V.krige GSoC 2009: Difference between revisions

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=== v.autokrige: Python porting and wxPython GUI addition  ===
=== v.krige: Python porting and [[wxGUI]] addition  ===
Anne Ghisla's [http://socghop.appspot.com/student_project/show/google/gsoc2009/osgeo/t124023165994 Google Summer of Code 2009 project], mentored by Martin Landa and Michael Barton
Anne Ghisla's [http://socghop.appspot.com/student_project/show/google/gsoc2009/osgeo/t124023165994 Google Summer of Code 2009 project], mentored by [[User:Landa|Martin Landa]] and Michael Barton


== Aim of the project ==
== Aim of the project ==


As GRASS presently lacks [[kriging]] capability, it is performed via an add-on, v.autokrige, that delegates analysis to R (package automap). This module is written in bash and has the classical autogenerated GUI. The project aims to rewrite the module in Python, creating a new GUI in wxPython that allows the user to refine parameters.
As GRASS presently lacks [[kriging]] capability, it is performed via an add-on, v.autokrige, that delegates analysis to R (package automap). This module is written in ksh and has the classical autogenerated GUI. The project aims to rewrite the module in Python, creating a new GUI in wxPython that allows the user to refine parameters.
I therefore plan to examinate present v.autokrige code and port it into Python, possibly improving it at the same time, and add a wxPython GUI. All time left will be dedicated to addition of further functionality, in respect of the most needed.
I therefore plan to examinate present v.autokrige code and port it into Python, possibly improving it at the same time, and add a wxPython GUI. All time left will be dedicated to addition of further functionality, in respect of the most needed.


== State of the art ==
== State of the art ==


[[File:Schermata-Kriging Module.png]]
'''V.krige is back to functionality in GRASS 7 trunk, from [http://trac.osgeo.org/grass/changeset/57146 r57146] - made during [[GRASS_Community_Sprint_Prague_2013]]'''
Soon more improvements and fixes will be available, and also be backported to GRASS 6.5. Until then, feel free to comment on [http://trac.osgeo.org/grass/query?status=assigned&status=new&status=reopened&description=~krig&order=priority the tickets on Trac] and on grass-dev mailing list.


'''Writing the wxPython interface''' - have a look at it from svn:
svn co https://svn.osgeo.org/grass/grass-addons/vector/v.autokrige2 v.autokrige2


It is quite complete, allows the user to choose among automap (default choice), gstat (advanced functions) and geoR.
[[File:Schermata-Kriging Module.png|600px]]
These three packages are not all required; if the user already uses R for kriging, the interface will load the package(s) present in R library. If none of the packages is available a popup message will ask for installation of at least one of the packages and abort. That is, crash gracefully and with clear explanation. I know what it means to crawl among missing dependencies and I don't want my users to be puzzled by inexplicable error messages.


Question: another layout can be a Choicebox with the three packages and in respect of the choice the drawing of corresponding widgets. Opinions welcome.


Anne vs. Sizers: 1 - 0! Now the window has the minimal size around the widgets. It costs two lines of code but AFAIK seems not possible to use only one.
Dependency check is performed on grass-python module, R, rpy2 and R packages gstat and rgrass7. If something is missing, the module won't start. Some graceful popup window will be set up in the near future. At the moment it aborts with a message in the shell.


On GRASS side, I succeeded in populating a wxChoicebox with vector layers of the mapset in use, furthermore discarding maps with no points. This second filter requires some time if there are lot of maps, so I'm considering to first set up the interface and in the meanwhile the user inspects the options perform this operation. It is not dead long (few seconds on my 2GB-RAM and Intel Core2Duo laptop, using spearfish dataset), but it creates an evident lag between the call of the module and the creation of interface.
Kriging relies on R package gstat, the most widespread. geoR tab is now hidden as it doesn't provide any functionality, but if anyone is interested in using it instead of gstat I'll put this todo higher in the list.


