def set_data_bunch(self):
self.data_bunch = TextDataBunch.from_df(
".",
self.train,
self.val,
tokenizer=self.coruscant_tokenizer,
vocab=self.coruscant_vocab,
include_bos=False,
include_eos=False,
text_cols=self.text_cols,
label_cols=self.label_cols,
bs=self.batch_size,
collate_fn=partial(pad_collate, pad_first=False, pad_idx=0),
)
def run_training_sample(sample_size=300, image_size=224, n_cycles=10,
with_focal_loss=False, with_oversampling=True,
with_weighted_loss=True,
confusion_matrix_filename='train_confusion_matrix'):
"""
:param sample_size: number of images per class
if the input file has less than the given number, only the existing ones are used
:param image_size:
Size of the image in image augmantation pre-processing
:param n_cycles:
epochs
:param with_focal_loss: bool
Use it if data is balanced
:param with_oversampling: bool
Use oversampling for the mintority class of COVID xrays to match the `sample_size`
:param with_weighted_loss: bool
Use weighted loss for unbalaned sample size in classes
:return:
"""
data = load_dataset(sample_size=sample_size, image_size=image_size)
callbacks = None
if with_oversampling:
callbacks = [partial(OverSamplingCallback)]
learn = cnn_learner(data, models.resnet50, metrics=accuracy,
callback_fns = callbacks
)
learn.model = torch.nn.DataParallel(learn.model)
# handle unbalanced data with weights
# ['COVID-19', 'normal', 'pneumonia']
if with_weighted_loss:
classes = {c:1 for c in learn.data.classes}
classes['COVID-19'] = 5
learn.loss_func = CrossEntropyLoss(weight=tensor(list(classes.values()),
dtype=torch.float, device=fastai.torch_core.defaults.device),
reduction='mean')
elif with_focal_loss:
learn.loss_func = FocalLoss()
learn.fit_one_cycle(n_cycles)
save_learner(learn, with_focal_loss=with_focal_loss, with_oversampling=with_oversampling,
sample_size=sample_size, with_weighted_loss=with_weighted_loss)
_save_classification_interpert(learn, confusion_matrix_filename=confusion_matrix_filename)
def train(self, graph, max_epoch=100, min_delta=0, patience=0):
model_num = self._model_num
self._model_num = self._model_num + 1
learn = Learner(self.data, graph.generate_model(), loss_func=self.loss_func, metrics=self.metrics,
callback_fns=[partial(ValueTrackingCallback,
value_holder=self.accuracy,
monitor=self.monitor,
min_delta=min_delta,
patience=patience)])
progress_disabled_ctx(learn)
learn.fit(max_epoch)
print(f'Saving model {model_num}...', end='')
graph.save(os.path.join(self.path, str(model_num)))
print(' Done!')
print(f'Model number: {model_num}\nBest accuracy: {self.accuracy.value}')
return model_num, self.accuracy.value.item()
def create_model(self):
# BERT model
bert_model_class = BertForSequenceClassification.from_pretrained(
'bert-base-uncased', num_labels=6)
# Loss function to be used is Binary Cross Entropy with Logistic Losses
loss_func = nn.BCEWithLogitsLoss()
