I have original data as a 700000's rows excel, with geometry data in hexwkb format. I want to plot it and make some spatial operations on it like intersect, distance and buffer, on a jupyter notebook. Half of the geometries are null. Part of the remaining ones have apparently invalid geometries.

I had succeed in plotting the first 100 lines, apparently with fine geometries, but I'm struggling to plot all the data.

This code worked for lines with no geometry problems:

Data example

id (int64) | geom (object)

1 | '0105000020E610000001000...

import pandas as pd
import geopandas as gpd
from shapely import wkb
from shapely.geometry import MultiLineString

trips= df.dropna(subset=['geom'])

# create column with converted geometry

def convert_to_hexwkb(geomString):
    geometry = wkb.loads(geomString, hex=True)
    return geometry
trips.drop('geom', axis=1, inplace=True)

# convert to GeoDataFrame


>> MULTILINESTRING ((-9.1474504470825 38.744022369385, -9.147529602050801 38.744121551514, -9.14...

# show trips map

>> got a nice map here

But when I run this to the entire data I get the following error given from the shapely -> geos library, during conversion of string to hexwkb:

WKBReadingError: Could not create geometry because of errors while reading input.

IllegalArgumentException: point array must contain 0 or >1 elements

I couldn't find how to apply Geopandas.GeoSeries.is_empty function to find empty geometries, because it was not a geodataframe at that point. Same for is_valid function from shapely library, since the field was not geometry type.

I've tried to delete exceptional rows with this:

for i, item in enumerate(trips['geom']):
    trips.at[i,'geometry'] = wkb.loads(item, hex=True)
    trips.drop([i], inplace=True)

And got the errors:

IllegalArgumentException: point array must contain 0 or >1 elements

WKBReadingError: Could not create geometry because of errors while reading input.

another exception occurred: KeyError: '[791] not found in axis' - This related with how the for cycle was constructed probably.

If I run this for debug:

def convert_to_hexwkb(geomString):
        geometry = wkb.loads(geomString, hex=True)
        return geometry
        return np.nan


I get these errors, multiplied for several lines:

ParseException: Unexpected EOF parsing WKB

ParseException: Premature end of HEX string

Any clue of what should I do to clean geometries of my dataset?

  • At least you can filter out trips which have exactly one point.
    – user30184
    May 11, 2020 at 20:27
  • What do you get when using trips = df.dropna(subset=['geom']).reset_index(drop=True) and then for loop? May 11, 2020 at 21:29
  • @KadirŞahbaz, made no difference, I've got the same errors.
    – danalif
    May 11, 2020 at 22:51

1 Answer 1


Try this:

import pandas as pd
import geopandas as gpd
import shapely
excel = r"C:\TEMP\ovrig_vag.xlsx" #Roads as multilinestrings wkb's, and various attributes
df = pd.read_excel(excel) #Create a pandas df
# df.shape
# Out: (474399, 11)

#I have a column named wkb. Modify some rows to make them invalid:
dfempty = df.sample(100)
dfempty["wkb"] = '' #Empty strings

dfnone = df.sample(100)
dfnone["wkb"] = None #None

dfabc = df.sample(100)
dfabc["wkb"] = 'abc' #Invalid string

def trywkb(wkb):
    """A function which tries to create a shapely geometry from a wkb,
        if the geometry is valid, it returns it and the string 'valid',
        if not returns the input wkb and the exception message"""
        geometry = shapely.from_wkb(wkb)
        return pd.Series([geometry, "valid"])
    except Exception as e:
        return pd.Series([wkb, str(e)])

df[["geometry", "validity"]] = df.apply(lambda x: trywkb(x.wkb), axis=1)
# df[["geometry", "validity"]].head(3)
# Out: 
#                                             geometry validity
# 0  MULTILINESTRING ((395958.5480000004 6133594.20...    valid
# 1  MULTILINESTRING ((396293.9639999997 6133965.64...    valid
# 2  MULTILINESTRING ((396325.72300000023 6133982.2...    valid

#There are valid geometries, and two types of invalid geometries:
# df.validity.unique()
# array(['valid', 'ParseException: Unexpected EOF parsing WKB',
#        'ParseException: Premature end of HEX string'], dtype=object)

#Create a geodataframe of the valid
dfvalid = df.loc[df["validity"]=="valid"]
gdf = gpd.GeoDataFrame(data=dfvalid, geometry=dfvalid["geometry"])

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