Reading and writing iMOD5 files in Python#

This example demonstrates how to work with iMOD5 files in Python using the imod package. It shows how to save, read, and manipulate iMOD5 files, including handling temporary directories and glob patterns for file selection.

For a full explanation of the iMOD5 file formats, see the iMOD5 documentation.

For a full overview of the supported iMOD5 features in iMOD Python, see iMOD5 backwards compatibility.


Raster data (IDF)#

Raster data in iMOD5 is stored in IDF files, which is a binary format for raster data. The imod.idf module provides functions to read and write IDF files. One IDF can only store data in two dimensions: y and x. It is similar to GeoTIFF in this regard.

We’ll start off with some example data to work with. Let’s load a layer model with geological layers.

import imod

layermodel = imod.data.hondsrug_layermodel()
layermodel
<xarray.Dataset> Size: 21MB
Dimensions:  (layer: 13, y: 200, x: 500)
Coordinates:
  * x        (x) float64 4kB 2.375e+05 2.375e+05 2.376e+05 ... 2.5e+05 2.5e+05
  * y        (y) float64 2kB 5.64e+05 5.64e+05 5.639e+05 ... 5.59e+05 5.59e+05
    dx       float64 8B ...
    dy       float64 8B ...
  * layer    (layer) int32 52B 1 2 3 4 5 6 7 8 9 10 11 12 13
Data variables:
    top      (layer, y, x) float32 5MB ...
    bottom   (layer, y, x) float32 5MB ...
    k        (layer, y, x) float32 5MB ...
    idomain  (layer, y, x) float32 5MB ...


This dataset contains multiple variables. We can take a closer look at the the “top” variable, which represents the top of every layer.

top = layermodel["top"]
top
<xarray.DataArray 'top' (layer: 13, y: 200, x: 500)> Size: 5MB
[1300000 values with dtype=float32]
Coordinates:
  * x        (x) float64 4kB 2.375e+05 2.375e+05 2.376e+05 ... 2.5e+05 2.5e+05
  * y        (y) float64 2kB 5.64e+05 5.64e+05 5.639e+05 ... 5.59e+05 5.59e+05
    dx       float64 8B ...
    dy       float64 8B ...
  * layer    (layer) int32 52B 1 2 3 4 5 6 7 8 9 10 11 12 13


Note that this DataArray has three dimensions: layer, y, x.

Let’s create a temporary directory to store our IDF files.

tmpdir = imod.util.temporary_directory()

As mentioned before, one IDF can only store data in two dimensions: y and x. iMOD Python therefore will save a 3D dataset as multiple IDF files. The layer index is stored in the file name, as the _l* suffix. iMOD Python will take the last part of the provided path as the name. We therefore end our path with top. This will result in files named top_l1.idf, top_l2.idf, etc.

idf_dir = tmpdir / "idf"
imod.idf.save(idf_dir / "top", top)

The IDF files are now stored in the temporary directory. We can list them using the glob method, which allows us to use wildcards to match file names

from pprint import pprint

idf_files = list(idf_dir.glob("*"))
pprint(idf_files)
[WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/idf/top_l1.idf'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/idf/top_l10.idf'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/idf/top_l11.idf'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/idf/top_l12.idf'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/idf/top_l13.idf'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/idf/top_l2.idf'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/idf/top_l3.idf'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/idf/top_l4.idf'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/idf/top_l5.idf'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/idf/top_l6.idf'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/idf/top_l7.idf'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/idf/top_l8.idf'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/idf/top_l9.idf')]

We can also read the IDF files back into a DataArray, we can either do that by directly providing a list of filenames (idf_files) to open, or by providing a path with a wildcard pattern (idf_dir / "top*"). The latter is more convenient, as it will automatically match all files that start with "top" in idf_dir. This means we can easily open the data without having to specify each file individually.

