gdalUtils 0.2.0 now on CRAN

I would like to announce a new R package "gdalUtils", now on CRAN. 
gdalUtils is a set of R wrappers for most of the GDAL utility
programs (http://gdal.org/gdal_utilities.html).  gdalUtils is a
collaboration between Matteo Mattiuzzi and me.

gdalUtils requires an already-installed GDAL on your system: 
http://trac.osgeo.org/gdal/wiki/DownloadingGdalBinaries

For Windows, I recommend installing QGIS Standalone 
(http://www.qgis.org/en/site/forusers/download.html) which appears
to have the most up-to-date binaries of GDAL for the Windows
operating system including support for HDF4/5 files.

Note that this is NOT a replacement for Roger Bivand's fantastic
rgdal package, it is a complementary package that simply provides
R-wrappers for functions like gdalwarp, gdal_translate, ogr2ogr,
etc.  We've tried to make the interface more R-like in terms of
input parameters, and have provided some additional features such
as (when relevant) returning outputs in Robert Hijman's raster
format.  The parameter naming and the documentation follows GDAL,
with permission from Frank Warmerdam (lead GDAL developer).

We have also provided some value-added functions such as 
batch_gdal_translate and get_subdatasets (for extracting
subdataset names from HDF4/5 and NetCDF files).

I will note the primary motivation for developing this package was 
initially to provide (finally) HDF4/5 file support to Windows
users (for Landsat and MODIS processing, among other things).
However, many of the GDAL functions provide additional capabilities
that R functions do not currently have, and they are quite a bit
faster than most of their R equivalents (compare
projectRaster_rigorous in my spatial.tools package to
gdalwarp(...,method="mode") for an example).

When you first fire it up, it may take a bit to search for a valid 
GDAL install on your computer.  If you have more than one (Windows 
users may find this), it will use the latest version.  We tried to 
make this system-agnostic, but let us know if you have any
problems getting the functions to work.  The best way to test is: 
library(gdalUtils) gdalinfo(version=TRUE) gdalinfo(formats=TRUE)

Cheers!

--j

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Very nice - haven't tried any working examples, but it installs on a
mac without problems and finds the gdal installation installed via
homebrew.

But I have some questions:

The automatic search is nice - but I unlinked gdal via homebrew, i.e.
the links to the binaries and libraries are not in the path anymore,
and I could not load gdalUtils anymore, as the gdalUtils did not find
the libraries anymore (understandable). But it seams, that gdalUtils
did not search for gdal, which is installed as a Framework as well.
Now I removed gdalUtils again and installed it again, with gdal still
unlinked, but it did not install as it did not find the gdal
libraries, despite gdal being available in a framework (see
http://www.kyngchaos.com/software/frameworks for the ones installed -
they are quite popular, and required, among GRASS and QGIS users on Mac).

Question 1:

Would it be possible, to include the gdal Frameworks in the search path?

At the end is a layout of the directory structure of the gdal frameworks.

Question 2:

Is it (or would it) be possible to manually set the installation of
gdal to be used? This would make comparison of versions of gdal as
well as reproducible research much easier.

Question 3:

I can't test it right now, but I assume that gdalUtils does search for
a new gdal installation if it can't find the one used before? Is there
a way of initiating the search (and selection) if a newer version has
been installed?

Thanks for a very neat package,

Rainer

Directory structure of the GDAL.Framework on a MAC:

/Library/Frameworks/GDAL.framework/
??? Headers -> Versions/Current/Headers
??? Programs -> Versions/Current/Programs
??? Resources -> Versions/Current/Resources
??? Versions
?   ??? 1.10
?   ?   ??? Headers
?   ?   ??? Libraries
?   ?   ?   ??? ogdi
?   ?   ??? PlugIns
?   ?   ??? Programs
?   ?   ??? Python
?   ?   ?   ??? 2.6
?   ?   ?   ?   ??? site-packages
?   ?   ?   ?       ??? osgeo
?   ?   ?   ??? 2.7
?   ?   ?       ??? site-packages
?   ?   ?           ??? osgeo
?   ?   ??? Resources
?   ?   ?   ??? doc
?   ?   ?   ?   ??? gdal
?   ?   ?   ?       ??? java
?   ?   ?   ?       ?   ??? org
?   ?   ?   ?       ?   ?   ??? gdal
?   ?   ?   ?       ?   ?       ??? gdal
?   ?   ?   ?       ?   ?       ??? gdalconst
?   ?   ?   ?       ?   ?       ??? ogr
?   ?   ?   ?       ?   ?       ??? osr
?   ?   ?   ?       ?   ??? resources
?   ?   ?   ?       ??? ogr
?   ?   ?   ??? gdal
?   ?   ??? unix
?   ?       ??? bin
?   ?       ??? include -> ../Headers
?   ?       ??? lib
?   ??? 1.9
?   ?   ??? Headers
?   ?   ??? Libraries
?   ?   ?   ??? ogdi
?   ?   ??? PlugIns
?   ?   ??? Programs
?   ?   ??? Python
?   ?   ?   ??? 2.6
?   ?   ?   ?   ??? site-packages
?   ?   ?   ?       ??? osgeo
?   ?   ?   ??? 2.7
?   ?   ?       ??? site-packages
?   ?   ?           ??? osgeo
?   ?   ??? Resources
?   ?   ?   ??? doc
?   ?   ?   ?   ??? gdal
?   ?   ?   ?       ??? java
?   ?   ?   ?       ?   ??? org
?   ?   ?   ?       ?   ?   ??? gdal
?   ?   ?   ?       ?   ?       ??? gdal
?   ?   ?   ?       ?   ?       ??? gdalconst
?   ?   ?   ?       ?   ?       ??? ogr
?   ?   ?   ?       ?   ?       ??? osr
?   ?   ?   ?       ?   ??? resources
?   ?   ?   ?       ??? ogr
?   ?   ?   ??? gdal
?   ?   ??? unix
?   ?       ??? bin
?   ?       ??? include -> ../Headers
?   ?       ??? lib
?   ??? Current -> 1.10
??? unix -> Versions/Current/unix

Cheers!

