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10 files changed

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‎AHLItoDICOMInterface/AHLIClientFactory.py

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"""
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AHLItoDICOM Module : This class contains the logic to create the AHLI boto3 client.
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SPDX-License-Identifier: Apache-2.0
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"""
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import boto3
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import tempfile
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import logging
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class AHLIClientFactory(object):
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def __init__(self) -> None:
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pass
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def __new__(self , aws_access_key : str = None , aws_secret_key : str = None , aws_accendpoint_url : str = None):
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try:
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session = boto3.Session()
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session._loader.search_paths.extend([tempfile.gettempdir()])
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AHLIclient = boto3.client('medical-imaging', aws_access_key_id = aws_access_key , aws_secret_access_key = aws_secret_key , endpoint_url=aws_accendpoint_url )
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return AHLIclient
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except Exception as AHLIErr:
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logging.error(f"[AHLIClientFactory] - {AHLIErr}")
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return None

‎AHLItoDICOMInterface/AHLIDataDICOMizer.py

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"""
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AHLItoDICOM Module : This class contains the logic to encapsulate the data and the pixels into a DICOM object.
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SPDX-License-Identifier: Apache-2.0
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"""
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from time import sleep
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from multiprocessing import Process , Queue
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import pydicom
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import logging
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from pydicom.sequence import Sequence
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from pydicom import Dataset , DataElement
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from pydicom.dataset import FileDataset, FileMetaDataset
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from pydicom.uid import UID
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import base64
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class AHLIDataDICOMizer():
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ds = Dataset()
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InstanceId = None
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thread_running = True
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AHLI_metadata = None
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process = None
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def __init__(self, InstanceId, AHLI_metadata) -> None:
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self.InstanceId = InstanceId
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self.DICOMizeJobs = Queue()
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self.DICOMizeJobsCompleted = Queue()
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self.AHLI_metadata = AHLI_metadata
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self.process = Process(target = self.ProcessJobs , args=(self.DICOMizeJobs, self.DICOMizeJobsCompleted, ))
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self.process.start()
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def AddDICOMizeJob(self,FetchJob):
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self.DICOMizeJobs.put(FetchJob)
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logging.debug("[AHLIFrameFetcher][AddFetchJob]["+self.InstanceId+"] - Fetch Job added "+str(FetchJob)+".")
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def ProcessJobs(self , DICOMizeJobs , DICOMizeJobsCompleted):
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while(self.thread_running):
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if not DICOMizeJobs.empty():
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self.status="busy"
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try:
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ImageFrame = DICOMizeJobs.get()
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vrlist = []
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file_meta = FileMetaDataset()
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self.ds = FileDataset(None, {}, file_meta=file_meta, preamble=b"\0" * 128)
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self.getDICOMVRs(self.AHLI_metadata["Study"]["Series"][ImageFrame["SeriesUID"]]["Instances"][ImageFrame["SOPInstanceUID"]]["DICOMVRs"] , vrlist)
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PatientLevel = self.AHLI_metadata["Patient"]["DICOM"]
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self.getTags(PatientLevel, self.ds , vrlist)
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StudyLevel = self.AHLI_metadata["Study"]["DICOM"]
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self.getTags(StudyLevel, self.ds , vrlist)
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SeriesLevel=self.AHLI_metadata["Study"]["Series"][ImageFrame["SeriesUID"]]["DICOM"]
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self.getTags(SeriesLevel, self.ds , vrlist)
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InstanceLevel=self.AHLI_metadata["Study"]["Series"][ImageFrame["SeriesUID"]]["Instances"][ImageFrame["SOPInstanceUID"]]["DICOM"]
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self.getTags(InstanceLevel , self.ds , vrlist)
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self.ds.file_meta.TransferSyntaxUID = pydicom.uid.ExplicitVRLittleEndian
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self.ds.is_little_endian = True
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self.ds.is_implicit_VR = False
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file_meta.MediaStorageSOPInstanceUID = UID(ImageFrame["SOPInstanceUID"])
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pixels = ImageFrame["PixelData"]
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if (pixels is not None):
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self.ds.PixelData = pixels.tobytes()
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vrlist.clear()
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DICOMizeJobsCompleted.put(self.ds)
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except Exception as FetchError:
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logging.error(f"[AHLIFrameFetcher][{str(self.InstanceId)}] - {FetchError}")
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else:
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self.status = 'idle'
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sleep(0.05)
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def getFramesDICOMized(self):
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if not self.DICOMizeJobsCompleted.empty():
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obj = self.DICOMizeJobsCompleted.get()
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return obj
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else:
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return None
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def getDataset(self):
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return self.ds
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def getDICOMVRs(self,taglevel, vrlist):
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for theKey in taglevel:
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vrlist.append( [ theKey , taglevel[theKey] ])
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logging.debug(f"[AHLIDataDICOMizer][getDICOMVRs] - List of private tags VRs: {vrlist}\r\n")
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def getTags(self,tagLevel, ds , vrlist):
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for theKey in tagLevel:
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try:
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try:
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tagvr = pydicom.datadict.dictionary_VR(theKey)
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except: #In case the vr is not in the pydicom dictionnary, it might be a private tag , listed in the vrlist
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tagvr = None
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for vr in vrlist:
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if theKey == vr[0]:
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tagvr = vr[1]
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datavalue=tagLevel[theKey]
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#print(f"{theKey} : {datavalue}")
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if(tagvr == 'SQ'):
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logging.debug(f"{theKey} : {tagLevel[theKey]} , {vrlist}")
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seqs = []
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for underSeq in tagLevel[theKey]:
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seqds = Dataset()
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self.getTags(underSeq, seqds, vrlist)
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seqs.append(seqds)
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datavalue = Sequence(seqs)
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continue
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if(tagvr == 'US or SS'):
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datavalue=tagLevel[theKey]
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if (int(datavalue) > 32767):
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tagvr = 'US'
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if( tagvr in [ 'OB' , 'OD' , 'OF', 'OL', 'OW', 'UN' ] ):
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base64_str = tagLevel[theKey]
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base64_bytes = base64_str.encode('utf-8')
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datavalue = base64.decodebytes(base64_bytes)
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if theKey == 'PrivateCreatorID': # Ignore this attribute, otherwise it creates an issue because it doesn't resolve to a DICOM tag
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continue
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data_element = DataElement(theKey , tagvr , datavalue )
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if data_element.tag.group != 2:
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try:
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if (int(data_element.tag.group) % 2) == 0 : # we are skipping all the private tags
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ds.add(data_element)
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except:
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continue
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except Exception as err:
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logging.debug(f"[AHLIDataDICOMizer][getTags] - {err}")
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continue
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def Dispose(self):
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self.thread_running = False
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self.process.terminate()

