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Re: [Imgcif-l] Adding references to external files to imgCIF

Dear James,
  The normalization was discussed ages ago and is consistent with DDL2
conventions, which
are more normalized than core cif.  The array sections were introduced when
we had to
start dealing with the Eiger.  It is routine in an eiger 16M data
collection to revert to a 4M
ROI (built into the hardware) when more speed is required.  Such
descriptions have to be
somewhere.  As speeds increase further, we will soon need to make more use
of
module-by-module ROIs, and we definitely will have to pull them in both
individually
and in groups instead of trying to only move full images.  What approach do
you suggest
for such cases?
  Regards,
    Herbert

On Thu, May 5, 2022 at 11:15 PM James H <jamesrhester@gmail.com> wrote:

> Thanks Herbert for making these updates. My apologies for taking so
> long to come back to them.
>
> I notice that the new 1.8.5 has moved the _array_data.external_data_*
> tags into a separate array_data_external_data loop. While I appreciate
> that a separate loop is as good a place as any, I would also have
> appreciated some discussion of this - perhaps I missed it? Anyway, I
> do not propose to dispute it now.
>
> More importantly, _array_data_external_data.frame seems to have
> acquired a format ARRAYID(start1:end1:stride1,start2:end2:stride2,
> ...) which I don't recall discussing, and there are now references in
> the definition to ARRAY_STRUCTURE_LIST which I believe miss the point
> that the ARRAY_STRUCTURE_LIST items are used to characterise the array
> after it has been obtained from the external data source, and are
> definitely *not* supposed to describe the layout of the data within
> the external data source. Likewise, ARRAY_ID refers to the layout of
> the data after they have been delivered, and so have no direct
> relevance to how the data are stored. I appreciate that C and Fortran
> layout should be considered by the author of the imgCIF file when
> describing what will be returned from the external source, but I'm not
> sure that this warning is particularly necessary here as the author
> will in any case be forced to consider the details of the
> format-specific behaviour when constructing the external data pointer.
>
> thanks,
> James.
>
> On Wed, 6 Apr 2022 at 23:39, Herbert J. Bernstein <yayahjb@gmail.com>
> wrote:
> >
> > Dear Colleagues,
> >
> >   I propose the following plan of action to get James' changes into the
> cif_img dictionary
> >
> >   0.  In both the yayahjb cbflib active branches:  main and
> CBFlib-0.9.7-devel, bring
> > the currently posted cif_img_1.8.5 dictionary up to an agreed level
> (which will be
> > called 1.8.6 if there are any changes) and make one last CBFlib 0.9.6
> release with
> > that as the default dictionary
> >   1.  Merge the current CBFlib_0.9.7-devel branch into main
> >   2.  Make that the default release in yayahjb
> >
> > If nobody objects, I plan to post the necessary pull requests and
> releases this weekend.
> >
> >
> >
> > On Wed, Apr 6, 2022 at 5:10 AM James H <jamesrhester@gmail.com> wrote:
> >>
> >> Dear All,
> >>
> >> Just a quick note: a further year later and the external data pointers
> >> work has not yet been merged, and neither has a further proposed data
> >> name [1]. On the bright side an implementation using these pointers
> >> has been published as a test of practicality [2]. It would of course
> >> be most welcome if imgCIF deliberative processes could get themselves
> >> to the point that these new data names are merged into the official
> >> version of the main dictionary, given that no issues have been
> >> identified.
> >>
> >> Meanwhile, in order to facilitate use of automated DDLm checking tools
> >> on data files using imgCIF data names, I have now generated (1) a
> >> direct translation of current version 1.8.4 into DDLm (2) a direct
> >> translation with added external data pointers to DDLm in a separate
> >> "journals-extension" branch. Both of these currently exist as pull
> >> requests on the https://github.com/COMCIFS/imgCIF repository, which is
> >> intended to hold the DDLm version of the imgCIF dictionary. Anyone is
> >> most welcome to comment on these pull requests of course, but I
> >> emphasise that they simply use a different dictionary language for
> >> defining the same data names, and therefore should have no
> >> implications for current imgCIF/CBF usage.
> >>
> >> best wishes,
> >> James.
> >>
> >> [1] pull request at https://github.com/yayahjb/cbflib/pull/39
> >> [2] https://github.com/jamesrhester/ImgCIFHandler.jl
> >>
> >> On Mon, 12 Apr 2021 at 16:38, James H <jamesrhester@gmail.com> wrote:
> >> >
> >> > Dear All,
> >> >
> >> > Over a year later I have now written up definitions in DDL2 for
> inclusion in imgCIF. The full definitions are at the Github issue (
> https://github.com/COMCIFS/imgCIF/issues/7). Please have a look and
> provide feedback here or there. Note that I have added datanames for
> specifying that the images are contained within compressed archives. I've
> checked a few known sources of images (proteindiffraction.org, zenodo, a
> uni repository) and this scheme seems to cover those bases. If you have
> time, please have a look at your favourite open archive of raw data to see
> if this scheme is sufficient for you to specify a particular image in that
> archive.  I've reproduced the examples from the definitions below.
