niftysim.ipynb

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   "source": [
    "case_number = 3"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "*Generate the mesh for FE model*"
   ]
  },
  {
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   "execution_count": null,
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   "outputs": [],
   "source": [
    "!python FEA-simualtions/mesh.py -i uncompressed_nrrd/UncompressedBreast{case_number}_resampled.nrrd -o uncompressed_nrrd/volmesh{case_number}.vtk"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "*Create XML file from the mesh an as input for the Niftysim Dockerfile*"
   ]
  },
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   "outputs": [],
   "source": [
    "# Based on the metadata of the corresponding compresssed phantom, the desired thickness is 65.0704 in the y-axis. This would be the final compressioon state no. 30.\n",
    "\n",
    "!python FEA-simualtions/writeNiftyModel.py -meshpath uncompressed_nrrd/volmesh{case_number}.vtk -output uncompressed_nrrd/volmesh{case_number}-model.xml -thickness 65.0704 -gravity 4905 -offset 15.0 -material NH -anisotropyRatio 0.0"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "*Running the Niftysim Docker Container to run the simulation*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
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   "outputs": [],
   "source": [
    "'''Update the -v path !!'''\n",
    "\n",
    "# Run Docker container with GPU support, mounting a volume, and using an interactive terminal\n",
    "!docker run --name niftysim_container --gpus all -v /home/hadeel/GNNs-BreastCompression:/home/data -d niftysim:2.5 tail -f /dev/null\n",
    "!docker ps\n",
    "# All nodal displacements\n",
    "# For each step you have to store the nodal displacemnet manually\n",
    "!docker exec niftysim_container /bin/bash -c \"cd /home/niftysim/release/source && ./niftysim -x /home/data/uncompressed_nrrd/volmesh{case_number}-model.xml -t -v -sport -print ND -device 0 -export-mesh /home/data/uncompressed_nrrd/niftysim_output/volmesh{case_number}_niftysim.vtk\"\n",
    "\n",
    "!docker stop niftysim_container\n",
    "!docker rm niftysim_container"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "*Get the compressed phantom from the output of Niftysim Docker container*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
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   },
   "outputs": [],
   "source": [
    "!python FEA-simualtions/extract_compressed_mesh.py uncompressed_nrrd/niftysim_output/volmesh{case_number}_niftysim.vtk uncompressed_nrrd/niftysim_output/volmesh{case_number}_compressed.vtk"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "*Reconstruct the NRRD image from the compressed phantom mesh*"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "vscode": {
     "languageId": "shellscript"
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   "outputs": [],
   "source": [
    "'''Update the -v path !!'''\n",
    "\n",
    "# Run Docker container with GPU support, mounting a volume, and using an interactive terminal\n",
    "!docker run --name reconstruct_container --gpus all -v /home/hadeel/GNNs-BreastCompression:/home/data -d reconstruct-image:latest tail -f /dev/null\n",
    "\n",
    "!docker ps\n",
    "\n",
    "!docker exec reconstruct_container /bin/bash -c \"cd /home/ReconstructImage/release && ./ReconstructImage /home/data/uncompressed_nrrd/volmesh{case_number}.vtk /home/data/uncompressed_nrrd/niftysim_output/volmesh{case_number}_compressed.vtk /home/data/uncompressed_nrrd/UncompressedBreast{case_number}_resampled.nrrd /home/data/uncompressed_nrrd/niftysim_output/compressedPhantom{case_number}.nrrd\"\n",
    "\n",
    "!docker stop reconstruct_container\n",
    "!docker rm reconstruct_container"
   ]
  }
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