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QGIS Planet

Gaining more WMS speed through enabling the QGIS cache directory

Interestingly the WMS caching is not enabled by default in QGIS. To better enjoy WMS/WMS-C/WMTS connections – if you have some disk space to dedicate – it is a good idea to enable the cache in these few steps:

Go to the menu entry Settings >> Options:

Enabling the QGIS WMS cache - step 1

Enabling the QGIS WMS cache – step 1

Go to tab “Network“. Therein, in “Cache settings“, select the “Directory” and choose a folder for the cache files. Be sure that there is free space for lots of megabytes can be stored there over time. And this directory should ideally be located on a fast disk (if you have several).

Here I choose the existing “tmp/” folder in my HOME directory and create inside a new folder “qgis_wms_cache”:

Enabling the QGIS WMS cache - step 2

Enabling the QGIS WMS cache – step 2: create new “qgis_wms_cache” cache folder

Eventually we change the “Default expiration period for WMS-C/WMTS tiles (hours)” to more than 24 hours (as it would be rather useless…). Here I change to 24*30 = 720 hours. And the cache size we increase as well, here to 250MB (written as 250000 since it is to be given in kilobytes):

Enabling the QGIS WMS cache - step 3

Enabling the QGIS WMS cache – step 3: increase expiration period for tiles and cache size

Now we press “OK” and close the dialog. Time to try out a WMS service, zoom back and forth… and:
Enjoy!

The post Gaining more WMS speed through enabling the QGIS cache directory appeared first on GFOSS Blog | GRASS GIS Courses.

New GRASS GIS 7.2.x stable release branch created

Towards the new stable release series

As of 24 May 2016, a new stable release branch was created for the upcoming GRASS GIS 7.2 release. This new branch includes all the many improvements which have been implemented in the former development version 7.1.svn.

What is a branch? In simple words, it is a kind of directory in the software development server (SVN in our case) in which no more development but only bugfixing happens. From a release branch, new stable releases are created and published.

The actual branches in the GRASS GIS project are:

  • very old stable: releasebranch_6_4 (used for bugfixing and to publish stable GRASS GIS 6.4.x releases) – very low release frequency (started in revision r34936)
  • old stable releasebranch_7_0 (used for bugfixing and to publish stable GRASS GIS 7.0.x releases) – perhaps one last release upcoming (branch started in revision r59487 but development already started in Apr 2008 in r31142)
  • new stable releasebranch_7_2 (used for bugfixing and to publish stable GRASS GIS 7.2.x releases) – upcoming series of stable releases (branch started in revision r68500)
  • trunk (used for development, with pseudo-name 7.3.svn) – under heavy development

Note to SVN users

The trunk branch with pseudo-name 7.1.svn has become 7.3.svn due to the creation of the new 7.2.svn release branch. You can simply continue to update from SVN, the version will be automatically updated.

If you used to work with the 7.0.svn release branch, consider to download the new 7.2.svn release branch, either from the weekly source code snapshot (here) or from the SVN server directly (here).

About GRASS GIS

The Geographic Resources Analysis Support System (http://grass.osgeo.org/), commonly referred to as GRASS GIS, is an Open Source Geographic Information System providing powerful raster, vector and geospatial processing capabilities in a single integrated software suite. GRASS GIS includes tools for spatial modeling, visualization of raster and vector data, management and analysis of geospatial data, and the processing of satellite and aerial imagery. It also provides the capability to produce sophisticated presentation graphics and hardcopy maps. GRASS GIS has been translated into about twenty languages and supports a huge array of data formats. It can be used either as a stand-alone application or as backend for other software packages such as QGIS and R geostatistics. It is distributed freely under the terms of the GNU General Public License (GPL). GRASS GIS is a founding member of the Open Source Geospatial Foundation (OSGeo).

The GRASS Development Team, May 2016

The post New GRASS GIS 7.2.x stable release branch created appeared first on GFOSS Blog | GRASS GIS Courses.

Markus Neteler joins the management of mundialis in Bonn

Press release

From March 2016 onwards, Dr. Markus Neteler, a prominent head of the Open Source GIS scene, will join the management board of mundialis GmbH & Co. KG in Bonn, Germany. Founded in 2015, mundialis combines remote sensing and satellite data analysis in the field of Big Data with Open Source WebGIS solutions.

Since 2008, Dr. Neteler was the head of the GIS and remote sensing unit at the Edmund Mach Foundation in Trento (Italy) and worked in this capacity on numerous projects related to biodiversity, environmental and agricultural research. He is also a founding member of the Open Source Geospatial Foundation (OSGeo), a nonprofit organization with headquarters in Delaware (USA), that promotes the development and use of free and open source geographic information systems (GIS). Since 1998 he coordinated the development of the well known GRASS GIS software project, a powerful Open Source GIS that supports processing of time series of several thousand raster, 3D raster or vector maps in a short time. Mongolia as seen by Sentinel-2A

Markus will keep his role as “Mr. GRASS” at mundialis, especially because the company also sees itself as a research and development enterprise that puts its focus on the open source interfaces between geoinformation and remote sensing. Although a new company, mundialis offers more than 50 years of experience in GIS, due to the background of its management. Besides Neteler, there are Till Adams and Hinrich Paulsen, both at the same time the founders and CEOs of terrestris in Bonn, a company that develops Open Source GIS solutions since 2002. These many years of experience in the construction of WebGIS and Geoportal architectures using free software as well as in the application of common OGC standards – are now combined with mundialis’ expertise in the processing of big data with spatial reference and remote sensing data.

Contact: http://www.mundialis.de/

The post Markus Neteler joins the management of mundialis in Bonn appeared first on GFOSS Blog | GRASS GIS Courses.

Markus Neteler

We are pleased to announce the first release candidate of GRASS GIS 7.0.3

What’s new in a nutshell

The new GRASS GIS 7.0.3RC1 release provides 160 stability fixes and manual improvements. Of particular interest is the new winGRASS 64 bit support.

About GRASS GIS 7: Its graphical user interface supports the user to make complex GIS operations as simple as possible. The updated Python interface to the C library permits users to create new GRASS GIS-Python modules in a simple way while yet obtaining powerful and fast modules. Furthermore, the libraries were significantly improved for speed and efficiency, along with support for huge files. A lot of effort has been invested to standardize parameter and flag names. Finally, GRASS GIS 7 comes with a series of new modules to analyse raster and vector data, along with a full temporal framework. For a detailed overview, see the list of new features. As a stable release series, 7.0.x enjoys long-term support.

Binaries/Installer download:

Source code download:

More details:

See also our detailed announcement:

  http://trac.osgeo.org/grass/wiki/Grass7/NewFeatures (overview of new 7.0 stable release series)

First time users may explore the first steps tutorial after installation.

