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utils.py
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import sys
import os
import glob
import numpy as np
import torch
import torch.optim as optim
from torch.optim import lr_scheduler
import math
from sklearn.metrics import f1_score, precision_score, recall_score, accuracy_score
from scipy.special import softmax
from Clf import *
from CBLoss import *
from FBeta_Loss import *
def load_conv_net(model_type, device):
'''
Function to load a CNN based on string input.
Inputs:
model_type [str]: specifies type of pre-trained model to load
device [torch.device]: cpu or gpu
instantiated using torch.device('cuda' if torch.cuda.is_available() else 'cpu')
Outputs:
conv_net [torch.nn]: CNN loaded onto specified device
input_size: image size suitable for CNN
'''
if model_type is not None:
if model_type.upper() == "EFFICIENTNET-B0":
from efficientnet_pytorch import EfficientNet
conv_net = EfficientNet.from_pretrained('efficientnet-b0').to(device)
conv_net._dropout = Identity()
conv_net._fc = Identity()
input_size = 224
elif model_type.upper() == "EFFICIENTNET-B1":
from efficientnet_pytorch import EfficientNet
conv_net = EfficientNet.from_pretrained('efficientnet-b1').to(device)
conv_net._dropout = Identity()
conv_net._fc = Identity()
input_size = 240
elif model_type.upper() == "MOBILENET-V2":
conv_net = torch.hub.load('pytorch/vision:v0.6.0', 'mobilenet_v2', pretrained=True).to(device)
conv_net.classifier = Identity()
input_size = 224
else:
print("Choose valid model.")
quit()
return conv_net, input_size
def choose_loss_fn(loss_fn, samples_per_cls, no_of_classes, weights_per_cls):
'''
Function that returns loss function object based on string input.
Inputs:
loss_fn [str]: specifies loss function to use
None: weighted cross entropy loss
fbetaX: FX soft loss (if X=1, then F1 soft loss)
focal: class balanced focal loss
sigmoid: class balanced sigmoid loss
samples_per_cls [np.array(n,)]: array storing count of samples for each of the n classes
no_of_classes [int]: number of classes
weights_per_cls [torch.tensor(n,)]: torch tensor of weights for each of the n classes, loaded onto device
Outputs:
criterion [torch.nn]: loss function object
'''
if loss_fn is None:
criterion = nn.CrossEntropyLoss(weight=weights_per_cls)
elif loss_fn[0:5] == "fbeta":
beta_val = float(loss_fn[5:])
criterion = FBetaLoss(beta=beta_val)
elif loss_fn == "focal" or loss_fn == "sigmoid":
criterion = CBLoss(samples_per_cls, no_of_classes, loss_fn, 0.9999, 0.5)
return criterion
def save_model(model, optimizer, epoch, accuracy, save_train_loss, save_val_loss, save_train_f1,
save_val_f1, save_train_acc, save_val_acc, clf_out, iteration, fine_tune):
'''
Function called within training which saves model to specified path. Saves model if model has best training/validation
loss, F1, or accuracy. Overrides models of previous best performance in each of the categories.
