[ITK-users] SimpleITK Anaconda Issue

Fri Aug 28 18:52:54 EDT 2015

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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