- Update 20/02/20 after further testing:
I have 2 other shapefiles (one for UK by Postcode Area and one by Parl Constituency). When using gv.Shape with these I do not need to set the projection used to plot successfully, unlike with the one discussed in my original post. I can also successfully produce choropleths for these using gv.Polygons:
When I checked the projection used by these it was {'init': 'epsg:4326'} so I changed the projection on my lad19 shapefile to match that:
gdf = gdf.to_crs(epsg=4326)
however when I attempted to produce the choropleth using gv.Polygons it failed with the same error as the first one that I documented previously.
This feel likes I am close to a solution, does any one have any suggestions?
- Original Start:
I have downloaded this UK shapefile: https://geoportal.statistics.gov.uk/datasets/local-authority-districts-december-2019-boundaries-uk-buc
I can successfully create an interactive UK Choropleth using the following code (gv.Shape method):
import pandas as pd
import numpy as np
import geopandas as gpd
import random
import copy
import feather
import matplotlib.pyplot as plt
import seaborn as sns
import plotly.graph_objects as go
import plotly.express as px
import panel as pn
import holoviews as hv
import geoviews as gv
import geoviews.feature as gf
import geoviews.tile_sources as gvts
import cartopy
import cartopy.feature as cf
from geoviews import opts
from holoviews import opts, streams
from holoviews.plotting.links import DataLink
from cartopy import crs as ccrs
import hvplot.pandas # noqa
import colorcet as cc
from colorcet.plotting import swatch
sns.set_style()
hv.extension("bokeh","plotly")
# TO SET NUMBER OF ROWS DISPLAYED:
pd.set_option("display.min_rows",0)
# TO SET NUMBER OF COLUMNS DISPLAYED:
pd.set_option("display.max_columns",0)
# LOAD SHAPEFILE USING gv.Shape
In [3]: shapefile = "../level3_LAD19_CONTAINS_4_LE
...: VELS_OF_DETAIL/Local_Authority_Districts_December_2019_Boundaries_UK_BUC
...: /Local_Authority_Districts_December_2019_Boundaries_UK_BUC.shp"
...: gv.Shape.from_shapefile(shapefile, crs=ccrs.OSGB())
Out[3]: :Polygons [Longitude,Latitude]
In [4]: # IDENTIFY WHICH ATTRIBUTES ARE IN SHAPEFILE - SO WE KNOW WHICH ATTRIBUTE TO JOIN ON:
...: shapes = cartopy.io.shapereader.Reader(shapefile)
...: list(shapes.records())[0]
Out[4]: <Record: <shapely.geometry.polygon.Polygon object at 0x1c34bc0550>, {'objectid': 1, 'lad19cd': 'E06000001', 'lad19nm': 'Hartlepool', 'lad19nmw': None, 'bng_e': 447160, 'bng_n': 531474, 'long': -1.27018, 'lat': 54.67614, 'st_areasha': 96845510.24630864, 'st_lengths': 50305.32505760145}, <fields>>
# LOAD DF THAT CONTAINS ALL 382 UK LOCAL AUTHORITY DISTRICTS:
In [5]: demo_file = pd.read_feather("../stack_overflow_demo_190320.feather")
...: demo_file.head()
Out[5]:
lad19_code lad19_name geography total_population
0 E06000047 County Durham Unitary Authority 526980
1 E06000005 Darlington Unitary Authority 106566
2 E06000001 Hartlepool Unitary Authority 93242
3 E06000002 Middlesbrough Unitary Authority 140545
4 E06000057 Northumberland Unitary Authority 320274
# SUCCESSFULLY PLOT UK CHOROPLETH:
In [6]: lad19_heatmap = gv.Shape.from_records(
...: shapes.records(),
...: demo_file,
...: on={"lad19cd":"lad19_code"},
...: value="total_population",
...: index="lad19_name", label = "Local Authority Districts UK Population",
...: crs=ccrs.OSGB()).opts(tools=["hover","tap"],
...: cmap = "Reds", colorbar=True,
...: hover_line_color="blue", hover_alpha=0.2,
...: line_width = 2, show_legend=True,
...: legend_position="top",
...: width = 600, height = 800)
...:
...: lad19_heatmap
Out[6]: :Polygons [Longitude,Latitude] (lad19_name,total_population)
My issue is that I want to move towards a more interactive plot, whereby the user selects a Polygon on the map on the left and a table and/or some other plots appear on the right for the given polygon / Local Authority District as per: http://holoviews.org/gallery/demos/bokeh/choropleth_data_link.html
To do this I had to switch from using gv.Shape to gv.Polygons and no matter what I try I can not get it to successfully work.