Inputs:
model [torch.nn]: model to be saved
optimizer [torch.optim]: optimizer object (also saved)
epoch [int]: epoch number
accuracy [float]: accuracy of classification for the given epoch
save_train_loss [bool]: true if saving model as it achieved best training loss
save_val_loss [bool]: true if saving model as it achieved best validation loss
save_train_f1 [bool]: true if saving model as it achieved best training F1
save_val_f1 [bool]: true if saving model as it achieved best validation F1
save_train_acc [bool]: true if saving model as it achieved best training accuracy
save_val_acc [bool]: true if saving model as it achieved best validation accuracy
clf_out [str]: path to where model is saved
iteration [int]: current ensembling iteration
fine_tune [bool]: true if saving a model that is being fine-tuned
'''
save_cond = [save_train_loss, save_val_loss, save_train_f1, save_val_f1, save_train_acc, save_val_acc]
prefix = ["t-loss", "v-loss", "t-f1", "v-f1", "t-acc", "v-acc"]
for i in range(len(save_cond)):
if clf_out is not None and save_cond[i]:
# delete previous model with same prefix
if fine_tune:
folder_path = clf_out + "ft/"
else:
folder_path = clf_out + str(iteration) + "/"
file_to_del = glob.glob( folder_path + "-" + prefix[i] + "*" )
if len(file_to_del) == 1:
os.remove(file_to_del[0])
# save clf
clf_save = folder_path + "-{}-{:02d}-{:.3f}-clf.tar".format(prefix[i], epoch, accuracy)
torch.save({
'epoch': epoch,
'model_state_dict': model.state_dict(),
'optimizer_state_dict': optimizer.state_dict(),
}, clf_save)
return
def print_scores(running_loss, data_length, phase, gt, pred):
'''
Utility function for printing model statistics - handled within training / testing / fine-tuning functions
'''
epoch_loss = running_loss / data_length[phase]
accuracy = accuracy_score(gt[phase].detach().cpu(), pred[phase].detach().cpu())
f1_class_scores = f1_score(gt[phase].detach().cpu(), pred[phase].detach().cpu(), average=None, labels=[0,1]).tolist()
string_out = " "
sys.stdout.write('%s\r' % string_out)
sys.stdout.flush()
if running_loss is not None:
print('{} \tLoss: {:.4f}, \tAccuracy: {:.4f}, \tF1: [{:.4f}, {:.4f}]'
.format(phase, epoch_loss, accuracy, f1_class_scores[0], f1_class_scores[1]))
return epoch_loss, accuracy, f1_class_scores
def clf_trainer(train_set, val_set, data_loader, data_length, end_epoch, batch_size,
conv_net, model, device, optimizer, scheduler, clf_out, loss_fn,
samples_per_cls, no_of_classes, weights_per_cls, iteration):
'''
Function for training a classification layer with fixed feature extractor.
Inputs:
train_set [BinaryDataset]: Dataset object for training set
val_set [BinaryDataset]: Dataset object for validation set
data_loader [dict]: dict of data loader objects
e.g. data_loader = {'Training': train_loader, 'Validation': val_loader}
where train_loader and val_loader are of type torch.utils.data.DataLoader
data_length [dict]: dict of data loader lengths
e.g. data_length = {'Training': len(train_loader), 'Validation': len(val_loader)}
where train_loader and val_loader are of type torch.utils.data.DataLoader
end_epoch [int]: number of epochs desired for training
batch_size [int]: batch size in training
conv_net [torch.nn]: feature extractor, loaded to device
model [torch.nn]: classification layer, loaded to device
device [torch.device]: cpu or gpu
instantiated using torch.device('cuda' if torch.cuda.is_available() else 'cpu')
optimizer [torch.optim]: optimizer object
scheduler [torch.optim.lr_scheduler]: learning rate scheduler object
clf_out [str]: path to where model is saved
loss_fn [str]: specifies loss function to use
samples_per_cls [np.array(n,)]: array storing count of samples for each of the n classes
no_of_classes [int]: number of classes
weights_per_cls [torch.tensor(n,)]: torch tensor of weights for each of the n classes, loaded onto device
iteration [int]: iteration in ensembling (i.e. 3rd iteration trains the 3rd classification layer)
'''
# save csv for training and validation sets
folder_path = clf_out + str(iteration) + "/"
if not os.path.exists(folder_path):
os.mkdir(folder_path)
train_set.df.to_csv(folder_path + "train_set_unique_labels.csv")
val_set.df.to_csv(folder_path + "val_set_unique_labels.csv")
# define variables for calculating statistics
pred_train = torch.zeros(len(train_set)).to(device)
labels_train = torch.zeros(len(train_set)).to(device)
pred_val = torch.zeros(len(val_set)).to(device)
labels_val = torch.zeros(len(val_set)).to(device)
pred = {'Training': pred_train, 'Validation': pred_val}
gt = {'Training': labels_train, 'Validation': labels_val}
min_train_loss = 999999999
min_val_loss = 999999999
max_train_f1 = 0
max_val_f1 = 0
max_train_acc = 0
max_val_acc = 0
# put feature extractor in evaluation mode (important for layers such as BN)
conv_net.eval()
# choose loss fn
criterion = choose_loss_fn(loss_fn, samples_per_cls, no_of_classes, weights_per_cls)
# training loop
for epoch in range(1, end_epoch + 1):
print('\nEpoch {}/{}'.format(epoch, end_epoch))
print('-' * 20)
# select between training or validation
for phase in ['Training']:#, 'Validation']:
if phase == 'Training':
model.train() # set classification layer to training mode
else:
