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Multiple point models refactor #12

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merged 24 commits into from
Feb 3, 2024
Merged

Multiple point models refactor #12

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4bc6b4c
cleaning of electrodes code
j-zimmermann Jan 13, 2024
48478d6
further code quality fixes
j-zimmermann Jan 13, 2024
f316686
fix example
j-zimmermann Jan 13, 2024
38ce0b7
fix code style in lead-dbs interface
j-zimmermann Jan 13, 2024
54c0e09
Merge branch 'LeadDBS_integration' into multiple_point_models_refactor
j-zimmermann Jan 17, 2024
6778915
move point model part from VCM
j-zimmermann Jan 18, 2024
1f26d2f
fix tuple
j-zimmermann Jan 19, 2024
0e26e29
fix frequency index
j-zimmermann Jan 19, 2024
7775318
fix field export
j-zimmermann Jan 19, 2024
8fa3a31
fix frequency index, run all tests
j-zimmermann Jan 21, 2024
a1833a5
export only real-valued data
j-zimmermann Jan 21, 2024
e62aebe
switch TimeDomain evaluation off for lattice and voxel lattice
j-zimmermann Jan 21, 2024
5284aa4
add more output
j-zimmermann Jan 21, 2024
da8581f
fix csv export
j-zimmermann Jan 21, 2024
228423a
print export frequency
j-zimmermann Jan 21, 2024
fca5f5e
always export
j-zimmermann Jan 23, 2024
fe4612e
first step towards new data structure
j-zimmermann Jan 28, 2024
316ea3b
first draft OOC
j-zimmermann Jan 30, 2024
0b54966
remove dask
j-zimmermann Jan 31, 2024
8352932
remove index and update name of pathway output
j-zimmermann Jan 31, 2024
4954306
fix VTA
j-zimmermann Feb 1, 2024
a2b3876
fix complex-number issue with h5py
j-zimmermann Feb 3, 2024
5601021
Merge branch 'LeadDBS_integration' into multiple_point_models_refactor
j-zimmermann Feb 3, 2024
8702d44
fix bug after merge and update manifest
j-zimmermann Feb 3, 2024
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1 change: 1 addition & 0 deletions MANIFEST.in
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Original file line number Diff line number Diff line change
Expand Up @@ -15,4 +15,5 @@ recursive-include input_files *.h5
recursive-include input_files *.json
recursive-include input_test_cases *.json
recursive-include input_test_cases *.md
recursive-include input_test_cases *.sh
recursive-include ossdbs *.py
101 changes: 52 additions & 49 deletions examples/MeshAPI/BrainVerciseMesh_SetMeshSizes.py
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Expand Up @@ -7,57 +7,60 @@
into account during the meshing
process.
"""
from ngsolve import Draw

