Difference between revisions of "GRASS GIS Jupyter notebooks"

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A Jupyter Notebook is a web application that allows you to create and share documents that contain scripts and code, equations, visualizations and explanatory text, combined.
A Jupyter Notebook is a web application that allows you to create and share documents that contain scripts and code, equations, visualizations and explanatory text, combined.
== Get started ==
Read the intro in the official documentation for [https://grass.osgeo.org/grass-stable/manuals/libpython/grass.jupyter.html grass.jupyter package].


== List of selected GRASS GIS Jupyter notebooks ==
== List of selected GRASS GIS Jupyter notebooks ==


''(please expand!)''
''(add yours to the list!)''


* https://github.com/wenzeslaus/try-grass-in-jupyter
Intro notebooks:
* https://github.com/wenzeslaus/try-grass-in-jupyter-with-bash
* [https://github.com/OSGeo/grass/blob/main/doc/notebooks Official notebooks in OSGeo/grass repo] ([https://mybinder.org/v2/gh/OSGeo/grass/main?urlpath=lab%2Ftree%2Fdoc%2Fnotebooks%2Fjupyter_example.ipynb jupyter_example.ipynb on Binder])
* [https://github.com/wenzeslaus/geospatial-modeling-course-jupyter/tree/master/notebooks 14 Jupyter Notebooks for learning geospatial analysis and modeling with GRASS GIS]
* [https://github.com/ncsu-geoforall-lab/grass-gis-workshop-foss4g-2022 Unleash the power of GRASS GIS with Jupyter (FOSS4G 2022 workshop)]
* [https://github.com/ncsu-geoforall-lab/grass-gis-workshop-FOSS4G-2021 GRASS GIS: From Beginner to Power User (FOSS4G 2021 workshop)]
* [https://github.com/wenzeslaus/try-grass-in-jupyter-with-bash wenzeslaus/try-grass-in-jupyter-with-bash] (experimental)
 
Collections:
* [https://github.com/wenzeslaus/geospatial-modeling-course-jupyter/tree/master/notebooks 14 Jupyter Notebooks for learning geospatial analysis and modeling with GRASS GIS] (Python and command line versions)
 
Image processing/OBIA:
* [https://github.com/neteler/jupyter_sentinel2_grass_gis GRASS GIS 8 and processing of multitemporal EO data]
* [https://github.com/tgrippa/Opensource_OBIA_processing_chain An open-source semi-automated processing chain for urban OBIA classification]
* [https://github.com/tgrippa/Opensource_OBIA_processing_chain An open-source semi-automated processing chain for urban OBIA classification]
Python and PyGRASS:
* [https://github.com/zarch/workshop-pygrass Workshop on PyGRASS using IPython notebook]
* [https://github.com/zarch/workshop-pygrass Workshop on PyGRASS using IPython notebook]
* [https://github.com/wenzeslaus/python-grass-addon How to write a Python GRASS GIS 7 addon]
* [https://github.com/wenzeslaus/foss4g-2022-developing-custom-grass-tools Developing custom GRASS tools (FOSS4G 2022 workshop)]
* [https://github.com/wenzeslaus/python-grass-addon How to write a Python GRASS GIS 7 addon (FOSS4G Europe 2015 workshop)]
* [https://github.com/lucadelu/docker-stacks/tree/geospatial/geospatial-notebook Jupyter Notebook Geospatial Python Stack]
* [https://github.com/lucadelu/docker-stacks/tree/geospatial/geospatial-notebook Jupyter Notebook Geospatial Python Stack]
R and GRASS GIS:
* [https://gist.github.com/joergsteinkamp/43fb13a82aeab9b5c0dcc4433f97f1a6 Simple Opensource GIS examples with GRASS GIS and R]
* [https://gist.github.com/joergsteinkamp/43fb13a82aeab9b5c0dcc4433f97f1a6 Simple Opensource GIS examples with GRASS GIS and R]
Wildfire Modeling:
* [https://github.com/acoiman/wildfire_modeling Wildfire Modeling in Yosemite National Park]


== Running a Jupyter notebook locally ==
== Running a Jupyter notebook locally ==
You can even change the code and explore your modified script(s).


=== Requirements ===
Both Jupyter and GRASS GIS have so called environments or sessions which need to be combined. Existing online environments with example notebooks are usually prepared to run right away, but locally, one must prepare the necessary software setup.


You need to have a working Jupyter installation:
=== Software requirements ===
<source lang="bash">
 
pip install jupyter
You need to have a working GRASS GIS installation.
</source>


=== How to run GRASS GIS from Jupyter notebook ===
You need to have a working Jupyter installation. If you are using ''pip'', you can install Jupyter using:


''(this section needs to be updated)''
<syntaxhighlight lang="bash">
pip install jupyter
</syntaxhighlight>


Running GRASS from Jupyter notebook requires that Jupyter notebook is installed on your system, and that you set up the [https://grass.osgeo.org/grass78/manuals/variables.html environment variables] for using GRASS.
GRASS GIS and the Python you used to install Jupyter need to know about each other.


