[cctbxbb] Adding columns to new *unmerged* MTZ object
Graeme.Winter at diamond.ac.uk
Graeme.Winter at diamond.ac.uk
Thu Feb 13 00:11:52 PST 2014
... and we want to write data out from DIALS which does want to be properly scaled by Aimless :o)
Also it is a good exercise anyway to pass as much information as possible down the wire - this is a good part of the motivation. May just require one or two small tweaks of iotbx...
Cheerio, Graeme
-----Original Message-----
From: Phil Evans [mailto:pre at mrc-lmb.cam.ac.uk]
Sent: 12 February 2014 20:04
To: cctbx mailing list
Subject: Re: [cctbxbb] Adding columns to new *unmerged* MTZ object
Pointless can read unmerged Scalepack files, which can go into Aimless, but it can't do any further scaling (probably unnecessary anyway) as the geometrical information is missing Phil
On 12 Feb 2014, at 18:14, Nathaniel Echols <nechols at lbl.gov> wrote:
> Random dumb question: does Aimless read unmerged Scalepack files? A
> few months ago I added a module in iotbx to export those, which might
> be simpler than dealing with the MTZ API. (Not that writing unmerged
> MTZ files would't be a good idea, but if you're looking for a quick
> solution that may not be the best route.)
>
> -Nat
>
>
> On Wed, Feb 12, 2014 at 4:48 AM, <Graeme.Winter at diamond.ac.uk> wrote:
> Hi Phil,
>
> Probably, but in the meantime using MTZ mean we can do things like
> running Aimless on the output data to see if we have made any kind of
> useful measurements :o)
>
> Has been a game though making full-on unmerged MTZ files!
>
> Cheerio, Graeme
>
>
> On 12 Feb 2014, at 12:29, Phil Evans <pre at mrc-lmb.cam.ac.uk> wrote:
>
> > I thought you DIALS guys were going to use a new file format Phil
> >
> >
> > On 12 Feb 2014, at 10:43, Graeme.Winter at Diamond.ac.uk wrote:
> >
> >> In related news....
> >>
> >> Should
> >>
> >> void
> >> object::adjust_column_array_sizes(int new_nref)
> >> {
> >> CMtz::MTZ* p = ptr();
> >> if (!p->refs_in_memory) return;
> >> if (new_nref > p->nref) {
> >> reserve(new_nref);
> >> for(int i=0;i<p->nxtal;i++) {
> >> for(int j=0;j<p->xtal[i]->nset;j++) {
> >> for(int k=0;k<p->xtal[i]->set[j]->ncol;k++) {
> >> CMtz::MTZCOL* col_k = p->xtal[i]->set[j]->col[k];
> >> int old_size = column_array_size(col_k);
> >> if (new_nref > old_size) {
> >> ccp4array_resize(col_k->ref, new_nref);
> >> for(int iref=old_size;iref<new_nref;iref++) {
> >> *(reinterpret_cast<union float_uint_uchar*>(
> >> &col_k->ref[iref])) = not_a_number_value_;
> >> }
> >> }
> >> }
> >> }
> >> }
> >> }
> >> }
> >>
> >> assign nref? otherwise repeated calling of this will keep on re-allocating the arrays
> >>
> >> Thanks Graeme
> >>
> >>
> >> On 12 Feb 2014, at 10:40, Graeme Winter <graeme.winter at diamond.ac.uk> wrote:
> >>
> >>> All,
> >>>
> >>> By adding
> >>>
> >>> m_out.adjust_column_array_sizes(len(mi))
> >>>
> >>> to the bpl wrapper and defining
> >>>
> >>> m_out.set_n_reflections(len(mi))
> >>>
> >>> in the object.h and bpl wrapper I can do what I want...
> >>>
> >>> I will add some tests and some warnings that this may make nonsense of the values... however before committing any comments on the interface? or behaviour?
> >>>
> >>> Thanks Graeme
> >>>
> >>>
> >>>
> >>> On 12 Feb 2014, at 09:11, <Graeme.Winter at diamond.ac.uk> <Graeme.Winter at diamond.ac.uk> wrote:
> >>>
> >>>> Hi Folks,
> >>>>
> >>>> I am trying to create a new MTZ file containing unmerged and it seems to be less simple than I would think - set_reals() on a column requires a set of Miller indices and values and does a lookup internally (which I don't want for unmerged values) and set_values() requires that the array is already the right size - when it starts off as size 0 and I have no idea how to make enough room in there from the Python API...
> >>>>
> >>>> Any clues? I have done quite a chunk of grepping around to try and figure this one out and have run out of ideas...
> >>>>
> >>>> Thanks Graeme_______________________________________________
> >>>> cctbxbb mailing list
> >>>> cctbxbb at phenix-online.org
> >>>> http://phenix-online.org/mailman/listinfo/cctbxbb
> >>>
> >>
> >> _______________________________________________
> >> cctbxbb mailing list
> >> cctbxbb at phenix-online.org
> >> http://phenix-online.org/mailman/listinfo/cctbxbb
> >
> > _______________________________________________
> > cctbxbb mailing list
> > cctbxbb at phenix-online.org
> > http://phenix-online.org/mailman/listinfo/cctbxbb
>
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb
>
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb
_______________________________________________
cctbxbb mailing list
cctbxbb at phenix-online.org
http://phenix-online.org/mailman/listinfo/cctbxbb
--
This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
More information about the cctbxbb
mailing list