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''(for discussions on the new GRASS GUI, see [[GRASS GUI|here]])''
''This page discusses usage of GRASS GIS and Python in a general way. If you just want to write a script to run in GRASS GIS, go to [[GRASS Python Scripting Library]] wiki page or [https://grass.osgeo.org/grass-stable/manuals/libpython/ Python API for GRASS GIS 7] documentation.''


==Python SIGs==
==Writing Python scripts in GRASS==
Python Special Interest Groups are focused collaborative efforts to develop, improve, or maintain specific Python resources. Each SIG has a charter, a coordinator, a mailing list, and a directory on the Python website. SIG membership is informal, defined by subscription to the SIG's mailing list. Anyone can join a SIG, and participate in the development discussions via the SIG's mailing list. Below is the list of currently active Python SIGs, with links to their resources.  
 
Python is a programming language which is more powerful than shell scripting but easier and more forgiving than C.
The Python script can contain simple module description definitions which will be processed with {{cmd|g.parser}}, as shown in the example below. In this way, with no extra coding a GUI can be built, inputs checked, and a skeleton help page can be generated automatically. In addition, it adds links to the GRASS message translation system. The library for "scripting" is "grass.script", typically used as:
 
<source lang="python">
import grass.script as gscript
</source>
 
The related files are at $GISBASE/etc/python/grass/script/*.py. See below for more details.
 
''Note: For code which needs access to the power of C, you can access the GRASS C library functions via [[GRASS and Python#Python Ctypes Interface|the Python "ctypes" interface]].''
 
=== How to write a Python GRASS GIS 7 addon ===
 
The tutorial "How to write a Python GRASS GIS 7 addon" is available here: https://github.com/wenzeslaus/python-grass-addon
 
=== Integrated Python shell ===
 
The [[wxGUI]] Layer Manager in GRASS GIS comes with a "Python Shell" which enables users to type and execute Python commands directly in wxGUI environment.
 
[[Image:wxgui-pyshell.png|center|400px|Embedded interactive Python Shell in wxGUI Layer Manager]]
 
=== Integrated Python editor ===
 
The [[wxGUI]] Layer Manager in GRASS GIS 7 comes with a "Simple Python Editor" which enables users to author Python scripts directly in the GRASS GIS GUI. Users can also run the script easily in the GRASS GIS environment with all the dependencies loaded. The editor comes with several examples, templates, and links to documentation.


See more at http://www.python.org/community/sigs/
[[File:Simple python editor v buffer.png|300px|thumb|right|Python interactive shell (console) and a simple Python editor are a powerful option for interacting with GRASS GIS as well as extending its functionality]]


==Writing Python scripts in GRASS==
=== External Python editors (IDE) ===
 
Besides the wxGUI Python shell and script editor, also advanced editors like '''Spyder''' (The Scientific PYthon Development EnviRonment) can be used in connection with GRASS GIS. For details, see [[Tools for Python programming]].
 
==== The correct editor settings for Python indentation ====
 
Be sure to use only white spaces and no tabs to indent Python code!
 
See: https://trac.osgeo.org/grass/wiki/Submitting/Python#Editorsettingsfor4-spaceindentation


Python is a programming language which is more powerful than shell scripting but easier and more forgiving than C.
Editor settings for 4-space indentation
The Python script can contain simple module description definitions which will be processed with {{cmd|g.parser}}, as shown in the example below. In this way with no extra coding a GUI can be built, inputs checked, and a skeleton help page can be generated automatically. In addition it adds links to the GRASS message translation system.
* '''Geany''' editor:
For code which needs access to the power of C, you can access the GRASS C library functions via the SWIG interface.
** Edit > Preferences > Editor > Intentation tab > Type: Spaces
* GNU Emacs:
** python-mode default
* spyder ...
* pycharm ...


* GRASS Python interface to library functions: http://download.osgeo.org/grass/grass6_progman/swig/
=== Using the GRASS Python Scripting Library ===
* GRASS Python scripting library: http://download.osgeo.org/grass/grass6_progman/pythonlib.html


Code style: Have a look at [http://trac.osgeo.org/grass/browser/grass/trunk/SUBMITTING_PYTHON SUBMITTING_PYTHON].
You can run Python scripts easily in a GRASS session.


=== Creating Python scripts that run in GRASS under MS-Windows ===
To write these scripts,
* check the code in lib/python/ which provides grass.script in order to support GRASS scripts written in Python.<br>
  See the [[GRASS Python Scripting Library]] for notes and examples.
* The scripts/ directory of GRASS contains a series of examples actually provided to the end users.


The environment variables have to be set as follows:
For the desired Python code style, have a look at [https://trac.osgeo.org/grass/wiki/Submitting/Python Submitting Python].
GISBASE= C:\GRASS-64
GISRC= C:\Documents and Settings\user\.grassrc6
LD_LIBRARY_PATH= C:\GRASS-64\lib
PATH= C:\GRASS-64\etc;C:\GRASS-64\etc\python;C:\GRASS-64\lib;C:\GRASS-64\bin;C:\GRASS-64\extralib;C:\GRASS-64\msys\bin;C:\Python26;
PYTHONLIB= C:\Python26
PYTHONPATH= C:\GRASS-64\etc\python
GRASS_SH= C:\GRASS-64\msys\bin\sh.exe


Some hints:
=== Creating Python scripts that call GRASS functionality from outside ===


# The Python interpreter (python.exe) needs to be in the PATH
For calling GRASS functionality from outside, see the [https://grass.osgeo.org/grass-stable/manuals/libpython/script.html#module-script.setup documentation] and also [[Working with GRASS without starting it explicitly]].
# Python needs to be associated with the .py extension
# PATHEXT needs to include .py if you want to be able to omit the extension
# PYTHONPATH needs to be set to %WINGISBASE%\etc\python


1-3 should be taken care of by the Python installer. 4 needs to be done by the startup (currently, this doesn't appear to be the case on MS-Windows).
Note: This is a more advanced use case of using GRASS' functionality from outside via Python. Commonly, a user will run GRASS Python script from inside a GRASS session, i.e. either from the command line or from the Python shell embedded in the wxGUI ([[:File:Wxgui-pyshell.png|screenshot]]).


