Object-Based Classification

[RODRIGO NUNES]

Hi colleagues, I have an issue when running the classification script from the RSGISLib_IntroTraining_Jan2017 course:

When I try to run the '16_PerformObjClass.py' script it gives an error:

> (py35) RNSOUSA@RODRIGO_NUNES:/mnt/c/RSGISLIB$ python 16_PerformObjClass.py

Traceback (most recent call last):

  File "16_PerformObjClass_LANDSAT.py", line 4, in <module>

    from rsgislib import rastergis

  File "/home/RNSOUSA/.conda/envs/py35/lib/python3.5/site-packages/rsgislib/rastergis/__init__.py", line 6, in <module>

    from ._rastergis import *

ImportError: libboost_filesystem.so.1.65.1: cannot open shared object file: No such file or directory

I am running the Miniconda 4.3.31, Python 3.5.4 and rsgislib 3.4.9 on Linux bash on Windows10.

Then I used the command: 

>  conda update -c conda-forge --all

And runned again, it gives:

(py35) RNSOUSA@RODRIGO_NUNES:/mnt/c/RSGISLIB$ python 16_PerformObjClass_LANDSAT.py

Traceback (most recent call last):

  File "16_PerformObjClass_LANDSAT.py", line 4, in <module>

    from rsgislib import rastergis

  File "/home/RNSOUSA/.conda/envs/py35/lib/python3.5/site-packages/rsgislib/rastergis/__init__.py", line 6, in <module>

    from ._rastergis import *

ImportError: /home/RNSOUSA/.conda/envs/py35/lib/python3.5/site-packages/rsgislib/rastergis/../../../.././libgdal.so.20: undefined symbol: _ZN6kmldom5ParseERKSsPSs

And after,

> conda update --all

After

> conda update --all

(osgeo) RNSOUSA@RODRIGO_NUNES:/mnt/c/RSGISLIB$ python 16_PerformObjClass.py

Traceback (most recent call last):

  File "16_PerformObjClass.py", line 3, in <module>

    from rsgislib import rastergis

  File "/home/RNSOUSA/.conda/envs/osgeo/lib/python3.6/site-packages/rsgislib/rastergis/__init__.py", line 6, in <module>

    from ._rastergis import *

ImportError: libboost_filesystem.so.1.65.1: cannot open shared object file: No such file or directory

Thanks

[Daniel Clewley]

Hi Rodrigo,

I’m not sure why this isn’t working. Could you try installing from scratch in a new environment and see if you have any luck with this?

conda create -n rsgislib-new -c conda-forge rsgislib

Thanks,

Dan

On 22 Jan 2018, at 15:01, RODRIGO NUNES <rodrigon...@gmail.com> wrote:

Hi colleagues, I have an issue when running the classification script from the RSGISLib_IntroTraining_Jan2017 course:

When I try to run the '16_PerformObjClass.py' script it gives an error:

> (py35) RNSOUSA@RODRIGO_NUNES:/mnt/c/RSGISLIB$ python 16_PerformObjClass.py

Traceback (most recent call last):

  File "16_PerformObjClass_LANDSAT.py", line 4, in <module>

    from rsgislib import rastergis

  File "/home/RNSOUSA/.conda/envs/py35/lib/python3.5/site-packages/rsgislib/rastergis/__init__.py", line 6, in <module>

    from ._rastergis import *

ImportError: libboost_filesystem.so.1.65.1: cannot open shared object file: No such file or directory

I am running the Miniconda 4.3.31, Python 3.5.4 and rsgislib 3.4.9 on Linux bash on Windows10.

I already used the command: 

>  conda update --all

Thanks

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[Daniel Clewley]

Have you also tried:

conda update --all

in the new environment?

Can you please make sure you keep rsgislib...@googlegroups.com cc’d when replying.

Thanks,

Dan

On 22 Jan 2018, at 21:42, RODRIGO NUNES <rodrigon...@gmail.com> wrote:

Hi Dan,

Still not working..

After running:

> conda create -n osgeo -c conda-forge rsgislib

> source activate osgeo

It gives..

> (osgeo) RNSOUSA@RODRIGO_NUNES:/mnt/c/RSGISLIB$ python 16_PerformObjClass_LANDSAT.py

Traceback (most recent call last):

  File "16_PerformObjClass_LANDSAT.py", line 4, in <module>

    from rsgislib import rastergis

  File "/home/RNSOUSA/.conda/envs/osgeo/lib/python3.6/site-packages/rsgislib/rastergis/__init__.py", line 6, in <module>

    from ._rastergis import *

ImportError: libopenblas.so.0: cannot open shared object file: No such file or directory

Rodrigo Nunes de Sousa

Biologist, Ph.D. candidate in Ecology and Biodiversity at UNESP - RC

E-mail: RODRIGON...@GMAIL.COM

Skype: rnsousa

2018-01-22 19:17 GMT-02:00 RODRIGO NUNES <rodrigon...@gmail.com>:

Thanks Dan.. I'll try it and call you back..