GRASS and R integration are really smooth with Python. In next days I'll build the minimum-option kriging procedure via automap, hopefully for next report.
The list of point layers is provided by VectorSelect class (gselect module) to provide uniformity of layout with wxGUI. The filtering is done once at the start of the module, then if the user adds a suitable point layer she/he will press the Refresh button to force addition to the list. Automatic refresh on popup has been tested as too time and resource consuming.
'''Variogram autofit is up and running!!''' The column with values in bound in the code and the data are not in spearfish, but it works!


Refactoring is approaching... on less than 150 lines of code. The creation of the wxNotebook pages for R packages is clearly factorizable. Marked on todo list.
== Installation ==
 
For GRASS 6.5 <r40048, it is easy to install it via [http://grass.osgeo.org/grass65/manuals/html65_user/g.extension.html g.extension] (for GRASS 6.4 it is an AddOn, from 6.5+/7 onwards included). Simply type in a GRASS shell:
 
g.extension v.krige
 
To install v.krige.py from source, please refer to [[Compile_and_Install#Scripts]]. Source is available on SVN:
 
svn co https://svn.osgeo.org/grass/grass-addons/vector/v.krige
 
'''The module requires GRASS >= 6.4 RC5''' - it uses the new version of grass-python library. At the moment, no backward compatibility with previous versions is provided.
 
The module has dependencies:
* R 2.x - no exhaustive tests on compatible versions. An up-to-date R package will do the job in 99% cases.
* R packages spgrass6 (for GRASS 6.*) or rgrass7 (for GRASS 7.*), gstat and maptools
* Python module rpy2
 
Be sure that ALL these dependencies are installed and operative. See below for platform-specific details.
 
=== Notes for Debian GNU/Linux ===
 
Install the dependiencies:
 
aptitude install R python-rpy2
 
'''Attention! python-rpy IS NOT SUITABLE.'''
 
To install R packages, use either R's function (as root):
 
install.packages("gstat", dep=T)
install.packages("spgrass6", dep=T)
install.packages("maptools", dep=T)
 
If you are running GRASS 7.*, install rgrass7 instead of spgrass6:
install.packages("rgrass7", dep=T)
 
Alternatively, you can install the packages using the brand new Debian packages [6]. To do so, add to repositories' list for 32bit:
deb http://debian.cran.r-project.org/cran2deb/debian-i386 testing/
 
or, for 64bit:
 
deb http://debian.cran.r-project.org/cran2deb/debian-amd64 testing/
 
and get the packages via
 
aptitude install r-cran-gstat r-cran-spgrass6 maptools
if you are using GRASS 6.*, or
aptitude install r-cran-gstat r-cran-rgrass7 maptools
if you are using GRASS 7.*
 
=== Notes for Windows ===
At this very moment, no backward compatibility with OSGeo4W's packaged GRASS 6.4svn2 is provided, nor with WinGRASS. Testing is planned, as latest  WinGRASS includes the most recent python library.
 
If you really need to run v.krige right now on Windows, I suggest to compile GRASS following [http://trac.osgeo.org/grass/wiki/CompileOnWindows this guide].
You could also use Linux in a virtual machine. Or install Linux in a separate partition of the HD. This is not as painful as it appears, there are lots of guides over the Internet to help you.


== Documentation ==
== Documentation ==


Kriging theory from Isaaks and Srivastava's "An Introduction to Applied Geostatistics" [0]. Great book.
Notes on v.krige usage, examples and tips are available in the module's help page, available via Help button if the GUI.
 
Kriging theory is available in Isaaks and Srivastava's "An Introduction to Applied Geostatistics" [1]. Another great book.
 
Developers documentation is available at Trac's wiki http://trac.osgeo.org/grass/wiki/wxGUIDevelopment/vkrige .


== Users feedback and other kriging software ==
== Users feedback and other kriging software ==
Line 41: Line 96:
** scripts including R and spgrass6: are the concrete basis upon which build the module.
** scripts including R and spgrass6: are the concrete basis upon which build the module.


