[ITK-users] SimpleITK Anaconda Issue

Sat Aug 29 11:12:35 EDT 2015

Hello,

That is great you got SimpleITK up and running by following those updated instructions for Anaconda.

Could you describe what you are trying to do and have a snippet of code?

Brad

On Aug 28, 2015, at 6:52 PM, Tassilo Klein <tjklein at gmail.com> wrote:

> Thanks Ziv,
> 
> I forgot to activate the environment before.
> 
> After following the steps, now I get a different error when trying to load an image, which worked some time before:
> 
> /home/tjklein/anaconda/envs/sitkpy3/lib/python2.7/site-packages/SimpleITK/SimpleITK.py in ReadImage(*args)
>    7726 
>    7727     """
> -> 7728     return _SimpleITK.ReadImage(*args)
>    7729 class HashImageFilter(ProcessObject):
>    7730     """
> 
> RuntimeError: Exception thrown in SimpleITK ReadImage: /home/blowekamp/anaconda/conda-bld/work/Code/IO/src/sitkImageSeriesReader.cxx:143:
> sitk::ERROR: The file in the series have unsupported 3 dimensions.
> 
> 
> On Thu, Aug 27, 2015 at 5:10 PM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <zivrafael.yaniv at nih.gov> wrote:
> Hi Tassilo,
> 
> Did you downgrade to libpng1.5 after creating the virtual environment? This is what I suggested in the thread you cited and was the solution at the time.  It no longer works because anaconda upgraded additional packages.
> 
> When you create the virtual environment with libpng set to 1.5 (conda create -n sitkpy anaconda libpng=1.5) all of the dependent packages are downgraded to work with this version of libpng and then you will not have this issue. The three steps are given in the FAQ that I pointed you to - I am assuming here you did not follow that solution, it is pasted below for your convenience:
> 
> conda create -n sitkpy anaconda libpng=1.5 
> conda install -c https://conda.binstar.org/simpleitk/channel/main SimpleITK 
> conda install libpng=1.5 
> 
> If you followed this set of instructions and it doesn't work, let us know and we will try to recreate the problem and find a solution.
> 
>           regards
>               Ziv
> 
> From: Tassilo Klein [tjklein at gmail.com]
> Sent: Thursday, August 27, 2015 4:56 PM
> To: Yaniv, Ziv Rafael (NIH/NLM/LHC) [C]
> Cc: insight-users at itk.org
> Subject: Re: [ITK-users] SimpleITK Anaconda Issue
> 
> Hi Ziv,
> 
> thanks. yes, that's what I did but then I get these  errors:
> 
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/font_manager.py in <module>()
>      56 import matplotlib
>      57 from matplotlib import afm
> ---> 58 from matplotlib import ft2font
>      59 from matplotlib import rcParams, get_cachedir
>      60 from matplotlib.cbook import is_string_like
> 
> ImportError: libpng16.so.16: cannot open shared object file: No such file or directory
> 
> On Thu, Aug 27, 2015 at 3:55 PM, Yaniv, Ziv Rafael (NIH/NLM/LHC) [C] <zivrafael.yaniv at nih.gov> wrote:
> Hello Tassilo,
> 
> Please follow the instructions found in our FAQ 'I am using the binary distribution of SimpleITK for Anaconda, why do I get an error about libpng?' found here: http://www.itk.org/Wiki/SimpleITK/FAQ
> 
> We are working on a more permanent solution for our next release.
> 
>                regards
>                       Ziv
> 
> From: Tassilo Klein [tjklein at gmail.com]
> Sent: Thursday, August 27, 2015 3:42 PM
> To: insight-users at itk.org
> Subject: [ITK-users] SimpleITK Anaconda Issue
> 
> Hi,
> 
> I have issues getting my SimpleITK running on a Linux machine.
> 
> I used to get errors:
> 
> http://public.kitware.com/pipermail/community/2015-May/009117.html
> 
> ImportError: libpng15.so.15: cannot open shared object file: No such
> 
> 
> Then I took an earlier version of libpng as mentioned here:
> 
> http://public.kitware.com/pipermail/community/2015-May/009120.html
> conda install libpng=1.5.13
> 
> 
> But then I get the following error:
> 
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/colorbar.py in <module>()
>      32 import matplotlib.artist as martist
>      33 import matplotlib.cbook as cbook
> ---> 34 import matplotlib.collections as collections
>      35 import matplotlib.colors as colors
>      36 import matplotlib.contour as contour
> 
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/collections.py in <module>()
>      25 import matplotlib.artist as artist
>      26 from matplotlib.artist import allow_rasterization
> ---> 27 import matplotlib.backend_bases as backend_bases
>      28 import matplotlib.path as mpath
>      29 from matplotlib import _path
> 
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/backend_bases.py in <module>()
>      54 
>      55 import matplotlib.tight_bbox as tight_bbox
> ---> 56 import matplotlib.textpath as textpath
>      57 from matplotlib.path import Path
>      58 from matplotlib.cbook import mplDeprecation
> 
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/textpath.py in <module>()
>      17 from matplotlib.path import Path
>      18 from matplotlib import rcParams
> ---> 19 import matplotlib.font_manager as font_manager
>      20 from matplotlib.ft2font import FT2Font, KERNING_DEFAULT, LOAD_NO_HINTING
>      21 from matplotlib.ft2font import LOAD_TARGET_LIGHT
> 
> /home/tjklein/anaconda/lib/python2.7/site-packages/matplotlib/font_manager.py in <module>()
>      56 import matplotlib
>      57 from matplotlib import afm
> ---> 58 from matplotlib import ft2font
>      59 from matplotlib import rcParams, get_cachedir
>      60 from matplotlib.cbook import is_string_like
> 
> ImportError: libpng16.so.16: cannot open shared object file: No such file or directory
> 
> 
> Any idea?
> 
> Best,
>  Tassilo
> 
> 
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