[ITK-users] SimpleITK Anaconda Issue

Tue Sep 1 12:02:12 EDT 2015

Hi,

well, it doesn't work for me. I am just trying to load a Nifti (.nii) image:

dwiImg = sitk.ReadImage(glob.glob(dataPath+'/*DWI*/*.nii'))

when getting the error. Reinstallation didn't help either. There is nothing
special about these files. It's MRIs.

home/tjklein/anaconda/envs/sitkpy/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.

Thanks,
 Tassilo

On Sat, Aug 29, 2015 at 11:12 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
wrote:

> 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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