About GRASS GIS

The Geographic Resources Analysis Support System (http://grass.osgeo.org/), commonly referred to as GRASS GIS, is an Open Source Geographic Information System providing powerful raster, vector and geospatial processing capabilities in a single integrated software suite. GRASS GIS includes tools for spatial modeling, visualization of raster and vector data, management and analysis of geospatial data, and the processing of satellite and aerial imagery. It also provides the capability to produce sophisticated presentation graphics and hardcopy maps. GRASS GIS has been translated into about twenty languages and supports a huge array of data formats. It can be used either as a stand-alone application or as backend for other software packages such as QGIS and R geostatistics. It is distributed freely under the terms of the GNU General Public License (GPL). GRASS GIS is a founding member of the Open Source Geospatial Foundation (OSGeo).

The GRASS Development Team, December 2015

The post appeared first on GFOSS Blog | GRASS GIS Courses.

GRASS GIS 7.0.2 released

What’s new in a nutshell

The new GRASS GIS 7.0.2 release provides 190 stability fixes and manual improvements.

About GRASS GIS 7: Its graphical user interface supports the user to make complex GIS operations as simple as possible. The updated Python interface to the C library permits users to create new GRASS GIS-Python modules in a simple way while yet obtaining powerful and fast modules. Furthermore, the libraries were significantly improved for speed and efficiency, along with support for huge files. A lot of effort has been invested to standardize parameter and flag names. Finally, GRASS GIS 7 comes with a series of new modules to analyse raster and vector data, along with a full temporal framework. For a detailed overview, see the list of new features. As a stable release series, 7.0.x enjoys long-term support.

Source code download:

Binaries download:

More details:

See also our detailed announcement:

  http://trac.osgeo.org/grass/wiki/Grass7/NewFeatures (overview of new 7.0 stable release series)First time users may explore the first steps tutorial after installation.

About GRASS GIS

The Geographic Resources Analysis Support System (http://grass.osgeo.org/), commonly referred to as GRASS GIS, is an Open Source Geographic Information System providing powerful raster, vector and geospatial processing capabilities in a single integrated software suite. GRASS GIS includes tools for spatial modeling, visualization of raster and vector data, management and analysis of geospatial data, and the processing of satellite and aerial imagery. It also provides the capability to produce sophisticated presentation graphics and hardcopy maps. GRASS GIS has been translated into about twenty languages and supports a huge array of data formats. It can be used either as a stand-alone application or as backend for other software packages such as QGIS and R geostatistics. It is distributed freely under the terms of the GNU General Public License (GPL). GRASS GIS is a founding member of the Open Source Geospatial Foundation (OSGeo).

The GRASS Development Team, November 2015

The post GRASS GIS 7.0.2 released appeared first on GFOSS Blog | GRASS GIS Courses.

GRASS GIS 7.0.1 released – 32 years of GRASS GIS

What’s new in a nutshellgrass7_logo_500px

This release addresses some minor issues found in the first GRASS GIS 7.0.0 release published earlier this year. The new release provides a series of stability fixes in the core system and the graphical user interface, PyGRASS improvements, some manual enhancements, and a few language translations.

This release is the 32nd birthday release of GRASS GIS.

New in GRASS GIS 7: Its new graphical user interface supports the user in making complex GIS operations as simple as possible. A new Python interface to the C library permits users to create new GRASS GIS-Python modules in a simple way while yet obtaining powerful and fast modules. Furthermore, the libraries were significantly improved for speed and efficiency, along with support for huge files. A lot of effort has been invested to standardize parameter and flag names. Finally, GRASS GIS 7 comes with a series of new modules to analyse raster and vector data, along with a full temporal framework. For a detailed overview, see the list of new features. As a stable release 7.0 enjoys long-term support.

Source code download:

Binaries download:

More details:

See also our detailed announcement:

  http://trac.osgeo.org/grass/wiki/Grass7/NewFeatures (overview of new stable release series)First time users may explore the first steps tutorial after installation.

About GRASS GIS

The Geographic Resources Analysis Support System (http://grass.osgeo.org/), commonly referred to as GRASS GIS, is an Open Source Geographic Information System providing powerful raster, vector and geospatial processing capabilities in a single integrated software suite. GRASS GIS includes tools for spatial modeling, visualization of raster and vector data, management and analysis of geospatial data, and the processing of satellite and aerial imagery. It also provides the capability to produce sophisticated presentation graphics and hardcopy maps. GRASS GIS has been translated into about twenty languages and supports a huge array of data formats. It can be used either as a stand-alone application or as backend for other software packages such as QGIS and R geostatistics. It is distributed freely under the terms of the GNU General Public License (GPL). GRASS GIS is a founding member of the Open Source Geospatial Foundation (OSGeo).

The GRASS Development Team, July 2015

The post GRASS GIS 7.0.1 released – 32 years of GRASS GIS appeared first on GFOSS Blog | GRASS GIS Courses.

QGIS 2.10 RPMs for Fedora 21, Centos 7, Scientific Linux 7

qgis-icon_smallThanks to the work of Volker Fröhlich and other Fedora/EPEL packagers I was able to create RPM packages of QGIS 2.10 Pisa for Fedora 21, Centos 7, and Scientific Linux 7 using the great COPR platform.

Repo: https://copr.fedoraproject.org/coprs/neteler/QGIS-2.10-Pisa/

The following packages can now be installed and tested on epel-7-x86_64 (Centos 7, Scientific Linux 7, etc.), and Fedora-21-x86_64:

  • qgis 2.10.1
  • qgis-debuginfo 2.10.1
  • qgis-devel 2.10.1
  • qgis-grass 2.10.1
  • qgis-python 2.10.1
  • qgis-server 2.10.1

Installation instructions (run as “root” user or use “sudo”):

su

# EPEL7:
yum install epel-release
yum update
wget -O /etc/yum.repos.d/qgis-2-10-epel-7.repo https://copr.fedoraproject.org/coprs/neteler/QGIS-2.10-Pisa/repo/epel-7/neteler-QGIS-2.10-Pisa-epel-7.repo
yum update
yum install qgis qgis-grass qgis-python

# Fedora 21:
dnf copr enable neteler/QGIS-2.10-Pisa
dnf update
dnf install qgis qgis-grass qgis-python

Enjoy!

The post QGIS 2.10 RPMs for Fedora 21, Centos 7, Scientific Linux 7 appeared first on GFOSS Blog | GRASS GIS Courses.

Sol Katz Award – Call for Nominations

The Open Source Geospatial Foundation would like to open nominations for the 2015 Sol Katz Award for Geospatial Free and Open Source Software.

The Sol Katz Award for Geospatial Free and Open Source Software (GFOSS) will be given to individuals who have demonstrated leadership in the GFOSS community. Recipients of the award will have contributed significantly through their activities to advance open source ideals in the geospatial realm.

Sol Katz was an early pioneer of GFOSS and left behind a large body of work in the form of applications, format specifications, and utilities while at the U.S. Bureau of Land Management. This early GFOSS archive provided both source code and applications freely available to the community. Sol was also a frequent contributor to many geospatial list servers, providing much guidance to the geospatial community at large.

