gsflow.builder.fishnet Module¶

class gsflow.builder.fishnet.GenerateFishnet(bbox, xcellsize, ycellsize, buffer=None)[source]¶

Class to build a fishnet model grid

The GenerateFishnet class creates a flopy.discretization.StructuredGrid object from basic geospatial information

Parameters

bboxshapefile, raster, [xmin, xmax, ymin, ymax]: bounding box for modelgrid. The bounding box can be a the extent read from a shapfile, the extent read in from a raster, or a list of [xmin, xmax, ymin, ymax]
xcellsizefloat: cell size in the x direction for fishnet
ycellsizefloat: cell size in the y direction for fishnet
bufferint: number of cells to buffer around the input geometry

Attributes

angrot
angrot_radians
botm
cross_section_vertices: Get a set of xvertices and yvertices ordered by node
delc
delr
delz
epsg
extent
grid_lines: Get the grid lines as a list
grid_type
idomain
is_complete
is_rectilinear: Test whether the grid is rectilinear (it is always so in the x and y directions, but not necessarily in the z direction).
is_regular: Test if the grid spacing is regular and equal in x, y and z directions.
is_regular_x: Test whether the grid spacing is regular in the x direction.
is_regular_xy: Test if the grid spacing is regular and equal in x and y directions.
is_regular_xz: Test if the grid spacing is regular and equal in x and z directions.
is_regular_y: Test whether the grid spacing is regular in the y direction.
is_regular_yz: Test if the grid spacing is regular and equal in y and z directions.
is_regular_z: Test if the grid spacing is regular in z direction.
is_valid
iverts
laycbd
lenuni
map_polygons: Get a list of matplotlib Polygon patches for plotting
ncol
ncpl
nlay
nnodes
nrow
nvert
prj
proj4
shape
thick: Get the cell thickness for a structured, vertex, or unstructured grid.
top
top_botm
top_botm_withnan: Same as top_botm array but with NaN where idomain==0 both above and below a cell.
units
verts
xcellcenters
xoffset
xvertices
xycenters: Return a list of two numpy one-dimensional float arrays for center x and y coordinates in model space - not offset or rotated.
xyedges: Return a list of two 1D numpy arrays: one with the cell edge x coordinate (size = ncol+1) and the other with the cell edge y coordinate (size = nrow+1) in model space - not offset or rotated.
xyzcellcenters: Return a list of three numpy float arrays: two two-dimensional arrays for center x and y coordinates, and one three-dimensional array for center z coordinates.
xyzextent
xyzvertices: Method to get all grid vertices in a layer
ycellcenters
yoffset
yvertices
zcellcenters
zedges: Return zedges for (column, row)==(0, 0).
zvertices
zverts_smooth: Get a unique z of cell vertices using bilinear interpolation of top and bottom elevation layers.

