Geselowitz ECG + Poisson reconstruction #85
Conversation
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 was
linked to
issues
Feb 11, 2024
AbdAlazezAhmed
changed the title
Comment on lines
+94
to
+99
|
|
||
| ecg_reconst_cache = Thunderbolt.Potse2006ECGPoissonReconstructionCache(problem, κ, κ) | ||
|
|
||
| u = zeros(Thunderbolt.solution_size(problem.A)) | ||
|
|
||
| κ = ConstantCoefficient(SymmetricTensor{2,3,Float64}((1.0, 0, 0, 1.0, 0, 1.0))) |
There was a problem hiding this comment.
Suggested change
| ecg_reconst_cache = Thunderbolt.Potse2006ECGPoissonReconstructionCache(problem, κ, κ) | |
| u = zeros(Thunderbolt.solution_size(problem.A)) | |
| κ = ConstantCoefficient(SymmetricTensor{2,3,Float64}((1.0, 0, 0, 1.0, 0, 1.0))) | |
| ecg_reconst_cache = Thunderbolt.Potse2006ECGPoissonReconstructionCache(problem, κ, κ) | |
| u = zeros(Thunderbolt.solution_size(problem.A)) | |
| κ = ConstantCoefficient(SymmetricTensor{2,3,Float64}((1.0, 0, 0, 1.0, 0, 1.0))) |
Comment on lines
+239
to
+251
| author="Ogiermann, Dennis | ||
| and Balzani, Daniel | ||
| and Perotti, Luigi E.", | ||
| editor="Ennis, Daniel B. | ||
| and Perotti, Luigi E. | ||
| and Wang, Vicky Y.", | ||
| title="The Effect of Modeling Assumptions on the ECG in Monodomain and Bidomain Simulations", | ||
| booktitle="Functional Imaging and Modeling of the Heart", | ||
| year="2021", | ||
| publisher="Springer International Publishing", | ||
| address="Cham", | ||
| pages="503--514", | ||
| isbn="978-3-030-78710-3" |
| (0.0, 50.0), | ||
| steady_state_initializer, | ||
| iocb_ | ||
| ) |
| @@ -54,6 +54,7 @@ struct ConstantCoefficient{T} | |||
| val::T | |||
| end | |||
|
|
|||
| Base.:(-)(cc::ConstantCoefficient) = ConstantCoefficient(-cc.val) | |||
There was a problem hiding this comment.
Why? I am not sure if we should do this, because this might be error prone for users (and internals).
| @@ -137,6 +138,8 @@ end | |||
| @inline _eval_sdt_coefficient(M::SVector{MS}, λ::SVector{λS}) where {MS, λS} = error("Incompatible dimensions! dim(M)=$MS dim(λ)=$λS") | |||
| @inline _eval_sdt_coefficient(M::SVector{rdim,<:Vec{sdim}}, λ::SVector{rdim}) where {rdim,sdim} = sum(i->λ[i] * M[i] ⊗ M[i], 1:rdim; init=zero(Tensor{2,sdim})) | |||
|
|
|||
| Base.:(-)(cc::SpectralTensorCoefficient) = SpectralTensorCoefficient(-cc.eigenvalues, cc.eigenvectors) | |||
|
|
||
| The important simplifications taken are: | ||
| 1. Surrounding volume is an infinite, homogeneous sphere with isotropic conductivity | ||
| 2. The extracellular space and surrounding volume share the same isotropic, homogeneous conductivity tensor | ||
| """ | ||
| struct Plonsey1964ECGGaussCache{BUF, CV, G} | ||
| struct Plonsey1964ECGGaussCache{BUF, CV, DH <: DofHandler, κT} |
There was a problem hiding this comment.
Suggested change
| struct Plonsey1964ECGGaussCache{BUF, CV, DH <: DofHandler, κT} | |
| struct Plonsey1964ECGGaussCache{BUF, CV, DH <: AbstractDofHandler, κT} |
Maybe?
| f = zeros(ndofs(dh_Z)) | ||
| v = zeros(size(Z,1)) | ||
|
|
||
| integrator = BilinearDiffusionIntegrator(-κ) |
There was a problem hiding this comment.
You can alternatively change the sign of the right hand side.
Comment on lines
+127
to
+129
| function _compute_lead_field(f, ∇Z, Z, op, p, electrodes::AbstractArray{Vec{3, T}}) where T | ||
| _add_electrode(f, op.dh, electrodes[1], true) | ||
| _add_electrode(f, op.dh, electrodes[2], false) |
There was a problem hiding this comment.
Do we need to add the electrodes every time?
Also, since we need 2 electrodes at a time why not simply a static array?
| function _compute_lead_field(f, ∇Z, Z, op, p, electrodes::AbstractArray{Vec{3, T}}) where T | ||
| _add_electrode(f, op.dh, electrodes[1], true) | ||
| _add_electrode(f, op.dh, electrodes[2], false) | ||
| (temp, _) = Krylov.cg(op.A,f, M=p, ldiv = true) |
There was a problem hiding this comment.
We should check for convergence failure here. Also, you can solve inplcae with Krylov.jl https://jso.dev/Krylov.jl/dev/solvers/spd/#Krylov.cg! .
| as proposed in [PotDubRicVinGul:2006:cmb](@cite) and mentioned in [OgiBalPer:2021:ema](@cite). Where κ is the bulk conductivity tensor, and κᵢ is the intracellular conductivity tensor. The cache includes the assembled | ||
| stiffness matrix with applied homogeneous Dirichlet boundary condition at the first vertex of the mesh. As the problem is solved for each timestep with only the right hand side changing. | ||
|
|
||
| TODO: Implement [BisPla:2011:bes](@cite) to improve the precision. |
There was a problem hiding this comment.
Is there some specific blocker for this?
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
For #71 and #72