Vis_VTK_STL_RT_structure.ipynb

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    "############################################################################\n",
    "#\n",
    "#  Program: Visualisation de structures VTK, STL ou RT Structure\n",
    "#\n",
    "#  Copyright (c) 2016 Jonathan Tranel - IDN-RJ\n",
    "#  All rights reserved.\n",
    "#     This software is distributed WITHOUT ANY WARRANTY; without even\n",
    "#     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR\n",
    "#     PURPOSE.  \n",
    "#\n",
    "############################################################################\n",
    "\n",
    "import sys\n",
    "import gdcm\n",
    "import dicom\n",
    "import os\n",
    "import vtkgdcm\n",
    "import numpy\n",
    "import vtk\n",
    "import itk\n",
    "sys.path.append('/usr/lib/python27/dist-packages/')\n",
    "import vtkDICOMPython\n",
    "\n",
    "from vtk.util.misc import vtkGetDataRoot\n",
    "\n",
    "#Chemin des DICOM images\n",
    "PathDicom=\"/home/jonathan/Bureau/DICOM/UH/\"\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
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   "outputs": [],
   "source": [
    "###########################################\n",
    "#Chapitre 1: Statistiques des DICOM images#\n",
    "###########################################\n",
    "\n",
    "# Lire les DICOM images      NB: par défaut, critère du image number\n",
    "reader = vtk.vtkDICOMImageReader()\n",
    "reader.SetDirectoryName(PathDicom)\n",
    "reader.Update()\n",
    "\n",
    "# Load dimensions using `GetDataExtent`\n",
    "ConstPixelDims = reader.GetOutput().GetDimensions()\n",
    "\n",
    "# Load spacing values\n",
    "ConstPixelSpacing = reader.GetPixelSpacing()\n",
    "\n",
    "print (\"Dimensions [Nb de pixels en x, en y, nombre de coupes]: \"+str(ConstPixelDims))\n",
    "\n",
    "from vtk.util import numpy_support\n",
    "# Get the 'vtkImageData' object from the reader\n",
    "imageData = reader.GetOutput()\n",
    "# Get the 'vtkPointData' object from the 'vtkImageData' object\n",
    "pointData = imageData.GetPointData()\n",
    "# Ensure that only one array exists within the 'vtkPointData' object\n",
    "assert (pointData.GetNumberOfArrays()==1)\n",
    "# Get the `vtkArray` (or whatever derived type) which is needed for the `numpy_support.vtk_to_numpy` function\n",
    "arrayData = pointData.GetArray(0)\n",
    "\n",
    "# Convert the `vtkArray` to a NumPy array\n",
    "GrosseMatrice = numpy_support.vtk_to_numpy(arrayData)\n",
    "# Reshape the NumPy array to 3D using 'ConstPixelDims' as a 'shape'\n",
    "GrosseMatrice = GrosseMatrice.reshape(ConstPixelDims, order='F')\n",
    "\n",
    "#Inversion   NB: critère de la position z\n",
    "GrosseMatrice2=GrosseMatrice[:,:,::-1]\n",
    "\n",
    "print (\"Dimensions de GrosseMatrice [Nb de pixels en x, en y, nombre de coupes]: \"+str(GrosseMatrice.shape))\n",
    "#print(\"Valeur du voxel max pour le fichier \"+str(lstFilesDCM[0])+\": \")\n",
    "\n",
    "print (\"UH maximal detecte: \"+str(GrosseMatrice2[:,:,1].max()))\n",
    "print (\"UH minimal detecte: \"+str(GrosseMatrice2[:,:,1].min()))\n"
   ]
  },