Sol unfortunately passed away in 1999 from Non-Hodgkin’s Lymphoma, but his legacy lives on in the open source world. Those interested in making a donation to the American Cancer Society, as per Sol’s family’s request, can do so at https://donate.cancer.org/index.

Nominations for the Sol Katz Award should be sent to SolKatzAward@osgeo.org with a description of the reasons for this nomination. Nominations will be accepted until 23:59 UTC on August 21st (http://www.timeanddate.com/worldclock/fixedtime.html?month=8&day=21&year=2015&hour=23&min=59&sec=59).
A recipient will be decided from the nomination list by the OSGeo selection committee.

The winner of the Sol Katz Award for Geospatial Free and Open Source Software will be announced at the FOSS4G-Seoul event in September. The hope is that the award will both acknowledge the work of community members, and pay tribute to one of its founders, for years to come.

It should be noted that past awardees and selection committee members are not eligible.

More info at the Sol Katz Award wiki page
http://wiki.osgeo.org/wiki/Sol_Katz_Award

Past Awardees:

2014: Gary Sherman
2013: Arnulf Christl
2012: Venkatesh Raghavan
2011: Martin Davis
2010: Helena Mitasova
2009: Daniel Morissette
2008: Paul Ramsey
2007: Steve Lime
2006: Markus Neteler
2005: Frank Warmerdam

Selection Committee 2015:

Jeff McKenna (chair)
Frank Warmerdam
Markus Neteler
Steve Lime
Paul Ramsey
Sophia Parafina
Daniel Morissette
Helena Mitasova
Martin Davis
Venkatesh Raghavan
Arnulf Christl
Gary Sherman

The post Sol Katz Award – Call for Nominations appeared first on GFOSS Blog | GRASS GIS Courses.

The man with the golden gun ( and some examples of installing and using QGIS on Windows)

I’m not Scaramanga (maybe a little bit of Nick Nack) but anyway, this article could be be a golden bullet for helping you to eliminate a lot of obstacles if you are using QGIS in some kind of class-room setup, networked environment and/or are struggling with the “new versions 3 times a year” policy of QGIS.

man-with-the-golden-gun-008

My interest for a hassle free and fast installation of QGIS stems from an experience last year: Some colleagues and I was giving a QGIS workshop for attendants from all over the world. We were told that QGIS was installed on all the computers in the “out-of-town” computer lab and indeed, the computers we checked had a working installation of QGIS. Next day, 15 minutes before the workshop should start, we discovered that the QGIS installations was either non-existent or badly mangled on a large portion of the rest of the computers. And no person with “local admin” rights within sight. It would be an understatement to say that the first hour of the workshop was an interesting time for us. Well, all’s well that ends well, and in the end the workshop was a success (Lucky us!)

A couple of months later I stumbled on this article “A QGIS class room setup on Windows ” – thanks to Richard Duivenvoorde – and tried the setup by copying the qgis program directory from the initial install to another “clean” computer. Alas, QGIS did work on some – but not on all of the computers, I tried it on. The QGIS installation had some dependencies to dll’s in the windows/system32 directory. If they already were present, the “copy” installation would work but otherwise it would fail. I discovered a somewhat complicated solution to the problem and publicized it in the article “How to make a ‘QGIS on a stick’ implementation

Then, some weeks ago at the “QGIS 2015 conference at Nødebo“, I had a chat with QGIS core developer Jürgen E. Fischer about my installation problems and viola! Two days after the chat, the OSGEO4W network installation contained the missing dll’s, Thanks Jürgen.

So now we have two bits of information:

  • By using the “–configpath” qualifier we can redirect where QGIS is looking for plugins, user selected values for options, values and files normally saved in the .qgis2 directory or in the registry.
  • The OSGeo4W network installation creates QGIS without any dependencies to external dll’s outside the installation directory. You could make an installation by simply copy an existing QGIS program directory to another computer.

This gives us some interesting possibilities:

  • Use case I : “QGIS on a stick”
    You can make a QGIS installation located on a memory stick and completely self contained; simply plug in the stick into a Windows computer and start QGIS by double clicking on the QGIS startup file.
  • Use case II: “Simple ‘xcopy’ installation of QGIS”
    Make an installation procedure for QGIS that consists of a simple copy of the QGIS program directory to a new computer. Like the answer to: “How the heck am I going to install QGIS on 24 computers in half an hour ?”
  • Use case III: “Network install of QGIS with floating profiles”
    Install QGIS on a network file share and put the QGIS setup information into the “Floating profile”. A large part of a user profile including will be cached on a central server in the windows domain. If the user logs on to another computer than the usual, his/her profile will automatically be copied to the new computer, giving the user his “normal” desktop and setups.
  • Use case IV: “QGIS on Citrix”
    Normally it ain’t my cup of tea to install any kind of program on a Citrix server where the program has a “canvas” area with fast changing images/pixels. For example: A GIS program like QGIS showing a map with an orthofoto background with millions of pixels – all with a slightly different hues of greens or browns.
    However, many IT departments swears by Citrix, so….
  • Use Case V: “Smart installation and update of a large amount of QGIS installations”
    If you have to install QGIS on dozens or hundreds of computers and keep the installation up-to-date, this is the use-case for you.

Step 1: Creating the common template..

First you have to create a common template for your future installation(s) whatever use case you implement afterwards. I use the 32-bit edition of the network installation as a basis for this although it’s perfectly possible to use the 64 bit version.

  1. Browse to http://qgis.org/en/site/forusers/download.html and click on OSGeo4W Network installer (32 bit) . This will download the installer.
  2. Start the installer and choose “Express Desktop Install”.
  3. Check “QGIS” and uncheck everything else.
  4. Check “I agree yadda yadda…” to every license message.This will install a default QGIS installation in directory C:\OSGeo4W and create a QGIS user directory in C:\Users\<my username>\.qgis2, i.e. the directory .qgis2 in your home directory. These 2 directories is the basis for the template. You can check the installation by starting QGIS from the “OSGeo4W” program group in “Start” –> “All Programs”. It should work without problems.
  5. Copy the C:\Users\<my username>\.qgis2 directory with contents to C:\OSGeo4W, so you’ll have a C:\OSGeo4W\.qgis2 directory.
  6. Copy the startup file for QGIS: C:\OSGeo4W\bin\QGIS.bat to C:\OSGeo4W\bin\QGIS.ref. This is insurance ! If you utterly mangle QGIS.bat in the next steps you have this file as a backup. Otherwise you are not going to use it for anything.
  7. Edit the file: C:\OSGeo4W\bin\QGIS.bat with a simple text editor like notepad.
    Insert 2 lines between line 2 and 3 in the bat file:

    call “%~dp0\o4w_env.bat”
    call “%OSGEO4W_ROOT%”\apps\grass\grass-6.4.4\etc\env.bat

    so it looks like this:

    call “%~dp0\o4w_env.bat”
    set QGIS_OAS=”%OSGEO4W_ROOT%”\.qgis2
    if exist “%OSGEO4W_ROOT%”\bin\QGIS_OAS.bat call “%OSGEO4W_ROOT%”\bin\QGIS_OAS.bat
    call “%OSGEO4W_ROOT%”\apps\grass\grass-6.4.4\etc\env.bat

    and replace the last line in the bat file:

    start “QGIS” /B “%OSGEO4W_ROOT%”\bin\qgis-bin.exe %*

    with this line:

    start “QGIS” /B “%OSGEO4W_ROOT%”\bin\qgis-bin.exe –configpath %QGIS_OAS% %*

    and save the result.

