def __init__(self, debug=False):
self.debug = debug
self.mode = "train"
self.both_to_tensor = ComposeJoint(
[[transforms.ToTensor(),
transforms.ToTensor()]])
return annotations.view(-1)
def get_valid_annotations_index(flatten_annotations, mask_out_value=255):
return torch.squeeze( torch.nonzero((flatten_annotations != mask_out_value )), 1)
number_of_classes = 21
labels = range(number_of_classes)
train_transform = ComposeJoint(
[
RandomHorizontalFlipJoint(),
#[ResizeAspectRatioPreserve(greater_side_size=348),
# ResizeAspectRatioPreserve(greater_side_size=348, interpolation=Image.NEAREST)],
# RandomScaleJoint(low=0.9, high=1.1),
# [CropOrPad(output_size=(348, 348)), CropOrPad(output_size=(348, 348), fill=255)],
[transforms.ToTensor(), None],
[transforms.Normalize((0.485, 0.456, 0.406), (0.229, 0.224, 0.225)), None],
[None, transforms.Lambda(lambda x: torch.from_numpy(np.asarray(x)).long()) ]
])
trainset = PascalVOCSegmentation('datasets',
download=False,
joint_transform=train_transform)
trainloader = torch.utils.data.DataLoader(trainset, batch_size=1,
shuffle=True, num_workers=2)
def run(sql_db_model):
""" Trains a Resnet-18 network on Endovis 2017.
Trains a Resnet-18 network previously trained on imagenet on the
data of Endovis 2017 challenge. The script trains a binary segmentation
network with an output stride of output_stride.
Parameters
----------
batch_size : int
Size of a batch to use during training.
learning_rate : float
Lerning rate to be used by optimization algorithm.
output_stride : int
Output stride of the network. Can we 32/16/8. Gives more
finegrained predictions but at a cost of more computation (8 is the best;
32 is the worst.
"""
batch_size = sql_db_model.batch_size
learning_rate = sql_db_model.learning_rate
output_stride = sql_db_model.output_stride
gpu_id = sql_db_model.gpu_id
os.environ["CUDA_VISIBLE_DEVICES"] = str(gpu_id)
experiment = Experiment(sql_db_model)
number_of_classes = 2
labels = range(number_of_classes)
train_transform = ComposeJoint([
# Crop to the actual view of the endoscop camera
[
transforms.CenterCrop((1024, 1280)),
transforms.CenterCrop((1024, 1280))
],
RandomHorizontalFlipJoint(),
RandomCropJoint(crop_size=(224, 224)),
[transforms.ToTensor(), None],
[
transforms.Normalize((0.485, 0.456, 0.406), (0.229, 0.224, 0.225)),
None
],
[
None,
transforms.Lambda(lambda x: torch.from_numpy(np.asarray(x)).long())
]
])
trainset = Endovis_Instrument_2017(
root=
'/home/daniil/.pytorch-segmentation-detection/datasets/endovis_2017',
dataset_type=0,
joint_transform=train_transform)
trainloader = torch.utils.data.DataLoader(trainset,
batch_size=batch_size,
shuffle=True,
num_workers=4)
valid_transform = ComposeJoint([
[
transforms.CenterCrop((1024, 1280)),
transforms.CenterCrop((1024, 1280))
], [transforms.ToTensor(), None],
[
transforms.Normalize((0.485, 0.456, 0.406), (0.229, 0.224, 0.225)),
None
],
[
None,
transforms.Lambda(lambda x: torch.from_numpy(np.asarray(x)).long())
]
])
valset = Endovis_Instrument_2017(
root=
'/home/daniil/.pytorch-segmentation-detection/datasets/endovis_2017',
dataset_type=0,
joint_transform=valid_transform,
train=False)
valset_loader = torch.utils.data.DataLoader(valset,
batch_size=1,
shuffle=False,
num_workers=1)
train_subset_sampler = torch.utils.data.sampler.SubsetRandomSampler(
xrange(223))
train_subset_loader = torch.utils.data.DataLoader(
dataset=trainset,
batch_size=1,
sampler=train_subset_sampler,
num_workers=2)
# Define the validation function to track MIoU during the training
def validate():
fcn.eval()
overall_confusion_matrix = None
for image, annotation in valset_loader:
image = Variable(image.cuda())
logits = fcn(image)
# First we do argmax on gpu and then transfer it to cpu
logits = logits.data
_, prediction = logits.max(1)
prediction = prediction.squeeze(1)
prediction_np = prediction.cpu().numpy().flatten()
annotation_np = annotation.numpy().flatten()
# Mask-out value is ignored by default in the sklearn
# read sources to see how that was handled
current_confusion_matrix = confusion_matrix(y_true=annotation_np,
y_pred=prediction_np,
labels=labels)
if overall_confusion_matrix is None:
overall_confusion_matrix = current_confusion_matrix
else:
overall_confusion_matrix += current_confusion_matrix
intersection = np.diag(overall_confusion_matrix)
ground_truth_set = overall_confusion_matrix.sum(axis=1)
predicted_set = overall_confusion_matrix.sum(axis=0)
union = ground_truth_set + predicted_set - intersection
intersection_over_union = intersection / union.astype(np.float32)
mean_intersection_over_union = np.mean(intersection_over_union)
fcn.train()
return mean_intersection_over_union
def validate_train():
fcn.eval()
overall_confusion_matrix = None
for image, annotation in train_subset_loader:
image = Variable(image.cuda())
logits = fcn(image)
# First we do argmax on gpu and then transfer it to cpu
logits = logits.data
_, prediction = logits.max(1)
prediction = prediction.squeeze(1)
prediction_np = prediction.cpu().numpy().flatten()
annotation_np = annotation.numpy().flatten()
