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Add animation documentation
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Mo8it
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65
README.adoc
65
README.adoc
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@ -1,4 +1,6 @@
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= ReCo.jl
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:source-highlighter: highlight.js
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:highlightjs-languages: bash, julia
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image:https://img.shields.io/badge/code%20style-blue-4495d1.svg[Code Style: Blue, link=https://github.com/invenia/BlueStyle]
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@ -12,7 +14,7 @@ The steps from the setup have to be followed before running anything in the foll
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To activate the environment, navigate to the main directory `/ReCo.jl` and then run the following to launch Julia:
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[source, bash]
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[source,bash]
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----
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cd ReCo.jl
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julia --threads auto
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@ -20,11 +22,11 @@ julia --threads auto
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`auto` automatically sets the number of threads to use. If you want to use a specific number `N` of threads, replace `auto` with `N`.
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=== Acitivating environment
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=== Activating environment
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After launching Julia, the package environment has to be activated by running the follwing in the REPL:
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[source, julia]
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[source,julia]
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----
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using Pkg
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Pkg.activate(".")
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@ -32,9 +34,9 @@ Pkg.activate(".")
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=== Install dependencies
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After activating the package environment, run the follwing to install the package dependencies:
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After activating the package environment, run the following to install the package dependencies:
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[source, julia]
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[source,julia]
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----
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Pkg.instantiate()
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----
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@ -43,36 +45,47 @@ Pkg.instantiate()
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You can import the package by running:
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[source, julia]
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[source,julia]
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----
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using ReCo
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----
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This will export the package methods that are intended to be used by the end user.
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This will export the package's methods that are intended to be used by the end user.
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== Help mode
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To access the documentation of the presented package methods further in this README, run `using ReCo` first. Then, enter the help mode by pressing `?` in the REPL. Now, enter the method's name followed by enter to see its documentation.
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== Run simulation
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Initialize a simulation with 100 particles having a self-propulsion velocity of 40.0 and return the relative path to the simulation directory:
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[source, julia]
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[source,julia]
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----
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sim_dir = init_sim(100, 40.0)
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----
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Run the simulation:
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[source, julia]
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[source,julia]
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----
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run_sim(sim_dir, duration=20.0)
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----
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The values for the number of particles, self-propulsion velocity and simulation duration are used here as an example. For more information about possible values and other optional arguments, press `?` in the REPL after running `using ReCo`. Then type `init_sim` or `run_sim` followed by pressing enter. This will show the method's documention.
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The values for the number of particles, self-propulsion velocity and simulation duration are used here as an example. For more information about possible values and other optional arguments, see the documentation of `init_sim` or `run_sim`.
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== Simulation visualization
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=== Animation
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//TODO
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To generate an animation of a simulation, run the following:
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[source,julia]
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----
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animate(sim_dir)
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----
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The method's documentation includes all possible optional arguments.
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=== Snapshot plot
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@ -81,50 +94,56 @@ The values for the number of particles, self-propulsion velocity and simulation
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== Run reinforcement learning
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Run a reinforcement learning process and return the environment helper and the the path of the process directory relative to the directory `ReCo.jl`:
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[source, julia]
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[source,julia]
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----
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env_helper, rl_dir = run_rl(ENVTYPE)
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----
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ENVTYPE has to be replaced by one of the environments named after the file names in the directory `ReCo.jl/RL/Envs`, for example: `LocalCOMEnv`. A description of an environment is included at the beginning of the corresponding file.
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`ENVTYPE` has to be replaced by one of the environments named after the file names in the directory `ReCo.jl/RL/Envs`, for example: `LocalCOMEnv`. A description of an environment is included at the beginning of the corresponding file.
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//TODO: Descriptions of envs
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For more information about all possible optional arguments, press `?` in the REPL after running `using ReCo`. Then type `run_rl` followed by pressing enter.
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The documentation of `run_rl` includes all possible optional arguments.
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=== Q-matrix
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`env_helper` has the abstract type `EnvHelper`. To access the Q-matrix, enter the following:
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[source, julia]
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[source,julia]
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----
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env_helper.shared.agent.policy.learner.approximator.table
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----
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To generate a LaTeX table with the states and actions combintation names for the Q-matrix, run the follwing:
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[source, julia]
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[source,julia]
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----
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include("src/RL/latex_table.jl")
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latex_rl_table(env_helper, FILENAME)
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----
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FILENAME has to be replaced by the wanted file name of the `.tex` file. This file can then be found under `ReCo.jl/exports/FILENAME`.
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`FILENAME` has to be replaced by the wanted file name without extension of the `.tex` file. This file can then be found under `ReCo.jl/exports/FILENAME.tex`.
