import numpy as np
from ..discretization import StructuredGrid, UnstructuredGrid
from ..utils import geometry
try:
import matplotlib.pyplot as plt
import matplotlib.colors
from matplotlib.collections import PatchCollection
from matplotlib.patches import Polygon
except ImportError:
plt = None
from . import plotutil
import warnings
warnings.simplefilter("always", PendingDeprecationWarning)
[docs]class PlotMapView(object):
"""
Class to create a map of the model. Delegates plotting
functionality based on model grid type.
Parameters
----------
modelgrid : flopy.discretiztion.Grid
The modelgrid class can be StructuredGrid, VertexGrid,
or UnstructuredGrid (Default is None)
ax : matplotlib.pyplot axis
The plot axis. If not provided it, plt.gca() will be used.
If there is not a current axis then a new one will be created.
model : flopy.modflow object
flopy model object. (Default is None)
layer : int
Layer to plot. Default is 0. Must be between 0 and nlay - 1.
extent : tuple of floats
(xmin, xmax, ymin, ymax) will be used to specify axes limits. If None
then these will be calculated based on grid, coordinates, and rotation.
Notes
-----
"""
def __init__(
self, model=None, modelgrid=None, ax=None, layer=0, extent=None
):
if plt is None:
s = (
"Could not import matplotlib. Must install matplotlib "
+ " in order to use ModelMap method"
)
raise ImportError(s)
self.model = model
self.layer = layer
self.mg = None
if model is not None:
self.mg = model.modelgrid
elif modelgrid is not None:
self.mg = modelgrid
else:
err_msg = "A model grid instance must be provided to PlotMapView"
raise AssertionError(err_msg)
if self.mg.grid_type not in ("structured", "vertex", "unstructured"):
err_msg = "Unrecognized modelgrid type {}"
raise TypeError(err_msg.format(self.mg.grid_type))
if ax is None:
try:
self.ax = plt.gca()
self.ax.set_aspect("equal")
except:
self.ax = plt.subplot(1, 1, 1, aspect="equal", axisbg="white")
else:
self.ax = ax
if extent is not None:
self._extent = extent
else:
self._extent = None
@property
def extent(self):
if self._extent is None:
self._extent = self.mg.extent
return self._extent
[docs] def plot_array(self, a, masked_values=None, **kwargs):
"""
Plot an array. If the array is three-dimensional, then the method
will plot the layer tied to this class (self.layer).
Parameters
----------
a : numpy.ndarray
Array to plot.
masked_values : iterable of floats, ints
Values to mask.
**kwargs : dictionary
keyword arguments passed to matplotlib.pyplot.pcolormesh
Returns
-------
quadmesh : matplotlib.collections.QuadMesh or
matplotlib.collections.PatchCollection
"""
if not isinstance(a, np.ndarray):
a = np.array(a)
if self.mg.grid_type == "structured":
if a.ndim == 3:
plotarray = a[self.layer, :, :]
elif a.ndim == 2:
plotarray = a
elif a.ndim == 1:
plotarray = a
else:
raise Exception("Array must be of dimension 1, 2, or 3")
elif self.mg.grid_type == "vertex":
if a.ndim == 3:
if a.shape[0] == 1:
a = np.squeeze(a, axis=0)
plotarray = a[self.layer, :]
elif a.shape[1] == 1:
a = np.squeeze(a, axis=1)
plotarray = a[self.layer, :]
else:
raise Exception("Array must be of dimension 1 or 2")
elif a.ndim == 2:
plotarray = a[self.layer, :]
elif a.ndim == 1:
plotarray = a
else:
raise Exception("Array must be of dimension 1 or 2")
elif self.mg.grid_type == "unstructured":
plotarray = a
else:
raise TypeError(
"Unrecognized grid type {}".format(self.mg.grid_type)
)
if masked_values is not None:
for mval in masked_values:
plotarray = np.ma.masked_values(plotarray, mval)
# add NaN values to mask
plotarray = np.ma.masked_where(np.isnan(plotarray), plotarray)
if "ax" in kwargs:
ax = kwargs.pop("ax")
else:
ax = self.ax
if self.mg.grid_type in ("structured", "vertex"):
xgrid = np.array(self.mg.xvertices)
ygrid = np.array(self.mg.yvertices)
if self.mg.grid_type == "structured":
quadmesh = ax.pcolormesh(xgrid, ygrid, plotarray)
else:
patches = [
Polygon(list(zip(xgrid[i], ygrid[i])), closed=True)
for i in range(xgrid.shape[0])
]
quadmesh = PatchCollection(patches)
quadmesh.set_array(plotarray)
else:
quadmesh = plotutil.plot_cvfd(
self.mg._vertices, self.mg._iverts, a=plotarray, ax=ax
)
# set max and min
if "vmin" in kwargs:
vmin = kwargs.pop("vmin")
else:
vmin = None
if "vmax" in kwargs:
vmax = kwargs.pop("vmax")
else:
vmax = None
quadmesh.set_clim(vmin=vmin, vmax=vmax)
# send rest of kwargs to quadmesh
quadmesh.set(**kwargs)
# add collection to axis
ax.add_collection(quadmesh)
# set limits
ax.set_xlim(self.extent[0], self.extent[1])
ax.set_ylim(self.extent[2], self.extent[3])
return quadmesh
[docs] def contour_array(self, a, masked_values=None, **kwargs):
"""
Contour an array. If the array is three-dimensional, then the method
will contour the layer tied to this class (self.layer).
Parameters
----------
a : numpy.ndarray
Array to plot.
masked_values : iterable of floats, ints
Values to mask.