import ossdbs
from ngsolve import Draw, Redraw

settings = \
{"Electrodes":
[{"Name": "BostonScientificVercise",
"Rotation[Degrees]": 0,
"Direction": {"x[mm]": 0, "y[mm]": 0, "z[mm]": 1},
"TipPosition": {"x[mm]": 0, "y[mm]": 0, "z[mm]": 0},
"EncapsulationLayer":
{"Thickness[mm]": 0.0, # indicates that no encapsulation is modelled
},
"Contacts":
[{"Contact_ID": 1,
"Active": True,
"Current[A]": 0.0,
"Voltage[V]": 1.0,
"Floating": False,
"SurfaceImpedance[Ohmm]": {"real": 0.0, "imag": 0.0},
"MaxMeshSizeEdge": 0.05
},
{"Contact_ID": 3,
"Active": True,
"Current[A]": 0.0,
"Voltage[V]": 0.0,
"Floating": False,
"SurfaceImpedance[Ohmm]": {"real": 0.0, "imag": 0.0},
"MaxMeshSizeEdge": 0.05
settings = {
"Electrodes": [
{
"Name": "BostonScientificVercise",
"Rotation[Degrees]": 0,
"Direction": {"x[mm]": 0, "y[mm]": 0, "z[mm]": 1},
"TipPosition": {"x[mm]": 0, "y[mm]": 0, "z[mm]": 0},
"EncapsulationLayer": {
"Thickness[mm]": 0.0, # indicates that no encapsulation is modelled
},
{"Contact_ID": 5,
"Active": False,
"Current[A]": 0.0,
"Voltage[V]": 0.0,
"Floating": False,
"SurfaceImpedance[Ohmm]": {"real": 0.0, "imag": 0.0},
"MaxMeshSize": 0.1
}]
}],
"MaterialDistribution":
{"MRIPath": "../BrainGeometryAPI/segmask.nii.gz"
},
"BrainRegion":
{"Center": {"x[mm]": 5, "y[mm]": 14, "z[mm]": -4.5},
"Dimension": {"x[mm]": 50.0, "y[mm]": 50.0, "z[mm]": 50.0},
"Shape": "Ellipsoid"
},
"Mesh":
{"LoadMesh": False,
"SaveMesh": False
}
}
"Contacts": [
{
"Contact_ID": 1,
"Active": True,
"Current[A]": 0.0,
"Voltage[V]": 1.0,
"Floating": False,
"SurfaceImpedance[Ohmm]": {"real": 0.0, "imag": 0.0},
"MaxMeshSizeEdge": 0.05,
},
{
"Contact_ID": 3,
"Active": True,
"Current[A]": 0.0,
"Voltage[V]": 0.0,
"Floating": False,
"SurfaceImpedance[Ohmm]": {"real": 0.0, "imag": 0.0},
"MaxMeshSizeEdge": 0.05,
},
{
"Contact_ID": 5,
"Active": False,
"Current[A]": 0.0,
"Voltage[V]": 0.0,
"Floating": False,
"SurfaceImpedance[Ohmm]": {"real": 0.0, "imag": 0.0},
"MaxMeshSize": 0.1,
},
],
}
],
"MaterialDistribution": {"MRIPath": "../BrainGeometryAPI/segmask.nii.gz"},
"BrainRegion": {
"Center": {"x[mm]": 5, "y[mm]": 14, "z[mm]": -4.5},
"Dimension": {"x[mm]": 50.0, "y[mm]": 50.0, "z[mm]": 50.0},
"Shape": "Ellipsoid",
},
"Mesh": {"LoadMesh": False, "SaveMesh": False},
"ExportElectrode": False,
}

mesh = ossdbs.generate_mesh(settings)
print(mesh.boundaries)
Expand All @@ -68,6 +71,6 @@

bnd_dict = {}
for idx in range(1, 9):
bnd_dict["E1C{}".format(idx)] = idx
bnd_dict[f"E1C{idx}"] = idx

Draw(mesh.boundary_coefficients(bnd_dict), mesh.ngsolvemesh, "bnd")
86 changes: 42 additions & 44 deletions examples/MeshAPI/BrainVerciseMesh_SetMeshSizes_Encap.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,53 +7,51 @@
into account during the meshing
process.
"""
from ngsolve import Draw

import ossdbs
from ngsolve import Draw, Redraw

ossdbs.set_logger()

