PACS integration is workign well

.dockerignore

@@ -1,7 +1,10 @@
 snapshots_knee_grading/*
 *.egg-info
 snapshots_release_kneel/*
+snapshots_release/*
 deepknee-frontend/*
 deepknee-backend-broker/*
+pacs-integration/*
+pics/*
 logs/*
 .git/

docker/Dockerfile.cpu

@@ -3,6 +3,8 @@ FROM miptmloulu/kneel:cpu
 
 MAINTAINER Aleksei Tiulpin, University of Oulu, Version 1.0
 
+RUN pip install pynetdicom
+
 RUN mkdir -p /opt/pkg-deepknee/
 COPY . /opt/pkg-deepknee/
 RUN pip install /opt/pkg-deepknee/

docker/Dockerfile.gpu

@@ -3,6 +3,8 @@ FROM miptmloulu/kneel:gpu
 
 MAINTAINER Aleksei Tiulpin, University of Oulu, Version 1.0
 
+RUN pip install pynetdicom
+
 RUN mkdir -p /opt/pkg-deepknee/
 COPY . /opt/pkg-deepknee/
 RUN pip install /opt/pkg-deepknee/

docker/docker-compose-cpu.yml

@@ -47,7 +47,7 @@ services:
     container_name: orthanc-pacs
     ports:
       - "6000:4242"
-      - "8042:8042"
+      - "6001:8042"
     volumes:
       - type: bind
         source: ../pacs-integration/orthanc.json
@@ -60,16 +60,20 @@ services:
         condition: service_started
       orthanc-pacs:
         condition: service_started
-    image: "miptmloulu/kneel:cpu"
+    image: "miptmloulu/deepknee:cpu"
     container_name: dicom-router
     volumes:
       - type: bind
         source: ../pacs-integration/change_polling.py
         target: /opt/change_polling.py
     entrypoint: ["python", "-u", "/opt/change_polling.py",
                  "--deepknee_addr", "http://deepknee",
+                 "--deepknee_port", "5001",
                  "--orthanc_addr", "http://orthanc-pacs",
-                 "--orthanc_port", "8042"]
+                 "--orthanc_http_port", "8042",
+                 "--orthanc_dicom_port", "4242",
+                 '--remote_pacs_addr', 'orthanc-pacs',
+                 '--remote_pacs_port', '4242']
   backend-broker:
     depends_on:
       - kneel

docker/docker-compose-gpu.yml

@@ -51,7 +51,7 @@ services:
     container_name: orthanc-pacs
     ports:
       - "6000:4242"
-      - "8042:8042"
+      - "6001:8042"
     volumes:
       - type: bind
         source: ../pacs-integration/orthanc.json
@@ -64,16 +64,20 @@ services:
         condition: service_started
       orthanc-pacs:
         condition: service_started
-    image: "miptmloulu/kneel:cpu"
+    image: "miptmloulu/deepknee:cpu"
     container_name: dicom-router
     volumes:
       - type: bind
         source: ../pacs-integration/change_polling.py
         target: /opt/change_polling.py
     entrypoint: ["python", "-u", "/opt/change_polling.py",
                  "--deepknee_addr", "http://deepknee",
+                 "--deepknee_port", "5001",
                  "--orthanc_addr", "http://orthanc-pacs",
-                 "--orthanc_port", "8042"]
+                 "--orthanc_http_port", "8042",
+                 "--orthanc_dicom_port", "4242",
+                 '--remote_pacs_addr', 'orthanc-pacs',
+                 '--remote_pacs_port', '4242']
   backend-broker:
     depends_on:
       - kneel

pacs-integration/change_polling.py

@@ -1,45 +1,120 @@
 # -*- coding: utf-8 -*-
-import queue
 import argparse
-import requests
 import base64
+import logging
+import queue
 import time
 
