From 1a4fa54e4287c1e5215e82d61ca33f231b9b4102 Mon Sep 17 00:00:00 2001
From: Vismayak Mohanarajan <mohanar2@illinois.edu>
Date: Wed, 10 Apr 2024 08:26:23 -0500
Subject: [PATCH] 339 Add galveston community app notebook with retrofit (#357)

* Create galveston_community_app_retrofit.ipynb

* Temporary store for retrofit_data

* Cleared cells and full test run done

* Update galveston_community_app_retrofit.ipynb

* Update galveston_community_app_retrofit.ipynb

* Update galveston_community_app_retrofit.ipynb

* Clean up

* Update CHANGELOG.md

* Update galveston_community_app_retrofit.ipynb

* Update notebooks_other.md
---
 CHANGELOG.md                                  |   1 +
 manual_jb/content/notebooks_other.md          |   1 +
 .../galveston_community_app_retrofit.ipynb    | 808 ++++++++++++++++++
 3 files changed, 810 insertions(+)
 create mode 100644 notebooks/galveston_community_app_retrofit.ipynb

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d07de6d2..4589db52 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -27,6 +27,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 ### Changed
 - Changed the mapping function used to generate the FEMA table [#343](https://github.com/IN-CORE/incore-docs/issues/343)
 - PyIncore-viz example notebook updated with new hazard dataset update [#335](https://github.com/IN-CORE/incore-docs/issues/335)
+- Added Galveston community notebook with retrofit [#337](https://github.com/IN-CORE/incore-docs/issues/337)
 
 ## [4.8.2] - 2024-02-07
 
diff --git a/manual_jb/content/notebooks_other.md b/manual_jb/content/notebooks_other.md
index b6764e53..46696679 100644
--- a/manual_jb/content/notebooks_other.md
+++ b/manual_jb/content/notebooks_other.md
@@ -17,6 +17,7 @@ Note that some Notebooks might not work with the latest version of pyIncore.
 [epf_repair_cost.ipynb](https://github.com/IN-CORE/incore-docs/blob/main/notebooks/epf_repair_cost.ipynb) <br />
 [epn_functionality.ipynb](https://github.com/IN-CORE/incore-docs/blob/main/notebooks/epn_functionality.ipynb) <br />
 [galveston_community_app.ipynb](https://github.com/IN-CORE/incore-docs/blob/main/notebooks/galveston_community_app.ipynb) <br />
+[galveston_community_app_retrofit.ipynb](https://github.com/IN-CORE/incore-docs/blob/main/notebooks/galveston_community_app_retrofit.ipynb) <br />
 [galveston_cge.ipynb](https://github.com/IN-CORE/incore-docs/blob/main/notebooks/galveston_cge.ipynb) <br />
 [housing household recovery](https://github.com/IN-CORE/incore-docs/blob/main/notebooks/housing_household_recovery.ipynb) <br />
 [housing_recovery.ipynb](https://github.com/IN-CORE/incore-docs/blob/main/notebooks/housing_recovery.ipynb) <br />
diff --git a/notebooks/galveston_community_app_retrofit.ipynb b/notebooks/galveston_community_app_retrofit.ipynb
new file mode 100644
index 00000000..80bd551e
--- /dev/null
+++ b/notebooks/galveston_community_app_retrofit.ipynb
@@ -0,0 +1,808 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "957d73f9",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import warnings\n",
+    "\n",
+    "warnings.filterwarnings(\"ignore\")\n",
+    "import pandas as pd\n",
+    "import geopandas as gpd\n",
+    "import numpy as np\n",
+    "import sys\n",
+    "import os\n",
+    "import matplotlib.pyplot as plt\n",
+    "import contextily as ctx\n",
+    "import copy\n",
+    "import math\n",
+    "from scipy.stats import norm\n",
+    "from pathlib import Path\n",
+    "\n",
+    "from pyincore import (\n",
+    "    IncoreClient,\n",
+    "    Dataset,\n",
+    "    DataService,\n",
+    "    HazardService,\n",
+    "    FragilityService,\n",
+    "    MappingSet,\n",