=== Running external commands from Python ===
=== Running external commands from Python ===
Line 45: Line 73:
Windows).
Windows).


=== Examples ===
=== Testing and installing Python extensions ===


==== Display example ====
==== Debugging ====
Example of Python script, which is processed by g.parser:


<source lang="python">
Make sure the script is executable:
#!/usr/bin/env python
 
#
    chmod +x /path/to/my.extension.py
############################################################################
 
#
During development, a Python script can be debugged using the Python Debugger (pdb):
# MODULE:     d.shadedmap
 
# AUTHOR(S):   Unknown; updated to GRASS 5.7 by Michael Barton
    python -m pdb /path/to/my.extension.py input=my_input_layer output=my_output_layer option=value -f
#              Converted to Python by Glynn Clements
 
# PURPOSE:    Uses d.his to drape a color raster over a shaded relief map
==== Installation ====
# COPYRIGHT:  (C) 2004,2008,2009 by the GRASS Development Team
 
#
Once you're happy with your script, you can put it in the scripts/ folder of your GRASS install. To do so, first create a directory named after your extension, then create a Makefile for it, and a HTML man page:
#             This program is free software under the GNU General Public
 
#              License (>=v2). Read the file COPYING that comes with GRASS
    cd /path/to/grass_src/
#              for details.
    cd scripts
#
    ls # it is useful to check out the existing scripts and their structure
#############################################################################
    mkdir my.extension
    cd my.extension
    cp path/to/my.extension.py .
    touch my.extension.html
    touch Makefile
 
Next step is to edit the Makefile. It is a very simple text file, the only thing to check is to put the right extension name (WITHOUT the .py file extension) after PGM:
 
    MODULE_TOPDIR = ../..
   
    PGM = my.extension
   
    include $(MODULE_TOPDIR)/include/Make/Script.make
   
    default: script
 
The HTML file would be generated automatically. If you want to add more precisions in it, you can do it (just make sure you start at DESCRIPTION. See existing scripts.)
 
In the /path/to/grass_src/scripts folder there is also a Makefile. Before building your new folder name should be added to the SUBDIRS list in this file to be built correctly.
 
You can then run "make" within the my.extension folder. Running "make" in the extension directory places the resulting files in the staging directory (path/to/grass_src/dist.<YOUR_ARCH>/). If you're running GRASS from the staging directory (/path/to/grass_src/bin.<YOUR_ARCH>/grass7), subsequent commands will used the updated files.
 
    # in your extension directory (/path/to/grass_src/scripts/my.extension/)
    make
    # Starting GRASS from the staging directory
    /path/to/grass_src/bin.<YOUR_ARCH>/grass7
    my.extension help
 
You can also run "make install" from the top level directory of your GRASS install (say /usr/local/src/grass_trunk/). Running "make install" from the top level just copies the whole of the dist.<YOUR_ARCH>/ directory to the installation directory (e.g. /usr/local/grass78) and the bin.<YOUR_ARCH>/grass78 bin file to the bin directory (e.g. /usr/local/bin), and fixes any embedded paths in scripts and configuration files.
 
    cd /path/to/grass_src
    make install
    # Starting GRASS as usual would work and show your extension available
    grass7
    my.extension help
 
=== Using the parser to get GUI and standardized CLI ===
 
Read the documentation for [https://grass.osgeo.org/grass-stable/manuals/libpython/script_intro.html GRASS GIS Python scripting with script package].


#%Module
For more details, see
#% description: Drapes a color raster over a shaded relief map using d.his
* [[Module command line parser]]
#%End
* [[GRASS Python Scripting Library#Parsing the options and flags]]
#%option
#% key: reliefmap
#% type: string
#% gisprompt: old,cell,raster
#% description: Name of shaded relief or aspect map
#% required : yes
#%end
#%option
#% key: drapemap
#% type: string
#% gisprompt: old,cell,raster
#% description: Name of raster to drape over relief map
#% required : yes
#%end
#%option
#% key: brighten
#% type: integer
#% description: Percent to brighten
#% options: -99-99
#% answer: 0
#%end


import sys
Be sure to use the standardized options such as G_OPT_R_INPUT or G_OPT_V_OUTPUT if possible. See the overview table of [https://grass.osgeo.org/grass-stable/manuals/parser_standard_options.html parser standard options] in the documentation.
from grass.script import core as grass


def main():
=== Using a version of Python different from the default installation ===
    drape_map = options['drapemap']
    relief_map = options['reliefmap']
    brighten = options['brighten']
    ret = grass.run_command("d.his", h_map = drape_map,  i_map = relief_map, brighten = brighten)
    sys.exit(ret)


if __name__ == "__main__":
Sometimes you don't want to use the default Python version installed on your system. You can control the interpreter used for building by overriding the PYTHON make variable, e.g.
    options, flags = grass.parser()
    main()


</source>
  make PYTHON=/path/to/python ...