--j

- --
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer at krugs.de

Skype:      RMkrug
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You might also try "gdal-config --prefix". Of course that wont work if
gdal-config not installed or in the path.

THK


On Thu, Jan 9, 2014 at 11:46 AM, Jonathan Greenberg <jgrn at illinois.edu>
wrote:

Rainer:

Responses below!

On Thu, Jan 9, 2014 at 2:28 AM, Rainer M Krug <Rainer at krugs.de> wrote:

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Very nice - haven't tried any working examples, but it installs on a
mac without problems and finds the gdal installation installed via
homebrew.

But I have some questions:

The automatic search is nice - but I unlinked gdal via homebrew, i.e.
the links to the binaries and libraries are not in the path anymore,
and I could not load gdalUtils anymore, as the gdalUtils did not find
the libraries anymore (understandable). But it seams, that gdalUtils
did not search for gdal, which is installed as a Framework as well.
Now I removed gdalUtils again and installed it again, with gdal still
unlinked, but it did not install as it did not find the gdal
libraries, despite gdal being available in a framework (see
http://www.kyngchaos.com/software/frameworks for the ones installed -
they are quite popular, and required, among GRASS and QGIS users on
Mac).

Quick question: did you try restarting R AFTER you unlinked the
homebrew version?  Here's why I ask: the first time you run ANY
gdalUtils in a session, what it does is spiders your system for
working GDAL installations (in fact, it looks for the frameworks
first).  After this first time, it won't re-scan the drive unless you
do one of two things: 1) restart R and re-load GDALUtils, or 2) run
gdal_setInstallation(rescan=TRUE)

Question 1:

Would it be possible, to include the gdal Frameworks in the search path?

These are the common locations it searches for, before it attempts a
brute-force search of your whole drive:

if (.Platform$OS=="unix")
{
common_locations <- c(
# UNIX systems
"/usr/bin",
"/usr/local/bin",
# Mac
# Kyngchaos frameworks:
"/Library/Frameworks/GDAL.framework/Programs",
# MacPorts:
"/opt/local/bin"
)
}
if (.Platform$OS=="windows")
{
common_locations <- c(
"C:\\Program Files",
"C:\\Program Files (x86)",
"C:\\OSGeo4W"
)
}

I use those frameworks, and the function worked for me, but let me
know if it failed to find yours (perhaps I'll strip the /Programs from
the search path?)  It is easy for me to add new search locations, so
if there are other common locations for ANY OS just let me know.

At the end is a layout of the directory structure of the gdal
frameworks.

Question 2:

Is it (or would it) be possible to manually set the installation of
gdal to be used? This would make comparison of versions of gdal as
well as reproducible research much easier.

Yes, we can add in this functionality at a future date.  Right now,
you can check to see what your installs are by:
gdal_setInstallation(rescan=TRUE)
getOption("gdalUtils_gdalPath")

In general, gdalUtils will use the first element of the
getOption("gdalUtils_gdalPath"), which is chosen by the most recent
version (by date).

Question 3:

I can't test it right now, but I assume that gdalUtils does search for
a new gdal installation if it can't find the one used before? Is there
a way of initiating the search (and selection) if a newer version has
been installed?

Yep, as I said either restart R or run:
gdal_setInstallation(rescan=TRUE)

Thanks for a very neat package,

Rainer

Directory structure of the GDAL.Framework on a MAC:

/Library/Frameworks/GDAL.framework/
??? Headers -> Versions/Current/Headers
??? Programs -> Versions/Current/Programs
??? Resources -> Versions/Current/Resources
??? Versions
?   ??? 1.10
?   ?   ??? Headers
?   ?   ??? Libraries
?   ?   ?   ??? ogdi
?   ?   ??? PlugIns
?   ?   ??? Programs
?   ?   ??? Python
?   ?   ?   ??? 2.6
?   ?   ?   ?   ??? site-packages
?   ?   ?   ?       ??? osgeo
?   ?   ?   ??? 2.7
?   ?   ?       ??? site-packages
?   ?   ?           ??? osgeo
?   ?   ??? Resources
?   ?   ?   ??? doc
?   ?   ?   ?   ??? gdal
?   ?   ?   ?       ??? java
?   ?   ?   ?       ?   ??? org
?   ?   ?   ?       ?   ?   ??? gdal
?   ?   ?   ?       ?   ?       ??? gdal
?   ?   ?   ?       ?   ?       ??? gdalconst
?   ?   ?   ?       ?   ?       ??? ogr
?   ?   ?   ?       ?   ?       ??? osr
?   ?   ?   ?       ?   ??? resources
?   ?   ?   ?       ??? ogr
?   ?   ?   ??? gdal
?   ?   ??? unix
?   ?       ??? bin
?   ?       ??? include -> ../Headers
?   ?       ??? lib
?   ??? 1.9
?   ?   ??? Headers
?   ?   ??? Libraries
?   ?   ?   ??? ogdi
?   ?   ??? PlugIns
?   ?   ??? Programs
?   ?   ??? Python
?   ?   ?   ??? 2.6
?   ?   ?   ?   ??? site-packages
?   ?   ?   ?       ??? osgeo
?   ?   ?   ??? 2.7
?   ?   ?       ??? site-packages
?   ?   ?           ??? osgeo
?   ?   ??? Resources
?   ?   ?   ??? doc
?   ?   ?   ?   ??? gdal
?   ?   ?   ?       ??? java
?   ?   ?   ?       ?   ??? org
?   ?   ?   ?       ?   ?   ??? gdal
?   ?   ?   ?       ?   ?       ??? gdal
?   ?   ?   ?       ?   ?       ??? gdalconst
?   ?   ?   ?       ?   ?       ??? ogr
?   ?   ?   ?       ?   ?       ??? osr
?   ?   ?   ?       ?   ??? resources
?   ?   ?   ?       ??? ogr
?   ?   ?   ??? gdal
?   ?   ??? unix
?   ?       ??? bin
?   ?       ??? include -> ../Headers
?   ?       ??? lib
?   ??? Current -> 1.10
??? unix -> Versions/Current/unix

Cheers!

