diff scripts/utils_spatial.py @ 4:e50c63cf96be branch-tests

rearranging folders

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/utils_spatial.py	Mon Sep 11 11:51:50 2017 +0100
@@ -0,0 +1,151 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Wed May 17 11:35:51 2017
+
+@author: mariapanteli
+"""
+import numpy as np
+import json
+import pysal # before shapely in util_plots
+import fiona
+import sys
+sys.path.append('../misc')
+import matplotlib.pyplot as plt
+
+
+def neighbors_from_json_file(data_countries, json_DB='../MergeBL-Smith/data/countries.json'):
+    neighbors = {}
+    with open(json_DB) as json_file:
+        countries_dict = json.load(json_file)
+    country_names = []
+    country_iso = []
+    country_borders_iso = []
+    for country_info in countries_dict:
+        country_names.append(country_info['name']['common'])
+        country_iso.append(country_info['cca3'])
+        country_borders_iso.append(country_info['borders'])
+    # temporary fixes of country names to match json data
+    country_names[country_names.index('United States')] = 'United States of America'
+    country_names[country_names.index('Tanzania')] = 'United Republic of Tanzania'
+    country_names[country_names.index('DR Congo')] = 'Democratic Republic of the Congo'
+    country_names[country_names.index('Czechia')] = 'Czech Republic'
+    for i, country in enumerate(data_countries):
+        neighbors[i] = {} 
+        if country in country_names:
+            if len(country_borders_iso[country_names.index(country)])>0:
+                # if country has neighbors according to json file
+                neighbors_iso = country_borders_iso[country_names.index(country)]
+                neighbors_names = [country_names[country_iso.index(nn)] for nn in neighbors_iso]
+                for neighbor in neighbors_names:
+                    if neighbor in data_countries:
+                        neighbor_idx = np.where(data_countries==neighbor)[0][0]
+                        neighbors[i][neighbor_idx] = 1.0                
+    w = pysal.weights.W(neighbors, id_order=range(len(data_countries)))
+    return w
+
+
+def get_countries_from_shapefile(shapefile):
+    shp = fiona.open(shapefile, 'r')
+    countries = []
+    if shp[0]["properties"].has_key("ADMIN"):
+        country_keyword = "ADMIN"
+    elif shp[0]["properties"].has_key("NAME"):
+        country_keyword = "NAME"
+    else:
+        country_keyword = "admin"
+    for line in shp:
+        countries.append(line["properties"][country_keyword])
+    shp.close()
+    return countries
+
+
+def replace_empty_neighbours_with_KNN(data_countries, w):
+    shapefile = "../MergeBL-Smith/shapefiles/ne_10m_admin_0_countries.shp"
+    no_neighbors_idx = w.islands
+    knn = 10
+    wknn = pysal.knnW_from_shapefile(shapefile, knn)
+    knn_countries = get_countries_from_shapefile(shapefile)
+    neighbors = w.neighbors
+    for nn_idx in no_neighbors_idx:
+        country = data_countries[nn_idx]
+        print country
+        if country not in knn_countries:
+            continue
+        knn_country_idx = knn_countries.index(country)
+        knn_country_neighbors = [knn_countries[nn] for nn in wknn.neighbors[knn_country_idx]]
+        for knn_nn in knn_country_neighbors:
+            if len(neighbors[nn_idx])>2:
+                continue
+            data_country_idx = np.where(data_countries==knn_nn)[0]
+            if len(data_country_idx)>0:
+                neighbors[nn_idx][data_country_idx[0]] = 1.0
+    w = pysal.weights.W(neighbors, id_order=range(len(data_countries)))
+    return w
+
+
+def get_neighbors_for_countries_in_dataset(Y):
+    # neighbors
+    data_countries = np.unique(Y)
+    w = neighbors_from_json_file(data_countries)
+    w = replace_empty_neighbours_with_KNN(data_countries, w)
+    return w, data_countries
+
+
+def from_weights_to_dict(w, data_countries):
+    w_dict = {}
+    for i in w.neighbors:
+        w_dict[data_countries[i]] = [data_countries[nn] for nn in w.neighbors[i]]
+    return w_dict
+
+
+def get_LH_HL_idx(lm, p_vals):
+    sig_idx = np.where(p_vals<0.05)[0]  
+    LH_idx = sig_idx[np.where(lm.q[sig_idx]==2)[0]]
+    HL_idx = sig_idx[np.where(lm.q[sig_idx]==4)[0]]
+    return LH_idx, HL_idx
+
+
+def print_Moran_outliers(y, w, data_countries):
+    lm = pysal.Moran_Local(y, w)
+    p_vals = lm.p_z_sim
+    LH_idx, HL_idx = get_LH_HL_idx(lm, p_vals)
+    print 'LH', zip(data_countries[LH_idx], p_vals[LH_idx])  # LH
+    print 'HL', zip(data_countries[HL_idx], p_vals[HL_idx])  # HL
+
+
+def plot_Moran_scatterplot(y, w, data_countries, out_file=None):
+    lm = pysal.Moran_Local(y, w)
+    p_vals = lm.p_z_sim
+    LH_idx, HL_idx = get_LH_HL_idx(lm, p_vals)
+    
+    ylt  = pysal.lag_spatial(lm.w, lm.y)
+    yt = lm.y
+    yt = (yt - np.mean(yt))/np.std(yt)
+    ylt = (ylt - np.mean(ylt))/np.std(ylt)
+    colors = plt.cm.spectral(np.linspace(0,1,5))
+    quad = np.zeros(yt.shape, dtype=int)
+    quad[np.bitwise_and(ylt > 0, yt > 0)]=1 # HH
+    quad[np.bitwise_and(ylt > 0, yt < 0)]=2 # LH
+    quad[np.bitwise_and(ylt < 0, yt < 0)]=3 # LL
+    quad[np.bitwise_and(ylt < 0, yt > 0)]=4 # HL
+    marker_color = colors[quad]
+    marker_size = 40*np.ones(yt.shape, dtype=int)
+    marker_size[LH_idx] = 140
+    marker_size[HL_idx] = 140
+    
+    plt.figure()
+    plt.scatter(yt, ylt, c=marker_color, s=marker_size, alpha=0.7)
+    plt.xlabel('Value')
+    plt.ylabel('Spatially Lagged Value')
+    plt.axvline(c='black', ls='--')
+    plt.axhline(c='black', ls='--')
+    plt.ylim(min(ylt)-0.5, max(ylt)+0.5)
+    plt.xlim(min(yt)-0.5, max(yt)+1.5)
+    for i in np.concatenate((LH_idx, HL_idx)):
+        plt.annotate(data_countries[i], (yt[i], ylt[i]), xytext=(yt[i]*1.1, ylt[i]*1.1),textcoords='data',arrowprops=dict(arrowstyle="->",connectionstyle="arc3"))
+    extreme_points = np.concatenate(([np.argmin(ylt)], [np.argmax(ylt)], np.where(yt>np.mean(yt)+2.8*np.std(yt))[0], np.where(ylt>np.mean(yt)+2.8*np.std(ylt))[0]))
+    extreme_points = np.array(list(set(extreme_points) - set(np.concatenate((LH_idx, HL_idx)))))
+    for i in extreme_points:
+        plt.annotate(data_countries[i], (yt[i]+0.1, ylt[i]))
+    if out_file is not None:
+        plt.savefig(out_file)