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On Thu, Oct 20, 2016 at 3:00 PM, Pedro Vicente < pedro.vicente@xxxxxxxxxxxxxxxxxx> wrote: > >>> This is making me think that we may want a spec for netcdf-json that > would be a subset of the hdf-json spec. > > that is one option; > other option is to make a JSON form of netCDF CDL , completely unaware of > HDF5 (just like the netCDF API is) > > http://www.unidata.ucar.edu/software/netcdf/workshops/ > 2011/utilities/CDL.html > yup. Are they mutually exclusive approaches? my thought was to make a netcdfJSON, then add features to make an hdfJSON. (and netcdfJSON would look a lot like CDL) So a netcdfJSON file would be a valid hdfJSON file, but not the other way around. Like a netcdf4 file is a valid hdf5 file now. -CHB > with the "data" part being optional, which was one of the goals of my > design, to transmit just metadata over the web, for a quick remote > inspection > > -Pedro > > ----- Original Message ----- > *From:* Chris Barker <chris.barker@xxxxxxxx> > *To:* John Readey <jreadey@xxxxxxxxxxxx> > *Cc:* Pedro Vicente <pedro.vicente@xxxxxxxxxxxxxxxxxx> ; netCDF Mail List > <netcdfgroup@xxxxxxxxxxxxxxxx> ; HDF Users Discussion List > <hdf-forum@xxxxxxxxxxxxxxxxxx> > *Sent:* Thursday, October 20, 2016 4:48 PM > *Subject:* Re: [netcdfgroup] How to dump netCDF to JSON? > > On Thu, Oct 20, 2016 at 12:02 PM, John Readey <jreadey@xxxxxxxxxxxx> > wrote: > >> So we came up with a scheme of Group, Dataset, and Datatype collections >> with a UUID to identify each object. That way if you a reference to a >> specific UUID, you can always access the object regardless of what >> shenanigans may be happening with the links in the file. >> >> >> >> It’s true that this makes path look ups a bit more cumbersome, but it’s a >> more general way of specify a directed graph (the HDF5 link structure) on a >> tree (the JSON hierarchy). >> > > Hmm -- interesting. I hadn't realized that HDF was this flexible. For my > part, I've only really used netcdf. > > This is making me think that we may want a spec for netcdf-json that would > be a subset of the hdf-json spec. > > That way they can be as compatible as possible without "cluttering up" the > netcdf spec too much. > > -CHB > > > > > >> >> >> John >> >> >> >> *From: *Pedro Vicente <pedro.vicente@xxxxxxxxxxxxxxxxxx> >> *Date: *Tuesday, October 18, 2016 at 9:37 PM >> *To: *John Readey <jreadey@xxxxxxxxxxxx>, Chris Barker < >> chris.barker@xxxxxxxx> >> *Cc: *netCDF Mail List <netcdfgroup@xxxxxxxxxxxxxxxx>, HDF Users >> Discussion List <hdf-forum@xxxxxxxxxxxxxxxxxx> >> >> *Subject: *Re: [netcdfgroup] How to dump netCDF to JSON? >> >> >> >> @John >> >> >> >> >> 1. Complete fidelity to all HDF5 features >> >> >> 2. Support graphs that are not acyclic. >> >> >> >> ok, understood. >> >> >> >> In my case I needed a simple schema for a particular set of files. >> >> >> >> But why didn't you start with the official HDF5 DDL >> >> >> >> https://support.hdfgroup.org/HDF5/doc/ddl.html >> >> >> >> and try to adapt to JSON? >> >> >> >> Same thing for netCDF, there is already an official CDL, so any JSON >> spec should be "identical". >> >> >> >> >> >> >> >> @Chris >> >> >> >> { >> "dset1" : ["dataset", "STAR_INT32", 2, [3, 4], [1, 2, 3, 4, 5, 6, 7, 8, >> 9, 10, 11, 12]] >> } >> >> >> >> >> * Do you need "rank"? >> >> >> >> sometimes a bit of redundancy is useful, to make it visually clear >> >> >> >> >> BTW, is a "dataset" in HDF the same thing as a "variable" in netcdf?) >> >> >> >> yes >> >> >> >> >>It would be really great to have this become an "official" spec -- if >> you want to get it there, you're probably going to need to develop it more >> out in the open with a wider community. These lists are