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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 bryn

    what do you mean by "The T1 and the electric field seem to be in opposite directions along the x-axis"?

    • the interpolated T1 image and the E-field?
    • is the interpolated T1 image NOT shown in the same position/orientation as the original T1 image from the modeler?
    • is the original T1 image (which you imported in the modeler) aligned/shown in the same position/orientation as the model?

    It would help if you would add screenshots to your question, with explanations of what each screenshot is trying to demonstrate.

    L Offline
    L Offline
    lucky_lin
    wrote last edited by
    #6

    @bryn What I mean is that the slice with index 0 in the T1 image and the slice with index 1 in the electric field are not on the same side of the head model along the x-axis. Additionally, I would like to know if it is possible to export the interpolated T1 image. I need the T1 structural image that corresponds to the simulated electric field to create a dataset.
    c2b26fe5-7cd7-465e-9e27-81b29b410516-image.png 8c9a6f68-03be-4d1c-8a88-8ce3eab8c903-image.png

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    • brynB Offline
      brynB Offline
      bryn
      ZMT
      wrote last edited by
      #7

      but are you using a slice field viewer to show the interpolated MRI slice? If not you basically are looking at the original MRI, with different grid and data ordering.

      L 1 Reply Last reply
      0
      • brynB bryn

        but are you using a slice field viewer to show the interpolated MRI slice? If not you basically are looking at the original MRI, with different grid and data ordering.

        L Offline
        L Offline
        lucky_lin
        wrote last edited by
        #8

        @bryn I don't know how to use the slice viewer to inspect the T1 image. I just want to export it.

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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]]
              
              L 1 Reply Last reply
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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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                      0
                      • 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

                          @bryn This is my code, I use v8.2.2

                          def run_simulation(value1, value2):
                              print(f"Running simulation for values: {value1}_{value2}")
                          
                              # Define the version to use for default values
                              # s2=time.time()
                          
                          #simulation
                              # Creating the simulation
                              simulation1 = emlf.ElectroQsOhmicSimulation()
                              simulation1.Name =f"{value1}_{value2}"
                          
                              # Mapping the components and entities
                              component__plane_x = simulation1.AllComponents["Plane X+"]
                              component__plane_x = simulation1.AllComponents["Plane X-"]
                              component__background = simulation1.AllComponents["Background"]
                              component__plane_y = simulation1.AllComponents["Plane Y+"]
                              component__plane_y = simulation1.AllComponents["Plane Y-"]
                              component__plane_z = simulation1.AllComponents["Plane Z+"]
                              component__plane_z = simulation1.AllComponents["Plane Z-"]
                              component__overall_field = simulation1.AllComponents["Overall Field"]
                          
