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Author Topic: Verifying installation
thiagoniki-
ti
Newbie
Posts: 3
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Post Verifying installation
on: January 30, 2015, 09:52
Quote

Dear all,

I am having problems verifying my installation which means it is not correct. I used the wiki and installed in my fedora from the source code. I am trying to run the simple_example file that comes with the installation but it seams that it does not find one of the functions. Here is the error I am getting:

---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
/usr/lib/python2.7/site-packages/IPython/utils/py3compat.pyc in execfile(fname, *where)
176 else:
177 filename = fname
--> 178 __builtin__.execfile(filename, *where)

/home/thiagovmlima/Software/NiftyRec/NiftyRec-2.0.1/apps/python_simple_phantom_example/simple_phantom_example.py in <module>()
118 for slice_index in range(M):
119 input_phantom_array[ 0:i.shape[0], slice_index, 0:i.shape[1] ]=i.astype(numpy.float32) # Put image array into the volume's slices
--> 120 NRsino=project(input_phantom_array, r.cameras, r.psf, r.attenuation, use_the_GPU) # Run et_project
121 print("Size of NiftyRec\'s sinogram:"+str(NRsino.shape))
122

/usr/lib/python2.7/site-packages/NiftyRec/NiftyRec.pyc in et_project(activity, cameras, psf, attenuation, gpu, background, background_attenuation, truncate_negative_values)
82 cameras = asarray(cameras,dtype=float32)
83
---> 84 L.et_array_project.restype = c_int
85 L.et_array_project.argtypes = [P(c_float), P(c_int), P(c_float), P(c_int), P(c_float), P(c_int), P(c_float), P(c_int), P(c_float), P(c_int), c_float, c_float, c_int, c_int]
86

/usr/lib64/python2.7/ctypes/__init__.pyc in __getattr__(self, name)
371 if name.startswith('__') and name.endswith('__'):
372 raise AttributeError(name)
--> 373 func = self.__getitem__(name)
374 setattr(self, name, func)
375 return func

/usr/lib64/python2.7/ctypes/__init__.pyc in __getitem__(self, name_or_ordinal)
376
377 def __getitem__(self, name_or_ordinal):
--> 378 func = self._FuncPtr((name_or_ordinal, self))
379 if not isinstance(name_or_ordinal, (int, long)):
380 func.__name__ = name_or_ordinal

AttributeError: /home/thiagovmlima/Software/NiftyRec/NiftyRec_install/lib/lib_et_array_interface.so: undefined symbol: et_array_project

Thank you for your help.

Thiago

thiagoniki-
ti
Newbie
Posts: 3
Permalink
Post Re: Verifying installation
on: February 3, 2015, 12:26
Quote

Testing in matlab it works better but I still get a problem with the installation. As I get similar error as described in the instructions for getting started with Matlab but instead of complaining of lib_et.dylib directly it complains of @rpath/CUDA.framework/Versions/A/CUDA. Any tips?

Here is the error I get:
Invalid MEX-file
'/Users/thiagovmlima/Software/NiftyRec/NiftyRec_install/niftyrec/matlab/et_project_mex.mexmaci64':
dlopen(/Users/thiagovmlima/Software/NiftyRec/NiftyRec_install/niftyrec/matlab/et_project_mex.mexmaci64,
6): Library not loaded: @rpath/CUDA.framework/Versions/A/CUDA
Referenced from: /usr/lib/lib_et.dylib
Reason: image not found

Error in et_project (line 91)
sinogram = et_project_mex(activity, cameras, attenuation, psf,
use_gpu, background, background_attenuation,
truncate_negative_values);

Error in et_demo_osem_2D (line 32)
ideal_sinogram = et_project(phantom, cameras, attenuation, psf,
GPU);

I did install without the CUDA.

Thank you
Thiago

thiagoniki-
ti
Newbie
Posts: 3
Permalink
Post Re: Verifying installation
on: February 3, 2015, 13:35
Quote

Dear all,

I have managed to sort my problem out, it was because since it tried with the python install before it ended up messing up my installation creating different libraries one in the standard installation folder and another in the chosen installation folder. Once I cleaned these up I was able to run the demos.

BW
Thiago

spedemon
Administrator
Posts: 22
Permalink
Post Re: Verifying installation
on: February 5, 2015, 17:40
Quote

Hi Thiago,

I am glad that you sorted out the problem with the Matlab installation. Please note that the Python interface of NiftyRec has been replaced by occiput.io (http://www.occiput.io), which provides a low level wrapper interface (called NiftyPy) and a high level interface for tomographic reconstruction (currently SPECT and PET are supported). If you are into Python, I encourage you to try occiput.io as the new interface is more flexible and easier to use than the Matlab interface. There are a few demos is the /notebooks folder of occiput.io.
The old NiftyRec Python wrapper has been removed in version 2.0.2.

Kind regards,
Stefano

snarf
Newbie
Posts: 2
Permalink
Post Re: Verifying installation
on: July 1, 2015, 05:27
Quote

Quote from spedemon on February 5, 2015, 17:40
The old NiftyRec Python wrapper has been removed in version 2.0.2.

Kind regards,
Stefano

Is there a way to test this version please ? Only the 2.0.1 is reachable on sourceforge.
Thanks,
Snarf

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