+    "    FragilityCurveSet,\n",
+    ")\n",
+    "from pyincore import HHRSOutputProcess\n",
+    "from pyincore.utils.dataprocessutil import DataProcessUtil\n",
+    "\n",
+    "\n",
+    "# importing pyIncone analyses:\n",
+    "from pyincore.analyses.buildingdamage import BuildingDamage\n",
+    "from pyincore.analyses.buildingfunctionality import BuildingFunctionality\n",
+    "from pyincore.analyses.combinedwindwavesurgebuildingdamage import (\n",
+    "    CombinedWindWaveSurgeBuildingDamage,\n",
+    ")\n",
+    "from pyincore.analyses.epfdamage import EpfDamage\n",
+    "from pyincore.analyses.montecarlofailureprobability import MonteCarloFailureProbability\n",
+    "from pyincore.analyses.housingunitallocation import HousingUnitAllocation\n",
+    "from pyincore.analyses.populationdislocation import (\n",
+    "    PopulationDislocation,\n",
+    "    PopulationDislocationUtil,\n",
+    ")\n",
+    "from pyincore.analyses.housingrecoverysequential import HousingRecoverySequential\n",
+    "from pyincore.analyses.socialvulnerability import SocialVulnerability\n",
+    "from pyincore.analyses.capitalshocks import CapitalShocks\n",
+    "from pyincore.analyses.galvestoncge import GalvestonCGEModel\n",
+    "import json"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4e50116d",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "client = IncoreClient()\n",
+    "# IN-CORE caches files on the local machine, it might be necessary to clear the memory\n",
+    "# client.clear_cache()\n",
+    "data_service = DataService(client)  # create data_service object for loading files\n",
+    "hazard_service = HazardService(client)\n",
+    "fragility_services = FragilityService(client)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "70388c7a-ed69-4efe-8114-f8567c14a9f6",
+   "metadata": {},
+   "source": [
+    "## Combined Building Damage with retrofit"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1b84e1cf-6266-42f2-9e32-764adf0a655a",
+   "metadata": {},
+   "source": [
+    "Retrofit is currently only for Surge-wave and flood damage"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "654c3396-d286-4034-ba9d-27381df68149",
+   "metadata": {},
+   "source": [
+    "### Wind building damage for Galveston, TX using Hurricane Ike"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3f759503-4477-41b8-a6f1-a17c904f3672",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "hazard_type = \"hurricane\"\n",
+    "\n",
+    "# Galveston Hurricane Ike\n",
+    "hazard_id = \"5fa5a228b6429615aeea4410\"\n",
+    "\n",
+    "# Galveston inventory data\n",
+    "# bldg_dataset_id = \"63053ddaf5438e1f8c517fed\" # Full city\n",
+    "bldg_dataset_id = \"63ff6b135c35c0353d5ed3ac\"  # Island Only\n",
+    "\n",
+    "# Retrofit planning\n",
+    "# retrofit_plan = \"660c605d099327393f82902b\"  # Galveston Retrofit Plan (Elevation - 10m)\n",
+    "retrofit_plan = \"660c5fa71fb1c519c6fd23bb\" # Galveston Retrofit Plan (Elevation - 5m)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5f1399f7-1bcd-431b-bf68-c9865df99ecd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Building Wind Fragility mapping\n",
+    "mapping_id = \"62fef3a6cef2881193f2261d\"\n",
+    "fragility_service = FragilityService(client)\n",
+    "mapping_set = MappingSet(fragility_service.get_mapping(mapping_id))\n",
+    "\n",
+    "# wind building damage\n",
+    "w_bldg_dmg = BuildingDamage(client)\n",
+    "w_bldg_dmg.load_remote_input_dataset(\"buildings\", bldg_dataset_id)\n",
+    "w_bldg_dmg.set_input_dataset(\"dfr3_mapping_set\", mapping_set)\n",
+    "w_bldg_dmg.set_parameter(\"result_name\", \"Galveston-w-retrofit-wind-dmg\")\n",
