Note

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.

Shapefile export demo

The goal of this notebook is to demonstrate ways to export model information to shapefiles. This example will cover: * basic exporting of information for a model, individual package, or dataset * custom exporting of combined data from different packages * general exporting and importing of geographic data from other sources

[1]:

import os

[2]:

import sys
from tempfile import TemporaryDirectory

import matplotlib as mpl
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd

import flopy

print(sys.version)
print("numpy version: {}".format(np.__version__))
print("matplotlib version: {}".format(mpl.__version__))
print("flopy version: {}".format(flopy.__version__))

3.8.17 (default, Jun  7 2023, 12:29:56)
[GCC 11.3.0]
numpy version: 1.24.4
matplotlib version: 3.7.1
flopy version: 3.4.1

[3]:

# temporary directory
temp_dir = TemporaryDirectory()
outdir = os.path.join(temp_dir.name, "shapefile_export")

# load an existing model
model_ws = "../../examples/data/freyberg"
m = flopy.modflow.Modflow.load(
    "freyberg.nam",
    model_ws=model_ws,
    verbose=False,
    check=False,
    exe_name="mfnwt",
)

[4]:

m.get_package_list()

[4]:

['DIS', 'BAS6', 'LPF', 'WEL', 'RIV', 'RCH', 'OC', 'PCG']

set the model coordinate information

the coordinate information where the grid is located in a projected coordinate system (e.g. UTM)

[5]:

grid = m.modelgrid
grid.set_coord_info(xoff=273170, yoff=5088657, epsg=26916)

/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/utils/crs.py:119: PendingDeprecationWarning: the epsg argument will be deprecated and will be removed in version 3.4. Use crs instead.
  warnings.warn(

[6]:

grid.extent

[6]:

(273170.0, 278170.0, 5088657.0, 5098657.0)

Declarative export using attached `.export()` methods

Export the whole model to a single shapefile

[7]:

fname = "{}/model.shp".format(outdir)
m.export(fname)

/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for delc array, DIS package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for delr array, DIS package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for laycbd array, DIS package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for nstp array, DIS package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for perlen array, DIS package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for steady array, DIS package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for tsmult array, DIS package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for chani array, LPF package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for layavg array, LPF package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for laytyp array, LPF package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for layvka array, LPF package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for laywet array, LPF package
  warn(

[8]:

ax = plt.subplot(1, 1, 1, aspect="equal")
extents = grid.extent
pc = flopy.plot.plot_shapefile(fname, ax=ax, edgecolor="k", facecolor="none")
ax.set_xlim(extents[0], extents[1])
ax.set_ylim(extents[2], extents[3])
ax.set_title(fname)

[8]:

Text(0.5, 1.0, '/tmp/tmp009ls4_r/shapefile_export/model.shp')

../_images/Notebooks_shapefile_export_example_10_1.png

[9]:

fname = "{}/wel.shp".format(outdir)
m.wel.export(fname)

Export a package to a shapefile

Export a FloPy list or array object

[10]:

m.lpf.hk

[10]:

<flopy.utils.util_array.Util3d at 0x7fdb142b56a0>

[11]:

fname = "{}/hk.shp".format(outdir)
m.lpf.hk.export("{}/hk.shp".format(outdir))

[12]:

ax = plt.subplot(1, 1, 1, aspect="equal")
extents = grid.extent
a = m.lpf.hk.array.ravel()
pc = flopy.plot.plot_shapefile(fname, ax=ax, a=a)
ax.set_xlim(extents[0], extents[1])
ax.set_ylim(extents[2], extents[3])
ax.set_title(fname)

[12]:

Text(0.5, 1.0, '/tmp/tmp009ls4_r/shapefile_export/hk.shp')

../_images/Notebooks_shapefile_export_example_16_1.png

[13]:

m.riv.stress_period_data

[13]:

<flopy.utils.util_list.MfList at 0x7fdaed82ebb0>

[14]:

m.riv.stress_period_data.export("{}/riv_spd.shp".format(outdir))

MfList.export() exports the whole grid by default, regardless of the locations of the boundary cells

sparse=True only exports the boundary cells in the MfList

[15]:

m.riv.stress_period_data.export("{}/riv_spd.shp".format(outdir), sparse=True)

wrote ../../../../home/runner/work/flopy/flopy/.docs/Notebooks

[16]:

m.wel.stress_period_data.export("{}/wel_spd.shp".format(outdir), sparse=True)

wrote ../../../../home/runner/work/flopy/flopy/.docs/Notebooks

Ad-hoc exporting using `recarray2shp`

The main idea is to create a recarray with all of the attribute information, and a list of geometry features (one feature per row in the recarray)
each geometry feature is an instance of the Point, LineString or Polygon classes in flopy.utils.geometry. The shapefile format requires all the features to be of the same type.
We will use pandas dataframes for these examples because they are easy to work with, and then convert them to recarrays prior to exporting.

