""" Classifier Network trainig
"""
import argparse
import json
import os
import sys
import time
from tqdm.autonotebook import tqdm
import torch
from torch import nn, optim
import torchinfo
import numpy as np
from sklearn.model_selection import train_test_split as sk_train_test_split
sys.path.append(os.getcwd())
import utilities.runUtils as rutl
import utilities.logUtils as lutl
from utilities.metricUtils import MultiClassMetrics
from algorithms.classifiers import ClassifierNet
from datacode.ultrasound_data import ClassifyDataFromCSV, get_class_weights
from datacode.augmentations import ClassifierTransform
print(f"Pytorch version: {torch.__version__}")
print(f"cuda version: {torch.version.cuda}")
device = 'cuda' if torch.cuda.is_available() else 'cpu'
print("Device Used:", device)
###============================= Configure and Setup ===========================
CFG = rutl.ObjDict(
data_folder = "/home/joseph.benjamin/WERK/fetal-ultrasound/data/Fetal-UltraSound/US-Planes-Heart-Views-V3",
balance_data = False, #while loading in dataloader; removed
seed = 1792, #previously 73
epochs = 100,
image_size = 256,
batch_size = 128,
workers = 16,
learning_rate = 1e-3,
weight_decay = 1e-6,
featx_arch = "resnet50",
featx_pretrain = "IMAGENET-1K" , # "IMAGENET-1K" or None
featx_freeze = False,
featx_bnorm = False,
featx_dropout = 0.5,
clsfy_layers = [5], #First mlp inwill be set w.r.t FeatureExtractor
clsfy_dropout = 0.0,
checkpoint_dir = "hypotheses/#dummy/Classify/trail-002",
disable_tqdm = False, #True--> to disable
restart_training = True
)
### ----------------------------------------------------------------------------
# CLI TAKES PRECENCE OVER JSON CONFIG
# e.g CLI overwrites the value set for featx-pretain in JSON while running
# without CLI default values form dict will be used
parser = argparse.ArgumentParser(description='Classification task')
parser.add_argument('--load-json', type=str, metavar='JSON',
help='Load settings from file in json format. Command line options override values in file.')
parser.add_argument('--seed', type=int, metavar='INT',
help='add batchnorm between feature extractor and classifier')
parser.add_argument('--featx-freeze', type=bool, metavar='BOOL',
help='freeze pretrain or not')
parser.add_argument('--featx-bnorm', type=bool, metavar='BOOL',
help='add batchnorm between feature extractor and classifier')
parser.add_argument('--featx-pretrain', type=str, metavar='PATH',
help='Set from where to load the prestrained weight from')
parser.add_argument('--checkpoint-dir', type=str, metavar='PATH',
help='Load settings from file in json format. Command line options override values in file.')
args = parser.parse_args()
if args.load_json:
with open(args.load_json, 'rt') as f:
CFG.__dict__.update(json.load(f))
for arg in vars(args):
att = getattr(args, arg)
if att: CFG.__dict__[arg] = att
### ----------------------------------------------------------------------------
CFG.gLogPath = CFG.checkpoint_dir
CFG.gWeightPath = CFG.checkpoint_dir + '/weights/'
### ============================================================================
def getDataLoaders(data_percent=None):
## Augumentations
train_transforms =ClassifierTransform(image_size=CFG.image_size, mode="train")
valid_transforms =ClassifierTransform(image_size=CFG.image_size, mode="infer")
## Dataset Class
traindataset = ClassifyDataFromCSV(CFG.data_folder,
CFG.data_folder+"/trainV3.csv",
transform = train_transforms,)
validdataset = ClassifyDataFromCSV(CFG.data_folder,
CFG.data_folder+"/validV3.csv",
transform = valid_transforms,)
class_weights, _ = get_class_weights(traindataset.targets, nclasses=5)
### Choose P% of data from train data
if data_percent and (data_percent < 100):
_idx, used_idx = sk_train_test_split( np.arange(len(traindataset)),