--j

- --
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer at krugs.de

Skype:      RMkrug
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--
Jonathan A. Greenberg, PhD
Assistant Professor
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
259 Computing Applications Building, MC-150
605 East Springfield Avenue
Champaign, IL  61820-6371
Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/
AIM: jgrn307, MSN: jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007

--
http://www.keittlab.org/

Rainer:

Responses below!

On Thu, Jan 9, 2014 at 2:28 AM, Rainer M Krug <Rainer at krugs.de>
wrote:


Very nice - haven't tried any working examples, but it installs on
a mac without problems and finds the gdal installation installed
via homebrew.

But I have some questions:

The automatic search is nice - but I unlinked gdal via homebrew,
i.e. the links to the binaries and libraries are not in the path
anymore, and I could not load gdalUtils anymore, as the gdalUtils
did not find the libraries anymore (understandable). But it seams,
that gdalUtils did not search for gdal, which is installed as a
Framework as well. Now I removed gdalUtils again and installed it
again, with gdal still unlinked, but it did not install as it did
not find the gdal libraries, despite gdal being available in a
framework (see http://www.kyngchaos.com/software/frameworks for the
ones installed - they are quite popular, and required, among GRASS
and QGIS users on Mac).

Quick question: did you try restarting R AFTER you unlinked the 
homebrew version?  Here's why I ask: the first time you run ANY 
gdalUtils in a session, what it does is spiders your system for 
working GDAL installations (in fact, it looks for the frameworks 
first).  After this first time, it won't re-scan the drive unless
you do one of two things: 1) restart R and re-load GDALUtils, or
2) run gdal_setInstallation(rescan=TRUE)

library(gdalUtils)

Question 1:

Would it be possible, to include the gdal Frameworks in the search
path?

These are the common locations it searches for, before it
attempts a brute-force search of your whole drive:

if (.Platform$OS=="unix") { common_locations <- c( # UNIX
systems "/usr/bin", "/usr/local/bin", # Mac # Kyngchaos
frameworks: "/Library/Frameworks/GDAL.framework/Programs", #
MacPorts: "/opt/local/bin" ) } if (.Platform$OS=="windows") { 
common_locations <- c( "C:\\Program Files", "C:\\Program Files
(x86)", "C:\\OSGeo4W" ) }

I use those frameworks, and the function worked for me, but let
me know if it failed to find yours (perhaps I'll strip the
/Programs from the search path?)  It is easy for me to add new
search locations, so if there are other common locations for ANY
OS just let me know.

At the end is a layout of the directory structure of the gdal
frameworks.

Question 2:

Is it (or would it) be possible to manually set the installation
of gdal to be used? This would make comparison of versions of gdal
as well as reproducible research much easier.

Yes, we can add in this functionality at a future date.  Right
now, you can check to see what your installs are by: 
gdal_setInstallation(rescan=TRUE) 
getOption("gdalUtils_gdalPath")

In general, gdalUtils will use the first element of the 
getOption("gdalUtils_gdalPath"), which is chosen by the most
recent version (by date).

Question 3:

I can't test it right now, but I assume that gdalUtils does search
for a new gdal installation if it can't find the one used before?
Is there a way of initiating the search (and selection) if a newer
version has been installed?

Yep, as I said either restart R or run: 
gdal_setInstallation(rescan=TRUE)

Thanks for a very neat package,

Rainer

Directory structure of the GDAL.Framework on a MAC:

/Library/Frameworks/GDAL.framework/ ??? Headers ->
Versions/Current/Headers ??? Programs -> Versions/Current/Programs 
??? Resources -> Versions/Current/Resources ??? Versions ?   ???
1.10 ?   ?   ??? Headers ?   ?   ??? Libraries ?   ?   ?   ???
ogdi ?   ?   ??? PlugIns ?   ?   ??? Programs ?   ?   ??? Python ?
?   ?   ??? 2.6 ?   ?   ?   ?   ??? site-packages ?   ?   ?   ?
??? osgeo ?   ?   ?   ??? 2.7 ?   ?   ?       ??? site-packages ?
?   ?           ??? osgeo ?   ?   ??? Resources ?   ?   ?   ???
doc ?   ?   ?   ?   ??? gdal ?   ?   ?   ?       ??? java ?   ?   ?
?       ?   ??? org ?   ?   ?   ?       ?   ?   ??? gdal ?   ?   ?
?       ?   ?       ??? gdal ?   ?   ?   ?       ?   ?       ???
gdalconst ?   ?   ?   ?       ?   ?       ??? ogr ?   ?   ?   ?
?   ?       ??? osr ?   ?   ?   ?       ?   ??? resources ?   ?   ?
?       ??? ogr ?   ?   ?   ??? gdal ?   ?   ??? unix ?   ?
??? bin ?   ?       ??? include -> ../Headers ?   ?       ??? lib ?
??? 1.9 ?   ?   ??? Headers ?   ?   ??? Libraries ?   ?   ?   ???
ogdi ?   ?   ??? PlugIns ?   ?   ??? Programs ?   ?   ??? Python ?
?   ?   ??? 2.6 ?   ?   ?   ?   ??? site-packages ?   ?   ?   ?
??? osgeo ?   ?   ?   ??? 2.7 ?   ?   ?       ??? site-packages ?
?   ?           ??? osgeo ?   ?   ??? Resources ?   ?   ?   ???
doc ?   ?   ?   ?   ??? gdal ?   ?   ?   ?       ??? java ?   ?   ?
?       ?   ??? org ?   ?   ?   ?       ?   ?   ??? gdal ?   ?   ?
?       ?   ?       ??? gdal ?   ?   ?   ?       ?   ?       ???
gdalconst ?   ?   ?   ?       ?   ?       ??? ogr ?   ?   ?   ?
?   ?       ??? osr ?   ?   ?   ?       ?   ??? resources ?   ?   ?
?       ??? ogr ?   ?   ?   ??? gdal ?   ?   ??? unix ?   ?
??? bin ?   ?       ??? include -> ../Headers ?   ?       ??? lib ?
??? Current -> 1.10 ??? unix -> Versions/Current/unix