Methods

`array_at_faces`(self, a, direction[, withnan])	Computes values at the center of cell faces using linear interpolation.
`array_at_verts`(self, a)	Interpolate array values at cell vertices.
`array_at_verts_basic`(self, a)	Computes values at cell vertices using neighbor averaging.
`cross_section_adjust_indicies`(self, k, cbcnt)	Method to get adjusted indicies by layer and confining bed for PlotCrossSection plotting
`cross_section_lay_ncpl_ncb`(self, ncb)	Get PlotCrossSection compatible layers, ncpl, and ncb variables
`cross_section_nodeskip`(self, nlay, xypts)	Get a nodeskip list for PlotCrossSection.
`cross_section_set_contour_arrays`(self, …)	Method to set countour array centers for rare instances where matplotlib contouring is prefered over trimesh plotting
`from_binary_grid_file`(file_path[, verbose])	Instantiate a StructuredGrid model grid from a MODFLOW 6 binary grid (*.grb) file.
`from_gridspec`(gridspec_file[, lenuni])
`get_cell_vertices`(self, \args, \\*kwargs)	Method to get a set of cell vertices for a single cell
`get_coords`(self, x, y)	Given x and y array-like values, apply rotation, scale and offset, to convert them from model coordinates to real-world coordinates.
`get_local_coords`(self, x, y)	Given x and y array-like values, apply rotation, scale and offset, to convert them from real-world coordinates to model coordinates.
`get_lrc`(self, nodes)	Get layer, row, column from a list of zero based MODFLOW node numbers.
`get_node`(self, lrc_list)	Get node number from a list of zero based MODFLOW layer, row, column tuples.
`get_number_plottable_layers`(self, a)	Calculate and return the number of 2d plottable arrays that can be obtained from the array passed (a)
`get_plottable_layer_shape`(self[, layer])	Determine the shape that is required in order to plot a 2d array for this grid.
`intersect`(self, x, y[, z, local, forgive])	Get the row and column of a point with coordinates x and y
`load_coord_info`(self[, namefile, reffile])	Attempts to load spatial reference information from the following files (in order): 1) usgs.model.reference 2) NAM file (header comment) 3) defaults
`load_from_file`(f)	Method to load a binary modelgrid file
`plot`(self, \\kwargs)	Plot the grid lines.
`read_usgs_model_reference_file`(self[, reffile])	read spatial reference info from the usgs.model.reference file https://water.usgs.gov/ogw/policy/gw-model/modelers-setup.html
`remove_confining_beds`(self, array)	Method to remove confining bed layers from an array
`saturated_thick`(self, array[, mask])	Get the saturated thickness for a structured, vertex, or unstructured grid.
`write`(self, f)	Method to save a binary copy of the modelgrid for later use
`write_shapefile`(self[, filename, epsg, prj])	Write a shapefile of the grid with just the row and column attributes.

attribs_from_namfile_header
get_plottable_layer_array
get_xcellcenters_for_layer
get_xvertices_for_layer
get_ycellcenters_for_layer
get_yvertices_for_layer
set_coord_info

array_at_faces(self, a, direction, withnan=True)¶

Computes values at the center of cell faces using linear interpolation.

Parameters

andarray: Values at cell centers, shape (nlay, row, ncol).
directionstr, possible values are ‘x’, ‘y’ and ‘z’: Direction in which values will be interpolated at cell faces.
withnanbool: If True (default), the result value will be set to NaN where the cell face sits between inactive cells. If False, not.

Returns

afacesndarray: Array values interpolated at cell vertices, shape as input extended by 1 along the specified direction.

array_at_verts(self, a)¶

Interpolate array values at cell vertices.

Parameters

andarray: Array values. Allowed shapes are: (nlay, nrow, ncol), (nlay, nrow, ncol+1), (nlay, nrow+1, ncol) and (nlay+1, nrow, ncol). * When the shape is (nlay, nrow, ncol), input values are considered at cell centers, and output values are computed by trilinear interpolation. * When the shape is extended in one direction, input values are considered at the center of cell faces in this direction, and output values are computed by bilinear interpolation in planes defined by these cell faces.

Returns

avertsndarray: Array values interpolated at cell vertices, shape (nlay+1, nrow+1, ncol+1).

Notes

Output values are smooth (continuous) even if top elevations or

bottom elevations are not constant across layers (i.e., in this case, vertices of neighboring cells are implicitly merged). * NaN values are assigned in accordance with inactive cells defined by idomain.

array_at_verts_basic(self, a)¶

Computes values at cell vertices using neighbor averaging.

Parameters

andarray: Array values at cell centers.