                              entity_0 = model.AllEntities()["Cz_Cylinder 1"]
                              entity_1 = model.AllEntities()["Fpz_Cylinder 1"]
                              entity_2 = model.AllEntities()["Fp1_Cylinder 1"]
                              entity_3 = model.AllEntities()["AF7_Cylinder 1"]
                              entity_4 = model.AllEntities()["F7_Cylinder 1"]
                              entity_5 = model.AllEntities()["FT7_Cylinder 1"]
                              entity_6 = model.AllEntities()["T7_Cylinder 1"]
                              entity_7 = model.AllEntities()["TP7_Cylinder 1"]
                              entity_8 = model.AllEntities()["P7_Cylinder 1"]
                              entity_9 = model.AllEntities()["PO7_Cylinder 1"]
                              entity_10 = model.AllEntities()["O1_Cylinder 1"]
                              entity_11 = model.AllEntities()["Oz_Cylinder 1"]
                              entity_12 = model.AllEntities()["O2_Cylinder 1"]
                              entity_13 = model.AllEntities()["PO8_Cylinder 1"]
                              entity_14 = model.AllEntities()["P8_Cylinder 1"]
                              entity_15 = model.AllEntities()["TP8_Cylinder 1"]
                              entity_16 = model.AllEntities()["T8_Cylinder 1"]
                              entity_17 = model.AllEntities()["FT8_Cylinder 1"]
                              entity_18 = model.AllEntities()["F8_Cylinder 1"]
                              entity_19 = model.AllEntities()["AF8_Cylinder 1"]
                              entity_20 = model.AllEntities()["Fp2_Cylinder 1"]
                              entity_21 = model.AllEntities()["AFz_Cylinder 1"]
                              entity_22 = model.AllEntities()["AF3_Cylinder 1"]
                              entity_23 = model.AllEntities()["F5_Cylinder 1"]
                              entity_24 = model.AllEntities()["FC5_Cylinder 1"]
                              entity_25 = model.AllEntities()["C5_Cylinder 1"]
                              entity_26 = model.AllEntities()["CP5_Cylinder 1"]
                              entity_27 = model.AllEntities()["P5_Cylinder 1"]
                              entity_28 = model.AllEntities()["PO3_Cylinder 1"]
                              entity_29 = model.AllEntities()["POz_Cylinder 1"]
                              entity_30 = model.AllEntities()["PO4_Cylinder 1"]
                              entity_31 = model.AllEntities()["P6_Cylinder 1"]
                              entity_32 = model.AllEntities()["CP6_Cylinder 1"]
                              entity_33= model.AllEntities()["C6_Cylinder 1"]
                              entity_34 = model.AllEntities()["FC6_Cylinder 1"]
                              entity_35 = model.AllEntities()["F6_Cylinder 1"]
                              entity_36 = model.AllEntities()["AF4_Cylinder 1"]
                              entity_37 = model.AllEntities()["Fz_Cylinder 1"]
                              entity_38 = model.AllEntities()["F1_Cylinder 1"]
                              entity_39 = model.AllEntities()["F3_Cylinder 1"]
                              entity_40 = model.AllEntities()["FC3_Cylinder 1"]
                              entity_41 = model.AllEntities()["C3_Cylinder 1"]
                              entity_42 = model.AllEntities()["CP3_Cylinder 1"]
                              entity_43 = model.AllEntities()["P3_Cylinder 1"]
                              entity_44 = model.AllEntities()["P1_Cylinder 1"]
                              entity_45 = model.AllEntities()["Pz_Cylinder 1"]
                              entity_46 = model.AllEntities()["P2_Cylinder 1"]
                              entity_47 = model.AllEntities()["P4_Cylinder 1"]
                              entity_48 = model.AllEntities()["CP4_Cylinder 1"]
                              entity_49 = model.AllEntities()["C4_Cylinder 1"]
                              entity_50 = model.AllEntities()["FC4_Cylinder 1"]
                              entity_51 = model.AllEntities()["F4_Cylinder 1"]
                              entity_52 = model.AllEntities()["F2_Cylinder 1"]
                              entity_53 = model.AllEntities()["FCz_Cylinder 1"]
                              entity_54 = model.AllEntities()["FC1_Cylinder 1"]
                              entity_55 = model.AllEntities()["C1_Cylinder 1"]
                              entity_56 = model.AllEntities()["CP1_Cylinder 1"]
                              entity_57 = model.AllEntities()["CPz_Cylinder 1"]
                              entity_58 = model.AllEntities()["CP2_Cylinder 1"]
                              entity_59 = model.AllEntities()["C2_Cylinder 1"]
                              entity_60 = model.AllEntities()["FC2_Cylinder 1"]
                              entity__bone_cortical = model.AllEntities()["Bone_cortical"]
                              entity__vein = model.AllEntities()["Vein"]
                              entity__other_tissues = model.AllEntities()["Other_tissues"]
                              entity__nerve_cranial_ii_optic = model.AllEntities()["Nerve_cranial_II_optic"]
                              entity__muscle_ocular = model.AllEntities()["Muscle_ocular"]
                              entity__bone_cancellous = model.AllEntities()["Bone_cancellous"]
                              entity__spinal_cord = model.AllEntities()["Spinal_cord"]
                              entity__skin = model.AllEntities()["Skin"]
                              entity__cerebrum_white_matter = model.AllEntities()["Cerebrum_white_matter"]
                              entity__eyes = model.AllEntities()["Eyes"]
                              entity__air_internal = model.AllEntities()["Air_internal"]
                              entity__mucosa = model.AllEntities()["Mucosa"]
                              entity__cerebrospinal_fluid = model.AllEntities()["Cerebrospinal_fluid"]
                              entity__dura = model.AllEntities()["Dura"]
                              entity__artery = model.AllEntities()["Artery"]
                              entity__cerebrum_grey_matter = model.AllEntities()["Cerebrum_grey_matter"]
                          