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   "cell_type": "code",
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    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Structure n°0: Brainstem \n",
      "Structure n°1: Cerebrum\n",
      "Structure n°2: Chiasm\n",
      "Structure n°3: Eye, Left \n",
      "Structure n°4: Eye, Right\n",
      "Structure n°5: Lens, Left\n",
      "Structure n°6: Lens, Right \n",
      "Structure n°7: MetFrontG \n",
      "Structure n°8: MetOccD1\n",
      "Structure n°9: MetOccD2\n",
      "Structure n°10: Optic Nerve, Left \n",
      "Structure n°11: Optic Nerve, Right\n",
      "Structure n°12: Optic Tract, Left \n",
      "Structure n°13: Optic Tract, Right\n"
     ]
    }
   ],
   "source": [
    "#####################################################################\n",
    "#Chapitre 2-1: Importer les RTStruc et DICOM Images et les visualiser#\n",
    "#####################################################################\n",
    "\n",
    "#Mettre ici le chemin du fichier RT Structure\n",
    "CheminRTStructure=\"/home/jonathan/Bureau/DICOM/RTStruc/RTST0173.dcm\"\n",
    "\n",
    "#Lister toutes les structures du RTStructure\n",
    "RTStruc=vtkgdcm.vtkGDCMPolyDataReader()\n",
    "RTStruc.SetFileName(CheminRTStructure)\n",
    "RTStruc.Update()\n",
    "Nb=RTStruc.GetRTStructSetProperties().GetNumberOfStructureSetROIs()\n",
    "\n",
    "for i in range (0,Nb):\n",
    "    print(\"Structure n°\"+str(i)+\": \"+RTStruc.GetRTStructSetProperties().GetStructureSetROIName(i))\n",
    "\n",
    "    \n",
    "#Mettre ici les RTStruc désirés (après lecture de la liste ci-dessous):\n",
    "\n",
    "n=8\n",
    "o=4"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {
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   "source": [
    "######################################################################\n",
    "#Chapitre 2-2: Importer les RTStruc et DICOM Images et les visualiser#\n",
    "######################################################################\n",
    "\n",
    "#Example stéréo Rangueil\n",
    "\n",
    "# Lire les DICOM images  NB: par défaut, critère du image number\n",
    "\n",
    "directory = vtkDICOMPython.vtkDICOMDirectory()\n",
    "directory.SetDirectoryName(PathDicom)\n",
    "directory.Update()\n",
    "\n",
    "readerImg = vtkDICOMPython.vtkDICOMReader()\n",
    "readerImg.SetFileNames(directory.GetFileNamesForSeries(0))\n",
    "readerImg.Update()\n",
    "\n",
    "dim = readerImg.GetOutput().GetDimensions()\n",
    "\n",
    "#Actor 1: DICOM images par Marching cubes\n",
    "#Fabrication de la surface 3D du DICOM images\n",
    "ImgMC = vtk.vtkMarchingCubes()\n",
    "ImgMC.SetInputConnection(readerImg.GetOutputPort())\n",
    "ImgMC.GenerateValues(1,1500,6000)\n",
    "ImgMC.Update()\n",
    "\n",
    "#Remplacer les polyDataNormals d'entrées avec les PolyData transformées\n",
    "NormalsMC=vtk.vtkPolyDataNormals()\n",
    "NormalsMC.SetInputConnection(ImgMC.GetOutputPort())\n",
    "#Normals.SetFeatureAngle(60)\n",
    "NormalsMC.Update()\n",
    "\n",
    "stripperMC=vtk.vtkStripper()\n",
    "stripperMC.SetInputConnection(NormalsMC.GetOutputPort())\n",
    "stripperMC.Update()\n",
    "\n",
    "\n",
