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Revert "added Vercise PAM files"
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This reverts commit ceff225.
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@j-zimmermann
j-zimmermann committed Sep 15, 2024
1 parent dee980b commit 9c512de
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Showing 3 changed files with 223 additions and 156 deletions.
105 changes: 29 additions & 76 deletions ...genceStudy/VTA/BostonScientificVerciseDirected/adjacent_contacts/run_convergence_study.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,6 @@

import json
import logging
import os
from copy import deepcopy

import numpy as np

Expand All @@ -20,25 +18,6 @@ def remove_file_handler(logger):
logger.removeHandler(h)


def save_input_dict(base_input_dict):
"""Save input dictionary for convergence run."""
input_dict = deepcopy(base_input_dict)
# add one layer to make sure input files get found
input_dict["MaterialDistribution"]["MRIPath"] = os.path.join(
"..", "..", input_dict["MaterialDistribution"]["MRIPath"]
)
input_dict["PointModel"]["Pathway"]["FileName"] = os.path.join(
"..", "..", input_dict["PointModel"]["Pathway"]["FileName"]
)
input_dict["PathwayFile"] = os.path.join("..", "..", input_dict["PathwayFile"])
input_dict["OutputPath"] = "./"

with open(
os.path.join(base_input_dict["OutputPath"], "input_dict.json"), "w"
) as fp:
json.dump(input_dict, fp, indent=2)


BASE_CONTACT = {
"Contact_ID": 1,
"Active": False,
Expand All @@ -52,32 +31,27 @@ def save_input_dict(base_input_dict):

electrode_name = "BostonScientificVerciseDirected"

with open("../../oss_dbs_parameters.json") as fp:
with open("../../base_settings.json") as fp:
base_input_dict = json.load(fp)


# adjust pathes
base_input_dict["MaterialDistribution"]["MRIPath"] = os.path.join(
"..", "..", base_input_dict["MaterialDistribution"]["MRIPath"]
)
base_input_dict["PointModel"]["Pathway"]["FileName"] = os.path.join(
"..", "..", base_input_dict["PointModel"]["Pathway"]["FileName"]
)
base_input_dict["PathwayFile"] = os.path.join(
"..", "..", base_input_dict["PathwayFile"]
)

# add electrode
base_input_dict["Electrodes"][0]["Name"] = electrode_name

# change contacts
base_input_dict["Electrodes"][0]["Contacts"][0]["Current[A]"] = 0.012
base_input_dict["Electrodes"][0]["Contacts"][1]["Current[A]"] = -0.004
base_input_dict["Electrodes"][0]["Contacts"][2]["Current[A]"] = -0.004
base_input_dict["Electrodes"][0]["Contacts"][3]["Current[A]"] = -0.004
# for PAM
base_input_dict["Scaling"] = 1.0
base_input_dict["ScalingIndex"] = None
# add contacts
contact_1_dict = BASE_CONTACT.copy()
contact_1_dict["Contact_ID"] = 1
contact_1_dict["Active"] = True
contact_1_dict["Voltage[V]"] = 1.0
contact_2_dict = BASE_CONTACT.copy()
contact_2_dict["Contact_ID"] = 2
contact_2_dict["Active"] = True
base_input_dict["Electrodes"][0]["Contacts"].append(contact_1_dict)
base_input_dict["Electrodes"][0]["Contacts"].append(contact_2_dict)

# update grid
base_input_dict["PointModel"]["Lattice"]["Shape"]["x"] = 60
base_input_dict["PointModel"]["Lattice"]["Shape"]["y"] = 60
base_input_dict["PointModel"]["Lattice"]["Shape"]["z"] = 120
base_input_dict["PointModel"]["Lattice"]["PointDistance[mm]"] = 0.125

# initially no adaptive refinement
base_input_dict["Mesh"]["AdaptiveMeshRefinement"] = {}
Expand All @@ -86,34 +60,26 @@ def save_input_dict(base_input_dict):
# first refinement level: Default
base_input_dict["Mesh"]["MeshingHypothesis"]["Type"] = "Default"
base_input_dict["Mesh"]["MeshingHypothesis"]["MaxMeshSize"] = 1e6
base_input_dict["OutputPath"] = "Results_PAM_default"
base_input_dict["OutputPath"] = "Results_VTA_default"
main_run(base_input_dict)
save_input_dict(base_input_dict)
ossdbs.api.run_PAM(base_input_dict)
remove_file_handler(_logger)