model.eval() # set classification layer to evaluate mode
running_loss = 0.0
save_train_loss = False
save_val_loss = False
save_train_f1 = False
save_val_f1 = False
save_train_acc = False
save_val_acc = False
# iterate over data.
for i, batch in enumerate(data_loader[phase], 0):
# grab data
inputs, labels = batch
# zero the parameter gradients
optimizer.zero_grad()
# forward pass
with torch.no_grad():
features = conv_net(inputs.to(device))
with torch.set_grad_enabled(phase=='Training'):
outputs = model(features)
# rare case where final batch in data has size 1 - add leading dimension
output_size = [int(x) for x in outputs.shape]
if len(output_size) == 1:
outputs = torch.unsqueeze(outputs,0)
# choose loss fn based on function input
loss = criterion(outputs, labels.to(device))
# catch NaNs
if math.isnan(loss):
print("\n\nCont'd: got undefined loss (nan)\n\n")
del loss, outputs, inputs, labels
continue
pred[phase][ i*batch_size : (batch_size*(i+1)) ] = torch.argmax(outputs, 1).float()
gt[phase][ i*batch_size : (batch_size*(i+1)) ] = labels
# backward pass + optimization (only if in training mode)
if phase == 'Training':
loss.backward()
optimizer.step()
running_loss += loss.item()
string_out = "Epoch [{}/{}]\tStep [{}/{}]\tLoss: {:.5}".format(epoch, end_epoch, i+1, data_length[phase], running_loss / (i+1))
sys.stdout.write('%s\r' % string_out)
sys.stdout.flush()
del loss, outputs, inputs, labels
# print loss, accuracy, class f1 scores, and harmonic mean f1 for whole epoch
epoch_loss, accuracy, f1_class_scores = print_scores(running_loss, data_length, phase, gt, pred)
if phase == 'Training':
if epoch_loss < min_train_loss:
min_train_loss = epoch_loss
save_train_loss = True
if f1_class_scores[1] > max_train_f1:
max_train_f1 = f1_class_scores[1]
save_train_f1 = True
if accuracy > max_train_acc:
max_train_acc = accuracy
save_train_acc = True
else:
if epoch_loss < min_val_loss:
min_val_loss = epoch_loss
save_val_loss = True
if f1_class_scores[1] > max_val_f1:
max_val_f1 = f1_class_scores[1]
save_val_f1 = True
if accuracy > max_val_acc:
max_val_acc = accuracy
save_val_acc = True
save_model(model, optimizer, epoch, accuracy, save_train_loss, save_val_loss, save_train_f1,
save_val_f1, save_train_acc, save_val_acc, clf_out, iteration, False)
scheduler.step()
del pred_train, labels_train, pred_val, labels_val, pred, gt
print("Training for iteration {:.0f} finished\n\n".format(iteration))
return
def fine_tune(train_set, val_set, data_loader, data_length, batch_size, cnn, device,
learning_rate, clf_out, loss_fn, samples_per_cls, no_of_classes, weights_per_cls):
'''
Function for fine-tuning CNN.
