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 "cells": [
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   "execution_count": 2,
   "id": "4783a1dd-e2b3-461c-8e61-5e6a36e41a7a",
   "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': 'master', 'modules': ['iraemmBrowser']}, 'SlicerLabkeyExtension': {'url': 'https://git0.fmf.uni-lj.si/studen/SlicerLabkeyExtension/archive/SlicerExtensionIndex.zip', 'branch': 'SlicerExtensionIndex', 'modules': ['labkeyBrowser']}, 'limfomiPET': {'url': 'https://git0.fmf.uni-lj.si/studen/limfomiPET/archive/master.zip', 'branch': 'master', 'modules': ['imageBrowser', 'segmentationBrowser']}, 'parseConfig': {'url': 'https://git0.fmf.uni-lj.si/studen/parseConfig/archive/master.zip', 'branch': 'master', 'modules': []}, 'orthancInterface': {'url': 'https://git0.fmf.uni-lj.si/studen/orthancInterface/archive/master.zip', 'branch': 'master', 'modules': []}, 'dynamicSPECT': {'url': 'https://git0.fmf.uni-lj.si/studen/dynamicSPECT/archive/master.zip', 'branch': 'master', 'modules': ['imageBrowser']}}\n",
      "{'url': 'https://git0.fmf.uni-lj.si/studen/labkeyInterface/archive/master.zip', 'branch': 'master', 'modules': []}\n",
      "File  C:\\Users\\studen\\temp\\labkeyInterface.zip: True\n",
      "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': 'master', 'modules': ['iraemmBrowser']}, 'SlicerLabkeyExtension': {'url': 'https://git0.fmf.uni-lj.si/studen/SlicerLabkeyExtension/archive/SlicerExtensionIndex.zip', 'branch': 'SlicerExtensionIndex', 'modules': ['labkeyBrowser']}, 'limfomiPET': {'url': 'https://git0.fmf.uni-lj.si/studen/limfomiPET/archive/master.zip', 'branch': 'master', 'modules': ['imageBrowser', 'segmentationBrowser']}, 'parseConfig': {'url': 'https://git0.fmf.uni-lj.si/studen/parseConfig/archive/master.zip', 'branch': 'master', 'modules': []}, 'orthancInterface': {'url': 'https://git0.fmf.uni-lj.si/studen/orthancInterface/archive/master.zip', 'branch': 'master', 'modules': []}, 'dynamicSPECT': {'url': 'https://git0.fmf.uni-lj.si/studen/dynamicSPECT/archive/master.zip', 'branch': 'master', 'modules': ['imageBrowser']}}\n",
      "{'url': 'https://git0.fmf.uni-lj.si/studen/orthancInterface/archive/master.zip', 'branch': 'master', 'modules': []}\n",
      "File  C:\\Users\\studen\\temp\\orthancInterface.zip: True\n"
     ]
    }
   ],
   "source": [
    "#load required libraries\n",
    "import sys\n",
    "import os\n",
    "import chardet\n",
    "import json\n",
    "import re\n",
    "import datetime\n",
    "\n",
    "#you should get nixSuite via git clone https://git0.fmf.uni-lj.si/studen/nixSuite.git\n",
    "#if you don't put it to $HOME/software/src/, you should update the path\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",
    "nixWrapper.loadLibrary('orthancInterface')\n",
    "import orthancInterface\n",
    "import orthancDatabaseBrowser\n",
    "\n",
    "def connectDB(server):\n",
    "    #check connectivity. This checks the configuration in $HOME/.labkey/network.json, \n",
    "    #where paths to certificates are stored\n",
    "    net=labkeyInterface.labkeyInterface()\n",
    "    fconfig=os.path.join(os.path.expanduser('~'),'.labkey','{}.json'.format(server))\n",
    "    net.init(fconfig)\n",
    "    #this reports the certificate used\n",
    "    try:\n",
    "        print('Using: {}'.format(net.connectionConfig['SSL']['user']))\n",
    "    except KeyError:\n",
    "        pass\n",
    "    #This gets a deafult CSRF code; It should report user name plus a long string of random hex numbers\n",
    "    net.getCSRF()\n",
    "    db=labkeyDatabaseBrowser.labkeyDB(net)\n",
    "    fb=labkeyFileBrowser.labkeyFileBrowser(net)\n",
    "    return db,fb\n",
    "\n",
    "def modifyRowsWithCheck(db,project,schema,query,entry,testFields):\n",
    "    mode='insert'\n",
    "    filters=[{'variable':x,'value':'{}'.format(entry[x]),'oper':'eq'} for x in testFields]\n",
    "    ds=db.selectRows(project,schema,query,filters)\n",
    "    finalEntry={}\n",
    "    if len(ds['rows'])==1:\n",
    "        finalEntry=ds['rows'][0]\n",
    "        mode='update'\n",
    "    for q in entry:\n",
    "        finalEntry[q]=entry[q];\n",
    "    print(db.modifyRows(mode,project,schema,query,[finalEntry]))\n",
    "\n",
    "def connectOrthanc(server):\n",
    "    net=orthancInterface.orthancInterface()\n",
    "    fconfig=os.path.join(os.path.expanduser('~'),'.labkey','{}.json'.format(server))\n",
    "    net.init(fconfig)\n",
    "    db=orthancDatabaseBrowser.orthancDB(net)\n",
    "    return db\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "b2682976-a44b-450d-88c2-ad69a3fde570",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "User: andrej studen CSRF: ea2151487c571c34c2860833e3685f60\n",
