Input/Output (IO)¶
This section documents various methods you can use to bring in data and write output to a file.
Module contents¶
Modules that read/write ModelGrids from various file formats.
- exception DataSizeError(size, expected_size)[source]
Bases:
Error
Raise this error if the size of data does not match the header.
- exception KeyTypeError(key, expected_type)[source]
Bases:
Error
Raise this error when a header’s key value is of the wrong type.
- exception KeyValueError(key, message)[source]
Bases:
Error
Raise this error when a header’s key value has a bad value.
- exception MismatchGridDataSizeError(size, expected_size)[source]
Bases:
Error
Raise this error if the data size does not match the grid size.
- exception MismatchGridXYLowerLeft(llc, expected_llc)[source]
Bases:
Error
Raise this error if the file lower left does not match the grid.
- exception MismatchGridXYSpacing(dx, expected_dx)[source]
Bases:
Error
Raise this error if the file cell size does not match the grid dx.
- exception MissingRequiredKeyError(key)[source]
Bases:
Error
Raise this error when a header is missing a required key.
- read_asc_header(asc_file)[source]
Read header information from an ESRI ASCII raster file.
- The header contains the following variables,
ncols: Number of cell columns
nrows: Number of cell rows
- xllcenter or xllcorner: X (column) coordinate of lower-left
coordinate of grid (by center or lower-left corner of the cell)
- yllcenter, yllcorner: Y (row) coordinate of lower-left
coordinate of grid (by center or lower-left corner of the cell)
cellsize: Grid spacing between rows and columns
nodata_value: No-data value (optional)
- Parameters
asc_file (file_like) – File-like object from which to read header.
- Returns
Header as key-value pairs.
- Return type
dict
- Raises
MissingRequiredKeyError – The header is missing a required key.
KeyTypeError – The header has the key but its values is of the wrong type.
Examples
>>> from io import StringIO >>> from landlab.io.esri_ascii import read_asc_header >>> contents = StringIO(''' ... nrows 100 ... ncols 200 ... cellsize 1.5 ... xllcenter 0.5 ... yllcenter -0.5 ... ''') >>> hdr = read_asc_header(contents) >>> hdr['nrows'], hdr['ncols'] (100, 200) >>> hdr['cellsize'] 1.5 >>> hdr['xllcenter'], hdr['yllcenter'] (0.5, -0.5)
MissingRequiredKey
is raised if the header does not contain all of the necessary keys.>>> contents = StringIO(''' ... ncols 200 ... cellsize 1.5 ... xllcenter 0.5 ... yllcenter -0.5 ... ''') >>> read_asc_header(contents) Traceback (most recent call last): MissingRequiredKeyError: nrows
KeyTypeError
is raises if a value is of the wrong type. For instance,nrows
andncols
must beint
.>>> contents = StringIO(''' ... nrows 100.5 ... ncols 200 ... cellsize 1.5 ... xllcenter 0.5 ... yllcenter -0.5 ... ''') >>> read_asc_header(contents) Traceback (most recent call last): KeyTypeError: Unable to convert nrows to <type 'int'>
- read_esri_ascii(asc_file, grid=None, reshape=False, name=None, halo=0)[source]
Read
RasterModelGrid
from an ESRI ASCII file.Read data from asc_file, an ESRI ASCII file, into a
RasterModelGrid
. asc_file is either the name of the data file or is a file-like object.The grid and data read from the file are returned as a tuple (grid, data) where grid is an instance of
RasterModelGrid
and data is a numpy array of doubles with that has been reshaped to have the number of rows and columns given in the header.- Parameters
asc_file (str of file-like) – Data file to read.
reshape (boolean, optional) – Reshape the returned array, otherwise return a flattened array.
name (str, optional) – Add data to the grid as a named field.
grid (grid , optional) – Adds data to an existing grid instead of creating a new one.
halo (integer, optional) – Adds outer border of depth halo to the grid.
- Returns
(grid, data) – A newly-created RasterModel grid and the associated node data.
- Return type
tuple
- Raises
DataSizeError – Data are not the same size as indicated by the header file.
MismatchGridDataSizeError – If a grid is passed, and the size of the grid does not agree with the size of the data.
MismatchGridXYSpacing – If a grid is passed, and the cellsize listed in the heading does not match the grid dx and dy.
MismatchGridXYLowerLeft – If a grid is passed and the xllcorner and yllcorner do not match that of the grid.