==== Example for embedding r.mapcalc (map algebra) ====
For controlling the interpreter used at run time:
* On Windows, Python scripts are invoked via %GRASS_PYTHON%, so changing that environment variable will change the interpreter.
* On Unix, GRASS_PYTHON is only used for components which use wxPython, e.g. wxGUI or the parameter dialogues which are displayed when modules are run without arguments.


grass.mapcalc() accepts a template string followed by keyword
Scripts rely upon the "#!/usr/bin/env python" line. You can control
arguments for the substitutions, e.g. (code snippets):
the interpreter used by scripts by creating a directory containing a
symlink named "python" which refers to your preferred version of the
interpreter, and placing that directory at the front of $PATH.


<source lang="python">
==Python extensions in GRASS GIS==
grass.mapcalc("${out} = ${rast1} + ${rast2}",
              out = options['output'],
              rast1 = options['raster1'],
              rast2 = options['raster2'])
</source>


''Best practice'': first copy all of the options[] into separate variables at the beginning of main(), i.e.:
=== Python Scripting Library ===


<source lang="python">
* See [[GRASS Python Scripting Library]]
def main():
    output = options['output']
    raster1 = options['raster1']
    raster2 = options['raster2']
    ...
    grass.mapcalc("${out} = ${rast1} + ${rast2}",
                  out = output,
                  rast1 = raster1,
                  rast2 = raster2)
</source>


==== Example for parsing category numbers ====
=== pyGRASS Library ===


Q: How to obtain the number of cells of a certain category?
pyGRASS is an object oriented Python Application Programming Interface (API) for GRASS GIS. pyGRASS wants to improve the integration between GRASS and Python, render the use of Python under GRASS more consistent with the language itself and make the GRASS scripting and programming activity easier and more natural to the final users. Some simple examples below.


A: It is recommended to use pipe_command() and parse the output, e.g.:
For more details, see '''[[Python/pygrass|pygrass]]'''


'''Example 1''':
<source lang="python">
<source lang="python">
      p = grass.pipe_command('r.stats',flags='c',input='map')
from grass.pygrass.modules import Module
      result = {}
 
      for line in p.stdout:
slope_aspect = Module("r.slope.aspect")
          [val,count] = line.strip().split()
slope_aspect(elevation='elevation', slope='slp', aspect='asp',
          result[int(val)] = int(count)
              format='degrees', overwrite=True)
      p.wait()
</source>
</source>


==Python extensions for GRASS GIS==
'''Example 2''', using "shortcuts":
=== wxPython GUI development for GRASS ===
<source lang="python">
#!/usr/bin/env python


* See the [[GRASS GUI]] wiki page
# simple example for pyGRASS usage: raster processing via modules approach


=== GRASS Python library ===
from grass.pygrass.modules.shortcuts import general as g
from grass.pygrass.modules.shortcuts import raster as r


See [http://download.osgeo.org/grass/grass6_progman/pythonlib.html GRASS Python library]
g.message("Filter elevation map by a threshold...")


==== Interfacing with NumPy ====
# set computational region
input = 'elevation'
g.region(raster=input)


''Glynn writes:''
# hardcoded:
# r.mapcalc('elev_100m = if(elevation > 100, elevation, null())', overwrite = True)
# with variables


The grass.script.array module defines a class "array" which is a
output = 'elev_100m'
subclass of numpy.memmap with .read() and .write() methods to
thresh = 100.0
read/write the underlying file via r.out.bin/r.in.bin.
r.mapcalc("%s = if(%s > %d, %s, null())" % (output, input, thresh, input), overwrite = True)
r.colors(map=output, color="elevation")
</source>


Example:


'''Example 3''', using "shortcuts" and external raster format support:
<source lang="python">
<source lang="python">
    import grass.script.array as garray
#!/usr/bin/env python
    a = garray.array()
 
    a.read("elevation.dem")
# simple example for pyGRASS usage: raster processing via Modules approach
    b = garray.array()
# Read GeoTIFF directly, write out GeoTIFF directly
    b[...] = (a / 50).astype(int) * 50    # or whatever
import os
     b.write("elev.50m")
import tempfile
</source>
from grass.pygrass.modules.shortcuts import general as g
from grass.pygrass.modules.shortcuts import raster as r
from grass.pygrass.modules import Module
 
# use alias name for GRASS GIS commands with more than one dot in name
r.external_out = Module('r.external.out')
 
# get the raster elevation map into GRASS without import
geotiff = 'elevation.tif' # with path
curr_raster='myraster'
r.external(input=geotiff, output=curr_raster)
 
# define output directory for files resulting from GRASS calculation:
gisdb = os.path.join(tempfile.gettempdir(), 'gisoutput')
try:
    os.stat(gisdb)
except:
     os.mkdir(gisdb)
g.message("Output will be written to %s" % gisdb)
 
# define where to store the resulting files and format
r.external_out(directory=gisdb, format='GTiff')


The size of the array is taken from the current region.
# do the GRASS GIS job
g.message("Filter elevation map by a threshold...")
# set computational region
g.region(raster=curr_raster)


The main drawback of using numpy is that you're limited by available
# generate GeoTIFF
memory. Using a subclass of numpy.memmap lets you use files which may
output = 'elev_100m.tif'
be much larger, but processing the entire array in one go is likely to
thresh = 100.0
produce in-memory results of a similar size.
r.mapcalc("%s = if(%s > %d, %s, null())" % (output, curr_raster, thresh, curr_raster), overwrite = True)
r.colors(map=output, color="elevation")


One may also use the scipy matlab interface:
# cease GDAL mode, back to GRASS data writing mode
   
r.external_out(flags = 'r')
    ### SH: in GRASS ###
# the resulting GeoTIFF file is in the gisdb directory
    r.out.mat input=elevation output=elev.mat
</source>


'''Example 4''':
<source lang="python">
<source lang="python">
    ### PY ###
#!/usr/bin/env python
    import scipy.io as sio
    # load data
# Example for pyGRASS usage - vector API
    elev = sio.loadmat('elev.mat')
 