                              # 创建一个映射表,将数字索引与实体名称关联起来
                              entity_mapping = {
                                  0: "Cz_Cylinder 1",
                                  1: "Fpz_Cylinder 1",
                                  2: "Fp1_Cylinder 1",
                                  3: "AF7_Cylinder 1",
                                  4: "F7_Cylinder 1",
                                  5: "FT7_Cylinder 1",
                                  6: "T7_Cylinder 1",
                                  7: "TP7_Cylinder 1",
                                  8: "P7_Cylinder 1",
                                  9: "PO7_Cylinder 1",
                                  10: "O1_Cylinder 1",
                                  11: "Oz_Cylinder 1",
                                  12: "O2_Cylinder 1",
                                  13: "PO8_Cylinder 1",
                                  14: "P8_Cylinder 1",
                                  15: "TP8_Cylinder 1",
                                  16: "T8_Cylinder 1",
                                  17: "FT8_Cylinder 1",
                                  18: "F8_Cylinder 1",
                                  19: "AF8_Cylinder 1",
                                  20: "Fp2_Cylinder 1",
                                  21: "AFz_Cylinder 1",
                                  22: "AF3_Cylinder 1",
                                  23: "F5_Cylinder 1",
                                  24: "FC5_Cylinder 1",
                                  25: "C5_Cylinder 1",
                                  26: "CP5_Cylinder 1",
                                  27: "P5_Cylinder 1",
                                  28: "PO3_Cylinder 1",
                                  29: "POz_Cylinder 1",
                                  30: "PO4_Cylinder 1",
                                  31: "P6_Cylinder 1",
                                  32: "CP6_Cylinder 1",
                                  33: "C6_Cylinder 1",
                                  34: "FC6_Cylinder 1",
                                  35: "F6_Cylinder 1",
                                  36: "AF4_Cylinder 1",
                                  37: "Fz_Cylinder 1",
                                  38: "F1_Cylinder 1",
                                  39: "F3_Cylinder 1",
                                  40: "FC3_Cylinder 1",
                                  41: "C3_Cylinder 1",
                                  42: "CP3_Cylinder 1",
                                  43: "P3_Cylinder 1",
                                  44: "P1_Cylinder 1",
                                  45: "Pz_Cylinder 1",
                                  46: "P2_Cylinder 1",
                                  47: "P4_Cylinder 1",
                                  48: "CP4_Cylinder 1",
                                  49: "C4_Cylinder 1",
                                  50: "FC4_Cylinder 1",
                                  51: "F4_Cylinder 1",
                                  52: "F2_Cylinder 1",
                                  53: "FCz_Cylinder 1",
                                  54: "FC1_Cylinder 1",
                                  55: "C1_Cylinder 1",
                                  56: "CP1_Cylinder 1",
                                  57: "CPz_Cylinder 1",
                                  58: "CP2_Cylinder 1",
                                  59: "C2_Cylinder 1",
                                  60: "FC2_Cylinder 1"
                              }
                          
                              # 确保输入的值是整数类型
                              value1 = int(value1)
                              value2 = int(value2)
                              # 根据输入的数字索引获取对应的实体名称
                              entity_name1 = entity_mapping.get(value1)
                              entity_name2 = entity_mapping.get(value2)
                          