    "mapperMC = vtk.vtkPolyDataMapper()\n",
    "mapperMC.SetInputConnection(stripperMC.GetOutputPort())\n",
    "mapperMC.ScalarVisibilityOff()\n",
    "actorMC = vtk.vtkActor()\n",
    "actorMC.SetMapper(mapperMC)\n",
    "actorMC.GetProperty().SetColor(0.7,1,0.5)\n",
    "\n",
    "#Actor 2: RT Structures\n",
    "# Lire la structure RT\n",
    "#n=6 #Numero du RT Structure\n",
    "RTStruc=vtkgdcm.vtkGDCMPolyDataReader()\n",
    "RTStruc.SetFileName(CheminRTStructure)\n",
    "RTStruc.Update()\n",
    "\n",
    "#Utiliser la matrice des DICOM images pour les lier avec les vtk\n",
    "Transf=vtk.vtkTransform()\n",
    "Transf.SetMatrix(readerImg.GetPatientMatrix())\n",
    "Transf.Inverse()\n",
    "Transf.Update()\n",
    "\n",
    "TransfFiltreN=vtk.vtkTransformPolyDataFilter()\n",
    "TransfFiltreN.SetInputConnection(RTStruc.GetOutputPort(n))\n",
    "TransfFiltreN.SetTransform(Transf)\n",
    "TransfFiltreN.Update()\n",
    "\n",
    "TransfFiltreO=vtk.vtkTransformPolyDataFilter()\n",
    "TransfFiltreO.SetInputConnection(RTStruc.GetOutputPort(o))\n",
    "TransfFiltreO.SetTransform(Transf)\n",
    "TransfFiltreO.Update()\n",
    "\n",
    "\n",
    "#Structure n\n",
    "mapperRTStrucN = vtk.vtkPolyDataMapper()\n",
    "mapperRTStrucN.SetInputConnection(TransfFiltreN.GetOutputPort())\n",
    "#Structure o\n",
    "mapperRTStrucO = vtk.vtkPolyDataMapper()\n",
    "mapperRTStrucO.SetInputConnection(TransfFiltreO.GetOutputPort())\n",
    "\n",
    "actorN = vtk.vtkActor()\n",
    "actorN.SetMapper(mapperRTStrucN)\n",
    "actorO = vtk.vtkActor()\n",
    "actorO.SetMapper(mapperRTStrucO)\n",
    "\n",
    "\n",
    "#Actor 3: DICOM images par coupes\n",
    "# Lire les DICOM images par coupes\n",
    "\n",
    "actorImg1 = vtk.vtkImageActor()#Afficher la 1ère coupe au choix\n",
    "actorImg1.SetInputData(readerImg.GetOutput())\n",
    "actorImg2 = vtk.vtkImageActor()#Afficher la 2ème coupe au choix\n",
    "actorImg2.SetInputData(readerImg.GetOutput())\n",
    "actorImg3 = vtk.vtkImageActor()#Afficher la 3ème coupe au choix\n",
    "actorImg3.SetInputData(readerImg.GetOutput())\n",
    "\n",
    "mapperImg1 = vtk.vtkImageSliceMapper().SafeDownCast(actorImg1.GetMapper())\n",
    "mapperImg2 = vtk.vtkImageSliceMapper().SafeDownCast(actorImg2.GetMapper())\n",
    "mapperImg3 = vtk.vtkImageSliceMapper().SafeDownCast(actorImg3.GetMapper())\n",
    "#mapperImg.SetSliceNumber(dim[2]/2)\n",
    "actorImg1.GetMapper()\n",
    "actorImg2.GetMapper()\n",
    "actorImg3.GetMapper()\n",
    "\n",
    "\n",
    "mapperImg1.SetSliceNumber(0)\n",
    "mapperImg2.SetSliceNumber(30)\n",
    "mapperImg3.SetSliceNumber(dim[2])\n",
    "\n",
    "# Create a rendering window and renderer\n",
    "ren = vtk.vtkRenderer()\n",
    "renWin = vtk.vtkRenderWindow()\n",
    "renWin.AddRenderer(ren)\n",
    "renWin.SetSize(1024, 1024)\n",
    "\n",
    "# Create a renderwindowinteractor\n",
    "iren = vtk.vtkRenderWindowInteractor()\n",
    "iren.SetRenderWindow(renWin)\n",
    "\n",
    "# Ajouter actor dans le renderer\n",
    "\n",
    "#Les images DICOM par coupes\n",
    "ren.AddActor(actorImg1)\n",
    "ren.AddActor(actorImg2)\n",
    "ren.AddActor(actorImg3)\n",
    "#Les images DICOM Marching cubes\n",
