SAGA modules (version 2.1.0) through SEXTANTE on Mac OSX

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SAGA modules (version 2.1.0) through SEXTANTE on Mac OSX

opeeters
Hi all,
I managed to successfully get SAGA installed from source on Mac OSX 10.6.8

Since the instructions on the SAGA wiki
(http://sourceforge.net/apps/trac/saga-gis/wiki/Compiling%20SAGA%20on%20Mac%20OS%20X)
did not seem to work well in my case, here is what I did:

on a system (in my case OSX 10.6.8) with Xcode 4.2, install:
- PROJ 4.7 (eg from here: http://www.kyngchaos.com/software/archive - if
you had PROJ 4.8 installed together with Qgis before, you will need to
reinstall PROJ 4.8 again after finishing the SAGA install, otherwise
Qgis will not open anymore)
- GDAL 1.8 (http://www.kyngchaos.com/software/archive)
- JasPer 1.900.1 ( http://www.ece.uvic.ca/~frodo/jasper/)
- wxWidgets post-2.9.3 (not needed if SAGA is installed without gui, I
guess, but I haven't tried)
- at least svn 1.7.x

$ svn checkout svn://svn.code.sf.net/p/saga-gis/code-0/trunk/saga-gis/
saga-gis
...
Checked out revision 1574.

$ cd ./saga-gis/
$ autoreconf -i

eg:
$ nano my-saga-config.sh

with this in it:
FEATURES="--enable-unicode --enable-debug --disable-gui"
CXX="/Developer/usr/bin/clang"
DEFINES="-D_FILE_OFFSET_BITS=64 -DWXUSINGDLL -D__WXMAC__ -D__WXOSX__
-D__WXOSX_COCOA__"
GDAL_H="-I/Library/Frameworks/GDAL.framework/Headers"
PROJ_H="-I/Library/Frameworks/PROJ.framework/Headers"
LIB_SRCH="-L/Library/Frameworks/PROJ.framework/unix/lib"
LINK_MISC="-arch x86_64 -mmacosx-version-min=10.6 -isysroot
/Developer/SDKs/MacOSX10.6.sdk -lstdc++"
./configure $FEATURES CXX="$CXX" CPPFLAGS="$DEFINES $GDAL_H $PROJ_H"
LDFLAGS="$LIB_SRCH $LINK_MISC"

$ chmod +x my-saga-config.sh
$ ./my-saga-config.sh

$ make

$ sudo make install

$ saga_cmd

_____________________________________________
   #####   ##   #####    ##
  ###     ###  ##       ###
   ###   # ## ##  #### # ##
    ### ##### ##    # #####
##### #   ##  ##### #   ##
_____________________________________________


...
...

Using saga_cmd from the command line on Mac OSX works!


Now the SEXTANTE in Qgis problem..

There is no option "SAGA folder" in the SEXTANTE configuration like you
have when installing on Windows. I haven't checked on Linux, but I guess
the Unixes don't need this, as long as saga_cmd is in the path, right?

Opening a SAGA module I get:
It seems that SAGA is not correctly installed in your system. Please
install it before running SAGA algorithms.

Is SAGA in SEXTANTE 1.0.8 maybe not yet compatible with the changes in
SAGA 2.1.0 ?

Regards,
Olav



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Re: SAGA modules (version 2.1.0) through SEXTANTE on Mac OSX

volaya
Olav,

Thanks for your contribution!

>
> There is no option "SAGA folder" in the SEXTANTE configuration like you have
> when installing on Windows. I haven't checked on Linux, but I guess the
> Unixes don't need this, as long as saga_cmd is in the path, right?

Right, Mac and Linux should work in the same way. Let me check,
because maybe in Mac it is performing the same check as in windows
(that is, checking that the SAGA folder is set...)

Looks like an easy to solve problem...i hope

Will keep you posted

Thanks again!