+import requests
+from pydicom import dcmread
+from pydicom.filebase import DicomBytesIO
+from pydicom.uid import ImplicitVRLittleEndian
+from pydicom.uid import generate_uid
+from pynetdicom import AE, VerificationPresentationContexts
 
 queue = queue.Queue()
 
 
 def ingestion_loop():
+    logger.log(logging.INFO, 'Creating application entity...')
+    ae = AE(ae_title=b'DEEPKNEE')
+    ae.requested_contexts = VerificationPresentationContexts
+    ae.add_requested_context('1.2.840.10008.5.1.4.1.1.1.1', transfer_syntax=ImplicitVRLittleEndian)
+
     current = 0
-    response = requests.get(f'{args.orthanc_addr}:{args.orthanc_port}/changes?since={current}&limit=10',
-                            auth=('deepknee', 'deepknee'))
+    base_url = f'{args.orthanc_addr}:{args.orthanc_http_port}'
+    response = requests.get(f'{base_url}/changes?since={current}&limit=10', auth=('deepknee', 'deepknee'))
     if response.status_code == 200:
-        print('Connection to orthanc is healthy.')
+        logger.log(logging.INFO, 'Connection to Orthanc via REST is healthy')
+
+    # Orthanc addr must have http, but DICOM communicates via sockets
+    assoc = ae.associate(args.orthanc_addr.split('http://')[1], args.orthanc_dicom_port)
+    if assoc.is_established:
+        logger.log(logging.INFO, 'Connection to Orthanc via DICOM is healthy')
+        assoc.release()
+
+    assoc = ae.associate(args.remote_pacs_addr, args.remote_pacs_port)
+    if assoc.is_established:
+        logger.log(logging.INFO, 'Connection to Remote PACS via DICOM is healthy')
+        assoc.release()
 