    What the edits mean:

    • Create an environment variable %QGIS_OAS% which works as a pointer to the location of the .qgis2 directory. Initially it points to the .qgis2 directory inside the OSGeo4W installation directory we created in (5).
    • Execute a command-file “QGIS_OAS.bat” if it exists. This command-file is the basis for all our different use-cases. There will be a different version for each use-case. Initially we don’t use this file.
    • Add the “–configpath %QGIS_OAS% qualifier to the actual start of QGIS. This means, that QGIS will look for all setup information, user-defined options, plugins and whatnot in the directory specified by the %QGIS_OAS% environment variable. And QGIS will not use any settings in the registry.
  8. Start QGIS by double clicking the revised C:\OSGeo4W\bin\QGIS.bat file and make all the changes to the initial setup of QGIS that should be included in your future QGIS installation(s). This could be change of language, default projection, extra plugins, snap options, yadda yadda yadda. Come on, make you dream QGIS setup !!

Thanks to the –configpath qualifier now on the start line for QGIS all these changes will be saved in the C:\OSGeo4W\.qgis2 directory. After this, you have a complete setup of QGIS – with your own changes – all located in the C:\OSGeo4W directory. This is the common template for all use cases.

Step 2: Do one of the use cases…

Use case I : “QGIS on a stick “

You have already done this use case. The template made in step 1 is a ready made “QGIS on a stick” installation:

  1. Copy the entire C:\OSGeo4W template directory from your computer to the root of your memory stick.
  2. Insert the memory stick into any Windows computer and start QGIS by double clicking on \OSGeo4W\bin\qgis.bat on the memory stick.
    QGIS will use \OSGeo4W\.qgis2 on the memory stick as the QGIS user directory.

Use case II : “Simple ‘xcopy’ installation of QGIS “

In this use case we will have to extend the template by creating the QGIS_OAS.bat file. This example will put the QGIS user directory “.qgis2” in the users home directory, just like the normal installation does – with one exception: This installation will not use the registry but save all user options in a ini-file placed in the QGIS user directory.

  1. Create the file C:\OSGeo4W\bin\QGIS_OAS.bat with the following content:
    set QGIS_OAS=”%USERPROFILE%”\.qgis2
    if exist %QGIS_OAS% exit /B
    xcopy “%OSGEO4W_ROOT%”\.qgis2 %QGIS_OAS% /e /i
    nircmd shortcut “””%OSGEO4W_ROOT%””\bin\qgis.bat” “~$folder.desktop$” “Start QGIS” “” “””%OSGEO4W_ROOT%””\bin\qgis-bin.exe” “0” “min” “””%OSGEO4W_ROOT%””\bin” “”

    (First the pointer to the QGIS user directory is changed to the “users home directory”\.qgis2. Secondly, The command file will check if the QGIS user directory exists in the users home directory. If it doesn’t exist, the command file will create a copy of the QGIS user directory template into the users home directory; create a shortcut to start QGIS and place this shortcut on the user’s desktop.)

  2. You can now install QGIS on a new PC by copying the entire C:\OSGeo4W directory to the new pc (using a memory-bird, network drive, zip-copy-unzip, whatever). The directory can be copied to any directory location on the new PC. Please note that some locations will require “local admin” rights for creating the new directory, for example if you copy it to “C:\Program Files”. I usually try the avoid this.

First time use on the new pc:

  • Start QGIS by double clicking on C:\OSGeo4W\bin\qgis.bat (or wherever you placed the OSGeo4W directory). When QGIS starts, the combined command files QGIS.BAT and QGIS_OAS.BAT will automatically create the QGIS user directory on the new pc; create a shortcut to QGIS on the user desktop and start QGIS.

After that you can start QGIS by double clicking on the shortcut placed on the desktop.

 

Use case III: “Network install of QGIS with floating profiles

This usage scenario will have the QGIS installation located in a directory on a common network file-share. A normal user need only to have read and execute rights to this directory. The QGIS user directory will be placed in the users “roaming profile” on the client PC, a special region which is cached to a central server.

The computers and users are members of a AD domain. If the user logs on to another pc in the domain, the “roaming profile”, including the desktop and the QGIS user directory, will automatically be copied the new computer and the user will see the usual desktop and applications.

With this setup, there is no dependencies to any particular client pc after the first start of QGIS by the user. If the user logs on any other client PC in the domain it will be possible for her to start QGIS simply by double clicking on the QGIS shortcut on desktop.

There is some requirements: The user has to have access to the common file share (!) and the network connection has to be stable and relatively fast.

In this use case we will do the following:

  1. Copy the QGIS directory C:\OSGeo4W to the common share: X:\QGIS\Current (The drive letter X: is arbitrary; it could be any drive letter). I will explain the naming scheme of the directory later.
  2. Create the file X:\QGIS\Current\bin\QGIS_OAS.bat with the following content
    set QGIS_OAS=”%APPDATA%”\.qgis2
    if exist %QGIS_OAS% exit /B
    xcopy “%OSGEO4W_ROOT%”\.qgis2 %QGIS_OAS% /e /i
    nircmd shortcut “””%OSGEO4W_ROOT%””\bin\qgis.bat” “~$folder.desktop$” “Start QGIS” “” “””%OSGEO4W_ROOT%””\bin\qgis-bin.exe” “0” “min” “””%OSGEO4W_ROOT%””\bin” “”

    (First, The QGIS_OAS environment variable points to the qgis user directory in the roaming profile. Secondly, the command file will check if the QGIS user directory exists. If it doesn’t, the command file will copy the QGIS user directory template to the users roaming profile; create a shortcut to start QGIS and place this shortcut on the user desktop.)

First time use on the new pc:

  • Start QGIS by double clicking on X:\QGIS\Current\bin\qgis.bat. When QGIS starts, the combined command files QGIS.BAT and QGIS_OAS.bat will automatically create the QGIS user directory on the new pc, create a shortcut on the user desktop and start QGIS.
  • After the first time you start QGIS by double clicking on the shortcut placed on the desktop.

