Re: [scipion-users] importing movies

[Juha H. <juh...@gm...>]

Dear Jose Miguel,

I prefer to collect movies as stacks instead of single frames but I would
say both scenarios are pretty common.

Best wishes,
Juha

--
Juha T. Huiskonen, PhD
Associate Professor
Principal Investigator

Oxford Particle Imaging Centre
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
University of Oxford

http://www.strubi.ox.ac.uk/strubi/research/huiskonen/
Email: ju...@st...
Tel.: +44 1865 287 844
Mob.: +44 7576 505 422

On Mon, Jul 11, 2016 at 5:25 PM, Jose Miguel de la Rosa Trevin <
del...@gm...> wrote:

> Indeed, the # has an special meaning, because it mark the ID of the item
> (either Micrograph or Movie) that will be used
> inside the set. The % character can do the work here.  In a general case I
> think that should be combined with the
> movies since the most common case is to have a dataset with more than one
> movie.
>
> I will let you know when you do any progress in this direction. I'm
> thinking that it can a bit more complicated when using
> this in an streaming mode. By the way, how do you usually collect movies,
> in a single stack or in separate frames, or both?
>
> Bests,
> Jose Miguel.
>
>
> On Mon, Jul 11, 2016 at 5:51 PM, Juha Huiskonen <juh...@gm...>
> wrote:
>
>> Dear Jose Miguel,
>>
>> May I suggest that wildcards "*" and "?" are reserved for general use and
>> "#" for digits [0-9], and "%" for specifying the pattern for all the frames
>> in one movie.
>>
>> So in my case
>>
>> movie_%%%%.mrc
>>
>> or
>>
>> mov*_%%%%.mrc
>>
>> would work. I hope that makes sense and would not be too complicated.
>>
>> Alternatively, a
>>
>> Best wishes,
>> Juha
>>
>>
>>
>> --
>> Juha T. Huiskonen, PhD
>> Associate Professor
>> Principal Investigator
>>
>> Oxford Particle Imaging Centre
>> Division of Structural Biology
>> Wellcome Trust Centre for Human Genetics
>> University of Oxford
>>
>> http://www.strubi.ox.ac.uk/strubi/research/huiskonen/
>> Email: ju...@st...
>> Tel.: +44 1865 287 844
>> Mob.: +44 7576 505 422
>>
>> On Mon, Jul 11, 2016 at 4:24 PM, Jose Miguel de la Rosa Trevin <
>> del...@gm...> wrote:
>>
>>> Dear Juha,
>>>
>>> Right now it is only possible to import frames contained in a single
>>> stack (mrcs or any other EM format).
>>> I have started a modification to support frames in individual frames,
>>> but it is in a development branch
>>> and is not ready yet. Something that we still have not clear is how we
>>> could allow to specify both the movie part
>>> and the frame part in the pattern without complicating things too
>>> much....so any suggestion about this is
>>> welcome.
>>>
>>> We have pending to generate some documentation pages about the types and
>>> options for each import case.
>>>
>>> Hope this helps,
>>> Jose Miguel.
>>>
>>>
>>> On Mon, Jul 11, 2016 at 4:37 PM, Juha Huiskonen <
>>> juh...@gm...> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I am trying to import one movie, that is stored as separate frames,
>>>> called
>>>>
>>>> movie_0001.mrc
>>>> movie_0002.mrc
>>>> ...
>>>> movie_0020.mrc
>>>>
>>>> For import, I tried using pattern movie_####.mrc which I was hoping
>>>> would do exactly what I wanted. However, it seems I got out 20 single frame
>>>> 'movies', instead of one 20-frame movie (SetOfMovies has 20 items).
>>>>
>>>> What am I doing wrong?
>>>>
>>>> Best wishes,
>>>> Juha
>>>>
>>>>
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>>
>>
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