test_size=data_percent/100, random_state=CFG.seed,
stratify=traindataset.targets)
traindataset = torch.utils.data.Subset(traindataset, sorted(used_idx))
lutl.LOG2CSV(sorted(used_idx), CFG.gLogPath +'/train_indices_used.csv')
torch.manual_seed(CFG.seed)
## Loaders Class
trainloader = torch.utils.data.DataLoader( traindataset, shuffle=True,
batch_size=CFG.batch_size, num_workers=CFG.workers,
pin_memory=True)
validloader = torch.utils.data.DataLoader( validdataset, shuffle=False,
batch_size=CFG.batch_size, num_workers=CFG.workers,
pin_memory=True)
lutl.LOG2DICTXT({"Train->":len(traindataset),
"class-weights":str(class_weights),
"TransformsClass": str(train_transforms.get_composition()),
},CFG.gLogPath +'/misc.txt')
lutl.LOG2DICTXT({"Valid->":len(validdataset),
"TransformsClass": str(valid_transforms.get_composition()),
},CFG.gLogPath +'/misc.txt')
return trainloader, validloader, class_weights
def getModelnOptimizer():
## pretrain setting
m_state = 0; torch_pretrain_flag = None
if os.path.isfile(CFG.featx_pretrain):
m_state = torch.load(CFG.featx_pretrain, map_location='cpu')
else: torch_pretrain_flag = CFG.featx_pretrain
model = ClassifierNet(arch=CFG.featx_arch,
fc_layer_sizes=CFG.clsfy_layers,
feature_freeze=CFG.featx_freeze,
feature_dropout=CFG.featx_dropout,
feature_bnorm=CFG.featx_bnorm,
classifier_dropout=CFG.clsfy_dropout,
torch_pretrain=torch_pretrain_flag )
## load from checkpoints
if m_state:
m_state = m_state["model"]
ret_msg = model.load_state_dict(m_state, strict=False)
lutl.LOG2TXT(f"Manual Pretrain Loaded...{CFG.featx_pretrain},{str(ret_msg)}",
CFG.gLogPath +'/misc.txt')
model_info = torchinfo.summary(model, (1, 3, CFG.image_size, CFG.image_size),
verbose=0)
lutl.LOG2TXT(model_info, CFG.gLogPath +'/misc.txt', console= False)
##--------------
optimizer = optim.AdamW(model.parameters(), lr=CFG.learning_rate,
weight_decay=CFG.weight_decay)
scheduler = False
return model.to(device), optimizer, scheduler
def getLossFunc(class_weights):
lossfn = nn.CrossEntropyLoss(weight=torch.tensor(class_weights,
dtype=torch.float32).to(device) )
return lossfn
def simple_main(data_percent=None):
### SETUP
rutl.START_SEED(CFG.seed)
gpu = 0
torch.cuda.set_device(gpu)
torch.backends.cudnn.benchmark = True
## paths and logs setup
if data_percent: CFG.gLogPath = CFG.checkpoint_dir+f"/{data_percent}_percent/"
CFG.gWeightPath = CFG.gLogPath+"/weights/"
if os.path.exists(CFG.gLogPath) and (not CFG.restart_training):
raise Exception("CheckPoint folder already exists and restart_training not enabled; Somethings Wrong!",
CFG.checkpoint_dir)
if not os.path.exists(CFG.gWeightPath): os.makedirs(CFG.gWeightPath)
with open(CFG.gLogPath+"/exp_cfg.json", 'a') as f:
json.dump(vars(CFG), f, indent=4)
### DATA ACCESS
trainloader, validloader, class_weights = getDataLoaders(data_percent)
### MODEL, OPTIM
model, optimizer, scheduler = getModelnOptimizer()
lossfn = getLossFunc(class_weights)
## Automatically resume from checkpoint if it exists and enabled
if os.path.exists(CFG.gWeightPath +'/checkpoint.pth') and CFG.restart_training:
ckpt = torch.load(CFG.gWeightPath +'/checkpoint.pth',
map_location='cpu')
start_epoch = ckpt['epoch']
model.load_state_dict(ckpt['model'])
optimizer.load_state_dict(ckpt['optimizer'])
lutl.LOG2TXT(f"Restarting Training from EPOCH:{start_epoch} of {CFG.gLogPath}", CFG.gLogPath +'/misc.txt')
else:
start_epoch = 0
### MODEL TRAINING
start_time = time.time()
best_acc = 0 ; best_loss = float('inf')
trainMetric = MultiClassMetrics(CFG.gLogPath)
validMetric = MultiClassMetrics(CFG.gLogPath)
for epoch in range(start_epoch, CFG.epochs):
## ---- Training Routine ----
model.train()
for img, tgt in tqdm(trainloader, disable=CFG.disable_tqdm):
img = img.to(device, non_blocking=True)
tgt = tgt.to(device, non_blocking=True)
optimizer.zero_grad()
