04_mixed_workflow.ipynb

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    "<font style=\"font-family:roboto;color:#455e6c;font-size:18px;text-align:justify\"> <b> Workflow mixing CompositionSpace and paraprobe-toolbox <br> </b> </font>\n",
    "This example combines both tools in that the parsing of the reconstruction and ranging definitions to NeXus is performed by paraprobe to create a<br>\n",
    "standardized input that is then consumed by CompositionSpace. The example shows the benefit that comes with using fewer file formats and data<br>\n",
    "representations in the field of atom probe to enable an exchange of data and metadata across different tools."
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   "source": [
    "from pyiron_workflow import Workflow\n",
    "from nodes.paraprobe import *\n",
    "from nodes.compositionspace import *\n",
    "from nodes.visualize import *"
   ]
  },
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   "source": [
    "config_file_path = 'experiment_params.yaml'\n",
    "results_file_path = 'CompositionSpace.Results.1.nxs'"
   ]
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    "wf = Workflow(\"demo\")\n",
    "wf.transcoder = transcoder_job()\n",
    "wf.ranger = ranger_job(wf.transcoder)\n",
    "wf.ranger_reporter = ranger_reporter(wf.ranger)\n",
    "\n",
    "wf.voxel = compositionspace_voxelize(\n",
    "    config_file_path=config_file_path,\n",
    "    results_file_path=results_file_path,\n",
    "    recon_file_path=wf.transcoder,\n",
    "    range_file_path=wf.ranger)\n",
    "wf.autophase = compositionspace_autophase(\n",
    "    config_file_path=config_file_path,\n",
    "    results_file_path=wf.voxel)\n",
    "wf.segmentation = compositionspace_segmentation(\n",
    "    config_file_path=config_file_path, \n",
    "    results_file_path=wf.autophase)\n",
    "wf.cluster = compositionspace_clustering(\n",
    "    config_file_path=config_file_path,\n",
    "    results_file_path=wf.segmentation)\n",
    "\n",
    "wf.xdmf = generate_xdmf(wf.cluster)\n",
    "wf.results = visualize_hdf(wf.cluster)"
   ]
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  {
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   "execution_count": 5,
   "id": "e5948227-7078-4470-b410-181875ee9a11",
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      "Computing SHA256 hash for file named Si.apt\n",
      "Computing SHA256 hash for file named Si.RNG\n",
      "Inspecting whether NeXus/HDF5 is used...\n",
      "The reconstruction and ranging come from files of technology\n",
      "partners but the paraprobe-toolbox uses NeXus/HDF5.\n",
      "Hence, paraprobe-transcoder will transcode to NeXus/HDF5.\n",
      "Writing configuration file ...\n",
      "PARAPROBE.Transcoder.Config.SimID.1.nxs was written successfully\n",
      "/entry1/transcode/reconstruction/path, /entry1/transcode/ranging/path\n",
      "True\n",
      "Processing configuration file: PARAPROBE.Transcoder.Config.SimID.1.nxs\n",
      "Processing reconstruction: Si.apt\n",
      "Processing ranging: Si.RNG\n",
      "Results file: PARAPROBE.Transcoder.Results.SimID.1.nxs\n",
      "Input reconstruction and ranging definitions use files from\n",
      "technology partners (POS, ePOS, APT, RRNG, RNG) or other\n",
      "file formats from the community. These will be transcoded to NeXus...\n",
      "Computing SHA256 hash for file named PARAPROBE.Transcoder.Config.SimID.1.nxs\n",
      "Reading Si.apt which is 37810040 B\n",
      "File describes 945211 ions\n",
      "Currently at byte_offset 540 B\n",
      "keyword: tofc, found_section: [([83, 69, 67,  0], 148, 2, [116, 111, 102,  99,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0], 1, 1, 1, 3, 32, 4, [110, 115,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0], 945211, 3780844)]\n",
      "Byte offset for reading data for section: tofc 3781532 B\n",
      "keyword: Mass, found_section: [([83, 69, 67,  0], 148, 2, [ 77,  97, 115, 115,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0], 1, 1, 1, 3, 32, 4, [68, 97,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  0], 945211, 3780844)]\n",
      "Byte offset for reading data for section: Mass 7562524 B\n",
      "keyword: XDet_mm, found_section: [([83, 69, 67,  0], 148, 2, [ 88,  68, 101, 116,  95, 109, 109,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0], 1, 1, 1, 3, 32, 4, [109, 109,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0], 945211, 3780844)]\n",
      "Byte offset for reading data for section: XDet_mm 11343516 B\n",
