Hi Elena Nice to hear from you.
I don’t think there is a solution to the problem which APIs wrote the file.
correct. but this is a problem for an application that wants to read both HDF5 and netCDF, say NCL, see below NCLs' team David Brown painful ways to decide which API to use. I just realized this problem 2 months ago, because I am trying to make a tool that reads both HDF5 and netCDF https://github.com/pedro-vicente/data-explorer if a user writes a netCDF file he should expect NCL to use the netCDF API to read it (and show netCDF things) if a user writes a pure HDF5 file he should expect NCL to use the HDF5 API to read it (and show HDF5 things) so, it is needed a way to "mark" a netCDF file as such , so that NCL "knows" that that file is * meant * to be read by netCDF.
Adding attributes, etc., really will not help. I can add an attribute to a “non-netCDF-4" HDF5 file and fool netCDF-4 library.
yes, true. that's what I said previously, the attribute approach is not 100 % "foolproof"
One should probably have a checker function that traverses an HDF5 file and tells if the file is compliant with the netCDF-4 convention.
I just did that https://github.com/pedro-vicente/netcdf-detect last week I sent an email with the subject " Detecting netCDF versus HDF5 -- PROPOSED SOLUTIONS --REQUEST FOR COMMENTS" I just realized I sent it twice by mistake to multiple email lists, and I got 8 emails with the same repeated content sorry about that the RFC proposed another way (not attribute related ) to deal with this I copy it here again SOLUTION 1: Add a flag to HDF5 source The hdf5 format specification, listed here https://www.hdfgroup.org/HDF5/doc/H5.format.html describes a sequence of bytes in the file layout that have special meaning for the HDF5 API. It is common practice, when designing a data format, so leave some fields "reserved for future use". This solution makes use of one of these empty "reserved for future use" spaces to save a byte (for example) that describes an enumerator of "HDF5 compatible formats". An "HDF5 compatible format" is a data format that uses the HDF5 API at a lower level (usually hidden from the user of the upper API), and providing its own API. The solution consists of writing a different enumerator value on the "reserved for future use" space. For example Value decimal 0 (current value): This file was generated by the HDF5 API (meaning the HDF5 only API) Value decimal 1: This file was generated by the netCDF API (using HDF5) Value decimal 2: This file was generated by <put here another HDF5 based format> and so on So, this solution is totally "foolproof". The writing of that byte in the netCDF file would be done by a * private * HDF5 function called by the netCDF API nc_create this allows the HDF Group to "keep track" of new HDF5 based formats. It allows to make the other format "HDF5 certified" . It's always a good thing to talk with the other HDF5 related organizations. I can pass anytime by the HDF office to explain this in detail best regardsby the way my previous email from today to hdf-forum was still put on moderator waiting list
could you please forward this email to "hdf-forum " ? ---------------------- Pedro Vicente pedro.vicente@xxxxxxxxxxxxxxxxxx https://twitter.com/_pedro__vicente http://www.space-research.org/----- Original Message ----- From: "Elena Pourmal" <epourmal@xxxxxxxxxxxx>
To: "Pedro Vicente" <pedro.vicente@xxxxxxxxxxxxxxxxxx> Cc: "HDF Users Discussion List" <hdf-forum@xxxxxxxxxxxxxxxxxx>; <netcdfgroup@xxxxxxxxxxxxxxxx> Sent: Sunday, April 24, 2016 7:10 PM Subject: Re: Detecting netCDF versus HDF5 All, I am probably missing something in this discussion. Since Pedro asked me to chime in and answer his question, I’ll try... [I am referring to Pedro’s initial question "Regarding the handling of both HDF5 and netCDF, it seems there is a potential issue, which is, how to tell if any HDF5 file was saved by the HDF5 API or by the netCDF API?”] netCDF-4 file is an HDF5 file. netCDF-4 is not a file format but a