From c707a20a75ca6e303b2637146a3512395338bf83 Mon Sep 17 00:00:00 2001
From: Joshua Coles <josh@coles.to>
Date: Mon, 6 Mar 2023 12:14:21 +0000
Subject: [PATCH] Quite a mess

---
 Cargo.lock                     |  1 +
 Cargo.toml                     |  1 +
 src/example_systems.rs         | 52 ++++++++++++++++++++++++++++++----
 src/main.rs                    | 49 +++++++++++++++++++++++---------
 src/system/model.rs            | 41 ++++++++++++++++++++-------
 src/system/spaces/grid.rs      | 11 +++++++
 src/system/spaces/hexagonal.rs | 11 +++++--
 src/system/spaces/nd.rs        |  2 +-
 src/system/spawner.rs          | 43 +++++++++++++++++++++++++++-
 9 files changed, 178 insertions(+), 33 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index c26123e..bef0d92 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -2723,6 +2723,7 @@ dependencies = [
  "num-integer",
  "rand",
  "serde",
+ "serde_json",
 ]
 
 [[package]]
diff --git a/Cargo.toml b/Cargo.toml
index 280ce63..f75ab3d 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -38,6 +38,7 @@ num-integer = "0.1.45"
 rand = { version = "0.8.5", features = ["default", "small_rng"] }
 csv = "1.1"
 serde = { version = "1.0.152", features = ["derive"] }
+serde_json = "1.0.93"
 
 [build-dependencies]
 cbindgen = "0.24.3"
diff --git a/src/example_systems.rs b/src/example_systems.rs
index 7ac13fd..f015d68 100644
--- a/src/example_systems.rs
+++ b/src/example_systems.rs
@@ -1,21 +1,52 @@
+use std::fs::File;
 use std::path::Path;
 use rand::rngs::SmallRng;
 use rand::{Rng, SeedableRng};
 use crate::system::model::DLASystem;
-use crate::system::{GriddedPosition, Position, Storage};
+use crate::system::{Position, Storage};
 use crate::system::spaces::grid::{Pos2D, VectorStorage};
+use crate::system::spaces::hexagonal::HexPosition;
 use crate::system::spaces::nd::{NDPosition, NDVectorStorage};
 use crate::system::spawner::{Spawner, UniformSpawner};
 use crate::system::sticker::{ProbabilisticSticking, SimpleSticking, Sticker};
 use crate::system::walker::{LocalRandomWalker, Walker};
 
-pub fn execute<R: Rng, P: Position, S: Storage<P>, W: Walker<P>, Sp: Spawner<P>, St: Sticker<P>>(sys: &mut DLASystem<R, P, S, W, Sp, St>, csv_path: &Path) {
+pub fn drive_system<R: Rng, P: Position, S: Storage<P>, W: Walker<P>, Sp: Spawner<P>, St: Sticker<P>>(sys: &mut DLASystem<R, P, S, W, Sp, St>, max_frames: Option<usize>) {
     while sys.running {
         sys.update();
-    }
 
-    sys.export_data(csv_path)
-        .expect("Failed to write");
+        match max_frames {
+            Some(max_frames) if max_frames <= sys.frame => {
+                sys.running = false;
+                eprintln!("System halted as it ran to {frame} frames (max_frames = {max_frames}) and did not complete", frame = sys.frame)
+            }
+            _ => {}
+        }
+    }
+}
+
+pub fn write_csv<R: Rng, P: Position, S: Storage<P>, W: Walker<P>, Sp: Spawner<P>, St: Sticker<P>>(sys: &DLASystem<R, P, S, W, Sp, St>, csv_path: &Path) {
+    let mut wtr = csv::Writer::from_path(csv_path)
+        .expect("Failed to open file");
+
+    // CSVs can only store the raw positions
+    let positions: Vec<&P> = sys.history
+        .iter()
+        .map(|line| &line.position)
+        .collect();
+
+    wtr.serialize(positions)
+        .unwrap();
+
+    wtr.flush()
+        .unwrap();
+}
+
+pub fn write_json<R: Rng, P: Position, S: Storage<P>, W: Walker<P>, Sp: Spawner<P>, St: Sticker<P>>(sys: &DLASystem<R, P, S, W, Sp, St>, output_path: &Path) {
+    let file = File::create(output_path).expect("Failed to open file");
+
+    serde_json::to_writer(file, &sys.history)
+        .expect("Failed to write json");
 }
 