      "keyword: YDet_mm, found_section: [([83, 69, 67,  0], 148, 2, [ 89,  68, 101, 116,  95, 109, 109,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0], 1, 1, 1, 3, 32, 4, [109, 109,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0], 945211, 3780844)]\n",
      "Byte offset for reading data for section: YDet_mm 15124508 B\n",
      "keyword: Multiplicity, found_section: [([83, 69, 67,  0], 148, 2, [ 77, 117, 108, 116, 105, 112, 108, 105,  99, 105, 116, 121,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0], 1, 1, 1, 1, 32, 4, [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], 945211, 3780844)]\n",
      "Byte offset for reading data for section: Multiplicity 18905500 B\n",
      "keyword: Detector Coordinates, found_section: [([83, 69, 67,  0], 148, 2, [ 68, 101, 116, 101,  99, 116, 111, 114,  32,  67, 111, 111, 114, 100, 105, 110,  97, 116, 101, 115,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0], 1, 1, 1, 3, 32, 8, [109, 109,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0], 945211, 7561688)]\n",
      "Byte offset for reading data for section: Detector Coordinates 26467336 B\n",
      "keyword: Position, found_section: [([83, 69, 67,  0], 172, 2, [ 80, 111, 115, 105, 116, 105, 111, 110,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0], 1, 1, 1, 3, 32, 12, [110, 109,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0,   0], 945211, 11342532)]\n",
      "Byte offset for reading data for section: Position 37810040 B\n",
      "End of file at 37810040 B\n",
      "Reading section Position at 26467508\n",
      "Reading section Mass at 3781680\n",
      "Transcoded reconstruction and mass-to-charge-state-ratio values\n",
      "Si.RNG parsed successfully\n",
      "Transcoded ranging data for Si.RNG\n",
      "Supported file formats are *.analysis, *.env, *.h5, *.fig.txt, *.rng, *.rrng !\n",
      "Transcoded ranging definitions\n",
      "paraprobe-transcoder success\n",
      "Computing SHA256 hash for file named PARAPROBE.Transcoder.Results.SimID.1.nxs\n",
      "Writing configuration file ...\n",
      "PARAPROBE.Ranger.Config.SimID.1.nxs was written successfully\n",
      "paraprobe-ranger\n",
      "A tool of the paraprobe-toolbox supporting FAIR materials science research\n",
      "Supporting the community with strong-scaling and open tools for robust and automated uncertainty quantification...\n",
      "\n",
      "The compiled code of this tool uses the source code with the following GitSha:\n",
      "v0.4\n",
      "\"v0.5.1\"\n",
      "Preprocessor run\n",
      "Aug 26 2024\n",
      "23:47:39\n",
      "Paraprobe can be cited via the following papers...\n",
      "Collecting 5 publications for the tool to cite:\n",
      "Article\n",
      "M. K\"uhbach and P. Bajaj and A. Breen and E. A. J\"agle and B. Gault\n",
      "On Strong Scaling Open Source Tools for Mining Atom Probe Tomography Data\n",
      "Microscopy and Microanalysis, 2019, Volume 25, Supplement S2, pp298-299\n",
      "https://doi.org/10.1017/S1431927619002228\n",
      "\n",
      "\n",
      "Article\n",
      "M. K\"uhbach and P. Bajaj and H. Zhao and M. H. C\"{c}elik E. A. J\"agle and B. Gault\n",
      "On strong-scaling and open-source tools for analyzing atom probe tomography data\n",
      "npj Computational Materials, 2021, Volume 7, ppArticle number 21\n",
      "https://doi.org/10.1038/s41524-020-00486-1\n",
      "\n",
      "\n",
      "Article\n",
      "M. K\"uhbach and A. J. London  and J. Wang and D. K. Schreiber and F. Mendez-Martin and I. Ghamarian and H. Bilal and A. V.Ceguerra\n",
      "Community-Driven Methods for Open and Reproducible Software Tools for Analyzing Datasets from Atom Probe Microscopy\n",
      "Microscopy and Microanalysis, 2021, pp1-16\n",
      "https://doi.org/10.1017/S1431927621012241\n",
      "\n",
      "\n",
      "Article\n",
      "M. K\"uhbach and M. Kasemer and A. Breen and B. Gault\n",
      "Open and strong-scaling tools for atom-probe crystallography: high-throughput methods for indexing crystal structure and orientation\n",
      "Journal of Applied Crystallography, 2021, Volume 54, pp1490-1508\n",
      "https://doi.org/10.1107/S1600576721008578\n",
      "\n",
      "\n",
      "Preprint\n",
      "M. K\"uhbach and V. V. Rielli and S. Primig and A. Saxena and B. Jenkins and D. Mayweg and A. Reichmann and S. Kardos and L. Romaner and S. Brockhauser\n",
      "CGM paper\n",
      "arXiv, 2022\n",
      "https://arxiv.org/abs/2205.13510\n",
      "\n",
      "\n",
      "ConfigRanger::\n",
      "Reading configuration from PARAPROBE.Ranger.Config.SimID.1.nxs\n",
      "Reading configuration for task 0\n",
      "Ranging with existent ranging definitions\n",
      "cwd: __/home/kaiobach/Research/hu_hu_hu/sprint26/iuc09_dfg_demo/pyiron_apt__\n",