+    "w_bldg_dmg.set_parameter(\"hazard_type\", hazard_type)\n",
+    "w_bldg_dmg.set_parameter(\"hazard_id\", hazard_id)\n",
+    "w_bldg_dmg.set_parameter(\"num_cpu\", 8)\n",
+    "w_bldg_dmg.run_analysis()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "97c326dd-946a-4c6a-95af-15bd40e88feb",
+   "metadata": {},
+   "source": [
+    "## Surge-Wave building damage for Galveston"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f6730bfb-fc39-4343-becf-d08074996cae",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sw_bldg_dmg_retrofit = BuildingDamage(client)\n",
+    "sw_bldg_dmg_retrofit.load_remote_input_dataset(\"buildings\", bldg_dataset_id)\n",
+    "\n",
+    "# Surge-wave mapping\n",
+    "mapping_id = \"6303e51bd76c6d0e1f6be080\"\n",
+    "mapping_set = MappingSet(fragility_service.get_mapping(mapping_id))\n",
+    "\n",
+    "\n",
+    "sw_bldg_dmg_retrofit.load_remote_input_dataset(\"retrofit_strategy\", retrofit_plan)\n",
+    "sw_bldg_dmg_retrofit.set_input_dataset('dfr3_mapping_set', mapping_set)\n",
+    "sw_bldg_dmg_retrofit.set_parameter(\"result_name\", \"Galveston-w-retrofit-sw-dmg-w\")\n",
+    "sw_bldg_dmg_retrofit.set_parameter(\"hazard_type\", hazard_type)\n",
+    "sw_bldg_dmg_retrofit.set_parameter(\"hazard_id\", hazard_id)\n",
+    "sw_bldg_dmg_retrofit.set_parameter(\"num_cpu\", 8)\n",
+    "sw_bldg_dmg_retrofit.run_analysis()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3aa5aa02-4930-4824-9bbc-a2bd6e737092",
+   "metadata": {},
+   "source": [
+    "## Flood building damage for Galveston"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "194f3541-c98f-4e51-a824-cd0ccab34573",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# flood building damage\n",
+    "f_bldg_dmg_retrofit = BuildingDamage(client)\n",
+    "f_bldg_dmg_retrofit.load_remote_input_dataset(\"buildings\", bldg_dataset_id)\n",
+    "\n",
+    "# Flood mapping\n",
+    "mapping_id = \"62fefd688a30d30dac57bbd7\"\n",
+    "mapping_set = MappingSet(fragility_service.get_mapping(mapping_id))\n",
+    "\n",
+    "f_bldg_dmg_retrofit.load_remote_input_dataset(\"retrofit_strategy\", retrofit_plan)\n",
+    "f_bldg_dmg_retrofit.set_input_dataset('dfr3_mapping_set', mapping_set)\n",
+    "f_bldg_dmg_retrofit.set_parameter(\"result_name\", \"Galveston-w-retrofit-flood-dmg\")\n",
+    "f_bldg_dmg_retrofit.set_parameter(\"hazard_type\", hazard_type)\n",
+    "f_bldg_dmg_retrofit.set_parameter(\"hazard_id\", hazard_id)\n",
+    "f_bldg_dmg_retrofit.set_parameter(\"num_cpu\", 8)\n",
+    "f_bldg_dmg_retrofit.run_analysis()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a9112606-e97f-4ea1-a287-1563bed54693",
+   "metadata": {},
+   "source": [
+    "## Combine wind, wave and surge building damage"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f89c1e66-a8f2-44ac-a1d7-7ef676eea6dd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "surge_wave_damage_r = sw_bldg_dmg_retrofit.get_output_dataset(\"ds_result\")\n",
+    "wind_damage = w_bldg_dmg.get_output_dataset(\"ds_result\")  # no change\n",
+    "flood_damage_r = f_bldg_dmg_retrofit.get_output_dataset(\"ds_result\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b16dea3d-2fd2-483c-8c8a-84665df31d88",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "combined_bldg_dmg_retrofit = CombinedWindWaveSurgeBuildingDamage(client)\n",
+    "result_name = \"Galveston-w-retrofit-combined-dmg-w\"\n",
+    "combined_bldg_dmg_retrofit.set_input_dataset(\"surge_wave_damage\", surge_wave_damage_r)\n",
+    "combined_bldg_dmg_retrofit.set_input_dataset(\"wind_damage\", wind_damage)\n",
