def upload_benchmark_results(benchmark_bin, api_key=None):
hostname = socket.gethostname().lower()
results_dir = os.path.join(benchmark_bin, 'BenchmarkResults',
hostname)
if not os.path.exists(results_dir):
sys.stderr.write('Expected results directory does not exist: ' + results_dir)
sys.exit(1)
from girder_client import GirderClient
gc = GirderClient(apiUrl='https://data.kitware.com/api/v1')
gc.authenticate(apiKey=api_key)
# ITK/PerformanceBenchmarkingResults
folder_id = '5af50c818d777f06857985e3'
hostname_folder = gc.loadOrCreateFolder(hostname, folder_id, 'folder')
gc.upload(os.path.join(results_dir, '*.json'), hostname_folder['_id'],
leafFoldersAsItems=False, reuseExisting=True)
def upload_zipped_flat_media_files(
gc: GirderClient,
manager: JobManager,
folderId: str,
working_directory: Path,
create_subfolder=False,
):
"""Takes a flat folder of media files and/or annotation and generates a dataset from it"""
listOfFileNames = os.listdir(working_directory)
validation = gc.sendRestRequest('POST',
'/dive_dataset/validate_files',
json=listOfFileNames)
root_folderId = folderId
default_fps = gc.getFolder(root_folderId).get(
f"meta.{constants.FPSMarker}", -1)
if validation.get('ok', False):
manager.write(f"Annotations: {validation['annotations']}\n")
manager.write(f"Media: {validation['media']}\n")
dataset_type = validation['type']
manager.write(f"Type: {dataset_type}\n")
if create_subfolder != '':
sub_folder = gc.createFolder(
folderId,
create_subfolder,
reuseExisting=True,
)
root_folderId = str(sub_folder["_id"])
# Upload all resulting items back into the root folder
manager.updateStatus(JobStatus.PUSHING_OUTPUT)
# create a source folder to place the zipFile inside of
gc.upload(f'{working_directory}/*', root_folderId)
if dataset_type == constants.ImageSequenceType and default_fps == -1:
default_fps = 1
gc.addMetadataToFolder(
str(root_folderId),
{
constants.TypeMarker: dataset_type,
constants.FPSMarker: default_fps
},
)
# After uploading the default files we do a the postprocess for video conversion now
gc.sendRestRequest("POST",
f"/dive_rpc/postprocess/{str(root_folderId)}")
else:
manager.write(f"Message: {validation['message']}\n")
raise Exception("Could not Validate media Files")
def upload_benchmark_results(benchmark_bin, api_key=None):
hostname = socket.gethostname().lower()
results_dir = os.path.join(benchmark_bin, 'BenchmarkResults', hostname)
if not os.path.exists(results_dir):
sys.stderr.write('Expected results directory does not exist: ' +
results_dir)
sys.exit(1)
from girder_client import GirderClient
gc = GirderClient(apiUrl='https://data.kitware.com/api/v1')
gc.authenticate(apiKey=api_key)
# ITK/PerformanceBenchmarkingResults
folder_id = '5af50c818d777f06857985e3'
hostname_folder = gc.loadOrCreateFolder(hostname, folder_id, 'folder')
gc.upload(os.path.join(results_dir, '*.json'),
hostname_folder['_id'],
leafFoldersAsItems=False,
reuseExisting=True)
def upload_exported_zipped_dataset(
gc: GirderClient,
manager: JobManager,
folderId: str,
working_directory: Path,
create_subfolder='',
):
"""Uploads a folder that is generated from the export of a zip file and sets metadata"""
listOfFileNames = os.listdir(working_directory)
potential_meta_files = list(
filter(constants.metaRegex.match, listOfFileNames))
if len(potential_meta_files) == 0:
manager.write(
"Could not find meta.json or config.json file within the subdirectroy\n"
)
return
print(listOfFileNames)
# load meta.json to get datatype and verify list of files
meta = {}
for meta_name in potential_meta_files:
with open(f"{working_directory}/{meta_name}") as f:
meta = json.load(f)
type = meta[constants.TypeMarker]
if type == constants.ImageSequenceType:
imageData = meta['imageData']
for image in imageData:
if image["filename"] not in listOfFileNames:
manager.write(
"Could not find {item['filename']} file within the list of files\n"
)
return
elif type == constants.VideoType:
video = meta["video"]
if video["filename"] not in listOfFileNames:
manager.write(
"Could not find {item['filename']} file within the list of files\n"
)
return
# remove the auxilary directory so we don't have to tag them all
if constants.AuxiliaryFolderName in listOfFileNames and os.path.isdir(
f'{working_directory}/{constants.AuxiliaryFolderName}'):
shutil.rmtree(f'{working_directory}/{constants.AuxiliaryFolderName}')
root_folderId = folderId
if create_subfolder != '':
sub_folder = gc.createFolder(
folderId,
create_subfolder,
reuseExisting=True,
)
root_folderId = str(sub_folder['_id'])
manager.updateStatus(JobStatus.PUSHING_OUTPUT)
# create a source folder to place the zipFile inside of
gc.upload(f'{working_directory}/*', root_folderId)
# Now we set all the metadata for the folders and items
all_files = list(gc.listItem(root_folderId))
root_meta = {
"type": type,
"attributes": meta.get("attributes", None),
"customTypeStyling": meta.get("customTypeStyling", None),
"confidenceFilters": meta.get("confidenceFilters", None),
"fps": meta["fps"],
"version": meta["version"],
}
if type == constants.VideoType:
# set transcoded and non-transcoded versions
transcoded_video = list(
gc.listItem(root_folderId, name=video["filename"]))
if len(transcoded_video) == 1:
ffprobe = meta["ffprobe_info"]
avgFpsString = ffprobe["avg_frame_rate"]
dividend, divisor = [int(v) for v in avgFpsString.split('/')]
originalFps = dividend / divisor
transcoded_metadata = {
"codec": "h264",
"originalFps": originalFps,
"originalFpsString": avgFpsString,
"source_video": False,
"transcoder": "ffmpeg",
}
gc.addMetadataToItem(str(transcoded_video[0]['_id']),
transcoded_metadata)
# other video is tagged as the source video
for item in all_files:
if (item["name"].endswith(tuple(constants.validVideoFormats))
and item["name"] != video["filename"]):
source_metadata = {
"codec": ffprobe["codec_name"],
"originalFps": originalFps,
"originalFpsString": avgFpsString,
"source_video": False,
}
gc.addMetadataToItem(str(item['_id']), source_metadata)
root_meta["originalFps"] = originalFps
root_meta["originalFpsString"] = avgFpsString
# Need to tag folder Level data (annotate, and others)
root_meta[constants.DatasetMarker] = True
gc.addMetadataToFolder(root_folderId, root_meta)
gc.post(f'dive_rpc/postprocess/{root_folderId}', data={"skipJobs": True})