def parse_args() -> argparse.Namespace:
""" Parse the provided script arguments
Returns:
Parsed arguments in a namespace object
"""
parser = argparse.ArgumentParser(
description=
"Launches the registered algorithm workflow (via name) on the given set of media"
)
parser = tator.get_parser(parser=parser)
parser.add_argument('--project',
type=int,
required=True,
help='Unique project id')
parser.add_argument('--algorithm',
type=str,
required=True,
help='Name of registered algorithm to launch')
parser.add_argument('--media',
type=int,
required=True,
nargs='+',
help='Media IDs to process')
args = parser.parse_args()
logger.info(args)
return args
def parse_args() -> argparse.Namespace:
""" Process arguments
"""
parser = tator.get_parser()
parser.add_argument("--name", type=str, required=True, help="New project's name")
parser.add_argument("--create-state-latest-type", action="store_true", help="Create a state type with latest interpolation/frame association attributes")
parser.add_argument("--create-state-range-type", action="store_true", help="Create state types with attr_style_range interpolation/frame association")
parser.add_argument("--create-track-type", action="store_true", help="Create a state type with localization association")
args = parser.parse_args()
return args
def main():
""" Main routine of this script
"""
# Create the argument list and extract them
parser = tator.get_parser()
parser.add_argument('--project',
type=int,
required=True,
help='Unique project id')
parser.add_argument('--section',
type=str,
required=False,
help='Optional section name to process')
parser.add_argument(
'--output',
type=str,
required=False,
help='Filename of section csv report. Only use if section was provided.'
)
parser.add_argument(
'--disable-thumbnails',
action='store_true',
help='Ignore thumbnail creation, no thumbnails reported.')
parser.add_argument(
'--thumbnail-filename-pattern',
type=str,
required=False,
help=
'Default thumbnail filename is just the localization id. Use this string to specify otherwise.\n'
+
'Use all string to use media-id_frame-num_localization-id_all-attributes\n'
+
'Specify a specific set with: "media_id:frame_number:localization_id:Attribute Name 1:Attribute Name 2"\n'
+
'media_id, frame_number, localization_id are parameters that can be used\n'
+ 'split up the set with the colon\n' +
'Entire string needs to be encapsulated in double quotes\n' +
'This argument is ignored if disable-thumbnails is true')
args = parser.parse_args()
logger.info(args)
# Create the report(s) and thumbnail(s)
processProject(host=args.host,
token=args.token,
project_id=args.project,
section_name=args.section,
summary_filename=args.output,
disable_thumbnails=args.disable_thumbnails,
thumbnail_filename_pattern=args.thumbnail_filename_pattern)
def parse_args() -> argparse.Namespace:
""" Parse script arguments
"""
parser = tator.get_parser()
parser.add_argument("--project", type=int, required=True, help="Associated unique project ID.")
parser.add_argument("--media", type=int, nargs="+", required=True, help="List of media IDs to display.")
parser.add_argument("--multi-media-name", type=str, required=True, help="Name of multi-media file. Note *.multi extension is applied automatically.")
parser.add_argument("--layout-rows", type=int, required=True, help="Number of rows to use in the multi-gridview.")
parser.add_argument("--layout-cols", type=int, required=True, help="Number of columns to use in the multi-gridview.")
parser.add_argument("--quality", type=int, required=True, help="Video quality. 360 for 360p, 720 for 720p, etc.")
parser.add_argument("--section-name", type=str, help="If provided, the new multi media will be applied to the given section. If section with the name does not exist, one will be created.")
args = parser.parse_args()
return args
def parse_args() -> argparse.Namespace:
""" Parse the provided arguments
Returns parsed arguments in a namespace object.
