-
-
Notifications
You must be signed in to change notification settings - Fork 21
Add interactive reparametrization #463
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Open
sumiya11
wants to merge
5
commits into
master
Choose a base branch
from
interactive
base: master
Could not load branches
Branch not found: {{ refName }}
Loading
Could not load tags
Nothing to show
Loading
Are you sure you want to change the base?
Some commits from the old base branch may be removed from the timeline,
and old review comments may become outdated.
Open
Changes from all commits
Commits
Show all changes
5 commits
Select commit
Hold shift + click to select a range
File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
This file contains hidden or 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 |
|---|---|---|
|
|
@@ -32,3 +32,5 @@ Manifest.toml | |
| .vscode/ | ||
|
|
||
| # End of https://www.toptal.com/developers/gitignore/api/julia | ||
|
|
||
| .ipynb_checkpoints | ||
This file contains hidden or 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 hidden or 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 hidden or 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 hidden or 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 hidden or 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 | ||||
|---|---|---|---|---|---|---|
|
|
@@ -16,6 +16,13 @@ function vector_field_along(derivation::Dict{T, U}, directions::AbstractVector) | |||||
| return new_vector_field | ||||||
| end | ||||||
|
|
||||||
| function default_variable_names(new_states, new_params) | ||||||
| ( | ||||||
| states = map(i -> "X$i", 1:length(new_states)), | ||||||
| params = map(i -> "a$i", 1:length(new_params)), | ||||||
| ) | ||||||
| end | ||||||
|
|
||||||
| """ | ||||||
| reparametrize_with_respect_to(ode, new_states, new_params) | ||||||
|
|
||||||
|
|
@@ -27,7 +34,12 @@ Reparametrizes the `ode` using the given fractional states and parameters. | |||||
| - `new_states`: a vector of new states as fractions in `parent(ode)`. | ||||||
| - `new_params`: a vector of new parameters as fractions in `parent(ode)`. | ||||||
| """ | ||||||
| function reparametrize_with_respect_to(ode, new_states, new_params) | ||||||
| function reparametrize_with_respect_to( | ||||||
| ode::ODE{P}, | ||||||
| new_states, | ||||||
| new_params; | ||||||
| new_variable_names = default_variable_names(new_states, new_params), | ||||||
| ) where {P} | ||||||
| @assert length(new_states) > 0 | ||||||
| poly_ring = base_ring(parent(first(new_states))) | ||||||
| # Compute the new dynamics in terms of the original variables. | ||||||
|
|
@@ -52,7 +64,7 @@ function reparametrize_with_respect_to(ode, new_states, new_params) | |||||
| gen_tag_names(length(ode.u_vars), "Input"), | ||||||
| gen_tag_names(length(ode.y_vars), "Output"), | ||||||
| ) | ||||||
| @info """ | ||||||
| @debug """ | ||||||
| Tag names: | ||||||
| $tag_names | ||||||
| Generating functions: | ||||||
|
|
@@ -81,7 +93,7 @@ function reparametrize_with_respect_to(ode, new_states, new_params) | |||||
| if !isempty(ode.u_vars) | ||||||
| new_inputs = tag_inputs | ||||||
| end | ||||||
| @info """ | ||||||
| @debug """ | ||||||
| New state dynamics: | ||||||
| $new_dynamics_states | ||||||
| New output dynamics: | ||||||
|
|
@@ -94,14 +106,14 @@ function reparametrize_with_respect_to(ode, new_states, new_params) | |||||
| state = tags[i] | ||||||
| new_vars_vector_field[state] = new_dynamics_states[i] | ||||||
| end | ||||||
| @info "Converting variable names to human-readable ones" | ||||||
| internal_variable_names = map(i -> "X$i(t)", 1:length(new_states)) | ||||||
| parameter_variable_names = map(i -> "a$i", 1:length(new_params)) | ||||||
| @debug "Converting variable names to human-readable ones" | ||||||
| @assert length(new_variable_names.states) == length(new_states) | ||||||
| @assert length(new_variable_names.params) == length(new_params) | ||||||
| input_variable_names = map(i -> "u$i(t)", 1:length(tag_inputs)) | ||||||
| output_variable_names = map(i -> "y$i(t)", 1:length(tag_outputs)) | ||||||
| all_variable_names = vcat( | ||||||
