Re: [Pytom-mail] Tutorial files

[Kanika K. <kk...@uc...>]

Hello

Thank you! But there is still this error for me :(

Traceback (most recent call last):
  File "/usr/local/pytom/bin/reconstructTomogram.py", line 186, in <module>
    outMarkerFileName=outMarkerFileName, verbose=True)
  File "/usr/local/pytom/reconstruction/reconstructionFunctions.py", line
192, in alignWeightReconstruct
    vol_bp = tiltSeries.reconstructVolume(dims=voldims,
reconstructionPosition=recCent, binning=1)
  File "/usr/local/pytom/reconstruction/TiltAlignmentStructures.py", line
440, in reconstructVolume
    binning=binning)
  File "/usr/local/pytom/reconstruction/reconstructionStructures.py", line
423, in reconstructVolume
    vol_bp = vol(dims[0], dims[1], dims[2])
  File "/usr/local/pytom/pytomc/swigModules/pytom_volume.py", line 85, in
__init__
    this = _pytom_volume.new_vol(*args)
RuntimeError: Initialize of volume failed. Specified size is 0,0,0!

On Wed, Feb 24, 2016 at 11:09 AM, Thomas Hrabe <th...@gm...> wrote:

> Kanika,
>
> attached is the fixed call for your reconstruction.
>
> The two first parameters had to be replaced
>
> reconstructTomogram.py
> --tiltSeriesName
> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/tomo01_sorted
> --tiltSeriesFormat em
> --firstIndex 1 --lastIndex 41 --referenceIndex 21 --markerFile
> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark
> --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01
> --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em
> --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128
> --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0
>
> Works? (Worked for me)
>
> The tutorial will be fixed in a bit.
>
> Thomas
>
> On Feb 24, 2016, at 10:32 AM, Kanika Khanna <kk...@uc...> wrote:
>
> Hi,
>
> I used the following command as per the tutorial.
>
> reconstructTomogram.py --tiltSeriesPath
> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/
> --tiltSeriesPrefix tomo01_sorted --firstIndex 1 --lastIndex 41
> --referenceIndiex 21 --markerFile
> /home/kkhanna/Desktop/pytom-tutorial/RibosFromLysate/projections/markfile_temp.mark
> --referenceMarkerIndex 1 -- projectionTargets ./alignedProjections/tomo01
> --projectionBinning 4 --lowpassFilter 0.5 --tomogramFile tomogram.em
> --filetype em --tomogramSizeX 512 --tomogramSizeY 512 --tomogramSizeZ 128
> --reconstructionCenterX 0 --reconstructionCenterY 0 reconstructCenterZ 0
>
>
> On Wed, Feb 24, 2016 at 10:17 AM, Thomas Hrabe <th...@gm...> wrote:
>
>> Hi Kanika,
>>
>> can you please send the full terminal command and output you processed?
>>
>> Thomas
>>
>> On Feb 24, 2016, at 10:13 AM, Kanika Khanna <kk...@uc...> wrote:
>>
>> Hi,
>>
>> I downloaded the tutorial file.
>>
>> I have been trying to use it to reconstruct the tutorial data and I get
>> the following error when I run the script reconstructTomo.
>>
>>
>>
>> *sys.version_info(major=2, minor=7, micro=5, releaselevel='final',
>> serial=0)option --tiltSeriesPath not recognized*
>>
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>
>