+    "combined_bldg_dmg_retrofit.set_input_dataset(\"flood_damage\", flood_damage_r)\n",
+    "combined_bldg_dmg_retrofit.set_parameter(\"result_name\", result_name)\n",
+    "combined_bldg_dmg_retrofit.run_analysis()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ca8dc90e-b1c8-4ff3-99da-54e041700e07",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "combined_dmg_retrofit = combined_bldg_dmg_retrofit.get_output_dataset(\"ds_result\")\n",
+    "combined_dmg_retrofit_df = combined_dmg_retrofit.get_dataframe_from_csv(low_memory=False)\n",
+    "\n",
+    "# Display top 5 rows of output data\n",
+    "combined_dmg_retrofit_df.head()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4ad1f635-d4d2-44ed-987d-5db2114a154a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "combined_dmg_retrofit_rs = combined_bldg_dmg_retrofit.get_output_dataset(\"result\")\n",
+    "combined_dmg_retrofit_df_rs = combined_dmg_retrofit_rs.get_dataframe_from_csv(low_memory=False)\n",
+    "\n",
+    "# Display top 5 rows of output data\n",
+    "combined_dmg_retrofit_df_rs"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "828e824b",
+   "metadata": {},
+   "source": [
+    "### Archetype Mapping\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d975ad1d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "buildings = Dataset.from_data_service(bldg_dataset_id, data_service)\n",
+    "bldg_gdf = buildings.get_dataframe_from_shapefile()\n",
+    "bldg_gdf.head()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b055f2d7",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "arch_mapping = Dataset.from_data_service(\n",
+    "    \"63dc1f1362b9d001e6a1b485\", data_service\n",
+    ").get_dataframe_from_csv()\n",
+    "arch_mapping"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "61854765",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "max_dmg_state_df = DataProcessUtil.get_max_damage_state(combined_dmg_retrofit_df)\n",
+    "max_dmg_state_df"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "27114b4d",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ret_json = DataProcessUtil.create_mapped_dmg_result_gal(\n",
+    "    bldg_gdf, combined_dmg_retrofit_df_rs, arch_mapping, \"max_state\", \"arch_wind\"\n",
+    ")\n",
+    "ret_json"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "88a5d556",
+   "metadata": {},
+   "source": [
+    "## Electric Power Pole Damage\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ed824b73",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# EPF fragility mapping\n",
+    "epf_mapping_id = \"62fac92ecef2881193f22613\"\n",
+    "epf_mapping_set = MappingSet(fragility_service.get_mapping(epf_mapping_id))\n",
+    "\n",
+    "epf_dmg_hurricane_galveston = EpfDamage(client)\n",
+    "epf_dmg_hurricane_galveston.load_remote_input_dataset(\n",
+    "    \"epfs\", \"62fc000f88470b319561b58d\"\n",
+    ")\n",
+    "epf_dmg_hurricane_galveston.set_input_dataset(\"dfr3_mapping_set\", epf_mapping_set)\n",
+    "epf_dmg_hurricane_galveston.set_parameter(\n",
+    "    \"result_name\", \"Galveston-hurricane-epf-damage\"\n",
+    ")\n",
+    "epf_dmg_hurricane_galveston.set_parameter(\n",
+    "    \"fragility_key\", \"Non-Retrofit Fragility ID Code\"\n",
+    ")\n",
+    "epf_dmg_hurricane_galveston.set_parameter(\"hazard_type\", hazard_type)\n",
+    "epf_dmg_hurricane_galveston.set_parameter(\"hazard_id\", hazard_id)\n",
+    "epf_dmg_hurricane_galveston.set_parameter(\"num_cpu\", 8)\n",
+    "\n",
+    "# Run Analysis\n",
+    "epf_dmg_hurricane_galveston.run_analysis()\n",