| internal_variable_names, | ||||||
| parameter_variable_names, | ||||||
| new_variable_names.states, | ||||||
| new_variable_names.params, | ||||||
| input_variable_names, | ||||||
| output_variable_names, | ||||||
| ) | ||||||
|
|
@@ -237,3 +249,214 @@ function _reparametrize_global(ode::ODE{P}; prob_threshold = 0.99, seed = 42) wh | |||||
| new_ode = ODE{P}(new_vector_field, new_outputs, new_inputs) | ||||||
| return (new_ode = new_ode, new_vars = new_vars, implicit_relations = implicit_relations) | ||||||
| end | ||||||
|
|
||||||
| function reparametrize_interactive( | ||||||
| ode::ODE{P}; | ||||||
| prob_threshold = 0.99, | ||||||
| seed = 42, | ||||||
| loglevel = Logging.Info, | ||||||
| input::IO = stdin, | ||||||
| output::IO = stdout, | ||||||
| ) where {P} | ||||||
| restart_logging(loglevel = loglevel, stream = output) | ||||||
| with_logger(_si_logger[]) do | ||||||
| return _reparametrize_interactive(ode, prob_threshold, seed, input, output) | ||||||
| end | ||||||
| end | ||||||
|
|
||||||
| function _reparametrize_interactive( | ||||||
| ode::ODE{P}, | ||||||
| prob_threshold, | ||||||
| seed, | ||||||
| input, | ||||||
| output, | ||||||
| ) where {P} | ||||||
| Random.seed!(seed) | ||||||
| id_funcs = find_identifiable_functions( | ||||||
| ode, | ||||||
| with_states = true, | ||||||
| simplify = :strong, | ||||||
| prob_threshold = prob_threshold, | ||||||
| return_all = true, | ||||||
| loglevel = Logging.Warn, | ||||||
|
||||||
| ) | ||||||
| id_funcs_simple = find_identifiable_functions( | ||||||
| ode, | ||||||
| with_states = true, | ||||||
| simplify = :strong, | ||||||
| prob_threshold = prob_threshold, | ||||||
| loglevel = Logging.Warn, | ||||||
| ) | ||||||
| state = Dict( | ||||||
| :counter => 0, | ||||||
| :id_funcs => id_funcs, | ||||||
| :chosen_funcs => (states = empty(id_funcs), params = empty(id_funcs)), | ||||||
| :variable_names => (states = Vector{String}(), params = Vector{String}()), | ||||||
| ) | ||||||
| contains_states(poly::MPolyRingElem) = any(x -> degree(poly, x) > 0, ode.x_vars) | ||||||
| contains_states(func) = | ||||||
| contains_states(numerator(func)) || contains_states(denominator(func)) | ||||||
| function print_header(state) | ||||||
| println(output, "\n$(state[:counter]). Info.") | ||||||
| println(output, " Original states: $(join(string.(ode.x_vars), ", "))") | ||||||
| println(output, " Original parameters: $(join(string.(ode.parameters), ", "))") | ||||||
| println(output, " Identifiable functions: $(join(string.(id_funcs_simple), ", "))") | ||||||
| end | ||||||
| function print_state(state) | ||||||
| counter, chosen_funcs, variable_names = | ||||||
| state[:counter], state[:chosen_funcs], state[:variable_names] | ||||||
| if isempty(chosen_funcs.states) && isempty(chosen_funcs.params) | ||||||
| return | ||||||
| end | ||||||
| println(output, "\n$counter. Current selection:") | ||||||
| for (names, funcs) in [ | ||||||
| (variable_names.states, chosen_funcs.states), | ||||||
| (variable_names.params, chosen_funcs.params), | ||||||
| ] | ||||||
| for (name, func) in zip(names, funcs) | ||||||
| println(output, " ", name, " := ", func) | ||||||
| end | ||||||
| end | ||||||
| end | ||||||
| function make_choice(state) | ||||||
| counter, id_funcs = state[:counter], state[:id_funcs] | ||||||
| terminal = | ||||||
| REPL.TerminalMenus.default_terminal(in = input, out = output, err = output) | ||||||
| menu = MultiSelectMenu(vcat("Enter a custom function", map(string, id_funcs))) | ||||||
| choice = request( | ||||||
| terminal, | ||||||
| "\n$counter. Select identifiable function(s) for reparametrization.", | ||||||
| menu, | ||||||
| ) | ||||||
| if 1 in choice # a custom function | ||||||
| funcs = empty(id_funcs) | ||||||
| while true | ||||||
| varnames = map( | ||||||
| f -> chopsuffix(f, "(t)"), | ||||||
| string.(vcat(ode.x_vars, ode.parameters)), | ||||||
| ) | ||||||
| res = Base.prompt( | ||||||
| input, | ||||||
| output, | ||||||
| "\n$counter. Enter a rational function in the variables: $(join(varnames, ", "))\n", | ||||||
| ) | ||||||
| func = nothing | ||||||
| try | ||||||
| func = myeval( | ||||||
