from kaapana.operators.LocalGetInputDataOperator import LocalGetInputDataOperator
from kaapana.operators.LocalMinioOperator import LocalMinioOperator
from kaapana.operators.LocalWorkflowCleanerOperator import LocalWorkflowCleanerOperator
from example.ExtractStudyIdOperator import ExtractStudyIdOperator
from example.PoolJsonsOperator import PoolJsonsOperator
log = LoggingMixin().log
args = {
'ui_visible': True,
'owner': 'kaapana',
'start_date': days_ago(0),
'retries': 0,
'retry_delay': timedelta(seconds=30)
}
dag = DAG(dag_id='example-dcm-pool-study-ids',
default_args=args,
schedule_interval=None)
get_input = LocalGetInputDataOperator(dag=dag)
extract = ExtractStudyIdOperator(dag=dag)
pool_jsons = PoolJsonsOperator(dag=dag, input_operator=extract)
put_to_minio = LocalMinioOperator(dag=dag,
action='put',
action_operators=[pool_jsons])
clean = LocalWorkflowCleanerOperator(dag=dag, clean_workflow_dir=True)
get_input >> extract >> pool_jsons >> put_to_minio >> clean
'start_date': days_ago(0),
'retries': 0,
'retry_delay': timedelta(seconds=60)
}
dag = DAG(
dag_id='nnunet-install-model',
default_args=args,
concurrency=1,
max_active_runs=1,
schedule_interval=None
)
get_input = LocalGetInputDataOperator(
dag=dag,
check_modality=True,
parallel_downloads=5
)
get_ref_ct_series_from_seg = LocalGetRefSeriesOperator(
dag=dag,
input_operator=get_input,
search_policy="study_uid",
expected_file_count="all",
modality="OT",
parallel_downloads=5,
)
dcm2bin = Bin2DcmOperator(
dag=dag,
input_operator=get_ref_ct_series_from_seg,
from kaapana.operators.LocalDeleteFromElasticOperator import LocalDeleteFromElasticOperator
from kaapana.operators.LocalDeleteFromPacsOperator import LocalDeleteFromPacsOperator
from kaapana.operators.LocalGetInputDataOperator import LocalGetInputDataOperator
from kaapana.operators.LocalWorkflowCleanerOperator import LocalWorkflowCleanerOperator
log = LoggingMixin().log
args = {
'ui_visible': True,
'owner': 'kaapana',
'start_date': days_ago(0),
'retries': 1,
'retry_delay': timedelta(seconds=30)
}
dag = DAG(dag_id='delete-series-from-platform',
default_args=args,
concurrency=30,
max_active_runs=10,
schedule_interval=None)
get_input = LocalGetInputDataOperator(dag=dag, data_type="json")
delete_dcm_pacs = LocalDeleteFromPacsOperator(dag=dag,
delete_complete_study=False)
delete_dcm_elastic = LocalDeleteFromElasticOperator(
dag=dag, delete_complete_study=False)
clean = LocalWorkflowCleanerOperator(dag=dag)
get_input >> delete_dcm_pacs >> delete_dcm_elastic >> clean
'ui_visible': True,
'ui_dag_info': tasks,
'ui_forms': ui_forms,
'owner': 'kaapana',
'start_date': days_ago(0),
'retries': 0,
'retry_delay': timedelta(seconds=60)
}
dag = DAG(dag_id='nnunet-predict',
default_args=args,
concurrency=50,
max_active_runs=30,
schedule_interval=None)
get_input = LocalGetInputDataOperator(dag=dag, check_modality=True)
get_task_model = GetTaskModelOperator(dag=dag)
# get_task_model = GetContainerModelOperator(dag=dag)
dcm2nifti = DcmConverterOperator(dag=dag, output_format='nii.gz')
nnunet_predict = NnUnetOperator(dag=dag,
input_dirs=[dcm2nifti.operator_out_dir],
input_operator=dcm2nifti)
alg_name = nnunet_predict.image.split("/")[-1].split(":")[0]
nrrd2dcmSeg_multi = Itk2DcmSegOperator(dag=dag,
segmentation_operator=nnunet_predict,
input_type="multi_label_seg",
multi_label_seg_name=alg_name,
alg_name=alg_name)
dcmseg_send_multi = DcmSendOperator(dag=dag, input_operator=nrrd2dcmSeg_multi)
from kaapana.operators.LocalGetInputDataOperator import LocalGetInputDataOperator
from kaapana.operators.LocalWorkflowCleanerOperator import LocalWorkflowCleanerOperator
log = LoggingMixin().log
args = {
'ui_visible': False,
'owner': 'kaapana',
'start_date': days_ago(0),
'retries': 2,
'retry_delay': timedelta(seconds=30),
}
dag = DAG(dag_id='service-extract-metadata',
default_args=args,
concurrency=50,
max_active_runs=50,
schedule_interval=None)
get_input = LocalGetInputDataOperator(
dag=dag, operator_out_dir='extract-metadata-input')
extract_metadata = LocalDcm2JsonOperator(dag=dag,
input_operator=get_input,
delete_private_tags=True)
push_json = LocalJson2MetaOperator(dag=dag,
input_operator=get_input,
json_operator=extract_metadata)
clean = LocalWorkflowCleanerOperator(dag=dag, clean_workflow_dir=True)
get_input >> extract_metadata >> push_json >> clean