{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "704c900c-9af8-4a68-95e5-10a13a749a22",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "importDicom ver: 1.0.2\n",
      "loadDicom ver: 1.0.0\n",
      "loadPatient.load ver: 1.0.3\n",
      "User: andrej studen CSRF: 014d1d34b354fe0645d621f760feec80\n",
      "\n",
      "Adding series 1 f=http://onko-nix.onko-i.si:8080/labkey/_webdav/Test/Transfer/%40files/dicom/1.2.840.113704.1.1762661776.985.1253733606.8/2.16.840.1.114337.23840299283.22957.20190906170313.0/2.16.840.1.114337.23840299283.22957.20190906170313.0.0\n",
      "...................................................................................................Got 1 series\n",
      "Got 1 series\n",
      "....................................................................................................Added 100 files\n"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\studen\\AppData\\Local\\NA-MIC\\Slicer 4.11.20200930\\lib\\Python\\Lib\\site-packages\\urllib3\\connection.py:395: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
      "  SubjectAltNameWarning,\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "User: andrej studen CSRF: a2559dbbd284436b12f91b98557e3fdf\n",
      "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\studen\\AppData\\Local\\NA-MIC\\Slicer 4.11.20200930\\lib\\Python\\Lib\\site-packages\\urllib3\\connection.py:395: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
      "  SubjectAltNameWarning,\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx"
     ]
    },
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "C:\\Users\\studen\\AppData\\Local\\NA-MIC\\Slicer 4.11.20200930\\lib\\Python\\Lib\\site-packages\\urllib3\\connection.py:395: SubjectAltNameWarning: Certificate for merlin.fmf.uni-lj.si has no `subjectAltName`, falling back to check for a `commonName` for now. This feature is being removed by major browsers and deprecated by RFC 2818. (See https://github.com/urllib3/urllib3/issues/497 for details.)\n",
      "  SubjectAltNameWarning,\n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "xxxxxxxx"
     ]
    }
   ],
   "source": [
    "import sys\n",
    "import os\n",
    "import json\n",
    "import pydicom\n",
    "import importlib\n",
    "import numpy\n",
    "import Elastix \n",
    "import vtk\n",
    "import DicomRtImportExportPlugin\n",
    "import glob\n",
    "import zipfile\n",
    "\n",
    "#just load nix suite\n",
    "sys.path.append(os.path.join(os.path.expanduser('~'),'software','src','nixSuite','wrapper'))\n",
    "import nixWrapper\n",
    "\n",
    "nixWrapper.loadLibrary('labkeyInterface')\n",
    "import labkeyInterface\n",
    "\n",
    "#DB access at ONKO-NIX\n",
    "net=labkeyInterface.labkeyInterface()\n",
    "fconfig=os.path.join(os.path.expanduser('~'),'.labkey','network.json')\n",
    "net.init(fconfig)\n",
    "\n",
    "#DMR are at merlin\n",
    "netDMR=labkeyInterface.labkeyInterface()\n",
    "fconfigDMR=os.path.join(os.path.expanduser('~'),'.labkey','merlin.json')\n",
    "netDMR.init(fconfigDMR)\n",
    "\n",
    "import labkeyDatabaseBrowser\n",
    "db=labkeyDatabaseBrowser.labkeyDB(net)\n",
    "\n",
    "import labkeyFileBrowser\n",
    "fb=labkeyFileBrowser.labkeyFileBrowser(net)\n",
    "fbDMR=labkeyFileBrowser.labkeyFileBrowser(netDMR)\n",
    "\n",
    "#dicom tools\n",
    "nixWrapper.loadLibrary('DICOMtools')\n",
    "try:\n",
    "    importlib.reload(importDicom)\n",
    "except NameError:\n",
    "    import importDicom\n",
    "    \n",
    "try:\n",
    "    importlib.reload(loadDicom)\n",
    "except NameError:\n",
    "    import loadDicom\n",
    "\n",
    "    \n",
    "nixWrapper.loadLibrary('EMBRACE')\n",
    "try:\n",
    "    importlib.reload(loadPatient)\n",
    "except NameError:\n",
    "    import loadPatient\n",
    "\n",
    "project='EMBRACE/studija'\n",
    "iDicom=importDicom.importDicom()\n",
    "lDicom=loadDicom.loadDicom()\n",
    "\n",
    "try:\n",
    "    del elastix\n",
    "except NameError:\n",
    "    pass\n",
    "\n",
    "elastix = Elastix.ElastixLogic()\n",
    "\n",
    "registrationIndex = 29 #targeted EMBRACE\n",
    "registrationIndex = 30 #rigid EMBRACE\n",
    "RegistrationPresets_ParameterFilenames = 5\n",
    "parameterFilenames = elastix.getRegistrationPresets()[registrationIndex]\\\n",
    "    [RegistrationPresets_ParameterFilenames]\n",
    "\n",
    "ids=range(1,87)\n",
    "ids=range(6,7)\n",
    "\n",
    "shn = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)\n",
    "baseDir=os.path.join('z:\\\\','EMBRACE')\n",
    "if not os.path.isdir(baseDir):\n",
    "    os.makedirs(baseDir)\n",
    "\n",
    "transformLogic = slicer.vtkSlicerTransformLogic()\n",
    "\n",
    "exporter = DicomRtImportExportPlugin.DicomRtImportExportPluginClass()\n",
    "\n",
    "for id in ids:\n",
    "\n",
    "    label = 'LJU'+'{:03d}'.format(id)\n",