Inputs:
train_set [BinaryDataset]: Dataset object for training set
val_set [BinaryDataset]: Dataset object for validation set
data_loader [dict]: dict of data loader objects
e.g. data_loader = {'Training': train_loader, 'Validation': val_loader}
where train_loader and val_loader are of type torch.utils.data.DataLoader
data_length [dict]: dict of data loader lengths
e.g. data_length = {'Training': len(train_loader), 'Validation': len(val_loader)}
where train_loader and val_loader are of type torch.utils.data.DataLoader
batch_size [int]: batch size in training
cnn [torch.nn]: CNN, loaded to device
device [torch.device]: cpu or gpu
instantiated using torch.device('cuda' if torch.cuda.is_available() else 'cpu')
learning_rate [float]: learning rate applied to backpropagation
clf_out [str]: path to where model is saved
loss_fn [str]: specifies loss function to use
samples_per_cls [np.array(n,)]: array storing count of samples for each of the n classes
no_of_classes [int]: number of classes
weights_per_cls [torch.tensor(n,)]: torch tensor of weights for each of the n classes, loaded onto device
'''
# save csv for training and validation sets
folder_path = clf_out + "1/"
train_set.df.to_csv(folder_path + "train_set_unique_labels.csv")
val_set.df.to_csv(folder_path + "val_set_unique_labels.csv")
# define variables for calculating statistics
pred_train = torch.zeros(len(train_set)).to(device)
labels_train = torch.zeros(len(train_set)).to(device)
pred_val = torch.zeros(len(val_set)).to(device)
labels_val = torch.zeros(len(val_set)).to(device)
pred = {'Training': pred_train, 'Validation': pred_val}
gt = {'Training': labels_train, 'Validation': labels_val}
min_train_loss = 999999999
min_val_loss = 999999999
max_train_f1 = 0
max_val_f1 = 0
max_train_acc = 0
max_val_acc = 0
# set all layers to trainable
for param in cnn.parameters():
param.requires_grad = True
# setup optimizer and learning rate scheduler
scheduler_step = 33
optimizer = optim.SGD(cnn.parameters(), lr=learning_rate, momentum=0.9, weight_decay=5e-4)
scheduler = lr_scheduler.StepLR(optimizer, step_size=scheduler_step, gamma=0.2)
# choose loss fn
criterion = choose_loss_fn(loss_fn, samples_per_cls, no_of_classes, weights_per_cls)
# training loop
end_epoch = 101
for epoch in range(1, end_epoch):
print('\nEpoch {}/{}'.format(epoch, end_epoch))
print('-' * 20)
# select between training or validation
for phase in ['Training', 'Validation']:
if phase == 'Training':
cnn.train() # set classification layer to training mode
else:
cnn.eval() # set classification layer to evaluate mode
running_loss = 0.0
save_train_loss = False
save_val_loss = False
save_train_f1 = False
save_val_f1 = False
save_train_acc = False
save_val_acc = False
# iterate over data.
for i, batch in enumerate(data_loader[phase], 0):
# grab data
inputs, labels = batch
# zero the parameter gradients
optimizer.zero_grad()
# forward pass
with torch.set_grad_enabled(phase=='Training'):
outputs = cnn(inputs.to(device))
# rare case where final batch in data has size 1 - add leading dimension
output_size = [int(x) for x in outputs.shape]
if len(output_size) == 1:
outputs = torch.unsqueeze(outputs,0)
# choose loss fn based on function input
loss = criterion(outputs, labels.to(device))
# catch NaNs
if math.isnan(loss):
print("\n\nCont'd: got undefined loss (nan)\n\n")
del loss, outputs, inputs, labels
continue
pred[phase][ i*batch_size : (batch_size*(i+1)) ] = torch.argmax(outputs, 1).float()
gt[phase][ i*batch_size : (batch_size*(i+1)) ] = labels