Rodrigo Nunes de Sousa

Biologist, Ph.D. candidate in Ecology and Biodiversity at UNESP - RC

E-mail: RODRIGON...@GMAIL.COM

Skype: rnsousa

2018-01-22 19:11 GMT-02:00 Daniel Clewley <daniel....@gmail.com>:

Hi Rodrigo,

I’m not sure why this isn’t working. Could you try installing from scratch in a new environment and see if you have any luck with this?

conda create -n rsgislib-new -c conda-forge rsgislib

Thanks,

Dan

On 22 Jan 2018, at 15:01, RODRIGO NUNES <rodrigon...@gmail.com> wrote:

Hi colleagues, I have an issue when running the classification script from the RSGISLib_IntroTraining_Jan2017 course:

When I try to run the '16_PerformObjClass.py' script it gives an error:

> (py35) RNSOUSA@RODRIGO_NUNES:/mnt/c/RSGISLIB$ python 16_PerformObjClass.py

Traceback (most recent call last):

  File "16_PerformObjClass_LANDSAT.py", line 4, in <module>

    from rsgislib import rastergis

  File "/home/RNSOUSA/.conda/envs/py35/lib/python3.5/site-packages/rsgislib/rastergis/__init__.py", line 6, in <module>

    from ._rastergis import *

ImportError: libboost_filesystem.so.1.65.1: cannot open shared object file: No such file or directory

I am running the Miniconda 4.3.31, Python 3.5.4 and rsgislib 3.4.9 on Linux bash on Windows10.

I already used the command: 

>  conda update --all

Thanks

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[RODRIGO NUNES]

HI Dan,

How can I install the older version of rsgislib?

I tried downloading the rsgislib-2.0.0.tar.gz from bitbucket, from: https://bitbucket.org/petebunting/rsgislib/downloads/ ...

Extract the file and "cd" to the "\rsgislib-2.0.0\python" directory

And tried to install using the command > python ./setup.py install

Them received ERRORS:

(osgeo) RNSOUSA@THOROS:/mnt/c/iMAGENS/Janauaca/GRD_IW/rsgislib-2.0.0/python$ python ./setup.py install

running install

running build

running config_cc

unifing config_cc, config, build_clib, build_ext, build commands --compiler options

running config_fc

unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options

running build_src

build_src

building extension "imagecalc._imagecalc" sources

building extension "imageutils._imageutils" sources

building extension "segmentation._segmentation" sources

building extension "imagecalibration._imagecalibration" sources

building extension "rastergis._rastergis" sources

build_src: building npy-pkg config files

running build_py

running build_ext

customize UnixCCompiler

customize UnixCCompiler using build_ext

customize UnixCCompiler

customize UnixCCompiler using build_ext

building 'imagecalc._imagecalc' extension

compiling C++ sources

C compiler: g++ -pthread -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC

compile options: '-I../src/cmds -I../src -I/home/RNSOUSA/miniconda3/envs/osgeo/lib/python3.6/site-packages/numpy/core/include -I/home/RNSOUSA/miniconda3/envs/osgeo/include/python3.6m -c'

g++: src/imagecalc.cpp

sh: 1: g++: not found

sh: 1: g++: not found

error: Command "g++ -pthread -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I../src/cmds -I../src -I/home/RNSOUSA/miniconda3/envs/osgeo/lib/python3.6/site-packages/numpy/core/include -I/home/RNSOUSA/miniconda3/envs/osgeo/include/python3.6m -c src/imagecalc.cpp -o build/temp.linux-x86_64-3.6/src/imagecalc.o" failed with exit status 127

[Daniel Clewley]

Hi Rodrigo,

You need to build the C++ library first (in the main directory) using cmake. If you are building against the packages in conda you will need to make sure cmake finds them.

However, it looks like the error you are getting is because you don’t have a c++ compiler installed.

I don’t know if you saw my message yesterday to the list which relates to your previous problem:

I think the conda-forge builds of RSGISLib need to be updated for a different version of boost, there is a pull request open for it:

https://github.com/conda-forge/rsgislib-feedstock/pull/9

Should be fixed in the next couple of days - will post when it is for you to test. 

Thanks,

Dan

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[RODRIGO NUNES]

Thanks Dan,

T'll wait for the new build at conda-forge..

[RODRIGO NUNES]

HI Dan and Chewley, I installed and updated the new rsgislib build at conda-forge.

Although when I run the Object-Based Classification script ('16_PerformObjClass.py') it goes right until..

"....

Running Rasterise now...

Traceback (most recent call last):

  File "16_PerformObjClass.py", line 51, in <module>

    ratutils.populateClumpsWithClassTraining(clumpsImg, classesDict, tmpPath, classesIntColIn, classesNameCol)

  File "/home/RNSOUSA/.conda/envs/rsgislib-new/lib/python3.6/site-packages/rsgislib/rastergis/ratutils.py", line 1168, in populateClumpsWithClassTraining

    vectorutils.rasterise2Image(classShpFile, clumpsImg, classImgFile, gdalformat="KEA", burnVal=classIntVal)

  File "/home/RNSOUSA/.conda/envs/rsgislib-new/lib/python3.6/site-packages/rsgislib/vectorutils/__init__.py", line 96, in rasterise2Image

    raise e

  File "/home/RNSOUSA/.conda/envs/rsgislib-new/lib/python3.6/site-packages/rsgislib/vectorutils/__init__.py", line 73, in rasterise2Image

    inVectorLayer = inVectorDS.GetLayer(0)

AttributeError: 'NoneType' object has no attribute 'GetLayer' "

How to solve  this?