      "/home/kaiobach/Research/hu_hu_hu/sprint26/iuc09_dfg_demo/pyiron_apt/PARAPROBE.Transcoder.Results.SimID.1.nxs\n",
      "/home/kaiobach/Research/hu_hu_hu/sprint26/iuc09_dfg_demo/pyiron_apt/PARAPROBE.Transcoder.Results.SimID.1.nxs\n",
      "abs_path: __/home/kaiobach/Research/hu_hu_hu/sprint26/iuc09_dfg_demo/pyiron_apt/PARAPROBE.Transcoder.Results.SimID.1.nxs__\n",
      "InputfileDataset /home/kaiobach/Research/hu_hu_hu/sprint26/iuc09_dfg_demo/pyiron_apt/PARAPROBE.Transcoder.Results.SimID.1.nxs\n",
      "ReconstructionDatasetName /entry1/atom_probe/reconstruction/reconstructed_positions\n",
      "MassToChargeDatasetName /entry1/atom_probe/mass_to_charge_conversion/mass_to_charge\n",
      "cwd: __/home/kaiobach/Research/hu_hu_hu/sprint26/iuc09_dfg_demo/pyiron_apt__\n",
      "/home/kaiobach/Research/hu_hu_hu/sprint26/iuc09_dfg_demo/pyiron_apt/PARAPROBE.Transcoder.Results.SimID.1.nxs\n",
      "/home/kaiobach/Research/hu_hu_hu/sprint26/iuc09_dfg_demo/pyiron_apt/PARAPROBE.Transcoder.Results.SimID.1.nxs\n",
      "abs_path: __/home/kaiobach/Research/hu_hu_hu/sprint26/iuc09_dfg_demo/pyiron_apt/PARAPROBE.Transcoder.Results.SimID.1.nxs__\n",
      "InputfileIonTypes /home/kaiobach/Research/hu_hu_hu/sprint26/iuc09_dfg_demo/pyiron_apt/PARAPROBE.Transcoder.Results.SimID.1.nxs\n",
      "IonTypesGroupName /entry1/atom_probe/ranging/peak_identification\n",
      "Sensible defaults\n",
      "PracticalMassToChargeResolution 0.0005\n",
      "Configuration from file PARAPROBE.Ranger.Config.SimID.1.nxs was accepted\n",
      "This analysis has SimulationID SimID.1\n",
      "Results of this analysis are written to PARAPROBE.Ranger.Results.SimID.1.nxs\n",
      "\n",
      "Rank 0 initialized, we are now MPI_COMM_WORLD parallel using MPI_THREAD_FUNNELED\n",
      "Adding iontype ...\n",
      "id 1\n",
      "charge 2+\n",
      "isotope vector \n",
      "14, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 2\n",
      "charge 1+\n",
      "isotope vector \n",
      "14, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 3\n",
      "charge 1+\n",
      "isotope vector \n",
      "24, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 4\n",
      "charge 1+\n",
      "isotope vector \n",
      "14, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 5\n",
      "charge 1+\n",
      "isotope vector \n",
      "14, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 6\n",
      "charge 2+\n",
      "isotope vector \n",
      "14, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 7\n",
      "charge 2+\n",
      "isotope vector \n",
      "14, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 8\n",
      "charge 1+\n",
      "isotope vector \n",
      "24, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 9\n",
      "charge 2+\n",
      "isotope vector \n",
      "24, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 10\n",
      "charge 2+\n",
      "isotope vector \n",
      "24, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 11\n",
      "charge 1+\n",
      "isotope vector \n",
      "29, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 12\n",
      "charge 1+\n",
      "isotope vector \n",
      "29, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 13\n",
      "charge 1+\n",
      "isotope vector \n",
      "6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 14\n",
      "charge 2+\n",
      "isotope vector \n",
      "6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 15\n",
      "charge 1+\n",
      "isotope vector \n",
      "8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 16\n",
      "charge 1+\n",
      "isotope vector \n",
      "8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 17\n",
      "charge 1+\n",
      "isotope vector \n",
      "24, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 18\n",
      "charge 1+\n",
      "isotope vector \n",
      "24, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 19\n",
      "charge 1+\n",
      "isotope vector \n",
      "24, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 20\n",
      "charge 2+\n",
      "isotope vector \n",
      "24, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 21\n",
      "charge 2+\n",
      "isotope vector \n",
      "24, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 22\n",
      "charge 2+\n",
      "isotope vector \n",
      "24, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 23\n",
      "charge 1+\n",
      "isotope vector \n",
      "24, 8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 24\n",
      "charge 2+\n",
      "isotope vector \n",
      "24, 8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Adding iontype ...\n",
      "id 25\n",
      "charge 2+\n",
      "isotope vector \n",