# backward pass + optimization (only if in training mode)
if phase == 'Training':
loss.backward()
optimizer.step()
running_loss += loss.item()
string_out = "Epoch [{}/{}]\tStep [{}/{}]\tLoss: {:.5}".format(epoch, end_epoch, i+1, data_length[phase], running_loss / (i+1))
sys.stdout.write('%s\r' % string_out)
sys.stdout.flush()
del loss, outputs, inputs, labels
# print loss, accuracy, class f1 scores, and harmonic mean f1 for whole epoch
epoch_loss, accuracy, f1_class_scores = print_scores(running_loss, data_length, phase, gt, pred)
if phase == 'Training':
if epoch_loss < min_train_loss:
min_train_loss = epoch_loss
save_train_loss = True
if f1_class_scores[1] > max_train_f1:
max_train_f1 = f1_class_scores[1]
save_train_f1 = True
if accuracy > max_train_acc:
max_train_acc = accuracy
save_train_acc = True
else:
if epoch_loss < min_val_loss:
min_val_loss = epoch_loss
save_val_loss = True
if f1_class_scores[1] > max_val_f1:
max_val_f1 = f1_class_scores[1]
save_val_f1 = True
if accuracy > max_val_acc:
max_val_acc = accuracy
save_val_acc = True
save_model(cnn, optimizer, epoch, accuracy, save_train_loss, save_val_loss, save_train_f1,
save_val_f1, save_train_acc, save_val_acc, clf_out, None, True)
scheduler.step()
del pred_train, labels_train, pred_val, labels_val, pred, gt
print("Fine tuning complete.\n\n")
return
def clf_tester(dataset, data_loader, batch_size, conv_net, model, device):
'''
Function for classifying data in evaluation mode. Returns boolean array corresponding
Inputs:
dataset [BinaryDataset]: Dataset object for training set
data_loader [torch.utils.data.DataLoader]: data loader object for dataset
batch_size [int]: batch size for evaluation
conv_net [torch.nn]: feature extractor, loaded to device
model [torch.nn]: classification layer, loaded to device
device [torch.device]: cpu or gpu
instantiated using torch.device('cuda' if torch.cuda.is_available() else 'cpu')
Outputs:
positives [np.array(n,)]: array marking the correctly classified samples
e.g. [1,1,0,1,0,0] means that samples 0, 1, 3 were correctly classified
'''
# define variables for calculating statistics
pred = torch.zeros(len(dataset)).to(device)
gt = torch.zeros(len(dataset)).to(device)
# set model to evaluation mode
conv_net.eval()
model.eval()
running_loss = 0.0
# iterate over data.
for i, batch in enumerate(data_loader, 0):
string_out = "Step [{}/{}]".format(i+1, len(data_loader))
sys.stdout.write('%s\r' % string_out)
sys.stdout.flush()
# grab data
inputs, labels = batch
# forward pass
with torch.no_grad():
features = conv_net(inputs.to(device))
outputs = model(features)
# rare case where final batch in data has size 1 - add leading dimension
output_size = [int(x) for x in outputs.shape]
if len(output_size) == 1:
outputs = torch.unsqueeze(outputs,0)
pred[ i*batch_size : (batch_size*(i+1)) ] = torch.argmax(outputs, 1).float()
gt[ i*batch_size : (batch_size*(i+1)) ] = labels
del outputs, inputs, labels
# print loss, accuracy, class f1 scores, and harmonic mean f1 for whole epoch
accuracy = accuracy_score(gt.detach().cpu(), pred.detach().cpu())
f1_class_scores = f1_score(gt.detach().cpu(), pred.detach().cpu(), average=None, labels=[0,1]).tolist()
print('Accuracy: {:.4f}, \tF1: [{:.4f}, {:.4f}]'
.format(accuracy, f1_class_scores[0], f1_class_scores[1]))
positives = (pred == gt).cpu().numpy()
del pred, gt
print("\n\n")
return positives
def create_meta_data(train_set, val_set, test_set, data_loader, data_length,
batch_size, conv_net, device, data_out, clfs):
'''
Function for creating meta-data using logit outputs from each classification layer.
