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ZMT zurich med tech

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  4. The shape of the T1 image and the shape of the electric field are different

The shape of the T1 image and the shape of the electric field are different

Scheduled Pinned Locked Moved CAD Modeling
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  • brynB Offline
    brynB Offline
    bryn
    ZMT
    wrote last edited by bryn
    #9

    I sent you code (it can also be done in GUI) above to interpolate the T1w image onto the E-field/simulation grid. If you do that you can export it in the same format as you export the E-field (not as a nii.gz file, since the simulation grid is rectilinear which is not supported by nifti files).

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    • L Offline
      L Offline
      lucky_lin
      wrote last edited by lucky_lin
      #10

      @bryn Is the following code correct? I'm not sure if the input is correct.

      inputs1 = [model_to_grid_filter.Outputs[""]]
      field_data_text_exporter1 = analysis.exporters.FieldDataTextExporter(inputs=inputs1)
      field_data_text_exporter1.FileName = output_file1
      field_data_text_exporter1.UpdateAttributes()
      document.AllAlgorithms.Add(field_data_text_exporter1)
      field_data_text_exporter1.Update(overwrite=True)
      
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      • brynB Offline
        brynB Offline
        bryn
        ZMT
        wrote last edited by
        #11

        this does not include the interpolation...

        to access an output of an analysis algorithm you can use named outputs or indexed outputs, in your snippet above it may be easier to use the index '0'.

        inputs1 = [model_to_grid_filter.Outputs[0]]
        
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        • brynB bryn

          this does not include the interpolation...

          to access an output of an analysis algorithm you can use named outputs or indexed outputs, in your snippet above it may be easier to use the index '0'.

          inputs1 = [model_to_grid_filter.Outputs[0]]
          
          L Offline
          L Offline
          lucky_lin
          wrote last edited by
          #12

          @bryn Thank you!!! I'll give it a try!^^

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          • L Offline
            L Offline
            lucky_lin
            wrote last edited by lucky_lin
            #13

            @bryn After executing the code, an error occurred that prevented the export of the txt file.
            ae3e0fe4-e2a0-4c96-ba40-9524c85e6988-image.png

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            • brynB Offline
              brynB Offline
              bryn
              ZMT
              wrote last edited by
              #14

              looking at the error 'Unable to create destination file', I would guess you are trying to write to a directory that does not exist (yet) or without write permissions

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              • L Offline
                L Offline
                lucky_lin
                wrote last edited by
                #15

                However, the electric field data can be exported.
                image.png

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                • brynB Offline
                  brynB Offline
                  bryn
                  ZMT
                  wrote last edited by
                  #16

                  what does your code look like? I create the pipeline in the GUI and it seems to run fine for me (v9.0.0). The "To Python" function yields

                  # This script was auto-generated by Sim4Life version 9.0.1
                  
                  import numpy
                  import s4l_v1.analysis as analysis
                  import s4l_v1.document as document
                  import s4l_v1.model as model
                  import s4l_v1.units as units
                  from s4l_v1 import ReleaseVersion
                  from s4l_v1 import Unit
                  
                  try:
                      # Define the version to use for default values
                      ReleaseVersion.set_active(ReleaseVersion.version9_0)
                      
                      # Creating the analysis pipeline
                      # Adding a new ModelToGridFilter
                      inputs = []
                      model_to_grid_filter = analysis.core.ModelToGridFilter(inputs=inputs)
                      model_to_grid_filter.Name = "IXI025-Guys-0852-T1"
                      model_to_grid_filter.Entity = model.AllEntities()["IXI025-Guys-0852-T1"]
                      model_to_grid_filter.UpdateAttributes()
                      document.AllAlgorithms.Add(model_to_grid_filter)
                  
                      # Adding a new SimulationExtractor
                      simulation = document.AllSimulations["EM"]
                      simulation_extractor = simulation.Results()
                  
                      # Adding a new EmSensorExtractor
                      em_sensor_extractor = simulation_extractor["Overall Field"]
                      em_sensor_extractor.FrequencySettings.ExtractedFrequency = u"All"
                      document.AllAlgorithms.Add(em_sensor_extractor)
                  
                      # Adding a new FieldInterpolationFilter
                      inputs = [model_to_grid_filter.Outputs[0], em_sensor_extractor.Outputs["EM E(x,y,z,f0)"]]
                      field_interpolation_filter = analysis.core.FieldInterpolationFilter(inputs=inputs)
                      field_interpolation_filter.UpdateAttributes()
                      document.AllAlgorithms.Add(field_interpolation_filter)
                  
                      # Adding a new FieldDataTextExporter
                      inputs = [field_interpolation_filter.Outputs[""]]
                      field_data_text_exporter = analysis.exporters.FieldDataTextExporter(inputs=inputs)
                      field_data_text_exporter.FileName = u"D:\\temp\\ExportedFieldData-T1w.txt"
                      field_data_text_exporter.UpdateAttributes()
                      document.AllAlgorithms.Add(field_data_text_exporter)
                  
                  except Exception as exc:
                      import traceback
                      traceback.print_exc()
                      # Reset active version to default
                      ReleaseVersion.reset()
                      raise(exc)
                  
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                  • L Offline
                    L Offline
                    lucky_lin
                    wrote last edited by lucky_lin
                    #17
                    This post is deleted!
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                    • brynB Offline
                      brynB Offline
                      bryn
                      ZMT
                      wrote last edited by
                      #18

                      your code is still not using the FieldInterpolationFilter to interpolate the T1w image onto the same grid as the E-field. Note, the FieldDataTextExporter takes the output of the interpolator as input

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