V.krige GSoC 2009: Difference between revisions

From GRASS-Wiki
Jump to navigation Jump to search
(added fulltext reports)
 
(31 intermediate revisions by 6 users not shown)
Line 1: Line 1:
=== v.krige: 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 ==
Line 9: Line 9:
== State of the art ==
== State of the art ==


''' Breaking news: Ordinary kriging with gstat or automap is up and running!''' not all the options are available for gstat, anyway is it a great goal to see that the whole process ends in writing a GRASS raster map with the result. Note also that the module suggests a filename based on the input data map name. One step further towards the One-Click Interface.
'''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, with GRASS bindings and part of R bindings''' - have a look at it from svn:


svn co https://svn.osgeo.org/grass/grass-addons/vector/v.krige v.krige
[[File:Schermata-Kriging Module.png|600px]]


[[File:Schermata-Kriging Module.png|450px|left]]


It is quite complete, allows the user to choose among automap (default choice), gstat (advanced functions) and geoR.  
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.


'''Poll''': Automap and gstat pages are redundant. The underlying algorithms are for both from gstat. I therefore plan to remove automap page and set the "automatic variogram fit" checkbox in gstat's page.
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.


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.
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.
 
Question: another layout can be a Choicebox with the three packages and in respect of the choice the drawing of corresponding widgets. Opinions welcome. [Until now, all preferences went to the Notebook.]
 
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 a Refresh button to force addition to the list. Automatic refresh on popup has been tested as too time and resource consuming.


== Installation ==  
== Installation ==  


Please refer to [[Compile_and_Install#Scripts]].
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:


== Bulletin Board ==
g.extension v.krige


* '''TODOs'''
To install v.krige.py from source, please refer to [[Compile_and_Install#Scripts]]. Source is available on SVN:
** '''Document dependencies''' - continue fill up html template page
** Set '''CLI - in progress!'''
** '''Refactor''' all code. Interface must be separated from model (i.e. wx from R) in order to implement CLI
** Remove automap page and move "automatic variogram fit" checkbox into gstat page, if no objection comes up
** Continue integrating '''gstat functions'''


* '''IDEAS TO DISCUSS'''
svn co https://svn.osgeo.org/grass/grass-addons/vector/v.krige
** Filter the maps after interface creation - wx.CallAfter/threads... have to grep documentation and examples
** Initial '''sanity checks''':
*** Check '''dependencies''' all before interface load. If something is missing, a popup window will give a clear message.
*** Create a '''package''' to delegate dependencies check!
** '''Variogram fit''': in a separated window, with allowed interactive model fit, using Python plot libraries.


* '''BLOCKING ISSUE(S)'''
'''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 big refactorisation about interface-model separation. Will quite completely rewrite the module.


== Documentation ==
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


Kriging theory from Isaaks and Srivastava's "An Introduction to Applied Geostatistics" [0]. Great book.
Be sure that ALL these dependencies are installed and operative. See below for platform-specific details.


== Users feedback and other kriging software ==
=== Notes for Debian GNU/Linux ===


* 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.
Install the dependiencies:


* There are (have been) some GRASS modules that perform kriging, like:
aptitude install R python-rpy2
** 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 [1] is a valuable source of ispiration for interface design.  
'''Attention! python-rpy IS NOT SUITABLE.'''


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


Draft:
install.packages("gstat", dep=T)
* create a wxPython interface for ordinary kriging. Will follow Humane Interface rules [2].
install.packages("spgrass6", dep=T)
* integrate R package ''automap''
install.packages("maptools", dep=T)
* '''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)


== Weekly Reports, from SoC mailing list [3] ==
If you are running GRASS 7.*, install rgrass7 instead of spgrass6:
install.packages("rgrass7", dep=T)


=== Report #1, 29 May ===
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/


- Done
or, for 64bit:


I dedicated this week to documentation and discussion with users and
deb http://debian.cran.r-project.org/cran2deb/debian-amd64 testing/
developers.
- - Documentation: I'm reading "An introduction to Applied Geostatistics"
[2], as I need to understand the theory behind kriging functions
provided by R. On wxPython side, wxPython wiki is the main source of
information, together with the code of GRASS wxPython interface.
- - Community discussion: Feedback on interface design and R has been
collected on various mailing lists, mainly in this thread [3]. Also, a
group of Portuguese ArcGIS users is interested in giving advice and test
the new module.


- Planned for next week
and get the packages via


I plan to define which functions (and consequently which R packages) are
aptitude install r-cran-gstat r-cran-spgrass6 maptools
to be included into the module. I plan to first include package automap
if you are using GRASS 6.*, or
(a wrapper for gstat), then gstat advanced functions, then geoR (an
aptitude install r-cran-gstat r-cran-rgrass7 maptools
"ecological vicariant" of gstat), all alvailable on CRAN [4] . This will
if you are using GRASS 7.*
allow R users to keep using their preferred functions, as kriging
results are implementation-dependent.
Then I'll work on wxPython interface and get a draft as soon as
possible. The interfaces that I use as model are ArcGIS' kriging module
and Isatis. I won't replicate their structure, rather see what are the
provided features and create v.autokrige interface following Humane
Interface guidelines.


- Bottleneck(s)
=== 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.