# Considering this is a multi-label classification problem, we cant use simple accuracy as metrics here.
# we will use accuracy_thresh with threshold of 25% as our metric here.
acc_02 = partial(accuracy_thresh, thresh=0.25)
self.model = bert_model_class
# learner function
self.learner = Learner(self.data_bunch,
self.model,
loss_func=loss_func,
model_dir=self.model_dir,
metrics=acc_02)
def main(epochs):
Task.init(project_name="examples",
task_name="fastai with tensorboard callback")
path = untar_data(URLs.MNIST_SAMPLE)
data = ImageDataBunch.from_folder(path,
ds_tfms=(rand_pad(2, 28), []),
bs=64,
num_workers=0)
data.normalize(imagenet_stats)
learn = cnn_learner(data, models.resnet18, metrics=accuracy)
tboard_path = Path("data/tensorboard/project1")
learn.callback_fns.append(
partial(LearnerTensorboardWriter, base_dir=tboard_path, name="run0"))
accuracy(*learn.get_preds())
learn.fit_one_cycle(epochs, 0.01)
def train_unet(epochs=5, batch_size=1, lr=0.1, val_percent=0.1):
print("Start script")
if args.isgrid is False:
filename = "/media/adrian/E2B45A26B459FD8B/psfmaskmoving_zernike2d_128_n_1_s_0_p_0_b_0__noise_1_2dzernike_test/"
batch_size = int(batch_size // 1.5)
else:
filename = "/idiap/temp/ashajkofci/psfmaskmoving_zernike2d_128_n_1_s_0_p_0_b_0__noise_1_2dzernike_train/"
batch_size = batch_size
os.environ['TORCH_HOME'] = os.getcwd() + 'data'
#transform = transforms.Compose([
# transforms.ToPILImage(),
# transforms.RandomCrop([450, 450]),
# transforms.RandomVerticalFlip(),
# transforms.RandomHorizontalFlip(),
# transforms.ToTensor(),
# ])
all_files_list = glob.glob(filename + "*/*.png")
print('{} files found in {}'.format(len(all_files_list), filename))
all_files_list = [x for x in all_files_list if "_mask" not in x]
print('{} files found'.format(len(all_files_list)))
all_files_list = sorted(all_files_list, key=lambda name: int(name[-13:-4]))
print('{} files found'.format(len(all_files_list)))
#all_files_list = all_files_list[:100000]
#all_labels_list = lambda x: str(x).replace('.png', '_mask.png')
num_files = len(all_files_list)
print('{} files found'.format(len(all_files_list)))
print("Convert to Dataframe")
#df = pd.DataFrame({'data':all_files_list, 'label':all_labels_list})
df = pd.DataFrame(all_files_list)
print("Create transforms")
print("Create data")
#class MyImageList(ImageList):
# def open(self, fn):
# image = Image(grayloader(fn, onedim=True))
# return image
src = (MyImageImageList.from_df(df,
path='/').split_by_rand_pct(val_percent))
print("Creating dataloaders")
data_gen = get_data(bs=batch_size, size=224, src=src)
#dataset = DatasetFromFolder(filename, loader = grayloader, transform=transform, target_transform=transform)
#n_val = int(len(dataset) * val_percent)
#n_train = len(dataset) - n_val
#train, val = rs(dataset, [n_train, n_val])
#data = ImageDataBunch.create(train, val, bs=batch_size, num_workers=4)
#data.c = 2
#data.normalize(imagenet_stats)
#data_gen.show_batch(2)
#plt.show()
print("Creating learner")
#optar = partial(DiffGrad, version=1, betas=(.95, .999), eps=1e-6)
optar = partial(Ranger, betas=(0.95, 0.99), eps=1e-6)
selfattention = False
modelname = 'resnet34unetanneal'
learn = unet_learner(data_gen,
model_resnet34,
pretrained=True,
self_attention=selfattention,
norm_type=NormType.Weight,
loss_func=loss_with_flag,
y_range=(0., 1.0))
learn.model_dir = os.getcwd() + 'data'
learn.opt_func = optar
print("Summary...")
dt_string = datetime.now().strftime("%d-%m-%Y-%H:%M:%S")