convention how to store data that is described by the netCDF-4 data model in HDF5. I don’t think there is a solution to the problem which APIs wrote the file. One can write a pure C program that doesn’t call HDF5 or netCDF-4 library but writes an HDF5 file according to the HDF5 file format and to the netCDF-4 convention making it a netCDF-4 file. One should probably have a checker function that traverses an HDF5 file and tells if the file is compliant with the netCDF-4 convention. Adding attributes, etc., really will not help. I can add an attribute to a “non-netCDF-4" HDF5 file and fool netCDF-4 library. I can also write netCDF-4 file using just pure HDF5 library by following convention of the netCDF-4 library. I think the tool should follow Common Data Model and shield data formats from the user. What I am missing? Elena ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Elena Pourmal The HDF Group http://hdfgroup.org 1800 So. Oak St., Suite 203, Champaign IL 61820 217.531.6112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Apr 24, 2016, at 6:08 PM, Pedro Vicente <pedro.vicente@xxxxxxxxxxxxxxxxxx> wrote:
All I posted some code on github that solves the issue for older netCDF files, see below In reply to previous comments @ John CaronHere are the blogs: http://www.unidata.ucar.edu/blogs/developer/en/entry/netcdf4_shared_dimensionsI had seen some of your blogs but not the one above. By looking at the netCDF code I came out with the code below that uses detection of one of the "hidden" attributes described in that blog, and other one that is not described @ David BrownBut this is not ideal, because we onlywant to open files that are explicitly written using NetCDF4 as NetCDFHi David, yes, that's the issue. I think this piece of code I posted on github is the possible best solution for this: https://github.com/pedro-vicente/netcdf-detect @ Ed Hartnett I wrote that code by reading the comments you wrote on the files nc4file.c and nc4hdf.c here https://github.com/Unidata/netcdf-c/tree/master/libsrc4 do you agree with the solution? anyone feel free to use that code the C function is called is_netcdf() the netCDF API writes, if variables and dimensions are present in the file: 1) an attribute named "_Netcdf4Dimid" (in some cases) 2) an attribute named "NAME", (always), saved by the HDF5 Dimension Scales API, that contains the string "This is a netCDF dimension but not a netCDF variable." This utility tries to detect both attributes by traversing the HDF5 file, if either case is found, it returns a value of 1 the program includes 3 test cases: 2 cases that generate a file with 1) and 2) above (they are mutually exclusive, it seems) , and a third one that simply does nc_create nc_close in this case, the above attributes are not written, so the test will fail, like someone posted here before. I would say if someone writes this kind of file, it is irrelevant using HDF5 or netCDF , the files are virtually identical * another * case that would give a false positive is the case where someone tries to be a spoiler and uses the HDF5 API to write these 2 attributes "_Netcdf4Dimid" "This is a netCDF dimension but not a netCDF variable." The only real "spoiler proof" 100% solution is the SOLUTION 1 I posted before: to have HDF5 save a byte in the file that explicitly tells what kind of derived API it is. This function would be a private HDF5 function called by the derived API, say called on nc_create() So, it does not deal with attributes written by public APIs at all @ Elena Pourmal Hi Elena, how are you? Any change of discussing this solution? by the way some of my email on this thread sent to the hdf-forum last Friday is waiting for approval "Your mail to 'Hdf-forum' with the subject... Is being held until the list moderator can review it for approval. " The hdf-forum now requires approval by a moderator? that does not work very well on weekends for example ---------------------- Pedro Vicente pedro.vicente@xxxxxxxxxxxxxxxxxx https://twitter.com/_pedro__vicente