reloaded_top = imod.idf.open(idf_dir / "top*")
reloaded_top
<xarray.DataArray 'top' (layer: 13, y: 200, x: 500)> Size: 5MB
dask.array<stack, shape=(13, 200, 500), dtype=float32, chunksize=(1, 200, 500), chunktype=numpy.ndarray>
Coordinates:
  * x        (x) float64 4kB 2.375e+05 2.375e+05 2.376e+05 ... 2.5e+05 2.5e+05
  * y        (y) float64 2kB 5.64e+05 5.64e+05 5.639e+05 ... 5.59e+05 5.59e+05
    dx       float64 8B 25.0
    dy       float64 8B -25.0
  * layer    (layer) int64 104B 1 2 3 4 5 6 7 8 9 10 11 12 13


Note that the reloaded DataArray is represented differently than the original DataArray. This is because the DataArray is lazily loaded as a dask array, which means that the data is not actually loaded into memory until it is accessed. For example when plotting or saving data. This allows for more efficient memory usage, especially when working with large datasets. See the Lazy evaluation for more information.

Let’s plot the top layer:

reloaded_top.sel(layer=1).plot()
dx = 25.0, dy = -25.0, layer = 1
<matplotlib.collections.QuadMesh object at 0x00000251C8F5C770>

Point data (IPF)#

iMOD Stores point data in iMOD Point Format (IPF) files, which is a text format for point data. The imod.ipf module provides functions to read and write IPF files. Point data can be used to store timeseries of point observations, such as groundwater heads, as well as borelogs. In this example, we will focus on timeseries.

Let’s load some example point data.

heads = imod.data.head_observations()
heads
Unnamed: 0 id Filternummer time head filt_top filt_bot Meetpunt tov m NAP x y
0 0 B12A1745001 1 2007-12-28 NaN 9.29 8.29 9.86 226410 563800
1 2 B12A1745001 1 2008-01-28 9.03 9.29 8.29 9.86 226410 563800
2 3 B12A1745001 1 2008-02-14 8.70 9.29 8.29 9.86 226410 563800
3 4 B12A1745001 1 2008-02-28 8.53 9.29 8.29 9.86 226410 563800
4 5 B12A1745001 1 2008-03-17 8.63 9.29 8.29 9.86 226410 563800
... ... ... ... ... ... ... ... ... ... ...
60374 92 B17E2244001 1 2019-05-14 15.44 8.64 7.64 16.08 240586 543605
60375 93 B17E2244001 1 2019-05-28 15.28 8.64 7.64 16.08 240586 543605
60376 94 B17E2244001 1 2019-06-14 15.13 8.64 7.64 16.08 240586 543605
60377 95 B17E2244001 1 2019-06-28 14.88 8.64 7.64 16.08 240586 543605
60378 98 B17E2244001 1 2019-08-14 14.53 8.64 7.64 16.08 240586 543605

60379 rows × 10 columns



Let’s plot a timeseries for one specific observation point, for example the observation point with ID “B12A1745001”.

head_selected = heads.loc[heads["id"] == "B12A1745001"]
head_selected.sort_values("time").plot(x="time", y="head")
11 imod5 files
<Axes: xlabel='time'>

We can save this point data to an IPF file. The imod.ipf.save function allows us to save the point data to a file. We can specify the path where we want to save the file, as well as the data to save. Make sure to specify itype as 1, which is the type for timeseries data. The path should end with the name you want to give to your IPF.

ipf_dir = tmpdir / "ipf"
imod.ipf.save(ipf_dir / "heads", heads, itype=1)

The IPF files are now stored in the temporary directory. Let’s print a list of files:

ipf_files = list(ipf_dir.glob("*"))
pprint(ipf_files)
[WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1745001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1745002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1747001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1747002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1748001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1749001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1750001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1750002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1751001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1752001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1752002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1753001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1754001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1754002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1755001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1756001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1756002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1757001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1762001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1762002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1763001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1763002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1765001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1766001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1766002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1767001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1767002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1792001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1793001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1793002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1805001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1805002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1806001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1806002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1820001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1822001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1822002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1822003.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1898001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1898002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1899001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1900001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1901001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1902001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1903001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1903002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1904001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1905001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1906001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1906002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1907001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1907002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1908001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1909001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1909002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1910001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1910002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1911001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1911002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12A1912001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B0135001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B0135002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B0135003.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B0361001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B0361002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B0364001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1724001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1724002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1725001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1725002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1726001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1727001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1814001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1815001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1815002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1815003.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1816001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1828001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1829001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1830001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1835001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1836001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1836002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1837001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1838001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1854001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1855001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12B1856001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0254001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0254002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0255001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0255002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0255003.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0255004.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0256001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0256002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0257001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0257002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0258001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0258002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0259001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0259002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0260001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0260002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0261001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0261002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0261003.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0262001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0262002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0262003.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0265001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0266001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0267001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C0277001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1541001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1542001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1542002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1566001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1566002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1566003.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1566004.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1567001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1568001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1569001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1569002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1570001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1571001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1572001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1573001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1573002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1574001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1574002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1575001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1575002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1576001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1576002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1594001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1594002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1595001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1596001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1596002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1597001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1597002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1598001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1599001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1600001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1600002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1601001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1601002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1602001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1603001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1603002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1604001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1604002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1605001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1606001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1606002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1607001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1607002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1608001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B12C1634001.txt'),
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 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B17E2224001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B17E2224002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B17E2225001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B17E2225002.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B17E2225003.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B17E2225004.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/B17E2244001.txt'),
 WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/ipf/heads.ipf')]

Notice that timeseries are stored in a single textfile per observation point. We can read the IPF file and accompanying text files back into a DataFrame.

reloaded_heads = imod.ipf.read(ipf_dir / "heads.ipf")
reloaded_heads
time unnamed: 0 filternummer head filt_top filt_bot meetpunt tov m nap x y id
0 2007-12-28 0 1 NaN 9.29 8.29 9.86 226410 563800 B12A1745001
1 2008-01-28 2 1 9.03 9.29 8.29 9.86 226410 563800 B12A1745001
2 2008-02-14 3 1 8.70 9.29 8.29 9.86 226410 563800 B12A1745001
3 2008-02-28 4 1 8.53 9.29 8.29 9.86 226410 563800 B12A1745001
4 2008-03-17 5 1 8.63 9.29 8.29 9.86 226410 563800 B12A1745001
... ... ... ... ... ... ... ... ... ... ...
60374 2019-05-14 92 1 15.44 8.64 7.64 16.08 240586 543605 B17E2244001
60375 2019-05-28 93 1 15.28 8.64 7.64 16.08 240586 543605 B17E2244001
60376 2019-06-14 94 1 15.13 8.64 7.64 16.08 240586 543605 B17E2244001
60377 2019-06-28 95 1 14.88 8.64 7.64 16.08 240586 543605 B17E2244001
60378 2019-08-14 98 1 14.53 8.64 7.64 16.08 240586 543605 B17E2244001

60379 rows × 10 columns



Line data (GEN)#

iMOD stores line data in GEN files, which is a binary format for line data. The imod.gen module provides functions to read and write GEN files. We’ll create some dummy line data to store in a GEN file. iMOD5 primarily uses GEN to specify Horizontal Flow Barriers (HFB).

import shapely

x = [0.0, 14.0, 36.0, 50.0, 70.0]
y = [0.0, 20.0, 10.0, 30.0, 40.0]

ls = shapely.LineString(zip(x, y))
ls
<LINESTRING (0 0, 14 20, 36 10, 50 30, 70 40)>

We now have a geometry, but there is no data associated with it yet. Let’s create a GeoDataFrame with some data to associate with the line.

import geopandas as gpd

gdf = gpd.GeoDataFrame([100.0], geometry=[ls], columns=["resistance"])

We can save this line data to a GEN file with the imod.formats.gen.write function.

gen_dir = tmpdir / "gen"
# We'll have to create the directory first, as it does not exist yet.
gen_dir.mkdir(exist_ok=True)

imod.gen.write(
    gen_dir / "barrier.gen",
    gdf,
)

Let’s check that the file is saved in the specified directory.

gen_files = list(gen_dir.glob("*"))
pprint(gen_files)
[WindowsPath('C:/BuildAgent/temp/buildTmp/tmpbv347zcx/gen/barrier.gen')]

We can read the GEN file back into a GeoDataFrame with the imod.gen.read

reloaded_gdf = imod.gen.read(gen_dir / "barrier.gen")
reloaded_gdf
resistance feature_type geometry
0 100.0 line LINESTRING (0 0, 14 20, 36 10, 50 30, 70 40)


The GEN file also supports storing “3D data”, which allows you to store vertically oriented polygons, which you can use to insert partially-penetrating horizontal flow barriers in iMOD5 and iMOD Python.