      "24, 24, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "subgrpnm /entry1/atom_probe/ranging/peak_identification/ion26 does not exists !\n",
      "Reporting the rangeTable\n",
      "0\n",
      "id 0\n",
      "charge neutral\n",
      "isotope vector \n",
      "0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "1\n",
      "id 1\n",
      "charge 2+\n",
      "isotope vector \n",
      "14, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "2\n",
      "id 2\n",
      "charge 1+\n",
      "isotope vector \n",
      "14, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "3\n",
      "id 3\n",
      "charge 1+\n",
      "isotope vector \n",
      "24, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "4\n",
      "id 4\n",
      "charge 1+\n",
      "isotope vector \n",
      "14, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "5\n",
      "id 5\n",
      "charge 1+\n",
      "isotope vector \n",
      "14, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "6\n",
      "id 6\n",
      "charge 2+\n",
      "isotope vector \n",
      "14, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "7\n",
      "id 7\n",
      "charge 2+\n",
      "isotope vector \n",
      "14, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "8\n",
      "id 8\n",
      "charge 1+\n",
      "isotope vector \n",
      "24, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "9\n",
      "id 9\n",
      "charge 2+\n",
      "isotope vector \n",
      "24, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "10\n",
      "id 10\n",
      "charge 2+\n",
      "isotope vector \n",
      "24, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "11\n",
      "id 11\n",
      "charge 1+\n",
      "isotope vector \n",
      "29, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "12\n",
      "id 12\n",
      "charge 1+\n",
      "isotope vector \n",
      "29, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "13\n",
      "id 13\n",
      "charge 1+\n",
      "isotope vector \n",
      "6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "14\n",
      "id 14\n",
      "charge 2+\n",
      "isotope vector \n",
      "6, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "15\n",
      "id 15\n",
      "charge 1+\n",
      "isotope vector \n",
      "8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "16\n",
      "id 16\n",
      "charge 1+\n",
      "isotope vector \n",
      "8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "17\n",
      "id 17\n",
      "charge 1+\n",
      "isotope vector \n",
      "24, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "18\n",
      "id 18\n",
      "charge 1+\n",
      "isotope vector \n",
      "24, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "19\n",
      "id 19\n",
      "charge 1+\n",
      "isotope vector \n",
      "24, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "20\n",
      "id 20\n",
      "charge 2+\n",
      "isotope vector \n",
      "24, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "21\n",
      "id 21\n",
      "charge 2+\n",
      "isotope vector \n",
      "24, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "22\n",
      "id 22\n",
      "charge 2+\n",
      "isotope vector \n",
      "24, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "23\n",
      "id 23\n",
      "charge 1+\n",
      "isotope vector \n",
      "24, 8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "24\n",
      "id 24\n",
      "charge 2+\n",
      "isotope vector \n",
      "24, 8, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "25\n",
      "id 25\n",
      "charge 2+\n",
      "isotope vector \n",
      "24, 24, 8, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, \n",
      "mass-to-charge ranges.size() 1\n",
      "\n",
      "Computing the elemental decomposition of the these iontypes\n",
      "molecular ion decomposition for iontype 0\n",
      "0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 0\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 1\n",
      "14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 14\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 2\n",
      "14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 14\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 3\n",
      "24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 24\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 4\n",
      "14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 14\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 5\n",
      "14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 14\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 6\n",