* Obtained ArcGIS availability for comparison of interface and functionality, because it is AFAIK the widespread tool used for kriging. Also Isats [1] is a valuable source of ispiration for interface design.  
* Obtained ArcGIS availability for comparison of interface and functionality, because it is AFAIK the widespread tool used for kriging. Also Isats [2] is a valuable source of ispiration for interface design.  


== Planned Timeline ==
== Planned Timeline ==


Draft:
Draft and definitive:
* create a wxPython interface for ordinary kriging. Will follow Humane Interface rules [2].
* create a wxPython interface for ordinary kriging. Will follow Humane Interface rules [3].
* integrate R package ''automap''
* integrate R package ''automap''
* '''midterm deadline''': have a working module that performs ordinary kriging.
* '''midterm deadline''': have a working module that performs ordinary kriging.
* integrate more R functions from ''gstat'' and ''geoR'', giving the user the choice between gstat and geoR (kriging results vary in respect of implementation)
* integrate more R functions from ''gstat'' and ''geoR'', giving the user the choice between gstat and geoR (kriging results vary in respect of implementation)


Weekly reports are available on SoC mailing list [3]


=== References ===
* [0] Isaaks and Srivastava, 1989: "An Introduction to Applied Geostatistics",  (ISBN 0-19-505013-4)
* [1] http://www.geovariances.com/software/video-data-investigation-with-isatis-exploratory-data-analysis-ar0353.html
* [2] Jef Raskin, 2000: "The Humane Interface: New Directions for Designing Interactive Systems" (ISBN 0-201-37937-6)
* [3] http://lists.osgeo.org/pipermail/soc/


[[Category:GSoC]]
== References ==
* [0] Fowler, Beck, Brant, Opdyke, Roberts, 1999. "Refactoring. Improving the design of existing code" (ISBN-10: 0201485672; ISBN-13: 978-0201485677)
* [1] Isaaks and Srivastava, 1989: "An Introduction to Applied Geostatistics"  (ISBN 0-19-505013-4)
* [2] http://www.geovariances.com/software/video-data-investigation-with-isatis-exploratory-data-analysis-ar0353.html
* [3] Jef Raskin, 2000: "The Humane Interface: New Directions for Designing Interactive Systems" (ISBN 0-201-37937-6)
* [4] OSGeo SoC mailing list http://lists.osgeo.org/pipermail/soc/
* [5] CRAN: Spatial view http://cran.r-project.org/web/views/Spatial.html
* [6] cran2deb repository https://stat.ethz.ch/pipermail/r-sig-debian/2009-July/000805.html
 
{{GSoC}}
[[Category:R]]

Latest revision as of 21:21, 30 September 2015

v.krige: Python porting and wxGUI addition

Anne Ghisla's Google Summer of Code 2009 project, mentored by Martin Landa and Michael Barton

Aim of the project

As GRASS presently lacks kriging capability, it is performed via an add-on, v.autokrige, that delegates analysis to R (package automap). This module is written in ksh and has the classical autogenerated GUI. The project aims to rewrite the module in Python, creating a new GUI in wxPython that allows the user to refine parameters. I therefore plan to examinate present v.autokrige code and port it into Python, possibly improving it at the same time, and add a wxPython GUI. All time left will be dedicated to addition of further functionality, in respect of the most needed.

State of the art

V.krige is back to functionality in GRASS 7 trunk, from r57146 - made during GRASS_Community_Sprint_Prague_2013 Soon more improvements and fixes will be available, and also be backported to GRASS 6.5. Until then, feel free to comment on the tickets on Trac and on grass-dev mailing list.



Dependency check is performed on grass-python module, R, rpy2 and R packages gstat and rgrass7. If something is missing, the module won't start. Some graceful popup window will be set up in the near future. At the moment it aborts with a message in the shell.

Kriging relies on R package gstat, the most widespread. geoR tab is now hidden as it doesn't provide any functionality, but if anyone is interested in using it instead of gstat I'll put this todo higher in the list.

The list of point layers is provided by VectorSelect class (gselect module) to provide uniformity of layout with wxGUI. The filtering is done once at the start of the module, then if the user adds a suitable point layer she/he will press the Refresh button to force addition to the list. Automatic refresh on popup has been tested as too time and resource consuming.