                              # 检查实体名称是否存在
                              if entity_name1 is None:
                                  raise KeyError(f"Entity for value {value1} does not exist")
                              if entity_name2 is None:
                                  raise KeyError(f"Entity for value {value2} does not exist")
                          
                              # 获取对应的实体对象
                              entity_value1 = model.AllEntities()[entity_name1]
                              entity_value2 = model.AllEntities()[entity_name2]
                          
                              # 打印结果,确认是否正确
                              print(f"Entity for value1 ({value1}): {entity_value1}")
                              print(f"Entity for value2 ({value2}): {entity_value2}")
                          
                              # Editing QuasiStaticSetupSettings "Setup
                              quasi_static_setup_settings = [x for x in simulation1.AllSettings if isinstance(x, emlf.QuasiStaticSetupSettings) and x.Name == "Setup"][0]
                              quasi_static_setup_settings.Frequency = 2000.0, units.Hz
                          
                              # Adding a new MaterialSettings
                              material_settings = emlf.MaterialSettings()
                              components = [entity__skin]
                              mat = database["IT'IS LF 4.2"]["Skin"]
                              if mat is not None:
                                  simulation1.LinkMaterialWithDatabase(material_settings, mat)
                              else:
                                  # Fallback if material is not found
                                  material_settings.Name = "Skin"
                                  material_settings.MassDensity = 1109.0, Unit("kg/m^3")
                                  material_settings.ElectricProps.Conductivity = 0.1482971014492752, Unit("S/m")
                                  material_settings.ElectricProps.RelativePermittivity = 1135.619382618975
                              simulation1.Add(material_settings, components)
                          
                              # Adding a new MaterialSettings
                              material_settings = emlf.MaterialSettings()
                              components = [entity__air_internal]
                              mat = database["IT'IS LF 4.2"]["Air"]
                              if mat is not None:
                                  simulation1.LinkMaterialWithDatabase(material_settings, mat)
                              else:
                                  # Fallback if material is not found
                                  material_settings.Name = "Air 1"
                                  material_settings.MassDensity = 1.164091552938177, Unit("kg/m^3")
                              material_settings.Name = "Air 1"
                              simulation1.Add(material_settings, components)
                          
                              # Adding a new MaterialSettings
                              material_settings = emlf.MaterialSettings()
                              components = [entity__cerebrospinal_fluid]
                              mat = database["IT'IS LF 4.2"]["Cerebrospinal Fluid"]
                              if mat is not None:
                                  simulation1.LinkMaterialWithDatabase(material_settings, mat)
                              else:
                                  # Fallback if material is not found
                                  material_settings.Name = "Cerebrospinal Fluid"
                                  material_settings.MassDensity = 1007.0, Unit("kg/m^3")
                                  material_settings.ElectricProps.Conductivity = 1.878999709695023, Unit("S/m")
                                  material_settings.ElectricProps.RelativePermittivity = 108.9999972649334
                              simulation1.Add(material_settings, components)
                          
                              # Adding a new MaterialSettings
                              material_settings = emlf.MaterialSettings()
                              components = [entity__cerebrum_white_matter]
                              mat = database["IT'IS LF 4.2"]["Brain (White Matter)"]
                              if mat is not None:
                                  simulation1.LinkMaterialWithDatabase(material_settings, mat)
                              else:
                                  # Fallback if material is not found
                                  material_settings.Name = "Brain (White Matter)"
                                  material_settings.MassDensity = 1041.0, Unit("kg/m^3")
                                  material_settings.ElectricProps.Conductivity = 0.3479543931346832, Unit("S/m")
                                  material_settings.ElectricProps.RelativePermittivity = 69810.68883114036
                              simulation1.Add(material_settings, components)
                          