"""
parser = argparse.ArgumentParser(
description="Query localization based on media location")
parser = tator.get_parser(parser=parser)
parser.add_argument('--project',
type=int,
required=True,
help='Unique project id')
parser.add_argument('--section',
type=str,
required=True,
help='Section name of media to process')
parser.add_argument(
'--media_type_id',
type=int,
required=True,
help=
'ID of media type to process (required for numerical attribute filtering)'
)
parser.add_argument('--radius',
type=float,
required=True,
help='Radius (km) of location query')
parser.add_argument('--latitude',
type=float,
required=True,
help='Latitude of location query center point')
parser.add_argument('--longitude',
type=float,
required=True,
help='Longitude of location query center point')
parser.add_argument('--location_field',
type=str,
required=True,
help='Name of lat/lon field of media')
args = parser.parse_args()
logger.info(args)
return args
def parse_args() -> argparse.Namespace:
"""Parse the provided arguments
Returns parsed arguments in a namespace object.
"""
parser = argparse.ArgumentParser(description="Add attribute to existing type")
parser = tator.get_parser(parser=parser)
parser.add_argument("project", type=int, help="Unique project id")
parser.add_argument(
"localization_type_id", type=int, help="ID of localization type to add attribute to"
)
parser.add_argument("new_attribute", type=str, help="Attribute to add (JSON string)")
args = parser.parse_args()
logger.info(args)
return args
def parse_args() -> argparse.Namespace:
"""Parse the provided arguments
Returns parsed arguments in a namespace object.
"""
parser = argparse.ArgumentParser(description="Add attribute to existing type")
parser = tator.get_parser(parser=parser)
parser.add_argument("--project", type=int, required=True, help="Unique project id")
parser.add_argument(
"--state-type", type=int, required=True, help="The type of state to consider"
)
parser.add_argument(
"--state-file",
type=str,
help="The text file where the intermediate list of states will be stored or read from",
default="state_list.txt",
)
parser.add_argument(
"--version", nargs="*", type=int, help="The list of layers to retrieve states from"
)
parser.add_argument(
"--tracks-file",
type=str,
help="The text file where the intermediate list of filtered states will be stored or read from",
default="track_list.txt",
)
parser.add_argument(
"--roi",
type=int,
help="The id of the localization that defines the region of interest",
default=94684778,
)
group = parser.add_mutually_exclusive_group(required=False)
group.add_argument(
"--get-states", help="Stop processing after all states are retrieved", action="store_true"
)
group.add_argument(
"--filter-states", help="Stop processing after states are filtered", action="store_true"
)
args = parser.parse_args()
return args
def main():
""" Main routine of this script
"""
# Create the argument list and extract them
parser = argparse.ArgumentParser(
description="Create localizations report and thumbnails for the section(s) in the given project.")
parser = tator.get_parser(parser=parser)
parser.add_argument('--project', type=int, required=True,
help='Unique project id')
parser.add_argument('--section', type=str, required=False,
help='Optional section name to process')
parser.add_argument('--output', type=str, required=False,
help='Filename of section csv report. Only use if section was provided.')
parser.add_argument('--disable-thumbnails', action='store_true',
help='Ignore thumbnail creation, no thumbnails reported.')
parser.add_argument('--thumbnail-filename-pattern', type=str, required=False,
help='Default thumbnail filename is just the localization id. Use this string to specify otherwise. \n' +
'Use <all> to use "media-name_frame-num_localization-id_all-attributes.png" \n' +
'Specify a specific set with: "media_name:frame_number:localization_id:Attribute Name 1:Attribute Name 2" \n' +
'Note: media_name, frame_number, localization_id are the only parameters that can be used (outside of attributes). \n' +
'Split up the set with the colon\n' +
'Extension of media_name is not included. \n' +
'Entire string needs to be encapsulated in double quotes. \n' +
'This argument is ignored if disable-thumbnails is true. ')
parser.add_argument('--rerun-project', action='store_true',
help='Script will start at the last section it processed (using the current directory of csv filenames)). Do not combine with section option.')