pred = model.forward(img)
loss = lossfn(pred, tgt)
loss.backward()
# nn.utils.clip_grad_norm_(model.parameters(),
# max_norm=2.0, norm_type=2)
optimizer.step()
trainMetric.add_entry(torch.argmax(pred, dim=1), tgt, loss)
if scheduler: scheduler.step()
## save checkpoint states
state = dict(epoch=epoch + 1, model=model.state_dict(),
optimizer=optimizer.state_dict())
torch.save(state, CFG.gWeightPath +'/checkpoint.pth')
## ---- Validation Routine ----
model.eval()
with torch.no_grad():
for img, tgt in tqdm(validloader, disable=CFG.disable_tqdm):
img = img.to(device, non_blocking=True)
tgt = tgt.to(device, non_blocking=True)
pred = model.forward(img)
loss = lossfn(pred, tgt)
validMetric.add_entry(torch.argmax(pred, dim=1), tgt, loss)
## Log Metrics TODO Add balanced and F1
stats = dict(
epoch=epoch, time=int(time.time() - start_time),
trainloss = trainMetric.get_loss(),
trainacc = trainMetric.get_balanced_accuracy(),
trainF1 = trainMetric.get_f1score(),
validloss = validMetric.get_loss(),
validacc = validMetric.get_balanced_accuracy(),
validF1 = validMetric.get_f1score(),
)
lutl.LOG2DICTXT(stats, CFG.gLogPath+'/train-stats.txt')
## save best model
best_flag = False
if stats['validacc'] > best_acc:
torch.save(model.state_dict(), CFG.gWeightPath +'/bestmodel.pth')
best_acc = stats['validacc']
best_loss = stats['validloss']
best_flag = True
## Log detailed validation
detail_stat = dict(
epoch=epoch, time=int(time.time() - start_time),
best = best_flag,
validf1scr = validMetric.get_f1score(),
validbalacc = validMetric.get_balanced_accuracy(),
validacc = validMetric.get_accuracy(),
validreport = validMetric.get_class_report(),
validconfus = validMetric.get_confusion_matrix().tolist(),
)
lutl.LOG2DICTXT(detail_stat, CFG.gLogPath+'/validation-details.txt', console=False)
trainMetric.reset()
validMetric.reset(best_flag)
return CFG.gLogPath
def simple_test(saved_logpath):
### SETUP
rutl.START_SEED()
gpu = 0
torch.cuda.set_device(gpu)
torch.backends.cudnn.benchmark = True
### DATA ACCESS
test_transforms =ClassifierTransform(image_size=CFG.image_size,
mode="infer")
testdataset = ClassifyDataFromCSV( CFG.data_folder,
CFG.data_folder+"/testV3.csv",
transform = test_transforms,)
testloader = torch.utils.data.DataLoader( testdataset,
shuffle=False,
batch_size=CFG.batch_size,
num_workers=CFG.workers,
pin_memory=True)
lutl.LOG2DICTXT({"TEST->":len(testdataset),
"TransformsClass": str(test_transforms.get_composition()),
},saved_logpath +'/test-results.txt')
### MODEL
model = ClassifierNet(arch=CFG.featx_arch,
fc_layer_sizes=CFG.clsfy_layers,
feature_freeze=CFG.featx_freeze,
feature_dropout=CFG.featx_dropout,
feature_bnorm=CFG.featx_bnorm,
classifier_dropout=CFG.clsfy_dropout)
model = model.to(device)
model.load_state_dict(torch.load(saved_logpath+"/weights/bestmodel.pth"))
### MODEL TESTING
testMetric = MultiClassMetrics(saved_logpath)
model.eval()
start_time = time.time()
with torch.no_grad():
for img, tgt in tqdm(testloader, disable=CFG.disable_tqdm):
img = img.to(device, non_blocking=True)
tgt = tgt.to(device, non_blocking=True)
pred = model.forward(img)
testMetric.add_entry(torch.argmax(pred, dim=1), tgt)
## Log detailed validation
detail_stat = dict(
timetaken = int(time.time() - start_time),
testf1scr = testMetric.get_f1score(),
testbalacc = testMetric.get_balanced_accuracy(),
testacc = testMetric.get_accuracy(),
testreport = testMetric.get_class_report(),
testconfus = testMetric.get_confusion_matrix(
save_png= True, title="test").tolist(),
)
lutl.LOG2DICTXT(detail_stat, saved_logpath+'/test-results.txt',
console=True)
testMetric._write_predictions(title="test")
if __name__ == '__main__':
# logpth = simple_main()
# simple_test(logpth)
for p in [100, 50, 25, 10, 5, 1]:
logpth = simple_main(data_percent=p)
simple_test(logpth)