Develop stacked extinction coefficients computation

doc/analysis.rst

@@ -22,6 +22,14 @@ Analysis
    :show-inheritance:
 
 .. automodule:: ledsa.analysis.ExperimentData
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Stacked Multi-Camera Analysis
+------------------------------
+
+.. automodule:: ledsa.analysis.StackedExtinctionCoefficients
    :members:
    :undoc-members:
    :show-inheritance:

doc/cli_documentation.rst

@@ -1,4 +1,3 @@
-
 CLI Documentation
 =================
 
@@ -68,6 +67,26 @@ Analysis
 .. warning::
     Color Correction is in a test state and has not yet been sufficiently evaluated. The application may lead to incorrect results.
 
+Stacked Multi-Camera Analysis
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. list-table::
+   :widths: 20 50 30
+   :header-rows: 1
+
+   * - Argument
+     - Description
+     - Options
+   * - ``-conf_s [FILENAME]``, ``--config_stacked [FILENAME]``
+     - Create a template ``config_stacked.ini`` for multi-camera stacked analysis. The optional argument sets the output filename (default: ``config_stacked.ini``).
+     - ``--n_simulations N`` sets the number of simulation blocks in the template (default: 2).
+   * - ``--n_simulations N``
+     - Number of ``[simulation_N]`` blocks written into the template ``config_stacked.ini``. Only used together with ``-conf_s``.
+     - Default: 2
+   * - ``-as``, ``--analysis_stacked``
+     - Run the stacked multi-camera extinction coefficient calculation using ``config_stacked.ini`` in the current directory.
+     - --
+
 Coordinates
 ^^^^^^^^^^^
 
@@ -117,4 +136,4 @@ Demo
      - Optional: Path to setup simulation and image directories. Default to ``'.'``
    * - ``--run``
      - Run the LEDSA demo in the current working directory.
-     - --
+     - --

doc/config.rst

@@ -17,3 +17,11 @@ ConfigDataAnalysis
    :members:
    :undoc-members:
    :show-inheritance:
+
+ConfigDataStacked
+-----------------
+
+.. automodule:: ledsa.analysis.ConfigDataStacked
+   :members:
+   :undoc-members:
+   :show-inheritance:

