{ "cells": [ { "cell_type": "code", "execution_count": 7, "id": "56a291b4-cb7d-4524-93a4-ef6158d7e634", "metadata": {}, "outputs": [], "source": [ "import os\n", "import sys\n", "import importlib\n", "\n", "def connect(setup):\n", " nixSuite=os.path.join(os.path.expanduser('~'),'software','src','nixSuite')\n", " sys.path.append(os.path.join(nixSuite,'wrapper'))\n", " import nixWrapper\n", " nixWrapper.loadLibrary('labkeyInterface')\n", " import labkeyInterface\n", " import labkeyDatabaseBrowser\n", " import labkeyFileBrowser\n", " \n", " nixWrapper.loadLibrary('orthancInterface')\n", " import orthancInterface\n", " import orthancDatabaseBrowser\n", " import orthancFileBrowser\n", " importlib.reload(orthancFileBrowser)\n", " \n", " net=labkeyInterface.labkeyInterface()\n", " qfile='{}.json'.format(setup['server'])\n", " fconfig=os.path.join(os.path.expanduser('~'),'.labkey',qfile)\n", " net.init(fconfig)\n", " net.getCSRF()\n", " \n", " onet=orthancInterface.orthancInterface()\n", " onet.init(fconfig)\n", " \n", " return {\"db\":labkeyDatabaseBrowser.labkeyDB(net),\n", " \"fb\":labkeyFileBrowser.labkeyFileBrowser(net),\n", " \"odb\":orthancDatabaseBrowser.orthancDB(onet),\n", " \"ofb\":orthancFileBrowser.orthancFileBrowser(onet)}\n", "\n", "def getODBPatientMap(setup):\n", " #get participants from orthanc\n", " odb=setup['odb']\n", " pat=odb.getPatients()\n", " #pat=pat[0:100]\n", " pMap={p:odb.getPatientData(p)['MainDicomTags']['PatientID'] for p in pat}\n", " return {'patientMap':{pMap[p]:p for p in pMap}}\n", "\n", "def getOrthancPatientId(pMap,oid):\n", " try:\n", " return pMap[oid]\n", " except KeyError:\n", " pass\n", " oid=oid.replace('/','p')\n", " try:\n", " return pMap[oid]\n", " except:\n", " pass\n", " return None\n", "\n", "def setPatientOrtancId(setup,dryRun=True):\n", " #get the map (it takes a couple of minutes)\n", " #keep patientMap for reuse\n", " try:\n", " pMap=setup['patientMap']\n", " except KeyError:\n", " setup.update(getODBPatientMap(setup))\n", " pMap=setup['patientMap']\n", " \n", " #get dataset \n", " db=setup['db']\n", " qFilter=setup.get('qFilter',[])\n", " debug=setup.get('debug',False)\n", " ds=db.selectRows(setup['project'],setup['schema'],setup['query'],qFilter)\n", " rows=ds['rows']\n", " if debug:\n", " rows=rows[0:10]\n", " for r in rows:\n", " r['orthancPatientId']=getOrthancPatientId(pMap,r['idOIL'])\n", " print(rows)\n", " n=len(rows)\n", " print(f'Modify {n} rows')\n", " if dryRun:\n", " return\n", " db.modifyRows('update',setup['project'],setup['schema'],setup['query'],rows)\n", "\n", "def setOrthancStudyId(setup,dryRun=True):\n", " #get dataset \n", " db=setup['db']\n", " odb=setup['odb']\n", " qFilter=setup.get('qFilter',[])\n", " debug=setup.get('debug',False)\n", " ds=db.selectRows(setup['project'],setup['schema'],setup['query'],qFilter)\n", " rows=ds['rows']\n", " if debug:\n", " rows=rows[0:10]\n", " for r in rows:\n", " id=r['orthancPatientId']\n", " if not id:\n", " continue\n", " pd=odb.getPatientData(id)\n", " n=len(pd['Studies'])\n", " if n>1:\n", " r['comments']='Multiple studies'\n", " else:\n", " r['orthancStudyId']=pd['Studies'][0]\n", " n=len(rows)\n", " print(f'Modify {n} rows')\n", " if dryRun:\n", " return\n", " db.modifyRows('update',setup['project'],setup['schema'],setup['query'],rows)\n", " \n", "def parseData(setup,updateRow):\n", " #get dataset \n", " db=setup['db']\n", " odb=setup['odb']\n", " ofb=setup['ofb']\n", " baseDir=setup.get('baseDir',os.path.join(os.path.expanduser('~'),'temp'))\n", " \n", " qFilter=setup.get('qFilter',[])\n", " debug=setup.get('debug',False)\n", " ds=db.selectRows(setup['project'],setup['schema'],setup['query'],qFilter)\n", " rows=ds['rows']\n", " if debug:\n", " rows=rows[0:3]\n", " for r in rows:\n", " update=updateRow(setup,r)\n", " if not update:\n", " continue\n", " db.modifyRows('update',setup['project'],setup['schema'],setup['query'],[r])\n", "\n", "def printRow(setup,r):\n", " print(r)\n", " return False\n", " \n", "def getStudyZip(setup,r):\n", " sid=r['orthancStudyId']\n", " if not sid:\n", " return False\n", " fname=f'{sid}.zip'\n", " path=os.path.join(baseDir,fname)\n", " ofb.getZip('studies',sid,path,'archive') \n", " return False\n", "\n", "def getStudyData(setup,r):\n", " odb=setup['odb']\n", " ofb=setup['ofb']\n", " sid=r['orthancStudyId']\n", " if not sid:\n", " return False\n", " sd=odb.getStudyData(sid)\n", " series=sd['Series']\n", " print(series)\n", " return False\n", " \n", "def getStudyInstances(setup,r):\n", " odb=setup['odb']\n", " ofb=setup['ofb']\n", " sid=r['orthancStudyId']\n", " if not sid:\n", " return False\n", " sd=odb.getStudyData(sid)\n", " series=sd['Series']\n", " instances=[]\n", " for s in series:\n", " sed=odb.getSeriesData(s)\n", " print(sed['MainDicomTags']['Modality'])\n", " #instances.extend(sed['Instances'])\n", " print(instances)\n", " return False\n", "\n", "def copyDose(setup,r):\n", " db=setup['db']\n", " debug=setup.get('debug',False)\n", " if debug:\n", " print('copyDose')\n", " var='ParticipantId'\n", " qFilter=[{'variable':var,'value':r[var],'oper':'eq'}]\n", " ds=db.selectRows(setup['project'],setup['imagingSchema'],setup['imagingQuery'],qFilter)\n", " n=len(ds['rows'])\n", " print(f'copyDose: {n}')\n", " if n!=1:\n", " return False\n", " r['doseHeart']=ds['rows'][0]['doseHeart']\n", " if debug:\n", " print(r)\n", " return False\n", " return True\n", " " ] }, { "cell_type": "code", "execution_count": 8, "id": "200fce5d-ed18-434b-9824-a32ea96e83c9", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "loadLibrary\n", "remoteSourcesURL https://git0.fmf.uni-lj.si/studen/nixSuite/raw/master/remoteResources/resources.json\n", "{'labkeyInterface': {'url': 'https://git0.fmf.uni-lj.si/studen/labkeyInterface/archive/master.zip', 'branch': 'master', 'modules': []}, 'irAEMM': {'url': 'https://git0.fmf.uni-lj.si/studen/iraemm/archive/master.zip', 'branch': 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"stpServer={'project':'DCIS/Study','server':'onko-nix'}\n", "stpI={'schema':'study','query':'Imaging1'}\n", "stpRT={'schema':'study','query':'radiotherapy'}\n", "stpRTI={'imagingSchema':'study','imagingQuery':'Imaging1'}\n", "stpDB=connect(stpServer)\n", "stpD={'debug':True}\n", "stpF={'qFilter':[{'variable':'ParticipantId','value':'7','oper':'startswith'}]}\n", "setup=stpServer|stpDB|stpI|stpF\n", "#get the map (it takes a couple of minutes the first time it is run\n", "#setPatientOrthancId(setup,dryRun=False)\n", "#setOrthancStudyId(setup,dryRun=False)\n", "#parseData(setup,getStudyZip)\n", "setup1=stpServer|stpRT|stpRTI|stpDB\n", "parseData(setup1,copyDose)" ] }, { "cell_type": "code", "execution_count": null, "id": "440e864c-4678-4648-a5df-0b0caac98289", "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.0" } }, "nbformat": 4, "nbformat_minor": 5 }