# second refinement level: fine assumption
base_input_dict["Mesh"]["MeshingHypothesis"]["Type"] = "Fine"
base_input_dict["OutputPath"] = "Results_PAM_fine"
base_input_dict["OutputPath"] = "Results_VTA_fine"
main_run(base_input_dict)
save_input_dict(base_input_dict)
ossdbs.api.run_PAM(base_input_dict)
remove_file_handler(_logger)

# third refinement level: very fine assumption
base_input_dict["Mesh"]["MeshingHypothesis"]["Type"] = "VeryFine"
base_input_dict["OutputPath"] = "Results_PAM_very_fine"
base_input_dict["OutputPath"] = "Results_VTA_very_fine"
main_run(base_input_dict)
save_input_dict(base_input_dict)
ossdbs.api.run_PAM(base_input_dict)
remove_file_handler(_logger)

# fourth refinement: material refinement
base_input_dict["Mesh"]["MaterialRefinementSteps"] = 2
base_input_dict["OutputPath"] = "Results_PAM_material_refinement"
base_input_dict["OutputPath"] = "Results_VTA_material_refinement"
main_run(base_input_dict)
save_input_dict(base_input_dict)
ossdbs.api.run_PAM(base_input_dict)
remove_file_handler(_logger)
# reset material refinement
base_input_dict["Mesh"]["MaterialRefinementSteps"] = 0
Expand All @@ -127,10 +93,8 @@ def save_input_dict(base_input_dict):
edge_size = perimeter / 20.0
base_input_dict["Electrodes"][0]["Contacts"][0]["MaxMeshSizeEdge"] = edge_size
base_input_dict["Electrodes"][0]["Contacts"][1]["MaxMeshSizeEdge"] = edge_size
base_input_dict["OutputPath"] = "Results_PAM_edge_refinement"
base_input_dict["OutputPath"] = "Results_VTA_edge_refinement"
main_run(base_input_dict)
save_input_dict(base_input_dict)
ossdbs.api.run_PAM(base_input_dict)
remove_file_handler(_logger)

# sixth refinement: more edge refinement
Expand All @@ -142,10 +106,8 @@ def save_input_dict(base_input_dict):
edge_size = perimeter / 50.0
base_input_dict["Electrodes"][0]["Contacts"][0]["MaxMeshSizeEdge"] = edge_size
base_input_dict["Electrodes"][0]["Contacts"][1]["MaxMeshSizeEdge"] = edge_size
base_input_dict["OutputPath"] = "Results_PAM_fine_edge_refinement"
base_input_dict["OutputPath"] = "Results_VTA_fine_edge_refinement"
main_run(base_input_dict)
save_input_dict(base_input_dict)
ossdbs.api.run_PAM(base_input_dict)
remove_file_handler(_logger)

# seventh refinement: very fine edge refinement
Expand All @@ -157,41 +119,33 @@ def save_input_dict(base_input_dict):
edge_size = perimeter / 75.0
base_input_dict["Electrodes"][0]["Contacts"][0]["MaxMeshSizeEdge"] = edge_size
base_input_dict["Electrodes"][0]["Contacts"][1]["MaxMeshSizeEdge"] = edge_size
base_input_dict["OutputPath"] = "Results_PAM_very_fine_edge_refinement"
base_input_dict["OutputPath"] = "Results_VTA_very_fine_edge_refinement"
main_run(base_input_dict)
save_input_dict(base_input_dict)
ossdbs.api.run_PAM(base_input_dict)
remove_file_handler(_logger)

# eigth refinement: edge refinement + limit on voxel size
mri_image, _ = ossdbs.load_images(base_input_dict)
max_mesh_size = 10.0 * min(mri_image.voxel_sizes)
print(f"Imposing max mesh size of: {max_mesh_size:.2f}")
base_input_dict["Mesh"]["MeshingHypothesis"]["MaxMeshSize"] = max_mesh_size
base_input_dict["OutputPath"] = "Results_PAM_edge_voxel_refinement"
base_input_dict["OutputPath"] = "Results_VTA_edge_voxel_refinement"
main_run(base_input_dict)
save_input_dict(base_input_dict)
ossdbs.api.run_PAM(base_input_dict)
remove_file_handler(_logger)