    # retrive the actual array. the data set contains also the spatial reference
from grass.pygrass.modules.shortcuts import general as g
    elev.get('map_data')
from grass.pygrass.vector import VectorTopo
    data = elev.get('map_data')
from grass.pygrass.modules import Module
    # a first simple plot
    import pylab
    pylab.plot(data)
    pylab.show()
    # the contour plot
    pylab.contour(data)
    # obviously data needs to ne reversed
    import numpy as np
    data_rev = data[::-1]
    pylab.contour(data_rev)
    # => this is a quick plot. basemap mapping may provide a nicer map!
    #######
</source>


=== Python ctypes GRASS interface ===
vectmap = 'myzipcodes_wake'


Use this interface, if you need to call GRASS library functions from Python.
g.message("Importing SHAPE file ...")
ogrimport = Module('v.in.ogr')
ogrimport('/home/neteler/gis_data/zipcodes_wake.shp', output=vectmap)


Examples:
g.message("Assessing vector topology...")
zipcodes = VectorTopo(vectmap)


* GRASS 6.4: http://trac.osgeo.org/grass/browser/grass/branches/releasebranch_6_4/doc/python/example_ctypes.py
# Open the map with topology:
* GRASS 7: http://trac.osgeo.org/grass/browser/grass/trunk/doc/python/example_ctypes.py
zipcodes.open()


* Latest and greatest GRASS-Python examples: [[http://trac.osgeo.org/grass/browser/grass/trunk/scripts GRASS 7 Python scripts]]
# query number of topological features
areas  = zipcodes.number_of("areas")
islands = zipcodes.number_of("islands")
print 'Map: <' + vectmap + '> with %d areas and %d islands' % (areas, islands)


=== Python-SWIG-GRASS interface ===
dblink = zipcodes.dblinks[0]
print 'DB name:'
print dblink.database
table = dblink.table()
print 'Column names:'
print table.columns.names()
print 'Column types:'
print table.columns.types()


  Warning: The GRASS-SWIG interface isn't particularly stable and well understood. Please consider to use the Python ctypes GRASS above.
zipcodes.close()
</source>


There is a prototype GRASS-SWIG interface available (thanks to Sajith VK), find it in GRASS 6-CVS: '''swig/python/'''. Draft documentation is [http://download.osgeo.org/grass/grass6_progman/swig/ here]. It now wraps both raster and vector data C functions plus the general GIS (G_*()) functions.
* For more examples, see '''[[Python/pygrass|pygrass]]'''


Background: [http://www.swig.org SWIG] (Simplified Wrapper and Interface Generator) is:
=== Python Ctypes Interface ===


* A compiler that turns ANSI C/C++ declarations into scripting language interfaces.
This interface allows calling GRASS library functions from Python scripts. See [[Python Ctypes Examples]] for details.
* Completely automated (produces a fully working Python extension module).
* Language neutral. SWIG can also target Tcl, Perl, Guile, MATLAB (try PyLab+Matplotlib from python), etc...
* Attempts to eliminate the tedium of writing extension modules.


==== Python-SWIG examples ====
Examples:


* Latest and greatest: [[http://trac.osgeo.org/grass/browser/grass/trunk/scripts GRASS 7 Python scripts]]
* GRASS 7: [https://github.com/OSGeo/grass/blob/master/doc/python/raster_example_ctypes.py raster], [https://github.com/OSGeo/grass/blob/master/doc/python/vector_example_ctypes.py vector] example


* [[PythonSwigExamples|More complicated examples]]
* Latest and greatest: GRASS 7 Python {{src|scripts}}


Sample script for GRASS 6 raster access (use within GRASS, Spearfish session):
Sample script for GRASS raster access (use within GRASS, Spearfish session):
<source lang="python">
<source lang="python">
#!/usr/bin/env python
#!/usr/bin/env python
## TODO: update example to Ctypes


import os, sys
import os, sys
from grass.lib import grass
from grass.lib import grass
if "GISBASE" not in os.environ:
    print "You must be in GRASS GIS to run this program."
    sys.exit(1)


if len(sys.argv)==2:
if len(sys.argv)==2:
Line 289: Line 342:


# run within GRASS Spearfish session
# run within GRASS Spearfish session
# run this before starting python to append module search path:
#  export PYTHONPATH=/usr/src/grass70/swig/python
#  check with "import sys; sys.path"
# or:
#  sys.path.append("/usr/src/grass70/swig/python")
# FIXME: install the grass bindings in $GISBASE/lib/ ?
import os, sys
import os, sys
from grass.lib import grass
from grass.lib import grass
from grass.lib import vector as grassvect
from grass.lib import vector as grassvect
if "GISBASE" not in os.environ:
    print "You must be in GRASS GIS to run this program."
    sys.exit(1)


if len(sys.argv)==2:
if len(sys.argv)==2:
Line 335: Line 377:
</source>
</source>


==== TODO ====
=== Using ipython ===


* Implement modules support in a Python class using --interface-description and a Python-XML parser. This should be a generic class with module's name as parameter, returning back an object which describes the module (description, flags, parameters, status of not/required). See [http://trac.osgeo.org/grass/browser/grass/trunk/gui/wxpython/ GRASS 6 wxPython interface] for inspiration. Important is to auto-generate the GRASS-Python class at compile time with a Python script.
Using [https://ipython.org/ ipython] is great due to the TAB completion. Don't remember the function name or curious about what's offered? Hit TAB (maybe twice for a list).


