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Inter results fixes #136

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merged 3 commits into from
Nov 8, 2023
Merged

Inter results fixes #136

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e2d7738
Report based on number of iters, not time
jClugstor Nov 7, 2023
3a0d115
inter result constructor to start at 0 iters
jClugstor Nov 7, 2023
537d7a9
get rid of Seconds
jClugstor Nov 7, 2023
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27 changes: 13 additions & 14 deletions src/operations.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -110,22 +110,21 @@ function amr_get(df::DataFrame, sys::ODESystem, ::Val{:data})
end

#--------------------------------------------------------------------# IntermediateResults callback
# Publish intermediate results to RabbitMQ with at least `every` seconds in between callbacks
# Publish intermediate results to RabbitMQ with at least `every` iterations in between callbacks
mutable struct IntermediateResults
last_callback::Dates.DateTime # Track the last time the callback was called
every::Dates.TimePeriod # Callback frequency e.g. `Dates.Second(5)`
last_callback::Int # Track the last iteration the callback was called
every::Int # Callback frequency
id::String
iter::Int # Track how many iterations of the calibration have happened
function IntermediateResults(id::String; every=Dates.Second(0))
new(typemin(Dates.DateTime), every, id, 0)
function IntermediateResults(id::String; every = 10)
new(0, every, id, 0)
end
end

function (o::IntermediateResults)(integrator)
if o.last_callback + o.every ≤ Dates.now()
o.last_callback = Dates.now()
(; iter, f, t, u, p) = integrator

(; iter, f, t, u, p) = integrator
if o.last_callback + o.every == iter
o.last_callback = iter
state_dict = Dict(states(f.sys) .=> u)
param_dict = Dict(parameters(f.sys) .=> p)

Expand Down Expand Up @@ -170,7 +169,7 @@ function Simulate(o::OperationRequest)
end

function get_callback(o::OperationRequest, ::Type{Simulate})
DiscreteCallback((args...) -> true, IntermediateResults(o.id,every = Dates.Second(0)))
DiscreteCallback((args...) -> true, IntermediateResults(o.id,every = 10))
end

# callback for Simulate requests
Expand All @@ -195,7 +194,7 @@ end

# callback for Calibrate requests
function get_callback(o::OperationRequest, ::Type{Calibrate})
IntermediateResults(o.id,every = Dates.Second(0))
IntermediateResults(o.id,every = 10)
end

function Calibrate(o::OperationRequest)
Expand All @@ -211,7 +210,7 @@ function Calibrate(o::OperationRequest)
if :extra in keys(o.obj)
extrakeys = keys(o.obj.extra)
:num_chains in extrakeys && (num_chains = o.obj.extra.num_chains)
:num_iterations in extrakeys && (num_iterations = o.obj.extra.num_iterations)
:num_iterations in extrakeys && (num_iterations = o.obj.extra.num_iterations) # only for bayesian?
:calibrate_method in extrakeys && (calibrate_method = o.obj.extra.calibrate_method)
end
Calibrate(sys, o.timespan, priors, data, num_chains, num_iterations, calibrate_method, ode_method)
Expand All @@ -224,8 +223,8 @@ function solve(o::Calibrate; callback)
# bayesian datafit
if o.calibrate_method == "bayesian"
p_posterior = EasyModelAnalysis.bayesian_datafit(prob, o.priors, o.data;
nchains = 2,
niter = 100,
nchains = o.num_chains,
niter = o.num_iterations,
mcmcensemble = SimulationService.EasyModelAnalysis.Turing.MCMCSerial())

pvalues = last.(p_posterior)
Expand Down
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