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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
    #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.

      1 Reply Last reply
      0
      • 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)
          
          1 Reply Last reply
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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

                  1 Reply Last reply
                  0
                  • L Offline
                    L Offline
                    lucky_lin
                    wrote last edited by
                    #15

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

                    1 Reply Last reply
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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)
                      
                      1 Reply Last reply
                      0
                      • 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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