Cheers!

--j

Tim: thanks! We have something similar, where the package uses a 
Sys.which() to see if gdalinfo is available in the PATH as one of
its attempts to find a valid install.

Rainer et al: I pushed version 0.2.3 to R-forge (you'll need to SVN
it until R-forge builds the new package later today/tomorrow) which
now supports a fixed search_path parameter.  To use this:

gdal_setInstallation(search_path="/pathto/your/favorite/GDAL/",rescan=TRUE)

 If it finds a valid gdalinfo in that path, it will use that one
(thus forcing gdalUtils to use a specific install).  If it doesn't
find it, it will search as usual.  Note that I updated the help
for gdal_setInstallation to better explain how gdalUtils searches
for a valid install.

Here's the R-forge site: 
https://r-forge.r-project.org/projects/gdalutils/

--j

On Thu, Jan 9, 2014 at 12:10 PM, Tim Keitt <tkeitt at utexas.edu>
wrote:

You might also try "gdal-config --prefix". Of course that wont
work if gdal-config not installed or in the path.

THK


On Thu, Jan 9, 2014 at 11:46 AM, Jonathan Greenberg
<jgrn at illinois.edu> wrote:

Rainer:

Responses below!

On Thu, Jan 9, 2014 at 2:28 AM, Rainer M Krug <Rainer at krugs.de>
wrote:

Very nice - haven't tried any working examples, but it installs on
a mac without problems and finds the gdal installation installed
via homebrew.

But I have some questions:

The automatic search is nice - but I unlinked gdal via homebrew,
i.e. the links to the binaries and libraries are not in the path
anymore, and I could not load gdalUtils anymore, as the gdalUtils
did not find the libraries anymore (understandable). But it seams,
that gdalUtils did not search for gdal, which is installed as a
Framework as well. Now I removed gdalUtils again and installed it
again, with gdal still unlinked, but it did not install as it did
not find the gdal libraries, despite gdal being available in a
framework (see http://www.kyngchaos.com/software/frameworks for the
ones installed - they are quite popular, and required, among GRASS
and QGIS users on Mac).

Quick question: did you try restarting R AFTER you unlinked
the homebrew version?  Here's why I ask: the first time you
run ANY gdalUtils in a session, what it does is spiders your
system for working GDAL installations (in fact, it looks for
the frameworks first).  After this first time, it won't
re-scan the drive unless you do one of two things: 1) restart
R and re-load GDALUtils, or 2) run 
gdal_setInstallation(rescan=TRUE)

Question 1:

Would it be possible, to include the gdal Frameworks in the search
path?

These are the common locations it searches for, before it
attempts a brute-force search of your whole drive:

if (.Platform$OS=="unix") { common_locations <- c( # UNIX
systems "/usr/bin", "/usr/local/bin", # Mac # Kyngchaos
frameworks: "/Library/Frameworks/GDAL.framework/Programs", #
MacPorts: "/opt/local/bin" ) } if (.Platform$OS=="windows") 
{ common_locations <- c( "C:\\Program Files", "C:\\Program
Files (x86)", "C:\\OSGeo4W" ) }

I use those frameworks, and the function worked for me, but
let me know if it failed to find yours (perhaps I'll strip
the /Programs from the search path?)  It is easy for me to
add new search locations, so if there are other common
locations for ANY OS just let me know.

At the end is a layout of the directory structure of the gdal 
frameworks.

Question 2:

Is it (or would it) be possible to manually set the installation
of gdal to be used? This would make comparison of versions of gdal
as well as reproducible research much easier.

Yes, we can add in this functionality at a future date.
Right now, you can check to see what your installs are by: 
gdal_setInstallation(rescan=TRUE) 
getOption("gdalUtils_gdalPath")

In general, gdalUtils will use the first element of the 
getOption("gdalUtils_gdalPath"), which is chosen by the most
recent version (by date).

Question 3:

I can't test it right now, but I assume that gdalUtils does search
for a new gdal installation if it can't find the one used before?
Is there a way of initiating the search (and selection) if a newer
version has been installed?