parser.add_argument('--print-timing-info', action='store_true',
help='Print timing')
args = parser.parse_args()
logger.info(args)
# Create the report(s) and thumbnail(s)
process_project(
host=args.host,
token=args.token,
project_id=args.project,
section_name=args.section,
summary_filename=args.output,
disable_thumbnails=args.disable_thumbnails,
thumbnail_filename_pattern=args.thumbnail_filename_pattern,
rerun_project=args.rerun_project,
print_timing_info=args.print_timing_info)
def parse_args() -> argparse.Namespace:
""" Returns the arguments passed to the script
"""
parser = tator.get_parser()
parser.add_argument('--url', type=str, help='URL to rest service.')
parser.add_argument('--gid',
type=str,
default='',
help='Group ID for sending progress.')
parser.add_argument('--uid',
type=str,
default='',
help='Job ID for sending progress.')
parser.add_argument('--media', type=int, help='Media ID related to track.')
parser.add_argument('--track', type=int, help='Track ID to process.')
parser.add_argument(
'--algo',
type=str,
help='Algorithm to run. Options: fillgaps|extend|batchextend')
parser.add_argument('--work-folder',
type=str,
default='/work',
help='Work folder that clips will be downloaded to')
parser.add_argument(
'--extend-direction',
type=str,
help='Extension algorithm direction. Options: forward|backward')
parser.add_argument(
'--extend-detection-id',
type=int,
help='ID of detection to start the extension process with.')
parser.add_argument(
'--extend-max-coast',
type=int,
default=0,
help='Max coast frames to use with the extension algorithm.')
parser.add_argument(
'--extend-max-frames',
type=int,
help=
"Max number of frames to extend if provided. If not provided, only coasting or end of media will prohibit the extension"
)
return parser.parse_args()
def main() -> None:
""" Main routine of this script
"""
# Set the arguments and grab them
parser = tator.get_parser()
parser.add_argument(
'--project',
help='Unique project ID associated with the argo workflow',
required=True,
type=int)
parser.add_argument(
'--manifest',
help='Path to the argo manifest .yaml file to be uploaded',
required=True)
parser.add_argument('--algorithm_name',
help='Unique name of algorithm argo workflow',
required=True)
parser.add_argument('--files_per_job',
help='Number of files to process per job batch',
type=int,
required=True)
parser.add_argument('--description',
help='Description of algorithm workflow')
parser.add_argument('--cluster_id',
help='Cluster ID to run the workflow on',
type=int)
parser.add_argument('--categories',
help='List of categories this workflow belongs to',
nargs='+',
type=str)
args = parser.parse_args()
tator.util.register_algorithm(host=args.host,
token=args.token,
project=args.project,
manifest=args.manifest,
algorithm_name=args.algorithm_name,
files_per_job=args.files_per_job,
description=args.description,
cluster_id=args.cluster_id,
categories=args.categories)
def parse_args() -> argparse.Namespace:
""" Parse the provided arguments
Returns parsed arguments in a namespace object.
"""
parser = argparse.ArgumentParser(
description=
"Creates a file (media) summary for the provided project/section. Localization counts, state counts, and last session duration are recorded."
)
parser = tator.get_parser(parser=parser)
parser.add_argument('--project',
type=int,
required=True,
help='Unique project id')
parser.add_argument('--section',
type=str,
required=True,
help='Name of section to process')
args = parser.parse_args()
logger.info(args)
return args
#!/usr/bin/env python
""" This example shows how to download media.