**kwargs : dictionary
keyword arguments passed to matplotlib.pyplot.pcolormesh
Returns
-------
contour_set : matplotlib.pyplot.contour
"""
try:
import matplotlib.tri as tri
except ImportError:
err_msg = "matplotlib must be installed to use contour_array()"
raise ImportError(err_msg)
a = np.copy(a)
if not isinstance(a, np.ndarray):
a = np.array(a)
xcentergrid = np.array(self.mg.xcellcenters)
ycentergrid = np.array(self.mg.ycellcenters)
if self.mg.grid_type == "structured":
if a.ndim == 3:
plotarray = a[self.layer, :, :]
elif a.ndim == 2:
plotarray = a
elif a.ndim == 1:
plotarray = a
else:
raise Exception("Array must be of dimension 1, 2 or 3")
elif self.mg.grid_type == "vertex":
if a.ndim == 3:
if a.shape[0] == 1:
a = np.squeeze(a, axis=0)
plotarray = a[self.layer, :]
elif a.shape[1] == 1:
a = np.squeeze(a, axis=1)
plotarray = a[self.layer, :]
else:
raise Exception("Array must be of dimension 1 or 2")
elif a.ndim == 2:
plotarray = a[self.layer, :]
elif a.ndim == 1:
plotarray = a
else:
raise Exception("Array must be of dimension 1, 2 or 3")
else:
plotarray = a
# work around for tri-contour ignore vmin & vmax
# necessary block for tri-contour NaN issue
if "levels" not in kwargs:
if "vmin" not in kwargs:
vmin = np.nanmin(plotarray)
else:
vmin = kwargs.pop("vmin")
if "vmax" not in kwargs:
vmax = np.nanmax(plotarray)
else:
vmax = kwargs.pop("vmax")
levels = np.linspace(vmin, vmax, 7)
kwargs["levels"] = levels
# workaround for tri-contour nan issue
# use -2**31 to allow for 32 bit int arrays
plotarray[np.isnan(plotarray)] = -(2 ** 31)
if masked_values is None:
masked_values = [-(2 ** 31)]
else:
masked_values = list(masked_values)
if -(2 ** 31) not in masked_values:
masked_values.append(-(2 ** 31))
ismasked = None
if masked_values is not None:
for mval in masked_values:
if ismasked is None:
ismasked = np.isclose(plotarray, mval)
else:
t = np.isclose(plotarray, mval)
ismasked += t
if "ax" in kwargs:
ax = kwargs.pop("ax")
else:
ax = self.ax
if "colors" in kwargs.keys():
if "cmap" in kwargs.keys():
kwargs.pop("cmap")
plot_triplot = False
if "plot_triplot" in kwargs:
plot_triplot = kwargs.pop("plot_triplot")
if "extent" in kwargs:
extent = kwargs.pop("extent")
if self.mg.grid_type in ("structured", "vertex"):
idx = (
(xcentergrid >= extent[0])
& (xcentergrid <= extent[1])
& (ycentergrid >= extent[2])
& (ycentergrid <= extent[3])
)
plotarray = plotarray[idx]
xcentergrid = xcentergrid[idx]
ycentergrid = ycentergrid[idx]
plotarray = plotarray.flatten()
xcentergrid = xcentergrid.flatten()
ycentergrid = ycentergrid.flatten()
triang = tri.Triangulation(xcentergrid, ycentergrid)
if ismasked is not None:
ismasked = ismasked.flatten()
mask = np.any(
np.where(ismasked[triang.triangles], True, False), axis=1
)
triang.set_mask(mask)
contour_set = ax.tricontour(triang, plotarray, **kwargs)
if plot_triplot:
ax.triplot(triang, color="black", marker="o", lw=0.75)
ax.set_xlim(self.extent[0], self.extent[1])
ax.set_ylim(self.extent[2], self.extent[3])
return contour_set
[docs] def plot_inactive(self, ibound=None, color_noflow="black", **kwargs):
"""
Make a plot of inactive cells. If not specified, then pull ibound
from the self.ml
Parameters
----------
ibound : numpy.ndarray
ibound array to plot. (Default is ibound in 'BAS6' package.)
color_noflow : string
(Default is 'black')
Returns
-------
quadmesh : matplotlib.collections.QuadMesh
"""
if plt is None:
err_msg = "matplotlib must be installed to use plot_inactive()"
raise ImportError(err_msg)
if ibound is None:
if self.mg.idomain is None:
raise AssertionError("Ibound/Idomain array must be provided")
ibound = self.mg.idomain
plotarray = np.zeros(ibound.shape, dtype=np.int)
idx1 = ibound == 0
plotarray[idx1] = 1
plotarray = np.ma.masked_equal(plotarray, 0)
cmap = matplotlib.colors.ListedColormap(["0", color_noflow])
bounds = [0, 1, 2]
norm = matplotlib.colors.BoundaryNorm(bounds, cmap.N)
quadmesh = self.plot_array(plotarray, cmap=cmap, norm=norm, **kwargs)
return quadmesh
[docs] def plot_ibound(
self,
ibound=None,
color_noflow="black",
color_ch="blue",
color_vpt="red",
**kwargs
):
"""
Make a plot of ibound. If not specified, then pull ibound from the
self.ml
Parameters
----------
ibound : numpy.ndarray
ibound array to plot. (Default is ibound in the modelgrid)
color_noflow : string
(Default is 'black')
color_ch : string
Color for constant heads (Default is 'blue'.)
color_vpt: string
Color for vertical pass through cells (Default is 'red')
Returns
-------
quadmesh : matplotlib.collections.QuadMesh
"""
if plt is None:
err_msg = "matplotlib must be installed to use plot_ibound()"
raise ImportError(err_msg)
if ibound is None:
if self.model is not None:
if self.model.version == "mf6":
color_ch = color_vpt
if self.mg.idomain is None:
raise AssertionError("Ibound/Idomain array must be provided")
ibound = self.mg.idomain
plotarray = np.zeros(ibound.shape, dtype=np.int)
idx1 = ibound == 0
idx2 = ibound < 0
plotarray[idx1] = 1
plotarray[idx2] = 2
plotarray = np.ma.masked_equal(plotarray, 0)
cmap = matplotlib.colors.ListedColormap(["0", color_noflow, color_ch])
bounds = [0, 1, 2, 3]
norm = matplotlib.colors.BoundaryNorm(bounds, cmap.N)
quadmesh = self.plot_array(plotarray, cmap=cmap, norm=norm, **kwargs)
return quadmesh
[docs] def plot_grid(self, **kwargs):
"""
Plot the grid lines.