Victor
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Re: SAGA modules (version 2.1.0) through SEXTANTE on Mac OSX

John C. Tull-2
On Dec 19, 2012, at 2:49 AM, Victor Olaya <[hidden email]> wrote:

> Olav,
>
> Thanks for your contribution!
>
>>
>> There is no option "SAGA folder" in the SEXTANTE configuration like you have
>> when installing on Windows. I haven't checked on Linux, but I guess the
>> Unixes don't need this, as long as saga_cmd is in the path, right?
>
> Right, Mac and Linux should work in the same way. Let me check,
> because maybe in Mac it is performing the same check as in windows
> (that is, checking that the SAGA folder is set...)
>
> Looks like an easy to solve problem...i hope
>
> Will keep you posted
>
> Thanks again!
>
>
> Victor

It looks like I'm a little late to the party on this. I confirm the same. I look forward to a solution on this for OS X. We can work on grass, perhaps, once that is resolved.

Regards,
John

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Re: SAGA modules (version 2.1.0) through SEXTANTE on Mac OSX

volaya
There is actually the following check in the case of mac and linux:

            command = ["saga_cmd"]
            proc = subprocess.Popen(command, shell=True,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,stderr=subprocess.STDOUT,
universal_newlines=True).stdout
            for line in iter(proc.readline, ""):
                if "________" in line:
                    settings.setValue(SAGA_INSTALLED, True)
                    return
            return "It seems that SAGA is not correctly installed in
your system.\nPlease install it before running SAGA algorithms."

basically, it is a naive check to see if executing saga_cmd in a
console returns something that looks like the SAGA CMD header. It
works fin in linux, but it seems it is not working in Mac. Are you
sure saga is in your path? if so, what do you see when you execute
saga_cmd? maybe the header is different for some reason?

Thanks in advance!

2012/12/20 John C. Tull <[hidden email]>:

> On Dec 19, 2012, at 2:49 AM, Victor Olaya <[hidden email]> wrote:
>
>> Olav,
>>
>> Thanks for your contribution!
>>
>>>
>>> There is no option "SAGA folder" in the SEXTANTE configuration like you have
>>> when installing on Windows. I haven't checked on Linux, but I guess the
>>> Unixes don't need this, as long as saga_cmd is in the path, right?
>>
>> Right, Mac and Linux should work in the same way. Let me check,
>> because maybe in Mac it is performing the same check as in windows
>> (that is, checking that the SAGA folder is set...)
>>
>> Looks like an easy to solve problem...i hope
>>
>> Will keep you posted
>>
>> Thanks again!
>>
>>
>> Victor
>
> It looks like I'm a little late to the party on this. I confirm the same. I look forward to a solution on this for OS X. We can work on grass, perhaps, once that is resolved.
>
> Regards,
> John
>
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Re: SAGA modules (version 2.1.0) through SEXTANTE on Mac OSX

John C. Tull-2
Hi Victor,

Below are the outputs from my terminal. The error:library is a non-issue according to comments on the dev forum for saga.

Regards,
John


> which saga_cmd
> /usr/local/bin/saga_cmd
> saga_cmd
_____________________________________________
  #####   ##   #####    ##
 ###     ###  ##       ###
  ###   # ## ##  #### # ##
   ### ##### ##    # #####
##### #   ##  ##### #   ##
_____________________________________________


error: library

library search path: /usr/local/lib/saga

58 available module libraries:
- climate_tools
- contrib_a_perego
- docs_html
- docs_pdf
- geostatistics_grid
- geostatistics_points
- geostatistics_regression
- grid_analysis
- grid_calculus
- grid_calculus_bsl
- grid_filter
- grid_gridding
- grid_spline
- grid_tools
- grid_visualisation
- ihacres
- imagery_classification
- imagery_rga
- imagery_segmentation
- imagery_svm
- imagery_tools
- io_esri_e00
- io_gdal
- io_gps
- io_grid
- io_grid_grib2
- io_grid_image
- io_odbc
- io_shapes
- io_shapes_dxf
- io_table
- lectures_introduction
- pj_georeference
- pj_proj4
- pointcloud_tools
- recreations_fractals
- recreations_games
- shapes_grid
- shapes_lines
- shapes_points
- shapes_polygons
- shapes_tools
- sim_cellular_automata
- sim_ecosystems_hugget
- sim_erosion
- sim_fire_spreading
- sim_hydrology
- ta_channels
- ta_compound
- ta_hydrology
- ta_lighting
- ta_morphometry
- ta_preprocessor
- ta_profiles
- table_calculus
- table_tools
- tin_tools
- transect

type -h or --help for further information

On Dec 20, 2012, at 2:09 PM, Victor Olaya <[hidden email]> wrote:

> There is actually the following check in the case of mac and linux:
>
>            command = ["saga_cmd"]
>            proc = subprocess.Popen(command, shell=True,
> stdout=subprocess.PIPE,
> stdin=subprocess.PIPE,stderr=subprocess.STDOUT,
> universal_newlines=True).stdout
>            for line in iter(proc.readline, ""):
>                if "________" in line:
>                    settings.setValue(SAGA_INSTALLED, True)
>                    return
>            return "It seems that SAGA is not correctly installed in
> your system.\nPlease install it before running SAGA algorithms."
>
> basically, it is a naive check to see if executing saga_cmd in a
> console returns something that looks like the SAGA CMD header. It
> works fin in linux, but it seems it is not working in Mac. Are you
> sure saga is in your path? if so, what do you see when you execute
> saga_cmd? maybe the header is different for some reason?
>
> Thanks in advance!
>
> 2012/12/20 John C. Tull <[hidden email]>:
>> On Dec 19, 2012, at 2:49 AM, Victor Olaya <[hidden email]> wrote:
>>
>>> Olav,
>>>
>>> Thanks for your contribution!
>>>
>>>>
>>>> There is no option "SAGA folder" in the SEXTANTE configuration like you have
>>>> when installing on Windows. I haven't checked on Linux, but I guess the
>>>> Unixes don't need this, as long as saga_cmd is in the path, right?
>>>
>>> Right, Mac and Linux should work in the same way. Let me check,
>>> because maybe in Mac it is performing the same check as in windows
>>> (that is, checking that the SAGA folder is set...)
>>>
>>> Looks like an easy to solve problem...i hope
>>>
>>> Will keep you posted
>>>
>>> Thanks again!
>>>
>>>
>>> Victor
>>
>> It looks like I'm a little late to the party on this. I confirm the same. I look forward to a solution on this for OS X. We can work on grass, perhaps, once that is resolved.
>>
>> Regards,
>> John
>>

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Re: SAGA modules (version 2.1.0) through SEXTANTE on Mac OSX

opeeters
I have the same output as John
Olav

On 21/12/12 00:16, John C. Tull wrote:

> Hi Victor,
>
> Below are the outputs from my terminal. The error:library is a non-issue according to comments on the dev forum for saga.
>
> Regards,
> John
>
>
>> which saga_cmd
>> /usr/local/bin/saga_cmd
>> saga_cmd
> _____________________________________________
>    #####   ##   #####    ##
>   ###     ###  ##       ###
>    ###   # ## ##  #### # ##
>     ### ##### ##    # #####
> ##### #   ##  ##### #   ##
> _____________________________________________
>
>
> error: library
>
> library search path: /usr/local/lib/saga
>
> 58 available module libraries:
> - climate_tools
> - contrib_a_perego
> - docs_html
> - docs_pdf
> - geostatistics_grid
> - geostatistics_points
> - geostatistics_regression
> - grid_analysis
> - grid_calculus
> - grid_calculus_bsl
> - grid_filter
> - grid_gridding
> - grid_spline
> - grid_tools
> - grid_visualisation
> - ihacres
> - imagery_classification
> - imagery_rga
> - imagery_segmentation
> - imagery_svm
> - imagery_tools
> - io_esri_e00
> - io_gdal
> - io_gps
> - io_grid
> - io_grid_grib2
> - io_grid_image
> - io_odbc
> - io_shapes
> - io_shapes_dxf
> - io_table
> - lectures_introduction
> - pj_georeference
> - pj_proj4
> - pointcloud_tools
> - recreations_fractals
> - recreations_games
> - shapes_grid
> - shapes_lines
> - shapes_points
> - shapes_polygons
> - shapes_tools
> - sim_cellular_automata
> - sim_ecosystems_hugget
> - sim_erosion
> - sim_fire_spreading
> - sim_hydrology
> - ta_channels
> - ta_compound
> - ta_hydrology
> - ta_lighting
> - ta_morphometry
> - ta_preprocessor
> - ta_profiles
> - table_calculus
> - table_tools
> - tin_tools
> - transect
>
> type -h or --help for further information
>
> On Dec 20, 2012, at 2:09 PM, Victor Olaya <[hidden email]> wrote:
>
>> There is actually the following check in the case of mac and linux:
>>
>>             command = ["saga_cmd"]
>>             proc = subprocess.Popen(command, shell=True,
>> stdout=subprocess.PIPE,
>> stdin=subprocess.PIPE,stderr=subprocess.STDOUT,
>> universal_newlines=True).stdout
>>             for line in iter(proc.readline, ""):
>>                 if "________" in line:
>>                     settings.setValue(SAGA_INSTALLED, True)
>>                     return
>>             return "It seems that SAGA is not correctly installed in
>> your system.\nPlease install it before running SAGA algorithms."
>>
>> basically, it is a naive check to see if executing saga_cmd in a
>> console returns something that looks like the SAGA CMD header. It
>> works fin in linux, but it seems it is not working in Mac. Are you
>> sure saga is in your path? if so, what do you see when you execute
>> saga_cmd? maybe the header is different for some reason?
>>
>> Thanks in advance!
>>
>> 2012/12/20 John C. Tull <[hidden email]>:
>>> On Dec 19, 2012, at 2:49 AM, Victor Olaya <[hidden email]> wrote:
>>>
>>>> Olav,
>>>>
>>>> Thanks for your contribution!
>>>>
>>>>> There is no option "SAGA folder" in the SEXTANTE configuration like you have
>>>>> when installing on Windows. I haven't checked on Linux, but I guess the
>>>>> Unixes don't need this, as long as saga_cmd is in the path, right?
>>>> Right, Mac and Linux should work in the same way. Let me check,
>>>> because maybe in Mac it is performing the same check as in windows
>>>> (that is, checking that the SAGA folder is set...)
>>>>
>>>> Looks like an easy to solve problem...i hope
>>>>
>>>> Will keep you posted
>>>>
>>>> Thanks again!
>>>>
>>>>
>>>> Victor
>>> It looks like I'm a little late to the party on this. I confirm the same. I look forward to a solution on this for OS X. We can work on grass, perhaps, once that is resolved.
>>>
>>> Regards,
>>> John
>>>

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Re: SAGA modules (version 2.1.0) through SEXTANTE on Mac OSX

opeeters
In reply to this post by volaya
A quick and dirty circumvention of the check is to change line 373 in
~/.qgis/python/plugins/sextante/saga/SagaAlgorithm.py
to:
if "" in line:
(restart Qgis)

this way the modules do open since the check is basically disabled.
The original code should also though. Maybe it's encoding related.
When I execute a Saga module, this happens during saving the output:

An error has occured while executing Python code:

Traceback (most recent call last):
   File
"/Users/myaccount/.qgis//python/plugins/sextante/gui/OutputSelectionPanel.py",
line 95, in saveToFile
     self.text.setText(str(filename))
UnicodeEncodeError: 'ascii' codec can't encode character u'\xff' in
position 2: ordinal not in range(128)

Should I have compiled with a different locale set?