| Meta.parse(res), | ||||||
| Dict(Symbol.(varnames) .=> vcat(ode.x_vars, ode.parameters)), | ||||||
| ) | ||||||
| catch e | ||||||
| @info "" e | ||||||
| printstyled( | ||||||
| output, | ||||||
| "\n ==> Error when parsing $res. Trying again..\n", | ||||||
| bold = true, | ||||||
| ) | ||||||
| continue | ||||||
| end | ||||||
| ffring = fraction_field(parent(ode)) | ||||||
| funcs = [ffring(func)] | ||||||
| if all( | ||||||
| field_contains( | ||||||
| RationalFunctionField(id_funcs_simple), | ||||||
| funcs, | ||||||
| prob_threshold, | ||||||
| ), | ||||||
| ) | ||||||
| break | ||||||
| else | ||||||
| printstyled( | ||||||
| output, | ||||||
| "\n ==> The given function $(funcs[1]) is not identifiable. Trying again..\n", | ||||||
| bold = true, | ||||||
| ) | ||||||
| continue | ||||||
| end | ||||||
| end | ||||||
| else | ||||||
| funcs = id_funcs[sort(collect(choice)) .- 1] | ||||||
| end | ||||||
| funcs | ||||||
| end | ||||||
| function query_names(state, funcs) | ||||||
| counter, chosen_funcs, variable_names = | ||||||
| state[:counter], state[:chosen_funcs], state[:variable_names] | ||||||
| new_states = filter(contains_states, funcs) | ||||||
| new_params = setdiff(funcs, new_states) | ||||||
| idx_states, idx_params = length(chosen_funcs.states), length(chosen_funcs.params) | ||||||
| append!(chosen_funcs.states, new_states) | ||||||
| append!(chosen_funcs.params, new_params) | ||||||
| default_names = default_variable_names(chosen_funcs.states, chosen_funcs.params) | ||||||
| for (kind, vars, defaults, new_vars, idx) in [ | ||||||
| ("state", new_states, default_names.states, variable_names.states, idx_states), | ||||||
| ( | ||||||
| "parameter", | ||||||
| new_params, | ||||||
| default_names.params, | ||||||
| variable_names.params, | ||||||
| idx_params, | ||||||
| ), | ||||||
| ] | ||||||
| for (i, var) in enumerate(vars) | ||||||
| default = defaults[idx + i] | ||||||
| res = Base.prompt( | ||||||
| input, | ||||||
| output, | ||||||
| "\n$counter. Enter a name for the new $kind: $var. Leave empty for default: $default.\n", | ||||||
| ) | ||||||
| if isnothing(res) || (res isa String && isempty(strip(res))) | ||||||
| res = default | ||||||
| end | ||||||
| push!(new_vars, res) | ||||||
| printstyled(output, " ==> New variable: $res := $var\n", bold = true) | ||||||
| end | ||||||
| end | ||||||
| end | ||||||
| function try_to_reparametrize(state) | ||||||
| counter, chosen_funcs, variable_names, id_funcs = | ||||||
| state[:counter], state[:chosen_funcs], state[:variable_names], state[:id_funcs] | ||||||
| rff = RationalFunctionField(vcat(chosen_funcs.states, chosen_funcs.params)) | ||||||
| state[:id_funcs] = id_funcs[.! field_contains(rff, id_funcs, prob_threshold)] | ||||||
| if isempty(chosen_funcs.states) | ||||||
| printstyled( | ||||||
| output, | ||||||
| "\n ==> Please select at least one new state in order to reparametrize.\n", | ||||||
| bold = true, | ||||||
| ) | ||||||
| return nothing | ||||||
| end | ||||||
| try | ||||||
| new_vector_field, new_inputs, new_outputs, new_vars, implicit_relations = | ||||||
| reparametrize_with_respect_to( | ||||||
| ode, | ||||||
| chosen_funcs.states, | ||||||
| chosen_funcs.params, | ||||||
| new_variable_names = variable_names, | ||||||
| ) | ||||||
| new_ode = ODE{P}(new_vector_field, new_outputs, new_inputs) | ||||||
| return ( | ||||||
| new_ode = new_ode, | ||||||
| new_vars = new_vars, | ||||||
| implicit_relations = implicit_relations, | ||||||
| ) | ||||||
| catch e | ||||||
| printstyled( | ||||||
| output, | ||||||
| "\n ==> Selected functions is not enough to reparametrize. Please select more.\n", | ||||||
|
||||||
| "\n ==> Selected functions is not enough to reparametrize. Please select more.\n", | |
| "\n ==> Selected functions are not enough to reparametrize. Please select more.\n", |
Oops, something went wrong.
Oops, something went wrong.
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.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Inconsistent indentation: line 281 uses tabs while the rest of the file uses spaces. This should be changed to spaces for consistency.