=== Python-GRASS add-ons ===
Here an example how to connect to C functions directly from Python:


Stand-alone addons:
<source lang="python">
grass76
# ... in the GRASS GIS terminal
ipython
In [1]: from grass.lib import gis


# Jáchym Čepický's G-ps.map, a GUI to typeset printable maps with ps.map (http://193.84.38.2/~jachym/index.py?cat=gpsmap)
In [2]: gis.<TAB>
# Jáchym Čepický's v.pydigit, a GUI to v.edit (http://les-ejk.cz/?cat=vpydigit)
Display all 729 possibilities? (y or n)
# Jáchym Čepický's PyWPS, GRASS-Web Processing Service (http://pywps.wald.intevation.org)
gis.ARRAY                                gis.G_fatal_longjmp                      gis.G_set_key_value
gis.ArgumentError                        gis.G_file_name                          gis.G_set_keywords
gis.Array                                gis.G_file_name_misc                      gis.G_set_ls_exclude_filter
...
gis.G_fatal_error                        gis.G_set_gisrc_mode                      gis.wstring_at


=== Using GRASS gui.tcl in Python ===
In [2]: gis.G_message("Hello world")
 
Hello world
Here is some example code to use the grass automatically generated guis in python code. This could (should) all be bundled up and abstracted away so that the implementation can be replaced later.
</source>
 
<source lang="python">
import Tkinter
import os


# Startup (once):
A full ipython workshop is available here: https://github.com/wenzeslaus/python-grass-addon


tk = Tkinter.Tk()
=== wxPython GUI development ===
tk.eval ("wm withdraw .")
tk.eval ("source $env(GISBASE)/etc/gui.tcl")
# Here you could do various things to change what the gui does
# See gui.tcl and README.GUI


# Make a gui (per dialog)
* See the [[wxGUI]] wiki page
# This sets up a window for the command.
# This can be different to integrate with tkinter:
tk.eval ('set path ".dialog$dlg"')
tk.eval ('toplevel .dialog$dlg')
# Load the code for this command:
fd = os.popen ("d.vect --tcltk")
gui = fd.read()
# Run it
tk.eval(gui)
dlg = tk.eval('set dlg') # This is used later to get and set


# Get the current command in the gui we just made:
=== 3rd party Python software connected to GRASS GIS ===
currentcommand = tk.eval ("dialog_get_command " + dlg)


# Set the command in the dialog we just made:
* PyWPS (http://pywps.org/)
tk.eval ("dialog_set_command " + dlg + " {d.vect map=roads}")
* QGIS Processing plugin
</source>


== FAQ ==
== FAQ ==
Line 391: Line 421:
=== General guides ===
=== General guides ===


* [http://en.wikibooks.org/wiki/Python_Programming/ Wikibook Python Programming]
* [https://en.wikibooks.org/wiki/Python_Programming/ Wikibook Python Programming]
* [http://www.poromenos.org/tutorials/python Quick Python tutorial] for programmers of other languages
* [https://www.poromenos.org/tutorials/python Quick Python tutorial] for programmers of other languages
: [http://wiki.python.org/moin/BeginnersGuide/Programmers More Python tutorials] for programmers
*: [https://wiki.python.org/moin/BeginnersGuide/Programmers More Python tutorials] for programmers
* [http://www.python.org/dev/peps/pep-0008/ Python programming style guide]
* [https://www.python.org/dev/peps/pep-0008/ Python programming style guide]
* [https://wiki.python.org/moin/PythonEditors Python Editors]


=== Programming ===
=== Programming ===


* Python and GRASS:
* Python and GRASS:
** GRASS Python interface to library functions: http://download.osgeo.org/grass/grass6_progman/swig/ based on SWIG http://www.swig.org/
** Library interfaces: [GRASS Python Scripting Library https://grass.osgeo.org/grass78/manuals/libpython/]
** GRASS Python scripting library: http://download.osgeo.org/grass/grass6_progman/pythonlib.html
** Graphical user interface (GUI): [GRASS wxPython-based GUI https://grass.osgeo.org/grass-stable/manuals/wxGUI.html]
** PyWPS, GRASS-Web Processing Service http://pywps.wald.intevation.org
** PyWPS, GRASS-Web Processing Service: [[WPS]]


* Python and OSGeo:
* Python and OSGeo:
** [http://wiki.osgeo.org/wiki/OSGeo_Python_Library OSGeo Python Library]
** [https://wiki.osgeo.org/wiki/OSGeo_Python_Library OSGeo Python Library]


* Python and GDAL/OGR:
* Python and GDAL/OGR:
** [http://mapserver.gis.umn.edu/community/conferences/MUM3/workshop/python Open Source Python GIS Hacks Mum'03]
** [https://mapserver.gis.umn.edu/community/conferences/MUM3/workshop/python Open Source Python GIS Hacks Mum'03]
** http://hobu.biz/software/OSGIS_Hacks - Python OSGIS Hacks '05
** https://hobu.biz/software/OSGIS_Hacks - Python OSGIS Hacks '05
** http://zcologia.com/news/categorylist_html?cat_id=8
** https://zcologia.com/news/categorylist_html?cat_id=8
** http://www.perrygeo.net/wordpress/?p=4
** https://www.perrygeo.net/wordpress/?p=4


* Python bindings to PROJ:
* Python bindings to PROJ:
** http://www.cdc.noaa.gov/people/jeffrey.s.whitaker/python/pyproj.html
** https://www.cdc.noaa.gov/people/jeffrey.s.whitaker/python/pyproj.html


* Python and GIS:
* Python and GIS:
** [http://gispython.org/ Open Source GIS-Python Laboratory]
** [https://gispython.org/ Open Source GIS-Python Laboratory]


* Python and Statistics:
* Python and Statistics:
** [http://rpy.sourceforge.net/ RPy] - Python interface to the R-statistics programming language
** [https://rpy.sourceforge.net/ RPy] - Python interface to the R-statistics programming language