examples/postprocessing_stacked.ipynb

@@ -0,0 +1,226 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {
+    "collapsed": true,
+    "pycharm": {
+     "name": "#%% md\n"
+    }
+   },
+   "source": [
+    "# Dependencies"
+   ]
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": [
+    "import os\n",
+    "import numpy as np\n",
+    "\n",
+    "import matplotlib.pyplot as plt\n",
+    "from matplotlib import rcParams\n",
+    "from mpl_toolkits.axes_grid1.inset_locator import InsetPosition\n",
+    "import seaborn as sns\n",
+    "\n",
+    "from ledsa.postprocessing.simulation import StackedSimData"
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": "# Display Config",
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "rcParams['font.family'] = 'serif'\n",
+    "rcParams['font.size'] = 10\n",
+    "cm = 1 / 2.54"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "cell_type": "markdown",
+   "source": "# Load Simulation Data",
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": [
+    "# Input Dir (Simulations)\n",
+    "path_simulation = '/Path/to/simulation'\n",
+    "sim = StackedSimData(path_simulation)"
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "# Extinction Coefficients"
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Plot extinction coefficients as a function of time for a specific LED array and height"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": [
+    "# Parameters\n",
+    "led_array_id = 1  # LED array to analyze\n",
+    "window = 3  # Size of moving average window\n",
+    "color_channels = [0, 1, 2] # RGB channels\n",
+    "height = 2\n",
+    "\n",
+    "# Create figure\n",
+    "fig, ax = plt.subplots(figsize=(10, 6))\n",
+    "\n",
+    "# Plot extinction coefficients for each channel\n",
+    "for channel in color_channels:\n",
+    "    # Get extinction coefficients at specified height\n",
+    "    extco = sim.get_extco_at_height(channel=channel, height=height, window=window)\n",
+    "\n",
+    "    # Plot with different colors for each channel\n",
+    "    colors = ['red', 'green', 'blue']\n",
+    "    ax.plot(extco.index, extco.iloc[:, led_array_id],\n",
+    "            color=colors[channel],\n",
+    "            label=f'Channel {channel}')\n",
+    "\n",
+    "ax.set_xlabel('Time / s')\n",
+    "ax.set_ylabel('Extinction Coefficient / $\\mathrm{m^{-1}}$')\n",
+    "ax.set_title(f'Extinction Coefficients at Height {height} m, LED Array {led_array_id}')\n",
+    "ax.grid(True)\n",
+    "ax.legend()\n",
+    "plt.tight_layout()\n",
+    "plt.show()"
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Plot extinction coefficients as a function of height and LED array for a specific point in time"
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": [
+    "# Parameters\n",
+    "time = 200  # Time point to analyze in seconds\n",
+    "channel = 0  # RGB channels\n",
+    "window = 20  # Size of moving average window\n",
+    "\n",
+    "# Find closest time point to given time\n",
+    "closest_time = sim.get_closest_time(time)\n",
+    "\n",
+    "extco = sim.get_extco_at_time(channel=channel, time=closest_time, window=window, yaxis='height')\n",
+    "sns.heatmap(extco.iloc[::-1], cmap='jet', vmax=0.4, cbar_kws={'label': 'Extinction Coefficient / $\\mathrm{m^{-1}}$'})\n",
+    "plt.tight_layout()"
+   ],
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "markdown",
+   "source": "## Plot extinction coefficients as a function of height for a specific LED array and point in time\n"
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "# Parameters\n",
+    "time = 200  # Time point to analyze in seconds\n",
+    "window = 3  # Size of moving average window\n",
+    "led_array_id = 2  # LED array to analyze\n",
+    "color_channels = [0, 1, 2]  # RGB channels\n",
+    "\n",
+    "# Find closest time point to given time\n",
+    "closest_time = sim.get_closest_time(time)\n",
+    "\n",
+    "# Create figure\n",
+    "fig, ax = plt.subplots(figsize=(10, 6))\n",
+    "\n",
+    "# Plot extinction coefficients for each channel\n",
+    "for channel in color_channels:\n",
+    "    # Get extinction coefficients at specified time\n",
+    "    extco = sim.get_extco_at_time(channel=channel, time=closest_time, window=window, yaxis='height')\n",
+    "\n",
+    "    # Plot with different colors for each channel\n",
+    "    colors = ['red', 'green', 'blue']\n",
+    "    ax.plot(extco.iloc[:, led_array_id], extco.index,\n",
+    "            color=colors[channel],\n",
+    "            label=f'Channel {channel}')\n",
+    "\n",
+    "ax.set_xlabel('Extinction Coefficient / $\\mathrm{m^{-1}}$')\n",
+    "ax.set_ylabel('Height / m')\n",
+    "ax.set_title(f'Extinction Coefficients at Time {closest_time} s, LED Array {led_array_id}')\n",
+    "ax.grid(True)\n",
+    "ax.legend()\n",
+    "plt.tight_layout()\n",
+    "plt.show()\n"
+   ],
+   "metadata": {
+    "collapsed": false,
+    "pycharm": {
+     "name": "#%%\n"
+    }
+   },
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": "",
+   "outputs": [],
+   "execution_count": null
+  },
+  {
+   "metadata": {},
+   "cell_type": "code",
+   "source": "",
+   "outputs": [],
+   "execution_count": null
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 2
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython2",
+   "version": "2.7.6"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 0
+}

ledsa/__main__.py

@@ -6,7 +6,7 @@
 from ledsa.core.parser_arguments_declaration import (add_parser_arguments_tools, add_parser_arguments_data_extraction,
     add_parser_arguments_testing, add_parser_arguments_demo, add_parser_argument_analysis)
 from ledsa.core.parser_arguments_run import run_tools_arguments, run_data_extraction_arguments, run_testing_arguments, run_demo_arguments, \
-    run_analysis_arguments, run_analysis_arguments_with_extinction_coefficient
+    run_analysis_arguments, run_analysis_arguments_with_extinction_coefficient, run_stacked_analysis
 
 
 def main(argv: List[str]) -> None:
@@ -40,9 +40,10 @@ def main(argv: List[str]) -> None:
         run_data_extraction_arguments(args)
         run_analysis_arguments(args)
         run_analysis_arguments_with_extinction_coefficient(args)
+        run_stacked_analysis(args)
         run_testing_arguments(args)
 
 
 
 if __name__ == "__main__":
-    main(sys.argv[1:])
+    main(sys.argv[1:])