For example you can create a '''script''' called <tt>grass_jupyter.sh</tt> that contains the following lines:
On Linux, this will be usually true and no special steps are needed. GRASS GIS just uses the system Python and you presumably use pip which uses system Python too.
<source lang="bash">


# directory where GRASS GIS lives
On Windows, install Jupyter using the Python which is available in GRASS session. There is no system Python on Windows, so, e.g., installing Jupyter in conda and standalone GRASS GIS results in two different and disconnected Python installations. See this [https://github.com/chaedri/GIS714-assignments/blob/main/Topic1_Foundations/JupyterOnWindows_Tutorial.ipynb NCSU GIS714 Jupyter On Windows Tutorial] for installing Jupyter using pip which is linked with Python linked to GRASS GIS.
export GISBASE=`grass78 --config path`  # or define path to binaries like /usr/local/grass-7.8.dev
echo $GISBASE


# generate GISRC
=== Start Jupyter, then GRASS GIS ===
# Defines the system wide value while in a GRASS session
MYGISDBASE=$HOME/grassdata # Change this path to reflect your own
MYLOC=MyLoc # Change this location name to reflect your own
MYMAPSET=PERMANENT


# Set the global grassrc file to individual file name
<syntaxhighlight lang="bash">
MYGISRC="$HOME/.grassrc.$$"
jupyter lab
</syntaxhighlight>


echo "GISDBASE: $MYGISDBASE" > "$MYGISRC"
In a notebook, start the session using the [https://grass.osgeo.org/grass-stable/manuals/libpython/grass.jupyter.html grass.jupyter package].
echo "LOCATION_NAME: $MYLOC" >> "$MYGISRC"
echo "MAPSET: $MYMAPSET" >> "$MYGISRC"
echo "GRASS_GUI: text" >> "$MYGISRC"


# path to GRASS settings file
On Windows, due to a lack of system Python shared among all applications, it is easiest to start GRASS GIS (to get a command line with Python) and start Jupyter from there, see the [https://github.com/chaedri/GIS714-assignments/blob/main/Topic1_Foundations/JupyterOnWindows_Tutorial.ipynb NCSU GIS714 Jupyter On Windows Tutorial]. (The session in command line will be replaced by a new session in the notebook.)
export GISRC=$MYGISRC


export LD_LIBRARY_PATH=$GISBASE/lib:$LD_LIBRARY_PATH
=== Start GRASS GIS, then GRASS GIS ===
export PYTHONPATH=$GISBASE/etc/python:$PYTHONPATH
export PATH=$GISBASE/bin:$GISBASE/scripts:$PATH


# start the notebook in the notebook folder
If the above does not work for you or you want your notebooks to not deal with GRASS session at all, start GRASS shell and then start Jupyter from there, for example:
cd $HOME/notebooks # change to notebooks folder (example; update to your path)


nohup jupyter notebook --ip=0.0.0.0 --port=8888 --debug &
<syntaxhighlight lang="bash">
</source>
$ grass ...
GRASS > jupyter lab
</syntaxhighlight>


To easily use this script, add this line to your <tt>$HOME/.bashrc</tt> file:
This can be done in one command, avoiding need for an additional step in the GRASS shell:


<source lang="bash">
<syntaxhighlight lang="bash">
# update path to script accordingly
$ grass ... --exec jupyter lab
alias grass_notebook='sh $HOME/grass_jupyter.sh'
</syntaxhighlight>
</source>


From terminal, in your home directory:
For example:
<source lang="bash">
source .bashrc
</source>


Now you can start easily your notebook typing in the terminal:
<syntaxhighlight lang="bash">
<source lang="bash">
$ grass ~/data/world_wgs84/coastal --exec jupyter lab
grass_notebook
</syntaxhighlight>
</source>


==== Tools ====
== Tools ==


* [https://github.com/wenzeslaus/gdoc2py GRASS GIS focused converter from HTML with pre code tags to Jupyter Notebook]
* [https://github.com/wenzeslaus/gdoc2py GRASS GIS focused converter from HTML with pre code tags to Jupyter Notebook]
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[[Category: Documentation]]
[[Category: Documentation]]
[[Category: Python]]
[[Category: Python]]
[[Category: Tutorial]]

Latest revision as of 14:19, 19 July 2022

A Jupyter Notebook is a web application that allows you to create and share documents that contain scripts and code, equations, visualizations and explanatory text, combined.

Get started

Read the intro in the official documentation for grass.jupyter package.

List of selected GRASS GIS Jupyter notebooks

(add yours to the list!)

Intro notebooks:

Collections:

Image processing/OBIA:

Python and PyGRASS:

R and GRASS GIS:

Wildfire Modeling:

Running a Jupyter notebook locally

Both Jupyter and GRASS GIS have so called environments or sessions which need to be combined. Existing online environments with example notebooks are usually prepared to run right away, but locally, one must prepare the necessary software setup.

Software requirements

You need to have a working GRASS GIS installation.

You need to have a working Jupyter installation. If you are using pip, you can install Jupyter using:

pip install jupyter

GRASS GIS and the Python you used to install Jupyter need to know about each other.

On Linux, this will be usually true and no special steps are needed. GRASS GIS just uses the system Python and you presumably use pip which uses system Python too.

On Windows, install Jupyter using the Python which is available in GRASS session. There is no system Python on Windows, so, e.g., installing Jupyter in conda and standalone GRASS GIS results in two different and disconnected Python installations. See this NCSU GIS714 Jupyter On Windows Tutorial for installing Jupyter using pip which is linked with Python linked to GRASS GIS.

Start Jupyter, then GRASS GIS

jupyter lab

In a notebook, start the session using the grass.jupyter package.

On Windows, due to a lack of system Python shared among all applications, it is easiest to start GRASS GIS (to get a command line with Python) and start Jupyter from there, see the NCSU GIS714 Jupyter On Windows Tutorial. (The session in command line will be replaced by a new session in the notebook.)

Start GRASS GIS, then GRASS GIS

If the above does not work for you or you want your notebooks to not deal with GRASS session at all, start GRASS shell and then start Jupyter from there, for example:

$ grass ...
GRASS > jupyter lab

This can be done in one command, avoiding need for an additional step in the GRASS shell:

$ grass ... --exec jupyter lab

For example:

$ grass ~/data/world_wgs84/coastal --exec jupyter lab

Tools