39 Working with Shapely Base Geometries containing Z components#

Shapely Base Geometries can not only have an X and Y coordinate but also a Z component. The following introduces how GemGIS is handling Shapely Base Geometries with an additional Z component.

Set File Paths and download Tutorial Data#

If you downloaded the latest GemGIS version from the Github repository, append the path so that the package can be imported successfully. Otherwise, it is recommended to install GemGIS via pip install gemgis and import GemGIS using import gemgis as gg. In addition, the file path to the folder where the data is being stored is set. The tutorial data is downloaded using Pooch (https://www.fatiando.org/pooch/latest/index.html) and stored in the specified folder. Use pip install pooch if Pooch is not installed on your system yet.

[1]:

import gemgis as gg

file_path ='data/39_shapely_base_geometries_with_z_component/'

WARNING (theano.configdefaults): g++ not available, if using conda: `conda install m2w64-toolchain`
C:\Users\ale93371\Anaconda3\envs\test_gempy\lib\site-packages\theano\configdefaults.py:560: UserWarning: DeprecationWarning: there is no c++ compiler.This is deprecated and with Theano 0.11 a c++ compiler will be mandatory
  warnings.warn("DeprecationWarning: there is no c++ compiler."
WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.
WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions.

Point Data#

Points can easily be defined using an X, Y and Z coordinate.

[2]:

import gemgis as gg
from shapely.geometry import Point

point = Point(1,2,3)
point

WARNING (theano.configdefaults): g++ not available, if using conda: `conda install m2w64-toolchain`
C:\Users\ale93371\Anaconda3\envs\test_gempy\lib\site-packages\theano\configdefaults.py:560: UserWarning: DeprecationWarning: there is no c++ compiler.This is deprecated and with Theano 0.11 a c++ compiler will be mandatory
  warnings.warn("DeprecationWarning: there is no c++ compiler."
WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.
WARNING (theano.tensor.blas): Using NumPy C-API based implementation for BLAS functions.

[2]:
../../_images/getting_started_tutorial_39_shapely_base_geometries_with_z_component_4_1.svg
[3]:

point.wkt

[3]:

'POINT Z (1 2 3)'

Despite the Z component, the point is still a regular Shapely Point.

[4]:

type(point)

[4]:

shapely.geometry.point.Point

But the attribute that an object has a z component is now set to True.

[5]:

point.has_z

[5]:

True

Accessing the coordinates#

The coordinates can be accessed via attributes.

[6]:

point.x

[6]:

1.0

[7]:

point.y

[7]:

2.0

[8]:

point.z

[8]:

3.0

Creating a GeoDataFrame and extracting coordinates#

[9]:

import geopandas as gpd

gdf = gpd.GeoDataFrame(geometry=[point, point])
gdf

[9]:
geometry
0 POINT Z (1.00000 2.00000 3.00000)
1 POINT Z (1.00000 2.00000 3.00000)

Extracting Coordinates#

[10]:

gdf_xyz = gg.vector.extract_xyz_points(gdf=gdf)
gdf_xyz

[10]:
geometry X Y Z
0 POINT Z (1.00000 2.00000 3.00000) 1.00 2.00 3.00
1 POINT Z (1.00000 2.00000 3.00000) 1.00 2.00 3.00 
[11]:

gdf_xyz = gg.vector.extract_xyz(gdf=gdf)
gdf_xyz

[11]:
geometry X Y Z
0 POINT Z (1.00000 2.00000 3.00000) 1.00 2.00 3.00
1 POINT Z (1.00000 2.00000 3.00000) 1.00 2.00 3.00

LineString Data#

[12]:

import gemgis as gg
from shapely.geometry import LineString

linestring = LineString(([1,2,3], [4,5,6]))
linestring

[12]:
../../_images/getting_started_tutorial_39_shapely_base_geometries_with_z_component_20_0.svg
[13]:

linestring.wkt

[13]:

'LINESTRING Z (1 2 3, 4 5 6)'

Despite the Z component, the line is still a regular Shapely LineString.

[14]:

type(linestring)

[14]:

shapely.geometry.linestring.LineString

But the attribute that an object has a z component is now set to True.

[15]:

linestring.has_z

[15]:

True

Accessing the coordinates#

The coordinates can be accessed via attributes.

[16]:

list(linestring.coords)

[16]:

[(1.0, 2.0, 3.0), (4.0, 5.0, 6.0)]

Creating a GeoDataFrame and extracting coordinates#

[17]:

import geopandas as gpd

gdf = gpd.GeoDataFrame(geometry=[linestring, linestring])
gdf

[17]:
geometry
0 LINESTRING Z (1.00000 2.00000 3.00000, 4.00000...
1 LINESTRING Z (1.00000 2.00000 3.00000, 4.00000...