the way to get that >> started, but I suggest >> >> >>1) put it up somewhere that people can collaborate on it, make >> suggestions, capture the discussion, etc. gitHub is one really nice way to >> do that. See, for example the UGRID spec project: >> >> >> >> >> >> ok, anyone interested send me an off list email >> >> >> >> >> >> -Pedro >> >> >> >> >> >> >> >> ----- Original Message ----- >> >> *From:* John Readey <jreadey@xxxxxxxxxxxx> >> >> *To:* Chris Barker <chris.barker@xxxxxxxx> ; Pedro Vicente >> <pedro.vicente@xxxxxxxxxxxxxxxxxx> >> >> *Cc:* netCDF Mail List <netcdfgroup@xxxxxxxxxxxxxxxx> ; Charlie Zender >> <zender@xxxxxxx> ; HDF Users Discussion List >> <hdf-forum@xxxxxxxxxxxxxxxxxx> ; David Pearah <David.Pearah@xxxxxxxxxxxx> >> >> *Sent:* Tuesday, October 18, 2016 11:15 PM >> >> *Subject:* Re: [netcdfgroup] How to dump netCDF to JSON? >> >> >> >> Hey, >> >> >> >> The hdf5-json code is here: https://github.com/HDFGroup/hdf5-json and >> docs are here: http://hdf5-json.readthedocs.io/en/latest/. >> >> >> >> The package is both a library of HFD5 <-> JSON conversion functions and >> some simple scripts for converting HDF5 to JSON and vice-versa. E.g. >> >> $ python h5tojson.py –D <hdf5-file> >> >> outputs JSON minus the dataset data values. >> >> >> >> While it may not be the most elegant JSON schema, it’s designed with the >> following goals in mind: >> >> 1. Complete fidelity to all HDF5 features (i.e. the goal is that >> you should be able to take any HDF5 files, convert it to JSON, convert back >> to HDF5 and wind up with a file that is semantically equivalent to what you >> started with. >> >> 2. Support graphs that are not acyclic. I.e. a group structure >> like <root> links with A, and B. And A and B links to C. The output >> should only produce one representation of C. >> >> Since NetCDF doesn’t use all these features, it’s certainly possible to >> come up with something simpler for just netCDF files. >> >> >> >> Suggestions, feedback, and pull requests are welcome! >> >> >> >> Cheers, >> >> John >> >> >> >> *From: *Chris Barker <chris.barker@xxxxxxxx> >> *Date: *Friday, October 14, 2016 at 12:32 PM >> *To: *Pedro Vicente <pedro.vicente@xxxxxxxxxxxxxxxxxx> >> *Cc: *netCDF Mail List <netcdfgroup@xxxxxxxxxxxxxxxx>, Charlie Zender < >> zender@xxxxxxx>, John Readey <jreadey@xxxxxxxxxxxx>, HDF Users >> Discussion List <hdf-forum@xxxxxxxxxxxxxxxxxx>, David Pearah < >> David.Pearah@xxxxxxxxxxxx> >> *Subject: *Re: [netcdfgroup] How to dump netCDF to JSON? >> >> >> >> Pedro, >> >> >> >> When I first started reading this thread, I thought "there should be a >> spec for how to represent netcdf in JSON" >> >> >> >> and then I read: >> >> >> >> 1) The specification to convert netCDF/HDF5 to "a" JSON format (note the >> "a" here) >> >> >> >> Awesome -- that's exactly what we need -- as you say there is not one way >> to represent netcdf data in JSON, and probably far more than one "obvious" >> way. >> >> >> >> Without looking at your spec yet, I do think it should probably look as >> much like CDL as possible -- we are all familiar with that. >> >> >> >> (why Python? HDF5 developer tools should be all about writing in C/C++) >> >> >> >> Because Python is an excellent language with which to "drive" C/C++ >> libraries like HDF5 and netcdf4. If I were to do this, I'd sure use Python. >> Even if you want to get to a C++ implementation eventually, you'd probably >> benefit from prototyping and working out the kinks with a Python version >> first. >> >> >> >> But whoever is writing the code.... >> >> >> >> >> >> The specification is here >> >> http://www.space-research.org/ >> >> >> >> Just took a quick look -- nice start. >> >> >> >> I've only used HDF through the netcdf4 