‎AHLItoDICOMInterface/AHLIFrameFetcher.py

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"""
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AHLItoDICOM Module : This class contains the logic to query the Image pixel raster.
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SPDX-License-Identifier: Apache-2.0
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"""
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from multiprocessing import Process , Queue
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import logging
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from openjpeg import decode
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import io
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from .AHLIClientFactory import *
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class AHLIFrameFetcher:
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status = 'idle'
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FetchJobs = None
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FetchJobsCompleted = None
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FetchJobsInError = None
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InstanceId= None
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client = None
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thread_running = True
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process = None
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aws_access_key = None
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aws_secret_key = None
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AHLI_endpoint = None
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def __init__(self, InstanceId , aws_access_key , aws_secret_key , AHLI_endpoint):
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#mp.set_start_method('spawn')
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self.InstanceId = InstanceId
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self.FetchJobs = Queue()
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self.FetchJobsCompleted = Queue()
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self.FetchJobsInError = Queue()
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self.aws_secret_key = aws_access_key
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self.aws_secret_key = aws_secret_key
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self.AHLI_endpoint = AHLI_endpoint
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self.process = Process(target = self.ProcessJobs , args=(self.FetchJobs,self.FetchJobsCompleted, self.FetchJobsInError , self.aws_access_key , self.aws_secret_key , self.AHLI_endpoint))
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self.process.start()
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def AddFetchJob(self,FetchJob):
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self.FetchJobs.put(FetchJob)
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#print(f"[FrameFetcher][{self.InstanceId}] Job entry added")
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#print(FetchJob)
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logging.debug("[AHLIFrameFetcher][AddFetchJob]["+self.InstanceId+"] - Fetch Job added "+str(FetchJob)+".")
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def ProcessJobs(self,FetchJobs : Queue, FetchJobsCompleted : Queue , FetchJobsInError : Queue , aws_access_key : str = None , aws_secret_key : str = None , AHLI_endpoint : str = None):
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self.client = AHLIClientFactory( aws_access_key= aws_access_key , aws_secret_key=aws_secret_key , aws_accendpoint_url=AHLI_endpoint )
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while(self.thread_running):
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if not FetchJobs.empty():
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try:
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entry = FetchJobs.get(block=False)
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entry["PixelData"] = self.curieGetFramePixels(entry["datastoreId"], entry["studyId"], entry["frameId"])
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FetchJobsCompleted.put(entry)
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except:
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FetchJobsInError.put(entry)
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def getFramesFetched(self):
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if not self.FetchJobsCompleted.empty() :
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obj = self.FetchJobsCompleted.get(block=False)
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return obj
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else:
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return None
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def curieGetFramePixels(self, datastoreId, studyId, imageFrameId):
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try:
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res = self.client.get_image_frame(
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datastoreId=datastoreId,
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imageSetId=studyId,
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imageFrameId=imageFrameId)
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b = io.BytesIO()
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b.write(res['imageFrameBlob'].read())
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b.seek(0)
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d = decode(b)
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return d
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except:
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logging.info("[AHLIFramefetcher] - Frame could not be decoded.")
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return None
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def Dispose(self):
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self.thread_running = False
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self.process.terminate()

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