#writer = SummaryWriter(comment=f'PROJ_{args.nbgrid}_LR_{lr}_BS_{batch_size}_FP_{args.fakepenalty}_N_{args.network}')
name = f'{dt_string}_PROJ_{args.nbgrid}_LR_{lr}_BS_{batch_size}_N_{args.network}_ATT_{selfattention}_MODEL_{modelname}'
mycallback = partial(TensorboardLogger, path='runs', run_name=name)
learn.callback_fns.append(mycallback)
learn.model.layers = learn.model.layers[:-1]
print(learn.summary())
#learn.lr_find(stop_div = False, num_it=200)
#learn.recorder.plot(suggestion=True)
#plt.show()
flattenAnneal(learn, lr, epochs, 0.7)
#learn.fit_one_cycle(epochs, max_lr = lr)
torch.save(learn.model,
os.getcwd() + '/data/' + name + '_TORCH_INTERMEDIATE.pth')
learn.export(os.getcwd() + '/data/' + name + '_INTERMEDIATE_EXPORT.pth')
#learn.fit_one_cycle(epochs, max_lr=lr/5.0)
learn.unfreeze()
flattenAnneal(learn, lr / 5, epochs, 0.7)
mycallback = partial(TensorboardLogger,
path='runs',
run_name=name + '_UNFREEZE')
learn.callback_fns[-1] = mycallback
torch.save(learn.model, os.getcwd() + '/data/' + name + '_TORCH.pth')
learn.export(os.getcwd() + '/data/' + name + '_EXPORT.pth')
def train_unet(epochs=5, batch_size=1, lr=0.1, val_percent=0.1):
print("Start script")
if args.isgrid is False:
filename = "/media/adrian/OMENDATA/data/movementgenerator_data_multiple2/"
batch_size = int(batch_size//1.5)
else:
filename = "/idiap/temp/ashajkofci/movementgenerator_data_multiple2/"
batch_size = batch_size
os.environ['TORCH_HOME'] = os.getcwd()+'/data'
all_files_list = glob.glob(filename + "*/*.png")
print('{} files found in {}'.format(len(all_files_list), filename))
all_files_list = sorted(all_files_list, key=lambda name: int(name[-13:-4]))
print('{} files found'.format(len(all_files_list)))
print("Convert to Dataframe")
df = pd.DataFrame(all_files_list)
print("Create transforms")
print("Create data")
class MyImageList(ImageList):
def open(self, fn):
image = np.load(fn)['arr_0']
image = np.transpose(image, (2, 0, 1))
image[1] /= 128.0
image[0] /= 128.0
image[3] /= 5.0
image = torch.Tensor(image)
#print('{} {} {}'.format(image.min(), image.max(), image.mean()))
image = Image(image)
return image
class MyImageImageList(ImageImageList):
_label_cls = MyImageList
def open(self, fn):
return Image(grayloader(fn))
def get_data(bs, size):
data = (src.label_from_func(lambda x: str(x).replace('.png', '_mask.npy.npz'))
.transform(get_transforms(do_flip = False, max_zoom=1.0, max_warp=0.0, max_rotate=0, max_lighting=0.3), tfm_y=False)
.transform([rand_crop(), rand_crop()], tfm_y=True, size= size)
.databunch(bs=bs).normalize(imagenet_stats, do_y=False))
data.c = 4
return data
src = (MyImageImageList.from_df(df, path='/')
.split_by_rand_pct(val_percent))
print("Creating dataloaders")
data_gen = get_data(bs=batch_size, size=448)
#dataset = DatasetFromFolder(filename, loader = grayloader, transform=transform, target_transform=transform)
#n_val = int(len(dataset) * val_percent)
#n_train = len(dataset) - n_val
#train, val = rs(dataset, [n_train, n_val])
#data = ImageDataBunch.create(train, val, bs=batch_size, num_workers=4)
#data.c = 2
#data.normalize(imagenet_stats)
#data_gen.show_batch(2)
#plt.show()
print("Creating learner")
optar = partial(DiffGrad, version=1, betas=(.95, .999), eps=1e-6)
selfattention=False
modelname='resnet34'
learn = unet_learner(data_gen, model_resnet34, pretrained=True, loss_func = MSELossFlat(), self_attention=False)
learn.model_dir = os.getcwd()+'/data'
learn.opt_func = optar
print("Summary...")
dt_string = datetime.now().strftime("%d-%m-%Y-%H:%M:%S")
name =f'{dt_string}_PROJ_{args.nbgrid}_LR_{lr}_BS_{batch_size}_N_{args.network}_ATT_{selfattention}_MODEL_{modelname}'
mycallback = partial(TensorboardLogger, path='runs', run_name=name, run_type='unet')
learn.callback_fns.append(mycallback)
learn.callback_fns.append(partial(SaveModelCallback,every='improvement', name='{}/{}.pth'.format(dir_checkpoint, name)))
#learn.model.layers = learn.model.layers[:-1]
print(learn.summary())
#learn.lr_find(stop_div = False, num_it=200)
#learn.recorder.plot(suggestion=True)
#plt.show()
learn.fit_one_cycle(epochs, max_lr = lr)
torch.save(learn.model, 'data/'+name+'_TORCH_INTERMEDIATE.pth')
learn.unfreeze()
learn.fit_one_cycle(epochs, max_lr = slice(lr/50,lr/5))
learn.save(name+'_FINAL')
torch.save(learn.model, 'data/'+name+'_TORCH.pth')
def train_cnn2(epochs=5, batch_size=1, lr=0.1, val_percent=0.1):
print("Start script")
if args.isgrid is False:
filename = "/media/adrian/E2B45A26B459FD8B/movementgenerator_data_multiple/"
batch_size = int(batch_size//1.5)
else:
filename = "/idiap/temp/ashajkofci/movementgenerator_data_multiple/"
batch_size = batch_size
os.environ['TORCH_HOME'] = os.getcwd()+'/data'
#transform = transforms.Compose([
# transforms.ToPILImage(),
# transforms.RandomCrop([450, 450]),
# transforms.RandomVerticalFlip(),
# transforms.RandomHorizontalFlip(),
# transforms.ToTensor(),
# ])
all_files_list = glob.glob(filename + "*/*.png")
print('{} files found in {}'.format(len(all_files_list), filename))
all_files_list = sorted(all_files_list, key=lambda name: int(name[-13:-4]))
print('{} files found'.format(len(all_files_list)))
_file_csv = read_csv(os.path.expanduser(filename + "parameters.txt"), header=None)
_labels = _file_csv.values.astype(np.float)
print('{} labels found'.format(len(_labels)))
print('{} files found'.format(len(all_files_list)))
print("Convert to Dataframe")
df = pd.DataFrame(all_files_list)
print("Create transforms")
print("Create data")
class MyImageImageList(ImageList):
_label_cls = FloatList
def open(self, fn):
return Image(grayloader(fn))
def ff(input):
out = _labels[int(input[-13:-4])]
out[0] /= 255.0
out[1] /= 255.0
#out[3] /= 5.0
out = out.tolist()
return out
def get_data(bs, size):
data = (src.label_from_func(ff)
.transform(get_transforms(do_flip = False, max_zoom=1.0, max_warp=0.0, max_rotate=0, max_lighting=0.3), tfm_y=False)
.transform([rand_crop(), rand_crop()], tfm_y=False, size= size)
.databunch(bs=bs).normalize(imagenet_stats, do_y=False))
data.c = 120
return data
src = (MyImageImageList.from_df(df, path='/')
.split_by_rand_pct(val_percent))
print("Creating dataloaders")
data_gen = get_data(bs=batch_size, size=448)
#dataset = DatasetFromFolder(filename, loader = grayloader, transform=transform, target_transform=transform)
#n_val = int(len(dataset) * val_percent)
#n_train = len(dataset) - n_val
#train, val = rs(dataset, [n_train, n_val])
#data = ImageDataBunch.create(train, val, bs=batch_size, num_workers=4)
#data.c = 2
#data.normalize(imagenet_stats)
#data_gen.show_batch(2)
#plt.show()
optar = partial(DiffGrad, version=1, betas=(.95, .999), eps=1e-6)
def minmse(output, target):
all_losses = torch.zeros(20)
for i in range(20):
loss = torch.pow((output[:,i*5:i*5+4] - target[:, i*5:i*5+4]), 2).sum()
all_losses[i] = loss
return torch.min(all_losses)
class SmoothL1NoOrderLoss(_Loss):
__constants__ = ['reduction']
def __init__(self, size_average=None, reduce=None, reduction='mean'):
super(SmoothL1NoOrderLoss, self).__init__(size_average, reduce, reduction)
def forward(self, input, target):
nb_feat = 8
nb_points = 15
input = input.double()
target = target.double()
with torch.no_grad():
target2 = target.view(-1, nb_points, nb_feat)
#out_total = torch.zeros((target2.shape[0] * 15 * nb_feat))
final_target_total = torch.zeros((target2.shape[0] * nb_points * nb_feat)).double().cuda()
for batch_image in range(target2.shape[0]):