http://www.space-research.org/ ----- Original Message ----- From: "David Brown" <dbrown@xxxxxxxx> To: <netcdfgroup@xxxxxxxxxxxxxxxx> Sent: Saturday, April 23, 2016 3:06 PM Subject: Re: [netcdfgroup] netcdfgroup Digest, Vol 1126, Issue 2Since Pedro asked earlier about how NCL distinguishes between NetCDF4 and HDF5, I'm going to add my 2 cents to what now appears to be the longest thread ever on this mailing list. First a bit of background. Traditionally NCL has distinguished among file formats based solely on file extensions. If a file name ends with ".nc" then it is considered to be a NetCDF file and will be opened using the NetCDF library calls. Additionally there is an idiosyncratic feature where you can add an "virtual" extension to a file name to specify the format you want to use. For example, if the file is name "test", you can open it as "test.h5" to open it using HDF5 calls. Given this name NCL will look first for a file called "test.h5" and if that is not found then it will look for "test". You can even add extensions to files that already have them to open a file using another format: e.g. test.hdf.nc. But recent versions of NCL attempt to figure out the format of files that do not have recognized extensions. And that means we have definitely run into the issue that Pedro originally brought up. We want our HDF5 module to handle HDF5 files on their own terms, including, e.g., recognizing reference types. For now, we first try to see if the file can be opened using the NetCDF library, and if not, we try various versions of HDF. But this is not ideal, because we only want to open files that are explicitly written using NetCDF4 as NetCDF. So it is indeed welcome news that there will be global attributes added to explicitly identify the file as NetCDF4. However, it also would be nice if nc_inq_format or nc_inq_format_extended could be adjusted to give a definitive answer as to whether the file was created as NetCDF4. I have to admit I was quite surprised to discover that nc_inq_format_extended would not answer this seemingly obvious (to me at least) question. -Dave Brown NCL technical architect On Sat, Apr 23, 2016 at 10:21 AM, <netcdfgroup-request@xxxxxxxxxxxxxxxx> wrote:Send netcdfgroup mailing list submissions to netcdfgroup@xxxxxxxxxxxxxxxx To subscribe or unsubscribe via the World Wide Web, visit http://mailman.unidata.ucar.edu/mailman/listinfo/netcdfgroup or, via email, send a message with subject or body 'help' to netcdfgroup-request@xxxxxxxxxxxxxxxx You can reach the person managing the list at netcdfgroup-owner@xxxxxxxxxxxxxxxx When replying, please edit your Subject line so it is more specific than "Re: Contents of netcdfgroup digest..." Today's Topics: 1. Re: [CF-metadata] [Hdf-forum] Detecting netCDF versus HDF5 -- PROPOSED SOLUTIONS --REQUEST FOR COMMENTS (John Caron) ---------------------------------------------------------------------- Message: 1 Date: Fri, 22 Apr 2016 21:57:51 -0600 From: John Caron <jcaron1129@xxxxxxxxx> To: Pedro Vicente <pedro.vicente@xxxxxxxxxxxxxxxxxx> Cc: cf-metadata@xxxxxxxxxxxx, NetCDF-Java community <netcdf-java@xxxxxxxxxxxxxxxx>, netcdfgroup@xxxxxxxxxxxxxxxx Subject: Re: [netcdfgroup] [CF-metadata] [Hdf-forum] Detecting netCDF versus HDF5 -- PROPOSED SOLUTIONS --REQUEST FOR COMMENTS Message-ID: <CAN1vDkp3iYVaBcEvoC8irp83AVKT85Mq+h75PWU_L-dExjWcMA@xxxxxxxxxxxxxx> Content-Type: text/plain; charset="utf-8" Here are the blogs: http://www.unidata.ucar.edu/blogs/developer/en/entry/dimensions_scales http://www.unidata.ucar.edu/blogs/developer/en/entry/dimension_scale2 http://www.unidata.ucar.edu/blogs/developer/en/entry/dimension_scales_part_3 http://www.unidata.ucar.edu/blogs/developer/en/entry/netcdf4_shared_dimensions http://www.unidata.ucar.edu/blogs/developer/en/entry/netcdf4_use_of_dimension_scales On Fri, Apr 22, 2016 at 7:57 AM, Pedro Vicente < pedro.vicente@xxxxxxxxxxxxxxxxxx> wrote:John >>>i have written various blogs on the unidata site about why netcdf4 >>>!