Unsuccessful gv.Polygons Method:
# LOAD MY SHAPEFILE AS A GEOPANDAS DATAFRAME:
In [10]: gdf = gpd.read_file("../level3_LAD19_CONTAINS_4_LEVELS_OF_DETAIL/Local_Aut
...: hority_Districts_December_2019_Boundaries_UK_BUC/Local_Authority_Districts_December_2019_Boundaries_UK_B
...: UC.shp")
...: gdf.head()
Out[10]:
objectid lad19cd lad19nm lad19nmw bng_e bng_n long lat st_areasha st_lengths geometry
0 1 E06000001 Hartlepool None 447160 531474 -1.27018 54.676140 9.684551e+07 50305.325058 POLYGON ((448986.025 536729.674, 453194.600 53...
1 2 E06000002 Middlesbrough None 451141 516887 -1.21099 54.544670 5.290846e+07 34964.406313 POLYGON ((451752.698 520561.900, 452424.399 52...
2 3 E06000003 Redcar and Cleveland None 464361 519597 -1.00608 54.567520 2.486791e+08 83939.752513 POLYGON ((451965.636 521061.756, 454348.400 52...
3 4 E06000004 Stockton-on-Tees None 444940 518183 -1.30664 54.556911 2.071591e+08 87075.860824 POLYGON ((451965.636 521061.756, 451752.698 52...
4 5 E06000005 Darlington None 428029 515648 -1.56835 54.535339 1.988128e+08 91926.839545 POLYGON ((419709.299 515678.298, 419162.998 51...
# In the previous step I had no way to specify the projection used, so here I confirm that OSGB is used:
In [11]: gdf.crs
Out[11]: {'init': 'epsg:27700'}
I checked here https://spatialreference.org/ref/epsg/osgb-1936-british-national-grid/ and this appears to be the desired projection ie OSGB.
# PLOT JUST ON THE GDF (HAS PROJECTION VALUE SET), NOT THE MERGED DF AND GDF
In [12]:gv.Polygons(gdf, vdims='lad1nm'
...: ).opts(projection=ccrs.OSGB(),
...: tools=['hover','tap'],
...: width=450, height=600,
...: color_index='total_population',
...: colorbar=True
...: )
DataError: Expected Polygons instance to declare two key dimensions corresponding to the geometry coordinates but 3 dimensions were found which did not refer to any columns.
GeoPandasInterface expects a list of tabular data, for more information on supported datatypes see http://holoviews.org/user_guide/Tabular_Datasets.html
So I thought that I might have to explicitly set the kdims:
# PLOT JUST ON THE GDF, NOT THE MERGED DF AND GDF (HAS PROJECTION VALUE SET)
In [13]: gv.Polygons(gdf, kdims=["long","lat"],vdims='lad1nm'
...: ).opts(projection=ccrs.OSGB(),
...: tools=['hover','tap'],
...: width=450, height=600,
...: color_index='total_population',
...: colorbar=True
...: )
DataError: Expected Polygons instance to declare two key dimensions corresponding to the geometry coordinates but 1 dimensions were found which did not refer to any columns.
GeoPandasInterface expects a list of tabular data, for more information on supported datatypes see http://holoviews.org/user_guide/Tabular_Datasets.html
This gave me a very similar error to before.
From reading the user guide in these error message links it says "Tabular data has a fixed list of column headings, with values stored in an arbitrarily long list of rows. Spreadsheets, relational databases, CSV files, and many other typical data sources fit naturally into this format."
I have attempted this with gdf created from a shapefile and demo_file from csv and feather formats and neither worked successfully.
The final thing that I tried was merging gdf with demo_file df and then attempting to plot the choropleth again:
In [15]: # NEED TO MERGE demo_file DF WITH gdf BEFORE PLOTTING POLYGONS:
...: finalgdf = gpd.GeoDataFrame(pd.merge(demo_file, gdf, left_on="lad19_code",right_on="lad19cd"))
...: finalgdf.drop(columns=["lad19_code","lad19_name"],inplace=True)
...: finalgdf.head()
Out[15]:
geography total_population objectid lad19cd lad19nm lad19nmw bng_e bng_n long lat st_areasha st_lengths geometry
0 Unitary Authority 526980 45 E06000047 County Durham None 410381 532242 -1.84050 54.685131 2.231126e+09 264032.927496 POLYGON ((411575.398 556785.301, 413248.799 55...
1 Unitary Authority 106566 5 E06000005 Darlington None 428029 515648 -1.56835 54.535339 1.988128e+08 91926.839545 POLYGON ((419709.299 515678.298, 419162.998 51...
2 Unitary Authority 93242 1 E06000001 Hartlepool None 447160 531474 -1.27018 54.676140 9.684551e+07 50305.325058 POLYGON ((448986.025 536729.674, 453194.600 53...
3 Unitary Authority 140545 2 E06000002 Middlesbrough None 451141 516887 -1.21099 54.544670 5.290846e+07 34964.406313 POLYGON ((451752.698 520561.900, 452424.399 52...