> >> >
> >> > Of course, in a perfect world we would just give a DOI but those days
> are not yet upon us due to landing pages. Happy to be corrected on that.
> >> >
> >> > best wishes,
> >> > James.
> >> >
> >> > Examples
> >> > ========
> >> > #  The frames are contained in a single HDF5-format file accessible
> >> > #   at https://zenodo.org/record/12345/files/tartaric.h5. An array
> of 2D
> >> > #   images is found at HDF5 location /entry1/detector1/data
> >> >
> >> >      loop_
> >> >     _array_data.array_id
> >> >     _array_data.binary_id
> >> >     _array_data.external_format
> >> >     _array_data.location_uri
> >> >     _array_data.external_path
> >> >     _array_data.external_frame
> >> >     1 1 HDF5 https://zenodo.org/record/12345/files/tartaric.h5
> /entry1/detector1/data 1
> >> >     1 2 HDF5 https://zenodo.org/record/12345/files/tartaric.h5
> /entry1/detector1/data 2
> >> >     ...
> >> >
> >> >  #  Frames are contained in individual Smart6000 Bruker-format files
> >> >  #   accessible using https://uni_repo.edu/5341 in subdirectory run1.
> >> >
> >> >   loop_
> >> >     _array_data.array_id
> >> >     _array_data.binary_id
> >> >     _array_data.external_format
> >> >     _array_data.external_version
> >> >     _array_data.location_uri
> >> >     1 1 Bruker Smart6000 https://uni_repo.edu/5341/run1/tartaric.001
> >> >     1 2 Bruker Smart6000 https://uni_repo.edu/5341/run1/tartaric.002
> >> >     ...
> >> >
> >> > #  Frames with SMV format are contained at
> data.proteindiffraction.org in a tarred
> >> > #    archive compressed with bzip2.
> >> >
> >> >     loop_
> >> >     _array_data.array_id
> >> >     _array_data.binary_id
> >> >     _array_data.external_format
> >> >     _array_data.location_uri
> >> >     _array_data.external_archive_format
> >> >     _array_data.external_archive_path
> >> >     1 1 SMV
> >> >
> https://data.proteindiffraction.org/ssgcid/MyulA_01062_a_B12-sddc0001574_7k69.
tar.bz2
> >> >         TBZ
> >> >         MyulA_01062_a_B12-sddc0001574_7k69/data/317895h4_y_0001.img
> >> >     1 2 SMV
> >> >
> https://data.proteindiffraction.org/ssgcid/MyulA_01062_a_B12-sddc0001574_7k69.
tar.bz2
> >> >         TBZ
> >> >         MyulA_01062_a_B12-sddc0001574_7k69/data/317895h4_y_0002.img
> >> >
> >> >
> >> > On Tue, 5 Mar 2019 at 16:37, James Hester <jamesrhester@gmail.com>
> wrote:
> >> >>
> >> >> OK, I've drafted up some definitions (just the human-readable part
> for now) for you all to peruse.  Please look at
> https://github.com/COMCIFS/imgCIF/issues/7 and provide feedback here or
> there.
> >> >>
> >> >> all the the best,
> >> >> James.
> >> >>
> >> >> On Thu, 14 Feb 2019 at 14:39, James Hester <jamesrhester@gmail.com>
> wrote:
> >> >>>
> >> >>> Thanks for the support Herbert. Does anybody have any concerns or
> improvements to the data names that I sent originally? If not, I guess I
> will write up some formal dictionary definitions for your consideration.
> >> >>>
> >> >>> James.
> >> >>>
> >> >>> On Wed, 13 Feb 2019 at 21:39, Herbert J. Bernstein <
> yayahjb@gmail.com> wrote:
> >> >>>>
> >> >>>> Dear Colleagues,
> >> >>>>
> >> >>>>   Since 2012 NIAC and COMCIFS have worked cooperatively to make
> imgCIF/CBF and NeXus/HDF5 fully interoperable.  This is very
> >> >>>> far along, e.g.with NeXus/HDF5 NXtransformations having been added
> to NeXus/HDF5 to carry the same information as imgCIF/CBF AXIS.