I'm experiencing some difficulties, mainly with wxPython, as I never
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].
used it before, and also with kriging, for the same reason :) but I'm
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.
not worried nor blocked. Last year GSoC project was a bet and I
succeeded, this year it's even harder but I can rely on some more
experience and, as always, on mentor and community support.


[0] http://precisiongis.blogspot.com/2008/11/vautokrige.html
== Documentation ==
[1] http://grass.osgeo.org/wiki/V.autokrige_GSoC_2009
[2] "An introduction to Applied Geostatistics", E. H. Isaaks and R. M
Srivastava, 1989.
[3] https://stat.ethz.ch/pipermail/r-sig-geo/2009-May/005786.html
[4] http://cran.r-project.org/web/views/Spatial.html


=== Report #2, 5 June ===
Notes on v.krige usage, examples and tips are available in the module's help page, available via Help button if the GUI.


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


- - Ended "An Introduction to Applied Geostatistics", great source of
Developers documentation is available at Trac's wiki http://trac.osgeo.org/grass/wiki/wxGUIDevelopment/vkrige .
information of what the module is supposed to do. Now I can be both
developer and user, not discarding any of the hints of other users.
- - Some progress on the interface: I'm getting used of wxWidgets, even if
the lack of a graphical designer slows down my work. wxDesigner seems
good, but I think it is also good for me to learn the meaning of each
line of code. The interface is quite ready for automap and GRASS
integration.


- Planned for next week
== Users feedback and other kriging software ==


End of interface essential features and integration of automap most
* 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.
automated functions - ideally, the user will pick up the point layer
containing data and press OK.


- Bottleneck(s)
* 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.


The only bottleneck is wxWidgets handling, but not so much as one week ago.
* 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.  


=== Report #2.5, 11 June ===
== Planned Timeline ==


First of all, the interface is almost finished. See a screenshot on the
Draft and definitive:
wiki page [0].
* create a wxPython interface for ordinary kriging. Will follow Humane Interface rules [3].
The layout includes a notebook with a page for each R package (automap,
* integrate R package ''automap''
gstat and geoR), with the available options. Another layout could be a
* '''midterm deadline''': have a working module that performs ordinary kriging.
chiocebox wht the three packages on the top of Kriging section, that
* integrate more R functions from ''gstat'' and ''geoR'', giving the user the choice between gstat and geoR (kriging results vary in respect of implementation)
redraws the section accourding to the user's choice.
Let me know which one do you prefer, feel free also to suggest something
new.
 
The R-GRASS integration is on its way: autofitting the variogram on a
map obtained from a DEM sample [1] works in the proof of concept. rpy2
is extremely helpful and does not require much more code than the
original R code. More to come in the next days.
 
The idea for variogram fitting is to plot the variogram in a new frame
and add some controls like sliders and/or text boxes to fill up with
nugget, sill and range values. This will involve Python graphics, not R,
as the former is more flexible.
 
Comments, suggestions, critics are welcome!
 
=== Report #3, 12 June ===
 
this weekly report will be very short, as yesterday I sent this email
[0] and made little progress.
 
I'm having some problems in using autoKrige() function work, AFAIK
because of projection information handling [1].
 
=== Report #4, 19 June ===
 
this week I made steady progress on the module.
What I've done:
* renamed the module v.krige, as its features will go beyond automatic
kriging.
* addition of choicebox with only numerical columns, as interpolation
will be based on such variables
* refactoring on interface population - more to come
* started documentation page
 
Next week I plan to create the splashscreen during dependencies check
and data load, and examine how to integrate gstat functions.
 
=== Report #5, 26 June (at [http://wiki.osgeo.org/wiki/OSGeo_Hacking_Event_2009 OSGeo Bolsena Hacking Event]) ===
 
just few minutes ago I succeded in completing the kriging procedure with
gstat functions. It runs with a proof-of-concept dataset based on
spearfish data, see this tutorial [0].
Martin helped me a lot in getting the standard wxGUI comboboxes to run
properly with filters.


Next week I plan to adapt the interface to each R package's available
options and consider how to solve lag issues in populating interface.


The blocking issue about autoKrige() and projections is no more valid as
I create the grid myself based on GRASS region.


== References ==
== References ==
* [0] Isaaks and Srivastava, 1989: "An Introduction to Applied Geostatistics", (ISBN 0-19-505013-4)
* [0] Fowler, Beck, Brant, Opdyke, Roberts, 1999. "Refactoring. Improving the design of existing code" (ISBN-10: 0201485672; ISBN-13: 978-0201485677)
* [1] http://www.geovariances.com/software/video-data-investigation-with-isatis-exploratory-data-analysis-ar0353.html
* [1] Isaaks and Srivastava, 1989: "An Introduction to Applied Geostatistics"  (ISBN 0-19-505013-4)
* [2] Jef Raskin, 2000: "The Humane Interface: New Directions for Designing Interactive Systems" (ISBN 0-201-37937-6)  
* [2] http://www.geovariances.com/software/video-data-investigation-with-isatis-exploratory-data-analysis-ar0353.html
* [3] http://lists.osgeo.org/pipermail/soc/
* [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


[[Category:GSoC]]
{{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

Retrieved from "https://grasswiki.osgeo.org/w/index.php?title=V.krige_GSoC_2009&oldid=22040"