Merge pull request #13 from symbiotic-engineering/ocm

merge updates from ocm into oceans
symbiotic-engineering · Nov 16, 2023 · 1a2d416 · 1a2d416
2 parents 0d33fc3 + 4f9273c
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diff --git a/CITATION.cff b/CITATION.cff
@@ -18,6 +18,6 @@ authors:
   orcid: "https://orcid.org/0000-0002-2953-7253"
 title: "Marine Spatial Planning of a Wave-Powered Offshore Aquaculture Farm in the Northeast U.S."
 version: 1.0
-doi: ???
-date-released: ???
-url: "https://github.com/symbiotic-engineering/Aquaculture"
+doi: 10.5281/zenodo.7633738
+date-released: 2023-06-06
+url: "https://github.com/symbiotic-engineering/aquaculture"
diff --git a/README.md b/README.md
@@ -1,5 +1,8 @@
+[![DOI](https://zenodo.org/badge/467335021.svg)](https://zenodo.org/doi/10.5281/zenodo.7633737)
+![GitHub](https://img.shields.io/github/license/symbiotic-engineering/aquaculture)
+
 # Aquaculture
-This repository contains an "Marine spatial planning of offshore aquaculture with co-located wave energy", simulated through Python.
+This repository contains a Python to model an offshore aquaculture farm with co-located wave energy converters and determine potential sites using marine spatial planning.
 
 ## File Structure
 This repository consists of the following files:
@@ -8,16 +11,16 @@ This repository consists of the following files:
 - optimization: scripts and functions to perform a single objective optimization using brute-force.
 - env_bruteforce: script to perform brute-force for defined net pen parmeters.
 - run_sim_env: top-level script to perform the "marine spatial planning" optimization code using default values for defined environment with rasters and vectors of data.
-- gis/gis_handler: object to handle connection between GIS data and Python functions
-- gis/gis_example: examples of how to use the GIS handler to query and save data
-- gis/data: GIS files used in analysis including conflicts (.geojson) and conditions (.tif)
+- gis_handler: object to handle connection between GIS data and Python functions
+- scripts/: relevant scripts including examples of how to use the GIS handler to query and save data
+- data/: GIS files used in analysis including conflicts (.geojson) and conditions (.tif) *(stored externally on Zenodo)*
 - requirements.txt: list of the required libraries.
 
 ## How to use
-In order to run the "Marine spatial planning" optimization code and find optimal location for wave-powered aquaculture farm (WPAF) for constant net pen within the Northeast U.S., you can open and run the run_sim_env (.ipynb) file. *Note:* because geospatial data files are uploaded using git lfs, you must clone the repository or download them individually instead of downloading the repository as a zip.
+Relevant data files must be first downloaded from the Zenodo at [https://zenodo.org/records/10140826](https://zenodo.org/records/10140826) and placed in the data folder of this repository. In order to run the marine spatial planning optimization code and find optimal location for wave-powered aquaculture farm (WPAF) for constant net pen within the Northeast U.S, open and run the run_sim_env (.ipynb) file.
 
 ## Dependencies
-Python 3.8.8 is used to develop this package. 
+Python 3.9.18 is used to develop this package.
 For other required libraries, please refer to requirements.txt file.
 
 ## Context

diff --git a/data/readme.md b/data/readme.md
@@ -2,7 +2,7 @@
 
 This folder contains all necessary data files for the Python handler and model including rasters of oceanic conditions, vectors of potential conflicts, and a vector file with the included state and federal waters.
 
-Due to space limitations on GitHub, these files are hosted externally on Zenodo and must be downloaded separately. The current files can be downloaded from [Zenodo](https://zenodo.org) and placed in this directory with the following paths:
+Due to space limitations on GitHub, these files are hosted externally on Zenodo and must be downloaded separately. The current files can be downloaded from [Zenodo](https://zenodo.org/records/10140826) but may have minor deviations from those initially used in published results due to additional pre-processing and scaling. Once downloaded, the files should be placed in this directory with the following paths:
 
     ### Conditions
     /data/Surface Currents m-s (NODP 2016).tif
@@ -29,8 +29,4 @@ Due to space limitations on GitHub, these files are hosted externally on Zenodo
     /data/Shipping Lanes (OCS 2015).geojson
 
     ### Scope
-    /data/Northeast State and Federal Waters (OCM 2018).geojson
-
-    ### Time Series Information
-    /data/Load 24 hour.xlsx
-    /data/32_43.49_-67.88_2009.csv
+    /data/Northeast State and Federal Waters (OCM 2018).geojson
diff --git a/env_bruteforce.py b/env_bruteforce.py
@@ -60,8 +60,10 @@ def env_bruteforce(all_vars, *args):
     param.nom_dict['pen_diameter']=   30       #[m]
     param.nom_dict['pen_height']=     15       #[m]
     param.nom_dict['stock_density']=  20       #[kg/m^3]
-
-    #print(x.bnds)
+
+    x.bnds_old = x.bnds
+    x.bnds = [(38.4, 45.2), (-75.8, -65.7)]
+    print("Manually replaced {} with new bounds of {} to match previously calculated points.".format(x.bnds_old, x.bnds))
 
     if 'grid_resolution' in args[0]:
         grid_resolution = args[0]['grid_resolution']

diff --git a/gis_handler.py b/gis_handler.py
@@ -1,5 +1,5 @@
 # Python GIS Handler
-# SEA Lab at Cornell University, last updated: 11/11/23
+# SEA Lab at Cornell University, last updated: 11/14/23
 