Extracting Coordinates#

extract_xy_linestrings(..) will also work for extracting the xyz coordinates as the used Pandas explode(..) function also extracts the Z component of the LineString object. In the subsequent definition of the columns for the coordinates, an additional Z column will be created if a Value error would have been returned before that.

[18]:

gdf_xyz = gg.vector.extract_xy_linestrings(gdf=gdf)
gdf_xyz

[18]:
geometry X Y Z
0 POINT (1.00000 2.00000) 1.00 2.00 3.00
1 POINT (4.00000 5.00000) 4.00 5.00 6.00
2 POINT (1.00000 2.00000) 1.00 2.00 3.00
3 POINT (4.00000 5.00000) 4.00 5.00 6.00

However, a dedicated function to extract the X, Y and Z coordinates from a GeoDataFrame containing LineStrings with a Z component is also implemented in GemGIS -> extract_xyz_linestrings(...).

[19]:

gdf_xyz = gg.vector.extract_xyz_linestrings(gdf=gdf, reset_index=True)
gdf_xyz

[19]:
geometry points X Y Z
0 POINT (1.00000 2.00000) (1.0, 2.0, 3.0) 1.00 2.00 3.00
1 POINT (4.00000 5.00000) (4.0, 5.0, 6.0) 4.00 5.00 6.00
2 POINT (1.00000 2.00000) (1.0, 2.0, 3.0) 1.00 2.00 3.00
3 POINT (4.00000 5.00000) (4.0, 5.0, 6.0) 4.00 5.00 6.00

The coordinates can also be extracted using the common function extract_xyz(...).

[20]:

gdf_xyz = gg.vector.extract_xyz(gdf=gdf)
gdf_xyz

[20]:
geometry X Y Z
0 POINT (1.00000 2.00000) 1.00 2.00 3.00
1 POINT (4.00000 5.00000) 4.00 5.00 6.00
2 POINT (1.00000 2.00000) 1.00 2.00 3.00
3 POINT (4.00000 5.00000) 4.00 5.00 6.00

Polygon Data#

[21]:

import gemgis as gg
from shapely.geometry import Polygon

polygon = Polygon([[0, 0, 0], [1, 0, 0], [1, 1, 0], [0, 1, 0], [0, 0, 0]])
polygon

[21]:
../../_images/getting_started_tutorial_39_shapely_base_geometries_with_z_component_37_0.svg
[22]:

polygon.wkt

[22]:

'POLYGON Z ((0 0 0, 1 0 0, 1 1 0, 0 1 0, 0 0 0))'

Despite the Z component, the line is still a regular Shapely Polygon.

[23]:

type(polygon)

[23]:

shapely.geometry.polygon.Polygon

But the attribute that an object has a z component is now set to True.

[24]:

polygon.has_z

[24]:

True

Accessing the coordinates#

The coordinates can be accessed via attributes.

[25]:

list(polygon.exterior.coords)

[25]:

[(0.0, 0.0, 0.0),
 (1.0, 0.0, 0.0),
 (1.0, 1.0, 0.0),
 (0.0, 1.0, 0.0),
 (0.0, 0.0, 0.0)]

Creating a GeoDataFrame and extracting coordinates#

[26]:

import geopandas as gpd

gdf = gpd.GeoDataFrame(geometry=[polygon, polygon])
gdf

[26]:
geometry
0 POLYGON Z ((0.00000 0.00000 0.00000, 1.00000 0...
1 POLYGON Z ((0.00000 0.00000 0.00000, 1.00000 0...

Extracting Coordinates#

The coordinates can be extracted easily with extract_xyz(...). As the polygons are exploded into LineStrings during the process of extracting the coordinates, the functionality to extract coordinates from Polygons is already present.

[27]:

gdf_xyz = gg.vector.extract_xyz(gdf=gdf)
gdf_xyz

[27]:
geometry X Y Z
0 POINT (0.00000 0.00000) 0.00 0.00 0.00
1 POINT (1.00000 0.00000) 1.00 0.00 0.00
2 POINT (1.00000 1.00000) 1.00 1.00 0.00
3 POINT (0.00000 1.00000) 0.00 1.00 0.00
4 POINT (0.00000 0.00000) 0.00 0.00 0.00
5 POINT (0.00000 0.00000) 0.00 0.00 0.00
6 POINT (1.00000 0.00000) 1.00 0.00 0.00
7 POINT (1.00000 1.00000) 1.00 1.00 0.00
8 POINT (0.00000 1.00000) 0.00 1.00 0.00
9 POINT (0.00000 0.00000) 0.00 0.00 0.00