      "14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 14\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 7\n",
      "14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 14\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 8\n",
      "24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 24\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 9\n",
      "24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 24\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 10\n",
      "24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 24\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 11\n",
      "29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 29\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 12\n",
      "29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 29\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 13\n",
      "6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 6\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 14\n",
      "6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 6\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 15\n",
      "8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 8\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 16\n",
      "8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 8\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 17\n",
      "24 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 8\t\t multiplicity 1\n",
      "nprotons 24\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 18\n",
      "24 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 8\t\t multiplicity 1\n",
      "nprotons 24\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 19\n",
      "24 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 8\t\t multiplicity 1\n",
      "nprotons 24\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 20\n",
      "24 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 8\t\t multiplicity 1\n",
      "nprotons 24\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 21\n",
      "24 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 8\t\t multiplicity 1\n",
      "nprotons 24\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 22\n",
      "24 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 8\t\t multiplicity 1\n",
      "nprotons 24\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 23\n",
      "24 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 8\t\t multiplicity 2\n",
      "nprotons 24\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 24\n",
      "24 8 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 8\t\t multiplicity 2\n",
      "nprotons 24\t\t multiplicity 1\n",
      "molecular ion decomposition for iontype 25\n",
      "24 24 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \n",
      "element multiplier with multiplicity > 0\n",
      "nprotons 8\t\t multiplicity 1\n",
      "nprotons 24\t\t multiplicity 2\n",
      "/home/kaiobach/Research/hu_hu_hu/sprint26/iuc09_dfg_demo/pyiron_apt/PARAPROBE.Transcoder.Results.SimID.1.nxs read /entry1/atom_probe/ranging/peak_identification successfully\n",
      "Rank 0 loaded rng.nuclides.isotopes.size() 26 iontypes\n",
      "Rank MASTER all relevant input was loaded successfully\n",
      "Rank 0 applying existent ranging ...\n",
      "Multi-threaded ranging using 1 OpenMP threads\n",
      "Rank 0 completed local workpackage\n",
      "Rank 0 computing naive composition ...\n",
      "Multi-threaded computing of a naive composition using 1 OpenMP threads\n",
      "Rank 0 completed local workpackage\n",
      "Reporting naive composition\n",
      "0\t\t68201\n",
      "1\t\t684972\n",
      "2\t\t5799\n",
      "3\t\t430\n",
      "4\t\t22528\n",
      "5\t\t8784\n",
      "6\t\t37918\n",
      "7\t\t25075\n",
      "8\t\t148\n",
      "9\t\t459\n",
      "10\t\t170\n",
      "11\t\t231\n",
      "12\t\t452\n",
      "13\t\t427\n",
      "14\t\t279\n",
      "15\t\t854\n",
      "16\t\t501\n",
      "17\t\t872\n",
      "18\t\t231\n",
      "19\t\t185\n",
      "20\t\t77\n",
      "21\t\t176\n",
      "22\t\t140\n",
      "23\t\t383\n",
      "24\t\t259\n",
      "25\t\t85660\n",
      "Ion total computed 945211\n",
      "Ion total expected 945211\n",
      "sizeof(unsigned char) 1\n",
      "Packing boolean states stored in unsigned char into a bitfield\n",
      "8 bits in an unsigned char\n",
      "in.size() 945211\n",
      "byte_length 118152\n",
      "out.size() 118152\n",
      "Rank 0 has completed its workpackage\n",
      "paraprobe-ranger success\n",
      "shape (945211,)\n",
      "dim 0\n",
      "\tnp.min(xyz[:, axis_id]) -20.433578491210938 >>>> -23.0\n",
      "\tnp.max(xyz[:, axis_id]) 19.706375122070312 >>>> 22.0\n",