 # import necessary packages, namely geopandas and rasterio
 import pandas as pd

diff --git a/results/README.md b/results/README.md
@@ -0,0 +1,3 @@
+# Results Folder
+
+*This readme exists as a placeholder in the folder where generated results will be written.*
diff --git a/run_sim_env.ipynb b/run_sim_env.ipynb
@@ -34,7 +34,7 @@
     "\n",
     "# high fishing is above average, very high is more than one standard deviation above average\n",
     "conflicts = {'very high fishing traffic': 'data/Very High Fishing Vessel Traffic (NODP 2022).geojson',\n",
-    "#            'high fishing traffic': 'data/High Fishing Vessel Traffic.geojson',\n",
+    "#            'high fishing traffic': 'data/High Fishing Vessel Traffic (NODP 2022).geojson',\n",
     "             'marine protected areas': 'data/Marine Protected Areas (NMPAC 2020).geojson',\n",
     "             'danger zones': 'data/Danger Zones and Restricted Areas (OCM 2022).geojson',\n",
     "             'submarine': 'data/Submarine Transit Lanes (NODP 2016).geojson',\n",
@@ -57,6 +57,13 @@
     "tags": []
    },
    "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Manually replaced [(38.45, 45.19), (-75.78, -65.7)] with new bounds of [(38.4, 45.2), (-75.8, -65.7)] to match previously calculated points.\n"
+     ]
+    },
     {
      "name": "stderr",
      "output_type": "stream",
@@ -91,61 +98,61 @@
       "\u001b[1mbrute force without conflict consideration\u001b[0;0m\n",
       "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n",
       "\u001b[1mdesign variable:\u001b[0;0m\n",
-      "   pos_lat       43.950 m\n",
-      "   pos_long     -68.480 m\n",
+      "   pos_lat       43.700 m\n",
+      "   pos_long     -68.900 m\n",
       "----------------------------------------\n",
       "\u001b[1m objective function terms:\u001b[0;0m\n",
-      "   Objective_func 109680868.339\n",
+      "   Objective_func 97695103.359\n",
       "   fish_yield     2162986.542 [kg]\n",
       "----------------------------------------\n",
       "\u001b[1m wave energy converter:\u001b[0;0m\n",
-      "   wec number         18.000 [-]\n",
-      "   wave power          3.373 [kW/m]\n",
-      "   wec_P_ave           7.841 [kW]\n",
+      "   wec number         16.000 [-]\n",
+      "   wave power          3.717 [kW/m]\n",
+      "   wec_P_ave           8.821 [kW]\n",
       "   wec AEP        1237228.302 [kWh]\n",
       "----------------------------------------\n",
       "\u001b[1m price break down:\u001b[0;0m\n",
-      "   wec NPV              109131900.357 [$]\n",
+      "   wec NPV              97006133.651 [$]\n",
       "   pen price            12723450.247 [$]\n",
       "   fish feed price      5649211.910 [$]\n",
-      "   vessel travel NPV    548967.982 [$]\n",
+      "   vessel travel NPV    688969.708 [$]\n",
       "----------------------------------------\n",
       "\u001b[1m location validation:\u001b[0;0m\n",
-      "   conditions           5628    True\n",
+      "   conditions           5475    True\n",
       "Name: ok-conditions, dtype: object\n",
-      "   scope                5628    True\n",
+      "   scope                5475    True\n",
       "Name: ok-scope, dtype: object\n",
-      "   conflicts            5628    False\n",
+      "   conflicts            5475    True\n",
       "Name: ok-conflicts, dtype: object\n",
       "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n",
       "\u001b[1mbrute force with conflict consideration\u001b[0;0m\n",
       "++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n",
       "\u001b[1mdesign variable:\u001b[0;0m\n",
-      "   pos_lat       43.750 m\n",
-      "   pos_long     -68.880 m\n",
+      "   pos_lat       43.700 m\n",
+      "   pos_long     -68.900 m\n",
       "----------------------------------------\n",
       "\u001b[1m objective function terms:\u001b[0;0m\n",
-      "   Objective_func 109780028.495\n",
+      "   Objective_func 97695103.359\n",
       "   fish_yield     2162986.542 [kg]\n",
       "----------------------------------------\n",
       "\u001b[1m wave energy converter:\u001b[0;0m\n",
-      "   wec number         18.000 [-]\n",
-      "   wave power          3.462 [kW/m]\n",
-      "   wec_P_ave           7.841 [kW]\n",
+      "   wec number         16.000 [-]\n",
+      "   wave power          3.717 [kW/m]\n",
+      "   wec_P_ave           8.821 [kW]\n",
       "   wec AEP        1237228.302 [kWh]\n",
       "----------------------------------------\n",
       "\u001b[1m price break down:\u001b[0;0m\n",
-      "   wec NPV              109131900.357 [$]\n",
+      "   wec NPV              97006133.651 [$]\n",
       "   pen price            12723450.247 [$]\n",
       "   fish feed price      5649211.910 [$]\n",
-      "   vessel travel NPV    648128.137 [$]\n",
+      "   vessel travel NPV    688969.708 [$]\n",
       "----------------------------------------\n",
       "\u001b[1m location validation:\u001b[0;0m\n",
-      "   conditions           5422    True\n",
+      "   conditions           5475    True\n",
       "Name: ok-conditions, dtype: object\n",
-      "   scope                5422    True\n",
+      "   scope                5475    True\n",
       "Name: ok-scope, dtype: object\n",
-      "   conflicts            5422    True\n",
+      "   conflicts            5475    True\n",
       "Name: ok-conflicts, dtype: object\n"
      ]
     }
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,3 @@
		# Results Folder

		This readme exists as a placeholder in the folder where generated results will be written.