    "#ren.AddActor(actorMC)\n",
    "#Les structures\n",
    "ren.AddActor(actorN)\n",
    "ren.AddActor(actorO)\n",
    "\n",
    "\n",
    "#ren.GetActiveCamera().Zoom(1.5)\n",
    "\n",
    "# Enable user interface interactor\n",
    "iren.Initialize()\n",
    "renWin.Render()\n",
    "iren.Start()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {
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   "outputs": [],
   "source": [
    "######################################################################\n",
    "#Chapitre 3: Importer les VTK et DICOM Images et les visualiser#\n",
    "######################################################################\n",
    "\n",
    "\n",
    "#Example Cochon TheraneaM\n",
    "\n",
    "# Lire les DICOM images (version VTK)      NB: par défaut, critère du image number\n",
    "\n",
    "PathDicom2=\"/home/jonathan/Bureau/DICOMcochon/UH\"\n",
    "\n",
    "directory = vtkDICOMPython.vtkDICOMDirectory()\n",
    "directory.SetDirectoryName(PathDicom2)\n",
    "directory.Update()\n",
    "\n",
    "readerImg = vtkDICOMPython.vtkDICOMReader()\n",
    "readerImg.SetFileNames(directory.GetFileNamesForSeries(0))\n",
    "readerImg.Update()\n",
    "\n",
    "ImgMC = vtk.vtkMarchingCubes()\n",
    "ImgMC.SetInputConnection(readerImg.GetOutputPort())\n",
    "ImgMC.GenerateValues(1,150,300)\n",
    "ImgMC.Update()\n",
    "\n",
    "dim = readerImg.GetOutput().GetDimensions()\n",
    "\n",
    "#Remplacer les polyDataNormals d'entrées avec les PolyData transformées\n",
    "NormalsMC=vtk.vtkPolyDataNormals()\n",
    "NormalsMC.SetInputConnection(ImgMC.GetOutputPort())\n",
    "#Normals.SetFeatureAngle(60)\n",
    "NormalsMC.Update()\n",
    "\n",
    "stripperMC=vtk.vtkStripper()\n",
    "stripperMC.SetInputConnection(NormalsMC.GetOutputPort())\n",
    "stripperMC.Update()\n",
    "\n",
    "mapperMC = vtk.vtkPolyDataMapper()\n",
    "mapperMC.SetInputConnection(stripperMC.GetOutputPort())\n",
    "mapperMC.ScalarVisibilityOff()\n",
    "\n",
    "actorMC = vtk.vtkActor()\n",
    "actorMC.SetMapper(mapperMC)\n",
    "actorMC.GetProperty().SetColor(1,1,0.5)\n",
    "\n",
    "\n",
    "##########################################\n",
    "\n",
    "# Lire les structures VTK\n",
    "\n",
    "#1: Os\n",
    "filenameOs=\"/home/jonathan/Bureau/DICOMcochon/vtk/Francisco.vtk\"\n",
    "VolumeOs = vtk.vtkPolyDataReader()\n",
    "VolumeOs.SetFileName(filenameOs)\n",
    "VolumeOs.Update()\n",
    "\n",
    "#2: HolmiumG\n",
    "filenameHoG=\"/home/jonathan/Bureau/DICOMcochon/vtk/HolmiumG.vtk\"\n",
    "VolumeHoG = vtk.vtkPolyDataReader()\n",
    "VolumeHoG.SetFileName(filenameHoG)\n",
    "VolumeHoG.Update()\n",
    "\n",
    "#3: HolmiumD\n",
    "filenameHoD=\"/home/jonathan/Bureau/DICOMcochon/vtk/HolmiumD.vtk\"\n",
    "VolumeHoD = vtk.vtkPolyDataReader()\n",
    "VolumeHoD.SetFileName(filenameHoD)\n",
    "VolumeHoD.Update()\n",
    "\n",
    "################################################################\n",
    "#Utiliser la matrice des DICOM images pour les lier avec les vtk\n",
    "\n",
    "#Premièrement !\n",
    "Transf1=vtk.vtkTransform()\n",
    "Transf1.Scale(-1.,-1.,1.)\n",
    "Transf1.Update()\n",
    "\n",
