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ZMT zurich med tech

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  2. Sim4Life
  3. Analysis & Postprocessing
  4. Understand the h5 file structure

Understand the h5 file structure

Scheduled Pinned Locked Moved Analysis & Postprocessing
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  • S Offline
    S Offline
    Seif_Elkerdany
    wrote last edited by
    #1

    After running the simulation the results are saved on my computer as h5 file so I want to understand how the sensor readings are stored in the h5 file.
    I want to extract the current density value per voxel. Is it feasible if I have the result h5 file?

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    • brynB Offline
      brynB Offline
      bryn
      ZMT
      wrote last edited by
      #2

      The current density is computed on the fly in the sensor extractor in Sim4Life. It is not stored in the .h5 file.

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      • brynB Offline
        brynB Offline
        bryn
        ZMT
        wrote last edited by bryn
        #3

        to get the current density in Python you could use a script like

        import s4l_v1.document as document
        
        try:
            # add a SimulationExtractor for the simulation call "LF"
            simulation = document.AllSimulations["LF"]
            simulation_extractor = simulation.Results()
        
            # create an EmSensorExtractor
            em_sensor_extractor = simulation_extractor["Overall Field"]
            em_sensor_extractor.FrequencySettings.ExtractedFrequency = u"All"
            document.AllAlgorithms.Add(em_sensor_extractor)
        
            # update the pipeline, make sure current density is extracted
            em_sensor_extractor.Outputs["J(x,y,z,f0)"].Update()
        
            # get data
            current_density_field = em_sensor_extractor.Outputs["J(x,y,z,f0)"].Data
        
        except Exception as exc:
            import traceback
            traceback.print_exc()
        
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