"""
import logging
import sys
import os
import tator
logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
logger = logging.getLogger(__name__)
if __name__ == '__main__':
# Create a parser that includes media name and project name.
parser = tator.get_parser()
parser.add_argument('--media_name',
help='Name of media to download.',
required=True)
parser.add_argument('--project_name',
help='Name of project.',
required=True)
parser.add_argument('--save_path',
help='Directory to save the media.',
required=True)
args = parser.parse_args()
# Create the api.
tator_api = tator.get_api(args.host, args.token)
# Find the project.
continue
media_dict["s3_key"] = uuid_filename
for media_id in list(media_tracker.keys()):
if media_tracker[media_id]["upload_attempts_rem"] < 1:
media_tracker.pop(media_id)
failures.add("upload")
logger.info("Features uploaded to s3")
return failures
if __name__ == "__main__":
parser = argparse.ArgumentParser(description=__doc__)
tator.get_parser(parser)
parser.add_argument("--access-key", type=str, required=True)
parser.add_argument("--secret-key", type=str, required=True)
parser.add_argument("--s3-bucket", type=str, required=True)
parser.add_argument("--endpoint-url", type=str, required=True)
parser.add_argument("--attribute-name", type=str, required=True)
parser.add_argument("--work-dir", type=str, required=True)
parser.add_argument("--project-id", type=int, required=True)
parser.add_argument("--media-ids", type=int, nargs="*", required=True)
parser.add_argument("--frame-modulus", type=int, required=True)
parser.add_argument("--image-size", type=int, nargs=2, required=True)
parser.add_argument("--verbose", action="store_true")
parser.add_argument("--force-extraction", action="store_true")
args = parser.parse_args()
logger.info(f"ARGS: {args}")
def main():
""" Invokes the thumbnail classifier on a media in tator """
parser = argparse.ArgumentParser(description=__doc__)
parser = tator.get_parser(parser)
parser.add_argument("--strategy",
help="path to strategy file",
required=True)
parser.add_argument("media_ids", nargs="*",help="List of media ids")
args = parser.parse_args()
print(args)
host = os.getenv("TATOR_API_SERVICE")
if host:
host = host.replace('/rest', '')
token = os.getenv("TATOR_AUTH_TOKEN")
media_ids = None
media_ids_str = os.getenv("TATOR_MEDIA_IDS")
if media_ids_str:
media_ids = [int(x) for x in media_ids_str.split(',')]
# Override ENV with CLI
if host is None and args.host:
host = args.host
if args.token:
token = args.token
if args.media_ids:
media_ids = args.media_ids
api = tator.get_api(host, token)
with open(args.strategy) as fp:
strategy = yaml.safe_load(fp)
data_image = strategy['data_image']
print("Strategy:")
pprint(strategy)
extract_mode = strategy['tator'].get('extract_mode', 'state')
assert extract_mode in ['state','localization']
if extract_mode == 'state':
project = _safe_retry(api.get_state_type,strategy['tator']['track_type_id']).project
else:
project = _safe_retry(api.get_localization_type,strategy['tator']['track_type_id']).project
# Download the network files from docker
network_dir = tempfile.mkdtemp()
client=docker.from_env()
image=client.images.pull(data_image)
container=client.containers.create(data_image)
bits, stats = container.get_archive("/network")
network_tar = os.path.join(network_dir, "network.tar")
with open(network_tar, 'wb') as tar_file:
for chunk in bits:
tar_file.write(chunk)
container.remove()
with tarfile.TarFile(network_tar) as tar_file:
members = tar_file.getmembers()
for member in members:
tar_file.extract(member, network_dir)
# Remove tar file
os.remove(network_tar)
run_tracker(api,
project,
media_ids,
os.path.join(network_dir, 'network'),
strategy)
shutil.rmtree(network_dir)
#!/usr/bin/env python
""" This example demonstrates how to create a project and configure media
and metadata type definitions.
"""
import logging
import sys
import tator
logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
logger = logging.getLogger(__name__)
if __name__ == '__main__':
args = tator.get_parser().parse_args()
tator_api = tator.get_api(args.host, args.token)
# Create the project.
result = tator_api.create_project(project_spec={
'name': 'Test Project', 'summary': 'A test project.',
})
project = result.id
logger.info(result.message)
# Create image type.
result = tator_api.create_media_type(project, media_type_spec={
"name": "Test Images",
"description": "A test image type.",
"dtype": "image",
"attribute_types": [