* Bindings:
* Bindings:
** SIP (C/C++ bindings generator) http://directory.fsf.org/all/Python-SIP.html
** SIP (C/C++ bindings generator) http://directory.fsf.org/all/Python-SIP.html
** [http://www.cython.org/ Cython] - C-Extensions for Python (compile where speed is needed)
** [https://www.cython.org/ Cython] - C-Extensions for Python (compile where speed is needed)


* Other external projects
* Other external projects
** [http://www.scipy.org Scientific Python]
** [https://www.scipy.org Scientific Python]
** [http://wiki.python.org/moin/NumericAndScientific Numeric and Scientific]
** [https://wiki.python.org/moin/NumericAndScientific Numeric and Scientific]
** [http://w3.pppl.gov/~hammett/comp/python/python.html Info on Python for Scientific Applications]
** [https://w3.pppl.gov/~hammett/comp/python/python.html Info on Python for Scientific Applications]


=== Presentations ===
=== Presentations ===


From FOSS4G2006:
* https://www.slideshare.net/search/slideshow?q=pygrass
* [http://www.foss4g2006.org/materialDisplay.py?contribId=136&amp;sessionId=48&amp;materialId=slides&amp;confId=1 A Python sweeps in the GRASS] - A. Frigeri 2006
 
* [http://www.foss4g2006.org/materialDisplay.py?contribId=67&amp;sessionId=48&amp;materialId=slides&amp;confId=1 GRASS goes web: PyWPS] - J. Cepicky 2006
From FOSS4G2006 (initial historical steps):
* [https://www.foss4g2006.org/materialDisplay.py?contribId=136&amp;sessionId=48&amp;materialId=slides&amp;confId=1 A Python sweeps in the GRASS] - A. Frigeri 2006
* [https://www.foss4g2006.org/materialDisplay.py?contribId=67&amp;sessionId=48&amp;materialId=slides&amp;confId=1 GRASS goes web: PyWPS] - J. Cepicky 2006 (see also [[WPS]])
 
=== References ===
 
* Zambelli, P., Gebbert, S., Ciolli, M., 2013. ''Pygrass: An Object Oriented Python Application Programming Interface (API) for Geographic Resources Analysis Support System (GRASS) Geographic Information System (GIS)''. ISPRS International Journal of Geo-Information 2, 201–219. ([https://dx.doi.org/10.3390/ijgi2010201 DOI] | [https://www.mdpi.com/2220-9964/2/1/201/pdf PDF])
 
* GRASS GIS and the Python geospatial modules (Shapely, PySAL,...)
** See https://osgeo-org.1560.x6.nabble.com/GRASS-and-the-Python-geospatial-modules-Shapely-PySAL-td4985075.html


[[Category:Development]]
{{Python}}
[[Category:Linking to other languages]]
[[Category:Python]]

Latest revision as of 08:20, 8 December 2020

This page discusses usage of GRASS GIS and Python in a general way. If you just want to write a script to run in GRASS GIS, go to GRASS Python Scripting Library wiki page or Python API for GRASS GIS 7 documentation.

Writing Python scripts in GRASS

Python is a programming language which is more powerful than shell scripting but easier and more forgiving than C. The Python script can contain simple module description definitions which will be processed with g.parser, as shown in the example below. In this way, with no extra coding a GUI can be built, inputs checked, and a skeleton help page can be generated automatically. In addition, it adds links to the GRASS message translation system. The library for "scripting" is "grass.script", typically used as: 

import grass.script as gscript

The related files are at $GISBASE/etc/python/grass/script/*.py. See below for more details.

Note: For code which needs access to the power of C, you can access the GRASS C library functions via the Python "ctypes" interface.

How to write a Python GRASS GIS 7 addon

The tutorial "How to write a Python GRASS GIS 7 addon" is available here: https://github.com/wenzeslaus/python-grass-addon

Integrated Python shell

The wxGUI Layer Manager in GRASS GIS comes with a "Python Shell" which enables users to type and execute Python commands directly in wxGUI environment.

Embedded interactive Python Shell in wxGUI Layer Manager
Embedded interactive Python Shell in wxGUI Layer Manager

Integrated Python editor

The wxGUI Layer Manager in GRASS GIS 7 comes with a "Simple Python Editor" which enables users to author Python scripts directly in the GRASS GIS GUI. Users can also run the script easily in the GRASS GIS environment with all the dependencies loaded. The editor comes with several examples, templates, and links to documentation.

Python interactive shell (console) and a simple Python editor are a powerful option for interacting with GRASS GIS as well as extending its functionality

External Python editors (IDE)

Besides the wxGUI Python shell and script editor, also advanced editors like Spyder (The Scientific PYthon Development EnviRonment) can be used in connection with GRASS GIS. For details, see Tools for Python programming.

The correct editor settings for Python indentation

Be sure to use only white spaces and no tabs to indent Python code!

See: https://trac.osgeo.org/grass/wiki/Submitting/Python#Editorsettingsfor4-spaceindentation

Editor settings for 4-space indentation

  • Geany editor:
    • Edit > Preferences > Editor > Intentation tab > Type: Spaces
  • GNU Emacs:
    • python-mode default
  • spyder ...
  • pycharm ...

Using the GRASS Python Scripting Library

You can run Python scripts easily in a GRASS session.

To write these scripts,

  • check the code in lib/python/ which provides grass.script in order to support GRASS scripts written in Python.
 See the GRASS Python Scripting Library for notes and examples.
  • The scripts/ directory of GRASS contains a series of examples actually provided to the end users.

For the desired Python code style, have a look at Submitting Python.

