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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]]
        
        L 1 Reply Last reply
        0
        • 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

                    @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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