= hdf5, and what the unique signature for shared dimensions looks like, in >>>case you want details. yes, I am interested, I had the impression by looking at the code some years ago that netCDF writes some unique name attributes somewhere ---------------------- Pedro Vicente pedro.vicente@xxxxxxxxxxxxxxxxxx https://twitter.com/_pedro__vicente http://www.space-research.org/ ----- Original Message ----- *From:* John Caron <jcaron1129@xxxxxxxxx> *To:* Pedro Vicente <pedro.vicente@xxxxxxxxxxxxxxxxxx> *Cc:* cf-metadata@xxxxxxxxxxxx ; Discussion forum for the NeXus data format <nexus@xxxxxxxxxxxxxxx> ; netcdfgroup@xxxxxxxxxxxxxxxx ; Dennis Heimbigner <dmh@xxxxxxxx> ; NetCDF-Java community <netcdf-java@xxxxxxxxxxxxxxxx> *Sent:* Thursday, April 21, 2016 11:11 PM *Subject:* Re: [CF-metadata] [netcdfgroup] [Hdf-forum] Detecting netCDF versus HDF5 -- PROPOSED SOLUTIONS --REQUEST FOR COMMENTS 1) I completely agree with the idea of adding system metadata that indicates the library version(s) that wrote the file. 2) the way shared dimensions are implemented by netcdf4 is a unique signature that would likely identify (100 - epsilon) % of real data files in the wild. One could add such detection to the netcdf4 and/or hdf5 libraries, and/or write a utility program to detect. there are 2 variants: 2.1) one could write a netcdf4 file without shared dimensions, though im pretty sure no one does. but you could argue then that its fine to just treat it as an hdf5 file and read through hdf5 library 2.2) one could write a netcdf4 file with hdf5 library, if you knew what you are doing. i have heard of this happening. but then you could argue that its really a netcdf4 file and you should use netcdf library to read . i have written various blogs on the unidata site about why netcdf4 != hdf5, and what the unique signature for shared dimensions looks like, in case you want details. On Thu, Apr 21, 2016 at 4:18 PM, Pedro Vicente < pedro.vicente@xxxxxxxxxxxxxxxxxx> wrote:If you have hdf5 files that should be readable, then I will undertake tolook at them and see what the problem is.ok, thank you WRT to old files: We could produce a utility that would redef the fileand insert the _NCProperties attribute. This would allow someone to wholesale mark old files.Excellent idea , Dennis ---------------------- Pedro Vicente pedro.vicente@xxxxxxxxxxxxxxxxxx https://twitter.com/_pedro__vicente http://www.space-research.org/ ----- Original Message ----- From: <dmh@xxxxxxxx> To: "Pedro Vicente" <pedro.vicente@xxxxxxxxxxxxxxxxxx>; < cf-metadata@xxxxxxxxxxxx>; "Discussion forum for the NeXus data format" < nexus@xxxxxxxxxxxxxxx>; <netcdfgroup@xxxxxxxxxxxxxxxx> Sent: Thursday, April 21, 2016 5:02 PM Subject: Re: [netcdfgroup] [Hdf-forum] Detecting netCDF versus HDF5 -- PROPOSED SOLUTIONS --REQUEST FOR COMMENTS If you have hdf5 files that should be readable, then I will undertake tolook at them and see what the problem is. WRT to old files: We could produce a utility that would redef the file and insert the _NCProperties attribute. This would allow someone to wholesale mark old files. =Dennis Heimbigner Unidata On 4/21/2016 2:17 PM, Pedro Vicente wrote:Dennis I am in the process of adding a global attribute in the root groupthat captures both the netcdf library version and the hdf5 libraryversion whenever a netcdf file is created. The current form is _NCProperties="version=...|netcdflibversion=...|hdflibversion=..."ok, good to know, thank you > 1. I am open to suggestions about changing the format or addinginfo > to it.I personally don't care, anything that uniquely identifies a netCDF file (HDF5 based) as such will work 2. Of course this attribute will not exist in files written using olderversions of the netcdf library, but at least the process will havebegun.yes 3. This technically does not address the original issue because thereexist hdf5 files not written by netcdf that are still compatible with and can be read by netcdf. Not sure this case is important or not.there will always be HDF5 files not written by netcdf that netCDF will