filter_ori = target2[batch_image].unsqueeze(1)
data = input.view(-1, 1, nb_points * nb_feat)[batch_image].unsqueeze(0)
filter = filter_ori.clone()
m = filter.mean(axis=2).unsqueeze(2)
m2 = filter.sum(axis=2).view(-1, 1, 1)
filter.sub_(m)
filter.div_(m2)
filter[filter != filter] = 0.0
filter_for_mean = torch.ones((1, 1, filter.shape[2])).double().cuda() / filter.shape[2]
data_group_mean2 = F.conv1d(data, filter_for_mean, padding=0, stride=filter.shape[2])
data_group_mean2 = data_group_mean2.repeat_interleave(filter.shape[2])
d2 = (data - data_group_mean2)
filtered_data = (F.conv1d(d2.expand((-1, 1, -1)), filter, stride=nb_feat))
index_min = torch.argsort(filtered_data, dim=2, descending=True)
res = torch.argsort(index_min)
final_indexes = (res[0, :] == 0).nonzero()[:, 1].view(-1)
final_target = filter_ori[final_indexes, :, :]
#out_total[batch_image*data.view(-1).shape[0]:batch_image*data.view(-1).shape[0]+data.view(-1).shape[0]] = data.view(-1)
final_target_total[batch_image*data.view(-1).shape[0]:batch_image*data.view(-1).shape[0]+data.view(-1).shape[0]] = final_target.view(-1)
# print(out)
# print(final_target)
#loss += F.smooth_l1_loss(out, final_target, reduction=self.reduction)
#loss += (out - final_target).pow(2).mean()
return F.mse_loss(input.view(-1), final_target_total, reduction=self.reduction)
class LossMatern(nn.Module):
def __init__(self):
super(LossMatern, self).__init__()
def forward(self,output, target):
covar_module = gpytorch.kernels.MaternKernel(batch_shape= torch.Size([output.shape[0]]), nu=2.5).cuda()
class GaussianKernel():
def __init__(self):
pass
def forward(self, output, target):
return torch.exp(-(output-target)**2)
#covar_module = GaussianKernel()
nb_feat = 8
nb_points = 15
target = target.view(-1, nb_points, nb_feat)
output = output.view(-1, nb_points, nb_feat)
similarity_xx = covar_module(output, output).evaluate().mean(dim=2).mean(dim=1)
similarity_yy = covar_module(target, target).evaluate().mean(dim=2).mean(dim=1)
similarity_xy = covar_module(output, target).evaluate().mean(dim=2).mean(dim=1)
loss = similarity_xx + similarity_yy - 2*similarity_xy
return loss.mean()
def loss_matern(output, target):
covar_module = gpytorch.kernels.MaternKernel(batch_shape= torch.Size([output.shape[0]]), nu=2.5).cuda()
class GaussianKernel():
def __init__(self):
pass
def forward(self, output, target):
return torch.exp(-(output-target)**2)
#covar_module = GaussianKernel()
nb_feat = 8
nb_points = 15
target = target.view(-1, nb_points, nb_feat)
output = output.view(-1, nb_points, nb_feat)
similarity_xx = covar_module(output, output).evaluate().mean(dim=2).mean(dim=1)
similarity_yy = covar_module(target, target).evaluate().mean(dim=2).mean(dim=1)
similarity_xy = covar_module(output, target).evaluate().mean(dim=2).mean(dim=1)
loss = similarity_xx + similarity_yy - 2*similarity_xy
return loss.mean()
#target_full = target.view(-1, nb_feat*15)
#loss = 0.0
#for i in range(target.shape[0]):
# for ii in range(target.shape[1]):
# patch = target[i, ii, :][None, ...]
# ncc = NCC(patch)
# input = output[i][None,...][None, ...]
# ncc_results = ncc(input)
# position = np.unravel_index(ncc_results.argmax(), output.shape)[1]
# position = position - position % nb_feat
# loss +=((target_full[i,position:position+nb_feat] - output[i,position:position+nb_feat])**2).mean()
#loss /= target.shape[0]
#return loss
selfattention=False
modelname='resnet34'
a, b = data_gen.one_batch()
u = b.clone().double().cuda()
b = b.double().cuda()
#a = torch.Tensor([[[1,1,1], [0,0,0], [2,2,2], [0,0,0]]]).double().cuda()
#b = torch.Tensor([[[2,2,2], [0,0,85], [1,1,1], [0,0,0]]]).double().cuda()
b.requires_grad=True
#a.requires_grad=True
criterion = loss_matern
loss = criterion(b,u)
loss.backward()
#res = torch.autograd.gradcheck(LossMatern(), (b, u), eps=1e-3, atol=1e-3, raise_exception=True)
#print('Gradient check:{}'.format(res)) # res should be True if the gradients are correct.