     while True:
-        response = requests.get(f'{args.orthanc_addr}:{args.orthanc_port}/changes?since={current}&limit=10',
-                                auth=('deepknee', 'deepknee'))
+        response = requests.get(f'{base_url}/changes?since={current}&limit=10', auth=('deepknee', 'deepknee'))
         response = response.json()
         for change in response['Changes']:
+            # We must also filter by the imaged body part in the future
             if change['ChangeType'] == 'NewInstance':
-                response = requests.get(f'{args.orthanc_addr}:{args.orthanc_port}/instances/{change["ID"]}/file',
-                                        auth=('deepknee', 'deepknee'))
-                dicom_base64 = base64.b64encode(response.content).decode('ascii')
-
-                response = requests.post(f'{args.deepknee_addr}:{args.deepknee_port}/deepknee/predict/bilateral',
-                                         json={'dicom': dicom_base64})
-                if response.status_code != 200:
-                    print('Request has failed!')
+                logger.log(logging.INFO, 'Identified new received instance in Orthanc. '
+                                         'Checking if it has been created by DeepKnee...')
+                # We should not analyze the instances if they are produced by DeepKnee
+                # Checking if it was verified by DeepKnee
+                resp_verifier = requests.get(f'{base_url}/instances/{change["ID"]}/content/0040-a027',
+                                             auth=('deepknee', 'deepknee'))
+                resp_verifier.encoding = 'utf-8'
+                resp_content = requests.get(f'{base_url}/instances/{change["ID"]}/content/0070-0080',
+                                            auth=('deepknee', 'deepknee'))
+
+                resp_content.encoding = 'utf-8'
+
+                if resp_verifier.text.strip("\x00 ") == 'UniOulu-DeepKnee' and \
+                        resp_content.text.strip("\x00 ") == 'DEEPKNEE-XRAY':
+                    continue
+
+                # Once we are sure that the instance is new, we need to go ahead with teh analysis
+                response = requests.get(f'{base_url}/instances/{change["ID"]}/file', auth=('deepknee', 'deepknee'))
+
+                logger.log(logging.INFO, 'Instance has been retrieved from Orthanc')
+                dicom_raw_bytes = response.content
+                dcm = dcmread(DicomBytesIO(dicom_raw_bytes))
+
+                dicom_base64 = base64.b64encode(dicom_raw_bytes).decode('ascii')
+                logger.log(logging.INFO, 'Sending API request to DeepKnee core')
+                url = f'{args.deepknee_addr}:{args.deepknee_port}/deepknee/predict/bilateral'
+                response_deepknee = requests.post(url, json={'dicom': dicom_base64})
+
+                if response_deepknee.status_code != 200:
+                    logger.log(logging.INFO, 'DeepKnee analysis has failed')
                 else:
-                    response_res = response.json()
-                    print(response_res['R']['kl'], response_res['L']['kl'])
-                response = requests.delete(f'{args.orthanc_addr}:{args.orthanc_port}/instances/{change["ID"]}',
-                                           auth=('deepknee', 'deepknee'))
-                if response.status_code == 200:
-                    print('Instance has been removed from the orthanc router')
+                    logger.log(logging.INFO, 'Getting rid of the instance in Orthanc')
+                    if args.orthanc_addr.split('http://')[1] != args.remote_pacs_addr and \
+                            args.orthanc_dicom_port != args.remote_pacs_port:
+                        response = requests.delete(f'{base_url}/instances/{change["ID"]}',
+                                                   auth=('deepknee', 'deepknee'))
+                        if response.status_code == 200:
+                            logger.log(logging.INFO, 'Instance has been removed from the Orthanc')
+                    else:
+                        logger.log(logging.INFO, 'Remote PACS is DeepKnee. The instance will not be removed.')
+
+                    logger.log(logging.INFO, 'DeepKnee has successfully analyzed the image. Routing...')
+
+                    # Report
+                    deepknee_json = response_deepknee.json()
+                    dcm.add_new([0x40, 0xa160], 'LO', 'KL_right: {}, KL_left: {}'.format(deepknee_json['R']['kl'],
+                                                                                         deepknee_json['L']['kl']))
+                    # Verifier
+                    dcm.add_new([0x40, 0xa027], 'LO', 'UniOulu-DeepKnee')
+                    # Content label
+                    dcm.add_new([0x70, 0x80], 'CS', 'DEEPKNEE-XRAY')
+
+                    dcm[0x08, 0x8].value = 'DERIVED'
+                    # Instance_UUID
+                    current_uuid = dcm[0x08, 0x18].value
+                    dcm[0x08, 0x18].value = generate_uid(prefix='.'.join(current_uuid.split('.')[:-1])+'.')
+                    # Series UUID
+                    current_uuid = dcm[0x20, 0x0e].value
+                    dcm[0x20, 0x0e].value = generate_uid(prefix='.'.join(current_uuid.split('.')[:-1])+'.')
+                    logger.log(logging.INFO, 'Connecting to Orthanc over DICOM')
+                    assoc = ae.associate(args.remote_pacs_addr, args.remote_pacs_port)
+                    if assoc.is_established:
+                        logger.log(logging.INFO, 'Association with Orthanc has been established. Routing..')
+                        routing_status = assoc.send_c_store(dcm)
+                        logger.log(logging.INFO, f'Routing finished. Status: {routing_status}')
+                        assoc.release()
+
             else:
+                # Here there should be a code to remove the change from the pacs
+                # Now nothing is done here
                 pass
-
             current += 1
         time.sleep(1)
 
@@ -48,10 +123,17 @@ def ingestion_loop():
     parser = argparse.ArgumentParser()
     parser.add_argument('--deepknee_addr', default='http://127.0.0.1', help='DeepKnee address')
     parser.add_argument('--deepknee_port', default=5001, help='DeepKnee backend port')
+
     parser.add_argument('--orthanc_addr', default='http://127.0.0.1', help='The host address that runs Orthanc')
-    parser.add_argument('--orthanc_port', type=int, default=6001, help='Orthanc REST API port')
+    parser.add_argument('--orthanc_http_port', type=int, default=6001, help='Orthanc REST API port')
+    parser.add_argument('--orthanc_dicom_port', type=int, default=6000, help='Orthanc DICOM port')
+
     parser.add_argument('--remote_pacs_addr', default='http://127.0.0.1', help='Remote PACS IP addr')
-    parser.add_argument('--remote_pacs_port', type=int, default=8042, help='Remote PACS IP addr')
+    parser.add_argument('--remote_pacs_port', type=int, default=6000, help='Remote PACS port')
     args = parser.parse_args()
+
+    logging.basicConfig(format='%(asctime)s - %(name)s - %(levelname)s - %(message)s', level=logging.INFO)
+    logger = logging.getLogger(f'dicom-router')
+
     ingestion_loop()