                              # Adding a new MaterialSettings
                              material_settings = emlf.MaterialSettings()
                              components = [entity__mucosa]
                              mat = database["IT'IS LF 4.2"]["Mucous Membrane"]
                              if mat is not None:
                                  simulation1.LinkMaterialWithDatabase(material_settings, mat)
                              else:
                                  # Fallback if material is not found
                                  material_settings.Name = "Mucous Membrane"
                                  material_settings.MassDensity = 1102.0, Unit("kg/m^3")
                                  material_settings.ElectricProps.Conductivity = 0.4610075264456888, Unit("S/m")
                                  material_settings.ElectricProps.RelativePermittivity = 434932.19242741907
                              simulation1.Add(material_settings, components)
                          
                              # Adding a new MaterialSettings
                              material_settings = emlf.MaterialSettings()
                              components = [entity__dura]
                              mat = database["IT'IS LF 4.2"]["Dura"]
                              if mat is not None:
                                  simulation1.LinkMaterialWithDatabase(material_settings, mat)
                              else:
                                  # Fallback if material is not found
                                  material_settings.Name = "Dura"
                                  material_settings.MassDensity = 1174.0, Unit("kg/m^3")
                                  material_settings.ElectricProps.Conductivity = 0.06, Unit("S/m")
                                  material_settings.ElectricProps.RelativePermittivity = 5343.990898234167
                              simulation1.Add(material_settings, components)
                          
                              # Adding a new MaterialSettings
                              material_settings = emlf.MaterialSettings()
                              components = [entity__eyes]
                              mat = database["IT'IS LF 4.2"]["Eye (Aqueous Humor)"]
                              if mat is not None:
                                  simulation1.LinkMaterialWithDatabase(material_settings, mat)
                              else:
                                  # Fallback if material is not found
                                  material_settings.Name = "Eye (Aqueous Humor)"
                                  material_settings.MassDensity = 993.7770167788401, Unit("kg/m^3")
                                  material_settings.ElectricProps.Conductivity = 1.878999709695023, Unit("S/m")
                                  material_settings.ElectricProps.RelativePermittivity = 108.9999972649334
                              simulation1.Add(material_settings, components)
                          
                              # Adding a new MaterialSettings
                              material_settings = emlf.MaterialSettings()
                              components = [entity__artery, entity__vein]
                              mat = database["IT'IS LF 4.2"]["Blood"]
                              if mat is not None:
                                  simulation1.LinkMaterialWithDatabase(material_settings, mat)
                              else:
                                  # Fallback if material is not found
                                  material_settings.Name = "Blood"
                                  material_settings.MassDensity = 1049.75, Unit("kg/m^3")
                                  material_settings.ElectricProps.Conductivity = 0.6624597361833767, Unit("S/m")
                                  material_settings.ElectricProps.RelativePermittivity = 5258.608390020375
                              simulation1.Add(material_settings, components)
                          
                              # Adding a new MaterialSettings
                              material_settings = emlf.MaterialSettings()
                              components = [entity__spinal_cord]
                              mat = database["IT'IS LF 4.2"]["Spinal Cord"]
                              if mat is not None:
                                  simulation1.LinkMaterialWithDatabase(material_settings, mat)
                              else:
                                  # Fallback if material is not found
                                  material_settings.Name = "Spinal Cord"
                                  material_settings.MassDensity = 1075.0, Unit("kg/m^3")
                                  material_settings.ElectricProps.Conductivity = 0.6109538492063492, Unit("S/m")
                                  material_settings.ElectricProps.RelativePermittivity = 69911.4914652573
                              simulation1.Add(material_settings, components)
                          
                              # Adding a new MaterialSettings
                              material_settings = emlf.MaterialSettings()
                              components = [entity__nerve_cranial_ii_optic]
                              mat = database["IT'IS LF 4.2"]["Nerve"]
                              if mat is not None:
                                  simulation1.LinkMaterialWithDatabase(material_settings, mat)
                              else:
                                  # Fallback if material is not found
                                  material_settings.Name = "Nerve"
                                  material_settings.MassDensity = 1075.0, Unit("kg/m^3")
                                  material_settings.ElectricProps.Conductivity = 0.3479543931346832, Unit("S/m")
                                  material_settings.ElectricProps.RelativePermittivity = 69911.4914652573
                              simulation1.Add(material_settings, components)
                          