read as we are now. this is not really the issue, but you just made a further issue :-) the issue is that I would like an application that reads a netCDF (HDF5 based) file to decide to use the netCDF or HDF5 API. your attribute writing will do , for future files. for older nertCDF files there may be a way to detect the current attributes and data structures to see if we can make it "identify itself" as netCDF. A bit of debugging will confirm that, since Dimension Scales are used, that would be an (imperfect maybe) way to do it regarding the "further issue " above you could go one step further and for any HDF5 files not written by netcdf , you could make netCDF reject the file reading, because it's not "netCDF compliant". Since having netCDF read pure HDF5 files is not a problem (at least for me), I don't know if you would want to do this, just an idea. In my mind taking complexity and ambiguities of problems is always a good thing ah, I forgot one thing, related to this In the past I have found several pure HDF5 files that netCDF failed in reading. Since netCDF is HDF5 binary compatible, one would expect that all HDF5 files will be read by netCDF. Except if you specifically wrote something in the code that makes it to fail if some condition is not met, This was a while ago, I'll try to find those cases and I'll send a bug report to the bug report email ---------------------- Pedro Vicente pedro.vicente@xxxxxxxxxxxxxxxxxx https://twitter.com/_pedro__vicente http://www.space-research.org/ ----- Original Message ----- From: <dmh@xxxxxxxx> To: "Pedro Vicente" <pedro.vicente@xxxxxxxxxxxxxxxxxx>; "HDF Users Discussion List" <hdf-forum@xxxxxxxxxxxxxxxxxx>; < cf-metadata@xxxxxxxxxxxx>; "Discussion forum for the NeXus data format" <nexus@xxxxxxxxxxxxxxx>; <netcdfgroup@xxxxxxxxxxxxxxxx> Cc: "John Shalf" <jshalf@xxxxxxx>; <Richard.E.Ullman@xxxxxxxx>; "Marinelli, Daniel J. (GSFC-5810)" <daniel.j.marinelli@xxxxxxxx>; "Miller, Mark C." <miller86@xxxxxxxx> Sent: Thursday, April 21, 2016 2:30 PM Subject: Re: [netcdfgroup] [Hdf-forum] Detecting netCDF versus HDF5 -- PROPOSED SOLUTIONS --REQUEST FOR COMMENTS I am in the process of adding a global attribute in the root groupthat captures both the netcdf library version and the hdf5 library version whenever a netcdf file is created. The current form is _NCProperties="version=...|netcdflibversion=...|hdflibversion=..." Where version is the version of the _NCProperties attribute and the others are e.g. 1.8.18 or 4.4.1-rc1. Issues: 1. I am open to suggestions about changing the format or adding info to it. 2. Of course this attribute will not exist in files written using older versions of the netcdf library, but at least the process will have begun. 3. This technically does not address the original issue because there exist hdf5 files not written by netcdf that are still compatible with and can be read by netcdf. Not sure this case is important or not. =Dennis Heimbigner Unidata On 4/21/2016 9:33 AM, Pedro Vicente wrote:DETECTING HDF5 VERSUS NETCDF GENERATED FILES REQUEST FOR COMMENTS AUTHOR: Pedro Vicente AUDIENCE: 1) HDF, netcdf developers, Ed Hartnett Kent Yang 2) HDF, netcdf users, that replied to this thread Miller, Mark C. John Shalf 3 ) netcdf tools developers Mary Haley , NCL 4) HDF, netcdf managers and sponsors David Pearah , CEO HDF Group Ward Fisher, UCAR Marinelli, Daniel J. , Richard Ullmman, Christopher Lynnes, NASA 5) [CF-metadata] list After this thread started 2 months ago, there was an annoucement on the [CF-metadata] mail list about "a meeting to discuss current and future netCDF-CF efforts and directions. The meeting will be held on 24-26 May 2016 in Boulder, CO, USA at the UCAR Center Green facility." This would be a good topic to put on the agenda, maybe? THE PROBLEM: Currently it is impossible to detect if an HDF5 file was generated by the HDF5 API or by the netCDF API. See previous email about the reasons why. WHY THIS MATTERS: Software applications that need to handle both netCDF and HDF5 files