Examples
Assume that fop is the name of a file that contains text below (make sure you have your path correct): ncols 3 nrows 4 xllcorner 1. yllcorner 2. cellsize 10. NODATA_value -9999 0. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. ——– >>> from landlab.io import read_esri_ascii >>> (grid, data) = read_esri_ascii(‘fop’) # doctest: +SKIP >>> #grid is an object of type RasterModelGrid with 4 rows and 3 cols >>> #data contains an array of length 4*3 that is equal to >>> # [9., 10., 11., 6., 7., 8., 3., 4., 5., 0., 1., 2.] >>> (grid, data) = read_esri_ascii(‘fop’, halo=1) # doctest: +SKIP >>> #now the data has a nodata_value ring of -9999 around it. So array is >>> # [-9999, -9999, -9999, -9999, -9999, -9999, >>> # -9999, 9., 10., 11., -9999, >>> # -9999, 6., 7., 8., -9999, >>> # -9999, 3., 4., 5., -9999, >>> # -9999, 0., 1., 2. -9999, >>> # -9999, -9999, -9999, -9999, -9999, -9999]
- read_shapefile(file, dbf=None, store_polyline_vertices=True, points_shapefile=None, points_dbf=None, link_fields=None, node_fields=None, link_field_conversion=None, node_field_conversion=None, link_field_dtype=None, node_field_dtype=None, threshold=0.0)[source]
Read shapefile and create a NetworkModelGrid.
- There are a number of assumptions that are required about the shapefile.
The shapefile must be a polyline shapefile.
All polylines must be their own object (e.g. no multi-part polylines).
Polyline endpoints match perfectly.
You might notice that there is no
write_shapefile
function. If this is something you need for your work, please make a GitHub issue to start this process.- Parameters
file (str or file-like) – File path or file-like of a valid polyline shapefile
dbf (file-like, optional) – If file is file-like, the dbf must also be passed.
store_polyline_vertices (bool, optional) – If True (default), store the vertices of the polylines in the at_link fields
x_of_polyline
andy_of_polyline
.points_shapefile (str or file-like) – File path or file-like of a valid point shapefile.
points_dbf (file-like, optional) – If file is file-like, the dbf must also be passed.
link_fields (list, optional) – List of polyline shapefile attributes to import as landlab at-link fields. Default is to import all.
node_fields (list, optional) – List of point shapefile attributes to import as landlab at-node fields. Default is to import all.
link_field_conversion (dict, optional) – Dictionary mapping polyline shapefile field names to desired at link field names. Default is no remapping.
node_field_conversion (dict, optional) – Dictionary mapping node shapefile field names to desired at node field names. Default is no remapping.
link_field_dtype (dict, optional) – Dictionary mapping node shapefile field names to desired dtype. Default is no change to dtype.
node_field_dtype (dict, optional) – Dictionary mapping node shapefile field names to desired dtype. Default is no change to dtype.
threshold (float, optional) – Maximum distance between a point in the point shapefile and a polyline junction in the polyline shapefile. Units are the same as in the shapefiles. Default is zero (requiring perfect overlap).
- Returns
grid – The network model grid will have nodes at the endpoints of the polylines, and links that connect these nodes. Any fields associated with the shapefile will be added as at-link fields. If a point shapefile is provided those values will be added as at-node fields.
- Return type
NetworkModelGrid instance
Examples
First, we make a simple shapefile
>>> from io import BytesIO >>> import os
>>> import shapefile >>> shp = BytesIO() >>> shx = BytesIO() >>> dbf = BytesIO() >>> w = shapefile.Writer(shp=shp, shx=shx, dbf=dbf) >>> w.shapeType = shapefile.POLYLINE >>> w.field("spam", "N") >>> w.line([[[5,5],[10,10]]]) >>> w.record(37) >>> w.line([[[5,0],[5,5]]]) >>> w.record(100) >>> w.line([[[5,5],[0,10]]]) >>> w.record(239) >>> w.close()
Now create a NetworkModelGrid with read_shapefile:
>>> from landlab.io import read_shapefile >>> grid = read_shapefile(shp, dbf=dbf) >>> grid.nodes array([0, 1, 2, 3]) >>> grid.x_of_node array([ 5., 5., 0., 10.]) >>> grid.y_of_node array([ 0., 5., 10., 10.]) >>> grid.nodes_at_link array([[0, 1], [2, 1], [1, 3]]) >>> assert "spam" in grid.at_link >>> grid.at_link["spam"] array([100, 239, 37])
Next lets also include a points file. First create both shapefiles.
