def test_sample_interfaces_from_raster_error(dem):
from gemgis.raster import sample_interfaces
from gemgis.utils import set_extent
extent = set_extent(0, 972, 0, 1069)
with pytest.raises(TypeError):
sample_interfaces(raster=[dem],
extent=extent,
point_x=[[500, 500], [600, 600], [700, 700]],
point_y=[[500, 500], [600, 600], [700, 700]],
formation='surface')
with pytest.raises(TypeError):
sample_interfaces(raster=dem,
extent=[extent],
point_x=[[500, 500], [600, 600], [700, 700]],
point_y=[[500, 500], [600, 600], [700, 700]],
formation='surface')
with pytest.raises(TypeError):
sample_interfaces(raster=dem,
extent='extent',
point_x=([500, 500], [600, 600], [700, 700]),
point_y=[[500, 500], [600, 600], [700, 700]],
formation='surface')
with pytest.raises(TypeError):
sample_interfaces(raster=dem,
extent=extent,
point_x=[[500, 500], [600, 600], [700, 700]],
point_y=[[500, 500], [600, 600], [700, 700]],
formation=['surface'])
with pytest.raises(TypeError):
sample_interfaces(raster=[dem],
extent=extent,
formation='surface')
def clip_by_shape(raster: Union[rasterio.io.DatasetReader, np.ndarray],
shape: gpd.geodataframe.GeoDataFrame,
save: bool = True,
path: str = 'clipped.tif',
**kwargs) -> np.ndarray:
"""
Clipping a rasterio raster or np.ndarray by a given shape
Args:
raster: np.ndarray or rasterio object to be clipped
shape: GeoDataFrame containing the corner points of a shape
bbox_crs: str containing the crs of the bounding box
save: bool whether to save the clipped raster or not
path: str with the path where the rasterio object will be saved
Kwargs:
extent_raster: list of the extent of the raster (only for np.ndarray), if no extent is provided, the origin
of the array will be set to 0,0
Return:
np.ndarray of the clipped area
"""
# Checking that the raster is of type np.ndarray or a rasterio object
if not isinstance(raster, (np.ndarray, rasterio.io.DatasetReader)):
raise TypeError(
'Raster must be of type np.ndarray or a rasterio object')
# Checking if shape is of type GeoDataFrame
if not isinstance(shape, gpd.geodataframe.GeoDataFrame):
raise TypeError('Shape must be of type GeoDataFrame')
# Checking if argument save if of type bool
if not isinstance(save, bool):
raise TypeError('Saving option must be of type bool')
# Checking if path is of type string
if not isinstance(path, str):
raise TypeError('Path must be of type string')
# Creating bounding box from shape
bbox = set_extent(gdf=shape)
bbox[1] = bbox[1] + 1
bbox[3] = bbox[3] + 1
# Getting raster extent
extent_raster = kwargs.get('extent_raster',
[0, raster.shape[1], 0, raster.shape[0]])
# Clipping raster
clipped_array = clip_by_extent(raster,
bbox,
bbox_crs='EPSG:' + str(shape.crs.to_epsg()),
save=save,
path=path,
extent_raster=extent_raster)
return clipped_array
def test_sample_interfaces_from_raster_points3(dem):
from gemgis.raster import sample_interfaces
from gemgis.utils import set_extent
extent = set_extent(0, 972, 0, 1069)
interfaces = sample_interfaces(raster=dem.read(1),
extent=extent,
point_x=[500, 600, 700],
point_y=[500, 600, 700],
formation='surface')
assert isinstance(interfaces, pd.DataFrame)
assert {'X', 'Y', 'Z', 'formation'}.issubset(interfaces.columns)
assert len(interfaces) == 3
def test_sample_orientations_from_raster_points3(dem):
from gemgis.raster import sample_orientations
from gemgis.utils import set_extent
extent = set_extent(0, 972, 0, 1069)
orientations = sample_orientations(raster=dem.read(1),
extent=extent,
point_x=[500, 600, 700],
point_y=[500, 600, 700],
formation='surface')
assert isinstance(orientations, pd.DataFrame)
assert {'X', 'Y', 'Z', 'formation', 'dip', 'azimuth', 'polarity'}.issubset(orientations.columns)
assert len(orientations) == 3
def clip_by_shape(gdf: gpd.geodataframe.GeoDataFrame,
shape: gpd.geodataframe.GeoDataFrame,
inplace: bool = False) -> gpd.geodataframe.GeoDataFrame:
"""
Clipping vector data by extent
Args:
gdf: GeoDataFrame to be clipped
shape: GeoDataFrame acting as bbox
inplace: - bool - default False -> copy of the current gdf is created
Return:
gdf: GeoDataFrame with the clipped values
"""
# Checking if the gdf is of type GeoDataFrame
if not isinstance(gdf, gpd.geodataframe.GeoDataFrame):
