Re: [Pytom-mail] Tutorial files

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

The parameter is case sensitive -> fileType ?



> On Feb 24, 2016, at 12:01 PM, Kanika Khanna <kk...@uc...> wrote:
> 
> Sorry! Thanks for pointing that out. But now it is showing a different error! 
> 
> option --filetype Not recognized
> 
> On Wed, Feb 24, 2016 at 11:39 AM, Thomas Hrabe <th...@gm... <mailto:th...@gm...>> wrote:
> Hm, I see theres a gap between - and projectionTargets in your call?
> 
> 
> 
>> On Feb 24, 2016, at 11:09 AM, Thomas Hrabe <th...@gm... <mailto: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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>>> 
>> 
> 
>