>>> shp = BytesIO() >>> shx = BytesIO() >>> dbf = BytesIO() >>> w = shapefile.Writer(shp=shp, shx=shx, dbf=dbf) >>> w.shapeType = shapefile.POLYLINE >>> w.field("spam", "N") >>> w.line([[[5,5],[10,10]]]) >>> w.record(37) >>> w.line([[[5,0],[5,5]]]) >>> w.record(100) >>> w.line([[[5,5],[0,10]]]) >>> w.record(239) >>> w.close()
>>> p_shp = BytesIO() >>> p_shx = BytesIO() >>> p_dbf = BytesIO() >>> p_w = shapefile.Writer(shp=p_shp, shx=p_shx, dbf=p_dbf) >>> p_w.shapeType = shapefile.POINT >>> p_w.field("eggs", "N") >>> p_w.point(5, 0) >>> p_w.record(2) >>> p_w.point(5, 5) >>> p_w.record(4) >>> p_w.point(0, 10) >>> p_w.record(8) >>> p_w.point(10, 10) >>> p_w.record(6) >>> p_w.close()
Now read in both files together.
>>> grid = read_shapefile(shp, dbf=dbf, points_shapefile=p_shp, points_dbf=p_dbf) >>> grid.nodes array([0, 1, 2, 3]) >>> grid.x_of_node array([ 5., 5., 0., 10.]) >>> grid.y_of_node array([ 0., 5., 10., 10.]) >>> grid.nodes_at_link array([[0, 1], [2, 1], [1, 3]]) >>> assert "spam" in grid.at_link >>> grid.at_link["spam"] array([100, 239, 37]) >>> assert "eggs" in grid.at_node >>> grid.at_node["eggs"] array([2, 4, 8, 6])
- write_esri_ascii(path, fields, names=None, clobber=False)[source]
Write landlab fields to ESRI ASCII.
Write the data and grid information for fields to path in the ESRI ASCII format.
- Parameters
path (str) – Path to output file.
fields (field-like) – Landlab field object that holds a grid and associated values.
names (iterable of str, optional) – Names of the fields to include in the output file. If not provided, write all fields.
clobber (boolean) – If path exists, clobber the existing file, otherwise raise an exception.
Examples
>>> import numpy as np >>> import os >>> import tempfile >>> from landlab import RasterModelGrid >>> from landlab.io.esri_ascii import write_esri_ascii
>>> grid = RasterModelGrid((4, 5), xy_spacing=(2., 2.)) >>> _ = grid.add_field("air__temperature", np.arange(20.), at="node") >>> with tempfile.TemporaryDirectory() as tmpdirname: ... fname = os.path.join(tmpdirname, 'test.asc') ... files = write_esri_ascii(fname, grid) >>> for file in files: ... print(os.path.basename(file)) test.asc
>>> _ = grid.add_field("land_surface__elevation", np.arange(20.), at="node") >>> with tempfile.TemporaryDirectory() as tmpdirname: ... fname = os.path.join(tmpdirname, 'test.asc') ... files = write_esri_ascii(fname, grid) >>> files.sort() >>> for file in files: ... print(os.path.basename(file)) test_air__temperature.asc test_land_surface__elevation.asc
- write_obj(path, grid, field_for_z='topographic__elevation', clobber=False)[source]
Write landlab grid and one field to Wavefront OBJ.
- Parameters
path (str, or file-like) – Path to output file.
grid (Landlab grid object) – Landlab grid object that includes associated values.
field_for_z (str, optional) – Name of a field to use for the z-values of the OBJ file.
clobber (boolean, optional) – If path exists, clobber the existing file, otherwise raise an exception.
- Returns
The input path used to write the OBJ file.
- Return type
str or file-like
Examples
>>> import io >>> from landlab import HexModelGrid, RasterModelGrid >>> from landlab.io.obj import write_obj
>>> grid = HexModelGrid((3, 2), spacing=2.) >>> z = grid.add_zeros("topographic__elevation", at="node") >>> z[3] = 1.0
>>> obj_file = write_obj(io.StringIO(), grid) >>> print(obj_file.getvalue()) # landlabgrid # g landlabgrid v 1.0 0.0 0.0 v 3.0 0.0 0.0 v 0.0 1.732051 0.0 v 2.0 1.732051 1.0 v 4.0 1.732051 0.0 v 1.0 3.464102 0.0 v 3.0 3.464102 0.0 f 4// 1// 2// f 4// 3// 1// f 5// 4// 2// f 6// 3// 4// f 7// 4// 5// f 7// 6// 4//