Bokeh Mapping Counties - python-3.x

Question

I am attempting to modify this example with county data for Michigan. In short, it's working, but it seems to be adding some extra shapes here and there in the process of drawing the counties. I'm guessing that in some instances (where there are counties with islands), the island part needs to be listed as a separate "county", but I'm not sure about the other case, such as with Wayne county in the lower right part of the state.
Here's a picture of what I currently have:
Here's what I did so far:
Get county data from Bokeh's sample county data just to get the state abbreviation per state number (my second, main data source only has state numbers). For this example, I'll simplify it by just filtering for state number 26).
Get state coordinates ('500k' file) by county from the U.S. Census site.
Use the following code to generate an 'interactive' map of Michigan.
Note: To pip install shapefile (really pyshp), I think I had to download the .whl file from here and then do pip install [path to .whl file].
import pandas as pd
import numpy as np
import shapefile
from bokeh.models import HoverTool, ColumnDataSource
from bokeh.palettes import Viridis6
from bokeh.plotting import figure, show, output_notebook
shpfile=r'Path\500K_US_Counties\cb_2015_us_county_500k.shp'
sf = shapefile.Reader(shpfile)
shapes = sf.shapes()
#Here are the rows from the shape file (plus lat/long coordinates)
rows=[]
lenrow=[]
for i,j in zip(sf.shapeRecords(),sf.shapes()):
rows.append(i.record+[j.points])
if len(i.record+[j.points])!=10:
print("Found record with irrular number of columns")
fields1=sf.fields[1:] #Ignore first field as it is not used (maybe it's a meta field?)
fields=[seq[0] for seq in fields1]+['Long_Lat']#Take the first element in each tuple of the list
c=pd.DataFrame(rows,columns=fields)
try:
c['STATEFP']=c['STATEFP'].astype(int)
except:
pass
#cns=pd.read_csv(r'Path\US_Counties.csv')
#cns=cns[['State Abbr.','STATE num']]
#cns=cns.drop_duplicates('State Abbr.',keep='first')
#c=pd.merge(c,cns,how='left',left_on='STATEFP',right_on='STATE num')
c['Lat']=c['Long_Lat'].apply(lambda x: [e[0] for e in x])
c['Long']=c['Long_Lat'].apply(lambda x: [e[1] for e in x])
#c=c.loc[c['State Abbr.']=='MI']
c=c.loc[c['STATEFP']==26]
#latitudex, longitude=y
county_xs = c['Lat']
county_ys = c['Long']
county_names = c['NAME']
county_colors = [Viridis6[np.random.randint(1,6, size=1).tolist()[0]] for l in aland]
randns=np.random.randint(1,6, size=1).tolist()[0]
#county_colors = [Viridis6[e] for e in randns]
#county_colors = 'b'
source = ColumnDataSource(data=dict(
x=county_xs,
y=county_ys,
color=county_colors,
name=county_names,
#rate=county_rates,
))
output_notebook()
TOOLS="pan,wheel_zoom,box_zoom,reset,hover,save"
p = figure(title="Title", tools=TOOLS,
x_axis_location=None, y_axis_location=None)
p.grid.grid_line_color = None
p.patches('x', 'y', source=source,
fill_color='color', fill_alpha=0.7,
line_color="white", line_width=0.5)
hover = p.select_one(HoverTool)
hover.point_policy = "follow_mouse"
hover.tooltips = [
("Name", "#name"),
#("Unemployment rate)", "#rate%"),
("(Long, Lat)", "($x, $y)"),
]
show(p)
I'm looking for a way to avoid the extra lines and shapes.
Thanks in advance!

Answer 1

I have a solution to this problem, and I think I might even know why it is correct. First, let me show quote from Bryan Van de ven in a Google groups Bokeh discussion:
there is no built-in support for dealing with shapefiles. You will have to convert the data to the simple format that Bokeh understands. (As an aside: it would be great to have a contribution that made dealing with various GIS formats easier).
The format that Bokeh expects for patches is a "list of lists" of points. So something like:
xs = [ [patch0 x-coords], [patch1 x-coords], ... ]
ys = [ [patch1 y-coords], [patch1 y-coords], ... ]
Note that if a patch is comprised of multiple polygons, this is currently expressed by putting NaN values in the sublists. So, the task is basically to convert whatever form of polygon data you have to this format, and then Bokeh can display it.
So it seems like somehow you are ignoring NaNs or otherwise not handling multiple polygons properly. Here is some code that will download US census data, unzip it, read it properly for Bokeh, and make a data frame of lat, long, state, and county.
def get_map_data(shape_data_file, local_file_path):
url = "http://www2.census.gov/geo/tiger/GENZ2015/shp/" + \
shape_data_file + ".zip"
zfile = local_file_path + shape_data_file + ".zip"
sfile = local_file_path + shape_data_file + ".shp"
dfile = local_file_path + shape_data_file + ".dbf"
if not os.path.exists(zfile):
print("Getting file: ", url)
response = requests.get(url)
with open(zfile, "wb") as code:
code.write(response.content)
if not os.path.exists(sfile):
uz_cmd = 'unzip ' + zfile + " -d " + local_file_path
print("Executing command: " + uz_cmd)
os.system(uz_cmd)
shp = open(sfile, "rb")
dbf = open(dfile, "rb")
sf = shapefile.Reader(shp=shp, dbf=dbf)
lats = []
lons = []
ct_name = []
st_id = []
for shprec in sf.shapeRecords():
st_id.append(int(shprec.record[0]))
ct_name.append(shprec.record[5])
lat, lon = map(list, zip(*shprec.shape.points))
indices = shprec.shape.parts.tolist()
lat = [lat[i:j] + [float('NaN')] for i, j in zip(indices, indices[1:]+[None])]
lon = [lon[i:j] + [float('NaN')] for i, j in zip(indices, indices[1:]+[None])]
lat = list(itertools.chain.from_iterable(lat))
lon = list(itertools.chain.from_iterable(lon))
lats.append(lat)
lons.append(lon)
map_data = pd.DataFrame({'x': lats, 'y': lons, 'state': st_id, 'county_name': ct_name})
return map_data
The inputs to this command are a local directory where you want to download the map data to and the other input is the name of the shape file. I know there are at least two available maps from the url in the function above that you could call:
map_low_res = "cb_2015_us_county_20m"
map_high_res = "cb_2015_us_county_500k"
If the US census changes their url, which they certainly will one day, then you will need to change the input file name and the url variable. So, you can call the function above
map_output = get_map_data(map_low_res, ".")
Then you could plot it just as the code in the original question does. Add a color data column first ("county_colors" in the original question), and then set it to the source like this:
source = ColumnDataSource(map_output)
To make this all work you will need to import libraries such as requests, os, itertools, shapefile, bokeh.models.ColumnDataSource, etc...

Answer 2

One solution:
Use the 1:20,000,000 shape file instead of the 1:500,000 file.
It loses some detail around the shape of each county but does not have any extra shapes (and just a couple of extra lines).