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

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_im
g 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 wil
l 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 thi
s 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 i
n imgCIF. The full definitions are at the Github issue (https://github.com/COMCI
FS/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 (proteindiffrac
tion.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 tha
t 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 n
ot 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/dete
ctor1/data 1
>> >     1 2 HDF5 https://zenodo.org/record/12345/files/tartaric.h5 /entry1/dete
ctor1/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-sddc00
01574_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-sddc00
01574_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/issue
s/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 improve
ments 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> wr
ote:
>> >>>>
>> >>>> Dear Colleagues,
>> >>>>
>> >>>>   Since 2012 NIAC and COMCIFS have worked cooperatively to make imgCIF/C
BF and NeXus/HDF5 fully interoperable.  This is very
>> >>>> far along, e.g.with NeXus/HDF5 NXtransformations having been added to Ne
Xus/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 wi
th the metadata and a set of datafiles.  This structural division
>> >>>> may not be important for some smaller datasets with only a few hundred t
o a few thousand frames, but can be very important in
>> >>>> handling datasets with more frames than that that are encountered in ser
ial crystallography.  Even for the smaller datasets this approach can
>> >>>> help to solve a problem for archives and facilities that need to store m
etadata 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 relatio
nal 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 reinv
ention of the wheel.  This may avoid a lot of unnecessary transformation
>> >>>> of huge quantities of raw data in serial crystallography while making th
e 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> wr
ote:
>> >>>>>
>> >>>>> 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, whe
ther
>> >>>>> HDF5, or ADSC, or Bruker, or Rigaku, etc.) which would contain the meta
data
>> >>>>> pertaining to that collection. In such a situation, some way of referri
ng
>> >>>>> 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 for
mat
>> >>>>> 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 fi
le,
>> >>>>> 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 t
he
>> >>>>> "generate a summary metadata file" approach is possible.
>> >>>>>
>> >>>>> Could we just copy the HDF5 way of referring to objects in other HDF5 f
iles
>> >>>>> 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 s
hape
>> >>>>> > of the problem you are trying to solve
>> >>>>> >
>> >>>>> > Thanks & best wishes Graeme
>> >>>>> >
>> >>>>> > > On 13 Feb 2019, at 05:15, James Hester <jamesrhester@gmail.com> wro
te:
>> >>>>> > >
>> >>>>> > > Dear All,
>> >>>>> > >
>> >>>>> > > Recent Commdat discussion revealed a desire to reference external i
mages
>> >>>>> > > from within an imgCIF file. This would allow the metadata for a dat
aset
>> >>>>> > to
>> >>>>> > > be held within a single imgCIF file, while the frames themselves re
main
>> >>>>> > > separate. This avoids the impracticality of navigating through an
>> >>>>> > enormous
>> >>>>> > > mulit-frame imgCIF file in order to extract a relatively compact am
ount
>> >>>>> > of
>> >>>>> > > information.
>> >>>>> > >
>> >>>>> > > As a starting proposal, I suggest we extend the _array_data categor
y 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 enume
rated
>> >>>>> > > value would explain how to interpret _array_data.internal_path
>> >>>>> > > (2) _array_data.location_url           A URI for the file containin
g the
>> >>>>> > > image. A relative URL is relative to the location of the imgCIF fil
e
>> >>>>> > > (3) _array_data.internal_path        A format-specific string descr
ibing
>> >>>>> > > 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 loca
tion
>> >>>>> > > referenced with a DOI, with appropriate definitions of the path not
ation:
>> >>>>> > >
>> >>>>> > > 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/da
ta[0]
>> >>>>> > > 1 2 NXMX doi:x.y.z directory/run/masterfilename:/entry1/detector/da
ta[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 wo
uld
>> >>>>> > > refer to the data after it has been provided by the format. The for
m in
>> >>>>> > > which it is provided should be specified in the definition of each
value
>> >>>>> > of
>> >>>>> > > "_array_data.external_format".  So, for example, the various compre
ssion
>> >>>>> > > methods in HDF5 would be invisible if the data as returned are spec
ified
>> >>>>> > to
>> >>>>> > > be an array of Reals.
>> >>>>> > >
>> >>>>> > > From the point of view of initial data validation, it would be suff
icient
>> >>>>> > > to check that all referenced files are accessible, and that the pro
vided
>> >>>>> > > locations exist.
>> >>>>> > > 
>> >>>>> > > Thoughts?
>> >>>>> > > James.
>> >>>>> > >
>> >>>>> > > --
>> >>>>> > > T +61 (02) 9717 9907
>> >>>>> > > F +61 (02) 9717 3145
>> >>>>> > > M +61 (04) 0249 4148
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>> >>>>> > 
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