We are nearly there :-)

Olav


On 20/12/12 23:09, Victor Olaya wrote:

> There is actually the following check in the case of mac and linux:
>
>              command = ["saga_cmd"]
>              proc = subprocess.Popen(command, shell=True,
> stdout=subprocess.PIPE,
> stdin=subprocess.PIPE,stderr=subprocess.STDOUT,
> universal_newlines=True).stdout
>              for line in iter(proc.readline, ""):
>                  if "________" in line:
>                      settings.setValue(SAGA_INSTALLED, True)
>                      return
>              return "It seems that SAGA is not correctly installed in
> your system.\nPlease install it before running SAGA algorithms."
>
> basically, it is a naive check to see if executing saga_cmd in a
> console returns something that looks like the SAGA CMD header. It
> works fin in linux, but it seems it is not working in Mac. Are you
> sure saga is in your path? if so, what do you see when you execute
> saga_cmd? maybe the header is different for some reason?
>
> Thanks in advance!
>
> 2012/12/20 John C. Tull <[hidden email]>:
>> On Dec 19, 2012, at 2:49 AM, Victor Olaya <[hidden email]> wrote:
>>
>>> Olav,
>>>
>>> Thanks for your contribution!
>>>
>>>> There is no option "SAGA folder" in the SEXTANTE configuration like you have
>>>> when installing on Windows. I haven't checked on Linux, but I guess the
>>>> Unixes don't need this, as long as saga_cmd is in the path, right?
>>> Right, Mac and Linux should work in the same way. Let me check,
>>> because maybe in Mac it is performing the same check as in windows
>>> (that is, checking that the SAGA folder is set...)
>>>
>>> Looks like an easy to solve problem...i hope
>>>
>>> Will keep you posted
>>>
>>> Thanks again!
>>>
>>>
>>> Victor
>> It looks like I'm a little late to the party on this. I confirm the same. I look forward to a solution on this for OS X. We can work on grass, perhaps, once that is resolved.
>>
>> Regards,
>> John
>>

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Re: SAGA modules (version 2.1.0) through SEXTANTE on Mac OSX

Salvatore Larosa-2
Hi Olav,

2012/12/21 Olav Peeters <[hidden email]>
A quick and dirty circumvention of the check is to change line 373 in ~/.qgis/python/plugins/sextante/saga/SagaAlgorithm.py
to:
if "" in line:
(restart Qgis)

this way the modules do open since the check is basically disabled.
The original code should also though. Maybe it's encoding related.
When I execute a Saga module, this happens during saving the output:

An error has occured while executing Python code:

Traceback (most recent call last):
  File "/Users/myaccount/.qgis//python/plugins/sextante/gui/OutputSelectionPanel.py", line 95, in saveToFile
    self.text.setText(str(filename))
UnicodeEncodeError: 'ascii' codec can't encode character u'\xff' in position 2: ordinal not in range(128)


are you using the latest sextante version ? From your traceback it seem not.
line 95 [1] has been changed !

Unfortunately, that's an annoying error that affects several tools (much less now) in sextante when non-ascii chars are used !


Regards,

-SL

[1] - https://github.com/qgis/Quantum-GIS/blob/master/python/plugins/sextante/gui/OutputSelectionPanel.py#L95

 
Should I have compiled with a different locale set?

We are nearly there :-)

Olav



On 20/12/12 23:09, Victor Olaya wrote:
There is actually the following check in the case of mac and linux:

             command = ["saga_cmd"]
             proc = subprocess.Popen(command, shell=True,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,stderr=subprocess.STDOUT,
universal_newlines=True).stdout
             for line in iter(proc.readline, ""):
                 if "________" in line:
                     settings.setValue(SAGA_INSTALLED, True)
                     return
             return "It seems that SAGA is not correctly installed in
your system.\nPlease install it before running SAGA algorithms."

basically, it is a naive check to see if executing saga_cmd in a
console returns something that looks like the SAGA CMD header. It
works fin in linux, but it seems it is not working in Mac. Are you
sure saga is in your path? if so, what do you see when you execute
saga_cmd? maybe the header is different for some reason?

Thanks in advance!

2012/12/20 John C. Tull <[hidden email]>:
On Dec 19, 2012, at 2:49 AM, Victor Olaya <[hidden email]> wrote:

Olav,

Thanks for your contribution!

