'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]