-
Notifications
You must be signed in to change notification settings - Fork 4
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* Add hp refinement * refactor AdaptiveMeshRefinement * add examples --------- Co-authored-by: Kenichi Maeda <[email protected]> Co-authored-by: JPPayonk <[email protected]> Co-authored-by: Julius Zimmermann <[email protected]>
- Loading branch information
4 people
authored
Aug 30, 2024
1 parent
89a857b
commit 640584c
Showing
10 changed files
with
303 additions
and
74 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
117 changes: 117 additions & 0 deletions
117
examples/MeshAPI/BrainVerciseMesh_AdaptiveMeshRefinement.py
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,117 @@ | ||
| """ | ||
| Example of a full model geometry | ||
| with one Vercise electrode without | ||
| encapsulation layer. | ||
| The mesh is generated and adaptive | ||
| refinement is used. | ||
| """ | ||
| import logging | ||
|
|
||
| import ngsolve | ||
| from ngsolve import Draw | ||
|
|
||
| import ossdbs | ||
| from ossdbs.api import ( | ||
| create_bounding_box, | ||
| generate_electrodes, | ||
| load_images, | ||
| prepare_dielectric_properties, | ||
| prepare_solver, | ||
| prepare_stimulation_signal, | ||
| prepare_volume_conductor_model, | ||
| run_volume_conductor_model, | ||
| set_contact_and_encapsulation_layer_properties, | ||
| ) | ||
| from ossdbs.fem import ConductivityCF | ||
| from ossdbs.model_geometry import BrainGeometry, ModelGeometry | ||
| from ossdbs.utils.settings import Settings | ||
|
|
||
| ossdbs.set_logger(logging.INFO) | ||
|
|
||
| input_settings = { | ||
| "BrainRegion": { | ||
| "Center": {"x[mm]": -9.48, "y[mm]": 11.61, "z[mm]": 4.68}, | ||
| "Dimension": {"x[mm]": 40.0, "y[mm]": 40.0, "z[mm]": 40.0}, | ||
| "Shape": "Ellipsoid", | ||
| }, | ||
| "Electrodes": [ | ||
| { | ||
| "Name": "BostonScientificVercise", | ||
| "Rotation[Degrees]": 0, | ||
| "Direction": {"x[mm]": 0, "y[mm]": 0, "z[mm]": 1}, | ||
| "TipPosition": {"x[mm]": -9.48, "y[mm]": 11.61, "z[mm]": 4.68}, | ||
| "EncapsulationLayer": {"Thickness[mm]": 0.0}, | ||
| "Contacts": [ | ||
| { | ||
| "Contact_ID": 1, | ||
| "Active": True, | ||
| "Voltage[V]": 1.0, | ||
| }, | ||
| { | ||
| "Contact_ID": 3, | ||
| "Active": True, | ||
| "Voltage[V]": 0.0, | ||
| }, | ||
| ], | ||
| }, | ||
| ], | ||
| "MaterialDistribution": {"MRIPath": "../../input_files/Butenko_segmask.nii.gz"}, | ||
| "Mesh": { | ||
| "AdaptiveMeshRefinement": { | ||
| "Active": True, | ||
| "MaxIterations": 2, | ||
| "ErrorTolerance": 0.1, | ||
| }, | ||
| "HPRefinement": { | ||
| "Active": False, | ||
| "Levels": 2, | ||
| "Factor": 0.125, | ||
| }, | ||
| }, | ||
| "StimulationSignal": { | ||
| "Type": "Multisine", | ||
| "ListOfFrequencies": [1000.0], | ||
| }, | ||
| "ComputeImpedance": True, | ||
| } | ||
|
|
||
| settings = Settings(input_settings).complete_settings() | ||
|
|
||
| mri_image, dti_image = load_images(settings) | ||
|
|
||
| electrodes = generate_electrodes(settings) | ||
|
|
||
| brain_region = create_bounding_box(settings["BrainRegion"]) | ||