[17]:

from flopy.export.shapefile_utils import recarray2shp

combining data from different packages

write a shapefile of RIV and WEL package cells

[18]:

wellspd = pd.DataFrame(m.wel.stress_period_data[0])
rivspd = pd.DataFrame(m.riv.stress_period_data[0])
spd = pd.concat([wellspd, rivspd])
spd.head()

[18]:

	i	j	flux	stage	cond	rbot
0	8	15	-0.00820	NaN	NaN	NaN
1	10	12	-0.00410	NaN	NaN	NaN
2	19	13	-0.00390	NaN	NaN	NaN
3	25	9	-0.00083	NaN	NaN	NaN
4	28	5	-0.00072	NaN	NaN	NaN

[19]:

from flopy.utils.geometry import Polygon

vertices = []
for row, col in zip(spd.i, spd.j):
    vertices.append(grid.get_cell_vertices(row, col))
polygons = [Polygon(vrt) for vrt in vertices]
polygons

[19]:

[<flopy.utils.geometry.Polygon at 0x7fdaea5605b0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea57c0a0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea57c100>,
 <flopy.utils.geometry.Polygon at 0x7fdaea57c1c0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea57c220>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c760>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56cb20>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c250>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c190>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c100>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c070>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c220>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c340>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56cdf0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c7f0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56cd60>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56cbe0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56ca30>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c370>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c400>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c640>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c5b0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c520>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c910>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c850>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56cd00>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56cc40>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56ceb0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56cfa0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c2b0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56c580>,
 <flopy.utils.geometry.Polygon at 0x7fdaea56cbb0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea5182b0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea518340>,
 <flopy.utils.geometry.Polygon at 0x7fdaea5183d0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea518460>,
 <flopy.utils.geometry.Polygon at 0x7fdaea5184f0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea518580>,
 <flopy.utils.geometry.Polygon at 0x7fdaea518610>,
 <flopy.utils.geometry.Polygon at 0x7fdaea5186d0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea518760>,
 <flopy.utils.geometry.Polygon at 0x7fdaea5187f0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea5188e0>,
 <flopy.utils.geometry.Polygon at 0x7fdaea518970>,
 <flopy.utils.geometry.Polygon at 0x7fdaea518a00>,
 <flopy.utils.geometry.Polygon at 0x7fdaea518a90>]

[20]:

fname = "{}/bcs.shp".format(outdir)
recarray2shp(spd.to_records(), geoms=polygons, shpname=fname, epsg=grid.epsg)

wrote ../../../../home/runner/work/flopy/flopy/.docs/Notebooks

/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/utils/crs.py:119: PendingDeprecationWarning: the epsg argument will be deprecated and will be removed in version 3.4. Use crs instead.
  warnings.warn(

[21]:

ax = plt.subplot(1, 1, 1, aspect="equal")
extents = grid.extent
pc = flopy.plot.plot_shapefile(fname, ax=ax)
ax.set_xlim(extents[0], extents[1])
ax.set_ylim(extents[2], extents[3])
ax.set_title(fname)

[21]:

Text(0.5, 1.0, '/tmp/tmp009ls4_r/shapefile_export/bcs.shp')

../_images/Notebooks_shapefile_export_example_30_1.png

exporting other data

Suppose we have some well data with actual locations that we want to export to a shapefile

[22]:

welldata = pd.DataFrame(
    {
        "wellID": np.arange(0, 10),
        "q": np.random.randn(10) * 100 - 1000,
        "x_utm": np.random.rand(10) * 5000 + grid.xoffset,
        "y_utm": grid.yoffset + np.random.rand(10) * 10000,
    }
)
welldata.head()

