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  • Installing Sim4Life and configuring licenses

    35 123
    35 Topics
    123 Posts
    brynB
    I believe the Materials.db) is copied from C:\Program Files\Sim4LIfe XYZ\data\... when you first run Sim4Life.exe

  • Working with CAD models

    61 218
    61 Topics
    218 Posts
    L
    @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)

  • Working with models from the Virtual Population

    58 273
    58 Topics
    273 Posts
    brynB
    The tutorials are, unfortunately, not automatically synchronized to the cloud version yet. We can make the new ones available soon, though. Sorry for the inconvenience. If you send me an email (lloyd @ zmt.swiss), I can forward the notebook to you. Cheers, Bryn

  • FDTD, Low-Frequency, Neuron, Mode-Matching, Flow, Acoustics, etc...

    250 746
    250 Topics
    746 Posts
    brynB
    it seems to happen (in Sim4Life 9.0.0) when you switch to the analysis tag after sending a solver job on the cloud. I guess it can be ignored and will be fixed in an upcoming update-fix release

  • Postprocessing results

    116 335
    116 Topics
    335 Posts
    brynB
    Good question. The rotation of the camera around the view direction is not so easy to specify in the API. I can suggest the following workaround, in your target image the 'right' direction is negative Y cam = XRenderer.CameraSettings() # create a camera cam.Distance = 100 # instead, you could zoom to the bounding box, as shown in the Jupyter notebook examples cam.SetViewDirection(Vec3(0,0,-1), Vec3(0,-1,0)) # specify view direction and 'right' direction XRenderer.RestoreCamera(cam) # tell the GUI to use these camera settings

  • Scripting interface for Sim4Life

    137 430
    137 Topics
    430 Posts
    K
    The problem has been resolved! Thank you for your assistance!

  • Running Sim4Life over a network

    4 7
    4 Topics
    7 Posts
    ofliO
    Hi, Please allow me to share here the response we sent you via the Sim4Life support email so that other users can benefit from your questions. The default machine provides 500GB of storage, and you are running out of space for this project. If your results require more than 500GB, consider upgrading to a higher-tier machine with greater storage capacity. Alternatively, you could reduce the size of your simulation project by splitting it into multiple smaller simulations. This would allow you to continue using the default tier. Additionally, you might optimize your sensor settings, such as by creating smaller sensors and recording data for specific volumes of interest, rather than using an Overall Field sensor.
  • C

    Electrode with Nerve Model tutorial

    5
    0 Votes
    5 Posts
    231 Views
    H
    Hi @cbenj33 we are aware of the inconsistencies (we have changed the position of the nerve and electrode, which will be part of the next release happening soon). For now, I am emailing you the pdf version of this tutorial documentation and explanations regarding the errors.
  • M

    What does this mean?: Error : Geometry cache out of date, unable to continue voxeling.

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    0 Votes
    2 Posts
    250 Views
    brynB
    The voxeler (re-)uses cached information about the geometry (solids, wires, etc.). It looks up the information for each model entity and emits this message if the cached geometry was not found. Questions: are you running this in the GUI or a script/notebook? did you potentially delete (or modify) some of the entities assigned to the simulation (I guess in voxeler settings)? If you deleted the entity or modified it in the modeler (some operations preserve the instance, while others may create a new instance and delete the old one), this would explain the error. We could improve the error message by providing more helpful instructions.
  • K

    This topic is deleted!

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  • R

    Volt and sensitivity of transducer sim4lite

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    M
    Assuming a linear relation between voltage and pressure amplitude, you should be able to map the input voltage to the input pressure (I think its 1 MPa by default), and then use this as a scaling factor, but it's unclear to me what you mean with voltage at the focused area. What exactly do you mean by transducer sensitivity? You could run additional simulations where you shift the transducer or slightly change some parameters to get a sense of the sensitivity.
  • A

    How to Script the Import a Segmented NIfTI Volume as a Solid in Sim4Life?

    image model python
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    brynB
    Here is a simple implementation to write an iSEG tissue list file, given a dictionary mapping the label index to a name: https://github.com/dyollb/s4l-scripts/blob/df8e2241f87ca91d71138e9d2b3d4336dadb82dc/src/anisotropic_conductivity/load_labels.py#L44
  • vegogardenV

    This topic is deleted!

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  • J

    Cannot open .smash project file

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    J
    Thank you so much you are a godsend 🙏 You saved me a couple days worth of work!
  • L

