{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "1da1e1c8-1f5a-4c9e-aa4a-1baaa8c71df1",
   "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": [
    "import sys\n",
    "import os\n",
    "import importlib\n",
    "import numpy\n",
    "import random\n",
    "\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",
    "\n",
    "nixWrapper.loadLibrary('orthancInterface')\n",
    "import orthancInterface\n",
    "import orthancDatabaseBrowser\n",
    "import orthancFileBrowser"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "40fce609-1142-4746-a912-70481ff809be",
   "metadata": {},
   "outputs": [],
   "source": [
    "def initDB(site,returnFB=False):\n",
    "    net=labkeyInterface.labkeyInterface()\n",
    "    fconfig=os.path.join(os.path.expanduser('~'),'.labkey','{}.json'.format(site))\n",
    "    net.init(fconfig)\n",
    "    net.getCSRF()\n",
    "    if not returnFB:\n",
    "        return labkeyDatabaseBrowser.labkeyDB(net)\n",
    "    return labkeyDatabaseBrowser.labkeyDB(net),labkeyFileBrowser.labkeyFileBrowser(net)\n",
    "\n",
    "def initOrthanc(site,returnFB=False):\n",
    "    net=orthancInterface.orthancInterface()\n",
    "    fconfig=os.path.join(os.path.expanduser('~'),'.labkey','{}.json'.format(site))\n",
    "    net.init(fconfig)\n",
    "    if not returnFB:\n",
    "        return orthancDatabaseBrowser.orthancDB(net)\n",
    "    return orthancDatabaseBrowser.orthancDB(net),orthancFileBrowser.orthancFileBrowser(net)\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "id": "e7386af6-7b00-4607-a05e-5581db804869",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "User: andrej studen CSRF: 9b381ce234d4a838c53c6f93dab2f5a7\n"
     ]
    }
   ],
   "source": [
    "db,fb=initDB('onko-nix',returnFB=True)\n",
    "odb,ofb=initOrthanc('onko-nix',returnFB=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 69,
   "id": "5910e7dd-de77-4260-a23a-78e2a6baabb4",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "[-592.9801940917969, -867.9606628417969, -2823.0]\n",
      "[-1644.0222664799999, -2395.3331437499996, -4710.0]\n"
     ]
    }
   ],
   "source": [
    "def parsePos(x):\n",
    "    return [float(y) for y in x.split('\\\\')]\n",
    "\n",
    "def parseOrientation(x):\n",
    "    z=[float(y) for y in x.split('\\\\')]\n",
    "    O=[z[0:3],z[3:6]]\n",
    "    O.append(list(numpy.cross(numpy.array(O[0]),numpy.array(O[1]))))\n",
    "    return O\n",
    "\n",
    "def getGeometry(code,odb,seriesId):\n",
    "    #imagepositionpatient 0020-0032\n",
    "    #imageorientationpatient 0020-0037\n",
    "    #pixelSpacing 0028-0030\n",
    "    #instance number 0020-0013\n",
    "    #sliceThickness 0018-0050\n",
    "    \n",
    "    sd=odb.getData('series',seriesId)\n",
    "    firstId=sd['Instances'][0] \n",
    "    \n",
    "    #check to see if orientation changes (it doesn't)\n",
    "    #ior=[odb.getDicomField(y,'0020-0037') for y in sd[x]['Instances']] \n",
    "    #same=all(y==ior[0] for y in ior)\n",
    "    #print(same)\n",
    "    \n",
    "    #check to see if pixel spacing changes (it doesn't)\n",
    "    #ips=[odb.getDicomField(y,'0028-0030') for y in sd['Instances']] \n",
    "    #same=all(y==ips[0] for y in ips)\n",
    "    #print(same)\n",
    "    \n",
    "    #check to see if sliceThickness changes (it doesn't)\n",
    "    #ist=[odb.getDicomField(y,'0018-0050') for y in sd['Instances']]\n",
    "    #same=all(y==ist[0] for y in ist)\n",
    "    #print(same)\n",
    "        \n",
    "    ior=parseOrientation(odb.getDicomField(firstId,'0020-0037'))\n",
    "    ips=parsePos(odb.getDicomField(firstId,'0028-0030'))\n",
    "    ist=parsePos(odb.getDicomField(firstId,'0018-0050')) \n",
    "    ips.append(ist[0])\n",
    "        \n",
    "    for y in range(3):\n",
    "        ior[y]=[ips[y]*w for w in ior[y]]\n",
    "    \n",
    "    \n",
    "    ipos=[parsePos(odb.getDicomField(y,'0020-0032')) for y in sd['Instances']] \n",
    "    m=[[numpy.dot(numpy.array(v),numpy.array(x)) for x in ipos] for v in ior]\n",
    "    m=[numpy.min(numpy.array(x)) for x in m]\n",
    "    print(m)    \n",
    "    \n",
    "    return {f'{code}origin':m,f'{code}orientation':ior}\n",
    "    \n",
    "        \n",
    "        \n",
    "def getFile(db,odb):\n",
    "    project='/iPNUMMretro/Study'\n",
    "    schema='study'\n",
    "    query='Imaging1'\n",
    "    coreDir=os.path.join(os.path.expanduser('~'),'temp')\n",
    "    ds=db.selectRows(project,schema,query,[])\n",
    "    rows=ds['rows'][0:1]\n",
    "    imgs={'CT':'CT_orthancId','PET':'PETWB_orthancId'}\n",
    "    for r in rows:\n",
    "        code=r['pseudoCode']\n",
    "        doUpdate=False\n",
    "        if not code:\n",
    "            code='{:16x}'.format(random.randrange(16**16))\n",
    "            r['pseudoCode']=code\n",
    "            doUpdate=True\n",
    "            \n",
    "        fname=os.path.join(coreDir,f'{code}.npz')\n",
    "        arr={}\n",
    "        arr.update({x:numpy.load(odb.getNumpy('series',r[imgs[x]])) for x in imgs})\n",
    "        igeo={x:getGeometry(x,odb,r[imgs[x]]) for x in imgs}\n",
    "        _={arr.update(igeo[x]) for x in igeo}\n",
    "        #print(arr)\n",
    "        \n",
    "        \n",
    "        numpy.savez_compressed(fname,**arr)\n",
    "        if doUpdate:\n",
    "            db.modifyRows('update',project,schema,query,[r])\n",
    "        \n",
    "getFile(db,odb)\n",
    "    "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "05cb025f-1c44-4ddf-b859-8b8e9d2584a6",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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