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=== Rewards
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To access the rewards, run the following:
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[source, julia]
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[source,julia]
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----
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env_helper.shared.hook.rewards
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----
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To plot the rewards, run the following:
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[source, julia]
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[source,julia]
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----
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plot_rewards(rl_dir)
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----
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=== Mean kappa
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To plot the mean of kappa as the ratio of the eigenvalues of the gyration tensor, run the following:
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[source, julia]
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[source,julia]
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----
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include("analysis/mean_kappa.jl")
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plot_mean_kappa(; rl_dir=rl_dir, n_last_episodes=N_LAST_EPISODES)
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@ -134,11 +153,11 @@ plot_mean_kappa(; rl_dir=rl_dir, n_last_episodes=N_LAST_EPISODES)
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== Run analysis
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After running the following command blocks in the REPL, the output can be found in the directory `exports/graphics`.
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After running the following command blocks in the REPL, the output can be found in the directory `ReCo.jl/exports/graphics`.
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=== Mean squared displacement
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[source, julia]
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[source,julia]
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----
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include("analysis/mean_squared_displacement.jl")
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run_msd_analysis()
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@ -147,7 +166,7 @@ run_random_walk()
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=== Radial distribution function
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[source, julia]
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[source,julia]
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----
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include("analysis/radial_distribution_function/radial_distribution_function.jl")
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run_radial_distribution_analysis()
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@ -11,7 +11,7 @@ function latex_table(
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return nothing
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end
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function latex_rl_table(env_helper, filename::String)
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function latex_rl_table(env_helper, filename_without_extension::String)
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table = copy(env_helper.shared.agent.policy.learner.approximator.table)
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for col in 1:size(table)[2]
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@ -40,7 +40,7 @@ function latex_rl_table(env_helper, filename::String)
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df = DataFrames.DataFrame(table, states)
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DataFrames.insertcols!(df, 1, :Actions => actions)
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latex_table(df, filename)
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latex_table(df, "$filename_without_extension.tex")
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return nothing
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end
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@ -12,6 +12,13 @@ using ..ReCo: ReCo
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include("common.jl")
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const DEFAULT_FRAMERATE = 10
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const DEFAULT_SHOW_CENTER_OF_MASS = false
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const DEFAULT_SHOW_INTERACTION_CIRCLE = false
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const DEFAULT_SHOW_SKIN_CIRCLE = false
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const DEFAULT_SHOW_FRAME_DIFF = false
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const DEFAULT_SHOW_PROGRESS = false
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function animate_bundle!(args, sim_consts::ReCo.SimConsts)
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bundle_t = args.bundle.t
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bundle_c = args.bundle.c
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@ -141,14 +148,29 @@ function animate_bundle!(args, sim_consts::ReCo.SimConsts)
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return nothing
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end
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"""
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animate(sim_dir::String; <keyword arguments>)
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Animate a simulation.
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The output is `sim_dir/animation.mkv`.
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# Arguments
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- `framerate::Int64=$DEFAULT_FRAMERATE`: Framerate
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- `show_center_of_mass::Bool=$DEFAULT_SHOW_CENTER_OF_MASS`: Show center of mass as transparent white circle.
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- `show_interaction_circle::Bool=$DEFAULT_SHOW_INTERACTION_CIRCLE`: Show the interaction radius with a circle around every particle.
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- `show_skin_circle::Bool=$DEFAULT_SHOW_SKIN_CIRCLE`: Show the skin radius with a circle around every particle.
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- `show_frame_diff::Bool=$DEFAULT_SHOW_FRAME_DIFF`: Show translation of particles between two frames as lines connecting the old and new position. This is helpful to recognize unwanted jumps.
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- `show_progress::Bool=$DEFAULT_SHOW_PROGRESS`: Show animation progress bar.
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"""
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function animate(
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sim_dir::String;
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framerate::Int64=1,
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show_center_of_mass::Bool=false,
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show_interaction_circle::Bool=false,
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show_skin_circle::Bool=false,
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show_frame_diff::Bool=false,
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show_progress::Bool=true,
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framerate::Int64=DEFAULT_FRAMERATE,
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show_center_of_mass::Bool=DEFAULT_SHOW_CENTER_OF_MASS,
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show_interaction_circle::Bool=DEFAULT_SHOW_INTERACTION_CIRCLE,
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show_skin_circle::Bool=DEFAULT_SHOW_SKIN_CIRCLE,
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show_frame_diff::Bool=DEFAULT_SHOW_FRAME_DIFF,
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show_progress::Bool=DEFAULT_SHOW_PROGRESS,
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)
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println("Initializing GLMakie...")
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