Yep, as I said either restart R or run: 
gdal_setInstallation(rescan=TRUE)

Thanks for a very neat package,

Rainer

Directory structure of the GDAL.Framework on a MAC:

/Library/Frameworks/GDAL.framework/ ??? Headers ->
Versions/Current/Headers ??? Programs -> Versions/Current/Programs 
??? Resources -> Versions/Current/Resources ??? Versions ?   ???
1.10 ?   ?   ??? Headers ?   ?   ??? Libraries ?   ?   ?   ???
ogdi ?   ?   ??? PlugIns ?   ?   ??? Programs ?   ?   ??? Python ?
?   ?   ??? 2.6 ?   ?   ?   ?   ??? site-packages ?   ?   ?   ?
??? osgeo ?   ?   ?   ??? 2.7 ?   ?   ?       ??? site-packages ?
?   ?           ??? osgeo ?   ?   ??? Resources ?   ?   ?   ???
doc ?   ?   ?   ?   ??? gdal ?   ?   ?   ?       ??? java ?   ?   ?
?       ?   ??? org ?   ?   ?   ?       ?   ?   ??? gdal ?   ?   ?
?       ?   ?       ??? gdal ?   ?   ?   ?       ?   ?       ???
gdalconst ?   ?   ?   ?       ?   ?       ??? ogr ?   ?   ?   ?
?   ?       ??? osr ?   ?   ?   ?       ?   ??? resources ?   ?   ?
?       ??? ogr ?   ?   ?   ??? gdal ?   ?   ??? unix ?   ?
??? bin ?   ?       ??? include -> ../Headers ?   ?       ??? lib ?
??? 1.9 ?   ?   ??? Headers ?   ?   ??? Libraries ?   ?   ?   ???
ogdi ?   ?   ??? PlugIns ?   ?   ??? Programs ?   ?   ??? Python ?
?   ?   ??? 2.6 ?   ?   ?   ?   ??? site-packages ?   ?   ?   ?
??? osgeo ?   ?   ?   ??? 2.7 ?   ?   ?       ??? site-packages ?
?   ?           ??? osgeo ?   ?   ??? Resources ?   ?   ?   ???
doc ?   ?   ?   ?   ??? gdal ?   ?   ?   ?       ??? java ?   ?   ?
?       ?   ??? org ?   ?   ?   ?       ?   ?   ??? gdal ?   ?   ?
?       ?   ?       ??? gdal ?   ?   ?   ?       ?   ?       ???
gdalconst ?   ?   ?   ?       ?   ?       ??? ogr ?   ?   ?   ?
?   ?       ??? osr ?   ?   ?   ?       ?   ??? resources ?   ?   ?
?       ??? ogr ?   ?   ?   ??? gdal ?   ?   ??? unix ?   ?
??? bin ?   ?       ??? include -> ../Headers ?   ?       ??? lib ?
??? Current -> 1.10 ??? unix -> Versions/Current/unix

Cheers!

--j

-- Jonathan A. Greenberg, PhD Assistant Professor Global
Environmental Analysis and Remote Sensing (GEARS) Laboratory 
Department of Geography and Geographic Information Science 
University of Illinois at Urbana-Champaign 259 Computing
Applications Building, MC-150 605 East Springfield Avenue 
Champaign, IL  61820-6371 Phone: 217-300-1924 
http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN:
jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007

-- http://www.keittlab.org/

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1



On 01/09/14, 19:43 , Jonathan Greenberg wrote:

Tim: thanks! We have something similar, where the package uses a
Sys.which() to see if gdalinfo is available in the PATH as one of
its attempts to find a valid install.

Rainer et al: I pushed version 0.2.3 to R-forge (you'll need to SVN
it until R-forge builds the new package later today/tomorrow) which
now supports a fixed search_path parameter.  To use this:

gdal_setInstallation(search_path="/pathto/your/favorite/GDAL/",rescan=TRUE)

 If it finds a valid gdalinfo in that path, it will use that one
(thus forcing gdalUtils to use a specific install).  If it doesn't
find it, it will search as usual.  Note that I updated the help
for gdal_setInstallation to better explain how gdalUtils searches
for a valid install.

This sounds very useful. But to come back to the importing of rgdal,
which was causing my problem: As gdalUtils is quite useful without
rgdal, would it be possible to move rgdal to Enhances and to disable
the functions which require rgdal when rgdal is not installed?
And if rgdal is installed, to use the same gdal installation (I don't
know if this is the case already)?

Just a ciosmetic suggestion: it would be nice if, when loadu=ing the
package via library(gdalUtils), that the gdal version and path could
be printed.

Thanks,

Rainer

Here's the R-forge site:
https://r-forge.r-project.org/projects/gdalutils/

--j

On Thu, Jan 9, 2014 at 12:10 PM, Tim Keitt <tkeitt at utexas.edu>
wrote:

You might also try "gdal-config --prefix". Of course that wont
work if gdal-config not installed or in the path.

THK


On Thu, Jan 9, 2014 at 11:46 AM, Jonathan Greenberg
<jgrn at illinois.edu> wrote:

Rainer:

Responses below!

On Thu, Jan 9, 2014 at 2:28 AM, Rainer M Krug <Rainer at krugs.de>
wrote:

Very nice - haven't tried any working examples, but it installs on
a mac without problems and finds the gdal installation installed
via homebrew.

But I have some questions:

The automatic search is nice - but I unlinked gdal via homebrew,
i.e. the links to the binaries and libraries are not in the path
anymore, and I could not load gdalUtils anymore, as the gdalUtils
did not find the libraries anymore (understandable). But it seams,
that gdalUtils did not search for gdal, which is installed as a
Framework as well. Now I removed gdalUtils again and installed it
again, with gdal still unlinked, but it did not install as it did
not find the gdal libraries, despite gdal being available in a
framework (see http://www.kyngchaos.com/software/frameworks for the
ones installed - they are quite popular, and required, among GRASS
and QGIS users on Mac).