+    "epf_dmg_result = epf_dmg_hurricane_galveston.get_output_dataset(\"result\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "9e8e1ca0",
+   "metadata": {},
+   "source": [
+    "## Monte Carlo Failure Probability\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "761889f1-3dc1-448a-8ef4-6faf0fda0f69",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mc_retrofit = MonteCarloFailureProbability(client)\n",
+    "mc_retrofit.set_input_dataset(\"damage\", combined_dmg_retrofit)\n",
+    "mc_retrofit.set_parameter(\"result_name\", \"galveston_w_retrofit_combined_bldg_mc\")\n",
+    "mc_retrofit.set_parameter(\"num_cpu\", 8)\n",
+    "mc_retrofit.set_parameter(\"num_samples\", 100)\n",
+    "mc_retrofit.set_parameter(\"damage_interval_keys\", [\"DS_0\", \"DS_1\", \"DS_2\", \"DS_3\"])\n",
+    "mc_retrofit.set_parameter(\"failure_state_keys\", [\"DS_2\", \"DS_3\", \"DS_4\"])\n",
+    "mc_retrofit.run_analysis()\n",
+    "\n",
+    "gal_bldg_damage_mcs_samples_retrofit = mc_retrofit.get_output_dataset(\"sample_failure_state\")\n",
+    "gal_bldg_damage_mcs_samples_retrofit_df = gal_bldg_damage_mcs_samples_retrofit.get_dataframe_from_csv()\n",
+    "gal_bldg_damage_mcs_samples_retrofit_df.head()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "507233a6",
+   "metadata": {},
+   "source": [
+    "### Clustering\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d165ebb3-9ea4-40a8-83ba-19f134bc8cad",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ret_json = DataProcessUtil.create_mapped_func_result(\n",
+    "    bldg_gdf, gal_bldg_damage_mcs_samples_retrofit_df, arch_mapping, arch_col=\"arch_wind\"\n",
+    ")\n",
+    "with open(\"galveston_w_retrofit_mcs_cluster.json\", \"w\") as f:\n",
+    "    json.dump(ret_json, f, indent=2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "81ca775d-9c49-47ec-b3ef-e768552bac58",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "gal_bldg_failure_probability = mc_retrofit.get_output_dataset(\n",
+    "    \"failure_probability\"\n",
+    ")  # get buildings failure probabilities"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "837544c4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "mc = MonteCarloFailureProbability(client)\n",
+    "mc.set_input_dataset(\"damage\", epf_dmg_result)\n",
+    "mc.set_parameter(\"result_name\", \"epf_mc\")\n",
+    "mc.set_parameter(\"num_cpu\", 8)\n",
+    "mc.set_parameter(\"num_samples\", 100)\n",
+    "mc.set_parameter(\"damage_interval_keys\", [\"DS_0\", \"DS_1\", \"DS_2\", \"DS_3\"])\n",
+    "mc.set_parameter(\"failure_state_keys\", [\"DS_2\", \"DS_3\", \"DS_4\"])\n",
+    "mc.run_analysis()\n",
+    "\n",
+    "gal_pole_damage_mcs_samples = mc.get_output_dataset(\"sample_failure_state\")\n",
+    "gal_pole_damage_mcs_samples_df = gal_pole_damage_mcs_samples.get_dataframe_from_csv()\n",
+    "gal_pole_damage_mcs_samples_df.head()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "44c772d4",
+   "metadata": {},
+   "source": [
+    "## Building Functionality\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "81e795e5-c336-4abd-b79a-8a1358f4f9e2",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "gal_bldg_func_retrofit = BuildingFunctionality(client)\n",
+    "\n",
+    "gal_bldg_func_retrofit.set_input_dataset(\n",
+    "    \"building_damage_mcs_samples\", gal_bldg_damage_mcs_samples_retrofit\n",
+    ")\n",
+    "gal_bldg_func_retrofit.set_input_dataset(\"poles_damage_mcs_samples\", gal_pole_damage_mcs_samples)\n",
+    "gal_bldg_func_retrofit.load_remote_input_dataset(\n",
+    "    \"interdependency_dictionary\", \"63e5af0262d82d2f5a1058ea\"\n",
+    ")\n",
+    "\n",
+    "gal_bldg_func_retrofit.set_parameter(\"result_name\", \"gal_w_retrofit_mcs_functionality_probability\")\n",