Parameters
----------
kwargs : ax, colors. The remaining kwargs are passed into the
the LineCollection constructor.
Returns
-------
lc : matplotlib.collections.LineCollection
"""
if plt is None:
err_msg = "matplotlib must be installed to use plot_grid()"
raise ImportError(err_msg)
else:
from matplotlib.collections import LineCollection
if "ax" in kwargs:
ax = kwargs.pop("ax")
else:
ax = self.ax
if "colors" not in kwargs:
kwargs["colors"] = "0.5"
lc = LineCollection(self.mg.grid_lines, **kwargs)
ax.add_collection(lc)
ax.set_xlim(self.extent[0], self.extent[1])
ax.set_ylim(self.extent[2], self.extent[3])
return lc
[docs] def plot_bc(
self,
name=None,
package=None,
kper=0,
color=None,
plotAll=False,
**kwargs
):
"""
Plot boundary conditions locations for a specific boundary
type from a flopy model
Parameters
----------
name : string
Package name string ('WEL', 'GHB', etc.). (Default is None)
package : flopy.modflow.Modflow package class instance
flopy package class instance. (Default is None)
kper : int
Stress period to plot
color : string
matplotlib color string. (Default is None)
plotAll : bool
Boolean used to specify that boundary condition locations for all
layers will be plotted on the current ModelMap layer.
(Default is False)
**kwargs : dictionary
keyword arguments passed to matplotlib.collections.PatchCollection
Returns
-------
quadmesh : matplotlib.collections.QuadMesh
"""
if "ftype" in kwargs and name is None:
name = kwargs.pop("ftype")
# Find package to plot
if package is not None:
p = package
name = p.name[0]
elif self.model is not None:
if name is None:
raise Exception("ftype not specified")
name = name.upper()
p = self.model.get_package(name)
else:
raise Exception("Cannot find package to plot")
# trap for mf6 'cellid' vs mf2005 'k', 'i', 'j' convention
if isinstance(p, list) or p.parent.version == "mf6":
if not isinstance(p, list):
p = [p]
idx = np.array([])
for pp in p:
if pp.package_type in ("lak", "sfr", "maw", "uzf"):
t = plotutil.advanced_package_bc_helper(pp, self.mg, kper)
else:
try:
mflist = pp.stress_period_data.array[kper]
except Exception as e:
raise Exception(
"Not a list-style boundary package: " + str(e)
)
if mflist is None:
return
t = np.array(
[list(i) for i in mflist["cellid"]], dtype=int
).T
if len(idx) == 0:
idx = np.copy(t)
else:
idx = np.append(idx, t, axis=1)
else:
# modflow-2005 structured and unstructured grid
if p.package_type in ("uzf", "lak"):
idx = plotutil.advanced_package_bc_helper(p, self.mg, kper)
else:
try:
mflist = p.stress_period_data[kper]
except Exception as e:
raise Exception(
"Not a list-style boundary package: " + str(e)
)
if mflist is None:
return
if len(self.mg.shape) == 3:
idx = [mflist["k"], mflist["i"], mflist["j"]]
else:
idx = mflist["node"]
nlay = self.mg.nlay
# Plot the list locations
plotarray = np.zeros(self.mg.shape, dtype=np.int)
if plotAll and self.mg.grid_type != "unstructured":
pa = np.zeros(self.mg.shape[1:], dtype=np.int)
pa[tuple(idx[1:])] = 1
for k in range(nlay):
plotarray[k] = pa.copy()
else:
plotarray[tuple(idx)] = 1
# mask the plot array
plotarray = np.ma.masked_equal(plotarray, 0)
# set the colormap
if color is None:
# modflow 6 ftype fix, since multiple packages append _0, _1, etc:
key = name[:3].upper()
if key in plotutil.bc_color_dict:
c = plotutil.bc_color_dict[key]
else:
c = plotutil.bc_color_dict["default"]
else:
c = color
cmap = matplotlib.colors.ListedColormap(["0", c])
bounds = [0, 1, 2]
norm = matplotlib.colors.BoundaryNorm(bounds, cmap.N)
# create normalized quadmesh or patch object depending on grid type
quadmesh = self.plot_array(plotarray, cmap=cmap, norm=norm, **kwargs)
return quadmesh
[docs] def plot_shapefile(self, shp, **kwargs):
"""
Plot a shapefile. The shapefile must be in the same coordinates as
the rotated and offset grid.
Parameters
----------
shp : string or pyshp shapefile object
Name of the shapefile to plot
kwargs : dictionary
Keyword arguments passed to plotutil.plot_shapefile()
"""
if "ax" in kwargs:
ax = kwargs.pop("ax")
else:
ax = self.ax
patch_collection = plotutil.plot_shapefile(shp, ax, **kwargs)
return patch_collection
[docs] def plot_cvfd(self, verts, iverts, **kwargs):
"""
Plot a cvfd grid. The vertices must be in the same coordinates as
the rotated and offset grid.
Parameters
----------
verts : ndarray
2d array of x and y points.
iverts : list of lists
should be of len(ncells) with a list of vertex number for each cell
kwargs : dictionary
Keyword arguments passed to plotutil.plot_cvfd()
"""
if "ax" in kwargs:
ax = kwargs.pop("ax")
else:
ax = self.ax
patch_collection = plotutil.plot_cvfd(
verts, iverts, ax, self.layer, **kwargs
)
return patch_collection
[docs] def contour_array_cvfd(self, vertc, a, masked_values=None, **kwargs):
"""
Contour a cvfd array. If the array is three-dimensional, then the method
will contour the layer tied to this class (self.layer). The vertices
must be in the same coordinates as the rotated and offset grid.
