def register_dataset_items_from_datalake(organization_id, image_channel_id,
label_channel_id, dataset_name,
img_list_path):
"""
register datasets from datalake channel
:param dataset_id: target dataset id
:param channel_id: target channel
:param label_metadata_key: metadata key which label value is stored
:param max_size_for_label: max size of dataset items for each label value
:return:
"""
with open('dataset.json', 'r') as f:
dataset_props = json.load(f)
paths = [[fn.split('/')[-1] for fn in line.split()]
for line in open(img_list_path)]
img2label = {img: lbl for img, lbl in paths}
print('Getting data from datalake....')
client = DatalakeClient(organization_id=organization_id,
credential=credential)
label_channel = client.get_channel(label_channel_id)
label_list = label_channel.list_files(prefetch=True)
label2fileid = {
label.metadata['filename']: label.file_id
for label in label_list
}
image_channel = client.get_channel(image_channel_id)
file_iter = image_channel.list_files(limit=1000, prefetch=True)
dataset_items = []
for file_info in file_iter:
imgfile = file_info.metadata['filename']
labelfile = img2label[imgfile]
label_id = label2fileid[labelfile]
annotation = {
'channel_id': label_channel_id,
'file_id': label_id,
'filename': labelfile
}
item = create_request_element(image_channel_id, file_info, annotation)
dataset_items.append(item)
print('Registering dataset items....')
dataset_params = {
'organization_id': organization_id,
'name': dataset_name,
'type': 'segmentation',
'props': dataset_props
}
dataset_client = DatasetClient(organization_id=organization_id,
credential=credential)
dataset = dataset_client.datasets.create(dataset_name, 'segmentation',
dataset_params)
register_dataset_items(dataset, dataset_items)
def upload_datalake(file_path):
client = DatalakeClient()
datalake_client = DatalakeClient(organization_id=organization_id,
credential=credential)
channel = datalake_client.get_channel(channel_id)
metadata = {}
file = channel.upload_file(file_path, metadata=metadata)
return 0
def upload_image_datalake(image_path):
abeja_credential = {
'user_id': abeja_user_id,
'personal_access_token': abeja_personal_access_token
}
datalake_client = DatalakeClient(organization_id=abeja_organization_id,
credential=abeja_credential)
channel = datalake_client.get_channel(abeja_channel_id)
res = channel.upload_file(image_path)
datalake_file = channel.get_file(file_id=res.file_id)
content = datalake_file.get_file_info()
return content['download_url']
def register_dataset_items_from_datalake(organization_id, channel_id,
dataset_name, split, year,
max_workers):
"""
register datasets from datalake channel
Args:
organization_id:
channel_id:
dataset_name:
split:
year:
max_workers:
Returns:
"""
with open('dataset.json', 'r') as f:
dataset_props = json.load(f)
voc_dataset = voc_bbox_dataset.VOCBboxDataset(split=split, year=year)
nb_data = len(voc_dataset)
data = {}
for i in range(nb_data):
id, annotation = voc_dataset.get_annotations(i)
data[id] = annotation
print('Getting data from datalake....')
client = DatalakeClient(organization_id=organization_id,
credential=credential)
channel = client.get_channel(channel_id)
def file2id(file_info):
return file_info.metadata['filename'].split('.')[0]
file_iter = channel.list_files(limit=1000, prefetch=False)
dataset_items = []
for file_info in tqdm(file_iter):
if file2id(file_info) in data:
item = create_request_element(channel_id, file_info,
data[file2id(file_info)])
dataset_items.append(item)
print('Registering dataset items....')
dataset_client = DatasetClient(organization_id=organization_id,
credential=credential)
dataset = dataset_client.datasets.create(dataset_name,
dataset_props['type'],
dataset_props['props'])
register_dataset_items(dataset, dataset_items, max_workers=max_workers)
print('uploaded!')
def load_latest_file_from_datalake(channel_id):
datalake_client = DatalakeClient()
channel = datalake_client.get_channel(channel_id)
# load latest file path
for f in channel.list_files(sort='-uploaded_at'):
latest_file_path = f.download_url
latest_file_datetime = f.uploaded_at
print('load file uploaded at {} (UTC time).'.format(
latest_file_datetime))
break
return latest_file_path
def main(image_root_dir, channel_id, dataset_name, max_workers,
min_num_image_per_class):
image_root_dir = Path(image_root_dir)
props, label2id = build_props(image_root_dir, min_num_image_per_class)
datakale_client = DatalakeClient()
channel = datakale_client.get_channel(channel_id)
datasets_client = DatasetsClient()
dataset = datasets_client.datasets.create(name=dataset_name,
type='classification',
props=props)
ret = upload_images(channel,
dataset,
image_root_dir,
label2id,
max_workers=max_workers,
min_num_image_per_class=min_num_image_per_class)
print('finished!')