    "TransfFiltreOs=vtk.vtkTransformPolyDataFilter()\n",
    "TransfFiltreOs.SetInputConnection(VolumeOs.GetOutputPort())\n",
    "TransfFiltreOs.SetTransform(Transf1)\n",
    "TransfFiltreOs.Update()\n",
    "TransfFiltreHoG=vtk.vtkTransformPolyDataFilter()\n",
    "TransfFiltreHoG.SetInputConnection(VolumeHoG.GetOutputPort())\n",
    "TransfFiltreHoG.SetTransform(Transf1)\n",
    "TransfFiltreHoG.Update()\n",
    "TransfFiltreHoD=vtk.vtkTransformPolyDataFilter()\n",
    "TransfFiltreHoD.SetInputConnection(VolumeHoD.GetOutputPort())\n",
    "TransfFiltreHoD.SetTransform(Transf1)\n",
    "TransfFiltreHoD.Update()\n",
    "\n",
    "Transf=vtk.vtkTransform()\n",
    "Transf.SetMatrix(readerImg.GetPatientMatrix())\n",
    "Transf.Inverse()\n",
    "Transf.Update()\n",
    "\n",
    "TransfFiltreOs2=vtk.vtkTransformPolyDataFilter()\n",
    "TransfFiltreOs2.SetInputConnection(TransfFiltreOs.GetOutputPort())\n",
    "TransfFiltreOs2.SetTransform(Transf)\n",
    "TransfFiltreOs2.Update()\n",
    "TransfFiltreHoG2=vtk.vtkTransformPolyDataFilter()\n",
    "TransfFiltreHoG2.SetInputConnection(TransfFiltreHoG.GetOutputPort())\n",
    "TransfFiltreHoG2.SetTransform(Transf)\n",
    "TransfFiltreHoG2.Update()\n",
    "TransfFiltreHoD2=vtk.vtkTransformPolyDataFilter()\n",
    "TransfFiltreHoD2.SetInputConnection(TransfFiltreHoD.GetOutputPort())\n",
    "TransfFiltreHoD2.SetTransform(Transf)\n",
    "TransfFiltreHoD2.Update()\n",
    "\n",
    "#Deuxièmement !\n",
    "Transf2=vtk.vtkTransform()\n",
    "Transf2.Scale(1.,1.,-1.)\n",
    "Transf2.Update()\n",
    "\n",
    "TransfFiltreOs3=vtk.vtkTransformPolyDataFilter()\n",
    "TransfFiltreOs3.SetInputConnection(TransfFiltreOs2.GetOutputPort())\n",
    "TransfFiltreOs3.SetTransform(Transf2)\n",
    "TransfFiltreOs3.Update()\n",
    "TransfFiltreHoG3=vtk.vtkTransformPolyDataFilter()\n",
    "TransfFiltreHoG3.SetInputConnection(TransfFiltreHoG2.GetOutputPort())\n",
    "TransfFiltreHoG3.SetTransform(Transf2)\n",
    "TransfFiltreHoG3.Update()\n",
    "TransfFiltreHoD3=vtk.vtkTransformPolyDataFilter()\n",
    "TransfFiltreHoD3.SetInputConnection(TransfFiltreHoD2.GetOutputPort())\n",
    "TransfFiltreHoD3.SetTransform(Transf2)\n",
    "TransfFiltreHoD3.Update()\n",
    "\n",
    "\n",
    "#Activer cette section selon besoins\n",
    "\n",
    "NormalsOs=vtk.vtkPolyDataNormals()\n",
    "NormalsOs.SetInputConnection(TransfFiltreOs3.GetOutputPort())\n",
    "NormalsOs.Update()\n",
    "NormalsHoG=vtk.vtkPolyDataNormals()\n",
    "NormalsHoG.SetInputConnection(TransfFiltreHoG3.GetOutputPort())\n",
    "NormalsHoG.Update()\n",
    "NormalsHoD=vtk.vtkPolyDataNormals()\n",
    "NormalsHoD.SetInputConnection(TransfFiltreHoD3.GetOutputPort())\n",
    "NormalsHoD.Update()\n",
    "\n",
    "#1: Os\n",
    "mapperOs = vtk.vtkPolyDataMapper()\n",
    "mapperOs.SetInputConnection(NormalsOs.GetOutputPort())\n",
    "mapperOs.ScalarVisibilityOff()\n",
    "actorOs = vtk.vtkActor()\n",
    "actorOs.SetMapper(mapperOs)\n",
    "actorOs.GetProperty().SetColor(0.8,1,0.3)\n",
    "\n",
    "#2: HoG\n",
    "mapperHoG = vtk.vtkPolyDataMapper()\n",
    "mapperHoG.SetInputConnection(NormalsHoG.GetOutputPort())\n",
    "mapperHoG.ScalarVisibilityOff()\n",
    "actorHoG = vtk.vtkActor()\n",
