'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) clean = LocalWorkflowCleanerOperator(dag=dag) get_input >> get_task_model >> dcm2nifti >> nnunet_predict >> nrrd2dcmSeg_multi >> dcmseg_send_multi >> clean
'retry_delay': timedelta(seconds=60) } dag = DAG(dag_id='nnunet-predict', default_args=args, concurrency=10, max_active_runs=10, schedule_interval=None) get_input = LocalGetInputDataOperator(dag=dag, parallel_downloads=5, check_modality=True) get_task_model = GetTaskModelOperator(dag=dag) # get_task_model = GetContainerModelOperator(dag=dag) dcm2nifti = DcmConverterOperator(dag=dag, input_operator=get_input, output_format='nii.gz') nnunet_predict = NnUnetOperator(dag=dag, mode="inference", input_nifti_operators=[dcm2nifti], inf_preparation=True, inf_threads_prep=1, inf_threads_nifti=1) resample_seg = ResampleOperator( dag=dag, input_operator=nnunet_predict, original_img_operator=dcm2nifti, operator_out_dir=nnunet_predict.operator_out_dir)
'ui_forms': ui_forms, 'owner': 'kaapana', 'start_date': days_ago(0), 'retries': 1, 'retry_delay': timedelta(seconds=30) } dag = DAG(dag_id='radiomics-dcmseg', default_args=args, schedule_interval=None, concurrency=30, max_active_runs=15) get_input = LocalGetInputDataOperator(dag=dag, check_modality=True) dcmseg2nrrd = DcmSeg2ItkOperator(dag=dag) get_dicom = LocalGetRefSeriesOperator(dag=dag) dcm2nrrd = DcmConverterOperator(dag=dag, input_operator=get_dicom, output_format='nrrd') radiomics = RadiomicsOperator(dag=dag, mask_operator=dcmseg2nrrd, input_operator=dcm2nrrd) put_radiomics_to_minio = LocalMinioOperator(dag=dag, action='put', action_operators=[radiomics], file_white_tuples=('.xml')) clean = LocalWorkflowCleanerOperator(dag=dag) get_input >> dcmseg2nrrd >> radiomics get_input >> get_dicom >> dcm2nrrd >> radiomics >> put_radiomics_to_minio >> clean
"type": "boolean", "default": False, "readOnly": False, } } } } args = { 'ui_forms': ui_forms, 'ui_visible': True, 'owner': 'kaapana', 'start_date': days_ago(0), 'retries': 0, 'retry_delay': timedelta(seconds=30) } dag = DAG(dag_id='example-dcm2nrrd', default_args=args, schedule_interval=None) get_input = LocalGetInputDataOperator(dag=dag) convert = DcmConverterOperator(dag=dag, input_operator=get_input, output_format='nrrd') put_to_minio = LocalMinioOperator(dag=dag, action='put', action_operators=[convert], file_white_tuples=('.nrrd')) clean = LocalWorkflowCleanerOperator(dag=dag, clean_workflow_dir=True) get_input >> convert >> put_to_minio >> clean
from kaapana.operators.LocalWorkflowCleanerOperator import LocalWorkflowCleanerOperator from kaapana.operators.LocalMinioOperator import LocalMinioOperator 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-dcm2nrrd', default_args=args, schedule_interval=None ) get_input = LocalGetInputDataOperator(dag=dag) convert = DcmConverterOperator(dag=dag, output_format='nrrd') put_to_minio = LocalMinioOperator(dag=dag, action='put', action_operators=[convert], file_white_tuples=('.nrrd')) clean = LocalWorkflowCleanerOperator(dag=dag) get_input >> convert >> put_to_minio >> clean
input_operator=get_input, output_format="nii.gz", seg_filter=seg_filter, parallel_id='seg', ) get_ref_ct_series_from_seg = LocalGetRefSeriesOperator( dag=dag, input_operator=get_input, search_policy="reference_uid", parallel_downloads=5, modality=None ) dcm2nifti_ct = DcmConverterOperator( dag=dag, input_operator=get_ref_ct_series_from_seg, parallel_id='ct', output_format='nii.gz' ) resample_seg = ResampleOperator( dag=dag, input_operator=dcm2nifti_seg, original_img_operator=dcm2nifti_ct, operator_out_dir=dcm2nifti_seg.operator_out_dir ) check_seg = LocalSegCheckOperator( dag=dag, abort_on_error=True, move_data=False, input_operators=[dcm2nifti_seg, dcm2nifti_ct]