def get(self, visibility):
dbm = access.DBMan(LOST_CONFIG)
identity = get_jwt_identity()
user = dbm.get_user_by_id(identity)
default_group = dbm.get_group_by_name(user.user_name)
if visibility == VisLevel().USER:
if not user.has_role(roles.DESIGNER):
dbm.close_session()
return "You are not authorized.", 401
else:
root_leaves = dbm.get_all_label_trees(
group_id=default_group.idx)
trees = list()
for root_leaf in root_leaves:
trees.append(
LabelTree(dbm, root_leaf.idx).to_hierarchical_dict())
dbm.close_session()
return trees
if visibility == VisLevel().GLOBAL:
if not user.has_role(roles.ADMINISTRATOR):
dbm.close_session()
return "You are not authorized.", 401
else:
root_leaves = dbm.get_all_label_trees(global_only=True)
trees = list()
for root_leaf in root_leaves:
trees.append(
LabelTree(dbm, root_leaf.idx).to_hierarchical_dict())
dbm.close_session()
return trees
dbm.close_session()
return "You are not authorized.", 401
def get_voc_label_tree(dbm):
tree = LabelTree(dbm)
df = pd.read_csv('/code/backend/lost/pyapi/examples/label_trees/pascal_voc2012.csv')
root = tree.import_df(df)
if root is None:
name = df[df['parent_leaf_id'].isnull()]['name'].values[0]
tree = LabelTree(dbm, name=name)
return tree
def test_create_delete_tree(self):
dbm = DBMan(config.LOSTConfig())
tree = LabelTree(dbm)
root_leaf = tree.create_root(ROOT_NAME, external_id=ROOT_EXTERNAL_ID)
assert root_leaf.name == ROOT_NAME
assert root_leaf.external_id == ROOT_EXTERNAL_ID
assert tree.tree[root_leaf.idx] == root_leaf
tree.delete_tree()
def create_label_tree(self, name, external_id=None):
'''Create a new LabelTree
Args:
name (str): Name of the tree / name of the root leaf.
external_id (str): An external id for the root leaf.
Returns:
:class:`lost.logic.label.LabelTree`:
The created LabelTree.
'''
tree = LabelTree(self._dbm)
tree.create_root(name, external_id=external_id)
return tree
def __label_trees(self):
label_trees_json = list()
for label_tree in self.available_label_trees:
if len(label_tree.label_leaves) > 0:
label_trees_json.append(
LabelTree(self.dbm, label_tree.idx).to_hierarchical_dict())
return label_trees_json
def main(args):
lostconfig = config.LOSTConfig()
dbm = access.DBMan(lostconfig)
if args.csv_file is not None:
df = pd.read_csv(args.csv_file)
name = df[df['parent_leaf_id'].isnull()]['name'].values[0]
elif args.name is not None:
name = args.name
else:
logging.error(
"Either a *csv_file* or a *name* for a label tree needs to be provided!"
)
return
root_leaf = next(
filter(lambda x: x.name == name, dbm.get_all_label_trees()), None)
if root_leaf is None:
logging.warning('LabelTree not present in database! {}'.format(
args.csv_file))
else:
try:
LabelTree(dbm, root_leaf=root_leaf, logger=logging).delete_tree()
logging.info('Deleted tree with name: {}'.format(name))
except:
logging.error(
'Can not delete label tree. One of the labels is used by a pipeline!'
)
dbm.close_session()
def get(self, label_leaf_id):
dbm = access.DBMan(LOST_CONFIG)
identity = get_jwt_identity()
user = dbm.get_user_by_id(identity)
if not user.has_role(roles.DESIGNER):
dbm.close_session()
return "You are not authorized.", 401
else:
label_tree = LabelTree(dbm, root_id=label_leaf_id)
ldf = label_tree.to_df()
dbm.close_session()
f = BytesIO()
ldf.to_csv(f)
f.seek(0)
resp = make_response(f.read())
resp.headers[
"Content-Disposition"] = f"attachment; filename={label_tree.root.name}.csv"
resp.headers["Content-Type"] = "blob"
return resp
def test_import_df(self, tree_plus_childs):
df = tree_plus_childs.to_df()
df2 = df.copy()
root_idx = df2[df2['parent_leaf_id'].isnull()].index.values[0]
no_root_idx = df2[~df2['parent_leaf_id'].isnull()].index
df2.loc[root_idx, 'name'] = 'second tree'
df2.loc[root_idx, 'idx'] = 0
df2.loc[no_root_idx, 'parent_leaf_id'] = 0
dbm = DBMan(config.LOSTConfig())
tree2 = LabelTree(dbm)
root_leaf = tree2.import_df(df2)
if root_leaf is None:
raise Exception(
'A label tree with name "{}" already exists. Clean your Test Database!'