[22]:

	wellID	q	x_utm	y_utm
0	0	-911.884369	278103.149042	5.090547e+06
1	1	-1256.331476	274954.755881	5.094338e+06
2	2	-867.884383	277364.475936	5.089807e+06
3	3	-1106.352553	275848.349597	5.090261e+06
4	4	-1066.408697	275438.795933	5.092867e+06

[23]:

from flopy.utils.geometry import Point

geoms = [Point(x, y) for x, y in zip(welldata.x_utm, welldata.y_utm)]

fname = "{}/wel_data.shp".format(outdir)
recarray2shp(welldata.to_records(), geoms=geoms, shpname=fname, epsg=grid.epsg)

wrote ../../../../home/runner/work/flopy/flopy/.docs/Notebooks

/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/utils/crs.py:119: PendingDeprecationWarning: the epsg argument will be deprecated and will be removed in version 3.4. Use crs instead.
  warnings.warn(

[24]:

ax = plt.subplot(1, 1, 1, aspect="equal")
extents = grid.extent
pc = flopy.plot.plot_shapefile(fname, ax=ax, radius=100)
ax.set_xlim(extents[0], extents[1])
ax.set_ylim(extents[2], extents[3])
ax.set_title(fname)

[24]:

Text(0.5, 1.0, '/tmp/tmp009ls4_r/shapefile_export/wel_data.shp')

../_images/Notebooks_shapefile_export_example_35_1.png

Adding attribute data to an existing shapefile

Suppose we have a GIS coverage representing the river in the riv package

[25]:

from flopy.utils.geometry import LineString

### make up a linestring shapefile of the river reaches
i, j = m.riv.stress_period_data[0].i, m.riv.stress_period_data[0].j
x0 = grid.xyzcellcenters[0][i[0], j[0]]
x1 = grid.xyzcellcenters[0][i[-1], j[-1]]
y0 = grid.xyzcellcenters[1][i[0], j[0]]
y1 = grid.xyzcellcenters[1][i[-1], j[-1]]
x = np.linspace(x0, x1, m.nrow + 1)
y = np.linspace(y0, y1, m.nrow + 1)
l0 = zip(list(zip(x[:-1], y[:-1])), list(zip(x[1:], y[1:])))
lines = [LineString(l) for l in l0]

rivdata = pd.DataFrame(m.riv.stress_period_data[0])
rivdata["reach"] = np.arange(len(lines))
lines_shapefile = "{}/riv_reaches.shp".format(outdir)
recarray2shp(
    rivdata.to_records(index=False),
    geoms=lines,
    shpname=lines_shapefile,
    epsg=grid.epsg,
)

wrote ../../../../home/runner/work/flopy/flopy/.docs/Notebooks

/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/utils/crs.py:119: PendingDeprecationWarning: the epsg argument will be deprecated and will be removed in version 3.4. Use crs instead.
  warnings.warn(

[26]:

ax = plt.subplot(1, 1, 1, aspect="equal")
extents = grid.extent
pc = flopy.plot.plot_shapefile(lines_shapefile, ax=ax, radius=25)
ax.set_xlim(extents[0], extents[1])
ax.set_ylim(extents[2], extents[3])
ax.set_title(lines_shapefile)

[26]:

Text(0.5, 1.0, '/tmp/tmp009ls4_r/shapefile_export/riv_reaches.shp')

../_images/Notebooks_shapefile_export_example_38_1.png

shp2recarray reads a shapefile into a numpy record array, which can easily be converted to a DataFrame

[27]:

from flopy.export.shapefile_utils import shp2recarray

[28]:

linesdata = shp2recarray(lines_shapefile)
linesdata = pd.DataFrame(linesdata)
linesdata.head()

[28]:

	i	j	stage	cond	rbot	reach	geometry
0	0	14	20.100000	0.05	20.00	0	<flopy.utils.geometry.LineString object at 0x7...
1	1	14	19.870001	0.05	19.75	1	<flopy.utils.geometry.LineString object at 0x7...
2	2	14	19.650000	0.05	19.50	2	<flopy.utils.geometry.LineString object at 0x7...
3	3	14	19.420000	0.05	19.25	3	<flopy.utils.geometry.LineString object at 0x7...
4	4	14	19.190001	0.05	19.00	4	<flopy.utils.geometry.LineString object at 0x7...

[29]:

# make up some fluxes between the river and aquifer at each reach
q = np.random.randn(len(linesdata)) + 1
q

[29]:

array([ 2.61865333,  1.05397547,  1.64178625,  1.21848485, -0.06295135,
        1.60865054,  1.45192973,  0.48222747,  2.10313399,  1.15293395,
        0.15305871,  0.57394651,  1.39538578,  1.60751542,  2.78837505,
        0.39969362, -0.38677384,  2.23798962,  0.75979869,  0.8654239 ,
        2.16574949, -1.51628836,  0.95198874, -1.40363164,  1.80877395,
        2.10601343,  0.12221982,  1.81915855,  0.56300365,  2.08833654,
        2.89406891,  1.88513056,  1.1006853 ,  1.70897461,  1.55707153,
        2.48697102,  0.84086854, -0.24499531,  0.04111582,  0.7868679 ])

[30]:

linesdata["qreach"] = q
linesdata["qstream"] = np.cumsum(q)

[31]:

recarray2shp(
    linesdata.drop("geometry", axis=1).to_records(),
    geoms=linesdata.geometry.values,
    shpname=lines_shapefile,
    epsg=grid.epsg,
)

wrote ../../../../home/runner/work/flopy/flopy/.docs/Notebooks

/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/utils/crs.py:119: PendingDeprecationWarning: the epsg argument will be deprecated and will be removed in version 3.4. Use crs instead.
  warnings.warn(

[32]:

ax = plt.subplot(1, 1, 1, aspect="equal")
extents = grid.extent
pc = flopy.plot.plot_shapefile(lines_shapefile, ax=ax, radius=25)
ax.set_xlim(extents[0], extents[1])
ax.set_ylim(extents[2], extents[3])
ax.set_title(lines_shapefile)

[32]:

Text(0.5, 1.0, '/tmp/tmp009ls4_r/shapefile_export/riv_reaches.shp')

../_images/Notebooks_shapefile_export_example_47_1.png

Overriding the model’s modelgrid with a user supplied modelgrid

In some cases it may be necessary to override the model’s modelgrid instance with a seperate modelgrid. An example of this is if the model discretization is in feet and the user would like it projected in meters. Exporting can be accomplished by supplying a modelgrid as a kwarg in any of the export() methods within flopy. Below is an example:

[33]:

mg0 = m.modelgrid

# build a new modelgrid instance with discretization in meters
modelgrid = flopy.discretization.StructuredGrid(
    delc=mg0.delc * 0.3048,
    delr=mg0.delr * 0.3048,
    top=mg0.top,
    botm=mg0.botm,
    idomain=mg0.idomain,
    xoff=mg0.xoffset * 0.3048,
    yoff=mg0.yoffset * 0.3048,
)

# exporting an entire model
m.export("{}/freyberg.shp".format(outdir), modelgrid=modelgrid)

No CRS information for writing a .prj file.
Supply an valid coordinate system reference to the attached modelgrid object or .export() method.
No CRS information for writing a .prj file.
Supply an valid coordinate system reference to the attached modelgrid object or .export() method.

/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for delc array, DIS package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for delr array, DIS package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for laycbd array, DIS package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for nstp array, DIS package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for perlen array, DIS package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for steady array, DIS package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for tsmult array, DIS package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for chani array, LPF package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for layavg array, LPF package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for laytyp array, LPF package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for layvka array, LPF package
  warn(
/opt/hostedtoolcache/Python/3.8.17/x64/lib/python3.8/site-packages/flopy/export/shapefile_utils.py:307: UserWarning: Failed to get data for laywet array, LPF package
  warn(

And for a specific parameter the method is the same

[34]:

fname = "{}/hk.shp".format(outdir)
m.lpf.hk.export(fname, modelgrid=modelgrid)

No CRS information for writing a .prj file.
Supply an valid coordinate system reference to the attached modelgrid object or .export() method.

[35]:

ax = plt.subplot(1, 1, 1, aspect="equal")
extents = modelgrid.extent
a = m.lpf.hk.array.ravel()
pc = flopy.plot.plot_shapefile(fname, ax=ax, a=a)
ax.set_xlim(extents[0], extents[1])
ax.set_ylim(extents[2], extents[3])
ax.set_title(fname)

[35]:

Text(0.5, 1.0, '/tmp/tmp009ls4_r/shapefile_export/hk.shp')

../_images/Notebooks_shapefile_export_example_52_1.png

[36]:

try:
    # ignore PermissionError on Windows
    temp_dir.cleanup()
except:
    pass