    "actorHoG.SetMapper(mapperHoG)\n",
    "actorHoG.GetProperty().SetColor(1,0,1)\n",
    "\n",
    "#3: HoD\n",
    "mapperHoD = vtk.vtkPolyDataMapper()\n",
    "mapperHoD.SetInputConnection(NormalsHoD.GetOutputPort())\n",
    "mapperHoD.ScalarVisibilityOff()\n",
    "actorHoD = vtk.vtkActor()\n",
    "actorHoD.SetMapper(mapperHoD)\n",
    "actorHoD.GetProperty().SetColor(0.9,0.2,0.5)\n",
    "\n",
    "#Actor 3: DICOM images par coupes\n",
    "# Lire les DICOM images par coupes\n",
    "\n",
    "actorImg1 = vtk.vtkImageActor()#Afficher la 1ère coupe au choix\n",
    "actorImg1.SetInputData(readerImg.GetOutput())\n",
    "actorImg2 = vtk.vtkImageActor()#Afficher la 2ème coupe au choix\n",
    "actorImg2.SetInputData(readerImg.GetOutput())\n",
    "actorImg3 = vtk.vtkImageActor()#Afficher la 3ème coupe au choix\n",
    "actorImg3.SetInputData(readerImg.GetOutput())\n",
    "\n",
    "mapperImg1 = vtk.vtkImageSliceMapper().SafeDownCast(actorImg1.GetMapper())\n",
    "mapperImg2 = vtk.vtkImageSliceMapper().SafeDownCast(actorImg2.GetMapper())\n",
    "mapperImg3 = vtk.vtkImageSliceMapper().SafeDownCast(actorImg3.GetMapper())\n",
    "actorImg1.GetMapper()\n",
    "actorImg2.GetMapper()\n",
    "actorImg3.GetMapper()\n",
    "mapperImg1.SetSliceNumber(0)\n",
    "mapperImg2.SetSliceNumber(dim[2]/5)\n",
    "mapperImg3.SetSliceNumber(dim[2]/3)\n",
    "\n",
    "# Create a rendering window and renderer\n",
    "ren = vtk.vtkRenderer()\n",
    "renWin = vtk.vtkRenderWindow()\n",
    "renWin.AddRenderer(ren)\n",
    "renWin.SetSize(1024, 1024)\n",
    "\n",
    "# Create a renderwindowinteractor\n",
    "iren = vtk.vtkRenderWindowInteractor()\n",
    "iren.SetRenderWindow(renWin)\n",
    "\n",
    "# Assign actor to the renderer\n",
    "ren.AddActor(actorOs)\n",
    "ren.AddActor(actorHoD)\n",
    "ren.AddActor(actorHoG)\n",
    "ren.AddActor(actorMC)\n",
    "#Les images DICOM par coupes\n",
    "ren.AddActor(actorImg1)\n",
    "ren.AddActor(actorImg2)\n",
    "ren.AddActor(actorImg3)\n",
    "\n",
    "#ren.GetActiveCamera().Zoom(1.5)\n",
    "# Enable user interface interactor\n",
    "iren.Initialize()\n",
    "renWin.Render()\n",
    "iren.Start()\n",
    "\n",
    "\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": false,
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   "outputs": [],
   "source": [
    "################################################################################\n",
    "#Chapitre 4: Utilisation du Image Data Stencil pour Holmium isolé (version VTK)#\n",
    "################################################################################\n",
    "\n",
    "\n",
    "#Volume: HolmiumG\n",
    "filenameHoG=\"/home/jonathan/Bureau/DICOMcochon/vtk/HolmiumG.vtk\"\n",
    "VolumeHoG = vtk.vtkPolyDataReader()\n",
    "VolumeHoG.SetFileName(filenameHoG)\n",
    "VolumeHoG.Update()\n",
    "\n",
    "# Lire les DICOM images (version VTK)      NB: par défaut, critère du image number\n",
    "\n",
    "PathDicom2=\"/home/jonathan/Bureau/DICOMcochon/UH\"\n",
    "\n",
    "directory = vtkDICOMPython.vtkDICOMDirectory()\n",
    "directory.SetDirectoryName(PathDicom2)\n",
    "directory.Update()\n",
    "\n",
    "readerImg = vtkDICOMPython.vtkDICOMReader()\n",