cannot decide which API to use. This includes popular visualization tools like IDL, Matlab, NCL, HDF Explorer. SOLUTIONS PROPOSED: 2 SOLUTION 1: Add a flag to HDF5 source The hdf5 format specification, listed here https://www.hdfgroup.org/HDF5/doc/H5.format.html describes a sequence of bytes in the file layout that have special meaning for the HDF5 API. It is common practice, when designing a data format, so leave some fields "reserved for future use". This solution makes use of one of these empty "reserved for future use" spaces to save a byte (for example) that describes an enumerator of "HDF5 compatible formats". An "HDF5 compatible format" is a data format that uses the HDF5 API at a lower level (usually hidden from the user of the upper API), and providing its own API. This category can still be divide in 2 formats: 1) A "pure HDF5 compatible format". Example, NeXus http://www.nexusformat.org/ NeXus just writes some metadata (attributes) on top of the HDF5 API, that has some special meaning for the NeXus community 2) A "non pure HDF5 compatible format". Example, netCDF Here, the format adds some extra feature besides HDF5. In the case of netCDF, these are shared dimensions between variables. This sub-division between 1) and 2) is irrelevant for the problem and solution in question The solution consists of writing a different enumerator value on the "reserved for future use" space. For example Value decimal 0 (current value): This file was generated by the HDF5 API (meaning the HDF5 only API) Value decimal 1: This file was generated by the netCDF API (using HDF5) Value decimal 2: This file was generated by <put here another HDF5 based format> and so on The advantage of this solution is that this process involves 2 parties: the HDF Group and the other format's organization. This allows the HDF Group to "keep track" of new HDF5 based formats . It allows to make the other format "HDF5 certified" . SOLUTION 2: Add some metadata to the other API on top of HDF5 This is what Nexus uses. A Nexus file on creation writes several attributes on the root group, like "NeXus_version" and other numeric data. This is done using the public HDF5 API calls. The solution for netCDF consists of the same approach, just write some specific attributes, and a special netCDF API to write/read them. This solutions just requires the work of one party (the netCDF group) END OF RFC In reply to people that commented in the thread @John Shalf >>Perhaps NetCDF (and other higher-level APIs that are built on >>top >>of HDF5) should include an attribute attached >>to the root group that identifies the name and version of the >>API that created the file? (adopt this as a convention) yes, that's one way to do it, Solution 2 above @Mark Miller >>>Hmmm. Is there any big reason NOT to try to read a netCDF >>>produced HDF5 file with the native HDF5 library if someone so chooses? It's possible to read a netCDF file using HDF5, yes. There are 2 things that you will miss doing this: 1) the ability to inquire about shared netCDF dimensions. 2) the ability to read remotely with openDAP. Reading with HDF5 also exposes metadata that is supposed to be private to netCDF. See below >>>> And, attempting to read an HDF5 file produced by Silo using >>>> just the HDF5 library (e.g. w/o Silo) is a major pain. This I don't understand. Why not read the Silo file with the Silo API? That's the all purpose of this issue, each higher level API on top of HDF5 should be able to detect "itself". I am not familiar with Silo, but if Silo cannot do this, then you have the same design flaw that netCDF has. >>> In a cursory look over the libsrc4 sources in netCDF distro, I >>> see a few things that might give a hint a file was created with netCDF. . . >>>> First, in NC_CLASSIC_MODEL, an attribute gets attached to the root group named "_nc3_strict". So, the existence of an attribute on the root group by that name would suggest the HDF5 file was generated by netCDF. I think this is done only by the "old" netCDF3 