Oh .. and why did I use this particular naming scheme for the directory ? It is used to make it easy to update QGIS:

When you have a new version of QGIS, do the following:

  1. Make a template of the new qgis version as described in step 1 and use case III, but in another directory: X:\QGIS\Testing and leave the X:\QGIS\Current unchanged.
  2. Test the new installation. You might even let some of your users test it!! You can start the “testing” version of QGIS by double clicking on X:\QGIS\Testing\bin\qgis.bat
  3. When you are satisfied with the new installation:
    • Rename the directory X:\QGIS\Current to X:\QGIS\Deprecated
    • Rename the directory X:\QGIS\Testing to X:\QGIS\Current 

After the last rename operation all the networked users will execute the new version using their existing shortcut. This method will probably work with all minor updates (2.8 -> 2.10), but probably not with a major update (2.10 -> 3.0)

Use case IV : “QGIS on Citrix “

If you have a Citrix environment you probably have a personal network-based share for each an every user on the domain. For this use case I call this directory M:\Personal. But the naming convention can be anything.

The idea is to place the QGIS user directory on the personal network share, so there won’t be anything saved or registered on the Citrix server that’s user related:

Do the following:

  1. Create a working installation of QGIS on the Citrix sever using the techniques described in Step 1.
  2. Create the file C:\OSGeo4W\bin\QGIS_OAS.bat on the Citrix server with the following content:
    set QGIS_OAS=M:\Personal\.qgis2
    if exist %QGIS_OAS% exit /B
    xcopy “%OSGEO4W_ROOT%”\.qgis2 %QGIS_OAS% /e /i

    (First, The QGIS_OAS environment variable points to the qgis user directory placed on the users personal network share. In this case “M:\Personal”. Secondly, the command file will check if the QGIS user directory exists. If it doesn’t, the command file will copy the QGIS user directory template to the users personal network share.)

  3. Create the usual application startup definition for Citrix pointing to C:\OSGeo4W\bin\QGIS.bat on the Citrix server.

Bingo ! That’s it. I’ll leave the last use case “Smart installation and update of a large amount of QGIS installations” to a separate article, because it is more complicated than any of the previous use cases. I’ll try to publish that article in a week or so, so stay tuned !!

This article has a zip file “QgisOnAStick.zip” attached. It contains the revised QGIS.BAT file plus all the different types of QGIS_OAS bat files described in the article. The suffix is renamed to “.usecase_1”, “.usecase_2” and so on. Download the zip file and rename the suffix to “.bat” on the files you’re going to use.

A final note: I’ve used QGIS 2.8.2 in my tests. So the use cases works for this version of QGIS and will probably work for other QGIS 2.x versions.

Regardsbo

Bo Victor Thomsen

bvt@aestas.dk
AestasGIS
Denmark

Fun with docker and GRASS GIS software

GRASS GIS and dockerSometimes, we developers get reports via mailing list that this & that would not work on whatever operating system. Now what? Should we be so kind and install the operating system in question in order to reproduce the problem? Too much work… but nowadays it has become much easier to perform such tests without having the need to install a full virtual machine – thanks to docker.

Disclaimer: I don’t know much about docker yet, so take the code below with a grain of salt!

In my case I usually work on Fedora or Scientific Linux based systems. In order to quickly (i.e. roughly 10 min of automated installation on my slow laptop) try out issues of GRASS GIS 7 on e.g., Ubuntu, I can run all my tests in docker installed on my Fedora box:

# we need to run stuff as root user
su
# Fedora 21: install docker 
yum -y docker-io

# Fedora 22: install docker
dnf -y install docker

# enable service
systemctl start docker
systemctl enable docker

Now we have a running docker environment. Since we want to exchange data (e.g. GIS data) with the docker container later, we prepare a shared directory beforehand:

# we'll later map /home/neteler/data/docker_tmp to /tmp within the docker container
mkdir /home/neteler/data/docker_tmp

Now we can start to install a Ubuntu docker image (may be “any” image, here we use “Ubuntu trusty” in our example). We will share the X11 display in order to be able to use the GUI as well:

# enable X11 forwarding
xhost +local:docker

# search for available docker images
docker search trusty

# fetch docker image from internet, establish shared directory and display redirect
# and launch the container along with a shell
docker run -v /data/docker_tmp:/tmp:rw -v /tmp/.X11-unix:/tmp/.X11-unix \
       -e uid=$(id -u) -e gid=$(id -g) -e DISPLAY=unix$DISPLAY \
       --name grass70trusty -i -t corbinu/docker-trusty /bin/bash

In almost no time we reach the command line of this minimalistic Ubuntu container which will carry the name “grass70trusty” in our case (btw: read more about Working with Docker Images):

root@8e0f233c3d68:/# 
# now we register the Ubuntu-GIS repos and get GRASS GIS 7.0
add-apt-repository ppa:ubuntugis/ubuntugis-unstable
add-apt-repository ppa:grass/grass-stable
apt-get update
apt-get install grass7

This will take a while (the remaining 9 minutes or so of the overall 10 minutes).

Since I like cursor support on the command line, I launch (again?) the bash in the container session:

root@8e0f233c3d68:/# bash
# yes, we are in Ubuntu here
root@8e0f233c3d68:/# cat /etc/issue

Now we can start to use GRASS GIS 7, even with its graphical user interface from inside the docker container:

# create a directory for our data, it is mapped to /home/neteler/data/docker_tmp/
# on the host machine 
root@8e0f233c3d68:/# mkdir /tmp/grassdata
# create a new LatLong location from EPSG code
# (or copy a location into /home/neteler/data/docker_tmp/)
root@8e0f233c3d68:/# grass70 -c epsg:4326 ~/grassdata/latlong_wgs84
# generate some data to play with
root@8e0f233c3d68:/# v.random n=30 output=random30
# start the GUI manually (since we didn't start GRASS GIS right away with it before)
root@8e0f233c3d68:/# g.gui

Indeed, the GUI comes up as expected!

GRASS GIS 7 GUI in docker container

GRASS GIS 7 GUI in docker container

You may now perform all tests, bugfixes, whatever you like and leave the GRASS GIS session as usual.
To get out of the docker session:

root@8e0f233c3d68:/# exit    # leave the extra bash shell
root@8e0f233c3d68:/# exit    # leave docker session

# disable docker connections to the X server
[root@oboe neteler]# xhost -local:docker

To restart this session later again, you will call it with the name which we have earlier assigned:

[root@oboe neteler]# docker ps -a
# ... you should see "grass70trusty" in the output in the right column

# we are lazy and automate the start a bit
[root@oboe neteler]# GRASSDOCKER_ID=`docker ps -a | grep grass70trusty | cut -d' ' -f1`
[root@oboe neteler]# echo $GRASSDOCKER_ID 
[root@oboe neteler]# xhost +local:docker
[root@oboe neteler]# docker start -a -i $GRASSDOCKER_ID

### ... and so on as described above.

Enjoy.

The post Fun with docker and GRASS GIS software appeared first on GFOSS Blog | GRASS GIS Courses.

GRASS GIS 6.4.5RC1 released

GRASS GIS logoAfter months of development a first release candidate of GRASS GIS 6.4.5 is now available. This is a stability release of the GRASS GIS 6 line.