Installation

For GRASS 6.5 <r40048, it is easy to install it via g.extension (for GRASS 6.4 it is an AddOn, from 6.5+/7 onwards included). Simply type in a GRASS shell: 

g.extension v.krige

To install v.krige.py from source, please refer to Compile_and_Install#Scripts. Source is available on SVN: 

svn co https://svn.osgeo.org/grass/grass-addons/vector/v.krige

The module requires GRASS >= 6.4 RC5 - it uses the new version of grass-python library. At the moment, no backward compatibility with previous versions is provided.

The module has dependencies:

  • R 2.x - no exhaustive tests on compatible versions. An up-to-date R package will do the job in 99% cases.
  • R packages spgrass6 (for GRASS 6.*) or rgrass7 (for GRASS 7.*), gstat and maptools
  • Python module rpy2

Be sure that ALL these dependencies are installed and operative. See below for platform-specific details.

Notes for Debian GNU/Linux

Install the dependiencies: 

aptitude install R python-rpy2

Attention! python-rpy IS NOT SUITABLE.

To install R packages, use either R's function (as root): 

install.packages("gstat", dep=T)
install.packages("spgrass6", dep=T)
install.packages("maptools", dep=T)

If you are running GRASS 7.*, install rgrass7 instead of spgrass6: 

install.packages("rgrass7", dep=T)

Alternatively, you can install the packages using the brand new Debian packages [6]. To do so, add to repositories' list for 32bit: 

deb http://debian.cran.r-project.org/cran2deb/debian-i386 testing/

or, for 64bit: 

deb http://debian.cran.r-project.org/cran2deb/debian-amd64 testing/

and get the packages via 

aptitude install r-cran-gstat r-cran-spgrass6 maptools

if you are using GRASS 6.*, or 

aptitude install r-cran-gstat r-cran-rgrass7 maptools

if you are using GRASS 7.*

Notes for Windows

At this very moment, no backward compatibility with OSGeo4W's packaged GRASS 6.4svn2 is provided, nor with WinGRASS. Testing is planned, as latest WinGRASS includes the most recent python library.

If you really need to run v.krige right now on Windows, I suggest to compile GRASS following this guide. You could also use Linux in a virtual machine. Or install Linux in a separate partition of the HD. This is not as painful as it appears, there are lots of guides over the Internet to help you.

Documentation

Notes on v.krige usage, examples and tips are available in the module's help page, available via Help button if the GUI.

Kriging theory is available in Isaaks and Srivastava's "An Introduction to Applied Geostatistics" [1]. Another great book.

Developers documentation is available at Trac's wiki http://trac.osgeo.org/grass/wiki/wxGUIDevelopment/vkrige .

Users feedback and other kriging software

  • Call for users has been done on gfoss.it, grass-it and grass-users, r-sig-geo and r-sig-ecology mailing lists. Thanks to Giovanni Manghi and João Tiago from GFOSS.pt and Giovanni Allegri for user advices, and to Edzer Pebesma, Paul Hiemstra, Ebrahim Jahanshiri, Dylan Beaudette for support on R side.
  • There are (have been) some GRASS modules that perform kriging, like:
    • v.surf.krige, v.variogram: no longer developed by authors, difficult to port.
    • s.surf.krig: deprecated since GRASS 6 series.
    • scripts including R and spgrass6: are the concrete basis upon which build the module.
  • Obtained ArcGIS availability for comparison of interface and functionality, because it is AFAIK the widespread tool used for kriging. Also Isats [2] is a valuable source of ispiration for interface design.

Planned Timeline

Draft and definitive:

  • create a wxPython interface for ordinary kriging. Will follow Humane Interface rules [3].
  • integrate R package automap
  • midterm deadline: have a working module that performs ordinary kriging.
  • integrate more R functions from gstat and geoR, giving the user the choice between gstat and geoR (kriging results vary in respect of implementation)


References

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