35 Plotting Borehole Data with PyVista#

Borehole data or stratigraphic data can be plotted using GemGIS and PyVista.

Well data provided by the Geological Survey NRW.

a503056d4aa7465887e2cf9e03cdc073

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/35_plotting_borehole_data_with_pyvista/'

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]:

gg.download_gemgis_data.download_tutorial_data(filename="35_plotting_borehole_data_with_pyvista.zip", dirpath=file_path)

Loading Data#

For better visualization, a mesh is loaded displaying a surface in the subsurface. In addition, sample well data is loaded to demonstrate the visualization of well data.

[2]:

import pyvista as pv
import pandas as pd

mesh = pv.read(file_path + 'base.vtk')
mesh

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]:
HeaderData Arrays
PolyDataInformation
N Cells23095
N Points11782
X Bounds3.232e+07, 3.250e+07
Y Bounds5.691e+06, 5.799e+06
Z Bounds-3.445e+03, 1.945e+03
N Arrays1
NameFieldTypeN CompMinMax
Depth [m]Pointsfloat641-3.445e+031.945e+03
[3]:

sargs = dict(fmt="%.0f", color='black')

p = pv.Plotter(notebook=True)

p.add_mesh(mesh,scalar_bar_args=sargs, clim=[-3500, 2000])

p.set_background('white')
p.show_grid(color='black')
p.set_scale(1,1,5)
p.show()
../../_images/getting_started_tutorial_35_plotting_borehole_data_with_pyvista_6_0.png 
[4]:

data = pd.read_csv(file_path + 'Borehole_Data.csv')
data.head()

[4]:
Unnamed: 0 Index Name X Y Z Altitude Depth formation geometry
0 2091 GD1017 ForschungsbohrungMünsterland1 32386176.36 5763283.15 27.00 107.00 5956.00 OberCampanium POINT (32386176.36 5763283.15)
1 2092 GD1017 ForschungsbohrungMünsterland1 32386176.36 5763283.15 -193.00 107.00 5956.00 UnterCampanium POINT (32386176.36 5763283.15)
2 2093 GD1017 ForschungsbohrungMünsterland1 32386176.36 5763283.15 -268.00 107.00 5956.00 OberSantonium POINT (32386176.36 5763283.15)
3 2094 GD1017 ForschungsbohrungMünsterland1 32386176.36 5763283.15 -828.00 107.00 5956.00 MittelSantonium POINT (32386176.36 5763283.15)
4 2095 GD1017 ForschungsbohrungMünsterland1 32386176.36 5763283.15 -988.00 107.00 5956.00 UnterSantonium POINT (32386176.36 5763283.15) 
[5]:

data['formation'].unique()

[5]:

array(['OberCampanium', 'UnterCampanium', 'OberSantonium',
       'MittelSantonium', 'UnterSantonium', 'OberConiacium',
       'UnterConiacium', 'MittelTuronium', 'UnterTuronium',
       'OberCenomanium', 'MittelCenomanium', 'UnterCenomanium',
       'OberAlbium', 'MittelAlbium', 'EssenFM', 'BochumFM', 'WittenFM',
       'Carboniferous', 'Devonian', 'Quaternary', 'MittelConiacium'],
      dtype=object)

Defining Color Dict#

[6]:

color_dict = {
        'OberCampanium':'#3182bd', 'UnterCampanium':'#9ecae1',
        'OberSantonium': '#e6550d', 'MittelSantonium': '#fdae6b', 'UnterSantonium': '#fdd0a2',
        'OberConiacium': '#31a354', 'MittelConiacium': '#74c476', 'UnterConiacium': '#a1d99b',
        'OberTuronium': '#756bb1', 'MittelTuronium': '#9e9ac8', 'UnterTuronium': '#9e9ac8',
        'OberCenomanium': '#636363', 'MittelCenomanium': '#969696', 'UnterCenomanium': '#d9d9d9',
        'OberAlbium': '#637939', 'MittelAlbium': '#8ca252',
        'EssenFM': '#e7969c', 'BochumFM': '#7b4173', 'WittenFM': '#a55194',
        'Carboniferous': '#de9ed6', 'Devonian': '#de9ed6', 'Quaternary': '#de9ed6',
        }

Adding a row to the wells#

[7]:

grouped = data.groupby(['Index'])
df_groups = [grouped.get_group(x) for x in grouped.groups]

list_df = gg.visualization.add_row_to_boreholes(df_groups)

list_df[0].head()