Source code download:
http://grass.osgeo.org/grass64/source/
http://grass.osgeo.org/grass64/source/grass-6.4.5RC1.tar.gz

Binaries download:
http://grass.osgeo.org/download/software/#g64x

To get the GRASS GIS 6.4.5RC1 source code directly from SVN:
svn checkout http://svn.osgeo.org/grass/grass/tags/release_20150406_grass_6_4_5RC1

Key improvements:
Key improvements of the GRASS GIS 6.4.5RC1 release include stability fixes (esp. vector library), some fixes for wxPython3 support, some module fixes, and more message translations.

See also our detailed announcement:
http://trac.osgeo.org/grass/wiki/Release/6.4.5RC1-News

First time users should explore the first steps tutorial after installation:
http://grasswiki.osgeo.org/wiki/Quick_wxGUI_tutorial

Release candidate management at
http://trac.osgeo.org/grass/wiki/Grass6Planning

Please join us in testing this release candidate for the final release.

Consider to donate pizza or beer for the next GRASS GIS Community Sprint (following the FOSS4G Europe 2015 in Como):
http://grass.osgeo.org/donations/

Thanks to all contributors!

About GRASS GIS

The Geographic Resources Analysis Support System (http://grass.osgeo.org), commonly referred to as GRASS GIS, is an Open Source Geographic Information System providing powerful raster, vector and geospatial processing capabilities in a single integrated software suite. GRASS GIS includes tools for spatial modeling, visualization of raster and vector data, management and analysis of geospatial data, and the processing of satellite and aerial imagery. It also provides the capability to produce sophisticated presentation graphics and hardcopy maps. GRASS GIS has been translated into about twenty languages and supports a huge array of data formats. It can be used either as a stand-alone application or as backend for other software packages such as QGIS and R geostatistics. It is distributed freely under the terms of the GNU General Public License (GPL). GRASS GIS is a founding member of the Open Source Geospatial Foundation (OSGeo).

The GRASS Development Team, April 2015

The post GRASS GIS 6.4.5RC1 released appeared first on GFOSS Blog | GRASS GIS Courses.

Inofficial QGIS 2.8 RPMs for EPEL 7: Fedora 20, Fedora 21, Centos 7, Scientific Linux 7

qgis-icon_smallThanks to the work of Devrim Gündüz, Volker Fröhlich, Dave Johansen, Rex Dieter and other Fedora/EPEL packagers I had an easy going to prepare RPM packages of QGIS 2.8 Wien for Fedora 20 and 21, Centos 7, and Scientific Linux 7.

The base SRPM package I copied from Fedora’s koji server, modified the SPEC file in order to remove the now outdated PyQwt bindings (see bugzilla) and compiled QGIS 2.8 via the great COPR platform.

Repo: https://copr.fedoraproject.org/coprs/neteler/QGIS-2.8-Wien/

The following packages can now be installed and tested on epel-7-x86_64 (Centos 7, Scientific Linux 7, etc.), Fedora-20-x86_64, and Fedora-21-x86_64:

  • qgis 2.8.1
  • qgis-debuginfo 2.8.1
  • qgis-devel 2.8.1
  • qgis-grass 2.8.1
  • qgis-python 2.8.1
  • qgis-server 2.8.1

Installation instructions (run as “root” user or use “sudo”):

# EPEL7:
yum -y install epel-release
yum -y install wget
# https://copr.fedoraproject.org/coprs/neteler/python-OWSLib/
wget -O /etc/yum.repos.d/neteler-python-OWSLib-epel-7.repo https://copr.fedoraproject.org/coprs/neteler/python-OWSLib/repo/epel-7/neteler-python-OWSLib-epel-7.repo
yum -y update
yum -y install python-OWSLib
wget -O /etc/yum.repos.d/qgis-epel-7.repo https://copr.fedoraproject.org/coprs/neteler/QGIS-2.8-Wien/repo/epel-7/neteler-QGIS-2.8-Wien-epel-7.repo
yum update
yum install qgis qgis-grass qgis-python qgis-server

# Fedora 20:
wget -O /etc/yum.repos.d/qgis-epel-7.repo https://copr.fedoraproject.org/coprs/neteler/QGIS-2.8-Wien/repo/fedora-20/neteler-QGIS-2.8-Wien-fedora-20.repo
yum update
yum install qgis qgis-grass qgis-python qgis-server

# Fedora 21:
wget -O /etc/yum.repos.d/qgis-epel-7.repo https://copr.fedoraproject.org/coprs/neteler/QGIS-2.8-Wien/repo/fedora-21/neteler-QGIS-2.8-Wien-fedora-21.repo
yum update
yum install qgis qgis-grass qgis-python qgis-server

The other packages are optional (well, also qgis-grass, qgis-python, and qgis-server…).

Enjoy!

PS: Of course I hope that QGIS 2.8 officially hits EPEL7 anytime soon! My COPR repo is just a temporary bridge towards that goal.

EDIT 30 April 2015:

  • updated EPEL7 installation for python-OWSLib dependency

The post Inofficial QGIS 2.8 RPMs for EPEL 7: Fedora 20, Fedora 21, Centos 7, Scientific Linux 7 appeared first on GFOSS Blog | GRASS GIS Courses.

Compiling OTB Orfeo ToolBox software on Centos/Scientific Linux

The Orfeo ToolBox (OTB), an open-source C++ library for remote sensing images processing, is offering a wealth of algorithms to perform Image manipulation, Data pre-processing, Features extraction, Image Segmentation and Classification, Change detection, Hyperspectral processing, and SAR processing.

Since there is no (fresh) RPM package available for Centos or Scientific Linux, here some quick hints (no full tutorial, though) how to get OTB easily locally compiled. We are following the Installation Chapter.

Importantly, you need to have some libraries installed including GDAL. Be sure that it has been compiled with the “–with-rename-internal-libtiff-symbols” and ” –with-rename-internal-libgeotiff-symbols” flags to avoid namespace collision a.k.a segmentation fault of OTB as per “2.2.4 Building your own qualified Gdal“. We’ll configure and build with the GDAL-internal Tiff and Geotiff libraries that supports BigTiff files

# configure GDAL
./configure \
 --without-libtool \
 --with-geotiff=internal --with-libtiff=internal \
 --with-rename-internal-libtiff-symbols=yes \
 --with-rename-internal-libgeotiff-symbols=yes \
...
make
make install

The compilation of the OTB source code requires “cmake” and some other requirements which you can install via “yum install …”. Be sure to have the following structure for compiling OTB, i.e. store the source code in a subdirectory. The binaries will then be compiled in a “build” directory parallel to the OTB-SRC directory:

OTB-4.4.0/
|-- build/
`-- OTB-SRC/
    |-- Applications/
    |-- CMake/
    |-- CMakeFiles/
    |-- Code/
    |-- Copyright/
    |-- Examples/
    |-- Testing/
    `-- Utilities/