      "\tself.aabb3d axis_id 0, [-23.  22.], extent 45\n",
      "dim 1\n",
      "\tnp.min(xyz[:, axis_id]) -17.857210159301758 >>>> -20.0\n",
      "\tnp.max(xyz[:, axis_id]) 21.282995223999023 >>>> 24.0\n",
      "\tself.aabb3d axis_id 1, [-20.  24.], extent 44\n",
      "dim 2\n",
      "\tnp.min(xyz[:, axis_id]) -75.08065032958984 >>>> -78.0\n",
      "\tnp.max(xyz[:, axis_id]) -0.020034153014421463 >>>> 2.0\n",
      "\tself.aabb3d axis_id 2, [-78.   2.], extent 80\n",
      "np.max(self.voxel_identifier) 153609\n",
      "np.prod(self.extent) 158400\n",
      "ion1, ('Si ++', 1, array([[13.8745, 14.241 ]], dtype=float32)):\n",
      "\tSi\n",
      "\t1\n",
      "\t{'Si': 1}\n",
      "ion2, ('Si +', 2, array([[27.856, 28.595]], dtype=float32)):\n",
      "\tSi\n",
      "\t1\n",
      "\t{'Si': 1}\n",
      "ion3, ('Cr +', 3, array([[51.699, 54.243]], dtype=float32)):\n",
      "\tCr\n",
      "\t1\n",
      "\t{'Cr': 1}\n",
      "ion4, ('Si +', 4, array([[28.826, 29.255]], dtype=float32)):\n",
      "\tSi\n",
      "\t1\n",
      "\t{'Si': 1}\n",
      "ion5, ('Si +', 5, array([[29.783, 30.252]], dtype=float32)):\n",
      "\tSi\n",
      "\t1\n",
      "\t{'Si': 1}\n",
      "ion6, ('Si ++', 6, array([[14.407, 14.643]], dtype=float32)):\n",
      "\tSi\n",
      "\t1\n",
      "\t{'Si': 1}\n",
      "ion7, ('Si ++', 7, array([[14.912, 15.171]], dtype=float32)):\n",
      "\tSi\n",
      "\t1\n",
      "\t{'Si': 1}\n",
      "ion8, ('Cr +', 8, array([[49.612, 50.526]], dtype=float32)):\n",
      "\tCr\n",
      "\t1\n",
      "\t{'Cr': 1}\n",
      "ion9, ('Cr ++', 9, array([[25.771, 27.211]], dtype=float32)):\n",
      "\tCr\n",
      "\t1\n",
      "\t{'Cr': 1}\n",
      "ion10, ('Cr ++', 10, array([[24.895, 25.445]], dtype=float32)):\n",
      "\tCr\n",
      "\t1\n",
      "\t{'Cr': 1}\n",
      "ion11, ('Cu +', 11, array([[62.567, 63.496]], dtype=float32)):\n",
      "\tCu\n",
      "\t1\n",
      "\t{'Cu': 1}\n",
      "ion12, ('Cu +', 12, array([[64.619, 65.548]], dtype=float32)):\n",
      "\tCu\n",
      "\t1\n",
      "\t{'Cu': 1}\n",
      "ion13, ('C +', 13, array([[11.866, 12.198]], dtype=float32)):\n",
      "\tC\n",
      "\t1\n",
      "\t{'C': 1}\n",
      "ion14, ('C ++', 14, array([[5.896, 6.193]], dtype=float32)):\n",
      "\tC\n",
      "\t1\n",
      "\t{'C': 1}\n",
      "ion15, ('O +', 15, array([[15.858, 16.48 ]], dtype=float32)):\n",
      "\tO\n",
      "\t1\n",
      "\t{'O': 1}\n",
      "ion16, ('O +', 16, array([[17.838, 18.304]], dtype=float32)):\n",
      "\tO\n",
      "\t1\n",
      "\t{'O': 1}\n",
      "ion17, ('Cr O +', 17, array([[67.622, 69.574]], dtype=float32)):\n",
      "\tCr O\n",
      "\t2\n",
      "\t{'Cr': 1, 'O': 1}\n",
      "ion18, ('Cr O +', 18, array([[69.781, 70.156]], dtype=float32)):\n",
      "\tCr O\n",
      "\t2\n",
      "\t{'Cr': 1, 'O': 1}\n",
      "ion19, ('Cr O +', 19, array([[65.76 , 66.264]], dtype=float32)):\n",
      "\tCr O\n",
      "\t2\n",
      "\t{'Cr': 1, 'O': 1}\n",
      "ion20, ('Cr O ++', 20, array([[32.892, 33.275]], dtype=float32)):\n",
      "\tCr O\n",
      "\t2\n",
      "\t{'Cr': 1, 'O': 1}\n",
      "ion21, ('Cr O ++', 21, array([[33.898, 34.802]], dtype=float32)):\n",
      "\tCr O\n",
      "\t2\n",
      "\t{'Cr': 1, 'O': 1}\n",
      "ion22, ('Cr O ++', 22, array([[34.917, 35.231]], dtype=float32)):\n",
      "\tCr O\n",
      "\t2\n",
      "\t{'Cr': 1, 'O': 1}\n",
      "ion23, ('Cr O O +', 23, array([[83.595, 86.555]], dtype=float32)):\n",
      "\tCr O O\n",
      "\t2\n",
      "\t{'Cr': 1, 'O': 2}\n",
      "ion24, ('Cr O O ++', 24, array([[41.869, 43.181]], dtype=float32)):\n",
      "\tCr O O\n",
      "\t2\n",
      "\t{'Cr': 1, 'O': 2}\n",
      "ion25, ('Cr Cr O ++', 25, array([[57.819, 61.159]], dtype=float32)):\n",
      "\tCr Cr O\n",
      "\t2\n",
      "\t{'Cr': 2, 'O': 1}\n",
      "/entry1/voxelization/element1, C\n",
      "symbol C, idx 0, np.sum(elem_cnts[symbol]) 706, np.sum(total_cnts) 706\n",
      "/entry1/voxelization/element2, Cr\n",
      "symbol Cr, idx 1, np.sum(elem_cnts[symbol]) 174850, np.sum(total_cnts) 175556\n",
      "/entry1/voxelization/element3, Cu\n",
      "symbol Cu, idx 2, np.sum(elem_cnts[symbol]) 683, np.sum(total_cnts) 176239\n",
      "/entry1/voxelization/element4, O\n",
      "symbol O, idx 3, np.sum(elem_cnts[symbol]) 89980, np.sum(total_cnts) 266219\n",
      "/entry1/voxelization/element5, Si\n",
      "symbol Si, idx 4, np.sum(elem_cnts[symbol]) 785076, np.sum(total_cnts) 1051295\n",
      "n_ions 945211\n",
      "Reading iontypes from /entry1/iontypes/iontypes\n",
      "Ions total 945211, i.e. 0.945 mio\n",
      "\t7.2154 at.-%,\t\t[0], 68201\n",