 pub fn initial_config(seed: u64, max_particles: usize) -> DLASystem<SmallRng, Pos2D, VectorStorage, LocalRandomWalker, UniformSpawner, SimpleSticking> {
@@ -50,3 +81,14 @@ pub fn three_dimensional(seed: u64, max_particles: usize, stick_probability: f32
         max_particles,
     )
 }
+
+pub fn hex_grid(seed: u64, max_particles: usize, stick_probability: f32) -> DLASystem<SmallRng, HexPosition, VectorStorage, LocalRandomWalker, UniformSpawner, ProbabilisticSticking> {
+    DLASystem::new(
+        SmallRng::seed_from_u64(seed),
+        VectorStorage::new(1600),
+        LocalRandomWalker,
+        UniformSpawner,
+        ProbabilisticSticking { stick_probability },
+        max_particles,
+    )
+}
diff --git a/src/main.rs b/src/main.rs
index e5f993b..b854965 100644
--- a/src/main.rs
+++ b/src/main.rs
@@ -1,24 +1,34 @@
 #![feature(array_zip)]
 #![feature(generic_const_exprs)]
 
+use std::fs::File;
 use std::path::PathBuf;
 
 mod system;
 mod example_systems;
 
 use clap::Parser;
-use crate::example_systems::{execute, stick_probability, three_dimensional};
-use crate::system::model::DLASystem;
+use crate::example_systems::{drive_system, stick_probability, three_dimensional, write_csv, write_json};
+
+#[derive(clap::ValueEnum, Clone, Debug)]
+enum PreConfiguredSystem {
+    Grid2,
+    Grid3,
+    Hex
+}
 
 #[derive(Parser, Debug)]
 struct Cli {
-    #[arg(short, long, default_value_t = 2)]
-    dim: u32,
+    #[arg(value_enum, long, default_value_t = PreConfiguredSystem::Grid2)]
+    mode: PreConfiguredSystem,
+
+    #[arg(short, long)]
+    max_frames: Option<usize>,
 
     seed: u64,
     max_particles: usize,
     stick_probability: f32,
-    csv_path: PathBuf,
+    output: PathBuf,
 }
 
 fn main() {
@@ -26,27 +36,40 @@ fn main() {
 
     println!("Running: {:?}", cli);
 
-    match cli.dim {
-        2 => {
+    match cli.mode {
+        PreConfiguredSystem::Grid2 => {
             let mut sys = stick_probability(
                 cli.seed,
                 cli.max_particles,
                 cli.stick_probability,
             );
 
-            execute(&mut sys, &cli.csv_path);
-        },
+            drive_system(&mut sys, cli.max_frames);
+            write_csv(&mut sys, &cli.output);
+        }
 
-        3 => {
+        PreConfiguredSystem::Grid3 => {
             let mut sys = three_dimensional(
                 cli.seed,
                 cli.max_particles,
                 cli.stick_probability,
             );
 
-            execute(&mut sys, &cli.csv_path);
-        },
+            drive_system(&mut sys, cli.max_frames);
 
-        n => panic!("Model not compiled with {n} dimensional support")
+            write_json(&mut sys, &cli.output);
+        }
+
+        PreConfiguredSystem::Hex => {
+            let mut sys = three_dimensional(
+                cli.seed,
+                cli.max_particles,
+                cli.stick_probability,
+            );
+
+            drive_system(&mut sys, cli.max_frames);
+
+            write_json(&mut sys, &cli.output);
+        }
     }
 }
diff --git a/src/system/model.rs b/src/system/model.rs
index 26332da..2e3adb2 100644
--- a/src/system/model.rs
+++ b/src/system/model.rs
@@ -1,19 +1,45 @@
 use std::io;
 use std::path::Path;
 use rand::prelude::*;
+use serde::Serialize;
 use crate::system::{GriddedPosition, Position, Storage};
 use crate::system::spawner::Spawner;
 use crate::system::sticker::Sticker;
 use crate::system::walker::Walker;
 
