Re: [Pytom-mail] Tutorial files

[Thomas H. <th...@gm...>]

Hm, I see theres a gap between - and projectionTargets in your call?



> On 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... <mailto: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... <mailto: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... <mailto: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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>> 
>> 
>