raise TypeError('gdf must be of type GeoDataFrame')
# Checking if the shape is of type GeoDataFrame
if not isinstance(shape, gpd.geodataframe.GeoDataFrame):
raise TypeError('shape must be of type GeoDataFrame')
# Checking if inplace is of type bool
if not isinstance(inplace, bool):
raise TypeError('Inplace must be of type bool')
# Create deep copy of gdf
if not inplace:
gdf = gdf.copy(deep=True)
# Setting the extent
extent = set_extent(gdf=shape)
# Clipping the gdf
gdf = clip_by_extent(gdf, extent, inplace=inplace)
return gdf
def plot_data(geo_data,
show_basemap: bool = False,
show_geolmap: bool = False,
show_topo: bool = False,
show_interfaces: bool = False,
show_orientations: bool = False,
show_customsections: bool = False,
show_wms: bool = False,
show_legend: bool = True,
show_hillshades: bool = False,
show_slope: bool = False,
show_aspect: bool = False,
show_contours: bool = False,
add_to_extent: float = 0,
hide_topo_left: bool = False,
**kwargs):
"""Plot Input Data
Args:
geo_data: GemPy Geo Data Class containing the raw data
show_basemap: bool - showing the basemap
show_geolmap: bool - showing the geological map
show_topo: bool - showing the topography/digital elevation model
show_interfaces: bool - showing the interfaces
show_orientations: bool - showing orientations
show_customsections: bool - showing custom sections
show_wms: bool - showing a WMS layer
show_legend: bool - showing the legend of interfaces
show_hillshades: bool - showing hillshades
show_slope: bool - showing the slope of the DEM
show_aspect: bool - showing the aspect of the DEM
show_contours: bool - showing the contours of the DEM
add_to_extent: float - number of meters to add to the extent of the plot in each direction
hide_topo_left: bool - if set to True, the topography will not be shown in the left plot
Kwargs:
cmap_basemap: str/cmap for basemap
cmap_geolmap: str/cmap for geological map
cmap_topo: str/cmap for topography
cmap_hillshades: str/cmap for hillshades
cmap_slope: str/cmap for slope
cmap_aspect: str/cmap for aspect
cmap_interfaces: str/cmap for interfaces
cmap_orientations: str/cmap for orientations
cmap_wms: str/cmap for WMS Service
cmap_contours: str/cmap for contour lines
"""
# Converting GeoDataFrame extent to list extent
if isinstance(geo_data.extent, gpd.geodataframe.GeoDataFrame):
geo_data.extent = set_extent(gdf=geo_data.extent)
# Getting and checking kwargs
cmap_basemap = kwargs.get('cmap_basemap', 'gray')
if not isinstance(cmap_basemap, (str, type(None))):
raise TypeError('Colormap must be of type string')
# Getting and checking kwargs
cmap_geolmap = kwargs.get('cmap_geolmap', 'gray')
if not isinstance(cmap_geolmap, (str, type(None), list)):
raise TypeError('Colormap must be of type string')
cmap_topo = kwargs.get('cmap_topo', 'gist_earth')
if not isinstance(cmap_topo, (str, type(None))):
raise TypeError('Colormap must be of type string')
cmap_contours = kwargs.get('cmap_contours', 'gist_earth')
if not isinstance(cmap_contours, (str, type(None))):
raise TypeError('Colormap must be of type string')
cmap_hillshades = kwargs.get('cmap_hillshades', 'gray')
if not isinstance(cmap_hillshades, (str, type(None))):
raise TypeError('Colormap must be of type string')
cmap_slope = kwargs.get('cmap_slope', 'RdYlBu_r')
if not isinstance(cmap_slope, (str, type(None))):
raise TypeError('Colormap must be of type string')
cmap_aspect = kwargs.get('cmap_aspect', 'twilight_shifted')
if not isinstance(cmap_aspect, (str, type(None))):
raise TypeError('Colormap must be of type string')
cmap_interfaces = kwargs.get('cmap_interfaces', 'gray')
if not isinstance(cmap_interfaces, (list, str, type(None))):
raise TypeError('Colormap must be of type string')
cmap_orientations = kwargs.get('cmap_orientations', 'gray')
if not isinstance(cmap_orientations, (list, str, type(None))):
raise TypeError('Colormap must be of type string')
cmap_wms = kwargs.get('cmap_wms', None)
if not isinstance(cmap_wms, (str, type(None))):
raise TypeError('Colormap must be of type string')
# Create figure and axes
fig, (ax1, ax2) = plt.subplots(ncols=2,
sharex='all',
sharey='all',
figsize=(20, 10))
# Plot basemap
if show_basemap:
if not isinstance(geo_data.basemap, type(None)):