Parameters
----------
vertc : np.ndarray
Array with of size (nc, 2) with centroid location of cvfd
a : numpy.ndarray
Array to plot.
masked_values : iterable of floats, ints
Values to mask.
**kwargs : dictionary
keyword arguments passed to matplotlib.pyplot.pcolormesh
Returns
-------
contour_set : matplotlib.pyplot.contour
"""
try:
import matplotlib.tri as tri
except ImportError:
err_msg = "matplotlib must be updated to use contour_array()"
raise ImportError(err_msg)
if "ncpl" in kwargs:
nlay = self.layer + 1
ncpl = kwargs.pop("ncpl")
if isinstance(ncpl, int):
i = int(ncpl)
ncpl = np.ones((nlay,), dtype=np.int) * i
elif isinstance(ncpl, list) or isinstance(ncpl, tuple):
ncpl = np.array(ncpl)
i0 = 0
i1 = 0
for k in range(nlay):
i0 = i1
i1 = i0 + ncpl[k]
# retain vertc in selected layer
vertc = vertc[i0:i1, :]
else:
i0 = 0
i1 = vertc.shape[0]
plotarray = a[i0:i1]
ismasked = None
if masked_values is not None:
for mval in masked_values:
if ismasked is None:
ismasked = np.isclose(plotarray, mval)
else:
t = np.isclose(plotarray, mval)
ismasked += t
# add NaN values to mask
if ismasked is None:
ismasked = np.isnan(plotarray)
else:
ismasked += np.isnan(plotarray)
if "ax" in kwargs:
ax = kwargs.pop("ax")
else:
ax = self.ax
if "colors" in kwargs.keys():
if "cmap" in kwargs.keys():
kwargs.pop("cmap")
triang = tri.Triangulation(vertc[:, 0], vertc[:, 1])
if ismasked is not None:
ismasked = ismasked.flatten()
mask = np.any(
np.where(ismasked[triang.triangles], True, False), axis=1
)
triang.set_mask(mask)
contour_set = ax.tricontour(triang, plotarray, **kwargs)
return contour_set
[docs] def plot_vector(
self,
vx,
vy,
istep=1,
jstep=1,
normalize=False,
masked_values=None,
**kwargs
):
"""
Plot a vector.
Parameters
----------
vx : np.ndarray
x component of the vector to be plotted (non-rotated)
array shape must be (nlay, nrow, ncol) for a structured grid
array shape must be (nlay, ncpl) for a unstructured grid
vy : np.ndarray
y component of the vector to be plotted (non-rotated)
array shape must be (nlay, nrow, ncol) for a structured grid
array shape must be (nlay, ncpl) for a unstructured grid
istep : int
row frequency to plot (default is 1)
jstep : int
column frequency to plot (default is 1)
normalize : bool
boolean flag used to determine if vectors should be normalized
using the vector magnitude in each cell (default is False)
masked_values : iterable of floats
values to mask
kwargs : matplotlib.pyplot keyword arguments for the
plt.quiver method
Returns
-------
quiver : matplotlib.pyplot.quiver
result of the quiver function
"""
if "pivot" in kwargs:
pivot = kwargs.pop("pivot")
else:
pivot = "middle"
if "ax" in kwargs:
ax = kwargs.pop("ax")
else:
ax = self.ax
# get actual values to plot
if self.mg.grid_type == "structured":
x = self.mg.xcellcenters[::istep, ::jstep]
y = self.mg.ycellcenters[::istep, ::jstep]
u = vx[self.layer, ::istep, ::jstep]
v = vy[self.layer, ::istep, ::jstep]
else:
x = self.mg.xcellcenters[::istep]
y = self.mg.ycellcenters[::istep]
u = vx[self.layer, ::istep]
v = vy[self.layer, ::istep]
# if necessary, copy to avoid changing the passed values
if masked_values is not None or normalize:
import copy
u = copy.copy(u)
v = copy.copy(v)
# mask values
if masked_values is not None:
for mval in masked_values:
to_mask = np.logical_or(u == mval, v == mval)
u[to_mask] = np.nan
v[to_mask] = np.nan
# normalize
if normalize:
vmag = np.sqrt(u ** 2.0 + v ** 2.0)
idx = vmag > 0.0
u[idx] /= vmag[idx]
v[idx] /= vmag[idx]
# rotate and plot, offsets must be zero since
# these are vectors not locations
urot, vrot = geometry.rotate(u, v, 0.0, 0.0, self.mg.angrot_radians)
# plot with quiver
quiver = ax.quiver(x, y, urot, vrot, pivot=pivot, **kwargs)
return quiver
[docs] def plot_specific_discharge(
self, spdis, istep=1, jstep=1, normalize=False, **kwargs
):
"""
DEPRECATED. Use plot_vector() instead, which should follow after
postprocessing.get_specific_discharge().
Method to plot specific discharge from discharge vectors
provided by the cell by cell flow output file. In MODFLOW-6
this option is controled in the NPF options block. This method
uses matplotlib quiver to create a matplotlib plot of the output.
Parameters
----------
spdis : np.recarray
specific discharge recarray from cbc file
istep : int
row frequency to plot. (Default is 1.)
jstep : int
column frequency to plot. (Default is 1.)
kwargs : matplotlib.pyplot keyword arguments for the
plt.quiver method.