There is no option "SAGA folder" in the SEXTANTE configuration like you have
when installing on Windows. I haven't checked on Linux, but I guess the
Unixes don't need this, as long as saga_cmd is in the path, right?
Right, Mac and Linux should work in the same way. Let me check,
because maybe in Mac it is performing the same check as in windows
(that is, checking that the SAGA folder is set...)

Looks like an easy to solve problem...i hope

Will keep you posted

Thanks again!


Victor
It looks like I'm a little late to the party on this. I confirm the same. I look forward to a solution on this for OS X. We can work on grass, perhaps, once that is resolved.

Regards,
John


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--
Salvatore Larosa
linkedIn: http://linkedin.com/in/larosasalvatore
twitter: @lrssvt
skype: s.larosa
IRC: lrssvt on freenode

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Re: SAGA modules (version 2.1.0) through SEXTANTE on Mac OSX

opeeters
Hi Salvatore,
I'm on version 1.0.8 installed through the Python Plugin Installer.
I guess these latest changes on github have not yet made into the packaged version...
I will try again with sextante from source... tomorrow ;-)
Olav


      On 22/12/12 00:16, Salvatore Larosa wrote:
Hi Olav,

2012/12/21 Olav Peeters <[hidden email]>
A quick and dirty circumvention of the check is to change line 373 in ~/.qgis/python/plugins/sextante/saga/SagaAlgorithm.py
to:
if "" in line:
(restart Qgis)

this way the modules do open since the check is basically disabled.
The original code should also though. Maybe it's encoding related.
When I execute a Saga module, this happens during saving the output:

An error has occured while executing Python code:

Traceback (most recent call last):
  File "/Users/myaccount/.qgis//python/plugins/sextante/gui/OutputSelectionPanel.py", line 95, in saveToFile
    self.text.setText(str(filename))
UnicodeEncodeError: 'ascii' codec can't encode character u'\xff' in position 2: ordinal not in range(128)


are you using the latest sextante version ? From your traceback it seem not.
line 95 [1] has been changed !

Unfortunately, that's an annoying error that affects several tools (much less now) in sextante when non-ascii chars are used !


Regards,

-SL

[1] - https://github.com/qgis/Quantum-GIS/blob/master/python/plugins/sextante/gui/OutputSelectionPanel.py#L95

 
Should I have compiled with a different locale set?

We are nearly there :-)

Olav



On 20/12/12 23:09, Victor Olaya wrote:
There is actually the following check in the case of mac and linux:

             command = ["saga_cmd"]
             proc = subprocess.Popen(command, shell=True,
stdout=subprocess.PIPE,
stdin=subprocess.PIPE,stderr=subprocess.STDOUT,
universal_newlines=True).stdout
             for line in iter(proc.readline, ""):
                 if "________" in line:
                     settings.setValue(SAGA_INSTALLED, True)
                     return
             return "It seems that SAGA is not correctly installed in
your system.\nPlease install it before running SAGA algorithms."

basically, it is a naive check to see if executing saga_cmd in a
console returns something that looks like the SAGA CMD header. It
works fin in linux, but it seems it is not working in Mac. Are you
sure saga is in your path? if so, what do you see when you execute
saga_cmd? maybe the header is different for some reason?

Thanks in advance!

2012/12/20 John C. Tull <[hidden email]>:
On Dec 19, 2012, at 2:49 AM, Victor Olaya <[hidden email]> wrote:

Olav,

Thanks for your contribution!

There is no option "SAGA folder" in the SEXTANTE configuration like you have
when installing on Windows. I haven't checked on Linux, but I guess the
Unixes don't need this, as long as saga_cmd is in the path, right?
Right, Mac and Linux should work in the same way. Let me check,
because maybe in Mac it is performing the same check as in windows
(that is, checking that the SAGA folder is set...)

Looks like an easy to solve problem...i hope

Will keep you posted

Thanks again!


Victor
It looks like I'm a little late to the party on this. I confirm the same. I look forward to a solution on this for OS X. We can work on grass, perhaps, once that is resolved.

Regards,
John


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Salvatore Larosa
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