      "\t72.4676 at.-%,\tSi ++\t[1], 684972\n",
      "\t0.6135 at.-%,\tSi +\t[2], 5799\n",
      "\t0.0455 at.-%,\tCr +\t[3], 430\n",
      "\t2.3834 at.-%,\tSi +\t[4], 22528\n",
      "\t0.9293 at.-%,\tSi +\t[5], 8784\n",
      "\t4.0116 at.-%,\tSi ++\t[6], 37918\n",
      "\t2.6528 at.-%,\tSi ++\t[7], 25075\n",
      "\t0.0157 at.-%,\tCr +\t[8], 148\n",
      "\t0.0486 at.-%,\tCr ++\t[9], 459\n",
      "\t0.018 at.-%,\tCr ++\t[10], 170\n",
      "\t0.0244 at.-%,\tCu +\t[11], 231\n",
      "\t0.0478 at.-%,\tCu +\t[12], 452\n",
      "\t0.0452 at.-%,\tC +\t[13], 427\n",
      "\t0.0295 at.-%,\tC ++\t[14], 279\n",
      "\t0.0904 at.-%,\tO +\t[15], 854\n",
      "\t0.053 at.-%,\tO +\t[16], 501\n",
      "\t0.0923 at.-%,\tCr O +\t[17], 872\n",
      "\t0.0244 at.-%,\tCr O +\t[18], 231\n",
      "\t0.0196 at.-%,\tCr O +\t[19], 185\n",
      "\t0.0081 at.-%,\tCr O ++\t[20], 77\n",
      "\t0.0186 at.-%,\tCr O ++\t[21], 176\n",
      "\t0.0148 at.-%,\tCr O ++\t[22], 140\n",
      "\t0.0405 at.-%,\tCr O O +\t[23], 383\n",
      "\t0.0274 at.-%,\tCr O O ++\t[24], 259\n",
      "\t9.0625 at.-%,\tCr Cr O ++\t[25], 85660\n",
      "Aggregate information for unique molecular ions (considering charge state)\n",
      "\t7.2154 at.-%,\t\t[0], 68201\n",
      "\t79.1321 at.-%,\tSi ++\t[1, 6, 7], 747965\n",
      "\t3.9262 at.-%,\tSi +\t[2, 4, 5], 37111\n",
      "\t0.0612 at.-%,\tCr +\t[3, 8], 578\n",
      "\t0.0665 at.-%,\tCr ++\t[9, 10], 629\n",
      "\t0.0723 at.-%,\tCu +\t[11, 12], 683\n",
      "\t0.0452 at.-%,\tC +\t[13], 427\n",
      "\t0.0295 at.-%,\tC ++\t[14], 279\n",
      "\t0.1434 at.-%,\tO +\t[15, 16], 1355\n",
      "\t0.1363 at.-%,\tCr O +\t[17, 18, 19], 1288\n",
      "\t0.0416 at.-%,\tCr O ++\t[20, 21, 22], 393\n",
      "\t0.0405 at.-%,\tCr O O +\t[23], 383\n",
      "\t0.0274 at.-%,\tCr O O ++\t[24], 259\n",
      "\t9.0625 at.-%,\tCr Cr O ++\t[25], 85660\n",
      "Aggregate information for unique molecular ions (ignoring charge state)\n",
      "\t7.2154 at.-%,\t\t[0], 68201\n",
      "\t83.0583 at.-%,\tSi\t[1, 2, 4, 5, 6, 7], 785076\n",
      "\t0.1277 at.-%,\tCr\t[3, 8, 9, 10], 1207\n",
      "\t0.0723 at.-%,\tCu\t[11, 12], 683\n",
      "\t0.0747 at.-%,\tC\t[13, 14], 706\n",
      "\t0.1434 at.-%,\tO\t[15, 16], 1355\n",
      "\t0.1778 at.-%,\tCr O\t[17, 18, 19, 20, 21, 22], 1681\n",
      "\t0.0679 at.-%,\tCr O O\t[23, 24], 642\n",
      "\t9.0625 at.-%,\tCr Cr O\t[25], 85660\n",
      "Composition matrix has 5 elements\n",
      "Populating composition table for element1\n",
      "Populating composition table for element2\n",
      "Populating composition table for element3\n",
      "Populating composition table for element4\n",
      "Populating composition table for element5\n",
      "Composition matrix has 5 elements\n",
      "Populating composition table for element1\n",
      "Populating composition table for element2\n",
      "Populating composition table for element3\n",
      "Populating composition table for element4\n",
      "Populating composition table for element5\n",
      "Composition matrix has 5 elements\n",
      "Populating composition table for element1\n",
      "Populating composition table for element2\n",
      "Populating composition table for element3\n",
      "Populating composition table for element4\n",
      "Populating composition table for element5\n",
      "Using results with automated phase assignment\n",
      "np.shape(X_train) (158400, 2)\n",
      "GaussianMixture ML analysis with n_cluster 1\n",
      "Using results with automated phase assignment\n",
      "np.shape(X_train) (158400, 2)\n",
      "GaussianMixture ML analysis with n_cluster 2\n",
      "Using results with automated phase assignment\n",
      "np.shape(X_train) (158400, 2)\n",
      "GaussianMixture ML analysis with n_cluster 3\n",
      "Using results with automated phase assignment\n",
      "np.shape(X_train) (158400, 2)\n",
      "GaussianMixture ML analysis with n_cluster 4\n",
      "Using results with automated phase assignment\n",
      "np.shape(X_train) (158400, 2)\n",
      "GaussianMixture ML analysis with n_cluster 5\n",
      "DBScan configuration: eps 3 nm, min_samples 5\n",
      "['cluster_analysis0', 'cluster_analysis1', 'cluster_analysis2', 'cluster_analysis3', 'cluster_analysis4', 'result', 'sequence_index']\n",
      "cluster_analysis0\n",
      "ic_run_id 0 >>>>\n",
      "np.shape(all_vxl_pos) (158400, 3) list(set(phase_identifier) [0]\n",
      "\tLoop 0\n",
      "\tnp.shape(trg_vxl_pos) (158400, 3)\n",
      "\tnp.shape(trg_vxl_idx) (158400,)\n",
      "\t1\n",
      "\ttype(db.labels_) <class 'numpy.ndarray'> dtype int64\n",
      "[0]\n",
      "cluster_analysis1\n",
      "ic_run_id 1 >>>>\n",