+#[derive(Serialize)]
+pub struct HistoryLine<P: Position> {
+    pub frame: usize,
+    pub cluster_radius: f32,
+    pub fd: f32,
+    pub position: P,
+}
+
 pub struct DLASystem<R: Rng, P: Position, S: Storage<P>, W: Walker<P>, Sp: Spawner<P>, St: Sticker<P>> {
     rng: R,
+
+    /*
+     * These object encapsulate the behaviour of our particular model.
+     */
+
+    /*
+     * The space, along with the chosen position choose the embedding space that the cluster grows
+     * in.
+     */
     space: S,
+
+    /*
+     * Walkers allow us to choose between different particle movement behaviours, eg random or
+     * biased walker
+     */
     walker: W,
     spawner: Sp,
     sticker: St,
 
+    pub frame: usize,
     pub running: bool,
+    pub history: Vec<HistoryLine<P>>,
+
     max_particles: usize,
     particles: Vec<P>,
     active_particle: Option<P>,
@@ -36,7 +62,10 @@ impl<R: Rng, P: Position, S: Storage<P>, W: Walker<P>, Sp: Spawner<P>, St: Stick
 
             space,
             walker,
+
+            frame: 0,
             particles: vec![],
+            history: vec![],
             active_particle: None,
 
             add_ratio: 1.2,
@@ -53,6 +82,7 @@ impl<R: Rng, P: Position, S: Storage<P>, W: Walker<P>, Sp: Spawner<P>, St: Stick
     }
 
     pub fn update(&mut self) {
+        self.frame += 1;
         if self.active_particle.is_some() {
             self.move_particle();
         } else if self.particles.len() < self.max_particles {
@@ -106,16 +136,7 @@ impl<R: Rng, P: Position, S: Storage<P>, W: Walker<P>, Sp: Spawner<P>, St: Stick
                 self.kill_circle = self.kill_ratio * self.add_circle;
             }
         }
-    }
 
-    pub fn export_data(&self, path: &Path) -> io::Result<()> {
-        let mut wtr = csv::Writer::from_path(path)?;
-
-        for particle in &self.particles {
-            wtr.serialize(particle)?;
-        }
-
-        wtr.flush()?;
-        Ok(())
+        self.history.push(HistoryLine { frame: self.frame, position: p0.clone(), cluster_radius: self.cluster_radius, fd: (self.particles.len() as f32).ln() / self.cluster_radius.ln() });
     }
 }
diff --git a/src/system/spaces/grid.rs b/src/system/spaces/grid.rs
index b3bec1c..3d83f7d 100644
--- a/src/system/spaces/grid.rs
+++ b/src/system/spaces/grid.rs
@@ -4,6 +4,7 @@ use num_integer::Integer;
 use rand::Rng;
 use crate::system::{GriddedPosition, Position, Storage};
 use serde::{Serialize, Deserialize};
+use crate::system::spaces::hexagonal::HexPosition;
 
 pub struct VectorStorage {
     backing: Vec<bool>,
@@ -91,3 +92,13 @@ impl Storage<Pos2D> for VectorStorage {
         self.backing[position.linear_index(self.grid_size)] = true;
     }
 }
+
+impl Storage<HexPosition> for VectorStorage {
+    fn at(&self, position: &HexPosition) -> bool {
+        return self.backing[position.linear_index(self.grid_size)];
+    }
+
+    fn deposit(&mut self, position: &HexPosition) {
+        self.backing[position.linear_index(self.grid_size)] = true;
+    }
+}
diff --git a/src/system/spaces/hexagonal.rs b/src/system/spaces/hexagonal.rs
index 0d76a6c..7567f7f 100644
--- a/src/system/spaces/hexagonal.rs
+++ b/src/system/spaces/hexagonal.rs
@@ -32,8 +32,10 @@ impl GriddedPosition for HexPosition {
     }
 
     fn linear_index(&self, grid_size: u32) -> usize {
-        todo!()
-        // ((self.q + grid_size / 2) + grid_size * self.r) as usize
+        let q = (self.q + (grid_size as i32 / 2)) as usize;
+        let r = (self.r + (grid_size as i32 / 2)) as usize;
+
+        r * (grid_size as usize) + q
     }
 }
 