Returns
-------
quiver : matplotlib.pyplot.quiver
quiver plot of discharge vectors
"""
warnings.warn(
"plot_specific_discharge() has been deprecated. Use "
"plot_vector() instead, which should follow after "
"postprocessing.get_specific_discharge()",
DeprecationWarning,
)
if "pivot" in kwargs:
pivot = kwargs.pop("pivot")
else:
pivot = "middle"
if "ax" in kwargs:
ax = kwargs.pop("ax")
else:
ax = self.ax
if isinstance(spdis, list):
print(
"Warning: Selecting the final stress period from Specific"
" Discharge list"
)
spdis = spdis[-1]
if self.mg.grid_type == "structured":
ncpl = self.mg.nrow * self.mg.ncol
else:
ncpl = self.mg.ncpl
nlay = self.mg.nlay
qx = np.zeros((nlay * ncpl))
qy = np.zeros((nlay * ncpl))
idx = np.array(spdis["node"]) - 1
qx[idx] = spdis["qx"]
qy[idx] = spdis["qy"]
if self.mg.grid_type == "structured":
qx.shape = (self.mg.nlay, self.mg.nrow, self.mg.ncol)
qy.shape = (self.mg.nlay, self.mg.nrow, self.mg.ncol)
x = self.mg.xcellcenters[::istep, ::jstep]
y = self.mg.ycellcenters[::istep, ::jstep]
u = qx[:, ::istep, ::jstep]
v = qy[:, ::istep, ::jstep]
else:
qx.shape = (self.mg.nlay, self.mg.ncpl)
qy.shape = (self.mg.nlay, self.mg.ncpl)
x = self.mg.xcellcenters[::istep]
y = self.mg.ycellcenters[::istep]
u = qx[:, ::istep]
v = qy[:, ::istep]
# normalize
if normalize:
vmag = np.sqrt(u ** 2.0 + v ** 2.0)
idx = vmag > 0.0
u[idx] /= vmag[idx]
v[idx] /= vmag[idx]
u[u == 0] = np.nan
v[v == 0] = np.nan
u = u[self.layer, :]
v = v[self.layer, :]
# Rotate and plot, offsets must be zero since
# these are vectors not locations
urot, vrot = geometry.rotate(u, v, 0.0, 0.0, self.mg.angrot_radians)
quiver = ax.quiver(x, y, urot, vrot, pivot=pivot, **kwargs)
return quiver
[docs] def plot_discharge(
self,
frf=None,
fff=None,
flf=None,
head=None,
istep=1,
jstep=1,
normalize=False,
**kwargs
):
"""
DEPRECATED. Use plot_vector() instead, which should follow after
postprocessing.get_specific_discharge().
Use quiver to plot vectors.
Parameters
----------
frf : numpy.ndarray
MODFLOW's 'flow right face'
fff : numpy.ndarray
MODFLOW's 'flow front face'
flf : numpy.ndarray
MODFLOW's 'flow lower face' (Default is None.)
head : numpy.ndarray
MODFLOW's head array. If not provided, then will assume confined
conditions in order to calculated saturated thickness.
istep : int
row frequency to plot. (Default is 1.)
jstep : int
column frequency to plot. (Default is 1.)
normalize : bool
boolean flag used to determine if discharge vectors should
be normalized using the magnitude of the specific discharge in each
cell. (default is False)
kwargs : dictionary
Keyword arguments passed to plt.quiver()
Returns
-------
quiver : matplotlib.pyplot.quiver
Vectors of specific discharge.
"""
warnings.warn(
"plot_discharge() has been deprecated. Use "
"plot_vector() instead, which should follow after "
"postprocessing.get_specific_discharge()",
DeprecationWarning,
)
if self.mg.grid_type != "structured":
err_msg = "Use plot_specific_discharge for " "{} grids".format(
self.mg.grid_type
)
raise NotImplementedError(err_msg)
else:
if self.mg.top is None:
err = (
"StructuredModelGrid must have top and "
"botm defined to use plot_discharge()"
)
raise AssertionError(err)
ib = np.ones((self.mg.nlay, self.mg.nrow, self.mg.ncol))
if self.mg.idomain is not None:
ib = self.mg.idomain
delr = self.mg.delr
delc = self.mg.delc
top = np.copy(self.mg.top)
botm = np.copy(self.mg.botm)
laytyp = None
hnoflo = 999.0
hdry = 999.0
laycbd = None
if self.model is not None:
if self.model.laytyp is not None:
laytyp = self.model.laytyp
if self.model.hnoflo is not None:
hnoflo = self.model.hnoflo
if self.model.hdry is not None:
hdry = self.model.hdry
if self.model.laycbd is not None:
laycbd = self.model.laycbd
if laycbd is not None and 1 in laycbd:
active = np.ones((botm.shape[0],), dtype=np.int)
kon = 0
for cbd in laycbd:
if cbd > 0:
kon += 1
active[kon] = 0
botm = botm[active == 1]
# If no access to head or laytyp, then calculate confined saturated
# thickness by setting laytyp to zeros
if head is None or laytyp is None:
head = np.zeros(botm.shape, np.float32)
laytyp = np.zeros((botm.shape[0],), dtype=np.int)
# calculate the saturated thickness
sat_thk = plotutil.PlotUtilities.saturated_thickness(
head, top, botm, laytyp, [hnoflo, hdry]
)
# Calculate specific discharge
qx, qy, qz = plotutil.PlotUtilities.centered_specific_discharge(
frf, fff, flf, delr, delc, sat_thk
)
ib = ib.ravel()
qx = qx.ravel()
qy = qy.ravel()
del qz
temp = []
for ix, val in enumerate(ib):
if val != 0:
temp.append((ix + 1, qx[ix], qy[ix]))
spdis = np.recarray(
(len(temp),),
dtype=[("node", np.int), ("qx", np.float), ("qy", np.float)],
)
for ix, tup in enumerate(temp):
spdis[ix] = tup
return self.plot_specific_discharge(
spdis, istep=istep, jstep=jstep, normalize=normalize, **kwargs
)
[docs] def plot_pathline(self, pl, travel_time=None, **kwargs):
"""
Plot the MODPATH pathlines.