def train_data_loader(channel_id: str, file_id: str, label_field: str, input_fileds: list = None):
datalake_client = DatalakeClient()
channel = datalake_client.get_channel(channel_id)
datalake_file = channel.get_file(file_id)
datalake_file.get_content(cache=True)
csvfile = Path(ABEJA_STORAGE_DIR_PATH, channel_id, file_id)
if input_fileds:
train = pd.read_csv(csvfile, usecols=input_fileds+[label_field])
else:
train = pd.read_csv(csvfile)
y_train = train[label_field].values
cols_drop = [c for c in train.columns if train[c].dtype == 'O'] + [label_field]
train.drop(cols_drop, axis=1, inplace=True)
X_train = train
cols_train = X_train.columns.tolist()
del train
return X_train, y_train, cols_train
def register_dataset_items_from_datalake(organization_id,
channel_id,
dataset_name,
label_metadata_key):
with open('dataset.json', 'r') as f:
dataset_props = json.load(f)
print('Getting data from datalake....')
client = DatalakeClient(organization_id=organization_id,
credential=credential)
channel = client.get_channel(channel_id)
def to_annotation(file_info):
label = file_info.metadata[label_metadata_key]
label_id = label2id[label]
return [{label_metadata_key: label,
'label_id': label_id,
'category_id': 0}]
file_iter = channel.list_files(limit=1000, prefetch=False)
label2id = {
x['label']: x['label_id']
for x in dataset_props['props']['categories'][0]['labels']
}
dataset_items = []
for file_info in file_iter:
item = create_request_element(channel_id, file_info,
data_id=int(file_info.metadata['filename'].split('.')[0]),
annotation=to_annotation(file_info))
dataset_items.append(item)
if len(dataset_items) % 1000 == 0:
print(len(dataset_items))
print('Registering dataset items....')
dataset_client = DatasetClient(organization_id=organization_id,
credential=credential)
dataset = dataset_client.datasets.create(dataset_name,
dataset_props['type'],
dataset_props['props'])
register_dataset_items(dataset, dataset_items)
def __init__(self,
root,
dataset_id,
transform=None,
target_transform=None,
transforms=None,
prefetch=False,
use_cache=True,
indices=None):
super(AbejaDataset, self).__init__(root, transforms, transform,
target_transform)
datasets_client = DatasetsClient()
self.datalake_client = DatalakeClient()
dataset = datasets_client.get_dataset(dataset_id)
self.labels = dataset.props['categories'][0]['labels']
self.palette = create_palette(self.labels)
self.use_cache = use_cache
self.datalake_files = list()
idx = 0
for item in dataset.dataset_items.list(prefetch=prefetch):
if indices is not None and not idx in indices:
idx += 1
continue
if 'segmentation-image' in item.attributes:
data_uri = item.attributes['segmentation-image']['combined'][
'data_uri']
else:
# FIXME: DEPRECATED. Type 'segmentation' is invalid on the latest spec.
data_uri = item.attributes['segmentation']['combined'][
'data_uri']
m = re.search(r'datalake://(.+?)/(.+?)$', data_uri)
src_data = item.source_data[0]
self.datalake_files.append(
DataLakeObj(m.group(1), m.group(2), src_data))
idx += 1
'pottedplant': 15,
'sheep': 16,
'sofa': 17,
'train': 18,
'tvmonitor': 19
}
# get DataLake channel id
organization_url = urljoin(
ANNOTATION_API,
"/api/v1/organizations/{}/projects/{}".format(ANNOTATION_ORGANIZATION_ID,
ANNOTATION_PROJECT_ID))
res = requests.get(organization_url, headers=headers)
res.raise_for_status()
channel_id = res.json()['data_lake_channels'][0]['channel_id']
client = DatalakeClient(organization_id=organization_id, credential=credential)
datalake_channel = client.get_channel(channel_id)
# get annotation task url
task_url = urljoin(
ANNOTATION_API, "/api/v1/organizations/{}/projects/{}/tasks/".format(
ANNOTATION_ORGANIZATION_ID, ANNOTATION_PROJECT_ID))
page = 1
while True:
res = requests.get(task_url, headers=headers, params={'page': page})
res.raise_for_status()
res_body = res.json()
# check if project has data
if len(res_body) == 0:
def main():
"""auto-annotation for image segmentation"""
page = 1
delay = 10
while True:
# get annotation tasks
task_url = urljoin(
annotation_api,
'/api/v1/organizations/{}/projects/{}/tasks/'.format(
annotation_organization_id, annotation_project_id))
res_task_url = requests.get(task_url,
headers=headers,
params={'page': page})
res_task_url.raise_for_status()
# check if project has data
if len(res_task_url.json()) == 0:
break
for task in tqdm(res_task_url.json()):
# load image from DataLake channel-in
client = DatalakeClient(organization_id=organization_id,
credential=credential)
channel = client.get_channel(channel_id_in)
metadata = task['metadata'][0]
input_img = channel.get_file(metadata['file_id'])
content_type = input_img.get_file_info()['content_type']
input_img_io = io.BytesIO(input_img.get_content())