@@ -49,6 +51,9 @@ impl Position for HexPosition {
     }
 
     fn from_cartesian(cartesian: [f32; Self::DIM]) -> Self {
-        todo!()
+        let q = (1.0f32/3.0f32).sqrt() * cartesian[0] - 1.0/3.0 * cartesian[1];
+        let r = 2.0/3.0 * cartesian[1];
+
+        Self { q: q as i32, r: r as i32 }
     }
 }
diff --git a/src/system/spaces/nd.rs b/src/system/spaces/nd.rs
index a3fd62e..64e20b8 100644
--- a/src/system/spaces/nd.rs
+++ b/src/system/spaces/nd.rs
@@ -2,7 +2,7 @@ use std::ops::Add;
 use num_integer::Integer;
 use rand::Rng;
 use serde::{Serialize, Serializer};
-use serde::ser::{SerializeMap, SerializeSeq, SerializeStruct};
+use serde::ser::SerializeStruct;
 use crate::system::{GriddedPosition, Position};
 use crate::system::Storage;
 
diff --git a/src/system/spawner.rs b/src/system/spawner.rs
index 22d75fa..5bdcca7 100644
--- a/src/system/spawner.rs
+++ b/src/system/spawner.rs
@@ -2,6 +2,7 @@ use std::f32::consts::PI;
 use rand::Rng;
 use crate::system::Position;
 use crate::system::spaces::grid::Pos2D;
+use crate::system::spaces::hexagonal::HexPosition;
 use crate::system::spaces::nd::NDPosition;
 
 pub trait Spawner<P: Position> {
@@ -19,11 +20,51 @@ impl Spawner<Pos2D> for UniformSpawner {
     }
 }
 
+impl Spawner<HexPosition> for UniformSpawner {
+    fn spawn<R: Rng>(&self, rng: &mut R, radius: f32) -> HexPosition {
+        let theta = rng.gen_range(0f32..1.0) * 2.0 * PI;
+        let (x, y) = (radius * theta.cos(), radius * theta.sin());
+
+        HexPosition::from_cartesian([x, y])
+    }
+}
+
 impl Spawner<NDPosition<3>> for UniformSpawner {
     fn spawn<R: Rng>(&self, rng: &mut R, radius: f32) -> NDPosition<3> {
         let theta = rng.gen_range(0f32..1.0) * 2.0 * PI;
         let phi = rng.gen_range(0f32..1.0) * 2.0 * PI;
-        let (x, y, z) = (radius * theta.cos(), radius * theta.sin(), radius * theta.sin());
+
+        let (x, y, z) = (
+            radius * theta.sin() * phi.cos(),
+            radius * theta.sin() * phi.sin(),
+            radius * theta.cos()
+        );
+
         NDPosition::<3>::from_cartesian([x, y, z])
     }
 }
+
+// Does not work due to const generics issue, for now specialise for each dimension needed.
+// pub struct NDUniformSpawner<const DIM: usize>;
+//
+// impl<const DIM: usize> Spawner<NDPosition<DIM>> for NDUniformSpawner<DIM> {
+//     fn spawn<R: Rng>(&self, rng: &mut R, radius: f32) -> NDPosition<DIM> {
+//         let mut a: [f32; DIM] = [0f32; DIM];
+//
+//         for i in 0..DIM {
+//             a[i] = rng.gen_range(0f32..1f32);
+//         }
+//
+//         let norm = a.iter().sum::<f32>()
+//             .sqrt();
+//
+//         for i in 0..DIM {
+//             a[i] = a[i] * radius / norm;
+//         }
+//
+//         unsafe {
+//             let b = transmute(a);
+//             NDPosition::from_cartesian(b)
+//         }
+//     }
+// }