Creating Python scripts that call GRASS functionality from outside

For calling GRASS functionality from outside, see the documentation and also Working with GRASS without starting it explicitly.

Note: This is a more advanced use case of using GRASS' functionality from outside via Python. Commonly, a user will run GRASS Python script from inside a GRASS session, i.e. either from the command line or from the Python shell embedded in the wxGUI (screenshot).

Running external commands from Python

For information on running external commands from Python, see: http://docs.python.org/lib/module-subprocess.html

Avoid using the older os.* functions. Section 17.1.3 lists equivalents using the Popen() interface, which is more robust (particularly on Windows).

Testing and installing Python extensions

Debugging

Make sure the script is executable: 

   chmod +x /path/to/my.extension.py

During development, a Python script can be debugged using the Python Debugger (pdb): 

   python -m pdb /path/to/my.extension.py input=my_input_layer output=my_output_layer option=value -f

Installation

Once you're happy with your script, you can put it in the scripts/ folder of your GRASS install. To do so, first create a directory named after your extension, then create a Makefile for it, and a HTML man page: 

   cd /path/to/grass_src/
   cd scripts
   ls # it is useful to check out the existing scripts and their structure
   mkdir my.extension
   cd my.extension
   cp path/to/my.extension.py .
   touch my.extension.html
   touch Makefile

Next step is to edit the Makefile. It is a very simple text file, the only thing to check is to put the right extension name (WITHOUT the .py file extension) after PGM: 

   MODULE_TOPDIR = ../..
   
   PGM = my.extension
   
   include $(MODULE_TOPDIR)/include/Make/Script.make
   
   default: script

The HTML file would be generated automatically. If you want to add more precisions in it, you can do it (just make sure you start at DESCRIPTION. See existing scripts.)

In the /path/to/grass_src/scripts folder there is also a Makefile. Before building your new folder name should be added to the SUBDIRS list in this file to be built correctly.

You can then run "make" within the my.extension folder. Running "make" in the extension directory places the resulting files in the staging directory (path/to/grass_src/dist.<YOUR_ARCH>/). If you're running GRASS from the staging directory (/path/to/grass_src/bin.<YOUR_ARCH>/grass7), subsequent commands will used the updated files. 

   # in your extension directory (/path/to/grass_src/scripts/my.extension/)
   make
   # Starting GRASS from the staging directory
   /path/to/grass_src/bin.<YOUR_ARCH>/grass7
   my.extension help

You can also run "make install" from the top level directory of your GRASS install (say /usr/local/src/grass_trunk/). Running "make install" from the top level just copies the whole of the dist.<YOUR_ARCH>/ directory to the installation directory (e.g. /usr/local/grass78) and the bin.<YOUR_ARCH>/grass78 bin file to the bin directory (e.g. /usr/local/bin), and fixes any embedded paths in scripts and configuration files. 

   cd /path/to/grass_src
   make install
   # Starting GRASS as usual would work and show your extension available
   grass7
   my.extension help

Using the parser to get GUI and standardized CLI

Read the documentation for GRASS GIS Python scripting with script package.

For more details, see

Be sure to use the standardized options such as G_OPT_R_INPUT or G_OPT_V_OUTPUT if possible. See the overview table of parser standard options in the documentation.

Using a version of Python different from the default installation

Sometimes you don't want to use the default Python version installed on your system. You can control the interpreter used for building by overriding the PYTHON make variable, e.g. 

 make PYTHON=/path/to/python ...

For controlling the interpreter used at run time:

  • On Windows, Python scripts are invoked via %GRASS_PYTHON%, so changing that environment variable will change the interpreter.
  • On Unix, GRASS_PYTHON is only used for components which use wxPython, e.g. wxGUI or the parameter dialogues which are displayed when modules are run without arguments.

Scripts rely upon the "#!/usr/bin/env python" line. You can control the interpreter used by scripts by creating a directory containing a symlink named "python" which refers to your preferred version of the interpreter, and placing that directory at the front of $PATH.

Python extensions in GRASS GIS

Python Scripting Library

pyGRASS Library

pyGRASS is an object oriented Python Application Programming Interface (API) for GRASS GIS. pyGRASS wants to improve the integration between GRASS and Python, render the use of Python under GRASS more consistent with the language itself and make the GRASS scripting and programming activity easier and more natural to the final users. Some simple examples below.

For more details, see pygrass

Example 1: 

from grass.pygrass.modules import Module

slope_aspect = Module("r.slope.aspect")
slope_aspect(elevation='elevation', slope='slp',  aspect='asp', 
               format='degrees', overwrite=True)

Example 2, using "shortcuts": 

#!/usr/bin/env python

# simple example for pyGRASS usage: raster processing via modules approach

from grass.pygrass.modules.shortcuts import general as g
from grass.pygrass.modules.shortcuts import raster as r

g.message("Filter elevation map by a threshold...")

# set computational region
input = 'elevation'
g.region(raster=input)

# hardcoded:
# r.mapcalc('elev_100m = if(elevation > 100, elevation, null())', overwrite = True)
# with variables

output = 'elev_100m'
thresh = 100.0
r.mapcalc("%s = if(%s > %d, %s, null())" % (output, input, thresh, input), overwrite = True)
r.colors(map=output, color="elevation")


Example 3, using "shortcuts" and external raster format support: 

#!/usr/bin/env python

# simple example for pyGRASS usage: raster processing via Modules approach
# Read GeoTIFF directly, write out GeoTIFF directly
import os
import tempfile
from grass.pygrass.modules.shortcuts import general as g
from grass.pygrass.modules.shortcuts import raster as r
from grass.pygrass.modules import Module