Now it is time to configure everything for OTB. Since I didn’t want to bother with “ccmake”, below the magic lines to compile and install OTB into its own subdirectory within /usr/local/. We’ll use as many internal libraries as possible according to the table in the installation guide. The best way is to save the following lines as a text script “cmake_otb.sh” for easier (re-)use, then run it:

#!/bin/sh

OTBVER=4.4.0
(
mkdir -p build
cd build

cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr/local/otb-$OTBVER \
      -DOTB_USE_EXTERNAL_ITK=OFF -DOTB_USE_EXTERNAL_OSSIM=OFF \
      -DOTB_USE_EXTERNAL_EXPAT=OFF -DOTB_USE_EXTERNAL_BOOST=OFF \
      -DOTB_USE_EXTERNAL_TINYXML=OFF -DOTB_USE_EXTERNAL_LIBKML=OFF \
      -DOTB_USE_EXTERNAL_MUPARSER=OFF \
       ../OTB-SRC/

make -j4
# note: we assume to have write permission in /usr/local/otb-$OTBVER
make install
)

That’s it!

In order to use the freshly compiled OTB, be sure to add the new directories for the binaries and the libraries to your PATH and LD_LIBRARY_PATH variables, e.g. in $HOME/.bashrc:

export PATH=$PATH:/usr/local/bin:/usr/local/otb-4.4.0/bin
export LD_LIBRARY_PATH=/usr/local/lib:/usr/local/lib64/:/usr/local/otb-4.4.0/lib/otb/

Enjoy OTB! And thanks to the OTB developers for making it available.

The post Compiling OTB Orfeo ToolBox software on Centos/Scientific Linux appeared first on GFOSS Blog | GRASS GIS Courses.

New stable release of GRASS GIS 7.0.0!

The GRASS GIS Development team has announced the release of the new major version GRASS GIS 7.0.0. This version provides many new functionalities including spatio-temporal database support, image segmentation, estimation of evapotranspiration and emissivity from satellite imagery, automatic line vertex densification during reprojection, more LIDAR support and a strongly improved graphical user interface experience. GRASS GIS 7.0.0 also offers significantly improved performance for many raster and vector modules: “Many processes that would take hours now take less than a minute, even on my small laptop!” explains Markus Neteler, the coordinator of the development team composed of academics and GIS professionals from around the world. The software is available for Linux, MS-Windows, Mac OSX and other operating systems.

Detailed announcement and software download:
http://grass.osgeo.org/news/42/15/GRASS-GIS-7-0-0/

About GRASS GIS
The Geographic Resources Analysis Support System (http://grass.osgeo.org/), commonly referred to as GRASS GIS, is an open source Geographic Information System providing powerful raster, vector and geospatial processing capabilities in a single integrated software suite. GRASS GIS includes tools for spatial modeling, visualization of raster and vector data, management and analysis of geospatial data, and the processing of satellite and aerial imagery. It also provides the capability to produce sophisticated presentation graphics and hardcopy maps. GRASS GIS has been translated into about twenty languages and supports a huge array of data formats. It can be used either as a stand-alone application or as backend for other software packages such as QGIS and R geostatistics. It is distributed freely under the terms of the GNU General Public License (GPL). GRASS GIS is a founding member of the Open Source Geospatial Foundation (OSGeo).

The post New stable release of GRASS GIS 7.0.0! appeared first on GFOSS Blog | GRASS GIS Courses.

Happy 9th Birthday, OSGeo!

Press release by Jeff McKenna, OSGeo Foundation President

9 years ago today was the first ever meeting of the OSGeo foundation, in Chicago U.S.A. (initial press release). Thanks to those passionately involved back then, and the thousands contributing since, now our community has expanded and has reached many countries all over world. Congratulations to everyone for continuing to share the passion for Open Source geospatial.

Here is a glimpse at some of the exciting events happening around the world this year:

The post Happy 9th Birthday, OSGeo! appeared first on GFOSS Blog | GRASS GIS Courses.

GRASS GIS 7: Vector data reprojection with automated vertex densification

GRASS GIS 7 just got better: When reprojecting vector data, now automated vertex densification is applied. This reduces the reprojection error for long lines (or polygon boundaries). The needed improvement has been kindly added in v.proj by Markus Metz.

1. Example

As an (extreme?) example, we generate a box in LatLong/WGS84 (EPSG: 4326) which is of 10 degree side length (see below for screenshot and at bottom for SHAPE file download of this “box” map):

[neteler@oboe ~]$ grass70 ~/grassdata/latlong/grass7/
# for the ease of generating the box, set computational region:
g.region n=60 s=40 w=0 e=30 res=10 -p
projection: 3 (Latitude-Longitude)
zone:       0
datum:      wgs84
ellipsoid:  wgs84
north:      60N
south:      40N
west:       0
east:       30E
nsres:      10
ewres:      10
rows:       2
cols:       3
cells:      6
# generate the box according to current computational region:
v.in.region box_latlong_10deg
exit

Next we start GRASS GIS in a metric projection, here the EU LAEA:

# EPSG 3035, metric EU LAEA:
grass70 ~/grassdata/europe_laea/user1/
GRASS 7.0.0svn (europe_laea): >

Now we first reproject the map the “traditional way” (no vertex densification as in most GIS, here enforced by smax=0):

v.proj box_latlong_10deg out=box_latlong_10deg_no_densification
location=latlong mapset=grass7 smax=0

Then we do a second reprojection with new automated vertex densification (here we use the default values for smax which is a 10km vertex distance in the reprojected map by default):

v.proj box_latlong_10deg out=box_latlong_10deg_yes_densification
location=latlong mapset=grass7

Eventually we can compare both reprojected maps:

g.region vect=box_latlong_10deg_no_densification

# compare:
d.mon wx0
d.vect box_latlong_10deg_no_densification color=red
d.vect box_latlong_10deg_yes_densification color=green fill_color=none
Comparison of the reprojection of a 10 degree large LatLong box to the metric EU LAEA (EPSG 3035): before in red and new in green. The grid is based on WGS84 at 5 degree spacing.

Comparison of the reprojection of a 10 degree large LatLong box to the metric EU LAEA (EPSG 3035): before in red and new in green. The grid is based on WGS84 at 5 degree spacing.

The result shows how nicely the projection is now performed in GRASS GIS 7: the red line output is old, the green color line is the new output (its area filling is not shown).

Consider to benchmark this with other GIS… the reprojected map should not become a simple trapezoid.

2. Sample dataset download

Download of box_latlong_10deg.shp for own tests (1kB).

The post GRASS GIS 7: Vector data reprojection with automated vertex densification appeared first on GFOSS Blog | GRASS GIS Courses.