ax1.imshow(np.flipud(geo_data.basemap),
origin='lower',
cmap=cmap_basemap,
extent=geo_data.extent[:4])
# Plot geological map
if show_geolmap:
if isinstance(geo_data.geolmap, np.ndarray):
ax1.imshow(np.flipud(geo_data.geolmap),
origin='lower',
cmap=cmap_geolmap,
extent=geo_data.extent[:4])
else:
geo_data.geolmap.plot(ax=ax1,
column='formation',
alpha=0.75,
legend=True,
cmap=ListedColormap(cmap_geolmap),
aspect='equal')
# Plot WMS Layer
if show_wms:
if not isinstance(geo_data.wms, type(None)):
ax1.imshow(np.flipud(geo_data.wms),
origin='lower',
cmap=cmap_wms,
extent=geo_data.extent[:4])
# Plot topography
if show_topo:
if not hide_topo_left:
if not isinstance(geo_data.raw_dem, type(None)):
if isinstance(geo_data.raw_dem, np.ndarray):
ax1.imshow(np.flipud(geo_data.raw_dem),
origin='lower',
cmap=cmap_topo,
extent=geo_data.extent[:4],
alpha=0.5)
# Set labels, grid and limits
ax1.set_xlabel('X')
ax1.set_ylabel('Y')
ax1.grid()
ax1.set_ylim(geo_data.extent[2] - add_to_extent,
geo_data.extent[3] + add_to_extent)
ax1.set_xlim(geo_data.extent[0] - add_to_extent,
geo_data.extent[1] + add_to_extent)
# Plot basemap
if show_basemap:
if not isinstance(geo_data.basemap, type(None)):
ax2.imshow(np.flipud(geo_data.basemap),
origin='lower',
cmap=cmap_basemap,
extent=geo_data.extent[:4])
# Plot geolmap
if show_geolmap:
if isinstance(geo_data.geolmap, np.ndarray):
ax2.imshow(np.flipud(geo_data.geolmap),
origin='lower',
cmap=cmap_geolmap,
extent=geo_data.extent[:4])
else:
geo_data.geolmap.plot(ax=ax2,
column='formation',
alpha=0.75,
legend=True,
cmap=ListedColormap(cmap_geolmap),
aspect='equal')
# Plot topography
if show_topo:
if not isinstance(geo_data.raw_dem, type(None)):
if isinstance(geo_data.raw_dem, np.ndarray):
ax2.imshow(np.flipud(geo_data.raw_dem),
origin='lower',
cmap=cmap_topo,
extent=geo_data.extent[:4],
alpha=0.5)
else:
geo_data.raw_dem.plot(ax=ax2,
column='Z',
legend=False,
linewidth=5,
cmap=cmap_topo,
aspect='equal')
# Plot contours
if show_contours:
if not isinstance(geo_data.contours, type(None)):
geo_data.contours.plot(ax=ax2,
column='Z',
legend=False,
linewidth=5,
cmap=cmap_contours,
aspect='equal')
# Plot WMS Layer
if show_wms:
if not isinstance(geo_data.wms, type(None)):
ax2.imshow(np.flipud(geo_data.wms),
origin='lower',
cmap=cmap_wms,
extent=geo_data.extent[:4])
# Plot hillshades
if show_hillshades:
if not isinstance(geo_data.hillshades, type(None)):
ax2.imshow(np.flipud(geo_data.hillshades),
origin='lower',
cmap=cmap_hillshades,
extent=geo_data.extent[:4])
# Plot slope
if show_slope:
if not isinstance(geo_data.slope, type(None)):
ax2.imshow(np.flipud(geo_data.slope),
origin='lower',
cmap=cmap_slope,
extent=geo_data.extent[:4])
# Plot aspect
if show_aspect:
if not isinstance(geo_data.aspect, type(None)):
ax2.imshow(np.flipud(geo_data.aspect),
origin='lower',
cmap=cmap_aspect,
extent=geo_data.extent[:4])
# Plot interfaces and orientations
if show_interfaces:
if not isinstance(geo_data.raw_i, type(None)):
if all(geo_data.raw_i.geom_type == 'Point'):
geo_data.raw_i.plot(ax=ax2,
column='formation',
legend=show_legend,
s=200,
aspect='equal')
elif all(geo_data.raw_i.geom_type == 'LineString'):
geo_data.raw_i.plot(ax=ax2,
column='formation',
legend=show_legend,
linewidth=5,
cmap=cmap_interfaces,
aspect='equal')
else:
if not cmap_interfaces:
geo_data.raw_i.plot(ax=ax2,
column='formation',
legend=show_legend,
aspect='equal')
else:
geo_data.raw_i.plot(ax=ax2,
column='formation',
legend=show_legend,
cmap=ListedColormap(cmap_interfaces),
aspect='equal')
if show_orientations:
if not isinstance(geo_data.raw_o, type(None)):
geo_data.raw_o.plot(ax=ax2,
column='formation',
legend=True,
s=200,
aspect='equal',
cmap=cmap_orientations)
# Plot custom sections
if show_customsections:
if not isinstance(geo_data.customsections, type(None)):
geo_data.customsections.plot(ax=ax2,
legend=show_legend,
linewidth=5,
color='red',
aspect='equal')
# Set labels, grid and limits
ax2.set_xlabel('X')
ax2.set_ylabel('Y')
ax2.grid()
ax2.set_ylim(geo_data.extent[2] - add_to_extent,
geo_data.extent[3] + add_to_extent)
ax2.set_xlim(geo_data.extent[0] - add_to_extent,
geo_data.extent[1] + add_to_extent)
return fig, ax1, ax2