# Mask-out value is ignored by default in the sklearn
# read sources to see how that was handled
current_confusion_matrix = confusion_matrix(y_true=annotation_np,
y_pred=prediction_np,
labels=labels)
if overall_confusion_matrix is None:
overall_confusion_matrix = current_confusion_matrix
else:
overall_confusion_matrix += current_confusion_matrix
intersection = np.diag(overall_confusion_matrix)
ground_truth_set = overall_confusion_matrix.sum(axis=1)
predicted_set = overall_confusion_matrix.sum(axis=0)
union = ground_truth_set + predicted_set - intersection
intersection_over_union = intersection / union.astype(np.float32)
mean_intersection_over_union = np.mean(intersection_over_union)
fcn.train()
return mean_intersection_over_union
loss_current_iteration = 0
loss_history = []
loss_iteration_number_history = []
validation_current_iteration = 0
validation_history = []
validation_iteration_number_history = []
train_validation_current_iteration = 0
train_validation_history = []
train_validation_iteration_number_history = []
fcn = resnet_dilated.Resnet18_8s(num_classes=2)
fcn.cuda()
fcn.train()
criterion = nn.CrossEntropyLoss(size_average=False).cuda()
optimizer = optim.Adam(fcn.parameters(),
lr=learning_rate,
weight_decay=0.0001)
best_validation_score = 0
current_validation_score = 0
iter_size = 20
epochs = range(10)
for epoch in epochs: # loop over the dataset multiple times
running_loss = 0.0
for i, data in enumerate(trainloader, 0):
# get the inputs
img, anno = data
# We need to flatten annotations and logits to apply index of valid
# annotations. All of this is because pytorch doesn't have tf.gather_nd()
anno_flatten = flatten_annotations(anno)
index = get_valid_annotations_index(anno_flatten,
mask_out_value=255)
anno_flatten_valid = torch.index_select(anno_flatten, 0, index)
# wrap them in Variable
# the index can be acquired on the gpu
img, anno_flatten_valid, index = Variable(img.cuda()), Variable(
anno_flatten_valid.cuda()), Variable(index.cuda())
# zero the parameter gradients
optimizer.zero_grad()
# forward + backward + optimize
logits = fcn(img)
logits_flatten = flatten_logits(logits, number_of_classes=2)
logits_flatten_valid = torch.index_select(logits_flatten, 0, index)
loss = criterion(logits_flatten_valid, anno_flatten_valid)
loss.backward()
optimizer.step()
# Be very carefull about the things that you append to the results
# array, once we accidently put a gpu tensor there which got pickeled
# and unpickled later on, taking the gpu memory and causing unobvious problems
running_loss += (loss.data[0].cpu().clone().numpy() /
logits_flatten_valid.size(0))
if i % 2 == 1:
loss_history.append(running_loss / 2)
loss_iteration_number_history.append(loss_current_iteration)
experiment.add_next_iteration_results(
training_loss=running_loss / 2)
loss_current_iteration += 1
running_loss = 0.0
#print("Iteration #{}; Epoch #{}".format(i, epoch) )
current_validation_score = validate()
validation_history.append(current_validation_score)
validation_iteration_number_history.append(
validation_current_iteration)
validation_current_iteration += 1
current_train_validation_score = validate_train()
train_validation_history.append(current_train_validation_score)
train_validation_iteration_number_history.append(
train_validation_current_iteration)
train_validation_current_iteration += 1
experiment.add_next_iteration_results(
training_accuracy=current_train_validation_score,
validation_accuracy=current_validation_score)
# Save the model if it has a better MIoU score.
if current_validation_score > best_validation_score:
model_save_path = experiment.get_best_model_file_save_path()
torch.save(fcn.state_dict(), model_save_path)
#torch.save(fcn.state_dict(), 'resnet_18_8s_best.pth')
best_validation_score = current_validation_score
experiment.update_best_iteration_results(
validation_accuracy=current_validation_score)
print('Finished Training')
print('Best validation score is: ' + str(best_validation_score))
return 'success'
# [transforms.ToTensor(), None],
# [transforms.Normalize((0.485, 0.456, 0.406), (0.229, 0.224, 0.225)), None],
# [None, transforms.Lambda(lambda x: torch.from_numpy(np.asarray(x)).long()) ]
# ])
# trainset = PascalVOCSegmentation('datasets',
# download=False,
# joint_transform=train_transform)
# trainloader = torch.utils.data.DataLoader(trainset, batch_size=100,
# shuffle=True, num_workers=4)
valid_transform = ComposeJoint(
[
[transforms.ToTensor(), None],
[transforms.Normalize((0.485, 0.456, 0.406), (0.229, 0.224, 0.225)), None],
[None, transforms.Lambda(lambda x: torch.from_numpy(np.asarray(x)).long())]
])
valset = PascalVOCSegmentation('datasets',
train=False,
download=False,
joint_transform=valid_transform)
valset_loader = torch.utils.data.DataLoader(valset, batch_size=1,
shuffle=False, num_workers=0)
# train_subset_sampler = torch.utils.data.sampler.SubsetRandomSampler(xrange(904))
# train_subset_loader = torch.utils.data.DataLoader(dataset=trainset, batch_size=1,
# sampler=train_subset_sampler,