Quick question: did you try restarting R AFTER you unlinked
the homebrew version?  Here's why I ask: the first time you
run ANY gdalUtils in a session, what it does is spiders your
system for working GDAL installations (in fact, it looks for
the frameworks first).  After this first time, it won't
re-scan the drive unless you do one of two things: 1) restart
R and re-load GDALUtils, or 2) run
gdal_setInstallation(rescan=TRUE)

Question 1:

Would it be possible, to include the gdal Frameworks in the search
path?

These are the common locations it searches for, before it
attempts a brute-force search of your whole drive:

if (.Platform$OS=="unix") { common_locations <- c( # UNIX
systems "/usr/bin", "/usr/local/bin", # Mac # Kyngchaos
frameworks: "/Library/Frameworks/GDAL.framework/Programs", #
MacPorts: "/opt/local/bin" ) } if (.Platform$OS=="windows")
{ common_locations <- c( "C:\\Program Files", "C:\\Program
Files (x86)", "C:\\OSGeo4W" ) }

I use those frameworks, and the function worked for me, but
let me know if it failed to find yours (perhaps I'll strip
the /Programs from the search path?)  It is easy for me to
add new search locations, so if there are other common
locations for ANY OS just let me know.

At the end is a layout of the directory structure of the gdal
frameworks.

Question 2:

Is it (or would it) be possible to manually set the installation
of gdal to be used? This would make comparison of versions of gdal
as well as reproducible research much easier.

Yes, we can add in this functionality at a future date.
Right now, you can check to see what your installs are by:
gdal_setInstallation(rescan=TRUE)
getOption("gdalUtils_gdalPath")

In general, gdalUtils will use the first element of the
getOption("gdalUtils_gdalPath"), which is chosen by the most
recent version (by date).

Question 3:

I can't test it right now, but I assume that gdalUtils does search
for a new gdal installation if it can't find the one used before?
Is there a way of initiating the search (and selection) if a newer
version has been installed?

Yep, as I said either restart R or run:
gdal_setInstallation(rescan=TRUE)

Thanks for a very neat package,

Rainer

Directory structure of the GDAL.Framework on a MAC:

/Library/Frameworks/GDAL.framework/ ??? Headers ->
Versions/Current/Headers ??? Programs -> Versions/Current/Programs
??? Resources -> Versions/Current/Resources ??? Versions ?   ???
1.10 ?   ?   ??? Headers ?   ?   ??? Libraries ?   ?   ?   ???
ogdi ?   ?   ??? PlugIns ?   ?   ??? Programs ?   ?   ??? Python ?
?   ?   ??? 2.6 ?   ?   ?   ?   ??? site-packages ?   ?   ?   ?
??? osgeo ?   ?   ?   ??? 2.7 ?   ?   ?       ??? site-packages ?
?   ?           ??? osgeo ?   ?   ??? Resources ?   ?   ?   ???
doc ?   ?   ?   ?   ??? gdal ?   ?   ?   ?       ??? java ?   ?   ?
?       ?   ??? org ?   ?   ?   ?       ?   ?   ??? gdal ?   ?   ?
?       ?   ?       ??? gdal ?   ?   ?   ?       ?   ?       ???
gdalconst ?   ?   ?   ?       ?   ?       ??? ogr ?   ?   ?   ?
?   ?       ??? osr ?   ?   ?   ?       ?   ??? resources ?   ?   ?
?       ??? ogr ?   ?   ?   ??? gdal ?   ?   ??? unix ?   ?
??? bin ?   ?       ??? include -> ../Headers ?   ?       ??? lib ?
??? 1.9 ?   ?   ??? Headers ?   ?   ??? Libraries ?   ?   ?   ???
ogdi ?   ?   ??? PlugIns ?   ?   ??? Programs ?   ?   ??? Python ?
?   ?   ??? 2.6 ?   ?   ?   ?   ??? site-packages ?   ?   ?   ?
??? osgeo ?   ?   ?   ??? 2.7 ?   ?   ?       ??? site-packages ?
?   ?           ??? osgeo ?   ?   ??? Resources ?   ?   ?   ???
doc ?   ?   ?   ?   ??? gdal ?   ?   ?   ?       ??? java ?   ?   ?
?       ?   ??? org ?   ?   ?   ?       ?   ?   ??? gdal ?   ?   ?
?       ?   ?       ??? gdal ?   ?   ?   ?       ?   ?       ???
gdalconst ?   ?   ?   ?       ?   ?       ??? ogr ?   ?   ?   ?
?   ?       ??? osr ?   ?   ?   ?       ?   ??? resources ?   ?   ?
?       ??? ogr ?   ?   ?   ??? gdal ?   ?   ??? unix ?   ?
??? bin ?   ?       ??? include -> ../Headers ?   ?       ??? lib ?
??? Current -> 1.10 ??? unix -> Versions/Current/unix

Cheers!

--j

-- Jonathan A. Greenberg, PhD Assistant Professor Global
Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign 259 Computing
Applications Building, MC-150 605 East Springfield Avenue
Champaign, IL  61820-6371 Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN:
jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007

-- http://www.keittlab.org/

- --
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation
Biology, UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :       +33 - (0)9 53 10 27 44
Cell:       +33 - (0)6 85 62 59 98
Fax :       +33 - (0)9 58 10 27 44

Fax (D):    +49 - (0)3 21 21 25 22 44

email:      Rainer at krugs.de

Skype:      RMkrug
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Ok, pushed a new version (0.2.4) to R-forge following these 
suggestions (rgdal and raster are now moved to "Suggests", and the 
examples should hopefully be updated to support it).

str(getOption("gdalUtils_gdalPath"))

Rainer: would you mind testing this out?  Try it with and without 
outputRaster=TRUE (it should fail on outputRaster=TRUE if you
don't have rgdal installed).