> >> >>>> What James has suggested will allow imgcif/CBF to carry the same
> dataset structure information as is conveyed in the external links of
> >> >>>> an Eiger dataset, which divides the collected data into a master
> file with the metadata and a set of datafiles.  This structural division
> >> >>>> may not be important for some smaller datasets with only a few
> hundred to a few thousand frames, but can be very important in
> >> >>>> handling datasets with more frames than that that are encountered
> in serial crystallography.  Even for the smaller datasets this approach can
> >> >>>> help to solve a problem for archives and facilities that need to
> store metadata in a relational database while the data itself has been
> parked in
> >> >>>> raw file systems, non-relational databases, zenodo, etc.  As with
> almost all of CIF, imgCIF/CBF metadata maps very easily and directly
> >> >>>> into relational tables, while putting NeXus/HDF5 metadata into a
> relational database first requires exactly the same sort of transformations
> >> >>>> as we have already designed to map NeXus/HDF5 metadata into
> imgCIF/CBF   To me it seems that James' suggestion is not a reinvention
> >> >>>> of this particular wheel, but may be an important step in avoiding
> reinvention of the wheel.  This may avoid a lot of unnecessary
> transformation
> >> >>>> of huge quantities of raw data in serial crystallography while
> making the metadata more accessible.
> >> >>>>
> >> >>>>   I would suggest giving James' suggestion serious consideration.
> >> >>>>
> >> >>>>   Regards,
> >> >>>>     Herbert
> >> >>>> while putting
> >> >>>>
> >> >>>> On Wed, Feb 13, 2019 at 4:02 AM James Hester <
> jamesrhester@gmail.com> wrote:
> >> >>>>>
> >> >>>>> Dear Graeme,
> >> >>>>>
> >> >>>>> The context of this is the idea that a single imgCIF file could be
> >> >>>>> generated from a collection of raw image files (in whatever
> format, whether
> >> >>>>> HDF5, or ADSC, or Bruker, or Rigaku, etc.) which would contain
> the metadata
> >> >>>>> pertaining to that collection. In such a situation, some way of
> referring
> >> >>>>> to the raw frames from within the imgCIF file is required.
> >> >>>>>
> >> >>>>> I agree that a perfectly reasonable approach is not to generate
> any new
> >> >>>>> file at all, and simply to access the metadata directly in
> whatever format
> >> >>>>> happens to be there. This was my initial impulse as well and it
> took me a
> >> >>>>> while to understand that the actual proposal was to create an
> imgCIF file,
> >> >>>>> rather than just use imgCIF datanames for specification
> purposes.  From a
> >> >>>>> semantic point of view both amount to the same thing so my only
> real
> >> >>>>> motivation here is to add an image linking facility to imgCIF so
> that the
> >> >>>>> "generate a summary metadata file" approach is possible.
> >> >>>>>
> >> >>>>> Could we just copy the HDF5 way of referring to objects in other
> HDF5 files
> >> >>>>> as a quick solution?
> >> >>>>>
> >> >>>>> all the best,
> >> >>>>> James.
> >> >>>>>
> >> >>>>> On Wed, 13 Feb 2019 at 19:03, Graeme.Winter@Diamond.ac.uk <
> >> >>>>> Graeme.Winter@diamond.ac.uk> wrote:
> >> >>>>>
> >> >>>>> > Dear James,
> >> >>>>> >
> >> >>>>> > On the face of it, this looks a lot to me like a reinvention of
> HDF5 -
> >> >>>>> > perhaps with specific semantics - and there is already a
> (complete?)
> >> >>>>> > mapping from imgCIF to HDF5 / NeXus
> >> >>>>> >
> >> >>>>> > Have I missed something? No offence meant, trying to understand
> the shape
> >> >>>>> > of the problem you are trying to solve
> >> >>>>> >
> >> >>>>> > Thanks & best wishes Graeme
> >> >>>>> >
> >> >>>>> > > On 13 Feb 2019, at 05:15, James Hester <
> jamesrhester@gmail.com> wrote:
> >> >>>>> > >
> >> >>>>> > > Dear All,
> >> >>>>> > >
> >> >>>>> > > Recent Commdat discussion revealed a desire to reference
> external images
> >> >>>>> > > from within an imgCIF file. This would allow the metadata for
> a dataset
> >> >>>>> > to
> >> >>>>> > > be held within a single imgCIF file, while the frames
> themselves remain
> >> >>>>> > > separate. This avoids the impracticality of navigating
> through an
> >> >>>>> > enormous
> >> >>>>> > > mulit-frame imgCIF file in order to extract a relatively
> compact amount
> >> >>>>> > of
> >> >>>>> > > information.
