = -1
return dict(pretrain_enc=enc,
pretrain_algo=algo,
pretrain_exp=exp,
pretrain_ckpt=ckpt,
inference_prec=inference_prec)
def merge_dict(main_dict, new_dict):
for k, v in new_dict.items():
if k not in main_dict:
main_dict[k] = []
main_dict[k].append(v)
return main_dict
def array2list(x):
if isinstance(x, np.ndarray):
return x.tolist()
return list(x)
def summarize_reulsts(results_dict, ignore_keys = ['folds']):
summary = {}
for k, v in results_dict.items():
if k in ignore_keys: continue
summary[f"{k}_avg"] = np.mean(v)
# summary[f"{k}_std"] = np.std(v)
return summary
def seed_torch(seed=7):
import random
device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
random.seed(seed)
os.environ['PYTHONHASHSEED'] = str(seed)
np.random.seed(seed)
torch.manual_seed(seed)
if device.type == 'cuda':
torch.cuda.manual_seed(seed)
torch.cuda.manual_seed_all(seed) # if you are using multi-GPU.
torch.backends.cudnn.benchmark = False
torch.backends.cudnn.deterministic = True
def read_splits(args, fold_idx=None):
splits_csvs = {}
split_names = args.split_names.split(',')
print(f"Using the following split names: {split_names}")
for split in split_names:
if fold_idx is not None:
split_path = j_(args.split_dir, f'{split}_{fold_idx}.csv')
else:
split_path = j_(args.split_dir, f'{split}.csv')
if os.path.isfile(split_path):
df = pd.read_csv(split_path)#.sample(frac=1, random_state=0).head(25).reset_index(drop=True)
assert 'Unnamed: 0' not in df.columns
splits_csvs[split] = df
return splits_csvs
class AverageMeter(object):
"""Computes and stores the average and current value"""
def __init__(self, name='unk', fmt=':f'):
self.name = name
self.fmt = fmt
self.reset()
def reset(self):
self.val = 0
self.avg = 0
self.sum = 0
self.count = 0
def update(self, val, n=1):
self.val = val
self.sum += val * n
self.count += n
self.avg = self.sum / self.count
def __str__(self):
fmtstr = '{name} {val' + self.fmt + '} ({avg' + self.fmt + '})'
return fmtstr.format(**self.__dict__)
def get_lr_scheduler(args, optimizer, dataloader):
scheduler_name = args.lr_scheduler
warmup_steps = args.warmup_steps
warmup_epochs = args.warmup_epochs
epochs = args.max_epochs if hasattr(args, 'max_epochs') else args.epochs
assert not (warmup_steps > 0 and warmup_epochs > 0), "Cannot have both warmup steps and epochs"
accum_steps = args.accum_steps
if warmup_steps > 0:
warmup_steps = warmup_steps
elif warmup_epochs > 0:
warmup_steps = warmup_epochs * (len(dataloader) // accum_steps)
else:
warmup_steps = 0
if scheduler_name=='constant':
lr_scheduler = get_constant_schedule_with_warmup(optimizer=optimizer,
num_warmup_steps=warmup_steps)
elif scheduler_name=='cosine':
lr_scheduler = get_cosine_schedule_with_warmup(optimizer=optimizer,
num_warmup_steps=warmup_steps,
num_training_steps=(len(dataloader) // accum_steps * epochs),
)
elif scheduler_name=='linear':
lr_scheduler = get_linear_schedule_with_warmup(
optimizer=optimizer,
num_warmup_steps=warmup_steps,
num_training_steps=(len(dataloader) // accum_steps) * epochs,
)
return lr_scheduler
def get_optim(args, model=None, parameters=None):
def exclude(
n, p): return p.ndim < 2 or "bn" in n or "ln" in n or "bias" in n or 'logit_scale' in n
def include(n, p): return not exclude(n, p)
if parameters is None:
named_parameters = list(model.named_parameters())
gain_or_bias_params = [
p for n, p in named_parameters if exclude(n, p) and p.requires_grad]
rest_params = [p for n, p in named_parameters if include(
n, p) and p.requires_grad]
parameters = [
{"params": gain_or_bias_params, "weight_decay": 0.},
{"params": rest_params, "weight_decay": args.wd},
]
if args.opt == "adamW":
optimizer = optim.AdamW(parameters, lr=args.lr)
elif args.opt == 'sgd':
optimizer = optim.SGD(parameters, lr=args.lr, momentum=0.9)
elif args.opt == 'RAdam':
optimizer = optim.RAdam(parameters, lr=args.lr)
else:
raise NotImplementedError
return optimizer
def print_network(net):
num_params = 0
num_params_train = 0
logging.info(str(net))
# print(str(net))
for param in net.parameters():
n = param.numel()
num_params += n
if param.requires_grad:
num_params_train += n
logging.info(f'Total number of parameters: {num_params}')
logging.info(f'Total number of trainable parameters: {num_params_train}')
# print('Total number of parameters: %d' % num_params)
# print('Total number of trainable parameters: %d' % num_params_train)
class EarlyStopping:
"""Early stops the training if validation loss doesn't improve after a given patience."""
def __init__(self, save_dir, patience=20, min_stop_epoch=50, verbose=False, better='min'):
"""
train_args:
patience (int): How long to wait after last time validation loss improved.
Default: 20
min_stop_epoch (int): Earliest epoch possible for stopping
verbose (bool): If True, prints a message for each validation loss improvement.
Default: False
"""
self.patience = patience
self.patience_counter = 0
self.min_stop_epoch = min_stop_epoch
self.better = better
self.verbose = verbose
self.best_score = None
self.save_dir = save_dir
if better == 'min':
self.best_score = np.Inf
else:
self.best_score = -np.Inf
self.early_stop = False
self.counter = 0
def is_new_score_better(self, score):
if self.better == 'min':
return score < self.best_score
else:
return score > self.best_score
def __call__(self, epoch, score, save_ckpt_fn, save_ckpt_kwargs):
is_better = self.is_new_score_better(score)
if is_better:
print(
f'score improved ({self.best_score:.6f} --> {score:.6f}). Saving model ...')
self.save_checkpoint(save_ckpt_fn, save_ckpt_kwargs)
self.counter = 0
self.best_score = score
else:
self.counter += 1
print(
f'EarlyStopping counter: {self.counter} out of {self.patience}')
if self.counter >= self.patience and epoch >= (self.min_stop_epoch - 1):
self.early_stop = True
return self.early_stop
def save_checkpoint(self, save_ckpt_fn, save_ckpt_kwargs):
'''Saves model when score improves.'''
if 'save_dir' in save_ckpt_kwargs:
save_ckpt_fn(**save_ckpt_kwargs)
else:
save_ckpt_fn(save_dir=self.save_dir, **save_ckpt_kwargs)
def save_checkpoint(config, epoch, model, score, save_dir, fname=None):
save_state = {'model': model.state_dict(),
'score': score,
'epoch': epoch,
'config': config}
if fname is None:
save_path = j_(save_dir, f'ckpt_epoch_{epoch}.pth')
else:
save_path = j_(save_dir, fname)
torch.save(save_state, save_path)