settings = \
{"Electrodes":
[{"Name": "BostonScientificVercise",
"Rotation[Degrees]": 0,
"Direction": {"x[mm]": 0, "y[mm]": 0, "z[mm]": 1},
"TipPosition": {"x[mm]": 0, "y[mm]": 0, "z[mm]": 0},
"EncapsulationLayer":
{"Thickness[mm]": 1.0,
"MaxMeshSize": 0.2
},
"Contacts":
[{"Contact_ID": 1,
"Active": True,
"Current[A]": 0.0,
"Voltage[V]": 1.0,
"Floating": False,
"SurfaceImpedance[Ohmm]": {"real": 0.0, "imag": 0.0},
"MaxMeshSizeEdge": 0.05
},
{"Contact_ID": 3,
"Active": True,
"Current[A]": 0.0,
"Voltage[V]": 0.0,
"Floating": False,
"SurfaceImpedance[Ohmm]": {"real": 0.0, "imag": 0.0},
"MaxMeshSizeEdge": 0.05
}]
},
],
"MaterialDistribution":
{"MRIPath": "../BrainGeometryAPI/segmask.nii.gz"
},
"BrainRegion":
{"Center": {"x[mm]": 5, "y[mm]": 14, "z[mm]": -4.5},
"Dimension": {"x[mm]": 50.0, "y[mm]": 50.0, "z[mm]": 50.0},
"Shape": "Ellipsoid"
},
"Mesh":
{"LoadMesh": False,
"SaveMesh": False
}
}
settings = {
"Electrodes": [
{
"Name": "BostonScientificVercise",
"Rotation[Degrees]": 0,
"Direction": {"x[mm]": 0, "y[mm]": 0, "z[mm]": 1},
"TipPosition": {"x[mm]": 0, "y[mm]": 0, "z[mm]": 0},
"EncapsulationLayer": {"Thickness[mm]": 1.0, "MaxMeshSize": 0.2},
"Contacts": [
{
"Contact_ID": 1,
"Active": True,
"Current[A]": 0.0,
"Voltage[V]": 1.0,
"Floating": False,
"SurfaceImpedance[Ohmm]": {"real": 0.0, "imag": 0.0},
"MaxMeshSizeEdge": 0.05,
},
{
"Contact_ID": 3,
"Active": True,
"Current[A]": 0.0,
"Voltage[V]": 0.0,
"Floating": False,
"SurfaceImpedance[Ohmm]": {"real": 0.0, "imag": 0.0},
"MaxMeshSizeEdge": 0.05,
},
],
},
],
"MaterialDistribution": {"MRIPath": "../BrainGeometryAPI/segmask.nii.gz"},
"BrainRegion": {
"Center": {"x[mm]": 5, "y[mm]": 14, "z[mm]": -4.5},
"Dimension": {"x[mm]": 50.0, "y[mm]": 50.0, "z[mm]": 50.0},
"Shape": "Ellipsoid",
},
"Mesh": {"LoadMesh": False, "SaveMesh": False},
"ExportElectrode": False,
}

mesh = ossdbs.generate_mesh(settings)
print(mesh.boundaries)
Expand All @@ -64,6 +62,6 @@

bnd_dict = {}
for idx in range(1, 9):
bnd_dict["E1C{}".format(idx)] = idx
bnd_dict[f"E1C{idx}"] = idx

Draw(mesh.boundary_coefficients(bnd_dict), mesh.ngsolvemesh, "bnd")
13 changes: 7 additions & 6 deletions input_test_cases/input_case4/input_multi_current.json
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Original file line number Diff line number Diff line change
Expand Up @@ -30,23 +30,24 @@
{
"Contact_ID": 1,
"Active": true,
"Current[A]": -0.003
"Current[A]": -0.003,
"Voltage[V]": 0
},
{
"Contact_ID": 2,
"Active": true,
"Floating": true,
"Current[A]": 0.001
}
,
{
"Contact_ID": 3,
"Active": true,
"Floating": true,
"Current[A]": 0.001
}
,
{
"Contact_ID": 4,
"Active": true,
"Floating": true,
"Current[A]": 0.001
}
],
Expand Down Expand Up @@ -97,7 +98,7 @@
"Solver": {
"Type": "CG",
"Preconditioner": "bddc",
"PreconditionerKwargs": {},
"PreconditionerKwargs": {"coarsetype": "local"},
"PrintRates": true,
"MaximumSteps": 200,
"Precision": 1e-8
Expand Down Expand Up @@ -133,4 +134,4 @@
"ComputeImpedance": false,
"ExportVTK": true,
"ExportElectrode": true
}
}
2 changes: 1 addition & 1 deletion input_test_cases/input_case7/input_vta.json
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Original file line number Diff line number Diff line change
Expand Up @@ -127,4 +127,4 @@
"ComputeImpedance": true,
"ExportVTK": true,
"ExportElectrode": true
}
}
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