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