print("Creating learner")
learn = cnn_learner(data_gen, model_resnet34, pretrained=True, loss_func = loss_matern)
learn.model_dir = os.getcwd()+'/data'
learn.opt_func = optar
print("Summary...")
dt_string = datetime.now().strftime("%d-%m-%Y-%H:%M:%S")
#writer = SummaryWriter(comment=f'PROJ_{args.nbgrid}_LR_{lr}_BS_{batch_size}_FP_{args.fakepenalty}_N_{args.network}')
name =f'{dt_string}_PROJ_{args.nbgrid}_LR_{lr}_BS_{batch_size}_N_{args.network}_ATT_{selfattention}_MODEL_{modelname}'
mycallback = partial(TensorboardLogger, path='runs', run_name=name)
learn.callback_fns.append(mycallback)
#learn.callback_fns.append(partial(SaveModelCallback,every='epoch', name='{}/{}.pth'.format(dir_checkpoint, name)))
#learn.model.layers = learn.model.layers[:-1]
print(learn.summary())
#learn.lr_find(stop_div = False, num_it=200)
#learn.recorder.plot(suggestion=True)
#plt.show()
learn.fit_one_cycle(epochs, max_lr = lr)
torch.save(learn.model, 'data/'+name+'_TORCH_INTERMEDIATE.pth')
learn.unfreeze()
learn.fit_one_cycle(epochs, max_lr = slice(lr/100,lr/10))
torch.save(learn.model, 'data/'+name+'_TORCH.pth')
learn.save(name+'_FINAL.pth')
def train_cnn(epochs=5, batch_size=1, lr=0.1, val_percent=0.1):
print("Start script")
if args.isgrid is False:
filename = "/media/adrian/E2B45A26B459FD8B/movementgenerator_data_realworld_big/"
batch_size = int(batch_size//1.5)
else:
filename = "/idiap/temp/ashajkofci/movementgenerator_data_realworld_big/"
batch_size = batch_size
os.environ['TORCH_HOME'] = os.getcwd()+'/data'
#transform = transforms.Compose([
# transforms.ToPILImage(),
# transforms.RandomCrop([450, 450]),
# transforms.RandomVerticalFlip(),
# transforms.RandomHorizontalFlip(),
# transforms.ToTensor(),
# ])
all_files_list = glob.glob(filename + "*/*.png")
print('{} files found in {}'.format(len(all_files_list), filename))
all_files_list = sorted(all_files_list, key=lambda name: int(name[-13:-4]))
print('{} files found'.format(len(all_files_list)))
_file_csv = read_csv(os.path.expanduser(filename + "parameters.txt"), header=None)
_labels = _file_csv.values.astype(np.float)
print('{} labels found'.format(len(_labels)))
print('{} files found'.format(len(all_files_list)))
print("Convert to Dataframe")
df = pd.DataFrame(all_files_list)
print("Create transforms")
print("Create data")
class MyImageImageList(ImageList):
_label_cls = FloatList
def open(self, fn):
return Image(grayloader(fn))
def ff(input):
out = _labels[int(input[-13:-4])]
out = out.tolist()
return out
def get_data(bs, size):
data = (src.label_from_func(ff)
.transform(get_transforms(do_flip = False, max_zoom=1.0, max_warp=0.0, max_rotate=0, max_lighting=0.3), tfm_y=False)
.transform([rand_crop(), rand_crop()], tfm_y=False, size= size)
.databunch(bs=bs).normalize(imagenet_stats, do_y=False))
data.c = 6
return data
src = (MyImageImageList.from_df(df, path='/')
.split_by_idx(list(range(int(val_percent*len(all_files_list))))))
print("Creating dataloaders")
patch_size = 112
data_gen = get_data(bs=batch_size, size=patch_size)
#dataset = DatasetFromFolder(filename, loader = grayloader, transform=transform, target_transform=transform)
#n_val = int(len(dataset) * val_percent)
#n_train = len(dataset) - n_val
#train, val = rs(dataset, [n_train, n_val])
#data = ImageDataBunch.create(train, val, bs=batch_size, num_workers=4)
#data.c = 2
#data.normalize(imagenet_stats)
#data_gen.show_batch(2)
#plt.show()
print("Creating learner")
optar = partial(DiffGrad, version=1, betas=(.95, .999), eps=1e-6)
selfattention=False
modelname='resnet34'
learn = cnn_learner(data_gen, model_resnet34, pretrained=True, loss_func = loss_with_flag)
learn.model_dir = os.getcwd()+'/data'
learn.opt_func = optar
print("Summary...")