Let’s create some 3D data first. iMOD Python has a convenience function to create a 3D polygon conveniently.

ztop = [0.0, 0.0, -10.0, 0.0, 0.0]
zbottom = [-20.0, -20.0, -20.0, -20.0, -20.0]

zpolygon = imod.prepare.linestring_to_trapezoid_zpolygons(x, y, ztop, zbottom)

gdf_polygon = gpd.GeoDataFrame(
    [100.0, 100.0, 100.0, 100.0], geometry=zpolygon, columns=["resistance"]
)
imod.gen.write(
    gen_dir / "barrier_3d.gen",
    gdf_polygon,
)

1D Network (ISG)#

iMOD5 stores store 1D networks in ISG files, which is a binary format primarily for surface water datasets. It supports all kinds of extra features such as associated bathymetries and weirs.

Given its complexity, ISG is not yet supported in iMOD Python. The workaround is to rasterize the ISGfiles to IDF files using the iMOD5 BATCH function ISGGRID.

Legend files (LEG)#

iMOD5 uses LEG files to store legend information for plotting. For example, the following LEG file defines a color legend for groundwater surface levels:

legend_str = """\
24,1,1,1,1,1,1,1
UPPERBND,LOWERBND,IRED,IGREEN,IBLUE,DOMAIN
200.0000,10.00000,75,0,0,"> 10.0 m"
10.00000,6.000000,115,0,0,"6.0-10.0 m"
6.000000,4.000000,166,0,0,"4.0-6.0 m"
4.000000,3.800000,191,0,0,"3.8-4.0 m"
3.800000,3.600000,217,0,0,"3.6-3.8 m"
3.600000,3.400000,237,0,0,"3.4-3.6 m"
3.400000,3.200000,255,42,0,"3.2-3.4 m"
3.200000,3.000000,255,85,0,"3.0-3.2 m"
3.000000,2.800000,254,115,0,"2.8-3.0 m"
2.800000,2.600000,254,140,0,"2.6-2.8 m"
2.600000,2.400000,254,170,0,"2.4-2.6 m"
2.400000,2.200000,254,191,10,"2.2-2.4 m"
2.200000,2.000000,254,196,20,"2.0-2.2 m"
2.000000,1.800000,254,221,51,"1.8-2.0 m"
1.800000,1.600000,254,255,0,"1.6-1.8 m"
1.600000,1.400000,254,255,115,"1.4-1.6 m"
1.400000,1.200000,255,255,190,"1.2-1.4 m"
1.200000,1.000000,209,255,115,"1.0-1.2 m"
1.000000,0.8000000,163,255,115,"0.8-1.0 m"
0.8000000,0.6000000,85,255,0,"0.6-0.8 m"
0.6000000,0.4000000,76,230,0,"0.4-0.6 m"
0.4000000,0.2000000,56,168,0,"0.2-0.4 m"
0.2000000,0.000000,38,115,0,"0.0-0.2 m"
0.000000,-200.0000,0,77,168,"<0.0 m"
"""

Let’s write this string to a file in our temporary directory.

legend_dir = tmpdir / "leg"
legend_dir.mkdir(exist_ok=True)
legend_path = legend_dir / "GWS_surface_level.leg"
with open(legend_path, "w") as f:
    f.write(legend_str)

We can read the LEG file using the imod.visualize.read_imod_legend function.

colors, levels, labels = imod.visualize.read_imod_legend(legend_path)

We can now use these colors and levels to plot a surface. In this case, we will plot the top layer of our layermodel.

imod.visualize.plot_map(top.sel(layer=1), colors=colors, levels=levels)
11 imod5 files
(<Figure size 640x480 with 2 Axes>, <Axes: >)

Project files (PRJ)#

iMOD5 uses PRJ files to store project information, basically the model definition. See the example for a full overview of importing a model from a projectfile into a MODFLOW6 model. We’ll show here how to open a projectfile here and convert the data to a MODFLOW 6 model.

Total running time of the script: (0 minutes 11.375 seconds)

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