[ITK-users] [ITK] SimpleITK Anaconda Issue

Tassilo Klein tjklein at gmail.com
Tue Sep 1 12:15:10 EDT 2015 

Sure, this this already. Same thing.

On Tue, Sep 1, 2015 at 12:13 PM, Kayhan Batmanghelich <
batmanghelich at gmail.com> wrote:

> Tassilo,
>
> Can you do test this, instead of glob which produce a lit of file, specify
> one file and try the ReadImage on one specific file and see if it works or
> not.
>
> Thanks,
> Kayhan
>
> On Tue, Sep 1, 2015 at 12:02 PM, Tassilo Klein <tjklein at gmail.com> wrote:
>
>> 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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