      "8294/16: 2017-07-07\n"
     ]
    }
   ],
   "source": [
    "setup={}\n",
    "setup['server']='onko-nix'\n",
    "setup['project']='limfomiPET/Study2023'\n",
    "setup['query']='missingTransfers'\n",
    "#setup['view']='Missing visit 1'\n",
    "setup['view']='Missing pre-treatment'\n",
    "\n",
    "def listOrthanc(setup):\n",
    "    db,fb=connectDB(setup['server'])\n",
    "    ds=db.selectRows(setup['project'],'study',setup['query'],[],setup['view'])\n",
    "    rows=ds['rows']\n",
    "    for r in rows:\n",
    "        imgs={}\n",
    "        idFilter={'variable':'PatientId','value':r['ParticipantId'],'oper':'eq'}\n",
    "        ds=db.selectRows('Orthanc/Database','study','Imaging',[idFilter])\n",
    "        for x in ds['rows']:\n",
    "            date=datetime.datetime.strptime(x['studyDate'],'%Y/%m/%d %H:%M:%S')\n",
    "            try:\n",
    "                imgs[date].append(x)\n",
    "            except KeyError:\n",
    "                imgs[date]=[x]\n",
    "            #print('{} {}'.format(date.strftime('%Y-%m-%d'),x['seriesDescription']))\n",
    "        #print(r['ParticipantId'])\n",
    "        dates=[d.strftime('%Y-%m-%d') for d in imgs]\n",
    "        print('{}: {}'.format(r['ParticipantId'],','.join(dates)))\n",
    "        \n",
    "            \n",
    "\n",
    "listOrthanc(setup)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "9740dbc3-17c0-4ab9-9680-44961590a0ab",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "User: andrej studen CSRF: 3fd61436be2b1f4f01f9c5be197d96eb\n",
      "Deleting 0 rows\n",
      "User: andrej studen CSRF: 4bb37bc5125387f1a054d520f1a6333e\n",
      "Inserting 1400 rows\n",
      "User: andrej studen CSRF: 9099dbaacb01d92900e4eb39b899a398\n"
     ]
    }
   ],
   "source": [
    "def copyDataset(modify=False):\n",
    "    db,fb=connectDB('onko-nix')\n",
    "    sourceProject='limfomiPET/Study'\n",
    "    sourceQuery='SUVanalysis'\n",
    "    targetProject='limfomiPET/Study'\n",
    "    targetQuery='SUVanalysisBackup'\n",
    "    \n",
    "    #prepare (and clear) target\n",
    "    ds=db.selectRows(targetProject,'study',targetQuery,[])\n",
    "    rows=ds['rows']\n",
    "    print('Deleting {} rows'.format(len(rows)))\n",
    "    if modify:\n",
    "        db.modifyRows('delete',targetProject,'study',targetQuery,rows)\n",
    "        \n",
    "    #copy from source\n",
    "    ds=db.selectRows(sourceProject,'study',sourceQuery,[])\n",
    "    rows=ds['rows']\n",
    "    #insert to target\n",
    "    print('Inserting {} rows'.format(len(rows)))\n",
    "    if modify:\n",
    "        db.modifyRows('insert',targetProject,'study',targetQuery,rows)\n",
    "        \n",
    "copyDataset(True)\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "id": "09d73d56-8d4a-488c-a11f-e8fb7e581ab1",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "User: andrej studen CSRF: 4762143c71425ffc69605ce515e80d93\n",
      "True\n",
      "Segmentation_2763_07-VISIT_1_adoma_220.nrrd 1: 5394\n",
      "Segmentation_2763_07-VISIT_1_adoma_220.nrrd 2: 0\n",
      "Segmentation_2763_07-VISIT_1_adoma_220.nrrd 4: 86125\n"
     ]
    }
   ],
   "source": [
    "import SimpleITK\n",
    "import numpy\n",
    "def getSegmentation():\n",
    "    db,fb=connectDB('onko-nix')\n",
    "    p='1965/16'\n",
    "    p='2763/07'\n",
    "    #p='4464/16'\n",
    "    pcode=p.replace('/','_')\n",
    "    idFilter={'variable':'ParticipantId','value':p,'oper':'eq'}\n",
    "    v='VISIT_1'\n",
    "    visitFilter={'variable':'visitCode','value':v,'oper':'eq'}\n",
    "    user='1037'\n",
    "    userFilter={'variable':'User','value':user,'oper':'eq'}\n",
    "    project='limfomiPET/Study'\n",
    "    ds=db.selectRows(project,'study','Segmentations',[idFilter,visitFilter,userFilter])\n",
    "    for r in ds['rows']:\n",
    "        url=fb.buildPathURL(project,['preprocessedImages',pcode,v,'Segmentations'])\n",
    "        remoteURL='/'.join([url,r['latestFile']])\n",
    "        print(fb.entryExists(remoteURL))\n",
    "        localPath=os.path.join(os.path.expanduser('~'),'Downloads',r['latestFile'])\n",
    "        fb.readFileToFile(remoteURL,localPath)\n",
    "        im=SimpleITK.ReadImage(localPath)\n",
    "        ar=SimpleITK.GetArrayFromImage(im)\n",
    "        for seg in [1,2,4]:\n",
    "            print('{} {}: {}'.format(r['latestFile'],seg,numpy.sum(ar==seg)))\n",
    "        \n",
    "getSegmentation()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "93f25f6e-344c-45ca-9c51-b292856eb5d4",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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