                              # Adding a new MaterialSettings
                              material_settings = emlf.MaterialSettings()
                              components = [entity__muscle_ocular]
                              mat = database["IT'IS LF 4.2"]["Muscle"]
                              if mat is not None:
                                  simulation1.LinkMaterialWithDatabase(material_settings, mat)
                              else:
                                  # Fallback if material is not found
                                  material_settings.Name = "Muscle"
                                  material_settings.MassDensity = 1090.4, Unit("kg/m^3")
                                  material_settings.ElectricProps.Conductivity = 0.4610075264456888, Unit("S/m")
                                  material_settings.ElectricProps.RelativePermittivity = 434932.19242741907
                              simulation1.Add(material_settings, components)
                          
                              # Adding a new MaterialSettings
                              material_settings = emlf.MaterialSettings()
                              components = [entity__bone_cortical]
                              mat = database["IT'IS LF 4.2"]["Bone (Cortical)"]
                              if mat is not None:
                                  simulation1.LinkMaterialWithDatabase(material_settings, mat)
                              else:
                                  # Fallback if material is not found
                                  material_settings.Name = "Bone (Cortical)"
                                  material_settings.MassDensity = 1908.0, Unit("kg/m^3")
                                  material_settings.ElectricProps.Conductivity = 0.00630199709513435, Unit("S/m")
                                  material_settings.ElectricProps.RelativePermittivity = 2702.3711256306647
                              simulation1.Add(material_settings, components)
                          
                              # Adding a new MaterialSettings
                              material_settings = emlf.MaterialSettings()
                              components = [entity__cerebrum_grey_matter]
                              mat = database["IT'IS LF 4.2"]["Brain (Grey Matter)"]
                              if mat is not None:
                                  simulation1.LinkMaterialWithDatabase(material_settings, mat)
                              else:
                                  # Fallback if material is not found
                                  material_settings.Name = "Brain (Grey Matter)"
                                  material_settings.MassDensity = 1044.5, Unit("kg/m^3")
                                  material_settings.ElectricProps.Conductivity = 0.4190548817650446, Unit("S/m")
                                  material_settings.ElectricProps.RelativePermittivity = 164062.99316639948
                              simulation1.Add(material_settings, components)
                          
                              # Adding a new MaterialSettings
                              material_settings = emlf.MaterialSettings()
                              components = [entity__other_tissues]
                              material_settings.ElectricProps.Conductivity = 0.087, Unit("S/m")
                              simulation1.Add(material_settings, components)
                          
                              # Adding a new MaterialSettings
                              material_settings = emlf.MaterialSettings()
                              components = [entity__bone_cancellous]
                              mat = database["IT'IS LF 4.2"]["Bone (Cancellous)"]
                              if mat is not None:
                                  simulation1.LinkMaterialWithDatabase(material_settings, mat)
                              else:
                                  # Fallback if material is not found
                                  material_settings.Name = "Bone (Cancellous)"
                                  material_settings.MassDensity = 1178.333333333333, Unit("kg/m^3")
                                  material_settings.ElectricProps.Conductivity = 0.08045952772338552, Unit("S/m")
                                  material_settings.ElectricProps.RelativePermittivity = 12320.035797440474
                              simulation1.Add(material_settings, components)
                          
                              # Editing BoundarySettings "Boundary Settings
                              boundary_settings = [x for x in simulation1.AllSettings if isinstance(x, emlf.BoundarySettings) and x.Name == "Boundary Settings"][0]
                              components = [component__plane_x, component__plane_x, component__plane_y, component__plane_y, component__plane_z, component__plane_z]
                              simulation1.Add(boundary_settings, components)
                              boundary_settings.BoundaryType = boundary_settings.BoundaryType.enum.Flux
                          
                              # Adding a new BoundarySettings
                              boundary_settings = emlf.BoundarySettings()
                              components = [entity_value1]
                              boundary_settings.Name = "Boundary Settings 1"
                              boundary_settings.DirichletValue = 1.0, units.Volts
                              simulation1.Add(boundary_settings, components)
                          