4 Unitary Authority 320274 54 E06000057 Northumberland None 395322 600699 -2.07523 55.300369 5.033705e+09 445104.766524 MULTIPOLYGON (((391123.704 649427.867, 391525....
In [18]: gv.Polygons(finalgdf, vdims='lad1nm',
...: ).opts(projection=ccrs.OSGB(),
...: tools=['hover','tap'],
...: width=450, height=600,
...: color_index='total_population',
...: colorbar=True
...: )
DataError: Expected Polygons instance to declare two key dimensions corresponding to the geometry coordinates but 3 dimensions were found which did not refer to any columns.
GeoPandasInterface expects a list of tabular data, for more information on supported datatypes see http://holoviews.org/user_guide/Tabular_Datasets.html
But as you can see I got the same error again.
An interesting point was that when I checked the projection used on my merged finalgdf, it came back as NoneType:
In [19]: type(finalgdf.crs)
Out[19]: NoneType
So I set it to OSGB:
In [20]: finalgdf.crs = {'init': 'epsg:27700'}
...: finalgdf.crs
Out[20]: {'init': 'epsg:27700'}
And then repeated my last plot attempt, however I just got the same error again:
In [21]: gv.Polygons(finalgdf, vdims='lad1nm',
...: ).opts(projection=ccrs.OSGB(),
...: tools=['hover','tap'],
...: width=450, height=600,
...: color_index='total_population',
...: colorbar=True
...: )
DataError: Expected Polygons instance to declare two key dimensions corresponding to the geometry coordinates but 3 dimensions were found which did not refer to any columns.
GeoPandasInterface expects a list of tabular data, for more information on supported datatypes see http://holoviews.org/user_guide/Tabular_Datasets.html
I am at a complete lose. Can anyone help me successfully recreate my UK choropleth using gv.Polygons instead of gv.Shape?
Failing that, if there was a way to successfully link my choropleth produced using gv.Shape to data tables and/or other plots as per in http://holoviews.org/gallery/demos/bokeh/choropleth_data_link.html then that would be great. I have tried and failed to get this working too.
Thanks
I am using OSX (10.15.2 (19C57)), firefox 74.0 (64-bit) and I am working in a Jupyter Notebook
Software Versions: (tried to include relevent ones as couldn't fit them all in here - if I am missing any let me know and I'll add them)
# Name Version Build Channel
_anaconda_depends 2019.03 py37_0
anaconda custom py37_1
anaconda-client 1.7.2 py37_0
anaconda-project 0.8.4 py_0
arrow-cpp 0.13.0 py37h8cfbac2_0
bokeh 1.4.0 py37_0
cairo 1.14.12 hc4e6be7_4
cartopy 0.17.0 py37haea56ea_1
colorcet 2.0.2 py_0 pyviz
cython 0.29.14 py37h0a44026_0
descartes 1.1.0 py_4 conda-forge
feather-format 0.4.0 py_1003 conda-forge
fingertips-py 0.2 pypi_0 pypi
flask 1.1.1 py_0
geopandas 0.6.1 py_0
geos 3.7.1 h0a44026_0
geoviews 1.6.5 py_0 pyviz
geoviews-core 1.6.5 py_0 pyviz
holoviews 1.12.7 py_0 pyviz
hvplot 0.5.2 py_0 pyviz
ipykernel 5.1.3 py37h39e3cac_0
ipython 7.9.0 py37h39e3cac_0
ipython_genutils 0.2.0 py37_0
ipywidgets 7.5.1 py_0
jupyter 1.0.0 py37_7
jupyter_client 5.3.4 py37_0
jupyter_console 6.0.0 py37_0
jupyter_core 4.6.1 py37_0
jupyterlab 1.2.3 pyhf63ae98_0
jupyterlab_server 1.0.6 py_0
markdown 3.1.1 py37_0
matplotlib 3.1.1 py37h54f8f79_0
notebook 6.0.2 py37_0
numpy 1.17.3 py37h4174a10_0
pandas 0.25.3 py37h0a44026_0
panel 0.8.0 py_0 pyviz
param 1.9.2 py_0 pyviz
parquet-cpp 1.5.1 2 conda-forge
plotly 4.3.0 py_0 plotly
plotly_express 0.4.1 py_0 plotly
proj4 5.2.0 h0a44026_1
pyarrow 0.13.0 py37hb37e6aa_0 conda-forge
python 3.7.5 h359304d_0
scikit-image 0.15.0 py37h0a44026_0
scikit-learn 0.21.3 py37h27c97d8_0
scipy 1.3.1 py37h1410ff5_0
seaborn 0.9.0 pyh91ea838_1
shapely 1.6.4 py37he8793f5_0
After further testing I created an additional question which more succinctly identifies the cause of this error and more importantly provides a solution:
gv.Polygons DataError When Using OSGB Projection
Closing this question as a duplicate.