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Geoconda

Geoconda

Description

Geoconda includes Python GIS packages and enables users easily to install new Python packags for their own use. It is an alternative installation to the GeoPython module.

Conda is a package management tool that is used to distribute and install software tools together with their dependencies. Geoconda installation is done with miniconda3, it includes Python3

Geoconda is a collection of python packages that facilitate the development of python scripts for geoinformatics applications. It includes following python packages (mostly the same as GeoPython):

  • cartopy - for map plotting (not included in GeoPython).
  • descartes - use Shapely or GeoJSON-like geometric objects as matplotlib paths and patches.
  • fiona - reads and writes spatial data files.
  • gdal - reads and writes spatial data files, and GDAL/OGR data manipulation tools.
  • geoalchemy2 (only in geoconda/3.7) - provides extensions to SQLAlchemy for working with spatial databases, primarly PostGIS.
  • geopandas - GeoPandas extends the datatypes used by pandas.
  • laspy - reading and writing .las and .laz files.
  • networkx - for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
  • pdal (only in geoconda/3.7) -  for lidar data management and analysis
  • pyfor - lidar analysis for forestry purposes.
  • pyproj - performs cartographic transformations and geodetic computations.
  • pysal - spatial analysis functions.
  • osmnx (only in geoconda/3.7) - download spatial geometries and construct, project, visualize, and analyze street networks from OpenStreetMap's APIs.
  • rasterio - access to geospatial raster data.
  • rasterstats - for summarizing geospatial raster datasets based on vector geometries. It includes functions for zonal statistics and interpolated point queries.
  • rtree - spatial indexing and search.
  • shapely - manipulation and analysis of geometric objects in the Cartesian plane.
  • spectral (only in geoconda/3.7) - for processing hyperspectral image data.
  • skimage - algorithms for image processing.
  • scikit-learn (only in geoconda/3.7) - machine learning for Python.
  • And many more, for retrieving the full list in Taito use: conda list
  • (snappy has its own conda environment, see SNAP)

Additionally geoconda includes:

  • spyder - Scientific PYthon Development EnviRonment with graphical interface (similar to RStudio for R). If you want to use Spyer, you should connect to taito-shell using -X connection or NoMachine for Windows users.
  • GDAL/OGR commandline tools and proj4, geos
  • PDAL command-line tools
  • And many more, see /appl/earth/geoconda/miniconda3/bin for full list.

Python has also packages for parallel computing, for example multiprocessing. In our examples there is two cases using Python multiprocessing: zonal statistics and focal mean.

If you want to use Python2, see also GeoPython module.

Geoconda can not be used simultaneously with geo-env (GeoPython) module

(If you think that some important GIS package for Python is missing from here, you can ask for installation from servicedesk@csc.fi.)

 


Available

Version on CSC's Servers

Taito: 3.6, 3.7 (version number is the same as Python version)


Usage

1. Using packages installed by CSC

To use software environments that are installed to Taito using Conda (either by CSC or yourself),  first load geoconda module:

module load geoconda

This loads latest geoconda module. If you want a specific version you can do:

module load geoconda/VERSION

After that you can use Python with GIS packages as with GeoPython.

For using the Spyder IDE give:

spyder

 

2. Adding more Python packages to packages included in GeoConda

You can add more packages to your own use, the details can be found from Python documention.

The packages are installed to your home directory under .local/lib/python3.6 or .local/lib/python3.7

The packages installed for GeoPython are not available together with GeoConda Python because of different Python versions.

 

3. Installing software for your own use with geoconda

You can use the geoconda module to install software to your personal Conda environments. Please see Conda environments documentation for details and CSC Bioconda documentation for example. The personal Conda environment does not include software included in GeoConda environment. The software is installed to:

/wrk/your_user_name/DONOTREMOVE/geoconda3_env


Discipline

Geosciences

References

Python spatial kirjastot.


Support


Manual