Landsat 8 captures Trentino in November 2014

The beautiful days in early November 2014 allowed to get some nice views of the Trentino (Northern Italy) – thanks to Landsat 8 and NASA’s open data policy:

Landsat 8: Northern Italy 1 Nov 2014
Landsat 8: Northern Italy 1 Nov 2014

Trento captured by Landsat8
Trento captured by Landsat8

Landsat 8: San Michele - 1 Nov 2014
Landsat 8: San Michele – 1 Nov 2014

The beauty of the landscape but also the human impact (landscape and condensation trails of airplanes) are clearly visible.

All data were processed in GRASS GIS 7 and pansharpened with i.fusion.hpf written by Nikos Alexandris.

The post Landsat 8 captures Trentino in November 2014 appeared first on GFOSS Blog | GRASS GIS Courses.

QGIS 2.6 ‘Brighton’ released

In the new release of QGIS 2.6.0 a series of new features have been added concerning

  • General: new features and bugfixes,
  • DXF export (improvements),
  • Map Composer (enhancements),
  • Processing (including a new modeler implementation),
  • QGIS Server (improvements),
  • Symbology (including user interface improvements),
  • User Interface with improvements.

A visual changelog is available for more details with lots of screenshots.

Congratulations to all QGIS developers! Looking forward to see the Fedora RPM available…

You can download QGIS 2.6 at http://qgis.org/en/site/forusers/download.html

The post QGIS 2.6 ‘Brighton’ released appeared first on GFOSS Blog | GRASS GIS Courses.

Selective data removal in an elevation map by means of floodfilling

Do you also sometimes get maps which contain zero (0) rather than NULL (no data) in some parts of the map? This can be easily solved with “floodfilling”, even in a GIS.

My original map looks like this (here, Trentino elevation model):

The light blue parts should be no data (NULL) rather than zero (0)...

Now what? In a paint software we would simply use bucket fill but what about GIS data? Well, we can do something similar using “clumping”. It requires a bit of computational time but works perfectly, even for large DEMs, e.g., all Italy at 20m resolution. Using the open source software GRASS GIS 7, we can compute all “clumps” (that are many for a floating point DEM!):

# first we set the computational region to the raster map:
g.region rast=pat_DTM_2008_derived_2m -p
r.clump pat_DTM_2008_derived_2m out=pat_DTM_2008_derived_2m_clump

The resulting clump map produced by r.clump is nicely colorized:

Clumped map derived from DEM (generated with r.clump)

As we can see, the area of interest (province) is now surrounded by three clumps. With a simple map algebra statement (r.mapcalc or GUI calculator) we can create a MASK by assigning these outer boundary clumps to NULL and the other “good” clumps to 1:

r.mapcalc "no_data_mask = if(pat_DTM_2008_derived_2m_clump == 264485050 || \
  pat_DTM_2008_derived_2m_clump == 197926480 || \
  pat_DTM_2008_derived_2m_clump == 3, null(), 1)"

This mask map looks like this:

Mask map from all clumps except for the large outer clumps

We now activate this MASK and generate a copy of the original map into a new map name by using map algebra again (this just keeps the data matched by the MASK). Eventually we remove the MASK and verify the result:

# apply the mask
r.mask no_data_mask
# generate a copy of the DEM, filter on the fly
r.mapcalc "pat_DTM_2008_derived_2m_fixed = pat_DTM_2008_derived_2m"
# assign a nice color table
r.colors pat_DTM_2008_derived_2m_fixed color=srtmplus
# remove the MASK
r.mask -r

And the final DEM is now properly cleaned up in terms of NULL values (no data):

DEM cleaned up for no data

Enjoy.

The post Selective data removal in an elevation map by means of floodfilling appeared first on GFOSS Blog | GRASS GIS Courses.

Rendering a brain CT scan in 3D with GRASS GIS 7

brainscan1Last year (2013) I “enjoyed” a brain CT scan in order to identify a post-surgery issue – luckily nothing found. Being in Italy, like all patients I received a CD-ROM with the scan data on it: so, something to play with! In this article I’ll show how to easily turn 2D scan data into a volumetric (voxel) visualization.

The CT scan data come in a DICOM format which ImageMagick is able to read and convert. Knowing that, we furthermore need the open source software packages GRASS GIS 7 and Paraview to get the job done.

First of all, we create a new XY (unprojected) GRASS location to import the data into:

# create a new, empty location (or use the Location wizard):
grass70 -c ~/grassdata/brain_ct

We now start GRASS GIS 7 with that location. After mounting the CD-ROM we navigate into the image directory therein. The directory name depends on the type of CT scanner which was used in the hospital. The file name suffix may be .IMA.

Now we count the number of images, convert and import them into GRASS GIS:

# list and count
LIST=`ls -1 *.IMA`
MAX=`echo $LIST | wc -w`

# import into XY location:
curr=1
for i in $LIST ; do

# pretty print the numbers to 000X for easier looping:
curr=`echo $curr | awk ‘{printf “%04d\n”, $1}’`
convert “$i” brain.$curr.png
r.in.gdal in=brain.$curr.png out=brain.$curr
r.null brain.$curr setnull=0
rm -f brain.$curr.png
curr=`expr $curr + 1`

done

At this point all CT slices are imported in an ordered way. For extra fun, we can animate the 2D slices in g.gui.animation:

Animation of brain scan slices
(click to enlarge)

# enter in one line:
g.gui.animation rast=`g.mlist -e rast separator=comma pattern=”brain*”`

The tool allows to export as animated GIF or AVI:

Animation of brain scan slices (click to enlarge)

Now it is time to generate a volume:

# first count number of available layers
g.mlist rast pat=”brain*” | wc -l

# now set 3D region to number of available layers (as number of depths)
g.region rast=brain.0003 b=1 t=$MAX -p3

At this point the computational region is properly defined to our 3D raster space. Time to convert the 2D slices into voxels by stacking them on top of each other:

# convert 2D slices to 3D slices:
r.to.rast3 `g.mlist rast pat=”brain*” sep=,` out=brain_vol

We can now look at the volume with GRASS GIS’ wxNVIZ or preferably the extremely powerful Paraview. The latter requires an export of the volume to VTK format:

# fetch some environment variables
eval `g.gisenv -s`
# export GRASS voxels to VTK 3D as 3D points, with scaled z values:
SCALE=2
g.message “Exporting to VTK format, scale factor: $SCALE”
r3.out.vtk brain_vol dp=2 elevscale=$SCALE \
output=${PREFIX}_${MAPSET}_brain_vol_scaled${SCALE}.vtk -p

Eventually we can open this new VTK file in Paraview for visual exploration:

# show as volume
# In Paraview: Properties: Apply; Display Repres: volume; etc.
paraview –data=brain_s1_vol_scaled2.vtk

markus_brain_ct_scan3 markus_brain_ct_scan4 markus_brain_ct_scan2

 

 

 

 

 

 

 

 

 

 

 

 

Fairly easy!

BTW: I have a scan of my non-smoker lungs as well :-)

The post Rendering a brain CT scan in 3D with GRASS GIS 7 appeared first on GFOSS Blog | GRASS GIS Courses.

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