def add_raw(token):
"""Add new channel to the project."""
project = Project.get(token)
if not project:
return abort(404, description=f'project {token} not found')
# Load channel from first array in attached file
try:
npz = np.load(request.files.get('file'))
except BadRequestKeyError: # could not get file from request.files
return abort(
400,
description=
'Attach a new channel file in a form under the file field.')
except TypeError:
return abort(
400,
description='Could not load the attached file. Attach an .npz file.'
)
channel = npz[npz.files[0]]
# Check channel is the right shape
expected_shape = (project.num_frames, project.width, project.height, 1)
if channel.shape != expected_shape:
raise ValueError(f'New channel must have shape {expected_shape}')
# Add channel to project
project.add_channel(channel)
return {'numChannels': project.num_channels}
def create_project_from_dropped_file():
"""
Create a new Project from drag & dropped file.
"""
start = timeit.default_timer()
loader = loaders.FileLoader(request)
project = Project.create(loader)
current_app.logger.info('Created project from %s in %s s.', loader.path,
timeit.default_timer() - start)
return jsonify({'projectId': project.token})
def semantic_labels(project_id, feature):
project = Project.get(project_id)
if not project:
return jsonify({'error': f'project {project_id} not found'}), 404
cell_info = project.labels.cell_info[feature]
cell_info = add_frame_div_parent(cell_info)
cell_info = reformat_cell_info(cell_info)
response = make_response(cell_info)
response.add_etag()
return response.make_conditional(request)
def create_project_from_url():
"""
Create a new Project from URL.
"""
start = timeit.default_timer()
url_form = request.form
loader = loaders.URLLoader(url_form)
project = Project.create(loader)
current_app.logger.info('Created project from %s in %s s.', loader.path,
timeit.default_timer() - start)
return jsonify({'projectId': project.token})
def get_project(token):
"""
Retrieve data from a project already in the Project table.
"""
start = timeit.default_timer()
project = Project.get(token)
if not project:
return abort(404, description=f'project {token} not found')
payload = project.make_first_payload()
current_app.logger.debug('Loaded project %s in %s s.', project.token,
timeit.default_timer() - start)
return jsonify(payload)
def raw(token, channel, frame):
project = Project.get(token)
if not project:
return abort(404, description=f'project {token} not found')
raw_array = project.get_raw_array(channel, frame)
content = gzip.compress(json.dumps(raw_array.tolist()).encode('utf8'), 5)
response = make_response(content)
response.headers['Content-length'] = len(content)
response.headers['Content-Encoding'] = 'gzip'
# gzip includes a timestamp that changes the md5 hash
# TODO: in Python >= 3.8, add mtime=0 to create stable md5 and use add_etag instead
etag = hashlib.md5(raw_array).hexdigest()
response.set_etag(etag)
return response.make_conditional(request)
def redo(token):
start = timeit.default_timer()
project = Project.get(token)
if not project:
return abort(404, description=f'project {token} not found')
payload = project.redo()
current_app.logger.debug(
'Redid action for project %s finished in %s s.',
token,
timeit.default_timer() - start,
)
return jsonify(payload)
def download_project():
"""
Download a DeepCell Label project as a .npz file
"""
id = request.args.get('id')
project = Project.get(id)
if not project:
return abort(404, description=f'project {id} not found')
format = request.args.get('format')
exporter = exporters.Exporter(project, format)
filestream = exporter.export()
return send_file(filestream,
as_attachment=True,
attachment_filename=exporter.path)
def labeled(token, feature, frame):
""" """
project = Project.get(token)
if not project:
return jsonify({'error': f'project {token} not found'}), 404
labeled_array = project.get_labeled_array(feature, frame).astype(np.int32)
content = gzip.compress(
json.dumps(labeled_array.tolist()).encode('utf8'), 5)
response = make_response(content)
response.headers['Content-length'] = len(content)
response.headers['Content-Encoding'] = 'gzip'
# gzip includes a timestamp that changes the md5 hash
# TODO: in Python >= 3.8, add mtime=0 to create stable md5 and use add_etag instead
etag = hashlib.md5(np.ascontiguousarray(labeled_array)).hexdigest()
response.set_etag(etag)
return response.make_conditional(request)
def edit(token, action_type):
"""
Edit the labeling of the project and
update the project in the database.
"""
start = timeit.default_timer()
# obtain 'info' parameter data sent by .js script
info = {k: json.loads(v) for k, v in request.values.to_dict().items()}
project = Project.get(token)
if not project:
return abort(404, description=f'project {token} not found')
# TODO: remove frame/feature/channel columns from db schema? or keep them around
# to load projects on the last edited frame
project.frame = info['frame']
project.feature = info['feature']
project.channel = info['channel']
del info['frame']
del info['feature']
del info['channel']
edit = Edit(project)
edit.dispatch_action(action_type, info)
project.create_memento(action_type)
project.update()
changed_frames = [frame.frame_id for frame in project.action.frames]
payload = {
'feature': project.feature,
'frames': changed_frames,
'labels': edit.labels_changed,
}
current_app.logger.debug(
'Finished action %s for project %s in %s s.',
action_type,
token,
timeit.default_timer() - start,
)
return jsonify(payload)
def upload_project_to_s3():
"""Upload .trk/.npz data file to AWS S3 bucket."""
start = timeit.default_timer()
id = request.form['id']
format = request.form['format']
bucket = request.form['bucket']
project = Project.get(id)
if not project:
return abort(404, description=f'project {id} not found')
# Save data file and send to S3 bucket
exporter = exporters.S3Exporter(project, format)
exporter.export(bucket)
# add "finished" timestamp and null out PickleType columns
# project.finish()
current_app.logger.debug(
'Uploaded %s to S3 bucket %s from project %s in %s s.',
exporter.path,
bucket,
id,
timeit.default_timer() - start,
)
return {}