> >> >>>>> > >
> >> >>>>> > > As a starting proposal, I suggest we extend the _array_data
> category with
> >> >>>>> > > the following three datanames:
> >> >>>>> > >
> >> >>>>> > > (1) _array_data.external_format    A value drawn from an
> enumerated list
> >> >>>>> > of
> >> >>>>> > > formats (e.g. "SMV","HDF5","Bruker"). The definition for each
> enumerated
> >> >>>>> > > value would explain how to interpret _array_data.internal_path
> >> >>>>> > > (2) _array_data.location_url           A URI for the file
> containing the
> >> >>>>> > > image. A relative URL is relative to the location of the
> imgCIF file
> >> >>>>> > > (3) _array_data.internal_path        A format-specific string
> describing
> >> >>>>> > > the location of the frame within the file identified by
> >> >>>>> > > _array_data.location_uri, interpreted according to the value
> given in
> >> >>>>> > > _array_data.external_format
> >> >>>>> > >
> >> >>>>> > > So for a multi-frame HDF5 file buried in a subdirectory of
> the location
> >> >>>>> > > referenced with a DOI, with appropriate definitions of the
> path notation:
> >> >>>>> > >
> >> >>>>> > > loop_
> >> >>>>> > > _array_data.array_id
> >> >>>>> > > _array_data.binary_id
> >> >>>>> > > _array_data.external_format
> >> >>>>> > > _array_data.location_uri
> >> >>>>> > > _array_data.internal_path
> >> >>>>> > > 1 1 NXMX doi:x.y.z
> directory/run/masterfilename:/entry1/detector/data[0]
> >> >>>>> > > 1 2 NXMX doi:x.y.z
> directory/run/masterfilename:/entry1/detector/data[1]
> >> >>>>> > > ...
> >> >>>>> > >
> >> >>>>> > > Or for a bunch of single-frame files generated by an ADSC
> detector in the
> >> >>>>> > > same directory as the imgCIF file
> >> >>>>> > >
> >> >>>>> > > _array_data.array_id
> >> >>>>> > > _array_data.binary_id
> >> >>>>> > > _array_data.external_format
> >> >>>>> > > _array_data.location_uri
> >> >>>>> > > 1 1 ADSC ./tartaric.001
> >> >>>>> > > 1 2 ADSC ./tartaric.002
> >> >>>>> > > 1 3 ADSC ./tartaric.003
> >> >>>>> > > ...
> >> >>>>> > >
> >> >>>>> > > The imgCIF data items describing the structure of the data
> array would
> >> >>>>> > > refer to the data after it has been provided by the format.
> The form in
> >> >>>>> > > which it is provided should be specified in the definition of
> each value
> >> >>>>> > of
> >> >>>>> > > "_array_data.external_format".  So, for example, the various
> compression
> >> >>>>> > > methods in HDF5 would be invisible if the data as returned
> are specified
> >> >>>>> > to
> >> >>>>> > > be an array of Reals.
> >> >>>>> > >
> >> >>>>> > > From the point of view of initial data validation, it would
> be sufficient
> >> >>>>> > > to check that all referenced files are accessible, and that
> the provided
> >> >>>>> > > locations exist.
> >> >>>>> > > 
> >> >>>>> > > Thoughts?
> >> >>>>> > > James.
> >> >>>>> > >
> >> >>>>> > > --
> >> >>>>> > > T +61 (02) 9717 9907
> >> >>>>> > > F +61 (02) 9717 3145
> >> >>>>> > > M +61 (04) 0249 4148
> >> >>>>> > > _______________________________________________
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> >> >>>>> > > imgcif-l@iucr.org
> >> >>>>> > > http://mailman.iucr.org/cgi-bin/mailman/listinfo/imgcif-l
> >> >>>>> > 
> >> >>>>> >
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> >> >>>>> T +61 (02) 9717 9907
> >> >>>>> F +61 (02) 9717 3145
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> >> >>> --
> >> >>> T +61 (02) 9717 9907
> >> >>> F +61 (02) 9717 3145
> >> >>> M +61 (04) 0249 4148
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> T +61 (02) 9717 9907
> >> >> F +61 (02) 9717 3145
> >> >> M +61 (04) 0249 4148
> >> >
> >> >
> >> >
> >> > --
> >> > T +61 (02) 9717 9907
> >> > F +61 (02) 9717 3145
> >> > M +61 (04) 0249 4148
> >>
> >>
> >>
> >> --
> >> T +61 (02) 9717 9907
> >> F +61 (02) 9717 3145
> >> M +61 (04) 0249 4148
> 
> 
> 
> --
> T +61 (02) 9717 9907
> F +61 (02) 9717 3145
> M +61 (04) 0249 4148
> 
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