dt_string = datetime.now().strftime("%d-%m-%Y-%H:%M:%S")
#writer = SummaryWriter(comment=f'PROJ_{args.nbgrid}_LR_{lr}_BS_{batch_size}_FP_{args.fakepenalty}_N_{args.network}')
name =f'{dt_string}_PROJ_{args.nbgrid}_LR_{lr}_BS_{batch_size}_N_{args.network}_ATT_{selfattention}_MODEL_{modelname}_PATCH_{patch_size}'
mycallback = partial(TensorboardLogger, path='runs', run_name=name)
learn.callback_fns.append(mycallback)
learn.callback_fns.append(partial(SaveModelCallback,every='improvement', name='{}/{}.pth'.format(dir_checkpoint, name)))
#learn.model.layers = learn.model.layers[:-1]
print(learn.summary())
#learn.lr_find(stop_div = False, num_it=200)
#learn.recorder.plot(suggestion=True)
#plt.show()
learn.fit_one_cycle(epochs, max_lr = lr)
torch.save(learn.model, 'data/'+name+'_TORCH_INTERMEDIATE.pth')
learn.unfreeze()
learn.fit_one_cycle(epochs, max_lr = slice(lr/20,lr/5))
learn.save(name+'_FINAL')
torch.save(learn.model, 'data/'+name+'_TORCH.pth')
print(f"Fast.ai version = {fastai.__version__}")
which_processor()
EPOCHS = 10
LEARNING_RATE = 1e-4
IM_SIZE = 300
BATCH_SIZE = 16
ARCHITECTURE = models.resnet18
path = Path('/app/classifier_data/')
data = (ImageList.from_folder(path).split_by_rand_pct(
valid_pct=0.2,
seed=10).label_from_folder().transform(size=IM_SIZE).databunch(
bs=BATCH_SIZE, num_workers=db_num_workers()).normalize(imagenet_stats))
print(f'number of classes: {data.c}')
print(data.classes)
learn = cnn_learner(
data,
ARCHITECTURE,
metrics=[accuracy],
callback_fns=[partial(TrainMetricsRecorder, show_graph=True)])
learn.unfreeze()
learn.fit(EPOCHS, LEARNING_RATE)
learn.export(file=Path("/app/classifier_model.pkl"))
_, validation_accuracy = learn.validate(learn.data.valid_dl,
metrics=[accuracy])
print(f'Accuracy on validation set: {100*float(validation_accuracy):3.2f}')
def get_metrics(thresh=0.2):
"""TODO"""
acc_thresh = partial(accuracy_thresh, thresh=thresh)
f_score = partial(fbeta, thresh=thresh)
metrics = [acc_thresh, f_score]
return metrics
PATH, 'train_v2.csv', folder='train-jpg',
suffix='.jpg').split_by_rand_pct(0.2).label_from_df(label_delim=' ')
data = origin_data.transform(transforms, size=256).databunch().normalize(
vision.imagenet_stats)
#---------------------OR to set batch size to avoid CUDA out of memory--------------------------------------------
# data = origin_data.transform(transforms, size=256).databunch()
# data.batch_size = 32
# data.normalize(vision.imagenet_stats)
#-------------------------------------------------------------------------------------------------------------------
# Show some sample images, labels are separated by semicolon
print(data.show_batch(rows=3, figsize=(12, 12), heatmap=False))
# In training pass, resnet34 is used again, but we use accuracy_thresh rather than accuracy
arch = vision.models.resnet50
# Define accuracy threshold and f2 score metrics
acc_thresh = vision.partial(metrics.accuracy_thresh, thresh=THRESHOLD)
f2_score = vision.partial(metrics.fbeta, thresh=THRESHOLD)
learner = vision.cnn_learner(data, arch, metrics=[acc_thresh, f2_score])
# Use LR finder to find good lr
learner.lr_find()
learner.recorder.plot()
LR = 0.01
learner.fit_one_cycle(EPOCHS, max_lr=LR)
learner.save('stage-1-34')
# Finetuning model
learner.unfreeze()
# Use LR finder to find good lr
learner.lr_find()
learner.recorder.plot()