format. >>>>> Also, I tested a simple case of nc_open, nc_def_dim, etc. nc_close to see what it produced. >>>> It appears to produce datasets for each 'dimension' defined >>>> with two attributes named "CLASS" and "NAME". This is because netCDF uses the HDF5 Dimension Scales API internally to keep track of shared dimensions. These are internal attributes of Dimension Scales. This approach would not work because an HDF5 only file with Dimension Scales would have the same attributes. >>>> I like John's suggestion here. >>>>>But, any code you add to any applications now will work >>>>>*only* for files that were produced post-adoption of this convention. yes. there are 2 actions to take here. 1) fix the issue for the future 2) try to retroactively have some workaround that makes possible now to differentiate a HDF5/netCDF files made before the adopted convention see below >>>> In VisIt, we support >140 format readers. Over 20 of those >>>> are different variants of HDF5 files (H5part, Xdmf, Pixie, Silo, Samrai, netCDF, Flash, Enzo, Chombo, etc., etc.) >>>>When opening a file, how does VisIt figure out which plugin to use? In particular, how do we avoid one poorly written reader plugin (which may be the wrong one for a given file) from preventing the correct one from being found. Its kinda a hard problem. Yes, that's the problem we are trying to solve. I have to say, that is quick a list of HDF5 based formats there. >>>> Some of our discussion is captured here. . . http://www.visitusers.org/index.php?title=Database_Format_Detection I"ll check it out, thank you for the suggestions @Ed Hartnett >>>I must admit that when putting netCDF-4 together I never >>>considered that someone might want to tell the difference between a "native" HDF5 file and a netCDF-4/HDF5 file. >>>>>Well, you can't think of everything. This is a major design flaw. If you are in the business of designing data file formats, one of the things you have to do is how to make it possible to identify it from the other formats. >>> I agree that it is not possible to canonically tell the difference. The netCDF-4 API does use some special attributes to track named dimensions, >>>>and to tell whether classic mode should be enforced. But it >>>>can easily produce files without any named dimensions, etc. >>>So I don't think there is any easy way to tell. I remember you wrote that code together with Kent Yang from the HDF Group. At the time I was with the HDF Group but unfortunately I did follow closely what you were doing. I don't remember any design document being circulated that explains the internals of the "how to" make the netCDF (classic) model of shared dimensions use the hierarchical group model of HDF5. I know this was done using the HDF5 Dimension Scales (that I wrote), but is there any design document that explains it? Maybe just some internal email exchange between you and Kent Yang? Kent, how are you? Do you remember having any design document that explains this? Maybe something like a unique private attribute that is written somewhere in the netCDF file? @Mary Haley, NCL NCL is a widely used tool that handles both netCDF and HDF5 Mary, how are you? How does NCL deal with the case of reading both pure HDF5 files and netCDF files that use HDF5? Would you be interested in joining a community based effort to deal with this, in case this is an issue for you? @David Pearah , CEO HDF Group I volunteer to participate in the effort of this RFC together with the HDF Group (and netCDF Group). Maybe we could make a "task force" between HDF Group, netCDF Group and any volunteer (such as tools developers that happen to be in these mail lists)? The "task force" would have 2 tasks: 1) make a HDF5 based convention for the future and 2) try to retroactively salvage the current design issue of netCDF My phone is 217-898-9356, you are welcome to call in anytime. ---------------------- Pedro Vicente pedro.vicente@xxxxxxxxxxxxxxxxxx <mailto: pedro.vicente@xxxxxxxxxxxxxxxxxx> https://twitter.com/_pedro__vicente