spec, so there may be richness >> needed that I'm missing, but my first thought is to a make greater use of >> "objects" in JSON (key-value structures, hash tables, dicts in python), >> rather than array position for heterogeneous structures. For instance, you >> have: >> >> >> >> a dataset >> >> >> { >> "dset1" : ["dataset", "STAR_INT32", 2, [3, 4], [1, 2, 3, 4, 5, 6, 7, 8, >> 9, 10, 11, 12]] >> } >> >> >> >> I would perhaps do that as something like: >> >> >> >> { >> >> ... >> >> "dset1":{"object_type": "dataset", >> >> "dtype": "INT32" >> >> "rank": 2, >> >> "dimensions": [3,4], >> >> "data": [[1,2,3,4], >> >> [5,6,7,8], >> >> [9,10,11,12]] >> >> } >> >> ... >> >> } >> >> >> >> NOTES: >> >> >> >> * I used nested arrays, rather than flattening the 2-d array -- this maps >> nicely to things like numpy arrays, for example -- not sure about the C++ >> world. (you can flatten and un-flatten numpy arrays easily, too, but this >> seems like a better mapping to the structure) And HDF is storing this all >> in chunks and who knows what -- so it's not a direct mapping to the memory >> layout anyway. >> >> >> >> * Do you need "rank"? -- can't you check the length of the dimensions >> array? >> >> >> >> * Do you need "object_type" -- will it always be a dataset? Or you could >> have something like: >> >> >> >> { >> >> ... >> >> "datasets": {"dset1": {the actual dataset object}, >> >> "dset2": {another dataset object}, >> >> .... >> >> } >> >> >> >> Then you don't need object_type or a name >> >> >> >> >> >> (BTW, is a "dataset" in HDF the same thing as a "variable" in netcdf?) >> >> >> >> I would like to make this some kind of "official" netCDF/HDF5 JSON format >> for the community, so I encourage anyone to read the specification >> >> >> >> If you see any flaw in the design or anything in the design that you >> would like to have change please let me know now >> >> >> >> done :-) >> >> >> >> It would be really great to have this become an "official" spec -- if you >> want to get it there, you're probably going to need to develop it more out >> in the open with a wider community. These lists are the way to get that >> started, but I suggest: >> >> >> >> 1) put it up somewhere that people can collaborate on it, make >> suggestions, capture the discussion, etc. gitHub is one really nice way to >> do that. See, for example the UGRID spec project: >> >> >> >> https://github.com/ugrid-conventions/ugrid-conventions >> >> >> >> (NOTE that that one got put on gitHub after there was a pretty complete >> draft spec, so there isn't THAT much discussion captured. But also note >> that that is too bad -- there is no good record of the decision process >> that led to the spec) >> >> >> >> At the moment it only (intentionally) uses common generic features of >> both netCDF and HDF5, which are the numeric atomic types and strings. >> >> >> >> Good plan. >> >> >> >> -Chris >> >> >> >> >> >> -- >> >> >> Christopher Barker, Ph.D. >> Oceanographer >> >> Emergency Response Division >> NOAA/NOS/OR&R (206) 526-6959 <%28206%29%20526-6959> voice >> 7600 Sand Point Way NE (206) 526-6329 <%28206%29%20526-6329> fax >> Seattle, WA 98115 (206) 526-6317 main reception >> >> Chris.Barker@xxxxxxxx >> >> > > > -- > > Christopher Barker, Ph.D. > Oceanographer > > Emergency Response Division > NOAA/NOS/OR&R (206) 526-6959 voice > 7600 Sand Point Way NE (206) 526-6329 fax > Seattle, WA 98115 (206) 526-6317 main reception > > Chris.Barker@xxxxxxxx > > -- Christopher Barker, Ph.D. Oceanographer Emergency Response Division NOAA/NOS/OR&R (206) 526-6959 voice 7600 Sand Point Way NE (206) 526-6329 fax Seattle, WA 98115 (206) 526-6317 main reception Chris.Barker@xxxxxxxx
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