                              # Adding a new BoundarySettings
                              boundary_settings = emlf.BoundarySettings()
                              components = [entity_value2]
                              boundary_settings.Name = "Boundary Settings 2"
                              boundary_settings.DirichletValue = -1.0, units.Volts
                              simulation1.Add(boundary_settings, components)
                          
                              # Editing GlobalGridSettings "Grid (Empty)
                              global_grid_settings = simulation1.GlobalGridSettings
                              global_grid_settings.PaddingMode = global_grid_settings.PaddingMode.enum.Manual
                              global_grid_settings.BottomPadding = numpy.array([0.0, 0.0, 0.0]), units.MilliMeters
                              global_grid_settings.TopPadding = numpy.array([0.0, 0.0, 0.0]), units.MilliMeters
                          
                              # Adding a new ManualGridSettings
                              manual_grid_settings = simulation1.AddManualGridSettings([entity_0, entity_1, entity_2,entity_3,entity_4,entity_5,entity_6,entity_7,entity_8,entity_9,entity_10,
                                                                                        entity_11,entity_12,entity_13,entity_14,entity_15,entity_16,entity_17,entity_18,entity_19,entity_20,
                                                                                        entity_21,entity_22,entity_23,entity_24,entity_25,entity_26,entity_27,entity_28,entity_29,entity_30,
                                                                                        entity_31,entity_32,entity_33,entity_34,entity_35,entity_36,entity_37,entity_38,entity_39,entity_40,
                                                                                        entity_41,entity_42,entity_43,entity_44,entity_45,entity_46,entity_47,entity_48,entity_49,entity_50,
                                                                                        entity_51,entity_52,entity_53,entity_54,entity_55,entity_56,entity_57,entity_58,entity_59,entity_60])
                              manual_grid_settings.MaxStep = numpy.array([1.0, 1.0, 1.0]), units.MilliMeters
                              manual_grid_settings.Resolution = numpy.array([0.3, 0.3, 0.3]), units.MilliMeters
                              manual_grid_settings.Priority = 0.0
                          
                              # Adding a new ManualGridSettings
                              manual_grid_settings = simulation1.AddManualGridSettings([entity__air_internal, entity__artery, entity__bone_cancellous, entity__bone_cortical, entity__cerebrospinal_fluid, entity__cerebrum_grey_matter, entity__cerebrum_white_matter, entity__dura, entity__eyes, entity__mucosa, entity__muscle_ocular, entity__nerve_cranial_ii_optic, entity__other_tissues, entity__skin, entity__spinal_cord, entity__vein])
                              manual_grid_settings.MaxStep = numpy.array([1.0, 1.0, 1.0]), units.MilliMeters
                              manual_grid_settings.Resolution = numpy.array([0.3, 0.3, 0.3]), units.MilliMeters
                              manual_grid_settings.Priority = 0.0
                          
                              # Editing AutomaticVoxelerSettings "Automatic Voxeler Settings
                              automatic_voxeler_settings = [x for x in simulation1.AllSettings if isinstance(x, emlf.AutomaticVoxelerSettings) and x.Name == "Automatic Voxeler Settings"][0]
                              components = [entity__air_internal, entity__artery, entity__bone_cancellous, entity__bone_cortical, entity__cerebrospinal_fluid, entity__cerebrum_grey_matter, entity__cerebrum_white_matter, entity__dura, entity__eyes, entity__mucosa, entity__muscle_ocular, entity__nerve_cranial_ii_optic, entity__other_tissues, entity__skin, entity__spinal_cord, entity__vein]
                              simulation1.Add(automatic_voxeler_settings, components)
                              automatic_voxeler_settings.Priority = 1
                          
                              # Adding a new AutomaticVoxelerSettings
                              automatic_voxeler_settings = emlf.AutomaticVoxelerSettings()
                              #components = [entity_f5__cylinder1, entity_p5__cylinder1]
                          