http://www.space-research.org/ ----- Original Message ----- *From:* Miller, Mark C. <mailto:miller86@xxxxxxxx> *To:* HDF Users Discussion List <mailto: hdf-forum@xxxxxxxxxxxxxxxxxx> *Cc:* netcdfgroup@xxxxxxxxxxxxxxxx <mailto:netcdfgroup@xxxxxxxxxxxxxxxx> ; Ward Fisher <mailto:wfisher@xxxxxxxx> *Sent:* Wednesday, March 02, 2016 7:07 PM *Subject:* Re: [Hdf-forum] Detecting netCDF versus HDF5 I like John's suggestion here. But, any code you add to any applications now will work *only* for files that were produced post-adoption of this convention. There are probably a bazillion files out there at this point that don't follow that convention and you probably still want your applications to be able to read them. In VisIt, we support >140 format readers. Over 20 of those are different variants of HDF5 files (H5part, Xdmf, Pixie, Silo, Samrai, netCDF, Flash, Enzo, Chombo, etc., etc.) When opening a file, how does VisIt figure out which plugin to use? In particular, how do we avoid one poorly written reader plugin (which may be the wrong one for a given file) from preventing the correct one from being found. Its kinda a hard problem. Some of our discussion is captured here. . . http://www.visitusers.org/index.php?title=Database_Format_Detection Mark From: Hdf-forum <hdf-forum-bounces@xxxxxxxxxxxxxxxxxx <mailto:hdf-forum-bounces@xxxxxxxxxxxxxxxxxx>> on behalf of John Shalf <jshalf@xxxxxxx <mailto:jshalf@xxxxxxx>> Reply-To: HDF Users Discussion List <hdf-forum@xxxxxxxxxxxxxxxxxx <mailto:hdf-forum@xxxxxxxxxxxxxxxxxx>> Date: Wednesday, March 2, 2016 1:02 PM To: HDF Users Discussion List <hdf-forum@xxxxxxxxxxxxxxxxxx <mailto:hdf-forum@xxxxxxxxxxxxxxxxxx>> Cc: "netcdfgroup@xxxxxxxxxxxxxxxx <mailto:netcdfgroup@xxxxxxxxxxxxxxxx>" <netcdfgroup@xxxxxxxxxxxxxxxx <mailto:netcdfgroup@xxxxxxxxxxxxxxxx>>, Ward Fisher <wfisher@xxxxxxxx <mailto:wfisher@xxxxxxxx>> Subject: Re: [Hdf-forum] Detecting netCDF versus HDF5 Perhaps NetCDF (and other higher-level APIs that are built on top of HDF5) should include an attribute attached to the root group that identifies the name and version of the API that created the file? (adopt this as a convention) -john On Mar 2, 2016, at 12:55 PM, Pedro Vicente <pedro.vicente@xxxxxxxxxxxxxxxxxx <mailto:pedro.vicente@xxxxxxxxxxxxxxxxxx>> wrote: Hi Ward As you know, Data Explorer is going to be a general purpose data reader for many formats, including HDF5 and netCDF. Here http://www.space-research.org/ Regarding the handling of both HDF5 and netCDF, it seems there is a potential issue, which is, how to tell if any HDF5 file was saved by the HDF5 API or by the netCDF API? It seems to me that this is not possible. Is this correct? netCDF uses an internal function NC_check_file_type to examine the first few bytes of a file, and for example for any HDF5 file the test is /* Look at the magic number */ /* Ignore the first byte for HDF */ if(magic[1] == 'H' && magic[2] == 'D' && magic[3] == 'F') { *filetype = FT_HDF; *version = 5; The problem is that this test works for any HDF5 file and for any netCDF file, which makes it impossible to tell which is which. Which makes it impossible for any general purpose data reader to decide to use the netCDF API or the HDF5 API. I have a possible solution for this , but before going any further, I would just like to confirm that 1) Is indeed not possible 2) See if you have a solid workaround for this, excluding the dumb ones, for example deciding on a extension .nc or .h5, or traversing the HDF5 file to see if it's non netCDF conforming one. Yes, to further complicate things, it is possible that the above test says OK for a HDF5 file, but then the read by the netCDF API fails because the file is a HDF5 non netCDF conformant Thanks ---------------------- Pedro Vicente pedro.vicente@xxxxxxxxxxxxxxxxxx <mailto:pedro.vicente@xxxxxxxxxxxxxxxxxx> http://www.space-research.org/ _______________________________________________ Hdf-forum is for HDF software users discussion. 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