      "np.shape(all_vxl_pos) (158400, 3) list(set(phase_identifier) [0, 1]\n",
      "\tLoop 0\n",
      "\tnp.shape(trg_vxl_pos) (110080, 3)\n",
      "\tnp.shape(trg_vxl_idx) (110080,)\n",
      "\t1\n",
      "\ttype(db.labels_) <class 'numpy.ndarray'> dtype int64\n",
      "[0]\n",
      "\tLoop 1\n",
      "\tnp.shape(trg_vxl_pos) (48320, 3)\n",
      "\tnp.shape(trg_vxl_idx) (48320,)\n",
      "\t1\n",
      "\ttype(db.labels_) <class 'numpy.ndarray'> dtype int64\n",
      "[0]\n",
      "cluster_analysis2\n",
      "ic_run_id 2 >>>>\n",
      "np.shape(all_vxl_pos) (158400, 3) list(set(phase_identifier) [0, 1, 2]\n",
      "\tLoop 0\n",
      "\tnp.shape(trg_vxl_pos) (110080, 3)\n",
      "\tnp.shape(trg_vxl_idx) (110080,)\n",
      "\t1\n",
      "\ttype(db.labels_) <class 'numpy.ndarray'> dtype int64\n",
      "[0]\n",
      "\tLoop 1\n",
      "\tnp.shape(trg_vxl_pos) (39046, 3)\n",
      "\tnp.shape(trg_vxl_idx) (39046,)\n",
      "\t2\n",
      "\ttype(db.labels_) <class 'numpy.ndarray'> dtype int64\n",
      "[-1  0]\n",
      "\tLoop 2\n",
      "\tnp.shape(trg_vxl_pos) (9274, 3)\n",
      "\tnp.shape(trg_vxl_idx) (9274,)\n",
      "\t2\n",
      "\ttype(db.labels_) <class 'numpy.ndarray'> dtype int64\n",
      "[-1  0]\n",
      "cluster_analysis3\n",
      "ic_run_id 3 >>>>\n",
      "np.shape(all_vxl_pos) (158400, 3) list(set(phase_identifier) [0, 1, 2, 3]\n",
      "\tLoop 0\n",
      "\tnp.shape(trg_vxl_pos) (110080, 3)\n",
      "\tnp.shape(trg_vxl_idx) (110080,)\n",
      "\t1\n",
      "\ttype(db.labels_) <class 'numpy.ndarray'> dtype int64\n",
      "[0]\n",
      "\tLoop 1\n",
      "\tnp.shape(trg_vxl_pos) (39046, 3)\n",
      "\tnp.shape(trg_vxl_idx) (39046,)\n",
      "\t2\n",
      "\ttype(db.labels_) <class 'numpy.ndarray'> dtype int64\n",
      "[-1  0]\n",
      "\tLoop 2\n",
      "\tnp.shape(trg_vxl_pos) (4339, 3)\n",
      "\tnp.shape(trg_vxl_idx) (4339,)\n",
      "\t2\n",
      "\ttype(db.labels_) <class 'numpy.ndarray'> dtype int64\n",
      "[-1  0]\n",
      "\tLoop 3\n",
      "\tnp.shape(trg_vxl_pos) (4935, 3)\n",
      "\tnp.shape(trg_vxl_idx) (4935,)\n",
      "\t2\n",
      "\ttype(db.labels_) <class 'numpy.ndarray'> dtype int64\n",
      "[-1  0]\n",
      "cluster_analysis4\n",
      "ic_run_id 4 >>>>\n",
      "np.shape(all_vxl_pos) (158400, 3) list(set(phase_identifier) [0, 1, 2, 3, 4]\n",
      "\tLoop 0\n",
      "\tnp.shape(trg_vxl_pos) (110080, 3)\n",
      "\tnp.shape(trg_vxl_idx) (110080,)\n",
      "\t1\n",
      "\ttype(db.labels_) <class 'numpy.ndarray'> dtype int64\n",
      "[0]\n",
      "\tLoop 1\n",
      "\tnp.shape(trg_vxl_pos) (39046, 3)\n",
      "\tnp.shape(trg_vxl_idx) (39046,)\n",
      "\t2\n",
      "\ttype(db.labels_) <class 'numpy.ndarray'> dtype int64\n",
      "[-1  0]\n",
      "\tLoop 2\n",
      "\tnp.shape(trg_vxl_pos) (1183, 3)\n",
      "\tnp.shape(trg_vxl_idx) (1183,)\n",
      "\t5\n",
      "\ttype(db.labels_) <class 'numpy.ndarray'> dtype int64\n",
      "[-1  0  1  2  3]\n",
      "\tLoop 3\n",
      "\tnp.shape(trg_vxl_pos) (4194, 3)\n",
      "\tnp.shape(trg_vxl_idx) (4194,)\n",
      "\t2\n",
      "\ttype(db.labels_) <class 'numpy.ndarray'> dtype int64\n",
      "[-1  0]\n",
      "\tLoop 4\n",
      "\tnp.shape(trg_vxl_pos) (3897, 3)\n",
      "\tnp.shape(trg_vxl_idx) (3897,)\n",
      "\t2\n",
      "\ttype(db.labels_) <class 'numpy.ndarray'> dtype int64\n",
      "[-1  0]\n",
      "result\n",
      "sequence_index\n",
      "Inspecting CompositionSpace.Results.1.nxs...\n",
      "Found dimensionality, uint64, (), 3\n",
      "Found extent, uint64, (3,), [45 44 80]\n",
      "Found origin, float64, (3,), [-23. -20. -78.]\n",
      "Found cell_dimensions, float64, (3,), [1. 1. 1.]\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "{'ranger_reporter__ranger_report': None,\n",
       " 'xdmf__result_file': 'CompositionSpace.Results.1.nxs.xdmf',\n",
       " 'results__visualize_hdf': <jupyterlab_h5web.widget.H5Web object>}"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "wf.run()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "f3f3b4a3-1910-4e4c-983d-f86621ad6109",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "data": {
      "application/x-hdf5": "/home/kaiobach/Research/hu_hu_hu/sprint26/iuc09_dfg_demo/pyiron_apt/CompositionSpace.Results.1.nxs",
      "text/plain": [
       "<jupyterlab_h5web.widget.H5Web object>"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "wf.outputs.results__visualize_hdf.value"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "d80ba0c8-84b1-464a-b38e-98026561aa76",
   "metadata": {},
   "outputs": [],
   "source": []
  }
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