                              components = [entity_value1, entity_value2]
                              automatic_voxeler_settings.Name = "electrodes"
                              simulation1.Add(automatic_voxeler_settings, components)
                              automatic_voxeler_settings.Priority = 0
                          
                              # Editing SolverSettings "Solver
                              solver_settings = simulation1.SolverSettings
                              solver_settings.NumberOfProcesses = 2
                          
                              # Update the materials with the new frequency parameters
                              simulation1.UpdateAllMaterials()
                          
                              # Update the grid with the new parameters
                              simulation1.UpdateGrid()
                          
                              #
                              simulation1.CreateVoxels(r"F:\Huilin\sim4life_pro\script\head_TI\head_TI-4.smash")
                          
                              # Add the simulation to the UI
                              document.AllSimulations.Add( simulation1 )
                              simulation1.RunSimulation(wait=True)
                          
                              # Output directory
                              output_dir = r"G:\MHL\TI_head\IXI025\interprate\tacs_2000Hz"
                          
                              # Output file
                              output_file1 = os.path.join(output_dir, f"{value1}_{value2}.txt")
                              output_file2 = os.path.join(output_dir, f"{value1}_{value2}_T1_interpolation.txt")
                          
                              # Add a new ModelToGridFilter
                              inputs = []
                              model_to_grid_filter = analysis.core.ModelToGridFilter(inputs=inputs)
                              model_to_grid_filter.Name = "Image"
                              model_to_grid_filter.Entity = model.AllEntities()["IXI025-Guys-0852-T1"]  # The model entity corresponding to the T1w-image
                              model_to_grid_filter.UpdateAttributes()
                          
                              simulation1 = document.AllSimulations[f"{value1}_{value2}"]
                              simulation_extractor1 = simulation1.Results()
                          
                              # Adding a new EmSensorExtractor
                              em_sensor_extractor1 = simulation_extractor1["Overall Field"]
                              em_sensor_extractor1.FrequencySettings.ExtractedFrequency = u"All"
                              document.AllAlgorithms.Add(em_sensor_extractor1)
                          
                              # Adding a new CurrentExtractor
                              inputs1 = [em_sensor_extractor1.Outputs["EM Potential(x,y,z,f0)"], em_sensor_extractor1.Outputs["J(x,y,z,f0)"]]
                              current_extractor1 = analysis.extractors.CurrentExtractor(inputs=inputs1)
                              current_extractor1.IsoSurfacePerCentThreshold = 30
                              current_extractor1.UpdateAttributes()
                              document.AllAlgorithms.Add(current_extractor1)
                          
                              # Adding a new DataTableHTMLViewer
                              output1 = current_extractor1.Outputs["Total Flux(J(x,y,z,f0))"]
                              output1.Update()
                              comp1 = output1.Data.GetComponent(0)
                              flux1 = np.real(comp1)[0]
                          
                              inputs1 = [em_sensor_extractor1.Outputs["EM E(x,y,z,f0)"]]
                              user_defined_field_normalizer1 = analysis.field.UserDefinedFieldNormalizer(inputs=inputs1)
                              user_defined_field_normalizer1.Target.Value = 1.0 / (flux1 * 1000)
                              user_defined_field_normalizer1.Name = f"{value1}_{value2}"
                              user_defined_field_normalizer1.UpdateAttributes()
                              document.AllAlgorithms.Add(user_defined_field_normalizer1)
                          
                              # Adding a new FieldDataTextExporter
                              inputs1 = [user_defined_field_normalizer1.Outputs["EM E(x,y,z,f0)"]]
                              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)
                          
                              inputs2 = [model_to_grid_filter.Outputs[0]]
                              field_data_text_exporter2 = analysis.exporters.FieldDataTextExporter(inputs=inputs2)
                              field_data_text_exporter2.FileName = output_file2
                              field_data_text_exporter2.UpdateAttributes()
                              document.AllAlgorithms.Add(field_data_text_exporter2)
                              field_data_text_exporter2.Update(overwrite=True)
                          
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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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