# ninth refinement: material refinement + edge refinement
base_input_dict["Mesh"]["MaterialRefinementSteps"] = 1
base_input_dict["Mesh"]["MeshingHypothesis"]["MaxMeshSize"] = 1e6
base_input_dict["OutputPath"] = "Results_PAM_edge_single_material_refinement"
base_input_dict["OutputPath"] = "Results_VTA_edge_single_material_refinement"
main_run(base_input_dict)
save_input_dict(base_input_dict)
ossdbs.api.run_PAM(base_input_dict)
remove_file_handler(_logger)
# reset material refinement
base_input_dict["Mesh"]["MaterialRefinementSteps"] = 0

# tenth refinement: material refinement + edge refinement
base_input_dict["Mesh"]["MaterialRefinementSteps"] = 2
base_input_dict["Mesh"]["MeshingHypothesis"]["MaxMeshSize"] = 1e6
base_input_dict["OutputPath"] = "Results_PAM_edge_double_material_refinement"
base_input_dict["OutputPath"] = "Results_VTA_edge_double_material_refinement"
main_run(base_input_dict)
save_input_dict(base_input_dict)
ossdbs.api.run_PAM(base_input_dict)
remove_file_handler(_logger)
# reset material refinement
base_input_dict["Mesh"]["MaterialRefinementSteps"] = 0
Expand All @@ -207,7 +161,6 @@ def save_input_dict(base_input_dict):
base_input_dict["Electrodes"][0]["Contacts"][1]["MaxMeshSizeEdge"] = edge_size
# adaptive refinement
base_input_dict["Mesh"]["AdaptiveMeshRefinement"]["Active"] = True
base_input_dict["OutputPath"] = "Results_PAM_best"

base_input_dict["OutputPath"] = "Results_VTA_best"
main_run(base_input_dict)
save_input_dict(base_input_dict)
ossdbs.api.run_PAM(base_input_dict)
165 changes: 165 additions & 0 deletions ...vergenceStudy/VTA/BostonScientificVerciseDirected/case_grounding/run_convergence_study.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1,165 @@
# gold standard:
# impedance error 0.1% and maximum element size equal
# to mesh size

import json
import logging

import numpy as np

import ossdbs
from ossdbs.main import main_run


def remove_file_handler(logger):
"""Remove file handler from logger instance."""
for h in logger.handlers:
if isinstance(h, logging.FileHandler):
logger.removeHandler(h)


BASE_CONTACT = {
"Contact_ID": 1,
"Active": False,
"Current[A]": 0.0,
"Voltage[V]": 0.0,
"Floating": False,
}

ossdbs.set_logger()
_logger = logging.getLogger("ossdbs")

electrode_name = "BostonScientificVerciseDirected"

with open("../../base_settings.json") as fp:
base_input_dict = json.load(fp)

# add electrode
base_input_dict["Electrodes"][0]["Name"] = electrode_name
# add contacts
contact_2_dict = BASE_CONTACT.copy()
contact_2_dict["Contact_ID"] = 2
contact_2_dict["Active"] = True
contact_2_dict["Voltage[V]"] = 1.0
base_input_dict["Electrodes"][0]["Contacts"].append(contact_2_dict)

# case grounding
surface_dict = {}
surface_dict["Name"] = "BrainSurface"
surface_dict["Active"] = True
surface_dict["Voltage[V]"] = 0.0
base_input_dict["Surfaces"] = [surface_dict]

# update grid
base_input_dict["PointModel"]["Lattice"]["Shape"]["x"] = 60
base_input_dict["PointModel"]["Lattice"]["Shape"]["y"] = 60
base_input_dict["PointModel"]["Lattice"]["Shape"]["z"] = 240
base_input_dict["PointModel"]["Lattice"]["PointDistance[mm]"] = 0.125

# initially no adaptive refinement
base_input_dict["Mesh"]["AdaptiveMeshRefinement"] = {}
base_input_dict["Mesh"]["AdaptiveMeshRefinement"]["Active"] = False

# first refinement level: Default
base_input_dict["Mesh"]["MeshingHypothesis"]["Type"] = "Default"
base_input_dict["Mesh"]["MeshingHypothesis"]["MaxMeshSize"] = 1e6
base_input_dict["OutputPath"] = "Results_VTA_default"
main_run(base_input_dict)
remove_file_handler(_logger)

# second refinement level: fine assumption
base_input_dict["Mesh"]["MeshingHypothesis"]["Type"] = "Fine"
base_input_dict["OutputPath"] = "Results_VTA_fine"
main_run(base_input_dict)
remove_file_handler(_logger)