Returns

avertsndarray: Array values at cell vertices, shape (a.shape[0]+1, a.shape[1]+1, a.shape[2]+1). NaN values are assigned in accordance with inactive cells defined by idomain.

cross_section_adjust_indicies(self, k, cbcnt)¶

Method to get adjusted indicies by layer and confining bed for PlotCrossSection plotting

Parameters

kint: zero based layer number
cbcntint: confining bed counter

Returns

tuple: (int, int, int) (adjusted layer, nodeskip layer, node: adjustment value based on number of confining beds and the layer)

cross_section_lay_ncpl_ncb(self, ncb)¶

Get PlotCrossSection compatible layers, ncpl, and ncb variables

Parameters

ncbint: number of confining beds

Returns

tuple(int, int, int) layers, ncpl, ncb

cross_section_nodeskip(self, nlay, xypts)¶

Get a nodeskip list for PlotCrossSection. This is a correction for UnstructuredGridPlotting

Parameters

nlayint: nlay is nlay + ncb
xyptsdict: dictionary of node number and xyvertices of a cross-section

Returns

listn-dimensional list of nodes to not plot for each layer

cross_section_set_contour_arrays(self, plotarray, xcenters, head, elev, projpts)¶

Method to set countour array centers for rare instances where matplotlib contouring is prefered over trimesh plotting

Parameters

plotarraynp.ndarray: array of data for contouring
xcentersnp.ndarray: xcenters array
zcentersnp.ndarray: zcenters array
headnp.ndarray: head array to adjust cell centers location
elevnp.ndarray: cell elevation array
projptsdict: dictionary of projected cross sectional vertices

Returns

tuple: (np.ndarray, np.ndarray, np.ndarray, bool): plotarray, xcenter array, ycenter array, and a boolean flag for contouring

property cross_section_vertices¶

Get a set of xvertices and yvertices ordered by node for plotting cross sections

Returns

xverts, yverts: (np.ndarray, np.ndarray)

classmethod from_binary_grid_file(file_path, verbose=False)¶

Instantiate a StructuredGrid model grid from a MODFLOW 6 binary grid (*.grb) file.

Parameters

file_pathstr: file path for the MODFLOW 6 binary grid file
verbosebool: Write information to standard output. Default is False.

Returns

returnStructuredGrid

get_cell_vertices(self, *args, **kwargs)¶

Method to get a set of cell vertices for a single cell: used in the Shapefile export utilities and plotting code

Parameters

node – (int) node number
i – (int) cell row number
j – (int) cell column number

Returns ——- list of x,y cell vertices

get_coords(self, x, y)¶: Given x and y array-like values, apply rotation, scale and offset, to convert them from model coordinates to real-world coordinates.

get_local_coords(self, x, y)¶: Given x and y array-like values, apply rotation, scale and offset, to convert them from real-world coordinates to model coordinates.

get_lrc(self, nodes)¶

Get layer, row, column from a list of zero based MODFLOW node numbers.

Returns

vlist of tuples containing the layer (k), row (i),: and column (j) for each node in the input list

get_node(self, lrc_list)¶

Get node number from a list of zero based MODFLOW layer, row, column tuples.

Returns

vlist of MODFLOW nodes for each layer (k), row (i),: and column (j) tuple in the input list

get_number_plottable_layers(self, a)¶

Calculate and return the number of 2d plottable arrays that can be obtained from the array passed (a)

Parameters

andarray: array to check for plottable layers

Returns

nplottableint: number of plottable layers

get_plottable_layer_shape(self, layer=None)¶

Determine the shape that is required in order to plot a 2d array for this grid. For a regular MODFLOW grid, this is (nrow, ncol). For a vertex grid, this is (ncpl,) and for an unstructured grid this is (ncpl[layer],).

Parameters

layerint: Has no effect unless grid changes by layer

Returns

shapetuple: required shape of array to plot for a layer

property grid_lines¶: Get the grid lines as a list

intersect(self, x, y, z=None, local=False, forgive=False)¶

Get the row and column of a point with coordinates x and y

When the point is on the edge of two cells, the cell with the lowest row or column is returned.