# use alias name for GRASS GIS commands with more than one dot in name
r.external_out = Module('r.external.out')

# get the raster elevation map into GRASS without import
geotiff = 'elevation.tif' # with path
curr_raster='myraster'
r.external(input=geotiff, output=curr_raster)

# define output directory for files resulting from GRASS calculation:
gisdb = os.path.join(tempfile.gettempdir(), 'gisoutput')
try:
    os.stat(gisdb)
except:
    os.mkdir(gisdb)
g.message("Output will be written to %s" % gisdb)

# define where to store the resulting files and format
r.external_out(directory=gisdb, format='GTiff')

# do the GRASS GIS job
g.message("Filter elevation map by a threshold...")
# set computational region
g.region(raster=curr_raster)

# generate GeoTIFF
output = 'elev_100m.tif'
thresh = 100.0
r.mapcalc("%s = if(%s > %d, %s, null())" % (output, curr_raster, thresh, curr_raster), overwrite = True)
r.colors(map=output, color="elevation")

# cease GDAL mode, back to GRASS data writing mode
r.external_out(flags = 'r')
# the resulting GeoTIFF file is in the gisdb directory

Example 4: 

#!/usr/bin/env python
 
# Example for pyGRASS usage - vector API

from grass.pygrass.modules.shortcuts import general as g
from grass.pygrass.vector import VectorTopo
from grass.pygrass.modules import Module

vectmap = 'myzipcodes_wake'

g.message("Importing SHAPE file ...")
ogrimport = Module('v.in.ogr')
ogrimport('/home/neteler/gis_data/zipcodes_wake.shp', output=vectmap)

g.message("Assessing vector topology...")
zipcodes = VectorTopo(vectmap)

# Open the map with topology:
zipcodes.open()

# query number of topological features
areas   = zipcodes.number_of("areas")
islands = zipcodes.number_of("islands")
print 'Map: <' + vectmap + '> with %d areas and %d islands' % (areas, islands)

dblink = zipcodes.dblinks[0]
print 'DB name:'
print dblink.database
table = dblink.table()
print 'Column names:'
print table.columns.names()
print 'Column types:'
print table.columns.types()

zipcodes.close()

Python Ctypes Interface

This interface allows calling GRASS library functions from Python scripts. See Python Ctypes Examples for details.

Examples:

  • Latest and greatest: GRASS 7 Python scripts

Sample script for GRASS raster access (use within GRASS, Spearfish session): 

#!/usr/bin/env python

## TODO: update example to Ctypes

import os, sys
from grass.lib import grass

if len(sys.argv)==2:
  input = sys.argv[1]
else:
  input = raw_input("Raster Map Name? ")

# initialize
grass.G_gisinit('')

# find map in search path
mapset = grass.G_find_cell2(input, '')

# determine the inputmap type (CELL/FCELL/DCELL) */
data_type = grass.G_raster_map_type(input, mapset)

infd = grass.G_open_cell_old(input, mapset)
inrast = grass.G_allocate_raster_buf(data_type)

rown = 0
while True:
    myrow = grass.G_get_raster_row(infd, inrast, rown, data_type)
    print rown, myrow[0:10]
    rown += 1
    if rown == 476:
        break

grass.G_close_cell(inrast)
grass.G_free(cell)

Sample script for vector access (use within GRASS, Spearfish session): 

#!/usr/bin/python

# run within GRASS Spearfish session
import os, sys
from grass.lib import grass
from grass.lib import vector as grassvect

if len(sys.argv)==2:
  input = sys.argv[1]
else:
  input = raw_input("Vector Map Name? ")

# initialize
grass.G_gisinit('')

# find map in search path
mapset = grass.G_find_vector2(input,'')

# define map structure
map = grassvect.Map_info()

# define open level (level 2: topology)
grassvect.Vect_set_open_level (2)

# open existing map
grassvect.Vect_open_old(map, input, mapset)

# query
print 'Vect map: ', input
print 'Vect is 3D: ', grassvect.Vect_is_3d (map)
print 'Vect DB links: ', grassvect.Vect_get_num_dblinks(map)
print 'Map Scale:  1:', grassvect.Vect_get_scale(map)
print 'Number of areas:', grassvect.Vect_get_num_areas(map)

# close map
grassvect.Vect_close(map)

Using ipython

Using ipython is great due to the TAB completion. Don't remember the function name or curious about what's offered? Hit TAB (maybe twice for a list).

Here an example how to connect to C functions directly from Python: 

grass76
# ... in the GRASS GIS terminal
ipython
In [1]: from grass.lib import gis

In [2]: gis.<TAB>
Display all 729 possibilities? (y or n)
gis.ARRAY                                 gis.G_fatal_longjmp                       gis.G_set_key_value
gis.ArgumentError                         gis.G_file_name                           gis.G_set_keywords
gis.Array                                 gis.G_file_name_misc                      gis.G_set_ls_exclude_filter
...
gis.G_fatal_error                         gis.G_set_gisrc_mode                      gis.wstring_at

In [2]: gis.G_message("Hello world")
Hello world

A full ipython workshop is available here: https://github.com/wenzeslaus/python-grass-addon

wxPython GUI development

3rd party Python software connected to GRASS GIS

FAQ

  • Q: Error message "execl() failed: Permission denied" - what to do?
A: Be sure that the execute bit of the script is set.

Links

General guides

Programming

  • Python and Statistics:
    • RPy - Python interface to the R-statistics programming language

Presentations

From FOSS4G2006 (initial historical steps):

References

  • Zambelli, P., Gebbert, S., Ciolli, M., 2013. Pygrass: An Object Oriented Python Application Programming Interface (API) for Geographic Resources Analysis Support System (GRASS) Geographic Information System (GIS). ISPRS International Journal of Geo-Information 2, 201–219. (DOI | PDF)
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