def test_from_df():
this_tests(ItemList.from_df)
df = pd.DataFrame(["123.png"], columns=["name"])
try:
ImageList.from_df(path="dummy_path", df=df)
except Exception as ex:
assert not isinstance(ex, TypeError)
def preprocess(dicom_paths):
dicom_paths = [f'{path}.png' for path in dicom_paths]
df = pd.DataFrame(dicom_paths, columns=['name'])
train_data_stats = torch.load('normal_stats')
images = ImageList.from_df(df, '.')
return images
df = pd.read_csv(LABELS)
nunique = list(df.nunique())[1:-1]
print(nunique)
df.head()
range(fold * len(df) // nfolds, (fold + 1) * len(df) // nfolds)
# +
stats = ([0.0692], [0.2051])
data = (ImageList.from_df(
df,
path='.',
folder=TRAIN,
suffix='.png',
cols='image_id',
convert_mode='L').split_by_idx(
range(fold * len(df) // nfolds,
(fold + 1) * len(df) // nfolds)).label_from_df(cols=[
'grapheme_root', 'vowel_diacritic', 'consonant_diacritic'
]).transform(
transform.get_transforms(do_flip=False, max_warp=0.1),
size=sz,
padding_mode='zeros').databunch(bs=bs)).normalize(stats)
data.show_batch()
# +
class Head(nn.Module):
def __init__(self, nc, n, ps=0.5):
super().__init__()
layers = [AdaptiveConcatPool2d(), Mish(), Flatten()] + \
def create_covidx_databunch(self):
bs = self.bs
data_path = DATA_DIR / "COVIDx"
assert data_path.exists()
train_df_path = data_path / f"train_split_{self.version}.txt"
# train set
LOGGER.info(f'Reading train_df from {train_df_path}')
self.train_df = (pd.read_csv(train_df_path,
header=None,
delimiter=" ",
index_col=0,
names=["name", "label",
"dataset"]).reset_index(drop=True))
self.train_df["name"] = ["train/" + f for f in self.train_df["name"]]
self.train_df["is_valid"] = False
# validation set
test_df_path = data_path / f"test_split_{self.version}.txt"
# train set
LOGGER.info(f'Reading test_df from {test_df_path}')
self.test_df = (pd.read_csv(data_path / test_df_path,
header=None,
delimiter=" ",
index_col=0,
names=["name", "label",
"dataset"]).reset_index(drop=True))
self.test_df["name"] = ["test/" + f for f in self.test_df["name"]]
self.test_df["is_valid"] = True
# merge
data_df = pd.concat([self.train_df,
self.test_df]).reset_index(drop=True)
data_df = data_df.drop("dataset", axis=1)
# import covidnet test set which is included in testset
covidnet_test_df = (pd.read_csv(data_path / "test_COVIDx4.txt",
header=None,
delimiter=" ",
index_col=0,
names=["name", "label"
]).reset_index(drop=True))
covidnet_test_df["name"] = [
"test/" + f for f in covidnet_test_df["name"]
]
# sanity check
a = set(covidnet_test_df.name)
b = set(self.train_df.name)
c = set(self.test_df.name)
assert a.intersection(b) == set()
assert a.intersection(c) == a
# create fastai databunch
tfms = get_dataaug_transformations()
np.random.seed(42)
src = (ImageList.from_df(
data_df,
data_path).split_from_df().label_from_df().transform(tfms,
size=224))
test = (ImageList.from_df(
covidnet_test_df,
data_path).split_none().label_from_df().transform(None, size=224))
data = (src.databunch(bs=bs).normalize(imagenet_stats))
data.add_test(test.train.x)
# check that proportion classes are same in train and valid
train_counts = np.unique(data.train_ds.y.items, return_counts=True)
LOGGER.info(
f'prop in train set: {train_counts[1]/ train_counts[1].sum()}')
valid_counts = np.unique(data.valid_ds.y.items, return_counts=True)
LOGGER.info(
f'prop in valid set: {valid_counts[1]/ valid_counts[1].sum()}')
test_counts = np.unique(test.y.items, return_counts=True)
LOGGER.info(
f'prop in test set: {test_counts[1]/ test_counts[1].sum()}')
return data, test
optar = partial(Ranger)
# In[25]:
CV=1
seed = CV
bs = 20
tfms = get_transforms(flip_vert=True, do_flip=True, max_zoom=1.05, max_lighting=0.2,
max_warp=0.05, max_rotate=5.)
data = (ImageList.from_df(df=image_df,path=DATA_BASE_PATH / 'train_images',cols='ImageId')
.split_from_df()
.label_from_df(cols='Detected',label_cls=FloatList)
.transform(tfms)
.databunch(bs=bs,num_workers=4)
.normalize(IMAGE_STATS_GLOBAL2)
)
from fastai.vision.models import resnet50
from models.efficientnet import EfficientNet
#making model
arch = 'efficientnet-b0'
model_name = f'{arch}-v1'
# Parameters for the entire model (stem, all blocks, and head)
md_ef = EfficientNet.from_pretrained(arch, num_classes=1, dropout_rate=0.5)
# md_ef = resnet50(pretrained=False, num_classes=1)
from densenet import densenet121, densenet161, densenet169
from resnet import (resnet50, resnet101, resnet152, resnext50_32x4d,
resnext101_32x8d)
from vgg import vgg13_bn, vgg16_bn, vgg19_bn
from se_resnet import se_resnet50, se_resnet101, se_resnet152
# In[1]
print(os.listdir("./input/"))
train_dir = "./input/train/train"
test_dir = "./input/test/train"
train = pd.read_csv('./input/train.csv')
test = pd.read_csv("./input/sample_submission.csv")
path = Path("./input")
device = torch.device('cuda:0')
test_img = ImageList.from_df(test, path=path / 'test', folder='test')
# In[2]
def predict(learn: Learner, name: str):
# submission.csv
preds, _ = learn.get_preds(ds_type=DatasetType.Test)
test['has_cactus'] = preds.numpy()[:, 0]
test.to_csv('submission_{}.csv'.format(name), index=False)
print('Finish creating submission_{}.csv'.format(name))
# loss.csv
id_ = range(len(learn.recorder.losses))
loss_df = pd.DataFrame({
'id': id_,
'loss': np.array(learn.recorder.losses)
})
def get_label_list(self, df_val, image_path):
il_val = ImageList.from_df(df_val, image_path,
cols='filename').split_none()
label_list = il_val.label_from_func(TestCnnLearners.get_label)
return label_list