    "    loadDicom.clearNodes()\n",
    "    \n",
    "    nodes=loadPatient.load(db,fb,fbDMR,iDicom,lDicom,project,label)\n",
    "    print('Segmentations: {}'.format(len(slicer.util.getNodesByClass(\"vtkMRMLSegmentationNode\"))))\n",
    "    \n",
    "    #debug \n",
    "    #seg=nodes['CTRS'].GetSegmentation()\n",
    "    #n=seg.GetNumberOfSegments()\n",
    "    #for i in numpy.arange(n):\n",
    "    #    sId=seg.GetNthSegmentID(int(i))\n",
    "    #    print(sId)\n",
    "    #continue\n",
    "\n",
    "    try:\n",
    "        fixedVolumeNode = nodes['DMR']\n",
    "        movingVolumeNode = nodes['CT']\n",
    "    except KeyError:\n",
    "        continue\n",
    "\n",
    "    transformNodeName = label+'_T2_DF'\n",
    "    #\n",
    "    transformNode=slicer.vtkMRMLGridTransformNode()\n",
    "    transformNode.SetName(transformNodeName)\n",
    "    slicer.mrmlScene.AddNode(transformNode)\n",
    "    \n",
    "    elastix.registerVolumes(fixedVolumeNode, movingVolumeNode, \\\n",
    "                            parameterFilenames = parameterFilenames, outputVolumeNode = None, \n",
    "                            outputTransformNode = transformNode, \\\n",
    "                            fixedVolumeMaskNode = None, movingVolumeMaskNode = None, \n",
    "                            forceDisplacementFieldOutputTransform = True)\n",
    "\n",
    "    \n",
    "    #dataManager.export(network, 'EMBRACE/Studija', patientID)\n",
    "    #create output dicom with MRI and migrated CTRS\n",
    "    oDir=os.path.join(baseDir,label)\n",
    "    if not os.path.isdir(oDir):\n",
    "        os.makedirs(oDir)\n",
    "    #transformNode=slicer.util.loadTransform(os.path.join(oDir,'Transform_R.h5'))\n",
    "    \n",
    "        \n",
    "    #remove all prior dicom files\n",
    "    dcmList=glob.glob(os.path.join(oDir,'*.dcm'))\n",
    "    for f in dcmList:\n",
    "        os.remove(f)\n",
    "    \n",
    "    for mode in ['CT','DMR']:\n",
    "        slicer.util.saveNode(nodes[mode],os.path.join(oDir,label+'_'+mode+'.nrrd'))\n",
    "    slicer.util.saveNode(transformNode,os.path.join(oDir,label+'_DF.nrrd'))\n",
    "    seg=nodes['CTRS'].GetSegmentation()\n",
    "    n=seg.GetNumberOfSegments()\n",
    "    \n",
    "    nodes['CTRS'].SetAndObserveTransformNodeID(transformNode.GetID())\n",
    "    \n",
    "    #transformLogic.hardenTransform(nodes['CTRS'])\n",
    "    for i in numpy.arange(n):\n",
    "        sId=seg.GetNthSegmentID(int(i))\n",
    "        print(sId)\n",
    "        seg.GetSegment(sId)\n",
    "        fname=os.path.join(oDir,label+'_{}.nrrd'.format(sId))\n",
    "        labelmapVolumeNode = slicer.mrmlScene.AddNewNodeByClass('vtkMRMLLabelMapVolumeNode')\n",
    "        \n",
    "        idArray = vtk.vtkStringArray()\n",
    "        idArray.InsertNextValue(sId)\n",
    "        slicer.vtkSlicerSegmentationsModuleLogic.ExportSegmentsToLabelmapNode(\n",
    "                  nodes['CTRS'], idArray, labelmapVolumeNode, nodes['DMR'])\n",
    "        slicer.util.saveNode(labelmapVolumeNode, fname)\n",
    "    \n",
    "    exportables=[]\n",
    "    for mode in ['CTRS','DMR']:\n",
    "        itemId=shn.GetItemByDataNode(nodes[mode])\n",
    "        exportables.extend(exporter.examineForExport(itemId))\n",
    "                                           \n",
    "    for exp in exportables:\n",
    "        exp.directory=oDir\n",
    "        exp.setTag('PatientID',label)\n",
    "        exp.setTag('PatientName',label)\n",
    "        exp.setTag('StudyDescription','contoursAligned')\n",
    "        exp.setTag('PatientID',label)\n",
    "        if exp.tag('Modality')=='CT':\n",
    "            exp.setTag('Modality','MR')\n",
    "            exp.setTag('ScanningSequence',nodes['metadataDMR']['scanningSequence'])\n",
    "            exp.setTag('SequenceVariant',nodes['metadataDMR']['sequenceVariant'])\n",
    "            \n",
    "    \n",
    "    exporter.export(exportables)\n",
    "   "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "id": "f2399104-5f88-4151-80fa-59ab4446a69e",
   "metadata": {},
   "outputs": [],
   "source": [
    "ids=range(3,5)\n",
    "for id in ids:\n",
    "    label = 'LJU'+'{:03d}'.format(id)\n",
    "    oDir=os.path.join(baseDir,label)\n",
    "    dcmList=glob.glob(os.path.join(oDir,'*.dcm'))\n",
    "    ozip=os.path.join(baseDir,label+'.zip')\n",
    "    with zipfile.ZipFile(ozip, 'w') as zf:\n",
    "        for f in dcmList:\n",
    "            zf.write(f)\n",
    "\n",
    "    rDir=fb.buildPathURL(project,[label])\n",
    "    rZip='{}/{}.zip'.format(rDir,label)\n",
    "    fb.writeFileToFile(ozip,rZip)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "3943dc9d-3070-4cdb-90e8-c79e2100745b",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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