| brain_model = BrainGeometry(settings["BrainRegion"]["Shape"], brain_region) | ||
|
|
||
| geometry = ModelGeometry(brain_model, electrodes) | ||
|
|
||
| set_contact_and_encapsulation_layer_properties(settings, geometry) | ||
| dielectric_properties = prepare_dielectric_properties(settings) | ||
| materials = settings["MaterialDistribution"]["MRIMapping"] | ||
|
|
||
| conductivity = ConductivityCF( | ||
| mri_image, | ||
| brain_region, | ||
| dielectric_properties, | ||
| materials, | ||
| geometry.encapsulation_layers, | ||
| complex_data=settings["EQSMode"], | ||
| dti_image=dti_image, | ||
| ) | ||
|
|
||
| mesh = ossdbs.generate_mesh(settings) | ||
|
|
||
| with ngsolve.TaskManager(): | ||
| solver = prepare_solver(settings) | ||
| volume_conductor = prepare_volume_conductor_model( | ||
| settings, geometry, conductivity, solver | ||
| ) | ||
| frequency_domain_signal = prepare_stimulation_signal(settings) | ||
|
|
||
| run_volume_conductor_model(settings, volume_conductor, frequency_domain_signal) | ||
|
|
||
| print("Number of elements before refinement:", mesh.ngsolvemesh.ne) | ||
| print("Number of elements after refinement:", volume_conductor.mesh.ngsolvemesh.ne) | ||
| print("Number degrees of freedom:", ngsolve.H1(volume_conductor.mesh.ngsolvemesh).ndof) | ||
| Draw(volume_conductor.mesh.ngsolvemesh) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| """ | ||
| Example of a full model geometry | ||
| with one Vercise electrode without | ||
| encapsulation layer. | ||
| The mesh is generated and then | ||
| refined at one surface. | ||
| """ | ||
| from ngsolve import Draw | ||
|
|
||
| import ossdbs | ||
|
|
||
| settings = { | ||
| "BrainRegion": { | ||
| "Center": {"x[mm]": -9.48, "y[mm]": 11.61, "z[mm]": 4.68}, | ||
| "Dimension": {"x[mm]": 40.0, "y[mm]": 40.0, "z[mm]": 40.0}, | ||
| "Shape": "Ellipsoid", | ||
| }, | ||
| "Electrodes": [ | ||
| { | ||
| "Name": "BostonScientificVercise", | ||
| "Rotation[Degrees]": 0, | ||
| "Direction": {"x[mm]": 0, "y[mm]": 0, "z[mm]": 1}, | ||
| "TipPosition": {"x[mm]": -9.48, "y[mm]": 11.61, "z[mm]": 4.68}, | ||
| "EncapsulationLayer": {"Thickness[mm]": 0.0}, | ||
| "Contacts": [ | ||
| { | ||
| "Contact_ID": 1, | ||
| "Active": True, | ||
| "Voltage[V]": 1.0, | ||
| }, | ||
| { | ||
| "Contact_ID": 3, | ||
| "Active": True, | ||
| "Voltage[V]": 0.0, | ||
| }, | ||
| ], | ||
| }, | ||
| ], | ||
| "Mesh": { | ||
| "LoadMesh": False, | ||
| "SaveMesh": False, | ||
| "AdaptiveMeshRefinement": { | ||
| "Active": False, | ||
| "MaxIterations": 2, | ||
| "ErrorTolerance": 0.1, | ||
| }, | ||
| "HPRefinement": { | ||
| "Active": True, | ||
| "Levels": 2, | ||
| "Factor": 0.125, | ||
| }, | ||
| }, | ||
| "ExportElectrode": False, | ||
| } | ||
|
|
||
| hp_mesh = ossdbs.generate_mesh(settings) | ||
| Draw(hp_mesh.ngsolvemesh) | ||
|
|
||
| settings["Mesh"]["HPRefinement"]["Active"] = False | ||
| mesh = ossdbs.generate_mesh(settings) | ||
|
|
||
| print("Number of elements before refinement:", mesh.ngsolvemesh.ne) | ||
| print("Number of elements after refinement:", hp_mesh.ngsolvemesh.ne) |
Oops, something went wrong.