--j

On Thu, Jan 9, 2014 at 2:15 PM, Rainer M Krug <Rainer at krugs.de>
wrote:


On 01/09/14, 19:43 , Jonathan Greenberg wrote:

Tim: thanks! We have something similar, where the package
uses a Sys.which() to see if gdalinfo is available in the
PATH as one of its attempts to find a valid install.

Rainer et al: I pushed version 0.2.3 to R-forge (you'll need
to SVN it until R-forge builds the new package later
today/tomorrow) which now supports a fixed search_path
parameter.  To use this:

gdal_setInstallation(search_path="/pathto/your/favorite/GDAL/",rescan=TRUE)

(thus forcing gdalUtils to use a specific install).  If it
doesn't find it, it will search as usual.  Note that I
updated the help for gdal_setInstallation to better explain
how gdalUtils searches for a valid install.

This sounds very useful. But to come back to the importing of
rgdal, which was causing my problem: As gdalUtils is quite useful
without rgdal, would it be possible to move rgdal to Enhances and
to disable the functions which require rgdal when rgdal is not
installed? And if rgdal is installed, to use the same gdal
installation (I don't know if this is the case already)?

Just a ciosmetic suggestion: it would be nice if, when loadu=ing
the package via library(gdalUtils), that the gdal version and path
could be printed.

Thanks,

Rainer

Here's the R-forge site: 
https://r-forge.r-project.org/projects/gdalutils/

--j

On Thu, Jan 9, 2014 at 12:10 PM, Tim Keitt
<tkeitt at utexas.edu> wrote:

You might also try "gdal-config --prefix". Of course that
wont work if gdal-config not installed or in the path.

THK


On Thu, Jan 9, 2014 at 11:46 AM, Jonathan Greenberg 
<jgrn at illinois.edu> wrote:

Rainer:

Responses below!

On Thu, Jan 9, 2014 at 2:28 AM, Rainer M Krug
<Rainer at krugs.de> wrote:

Very nice - haven't tried any working examples, but it
installs on a mac without problems and finds the gdal
installation installed via homebrew.

But I have some questions:

The automatic search is nice - but I unlinked gdal via
homebrew, i.e. the links to the binaries and libraries are
not in the path anymore, and I could not load gdalUtils
anymore, as the gdalUtils did not find the libraries anymore
(understandable). But it seams, that gdalUtils did not search
for gdal, which is installed as a Framework as well. Now I
removed gdalUtils again and installed it again, with gdal
still unlinked, but it did not install as it did not find the
gdal libraries, despite gdal being available in a framework
(see http://www.kyngchaos.com/software/frameworks for the 
ones installed - they are quite popular, and required, among
GRASS and QGIS users on Mac).

Quick question: did you try restarting R AFTER you
unlinked the homebrew version?  Here's why I ask: the
first time you run ANY gdalUtils in a session, what it
does is spiders your system for working GDAL
installations (in fact, it looks for the frameworks
first).  After this first time, it won't re-scan the
drive unless you do one of two things: 1) restart R and
re-load GDALUtils, or 2) run 
gdal_setInstallation(rescan=TRUE)

Question 1:

Would it be possible, to include the gdal Frameworks in the
search path?

These are the common locations it searches for, before
it attempts a brute-force search of your whole drive:

if (.Platform$OS=="unix") { common_locations <- c( #
UNIX systems "/usr/bin", "/usr/local/bin", # Mac #
Kyngchaos frameworks:
"/Library/Frameworks/GDAL.framework/Programs", # 
MacPorts: "/opt/local/bin" ) } if
(.Platform$OS=="windows") { common_locations <- c(
"C:\\Program Files", "C:\\Program Files (x86)",
"C:\\OSGeo4W" ) }

I use those frameworks, and the function worked for me,
but let me know if it failed to find yours (perhaps
I'll strip the /Programs from the search path?)  It is
easy for me to add new search locations, so if there
are other common locations for ANY OS just let me
know.

At the end is a layout of the directory structure of the
gdal frameworks.

Question 2:

Is it (or would it) be possible to manually set the
installation of gdal to be used? This would make comparison
of versions of gdal as well as reproducible research much
easier.

Yes, we can add in this functionality at a future
date. Right now, you can check to see what your
installs are by: gdal_setInstallation(rescan=TRUE) 
getOption("gdalUtils_gdalPath")

In general, gdalUtils will use the first element of
the getOption("gdalUtils_gdalPath"), which is chosen by
the most recent version (by date).

Question 3:

I can't test it right now, but I assume that gdalUtils does
search for a new gdal installation if it can't find the one
used before? Is there a way of initiating the search (and
selection) if a newer version has been installed?

Yep, as I said either restart R or run: 
gdal_setInstallation(rescan=TRUE)

Thanks for a very neat package,

Rainer

Directory structure of the GDAL.Framework on a MAC:

/Library/Frameworks/GDAL.framework/ ??? Headers -> 
Versions/Current/Headers ??? Programs ->
Versions/Current/Programs ??? Resources ->
Versions/Current/Resources ??? Versions ?   ??? 1.10 ?   ?
??? Headers ?   ?   ??? Libraries ?   ?   ?   ??? ogdi ?   ?
??? PlugIns ?   ?   ??? Programs ?   ?   ??? Python ? ?   ?
??? 2.6 ?   ?   ?   ?   ??? site-packages ?   ?   ?   ? ???
osgeo ?   ?   ?   ??? 2.7 ?   ?   ?       ??? site-packages
? ?   ?           ??? osgeo ?   ?   ??? Resources ?   ?   ?
??? doc ?   ?   ?   ?   ??? gdal ?   ?   ?   ?       ??? java
?   ?   ? ?       ?   ??? org ?   ?   ?   ?       ?   ?   ???
gdal ?   ?   ? ?       ?   ?       ??? gdal ?   ?   ?   ?
?   ?       ??? gdalconst ?   ?   ?   ?       ?   ?       ???
ogr ?   ?   ?   ? ?   ?       ??? osr ?   ?   ?   ?       ?
??? resources ?   ?   ? ?       ??? ogr ?   ?   ?   ??? gdal
?   ?   ??? unix ?   ? ??? bin ?   ?       ??? include ->
../Headers ?   ?       ??? lib ? ??? 1.9 ?   ?   ??? Headers
?   ?   ??? Libraries ?   ?   ?   ??? ogdi ?   ?   ???
PlugIns ?   ?   ??? Programs ?   ?   ??? Python ? ?   ?   ???
2.6 ?   ?   ?   ?   ??? site-packages ?   ?   ?   ? ??? osgeo
?   ?   ?   ??? 2.7 ?   ?   ?       ??? site-packages ? ?   ?
??? osgeo ?   ?   ??? Resources ?   ?   ?   ??? doc ?   ?   ?
?   ??? gdal ?   ?   ?   ?       ??? java ?   ?   ? ?       ?
??? org ?   ?   ?   ?       ?   ?   ??? gdal ?   ?   ? ?
?   ?       ??? gdal ?   ?   ?   ?       ?   ?       ??? 
gdalconst ?   ?   ?   ?       ?   ?       ??? ogr ?   ?   ?
? ?   ?       ??? osr ?   ?   ?   ?       ?   ??? resources ?
?   ? ?       ??? ogr ?   ?   ?   ??? gdal ?   ?   ??? unix ?
? ??? bin ?   ?       ??? include -> ../Headers ?   ?
??? lib ? ??? Current -> 1.10 ??? unix ->
Versions/Current/unix

Cheers!

--j

-- Jonathan A. Greenberg, PhD Assistant Professor Global 
Environmental Analysis and Remote Sensing (GEARS)
Laboratory Department of Geography and Geographic
Information Science University of Illinois at
Urbana-Champaign 259 Computing Applications Building,
MC-150 605 East Springfield Avenue Champaign, IL
61820-6371 Phone: 217-300-1924 
http://www.geog.illinois.edu/~jgrn/ AIM: jgrn307, MSN: 
jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007

-- http://www.keittlab.org/

Dear Jonathan,

First of all, congratulations on the package. It installed without a glitch
in all of my platforms: Mac, Windows and Linux.

However, I have a question on the speed of the wrapper functions.

In the past sometimes I caught myself using GDAL instead of R for some
routines when dealing with really large datasets (1GB+ shapefiles and 2GB+
rasters). Most of the routines were resampling and reprojection.

While R used to run for several hours, GDAL binaries finished the task in a
matter of seconds.

Unfortunately I don't have access to those previous large datasets to
perform some tests with the package, and this is why I ask you: do you think
that gdalUtils functions are as fast as the GDAL binaries?

Many thanks in advance. Congratulations once again for the very useful
package!

Greetings,
--
Thiago V. dos Santos
PhD student
Land and Atmospheric Science
University of Minnesota
http://www.laas.umn.edu/CurrentStudents/MeettheStudents/ThiagodosSantos/index.htm
Phone: (612) 323 9898


On Wednesday, January 8, 2014 4:43 PM, Jonathan Greenberg
<jgrn at illinois.edu> wrote:
I would like to announce a new R package "gdalUtils", now on CRAN.
gdalUtils is a set of R wrappers for most of the GDAL utility programs
(http://gdal.org/gdal_utilities.html).  gdalUtils is a collaboration
between Matteo Mattiuzzi and me.

gdalUtils requires an already-installed GDAL on your system:
http://trac.osgeo.org/gdal/wiki/DownloadingGdalBinaries

For Windows, I recommend installing QGIS Standalone
(http://www.qgis.org/en/site/forusers/download.html) which appears to
have the most up-to-date binaries of GDAL for the Windows operating
system including support for HDF4/5 files.

Note that this is NOT a replacement for Roger Bivand's fantastic rgdal
package, it is a complementary package that simply provides R-wrappers
for functions like gdalwarp, gdal_translate, ogr2ogr, etc.  We've
tried to make the interface more R-like in terms of input parameters,
and have provided some additional features such as (when relevant)
returning outputs in Robert Hijman's raster format.  The parameter
naming and the documentation follows GDAL, with permission from Frank
Warmerdam (lead GDAL developer).

We have also provided some value-added functions such as
batch_gdal_translate and get_subdatasets (for extracting subdataset
names from HDF4/5 and NetCDF files).

I will note the primary motivation for developing this package was
initially to provide (finally) HDF4/5 file support to Windows users
(for Landsat and MODIS processing, among other things).  However, many
of the GDAL functions provide additional capabilities that R functions
do not currently have, and they are quite a bit faster than most of
their R equivalents (compare projectRaster_rigorous in my
spatial.tools package to gdalwarp(...,method="mode") for an example).

When you first fire it up, it may take a bit to search for a valid
GDAL install on your computer.  If you have more than one (Windows
users may find this), it will use the latest version.  We tried to
make this system-agnostic, but let us know if you have any problems
getting the functions to work.  The best way to test is:
library(gdalUtils)
gdalinfo(version=TRUE)
gdalinfo(formats=TRUE)

Cheers!

--j

--
Jonathan A. Greenberg, PhD
Assistant Professor
Global Environmental Analysis and Remote Sensing (GEARS) Laboratory
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
259 Computing Applications Building, MC-150
605 East Springfield Avenue
Champaign, IL  61820-6371
Phone: 217-300-1924
http://www.geog.illinois.edu/~jgrn/
AIM: jgrn307, MSN: jgrn307 at hotmail.com, Gchat: jgrn307, Skype: jgrn3007