Parameters
----------
pl : list of rec arrays or a single rec array
rec array or list of rec arrays is data returned from
modpathfile PathlineFile get_data() or get_alldata()
methods. Data in rec array is 'x', 'y', 'z', 'time',
'k', and 'particleid'.
travel_time : float or str
travel_time is a travel time selection for the displayed
pathlines. If a float is passed then pathlines with times
less than or equal to the passed time are plotted. If a
string is passed a variety logical constraints can be added
in front of a time value to select pathlines for a select
period of time. Valid logical constraints are <=, <, >=, and
>. For example, to select all pathlines less than 10000 days
travel_time='< 10000' would be passed to plot_pathline.
(default is None)
kwargs : layer, ax, colors. The remaining kwargs are passed
into the LineCollection constructor. If layer='all',
pathlines are output for all layers
Returns
-------
lc : matplotlib.collections.LineCollection
"""
if plt is None:
err_msg = "matplotlib must be installed to use plot_pathline()"
raise ImportError(err_msg)
else:
from matplotlib.collections import LineCollection
# make sure pathlines is a list
if not isinstance(pl, list):
pl = [pl]
if "layer" in kwargs:
kon = kwargs.pop("layer")
if isinstance(kon, bytes):
kon = kon.decode()
if isinstance(kon, str):
if kon.lower() == "all":
kon = -1
else:
kon = self.layer
else:
kon = self.layer
if "marker" in kwargs:
marker = kwargs.pop("marker")
else:
marker = None
if "markersize" in kwargs:
markersize = kwargs.pop("markersize")
elif "ms" in kwargs:
markersize = kwargs.pop("ms")
else:
markersize = None
if "markercolor" in kwargs:
markercolor = kwargs.pop("markercolor")
else:
markercolor = None
if "markerevery" in kwargs:
markerevery = kwargs.pop("markerevery")
else:
markerevery = 1
if "ax" in kwargs:
ax = kwargs.pop("ax")
else:
ax = self.ax
if "colors" not in kwargs:
kwargs["colors"] = "0.5"
linecol = []
markers = []
for p in pl:
if travel_time is None:
tp = p.copy()
else:
if isinstance(travel_time, str):
if "<=" in travel_time:
time = float(travel_time.replace("<=", ""))
idx = p["time"] <= time
elif "<" in travel_time:
time = float(travel_time.replace("<", ""))
idx = p["time"] < time
elif ">=" in travel_time:
time = float(travel_time.replace(">=", ""))
idx = p["time"] >= time
elif "<" in travel_time:
time = float(travel_time.replace(">", ""))
idx = p["time"] > time
else:
try:
time = float(travel_time)
idx = p["time"] <= time
except:
errmsg = (
"flopy.map.plot_pathline travel_time "
+ "variable cannot be parsed. "
+ "Acceptable logical variables are , "
+ "<=, <, >=, and >. "
+ "You passed {}".format(travel_time)
)
raise Exception(errmsg)
else:
time = float(travel_time)
idx = p["time"] <= time
tp = p[idx]
# transform data!
x0r, y0r = geometry.transform(
tp["x"],
tp["y"],
self.mg.xoffset,
self.mg.yoffset,
self.mg.angrot_radians,
)
# build polyline array
arr = np.vstack((x0r, y0r)).T
# select based on layer
if kon >= 0:
kk = p["k"].copy().reshape(p.shape[0], 1)
kk = np.repeat(kk, 2, axis=1)
arr = np.ma.masked_where((kk != kon), arr)
else:
arr = np.ma.asarray(arr)
# append line to linecol if there is some unmasked segment
if not arr.mask.all():
linecol.append(arr)
if not arr.mask.all():
linecol.append(arr)
if marker is not None:
for xy in arr[::markerevery]:
if not xy.mask:
markers.append(xy)
# create line collection
lc = None
if len(linecol) > 0:
lc = LineCollection(linecol, **kwargs)
ax.add_collection(lc)
if marker is not None:
markers = np.array(markers)
ax.plot(
markers[:, 0],
markers[:, 1],
lw=0,
marker=marker,
color=markercolor,
ms=markersize,
)
return lc
[docs] def plot_timeseries(self, ts, travel_time=None, **kwargs):
"""
Plot the MODPATH timeseries.
Parameters
----------
ts : list of rec arrays or a single rec array
rec array or list of rec arrays is data returned from
modpathfile TimeseriesFile get_data() or get_alldata()
methods. Data in rec array is 'x', 'y', 'z', 'time',
'k', and 'particleid'.
travel_time : float or str
travel_time is a travel time selection for the displayed
pathlines. If a float is passed then pathlines with times
less than or equal to the passed time are plotted. If a
string is passed a variety logical constraints can be added
in front of a time value to select pathlines for a select
period of time. Valid logical constraints are <=, <, >=, and
>. For example, to select all pathlines less than 10000 days
travel_time='< 10000' would be passed to plot_pathline.
