54 Converting PyVista Mesh to ZMAP Grid
Contents
54 Converting PyVista Mesh to ZMAP Grid#
After creating a model, the resulting surfaces are often needed for further processing or visualization. One common grid type are ZMAP Grids (https://gdal.org/drivers/raster/zmap.html) common to the O&G industry and readable in GIS packages like ArcGIS or QGIS. In this notebook, we present methods to convert a PyVista mesh, the resulting surface when using GemPy for structural geological modeling to a ZMAP grid.
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 warnings
warnings.filterwarnings("ignore")
import gemgis as gg
import geopandas as gpd
import rasterio
import gempy as gp
import pyvista as pv
import matplotlib.pyplot as plt
import numpy as np
WARNING (theano.configdefaults): g++ not available, if using conda: `conda install m2w64-toolchain`
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]:
file_path ='data/54_converting_pyvista_mesh_to_zmap_grid/'
gg.download_gemgis_data.download_tutorial_data(filename="54_converting_pyvista_mesh_to_zmap_grid.zip", dirpath=file_path)
Creating GemPy Model#
Loading Topography#
[3]:
topo_raster = rasterio.open(file_path + 'raster1.tif')
Creating Interfaces#
[4]:
interfaces = gpd.read_file(file_path + 'interfaces1_lines.shp')
interfaces_coords = gg.vector.extract_xyz(gdf=interfaces, dem=topo_raster)
interfaces_coords.head()
[4]:
| formation | geometry | X | Y | Z | |
|---|---|---|---|---|---|
| 0 | Sand1 | POINT (0.256 264.862) | 0.26 | 264.86 | 353.97 |
| 1 | Sand1 | POINT (10.593 276.734) | 10.59 | 276.73 | 359.04 |
| 2 | Sand1 | POINT (17.135 289.090) | 17.13 | 289.09 | 364.28 |
| 3 | Sand1 | POINT (19.150 293.313) | 19.15 | 293.31 | 364.99 |
| 4 | Sand1 | POINT (27.795 310.572) | 27.80 | 310.57 | 372.81 |
Creating Orientations#
[5]:
orientations = gpd.read_file(file_path + 'orientations1.shp')
orientations = gg.vector.extract_xyz(gdf=orientations, dem=topo_raster)
orientations['polarity'] = 1
orientations
[5]:
| formation | dip | azimuth | geometry | X | Y | Z | polarity | |
|---|---|---|---|---|---|---|---|---|
| 0 | Ton | 30.50 | 180.00 | POINT (96.471 451.564) | 96.47 | 451.56 | 440.59 | 1 |
| 1 | Ton | 30.50 | 180.00 | POINT (172.761 661.877) | 172.76 | 661.88 | 556.38 | 1 |
| 2 | Ton | 30.50 | 180.00 | POINT (383.074 957.758) | 383.07 | 957.76 | 729.02 | 1 |
| 3 | Ton | 30.50 | 180.00 | POINT (592.356 722.702) | 592.36 | 722.70 | 601.55 | 1 |
| 4 | Ton | 30.50 | 180.00 | POINT (766.586 348.469) | 766.59 | 348.47 | 378.63 | 1 |
| 5 | Ton | 30.50 | 180.00 | POINT (843.907 167.023) | 843.91 | 167.02 | 282.61 | 1 |
| 6 | Ton | 30.50 | 180.00 | POINT (941.846 428.883) | 941.85 | 428.88 | 423.45 | 1 |
| 7 | Ton | 30.50 | 180.00 | POINT (22.142 299.553) | 22.14 | 299.55 | 368.05 | 1 |
Calculating GemPy Model#
[6]:
geo_model = gp.create_model('Model1')
gp.init_data(geo_model, [0, 972, 0, 1069, 300, 800], [50, 50, 50],
surface_points_df=interfaces_coords,
orientations_df=orientations,
default_values=True)
gp.map_stack_to_surfaces(geo_model,
{'Strata': ('Sand1', 'Ton')},
remove_unused_series=True)
geo_model.add_surfaces('Basement')
geo_model.set_topography(source='gdal', filepath=file_path + 'raster1.tif')
gp.set_interpolator(geo_model,
compile_theano=True,
theano_optimizer='fast_compile',
verbose=[],
update_kriging=False
)
sol = gp.compute_model(geo_model, compute_mesh=True)
Active grids: ['regular']
Cropped raster to geo_model.grid.extent.
depending on the size of the raster, this can take a while...
storing converted file...
Active grids: ['regular' 'topography']
Compiling theano function...
Level of Optimization: fast_compile
Device: cpu
Precision: float64
Number of faults: 0
Compilation Done!
Kriging values:
values
range 1528.9
$C_o$ 55655.83
drift equations [3]
[7]:
gpv = gp.plot_3d(geo_model,
image=False,
show_topography=True,
plotter_type='basic',
notebook=True,
show_lith=True,
show_boundaries=True)
Extracting Surfaces from the GemPy Model#
[8]:
mesh = gg.visualization.create_depth_maps_from_gempy(geo_model=geo_model, surfaces=['Sand1', 'Ton'])
mesh
[8]:
{'Sand1': [PolyData (0x28273f07b20)
N Cells: 4209
N Points: 2325
X Bounds: 9.720e+00, 9.623e+02
Y Bounds: 1.672e+02, 9.497e+02
Z Bounds: 3.050e+02, 7.250e+02
N Arrays: 1,
'#015482'],
'Ton': [PolyData (0x28273f079a0)
N Cells: 5396
N Points: 2891
X Bounds: 9.720e+00, 9.623e+02
Y Bounds: 2.799e+02, 1.058e+03
Z Bounds: 3.050e+02, 7.297e+02
N Arrays: 1,
'#9f0052']}
[9]:
p = pv.Plotter(notebook=True)
p.add_mesh(mesh['Sand1'][0], scalars = 'Depth [m]')
p.show_bounds()
p.show()
Creating the ZMAP Grid#
[11]:
z_values = gg.utils.extract_zmap_data(surface=mesh['Sand1'][0],
cell_width=5)
z_values[z_values == -9999] = np.nan
im = plt.imshow(np.flipud(z_values.T), cmap='viridis')
plt.gca().invert_yaxis()
plt.colorbar(im)
[11]:
<matplotlib.colorbar.Colorbar at 0x28276bc3c70>
[12]:
zmap_grid = gg.utils.create_zmap_grid(surface=mesh['Sand1'][0],
cell_width=5, comments=['Hi'], nodata=-9999
)
zmap_grid
[12]:
['!',
'! This ZMAP Grid was created using the GemGIS Package',
'! See https://github.com/cgre-aachen/gemgis for more information',
'!',
'! Hi',
'!',
'@ZMAP_GRID, GRID, 5',
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[13]:
gg.utils.save_zmap_grid(zmap_grid, path='ZMAP_Grid.dat')
ZMAP Grid successfully saved to file
Alternative#
Alternatively, the resulting NumPy array can also be saved using the gg.raster.save_as_tiff function.
[ ]: