Note

This page was generated from Notebooks/shapefile_export_example. Download as a Jupyter notebook (.ipynb) or Python script (.py) or launch interactively with Binder

.

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: 3.7.2
flopy version: 3.4.2

[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/tmpxs1d6w24/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 0x7f1944910610>

[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/tmpxs1d6w24/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 0x7f1944910af0>

[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 0x7f194167bb20>,
 <flopy.utils.geometry.Polygon at 0x7f1941650100>,
 <flopy.utils.geometry.Polygon at 0x7f19416509a0>,
 <flopy.utils.geometry.Polygon at 0x7f1941650df0>,
 <flopy.utils.geometry.Polygon at 0x7f19416500a0>,
 <flopy.utils.geometry.Polygon at 0x7f1941650e20>,
 <flopy.utils.geometry.Polygon at 0x7f19416501c0>,
 <flopy.utils.geometry.Polygon at 0x7f1941650850>,
 <flopy.utils.geometry.Polygon at 0x7f194166f460>,
 <flopy.utils.geometry.Polygon at 0x7f194166fdf0>,
 <flopy.utils.geometry.Polygon at 0x7f194166f8e0>,
 <flopy.utils.geometry.Polygon at 0x7f194166fe20>,
 <flopy.utils.geometry.Polygon at 0x7f194166feb0>,
 <flopy.utils.geometry.Polygon at 0x7f194166ffa0>,
 <flopy.utils.geometry.Polygon at 0x7f194166f100>,
 <flopy.utils.geometry.Polygon at 0x7f194166f130>,
 <flopy.utils.geometry.Polygon at 0x7f194166f1c0>,
 <flopy.utils.geometry.Polygon at 0x7f194166f0a0>,
 <flopy.utils.geometry.Polygon at 0x7f194166f6a0>,
 <flopy.utils.geometry.Polygon at 0x7f194166f640>,
 <flopy.utils.geometry.Polygon at 0x7f194166fbb0>,
 <flopy.utils.geometry.Polygon at 0x7f194166f730>,
 <flopy.utils.geometry.Polygon at 0x7f194166fbe0>,
 <flopy.utils.geometry.Polygon at 0x7f194166f3d0>,
 <flopy.utils.geometry.Polygon at 0x7f194166f2b0>,
 <flopy.utils.geometry.Polygon at 0x7f194166f2e0>,
 <flopy.utils.geometry.Polygon at 0x7f194166fa90>,
 <flopy.utils.geometry.Polygon at 0x7f194166f610>,
 <flopy.utils.geometry.Polygon at 0x7f194166f880>,
 <flopy.utils.geometry.Polygon at 0x7f194166f970>,
 <flopy.utils.geometry.Polygon at 0x7f194166fc40>,
 <flopy.utils.geometry.Polygon at 0x7f194166fa00>,
 <flopy.utils.geometry.Polygon at 0x7f194166fcd0>,
 <flopy.utils.geometry.Polygon at 0x7f194166fd00>,
 <flopy.utils.geometry.Polygon at 0x7f194166f760>,
 <flopy.utils.geometry.Polygon at 0x7f194166f370>,
 <flopy.utils.geometry.Polygon at 0x7f19416192b0>,
 <flopy.utils.geometry.Polygon at 0x7f1941619340>,
 <flopy.utils.geometry.Polygon at 0x7f19416193d0>,
 <flopy.utils.geometry.Polygon at 0x7f1941619490>,
 <flopy.utils.geometry.Polygon at 0x7f1941619520>,
 <flopy.utils.geometry.Polygon at 0x7f19416195b0>,
 <flopy.utils.geometry.Polygon at 0x7f19416196a0>,
 <flopy.utils.geometry.Polygon at 0x7f1941619730>,
 <flopy.utils.geometry.Polygon at 0x7f19416197c0>,
 <flopy.utils.geometry.Polygon at 0x7f1941619850>]

[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/tmpxs1d6w24/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	-949.858995	274308.783967	5.097899e+06
1	1	-1044.874138	276377.008814	5.097730e+06
2	2	-1100.535038	275659.675014	5.090648e+06
3	3	-854.955910	274540.281969	5.095267e+06
4	4	-1062.992874	276095.137951	5.089571e+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/tmpxs1d6w24/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/tmpxs1d6w24/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([ 2.21503528,  0.53574545,  1.35066259,  0.08877754,  2.19470019,
        1.66852015,  1.32223678,  0.73226893,  1.78233004, -0.05219243,
        1.78181563,  0.9470055 ,  2.66443477,  1.8107067 , -0.22769033,
        1.0440054 ,  1.6127676 ,  2.03245612,  0.95663194,  0.19795043,
        2.84463059, -0.64531693,  0.4613263 ,  0.30845682,  3.0810573 ,
        0.94206581,  0.38607183,  2.0758155 ,  1.15047488,  1.00335807,
       -0.15466015,  2.65838033,  1.47448651,  1.93603432,  0.39884021,
       -0.41629943,  0.65295213,  2.71222462,  2.16473365,  0.71629048])

[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/tmpxs1d6w24/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/tmpxs1d6w24/shapefile_export/hk.shp')

../_images/Notebooks_shapefile_export_example_52_1.png

[36]:

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