    "readerImg.SetFileNames(directory.GetFileNamesForSeries(0))\n",
    "readerImg.Update()\n",
    "\n",
    "################################################################\n",
    "#Utiliser la matrice des DICOM images pour les lier avec les vtk\n",
    "\n",
    "#Premièrement !\n",
    "Transf1=vtk.vtkTransform()\n",
    "Transf1.Scale(-1.,-1.,1.)\n",
    "Transf1.Update()\n",
    "TransfFiltreHoG=vtk.vtkTransformPolyDataFilter()\n",
    "TransfFiltreHoG.SetInputConnection(VolumeHoG.GetOutputPort())\n",
    "TransfFiltreHoG.SetTransform(Transf1)\n",
    "TransfFiltreHoG.Update()\n",
    "Transf=vtk.vtkTransform()\n",
    "Transf.SetMatrix(readerImg.GetPatientMatrix())\n",
    "Transf.Inverse()\n",
    "Transf.Update()\n",
    "TransfFiltreHoG2=vtk.vtkTransformPolyDataFilter()\n",
    "TransfFiltreHoG2.SetInputConnection(TransfFiltreHoG.GetOutputPort())\n",
    "TransfFiltreHoG2.SetTransform(Transf)\n",
    "TransfFiltreHoG2.Update()\n",
    "#Deuxièmement !\n",
    "Transf2=vtk.vtkTransform()\n",
    "Transf2.Scale(1.,1.,-1.)\n",
    "Transf2.Update()\n",
    "TransfFiltreHoG3=vtk.vtkTransformPolyDataFilter()\n",
    "TransfFiltreHoG3.SetInputConnection(TransfFiltreHoG2.GetOutputPort())\n",
    "TransfFiltreHoG3.SetTransform(Transf2)\n",
    "TransfFiltreHoG3.Update()\n",
    "NormalsHoG=vtk.vtkPolyDataNormals()\n",
    "NormalsHoG.SetInputConnection(TransfFiltreHoG3.GetOutputPort())\n",
    "NormalsHoG.Update()\n",
    "\n",
    "\n",
    "#Etape du stencil\n",
    "dataToStencil = vtk.vtkPolyDataToImageStencil()\n",
    "dataToStencil.SetInputConnection(NormalsHoG.GetOutputPort())\n",
    "dataToStencil.SetOutputSpacing(readerImg.GetOutput().GetSpacing())\n",
    "#dataToStencil.SetOutputOrigin(Origine)\n",
    "stencil = vtk.vtkImageStencil()\n",
    "stencil.SetInputConnection(readerImg.GetOutputPort())\n",
    "stencil.SetStencilConnection(dataToStencil.GetOutputPort())\n",
    "#stencil.ReverseStencilOn()\n",
    "stencil.SetBackgroundValue(0)\n",
    "stencil.Update()\n",
    "\n",
    "\n",
    "\n",
    "#Visualisation\n",
    "imageAppend=vtk.vtkImageAppend()\n",
    "imageAppend.AddInputConnection(stencil.GetOutputPort())\n",
    "viewer = vtk.vtkImageViewer()\n",
    "interator = vtk.vtkRenderWindowInteractor()\n",
    "viewer.SetInputConnection(imageAppend.GetOutputPort())\n",
    "viewer.SetupInteractor(interator)\n",
    "viewer.SetZSlice(130)\n",
    "viewer.SetSize(1024,1024)\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "viewer.Render()\n",
    "interator.Start()\n",
    "\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "###################################\n",
    "#Annexe 1: Visualiseur de stl seul#\n",
    "###################################\n",
    "\n",
    "filename = \"/home/jonathan/Bureau/DICOM/stl/MetFrontG.stl\"\n",
    " \n",
    "reader = vtk.vtkSTLReader()\n",
    "reader.SetFileName(filename)\n",
    "reader.Update()\n",
    "\n",
    "transform=vtk.vtkTransform()\n",
    "#transform.Scale(-1,-1,1)\n",
    "\n",
    "transformFilter=vtk.vtkTransformPolyDataFilter()\n",
    "transformFilter.SetInputConnection(reader.GetOutputPort())\n",
    "transformFilter.SetTransform(transform)\n",
    "transformFilter.Update()\n",