(default is None)
kwargs : layer, ax, colors. The remaining kwargs are passed
into the LineCollection constructor. If layer='all',
pathlines are output for all layers
Returns
-------
lo : list of Line2D objects
"""
if plt is None:
err_msg = "matplotlib must be installed to use plot_timeseries()"
raise ImportError(err_msg)
# make sure timeseries is a list
if not isinstance(ts, list):
ts = [ts]
if "layer" in kwargs:
kon = kwargs.pop("layer")
if isinstance(kon, bytes):
kon = kon.decode()
if isinstance(kon, str):
if kon.lower() == "all":
kon = -1
else:
kon = self.layer
else:
kon = self.layer
if "ax" in kwargs:
ax = kwargs.pop("ax")
else:
ax = self.ax
if "color" not in kwargs:
kwargs["color"] = "red"
linecol = []
for t in ts:
if travel_time is None:
tp = t.copy()
else:
if isinstance(travel_time, str):
if "<=" in travel_time:
time = float(travel_time.replace("<=", ""))
idx = t["time"] <= time
elif "<" in travel_time:
time = float(travel_time.replace("<", ""))
idx = t["time"] < time
elif ">=" in travel_time:
time = float(travel_time.replace(">=", ""))
idx = t["time"] >= time
elif "<" in travel_time:
time = float(travel_time.replace(">", ""))
idx = t["time"] > time
else:
try:
time = float(travel_time)
idx = t["time"] <= time
except:
errmsg = (
"flopy.map.plot_pathline travel_time "
+ "variable cannot be parsed. "
+ "Acceptable logical variables are , "
+ "<=, <, >=, and >. "
+ "You passed {}".format(travel_time)
)
raise Exception(errmsg)
else:
time = float(travel_time)
idx = t["time"] <= time
tp = ts[idx]
x0r, y0r = geometry.transform(
tp["x"],
tp["y"],
self.mg.xoffset,
self.mg.yoffset,
self.mg.angrot_radians,
)
# build polyline array
arr = np.vstack((x0r, y0r)).T
# select based on layer
if kon >= 0:
kk = t["k"].copy().reshape(t.shape[0], 1)
kk = np.repeat(kk, 2, axis=1)
arr = np.ma.masked_where((kk != kon), arr)
else:
arr = np.ma.asarray(arr)
# append line to linecol if there is some unmasked segment
if not arr.mask.all():
linecol.append(arr)
# plot timeseries data
lo = []
for lc in linecol:
if not lc.mask.all():
lo += ax.plot(lc[:, 0], lc[:, 1], **kwargs)
return lo
[docs] def plot_endpoint(
self,
ep,
direction="ending",
selection=None,
selection_direction=None,
**kwargs
):
"""
Plot the MODPATH endpoints.
Parameters
----------
ep : rec array
A numpy recarray with the endpoint particle data from the
MODPATH 6 endpoint file
direction : str
String defining if starting or ending particle locations should be
considered. (default is 'ending')
selection : tuple
tuple that defines the zero-base layer, row, column location
(l, r, c) to use to make a selection of particle endpoints.
The selection could be a well location to determine capture zone
for the well. If selection is None, all particle endpoints for
the user-sepcified direction will be plotted. (default is None)
selection_direction : str
String defining is a selection should be made on starting or
ending particle locations. If selection is not None and
selection_direction is None, the selection direction will be set
to the opposite of direction. (default is None)
kwargs : ax, c, s or size, colorbar, colorbar_label, shrink. The
remaining kwargs are passed into the matplotlib scatter
method. If colorbar is True a colorbar will be added to the plot.
If colorbar_label is passed in and colorbar is True then
colorbar_label will be passed to the colorbar set_label()
method. If shrink is passed in and colorbar is True then
the colorbar size will be set using shrink.
Returns
-------
sp : matplotlib.pyplot.scatter
"""
if plt is None:
err_msg = "matplotlib must be installed to use plot_endpoint()"
raise ImportError(err_msg)
ep = ep.copy()
direction = direction.lower()
if direction == "starting":
xp, yp = "x0", "y0"
elif direction == "ending":
xp, yp = "x", "y"
else:
errmsg = (
'flopy.map.plot_endpoint direction must be "ending" '
+ 'or "starting".'
)
raise Exception(errmsg)
if selection_direction is not None:
if (
selection_direction.lower() != "starting"
and selection_direction.lower() != "ending"
):
errmsg = (
"flopy.map.plot_endpoint selection_direction "
+ 'must be "ending" or "starting".'
)
raise Exception(errmsg)
else:
if direction.lower() == "starting":
selection_direction = "ending"
elif direction.lower() == "ending":
selection_direction = "starting"
# selection of endpoints
if selection is not None:
if isinstance(selection, int):
selection = tuple((selection,))
try:
if len(selection) == 1:
node = selection[0]
if selection_direction.lower() == "starting":
nsel = "node0"
else:
nsel = "node"
# make selection
idx = ep[nsel] == node
tep = ep[idx]
elif len(selection) == 3:
k, i, j = selection[0], selection[1], selection[2]
if selection_direction.lower() == "starting":
ksel, isel, jsel = "k0", "i0", "j0"
else:
ksel, isel, jsel = "k", "i", "j"
# make selection
idx = (ep[ksel] == k) & (ep[isel] == i) & (ep[jsel] == j)
tep = ep[idx]
else:
errmsg = (
"flopy.map.plot_endpoint selection must be "
+ "a zero-based layer, row, column tuple "
+ "(l, r, c) or node number (MODPATH 7) of "
+ "the location to evaluate (i.e., well location)."
)
raise Exception(errmsg)
except:
errmsg = (
"flopy.map.plot_endpoint selection must be a "
+ "zero-based layer, row, column tuple (l, r, c) "
+ "or node number (MODPATH 7) of the location "
+ "to evaluate (i.e., well location)."
)
raise Exception(errmsg)
# all endpoints
else:
tep = ep.copy()
if "ax" in kwargs:
ax = kwargs.pop("ax")
else:
ax = self.ax
# scatter kwargs that users may redefine
if "c" not in kwargs:
c = tep["time"] - tep["time0"]
else:
c = np.empty((tep.shape[0]), dtype="S30")
c.fill(kwargs.pop("c"))
s = 50
if "s" in kwargs:
s = float(kwargs.pop("s")) ** 2.0
elif "size" in kwargs:
s = float(kwargs.pop("size")) ** 2.0
# colorbar kwargs
createcb = False
if "colorbar" in kwargs:
createcb = kwargs.pop("colorbar")
colorbar_label = "Endpoint Time"
if "colorbar_label" in kwargs:
colorbar_label = kwargs.pop("colorbar_label")
shrink = 1.0
if "shrink" in kwargs:
shrink = float(kwargs.pop("shrink"))
# transform data!
x0r, y0r = geometry.transform(
tep[xp],
tep[yp],
self.mg.xoffset,
self.mg.yoffset,
self.mg.angrot_radians,
)
# build array to plot
arr = np.vstack((x0r, y0r)).T
# plot the end point data
sp = ax.scatter(arr[:, 0], arr[:, 1], c=c, s=s, **kwargs)
# add a colorbar for travel times
if createcb:
cb = plt.colorbar(sp, ax=ax, shrink=shrink)
cb.set_label(colorbar_label)
return sp
[docs]class DeprecatedMapView(PlotMapView):
"""
Deprecation handler for the PlotMapView class
Parameters
----------
model : flopy.modflow.Modflow object
modelgrid : flopy.discretization.Grid object
ax : matplotlib.pyplot.axes object
layer : int
model layer to plot, default is layer 1
extent : tuple of floats
(xmin, xmax, ymin, ymax) will be used to specify axes limits. If None
then these will be calculated based on grid, coordinates, and rotation.