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[7]:
Unnamed: 0 Index Name X Y Z Altitude Depth formation geometry
0 nan GD1017 ForschungsbohrungMünsterland1 32386176.36 5763283.15 107.00 107.00 5956.00 NaN
0 2091.00 GD1017 ForschungsbohrungMünsterland1 32386176.36 5763283.15 27.00 107.00 5956.00 OberCampanium POINT (32386176.36 5763283.15)
1 2092.00 GD1017 ForschungsbohrungMünsterland1 32386176.36 5763283.15 -193.00 107.00 5956.00 UnterCampanium POINT (32386176.36 5763283.15)
2 2093.00 GD1017 ForschungsbohrungMünsterland1 32386176.36 5763283.15 -268.00 107.00 5956.00 OberSantonium POINT (32386176.36 5763283.15)
3 2094.00 GD1017 ForschungsbohrungMünsterland1 32386176.36 5763283.15 -828.00 107.00 5956.00 MittelSantonium POINT (32386176.36 5763283.15)

Creating Lines From Points#

[8]:

lines = gg.visualization.create_lines_from_points(df=list_df[0])
lines

[8]:
PolyDataInformation
N Cells39
N Points20
X Bounds3.239e+07, 3.239e+07
Y Bounds5.763e+06, 5.763e+06
Z Bounds-5.849e+03, 1.070e+02
N Arrays0

Creating Borehole Tubes#

[9]:

tubes, df_groups = gg.visualization.create_borehole_tubes(df=data,
                                               min_length= 10,
                                               radius=1000)
tubes[0]

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[9]:
HeaderData Arrays
PolyDataInformation
N Cells418
N Points1520
X Bounds3.239e+07, 3.239e+07
Y Bounds5.762e+06, 5.764e+06
Z Bounds-5.849e+03, 1.070e+02
N Arrays2
NameFieldTypeN CompMinMax
scalarsPointsint3210.000e+001.900e+01
TubeNormalsPointsfloat323-1.000e+001.000e+00
[10]:

tubes[0].plot()
../../_images/getting_started_tutorial_35_plotting_borehole_data_with_pyvista_17_0.png 
[11]:

labels = gg.visualization.create_borehole_labels(df=data)
labels

[11]:
HeaderData Arrays
PolyDataInformation
N Cells2
N Points2
X Bounds3.239e+07, 3.240e+07
Y Bounds5.753e+06, 5.763e+06
Z Bounds6.000e+01, 1.070e+02
N Arrays1
NameFieldTypeN CompMinMax
LabelsPoints1nannan

Creating Borehole Tube and Labels#

[12]:

tubes, labels, df_groups = gg.visualization.create_boreholes_3d(df=data,
                                                                min_length=10,
                                                                color_dict=color_dict,
                                                                radius=1000)
tubes

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[12]:
InformationBlocks
MultiBlockValues
N Blocks2
X Bounds32385176.360, 32404939.830
Y Bounds5751889.550, 5764283.150
Z Bounds-5849.000, 107.000
IndexNameType
0Block-00PolyData
1Block-01PolyData
[13]:

tubes[0]

[13]:
HeaderData Arrays
PolyDataInformation
N Cells418
N Points1520
X Bounds3.239e+07, 3.239e+07
Y Bounds5.762e+06, 5.764e+06
Z Bounds-5.849e+03, 1.070e+02
N Arrays2
NameFieldTypeN CompMinMax
scalarsPointsint3210.000e+001.900e+01
TubeNormalsPointsfloat323-1.000e+001.000e+00
[14]:

labels

[14]:
HeaderData Arrays
PolyDataInformation
N Cells2
N Points2
X Bounds3.239e+07, 3.240e+07
Y Bounds5.753e+06, 5.763e+06
Z Bounds6.000e+01, 1.070e+02
N Arrays1
NameFieldTypeN CompMinMax
LabelsPoints1nannan
[15]:

sargs = dict(fmt="%.0f", color='black')

p = pv.Plotter(notebook=True)

p.add_mesh(mesh,scalar_bar_args=sargs, clim=[-3500, 2000], opacity=0.7)
p.add_point_labels(labels, "Labels", point_size=5, font_size=10)
p.add_mesh(tubes, show_scalar_bar=False)

p.set_background('white')
p.show_grid(color='black')
p.set_scale(1,1,5)
p.show()
../../_images/getting_started_tutorial_35_plotting_borehole_data_with_pyvista_23_0.png 
[16]:

sargs = dict(fmt="%.0f", color='black')

p = pv.Plotter(notebook=True)

p.add_mesh(mesh,scalar_bar_args=sargs, clim=[-3500, 2000], opacity=0.7)
p.add_point_labels(labels, "Labels", point_size=5, font_size=10)

for j in range(len(tubes)):
        df_groups[j] = df_groups[j][1:]
        p.add_mesh(mesh=tubes[j], cmap=[color_dict[i] for i in df_groups[j]['formation'].unique()], show_scalar_bar=False)

p.set_background('white')
p.show_grid(color='black')
p.set_scale(1,1,5)
p.show()
../../_images/getting_started_tutorial_35_plotting_borehole_data_with_pyvista_24_0.png