    "\n",
    "print(transformFilter.GetOutput().GetBounds())\n",
    "    \n",
    "mapper = vtk.vtkPolyDataMapper()\n",
    "if vtk.VTK_MAJOR_VERSION <= 5:\n",
    "    mapper.SetInput(reader.GetOutput())\n",
    "else:\n",
    "    mapper.SetInputConnection(reader.GetOutputPort())\n",
    "\n",
    "actor = vtk.vtkActor()\n",
    "actor.SetMapper(mapper)\n",
    "\n",
    "# Create a rendering window and renderer\n",
    "ren = vtk.vtkRenderer()\n",
    "renWin = vtk.vtkRenderWindow()\n",
    "renWin.AddRenderer(ren)\n",
    "renWin.SetSize(1024, 1024)\n",
    "# Create a renderwindowinteractor\n",
    "iren = vtk.vtkRenderWindowInteractor()\n",
    "iren.SetRenderWindow(renWin)\n",
    " \n",
    "# Assign actor to the renderer\n",
    "ren.AddActor(actor)\n",
    "\n",
    "# Enable user interface interactor\n",
    "iren.Initialize()\n",
    "renWin.Render()\n",
    "iren.Start()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "############################################\n",
    "#Annexe 2: Visualiseur de RTStructure seule#\n",
    "############################################\n",
    "\n",
    "n=6 #Numero du RT Structure\n",
    "RTStruc=vtkgdcm.vtkGDCMPolyDataReader()\n",
    "RTStruc.SetFileName(\"/home/jonathan/Bureau/DICOM/RTStruc/RTST0173.dcm\")\n",
    "RTStruc.Update()\n",
    "\n",
    "\n",
    "\n",
    "mapper = vtk.vtkPolyDataMapper()\n",
    "mapper.SetInputConnection(RTStruc.GetOutputPort(n))\n",
    "actor = vtk.vtkActor()\n",
    "actor.SetMapper(mapper)\n",
    " \n",
    "# Create a rendering window and renderer\n",
    "ren = vtk.vtkRenderer()\n",
    "renWin = vtk.vtkRenderWindow()\n",
    "renWin.AddRenderer(ren)\n",
    "renWin.SetSize(1024, 1024)\n",
    "\n",
    "# Create a renderwindowinteractor\n",
    "iren = vtk.vtkRenderWindowInteractor()\n",
    "iren.SetRenderWindow(renWin)\n",
    " \n",
    "# Assign actor to the renderer\n",
    "ren.AddActor(actor)\n",
    " \n",
    "# Enable user interface interactor\n",
    "iren.Initialize()\n",
    "renWin.Render()\n",
    "iren.Start()\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "###################################\n",
    "#Annexe 3: Visualiseur de vtk seul#\n",
    "##################################\n",
    "\n",
    "filename=\"/home/jonathan/Bureau/DICOMcochon/vtk/Segment_Os.vtk\"\n",
    "RTStruc = vtk.vtkPolyDataReader()\n",
    "RTStruc.SetFileName(filename)\n",
    "RTStruc.Update()\n",
    "\n",
    "mapper = vtk.vtkPolyDataMapper()\n",
    "mapper.SetInputConnection(RTStruc.GetOutputPort())\n",
    "actor = vtk.vtkActor()\n",
    "actor.SetMapper(mapper)\n",
    " \n",
    "# Create a rendering window and renderer\n",
    "ren = vtk.vtkRenderer()\n",
    "renWin = vtk.vtkRenderWindow()\n",
    "renWin.AddRenderer(ren)\n",
    "renWin.SetSize(1024, 1024)\n",
    "\n",
    "# Create a renderwindowinteractor\n",
    "iren = vtk.vtkRenderWindowInteractor()\n",
    "iren.SetRenderWindow(renWin)\n",
    " \n",
    "# Assign actor to the renderer\n",
    "ren.AddActor(actor)\n",
    " \n",
    "# Enable user interface interactor\n",
    "iren.Initialize()\n",
    "renWin.Render()\n",
    "iren.Start()\n"
   ]
  }
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