Inputs:
train_set [BinaryDataset]: Dataset object for training set
val_set [BinaryDataset]: Dataset object for validation set
data_loader [dict]: dict of data loader objects
e.g. data_loader = {'Training': train_loader, 'Validation': val_loader}
where train_loader and val_loader are of type torch.utils.data.DataLoader
data_length [dict]: dict of data loader lengths
e.g. data_length = {'Training': len(train_loader), 'Validation': len(val_loader)}
where train_loader and val_loader are of type torch.utils.data.DataLoader
end_epoch [int]: number of epochs desired for training
batch_size [int]: batch size in training
conv_net [torch.nn]: feature extractor, loaded to device
device [torch.device]: cpu or gpu
instantiated using torch.device('cuda' if torch.cuda.is_available() else 'cpu')
data_out [str]: path for saving meta data (saved as type np.array)
clfs [list]: list where each element is a classification layer (already loaded to device)
'''
boost_data_train = torch.zeros(len(train_set), len(clfs) * 2).to(device)
boost_data_val = torch.zeros(len(val_set), len(clfs) * 2).to(device)
boost_data_test = torch.zeros(len(test_set), len(clfs) * 2).to(device)
boost_data = {'Training': boost_data_train, 'Validation': boost_data_val, 'Testing': boost_data_test}
labels_train = torch.zeros(len(train_set)).to(device)
labels_val = torch.zeros(len(val_set)).to(device)
labels_test = torch.zeros(len(test_set)).to(device)
gt = {'Training': labels_train, 'Validation': labels_val, 'Testing': labels_test}
conv_net.eval()
for i in range(len(clfs)):
clfs[i].eval()
# select between training or validation
for phase in ['Training', 'Validation', 'Testing']:
# iterate over data.
for i, batch in enumerate(data_loader[phase], 0):
string_out = "Step [{}/{}]".format(i+1, len(data_loader[phase]))
sys.stdout.write('%s\r' % string_out)
sys.stdout.flush()
# grab data
inputs, labels = batch
# forward pass
with torch.no_grad():
features = conv_net(inputs.to(device))
ens_in = torch.randn(0).to(device)
for j in range(len(clfs)):
with torch.no_grad():
ens_in = torch.cat((ens_in, clfs[j](features)), dim=1)
boost_data[phase][ i*batch_size : (batch_size*(i+1)), : ] = ens_in
gt[phase][ i*batch_size : (batch_size*(i+1)) ] = labels
# save for offline
boost_data_train = boost_data["Training"].cpu().detach().numpy()
boost_data_val = boost_data["Validation"].cpu().detach().numpy()
boost_data_test = boost_data["Testing"].cpu().detach().numpy()
np.save(data_out + "boost_data_train.npy", boost_data_train)
np.save(data_out + "boost_data_val.npy", boost_data_val)
np.save(data_out + "boost_data_test.npy", boost_data_test)
boost_labels_train = gt["Training"].cpu().detach().numpy()
boost_labels_val = gt["Validation"].cpu().detach().numpy()
boost_labels_test = gt["Testing"].cpu().detach().numpy()
np.save(data_out + "boost_labels_train.npy", boost_labels_train)
np.save(data_out + "boost_labels_val.npy", boost_labels_val)
np.save(data_out + "boost_labels_test.npy", boost_labels_test)
return
def fn_and_fp(y_test, test_preds):
# count false positives and false negatives
fn = 0
fp = 0
for i in range(y_test.shape[0]):
if test_preds[i] == 0 and y_test[i] == 1:
fn += 1
elif test_preds[i] == 1 and y_test[i] == 0:
fp += 1
print("# false negatives: ", fn)
print("# false positives: ", fp)
return
def softmax_transform(X):
X_softmax = np.empty(X.shape)
num_clf = int(X.shape[1] / 2)
for i in range(num_clf):
X_softmax[:,i:i+2] = softmax(X[:,i:i+2], axis=1)
return X_softmax
def model_average(X):
# X needs to be in softmax form
num_clf = int(X.shape[1] / 2)
X_logit_avg = np.zeros((X.shape[0],2))
for i in range(num_clf):
X_logit_avg[:,0:2] = X_logit_avg[:,0:2] + X[:,i:i+2]
return np.argmax(X_logit_avg, axis=1)
def majority_voting(X):
# X needs to be in softmax form
num_clf = int(X.shape[1] / 2)
X_votes = np.zeros((X.shape[0],2))
for i in range(X.shape[0]):
for j in range(num_clf):
if X[i,2*j+1] > X[i,2*j]:
X_votes[i,1] += 1
else:
X_votes[i,0] += 1
return np.argmax(X_votes, axis=1)