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Feb 7, 2014

Participants: Nicholas Schwarz(ANL), Arthur Glowacki(ANL), Ulrik Pedersen(Diamond), Alan Greer(Diamond), Nick Rees(Diamond)


  1) Discuss test results from new HDF5 plugin code
  2) Progress report on libxml2 in ADBinaries
  3) Go over git workflow ( make branch hdf5_xml for ADBinaries submodule?)


Alan will look into xml layout issue where if you remove the root group it does not correctly format the layout of the hdf5 file.
Ulrik is working on test / integrating SWMR features from HDF5 group
Arthur will work on reading the xml layout as a waveform or file

Next meeting will be the area detector workshop meeting

Jan 24, 2014

Participants: Nicholas Schwarz(ANL), Arthur Glowacki(ANL), Ulrik Pedersen(Diamond), Alan Greer(Diamond), Nick Rees(Diamond)


  1) Review where we left off since last meeting
  2) Talk about updates made since last meeting
  3) Go over results from testing
  4) Talk about next steps
  4a) Next steps: Windows support with libxml2


Reviewed the test results from Arthur's tests. Alan updated the source code and said fixes are available on github.

Discussed the process for contributing code to the area detector github repo. They are as follow:

1) Create a fork of the hdf5_xml branch

2) Make changes on your fork.

3) Pull and mearge with the main hdf5_xml branch

4) Send a pull request to hdf5_xml branch maintainer

ANL will maintain and update the HDF5 writer plugin ADL files for MEDM.

We decided to stick with 2 spaces for a tab in the source code to keep the file consistent.

Arthur will work on adding libxml2 to Windows build of Area Detector

The next meeting is scheduled for Feb 7, 2014 9:00 am central.

Dec 11, 2013

Participants: Nicholas Schwarz(ANL), Arthur Glowacki(ANL), Ulrik Pedersen(Diamond), Alan Greer(Diamond)

Agenda: Review HDF5 XML format and discuss adding features to it. XML Design Ideas 1


A lot of progress on updates to HDF5 plugin. Alan sent us (ANL) a package of the current source code to try out. Ulrik plans on putting the updates onto the new github repo that Mark created for area detector.

Current plugin does not support OnFileOpen and OnFileClose, it saves OnFrame. If it is saving to a dataset, the data is appended. The xml data has to be read in from a file. We talked about adding feature that it would read in the XML data as a waveform. This work would be done by ANL.

If there is no XML defined then the plugin falls back to the previous version. There is some hard coded xml in the source code that defines the previous version.

The plugin supports the value attribute in the XML tag only ( <dataset value="1"></dataset> ) but does not look inbetween the tags ( <dataset>1</dataset> ). It was agreed that both should be supported in the future (by ANL).

HDF5 Attributes will only support OnFileOpen or OnFileClose. It does not make sense to have OnFrame since no data will be appended to attributes.

detector_switch tag was added to tell where the data is saved if multiple datasets point to the images array. The name will be changed in the future for better comprehension.

NDAttributes are saved to the group if the tag ndattr_default=“true” exists. If it does not than a group called /NDAttributes is created in the file and the values are saved there.

We created a schema from a generator but plan to manually tweak it.
Minor issue:
 -If there is no end xml tag, the plugin crashes. ( <dataset /> causes crash, <dataset></dataset> is ok )

Next meeting is planned to be around middle of Jan 2014.

Nov 25, 2013

Participants: Nicholas Schwarz(ANL), Arthur Glowacki(ANL), Ulrik Pedersen(Diamond), Nick Rees(Diamond), Alan Greer(Diamond)

Agenda: Establish that Alan will be doing the finished plugin and understand each others requirements


Moved date to the 16th of December to look at first release.

Final product delivery by early / mid Feb

Arthur will work on converting current XML to new definition.

Nov 11, 2013

Participants: Nicholas Schwarz(ANL), Arthur Glowack(ANL)i, Ulrik Pedersen(Diamond), Nick Rees(Diamond)

Agenda: Video conference to discuss collaboration effort for unified HDF5 writer plugin


As Ulrik mentioned in a recent e-mail. Nick Rees and Ulrik have a contractor, Alan, assigned to work on merging XML parsing code from Diamond’s parallel HDF5 plug-in into the one in the general Area Detector distribution. This work should mostly be done by the end of the calendar year. Nick Rees mentioned that he’d like Diamond to lead this effort. I think that’s a great idea. 
We at the APS want to make certain that the functionality, format, output, etc. meet our requirements so that we can do away with the other two HDF5 plug-ins, use one, and use one that’s included as a part of the Area Detector distirbution.
Nick Rees recorded a general list of requirements for the plug-in. Can Nick put those online somewhere or send them around? We can volunteer our wiki,, if there’s no other convenient way to share them. That way all of us can modify them as needed.
Arthur produced a small XML file that we currently use with Tim Madden’s Area Detector plug-in. He can make one or two more with more data in them. Arthur can also generate some files with the current NeXuS plug-in so we can test compatibility.
Ulrik, can you send some example XML files from your parallel plug-in or put them online?
It would also be great to have somewhere accessible by all to put the code. We can offer our SVN repository for this if it helps. The goal wouldn’t be to use it as a permanent repository for the final work. That would presumably be the repository Mark manages. But it would be a great place to see the development progress, and where we could check out updates, test them, offer feedback, etc.
We will meet again on 25 November 2013 at 10 AM CST via Polycom to discuss current state, progress, etc.
On a side note: Nick and Ulrik mentioned the need for a HDF5 reader that streams data into the Area Detector pipeline. I can’t think of any of our customers that want this feature right now. (Does Mark know of anyone in APS/XSD that wants this?) Not having a customer makes it challenging for me to justify working on it. If this is something that’s pressing and needed on Diamond’s end, one possibility is to have your contractor work on that, and we can work on the XML part. Just a thought.

Oct 1, 2013

Participants: Nicholas Schwarz(ANL), Arthur Glowacki(ANL)

Agenda: Come up with initial deliverable

Status update:

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