Re: [Pytom-mail] Tutorial files

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

Deleting it from the call worked...

On Wed, Feb 24, 2016 at 12:36 PM, Thomas Hrabe <th...@gm...> wrote:

> 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...> 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...> 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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>>>
>>
>>
>>
>
>