    Heat generation rate and Heat transfer rate in a MQS/Thermal simulation

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    H
    In terms of the material settings in the thermal simulation: The heat transfer rate defines whether heat removal by perfusion should be considered. In the absence of this term, heat is only removed by thermal conduction (diffusion) and boundary conditions. The options provided for heat transfer rate affect whether perfusion is constant or affected by local thermoregulation (temperature (T) dependent perfusion, e.g., to account for vasodilation). As for the heat transfer rate, the heat generation rate term can be constant or affected by local thermoregulation (T dependent, reflecting increased metabolic activity with increasing temperature). It is also possible to introduce time-dependent heat generation, e.g., to model a heating battery. Baseline perfusion values (incl. variability information) are available in the IT'IS database and can be automatically assigned from sim4life: (http://www.itis.ethz.ch/virtual-population/tissue-properties/database/database-summary/). If non-constant perfusion should be applied or not depends on the tissue and temperature increase magnitude (e.g., muscle above 39 starts to have a strong perfusion increase). The conservativeness of a perfusion model choice is application-dependent. To simulate the heating effect of tissues over time, blood perfusion and heat generation rate (metabolic heat generation) of the tissue would also need to be considered. The perfusion is covered in the option "Heat Transfer Rate". All options that you can enter here are related to heat-transfer based removal of energy from the system. Perfusion can be adjusted by changing the type of hear transfer (None, Constant, Linear (T), Piecewise Linear (T). The constant term assumes constant perfusion, independent of tissue temperature. It is the default assigned when using the IT'IS tissue database in Sim4Life. Linear (T) or Piecewise Linear (T) assume temperature dependent perfusion. You can add your your transition temperatures using the little "+" icon. Please note that the linear coefficients represent the slope of the linear perfusion. Each transition temperature indicates the change of the perfusion rate.
  • Paria M.P

    Grid Convergence

    Solved
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    B
    To perform such a study, define your region or quantity of interest, then parametrize it. After a quantity has been parametrized, you can run multiple simulations using the built in Sweeper feature or using the Sim4Life Python API. There is an example in the Sim4Life manual titled 'Parametrized Patch Antenna' that shows how to use the Sweeper feature. If using the Python API, the easiest way would be to create a baseline simulation by hand, then right-click on the simulation name and select To Python. Then you would find the quantity of interest in the auto-generated script and assign it to a variable instead of the hardcoded value. Using a simple loop in Python, you can create multiple simulation that have identical setup except for parameters of interest. In your example, multiple simulations would be run with identical setup except for the grid resolution within a region of interest (e.g., a wire block surrounding a region of interest is placed in a manual grid settings folder, then Maximum Step is changed from 0.3 to 1.0 mm). Then in Analysis you extract a quantity of interest and compare how this value changes as a function of grid resolution. If the change in the value is small as you increase resolution, you can proceed in future simulations with a coarser resolution to save on run time. The exact convergence of the value needed depends on your application.
  • M

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  • D

    My S4L file isn't opening after it crashed

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    D
    @bryn Thank you Bryn. Managed to find a version that wasn't corrupted! Hope you have a nice day :)
  • L

    3D Surface model to Voxel and export

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    brynB
    Are you using Sim4Life lite (web version)? I recorded my screen while I voxeled Duke V2.0 and exported the voxels. There seems to be a glitch in the Reload button when I try to see the data that was saved in the Study: as a workaround the Reload button in the DATA tab works. I voxeled at 15mm, so the skin is not completely closed, but if you choose something like 5-10mm it should be enough to resolve thin layers (like the skin): BTW. if you are using a desktop version of Sim4Life, the workflow is similar, except that the software uses native Windows file dialogs to save/load files. https://youtu.be/uAQgQQpG3Bg
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  • glasshousemediaG

    This topic is deleted!

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  • A

    Simulate a concave multi-element ultrasound array

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    Assuming 'sim' is the acoustic simulation you're interested in and that 'elements' is a list of the elements (gotten from entities = model.AllEntities()) and that 'amp' and 'phase' are numpy arrays with the amplitude, phase values you're interested in assigning: # Print current simulation name print(sim.Name) # Remove all sources before adding them to_del = [] for s in sim.AllSettings: if isinstance(s,acoustic.SourceSettings): to_del.append(s) for d in to_del: sim.Remove(d) # Add sources with correct element and parameters for source_idx in np.arange(len(elements)): source_settings = acoustic.SourceSettings() source_settings.Amplitude = amp[source_idx] source_settings.Phase = phases[source_idx] sim.Add(source_settings, rings[source_idx]) print(rings[source_idx].Name, amp[source_idx], phases[source_idx]) Sorry I'm not providing a full example. Easiest way to do that would be to manually create the whole simulation without the sources (just make all sources as materials), then right click on simulation and select 'To Python...' and then add the lines above to your code You could do something like this to get the elements as a list: src_ents = [] entities = model.AllEntities() for e in entities: if 'Element' in e.Name: src_ents.append(e) Careful, I have no idea how the elements will be sorted in that case but you could use a fixed size numerical suffix and then sort them.
  • B

    File .Smash error

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    M
    Hallo, There should be, in the same folder where the smash project is, a file named as the smash file, but starting with a ".", like ".Name_of_the_File.smash.xxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxx". Try to drag that file directly into Sim4Life and save it with a different name. From there you should be able to go on with the models/simulations/analysis settings already saved.
  • L

    Cannot read document verion

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    L
    I have two versions installed (6.2.2 and 7.00) and I tried opening the file with both. I have now deleted the smash file that wasn't working and started over, but if it happens again, I will try the import option- thanks!
  • V

    Bone identification using RF signals

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  • S

    The file I created with Sim4Life light cannot be opened.

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    brynB
    If you don't have a full version, i think (untested) you can still recover the model by importing the smash file in the modeling tab.
  • P

    'Point Sensor Tool' is not available

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    M
    Sorry, don't have S4L with neuron available at the moment, but I looked at the tutorial and it seems to have changed. When you create the sensor settings can you try to drag and drop the axon to the sensor setting and then chose the section name? (That was the old way of doing it) Still, you should be able to run the simulation without a point sensor.. Sorry can't help more