+    "gal_bldg_func_retrofit.run_analysis()\n",
+    "\n",
+    "gal_bldg_func_retrofit_samples_df = gal_bldg_func_retrofit.get_output_dataset(\n",
+    "    \"functionality_samples\"\n",
+    ").get_dataframe_from_csv()\n",
+    "gal_bldg_func_retrofit_samples_df.head()"
+   ]
+  },
+  {
+   "cell_type": "raw",
+   "id": "91383ed4-b626-43e5-8ff3-918357be908f",
+   "metadata": {},
+   "source": [
+    "df_gal_bldg_retrofit_func_probability = gal_bldg_func_retrofit.get_output_dataset('functionality_probability').get_dataframe_from_csv()\n",
+    "df_gal_bldg_retrofit_func_probability = df_gal_bldg_retrofit_func_probability.rename(columns={\"building_guid\": \"guid\"})\n",
+    "func_prob_target = 0.40\n",
+    "df_gal_bldg_retrofit_func_probability.loc[df_gal_bldg_retrofit_func_probability['probability'].isna(), 'functionality'] = 1 # Assumed to be connected to an undamaged/unanalyzed power network for now.\n",
+    "df_gal_bldg_retrofit_func_probability.loc[df_gal_bldg_retrofit_func_probability['probability'] <= func_prob_target, 'functionality'] = 0 # Non-Functional\n",
+    "df_gal_bldg_retrofit_func_probability.loc[df_gal_bldg_retrofit_func_probability['probability'] > func_prob_target, 'functionality'] = 1 # Functional\n",
+    "df_gal_bldg_retrofit_func_probability.loc[df_gal_bldg_retrofit_func_probability['probability'].isna(), 'functionality_state'] = 'Functional' # Assumed to be connected to an undamaged/unanalyzed power network for now.\n",
+    "df_gal_bldg_retrofit_func_probability.loc[df_gal_bldg_retrofit_func_probability['probability'] <= func_prob_target, 'functionality_state'] = 'Non-Functional' # Non-Functional\n",
+    "df_gal_bldg_retrofit_func_probability.loc[df_gal_bldg_retrofit_func_probability['probability'] > func_prob_target, 'functionality_state'] = 'Functional' # Functional\n",
+    "df_gal_bldg_retrofit_func_probability.head()"
+   ]
+  },
+  {
+   "cell_type": "raw",
+   "id": "7cdcf98c-5ae1-4f8c-8107-bad56d935cc8",
+   "metadata": {},
+   "source": [
+    "### Plot of the distribution of functionality state for buildings\n",
+    "indexes = df_gal_bldg_retrofit_func_probability['functionality_state'].value_counts(normalize=True).mul(100).index.tolist()\n",
+    "values = df_gal_bldg_retrofit_func_probability['functionality_state'].value_counts(normalize=True).mul(100).tolist()\n",
+    "\n",
+    "fig, ax = plt.subplots(figsize=(4, 2.5), dpi=200)\n",
+    "\n",
+    "bars = ax.bar(x=indexes, height=values,)\n",
+    "\n",
+    "for bar in bars:\n",
+    "    ax.text(bar.get_x() + bar.get_width() / 2,\n",
+    "            bar.get_height() + 3,f'% {bar.get_height() :.1f}',\n",
+    "            horizontalalignment='center')\n",
+    "\n",
+    "fig.tight_layout()\n",
+    "ax.set_ylim([0,100])\n",
+    "ax.set_xlabel('Damage State', labelpad=15)\n",
+    "ax.set_ylabel('Percentage', labelpad=15)\n",
+    "ax.set_title('Functionality Percentage (Buildings and Substations) with Retrofit', pad=15)\n",
+    "ax.set(frame_on=False);"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "801cee9d-0170-4817-a98e-62ac7ffa7748",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "ret_json = DataProcessUtil.create_mapped_func_result(\n",
+    "    bldg_gdf, gal_bldg_func_retrofit_samples_df, arch_mapping, arch_col=\"arch_wind\"\n",
+    ")\n",
+    "with open(\"galveston_w_retrofit_bldg_func_cluster.json\", \"w\") as f:\n",
+    "    json.dump(ret_json, f, indent=2)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "08f62ae4",
+   "metadata": {},
+   "source": [