Parameters

xfloat: The x-coordinate of the requested point
yfloat: The y-coordinate of the requested point
zfloat: Optional z-coordinate of the requested point (will return layer, row, column) if supplied
local: bool (optional): If True, x and y are in local coordinates (defaults to False)
forgive: bool (optional): Forgive x,y arguments that fall outside the model grid and return NaNs instead (defaults to False - will throw exception)

Returns

rowint: The row number
colint: The column number

property is_rectilinear¶: Test whether the grid is rectilinear (it is always so in the x and y directions, but not necessarily in the z direction).

property is_regular¶: Test if the grid spacing is regular and equal in x, y and z directions.

property is_regular_x¶: Test whether the grid spacing is regular in the x direction.

property is_regular_xy¶: Test if the grid spacing is regular and equal in x and y directions.

property is_regular_xz¶: Test if the grid spacing is regular and equal in x and z directions.

property is_regular_y¶: Test whether the grid spacing is regular in the y direction.

property is_regular_yz¶: Test if the grid spacing is regular and equal in y and z directions.

property is_regular_z¶: Test if the grid spacing is regular in z direction.

load_coord_info(self, namefile=None, reffile='usgs.model.reference')¶: Attempts to load spatial reference information from the following files (in order): 1) usgs.model.reference 2) NAM file (header comment) 3) defaults

static load_from_file(f)[source]¶

Method to load a binary modelgrid file

Parameters

fstr: binary modelgrid file name

Returns

GenerateFishnet object

property map_polygons¶

Get a list of matplotlib Polygon patches for plotting

Returns

list of Polygon objects

plot(self, **kwargs)¶

Plot the grid lines.

Parameters

kwargsax, colors. The remaining kwargs are passed into the: the LineCollection constructor.

Returns

lcmatplotlib.collections.LineCollection

read_usgs_model_reference_file(self, reffile='usgs.model.reference')¶: read spatial reference info from the usgs.model.reference file https://water.usgs.gov/ogw/policy/gw-model/modelers-setup.html

remove_confining_beds(self, array)¶

Method to remove confining bed layers from an array

Parameters

arraynp.ndarray: array to remove quasi3d confining bed data from. Shape of axis 0 should be (self.lay + ncb) to remove beds
Returns
——-: np.ndarray

saturated_thick(self, array, mask=None)¶

Get the saturated thickness for a structured, vertex, or unstructured grid. If the optional array is passed then thickness is returned relative to array values (saturated thickness). Returned values ranges from zero to cell thickness if optional array is passed.

Parameters

arrayndarray: array of elevations that will be used to adjust the cell thickness
mask: float, list, tuple, ndarray: array values to replace with a nan value.

Returns

thickcalculated saturated thickness

property thick¶

Get the cell thickness for a structured, vertex, or unstructured grid.

Returns

thickcalculated thickness

property top_botm_withnan¶: Same as top_botm array but with NaN where idomain==0 both above and below a cell.

write(self, f)[source]¶

Method to save a binary copy of the modelgrid for later use

Parameters

fstr: filename

Returns

None

write_shapefile(self, filename='grid.shp', epsg=None, prj=None)¶: Write a shapefile of the grid with just the row and column attributes.

property xycenters¶: Return a list of two numpy one-dimensional float arrays for center x and y coordinates in model space - not offset or rotated.

property xyedges¶: Return a list of two 1D numpy arrays: one with the cell edge x coordinate (size = ncol+1) and the other with the cell edge y coordinate (size = nrow+1) in model space - not offset or rotated.

property xyzcellcenters¶: Return a list of three numpy float arrays: two two-dimensional arrays for center x and y coordinates, and one three-dimensional array for center z coordinates. Coordinates are given in real-world coordinates.

property xyzvertices¶

Method to get all grid vertices in a layer

Returns:: [] 2D array

property zedges¶: Return zedges for (column, row)==(0, 0).

property zverts_smooth¶

Get a unique z of cell vertices using bilinear interpolation of top and bottom elevation layers.

Returns

zvertsndarray, shape (nlay+1, nrow+1, ncol+1): z of cell vertices. NaN values are assigned in accordance with inactive cells defined by idomain.