"""
def __init__(
self, model=None, modelgrid=None, ax=None, layer=0, extent=None
):
super(DeprecatedMapView, self).__init__(
model=model, modelgrid=modelgrid, ax=ax, layer=layer, extent=extent
)
[docs] def plot_discharge(
self,
frf,
fff,
dis=None,
flf=None,
head=None,
istep=1,
jstep=1,
normalize=False,
**kwargs
):
"""
Use quiver to plot vectors. Deprecated method that uses
the old function call to pass the method to PlotMapView
Parameters
----------
frf : numpy.ndarray
MODFLOW's 'flow right face'
fff : numpy.ndarray
MODFLOW's 'flow front face'
dis : flopy.modflow.ModflowDis package
Depricated parameter
flf : numpy.ndarray
MODFLOW's 'flow lower face' (Default is None.)
head : numpy.ndarray
MODFLOW's head array. If not provided, then will assume confined
conditions in order to calculated saturated thickness.
istep : int
row frequency to plot. (Default is 1.)
jstep : int
column frequency to plot. (Default is 1.)
normalize : bool
boolean flag used to determine if discharge vectors should
be normalized using the magnitude of the specific discharge in each
cell. (default is False)
kwargs : dictionary
Keyword arguments passed to plt.quiver()
Returns
-------
quiver : matplotlib.pyplot.quiver
Vectors of specific discharge.
"""
if dis is not None:
self.mg = plotutil._depreciated_dis_handler(
modelgrid=self.mg, dis=dis
)
super(DeprecatedMapView, self).plot_discharge(
frf=frf,
fff=fff,
flf=flf,
head=head,
istep=1,
jstep=1,
normalize=normalize,
**kwargs
)
[docs]class ModelMap(object):
"""
Pending Depreciation: ModelMap acts as a PlotMapView factory
object. Please migrate to PlotMapView for plotting
functionality and future code compatibility
Parameters
----------
sr : flopy.utils.reference.SpatialReference
The spatial reference class (Default is None)
ax : matplotlib.pyplot axis
The plot axis. If not provided it, plt.gca() will be used.
If there is not a current axis then a new one will be created.
model : flopy.modflow object
flopy model object. (Default is None)
dis : flopy.modflow.ModflowDis object
flopy discretization object. (Default is None)
layer : int
Layer to plot. Default is 0. Must be between 0 and nlay - 1.
xul : float
x coordinate for upper left corner
yul : float
y coordinate for upper left corner. The default is the sum of the
delc array.
rotation : float
Angle of grid rotation around the upper left corner. A positive value
indicates clockwise rotation. Angles are in degrees.
extent : tuple of floats
(xmin, xmax, ymin, ymax) will be used to specify axes limits. If None
then these will be calculated based on grid, coordinates, and rotation.
length_multiplier : float
scaling factor for conversion from model units to another unit
length base ex. ft to m.
Notes
-----
ModelMap must know the position and rotation of the grid in order to make
the plot. This information is contained in the SpatialReference class
(sr), which can be passed. If sr is None, then it looks for sr in dis.
If dis is None, then it looks for sr in model.dis. If all of these
arguments are none, then it uses xul, yul, and rotation. If none of these
arguments are provided, then it puts the lower-left-hand corner of the
grid at (0, 0).
"""
def __new__(
cls,
sr=None,
ax=None,
model=None,
dis=None,
layer=0,
extent=None,
xul=None,
yul=None,
xll=None,
yll=None,
rotation=None,
length_multiplier=None,
):
from ..utils.reference import SpatialReferenceUnstructured
# from ..plot.plotbase import DeprecatedMapView
err_msg = (
"ModelMap will be replaced by "
"PlotMapView(); Calling PlotMapView()"
)
warnings.warn(err_msg, PendingDeprecationWarning)
modelgrid = None
if model is not None:
if (xul, yul, xll, yll, rotation) != (
None,
None,
None,
None,
None,
):
modelgrid = plotutil._set_coord_info(
model.modelgrid, xul, yul, xll, yll, rotation
)
elif sr is not None:
if length_multiplier is not None:
sr.length_multiplier = length_multiplier
if (xul, yul, xll, yll, rotation) != (
None,
None,
None,
None,
None,
):
sr.set_spatialreference(xul, yul, xll, yll, rotation)
if isinstance(sr, SpatialReferenceUnstructured):
if dis is not None:
modelgrid = UnstructuredGrid(
vertices=sr.verts,
iverts=sr.iverts,
xcenters=sr.xc,
ycenters=sr.yc,
top=dis.top.array,
botm=dis.botm.array,
ncpl=sr.ncpl,
)
else:
modelgrid = UnstructuredGrid(
vertices=sr.verts,
iverts=sr.iverts,
xcenters=sr.xc,
ycenters=sr.yc,
ncpl=sr.ncpl,
)
elif dis is not None:
modelgrid = StructuredGrid(
delc=sr.delc,
delr=sr.delr,
top=dis.top.array,
botm=dis.botm.array,
xoff=sr.xll,
yoff=sr.yll,
angrot=sr.rotation,
)
else:
modelgrid = StructuredGrid(
delc=sr.delc,
delr=sr.delr,
xoff=sr.xll,
yoff=sr.yll,
angrot=sr.rotation,
)
else:
pass
return DeprecatedMapView(
model=model, modelgrid=modelgrid, ax=ax, layer=layer, extent=extent
)