+    "# Capital Shocks\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "8b64b451-0049-47f1-8b04-d128fd98b28e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Create Capital shocks analysis\n",
+    "capital_shocks = CapitalShocks(client)\n",
+    "building_to_sectors_id = \"640200da475d895dfc2de1bd\"\n",
+    "# Load remote datasets\n",
+    "capital_shocks.load_remote_input_dataset(\"buildings_to_sectors\", building_to_sectors_id)\n",
+    "capital_shocks.load_remote_input_dataset(\"buildings\", bldg_dataset_id)\n",
+    "capital_shocks.set_input_dataset(\"failure_probability\", gal_bldg_failure_probability)\n",
+    "\n",
+    "capital_shocks.set_parameter(\n",
+    "    \"result_name\", \"gal_w_retrofit_sector_shocks\"\n",
+    ")  # name of csv file with results"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "94a9200a-029f-4ccf-ae27-e7f9b1dcea7c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Run capital shocks analysis\n",
+    "capital_shocks.run_analysis()\n",
+    "\n",
+    "sector_shocks_result = capital_shocks.get_output_dataset(\"sector_shocks\")\n",
+    "sector_shocks_result.get_dataframe_from_csv()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0ff5fc0a",
+   "metadata": {},
+   "source": [
+    "# CGE\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "471efa22",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "galveston_cge = GalvestonCGEModel(client)\n",
+    "\n",
+    "galveston_cge.set_parameter(\"model_iterations\", 1)\n",
+    "galveston_cge.load_remote_input_dataset(\"SAM\", \"641e1fccea308903b2b8c51a\")\n",
+    "galveston_cge.load_remote_input_dataset(\"BB\", \"641e1fff34810d74880b3985\")\n",
+    "galveston_cge.load_remote_input_dataset(\"MISCH\", \"641e21a702414a24a5436dfe\")\n",
+    "galveston_cge.load_remote_input_dataset(\"EMPLOY\", \"641e2152ea308903b2b8c51c\")\n",
+    "galveston_cge.load_remote_input_dataset(\"JOBCR\", \"641e209eea308903b2b8c51b\")\n",
+    "galveston_cge.load_remote_input_dataset(\"OUTCR\", \"641e20f134810d74880b3986\")\n",
+    "galveston_cge.set_input_dataset(\"sector_shocks\", sector_shocks_result)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bd952c8f",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "galveston_cge.run_analysis()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "34636105",
+   "metadata": {},
+   "source": [
+    "## Population Dislocation\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "5687353b",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "pop_dis = PopulationDislocation(client)\n",
+    "value_loss = \"60354810e379f22e16560dbd\"\n",
+    "bg_data = \"603545f2dcda03378087e708\"\n",
+    "# hua_result_id = \"63ee615d62b9d001e6a2b660\" # city\n",
+    "hua_result_id = \"63ff8e895367c2261b4cb2ef\"  # island\n",
+    "\n",
+    "pop_dis.load_remote_input_dataset(\"block_group_data\", bg_data)\n",
+    "pop_dis.load_remote_input_dataset(\"value_loss_param\", value_loss)\n",
+    "pop_dis.load_remote_input_dataset(\"housing_unit_allocation\", hua_result_id)\n",
+    "\n",
+    "pop_dis.set_input_dataset(\"building_dmg\", combined_dmg_retrofit)\n",
+    "\n",
+    "result_name = \"galveston-w-retrofit-pop-disl-results\"\n",
+    "seed = 1111\n",
+    "\n",
+    "pop_dis.set_parameter(\"result_name\", result_name)\n",
+    "pop_dis.set_parameter(\"seed\", seed)\n",
+    "pop_dis.run_analysis()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "be72da00",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "population_dislocation_result = pop_dis.get_output_dataset(\"result\")\n",
+    "population_dislocation_result_df = population_dislocation_result.get_dataframe_from_csv(\n",
+    "    low_memory=False\n",
