parse_simulation_outputs.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a class=\"anchor\" id=\"toc\"></a>\n",
    "# PARSE SIMULATION OUTPUTS\n",
    "\n",
    "This notebook provides the functions and scripts for parsing simulation files (`.json`) to results files (`.csv`).\n",
    "\n",
    "---\n",
    "- [WORKSPACE VARIABLES](#workspace-variables)\n",
    "- **[SYSTEM REPRESENTATION](#system-representation)**\n",
    "- **[CELL VARIABILITY](#cell-variability)**\n",
    "- **[NUTRIENT DYNAMICS](#nutrient-dynamics)**\n",
    "---"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The main parsing function (`parse_simulations`) iterates through each file in the data path and parses for each simulation instance, extracting fields each timepoint.\n",
    "\n",
    "The output files have the following headers:\n",
    "\n",
    "- `i` = simulation seed\n",
    "- `t` = timepoint\n",
    "- (`x`, `y`) OR (`u`, `v`, `w`) = rectangular OR hexagonal coordinates\n",
    "- `z` = z coordinate\n",
    "- `p` = position\n",
    "- `pop` = population\n",
    "- `state` = cell state\n",
    "- `volume` = cell volume (rounded)\n",
    "- `cycle` = average cell cycle length (rounded), -1 if N/A"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The `parse.py` file contains general parsing functions.\n",
    "\n",
    "Parsing can take some time, so parsed `.csv` files for all simulations are provided along with the raw simulation data."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from scripts.parse import *"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a class=\"anchor\" id=\"workspace-variables\"></a>\n",
    "\n",
    "### WORKSPACE VARIABLES \n",
    "<span style=\"float:right;\">[back to top](#toc)</span>\n",
    "\n",
    "Set up workspace variables for parsing simulations.\n",
    "\n",
    "- **`DATA_PATH`** is the path to data files (`.tar.xz` files of compressed simulation outputs)\n",
    "- **`RESULT_PATH`** is the path for result files (`.csv.xz` files generated by parsing)\n",
    "- **`EXCLUDE`** is a list of seeds to exclude from parsing."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "DATA_PATH = \"/path/to/data/files/\"\n",
    "RESULTS_PATH = \"/path/to/result/files/\"\n",
    "EXCLUDE = []"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a class=\"anchor\" id=\"system-representation\"></a>\n",
    "\n",
    "### SYSTEM REPRESENTATION\n",
    "<span style=\"float:right;\">[back to top](#toc)</span>\n",
    "\n",
    "Parse `SYSTEM_REPRESENTATION` simulations."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "parse_simulations(\"SYSTEM_REPRESENTATION\", DATA_PATH, RESULTS_PATH, EXCLUDE)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a class=\"anchor\" id=\"cell-variability\"></a>\n",
    "\n",
    "### CELL VARIABILITY\n",
    "<span style=\"float:right;\">[back to top](#toc)</span>\n",
    "\n",
    "Parse `CELL_VARIABILITY` simulations."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "parse_simulations(\"CELL_VARIABILITY\", DATA_PATH, RESULTS_PATH, EXCLUDE)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "<a class=\"anchor\" id=\"nutrient-dynamics\"></a>\n",
    "\n",
    "### NUTIENT DYNAMICS\n",
    "<span style=\"float:right;\">[back to top](#toc)</span>\n",
    "\n",
    "Parse `NUTRIENT_DYNAMICS` simulations."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "parse_simulations(\"NUTRIENT_DYNAMICS\", DATA_PATH, RESULTS_PATH, EXCLUDE)"
   ]
  }
 ],
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