# post image to the model
res_deployment_url = requests.post(
deployment_url,
data=input_img_io,
headers={'Content-Type': content_type},
auth=(user_id, personal_access_token))
res_deployment_url.raise_for_status()
# get predicted results
labels = res_deployment_url.json()['labels'][0]
b64 = res_deployment_url.json()['result']
output_img_io = io.BytesIO(base64.b64decode(b64))
# convert black color to transparency
img = Image.open(output_img_io).convert('RGBA')
pixdata = img.load()
width, height = img.size
for y in range(height):
for x in range(width):
if pixdata[x, y] == (0, 0, 0, 255):
pixdata[x, y] = (0, 0, 0, 0)
modified_img_io = io.BytesIO()
img.save(modified_img_io, format='PNG')
# upload output image to Datalake channel-out
upload_url = 'https://api.abeja.io//channels/{}/upload'.format(
channel_id_out)
res_upload_url = requests.post(
upload_url,
data=modified_img_io.getvalue(),
headers={'Content-type': 'image/png'},
auth=(user_id, personal_access_token))
res_upload_url.raise_for_status()
file_id = res_upload_url.json()['file_id']
# get file url
file_info_url = 'https://api.abeja.io//channels/{}/{}'.format(
channel_id_out, file_id)
res_file_info_url = requests.get(file_info_url,
auth=(user_id,
personal_access_token))
res_file_info_url.raise_for_status()
file_url = res_file_info_url.json()['download_url']
# FIXME multi label
information = [{
'class': labels['label'],
'color': labels['color'],
'file_id': file_id,
'file_url': file_url,
'id': labels['label_id']
}]
# register predicted result to annotation tool
preinference_url = urljoin(
task_url, "{}/preinferences".format(str(task['id'])))
res_preinference_url = requests.post(
preinference_url,
json={'information': information},
headers=headers)
res_preinference_url.raise_for_status()
print(res_preinference_url.json())
time.sleep(delay)
page = page + 1
class AbejaDataset(VisionDataset):
def __init__(self,
root,
dataset_id,
transform=None,
target_transform=None,
transforms=None,
prefetch=False,
use_cache=True,
indices=None):
super(AbejaDataset, self).__init__(root, transforms, transform,
target_transform)
datasets_client = DatasetsClient()
self.datalake_client = DatalakeClient()
dataset = datasets_client.get_dataset(dataset_id)
self.labels = dataset.props['categories'][0]['labels']
self.palette = create_palette(self.labels)
self.use_cache = use_cache
self.datalake_files = list()
idx = 0
for item in dataset.dataset_items.list(prefetch=prefetch):
if indices is not None and not idx in indices:
idx += 1
continue
if 'segmentation-image' in item.attributes:
data_uri = item.attributes['segmentation-image']['combined'][
'data_uri']
else:
# FIXME: DEPRECATED. Type 'segmentation' is invalid on the latest spec.
data_uri = item.attributes['segmentation']['combined'][
'data_uri']
m = re.search(r'datalake://(.+?)/(.+?)$', data_uri)
src_data = item.source_data[0]
self.datalake_files.append(
DataLakeObj(m.group(1), m.group(2), src_data))
idx += 1
def __getitem__(self, index):
"""
Args:
index (int): Index
Returns:
tuple: (image, target) where target is the image segmentation.
"""
channel = self.datalake_client.get_channel(
self.datalake_files[index].channel_id)
datalake_file = channel.get_file(self.datalake_files[index].file_id)
# source image
src_data = self.datalake_files[index].src_data
src_content = src_data.get_content(cache=self.use_cache)
src_file_like_object = io.BytesIO(src_content)
src_img = Image.open(src_file_like_object).convert('RGB')
# target image
content = datalake_file.get_content(cache=self.use_cache)
file_like_object = io.BytesIO(content)
target = Image.open(file_like_object).convert('RGB').quantize(
palette=self.palette)
if self.transforms is not None:
src_img, target = self.transforms(src_img, target)
return src_img, target
def __len__(self):
return len(self.datalake_files)
def num_class(self):
return len(self.labels) + 1 # label+background
from abeja.datalake import Client
from abeja.datalake.file import DatalakeFile
CHANNEL_ID = os.environ.get('CHANNEL_ID')
ORGANIZATION_ID = os.environ.get('ORGANIZATION_ID')
USER_ID = os.environ.get('USER_ID')
PERSONAL_ACCESS_TOKEN = os.environ.get('PERSONAL_ACCESS_TOKEN')
FIXTURE_IMAGE_PATH = 'integration_tests/fixtures/images'
credential = {
'user_id': USER_ID,
'personal_access_token': PERSONAL_ACCESS_TOKEN
}
client = Client(credential=credential, organization_id=ORGANIZATION_ID)
channel = client.get_channel(CHANNEL_ID)
def delete_all_files_in_channel(channel_id):
res = client.api.list_channel_files(channel_id)
for file in res['files']:
file_id = file['file_id']
client.api.delete_channel_file(channel_id, file_id)
class DatalakeIntegrationTest(TestCase):
def setUp(self):
delete_all_files_in_channel(CHANNEL_ID)
@classmethod