+    ")\n",
+    "population_dislocation_result_df.head()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "123208de",
+   "metadata": {},
+   "source": [
+    "## Housing Houshold Recovery Sequentials\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "183e1e00",
+   "metadata": {},
+   "source": [
+    "### Social Vulnerabilities\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cf28d307",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "social_vulnerability = SocialVulnerability(client)\n",
+    "\n",
+    "social_vulnerability.set_parameter(\"result_name\", \"gal_w_retrofit_social_vulnerabilty\")\n",
+    "social_vulnerability.load_remote_input_dataset(\n",
+    "    \"national_vulnerability_feature_averages\", \"63d178c2a011a9746c948115\"\n",
+    ")\n",
+    "social_vulnerability.load_remote_input_dataset(\n",
+    "    \"social_vulnerability_demographic_factors\", \"63d17e81a011a9746c94811b\"\n",
+    ")\n",
+    "social_vulnerability.run_analysis()\n",
+    "sv_result = social_vulnerability.get_output_dataset(\"sv_result\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6d697f61",
+   "metadata": {},
+   "source": [
+    "### HHRS\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9011551e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Population dislocation result aggregated to the block group level.\n",
+    "# Transition probability matrix per social vulnerability level.\n",
+    "transition_probability_matrix = \"60f5e2ae544e944c3cec0794\"\n",
+    "# Initial mass probability function for stage 0.\n",
+    "initial_probability_vector = \"60f5e918544e944c3cec668b\"  # this is only for galveston???\n",
+    "\n",
+    "# Create housing recovery instance\n",
+    "housing_recovery = HousingRecoverySequential(client)\n",
+    "\n",
+    "# Load input datasets\n",
+    "housing_recovery.set_input_dataset(\n",
+    "    \"population_dislocation_block\", population_dislocation_result\n",
+    ")\n",
+    "housing_recovery.load_remote_input_dataset(\"tpm\", transition_probability_matrix)\n",
+    "housing_recovery.load_remote_input_dataset(\n",
+    "    \"initial_stage_probabilities\", initial_probability_vector\n",
+    ")\n",
+    "\n",
+    "# Chain with SV output\n",
+    "housing_recovery.set_input_dataset(\"sv_result\", sv_result)\n",
+    "\n",
+    "# Initial value to seed the random number generator to ensure replication\n",
+    "seed = 1111\n",
+    "# A size of the analysis time step.\n",
+    "t_delta = 1.0\n",
+    "# Total duration.\n",
+    "t_final = 90.0\n",
+    "\n",
+    "\n",
+    "# Specify the result name\n",
+    "result_name = \"gal_w_retrofit_housing_recovery_result\"\n",
+    "\n",
+    "# Set analysis parameters\n",
+    "housing_recovery.set_parameter(\"result_name\", result_name)\n",
+    "housing_recovery.set_parameter(\"seed\", seed)\n",
+    "housing_recovery.set_parameter(\"t_delta\", t_delta)\n",
+    "housing_recovery.set_parameter(\"t_final\", t_final)\n",
+    "\n",
+    "housing_recovery.run()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "62a0730a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "HH_stagehistory_DF = housing_recovery.get_output_dataset(\n",
+    "    \"ds_result\"\n",
+    ").get_dataframe_from_csv()\n",
+    "timesteps = [\"1\", \"7\", \"13\", \"25\", \"49\", \"85\"]  # t0, t6, t12, t24, t48\n",
+    "HHRSOutputProcess.get_hhrs_stage_count(timesteps, HH_stagehistory_DF)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "f8f98416-c962-44f0-b656-600755264d6a",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.18"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}