# third refinement level: very fine assumption
base_input_dict["Mesh"]["MeshingHypothesis"]["Type"] = "VeryFine"
base_input_dict["OutputPath"] = "Results_VTA_very_fine"
main_run(base_input_dict)
remove_file_handler(_logger)

# fourth refinement: material refinement
base_input_dict["Mesh"]["MaterialRefinementSteps"] = 2
base_input_dict["OutputPath"] = "Results_VTA_material_refinement"
main_run(base_input_dict)
remove_file_handler(_logger)
# reset material refinement
base_input_dict["Mesh"]["MaterialRefinementSteps"] = 0

# fifth refinement: edge refinement
base_input_dict["Mesh"]["MeshingHypothesis"]["Type"] = "Default"
lead_diameter = ossdbs.electrodes.default_electrode_parameters[
electrode_name
].lead_diameter
perimeter = np.pi * lead_diameter
edge_size = perimeter / 20.0
base_input_dict["Electrodes"][0]["Contacts"][0]["MaxMeshSizeEdge"] = edge_size
base_input_dict["OutputPath"] = "Results_VTA_edge_refinement"
main_run(base_input_dict)
remove_file_handler(_logger)

# sixth refinement: more edge refinement
base_input_dict["Mesh"]["MeshingHypothesis"]["Type"] = "Default"
lead_diameter = ossdbs.electrodes.default_electrode_parameters[
electrode_name
].lead_diameter
perimeter = np.pi * lead_diameter
edge_size = perimeter / 50.0
base_input_dict["Electrodes"][0]["Contacts"][0]["MaxMeshSizeEdge"] = edge_size
base_input_dict["OutputPath"] = "Results_VTA_fine_edge_refinement"
main_run(base_input_dict)
remove_file_handler(_logger)

# seventh refinement: very fine edge refinement
base_input_dict["Mesh"]["MeshingHypothesis"]["Type"] = "Default"
lead_diameter = ossdbs.electrodes.default_electrode_parameters[
electrode_name
].lead_diameter
perimeter = np.pi * lead_diameter
edge_size = perimeter / 75.0
base_input_dict["Electrodes"][0]["Contacts"][0]["MaxMeshSizeEdge"] = edge_size
base_input_dict["OutputPath"] = "Results_VTA_very_fine_edge_refinement"
main_run(base_input_dict)
remove_file_handler(_logger)

# eigth refinement: edge refinement + limit on voxel size
mri_image, _ = ossdbs.load_images(base_input_dict)
max_mesh_size = 10.0 * min(mri_image.voxel_sizes)
print(f"Imposing max mesh size of: {max_mesh_size:.2f}")
base_input_dict["Mesh"]["MeshingHypothesis"]["MaxMeshSize"] = max_mesh_size
base_input_dict["OutputPath"] = "Results_VTA_edge_voxel_refinement"
main_run(base_input_dict)
remove_file_handler(_logger)

# ninth refinement: material refinement + edge refinement
base_input_dict["Mesh"]["MaterialRefinementSteps"] = 1
base_input_dict["Mesh"]["MeshingHypothesis"]["MaxMeshSize"] = 1e6
base_input_dict["OutputPath"] = "Results_VTA_edge_single_material_refinement"
main_run(base_input_dict)
remove_file_handler(_logger)
# reset material refinement
base_input_dict["Mesh"]["MaterialRefinementSteps"] = 0

# tenth refinement: material refinement + edge refinement
base_input_dict["Mesh"]["MaterialRefinementSteps"] = 2
base_input_dict["Mesh"]["MeshingHypothesis"]["MaxMeshSize"] = 1e6
base_input_dict["OutputPath"] = "Results_VTA_edge_double_material_refinement"
main_run(base_input_dict)
remove_file_handler(_logger)
# reset material refinement
base_input_dict["Mesh"]["MaterialRefinementSteps"] = 0

# finest level: voxel size + adaptive mesh refinement
max_mesh_size = min(mri_image.voxel_sizes)
base_input_dict["Mesh"]["MeshingHypothesis"]["MaxMeshSize"] = max_mesh_size
# one material refinement step
base_input_dict["Mesh"]["MaterialRefinementSteps"] = 1
# reset edge size
edge_size = 1e6
base_input_dict["Electrodes"][0]["Contacts"][0]["MaxMeshSizeEdge"] = edge_size
# adaptive refinement
base_input_dict["Mesh"]["AdaptiveMeshRefinement"]["Active"] = True

base_input_dict["OutputPath"] = "Results_VTA_best"
main_run(base_input_dict)
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