.format(df2.loc[root_idx, 'name']))
for key, val in tree2.tree.items():
print(val.to_df()[['idx', 'name', 'external_id',
'parent_leaf_id']])
for ll in tree2.root.label_leaves:
assert ll.name == CHILD_COW_NAME or ll.name == CHILD_HORSE_NAME
tree2.delete_tree()
def tree_plus_childs():
dbm = DBMan(config.LOSTConfig())
tree = LabelTree(dbm)
root_leaf = tree.create_root(ROOT_NAME, external_id=ROOT_EXTERNAL_ID)
horse = tree.create_child(tree.root.idx,
CHILD_HORSE_NAME,
external_id=CHILD_HORSE_EXTERNAL_ID)
cow = tree.create_child(tree.root.idx,
CHILD_COW_NAME,
external_id=CHILD_COW_EXTERNAL_ID)
yield tree # type: lost.logic.label.LabelTree
tree.delete_tree()
def get(self):
dbm = access.DBMan(LOST_CONFIG)
identity = get_jwt_identity()
user = dbm.get_user_by_id(identity)
if not user.has_role(roles.DESIGNER):
dbm.close_session()
return "You are not authorized.", 401
else:
root_leaves = dbm.get_all_label_trees()
trees = list()
for root_leaf in root_leaves:
trees.append(
LabelTree(dbm, root_leaf.idx).to_hierarchical_dict())
dbm.close_session()
return trees
def get_label_tree(self, name):
'''Get a LabelTree by name.
Args:
name (str): Name of the desired LabelTree.
Retruns:
:class:`lost.logic.label.LabelTree` or None:
If a label tree with the given name exists
it will be returned. Otherwise None
will be returned'''
root_list = self._dbm.get_all_label_trees()
root = next(filter(lambda x: x.name == name, root_list), None)
if root is None:
return None
else:
return LabelTree(self._dbm, root_leaf=root)
#!/usr/bin/env python3
import argparse
from lost.db import model, access
from lost.logic import config
from lost.logic.label import LabelTree
import logging
import os
import pandas as pd
logging.basicConfig(level=logging.INFO, format='(%(levelname)s): %(message)s')
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description='Import a label tree into this lost instance')
parser.add_argument('csv_file',
nargs='?',
action='store',
help='Path to the label tree in csv style.')
# parser.add_argument('group_name', nargs='?', action='store',
# help='Name of group that pipeline should be visible for.')
args = parser.parse_args()
lostconfig = config.LOSTConfig()
dbm = access.DBMan(lostconfig)
tree = LabelTree(dbm, logger=logging)
df = pd.read_csv(args.csv_file)
if tree.import_df(df) is None:
logging.warning('LabelTree already present in database! {}'.format(
args.csv_file))
dbm.close_session()
from lost.api.api import api
from lost.api.label.api_definition import label_leaf
from lost.api.label.parsers import update_label_parser, create_label_parser
from lost.db import model, roles, access
from lost.settings import LOST_CONFIG
from lost.logic.label import LabelTree
import logging
logger = logging.getLogger(__name__)
# Adding initial label tree if it doesn't exist
dbm = access.DBMan(LOST_CONFIG)
root_leaves = dbm.get_all_label_trees()
foundcovid = False
for root_leaf in root_leaves:
if LabelTree(dbm, root_leaf.idx).to_hierarchical_dict().get('name') == 'Covid19':
foundcovid = True
if not foundcovid:
rootlabel = model.LabelLeaf(name='Covid19',
abbreviation=None,
description='Covid19 dataset labels contains 5 labels',
external_id=None,
is_root=True)
rootlabel.parent_leaf_id = None
dbm.save_obj(rootlabel)
for l in ['Parenchyma', 'Emphysema', 'Ground glass', 'Crazy Paving', 'Consolidation']:
label = model.LabelLeaf(name=l,
abbreviation=None,
description=None,
external_id=None,
parent_leaf_id=rootlabel.idx,
import pandas as pd
logging.basicConfig(level=logging.INFO, format='(%(levelname)s): %(message)s')
if __name__ == "__main__":
parser = argparse.ArgumentParser(
description='Export a label tree to a csv file')
parser.add_argument('tree_name',
nargs='?',
action='store',
help='Name of the label tree.')
parser.add_argument('out_path',
nargs='?',
action='store',
help='Path to store the label tree in csv style.')
args = parser.parse_args()
lostconfig = config.LOSTConfig()
dbm = access.DBMan(lostconfig)
root_leaf = next(
filter(lambda x: x.name == args.tree_name, dbm.get_all_label_trees()),
None)
if root_leaf is None:
logging.warning('LabelTree "{}" not present in database!'.format(
args.tree_name))
else:
tree = LabelTree(dbm, root_leaf=root_leaf)
df = tree.to_df()
df.to_csv(args.out_path, index=False)
logging.info('Exported label tree to: {}'.format(args.out_path))
dbm.close_session()
def tree():
dbm = DBMan(config.LOSTConfig())
tree = LabelTree(dbm)
root_leaf = tree.create_root(ROOT_NAME, external_id=ROOT_EXTERNAL_ID)
yield tree
tree.delete_tree()