[x3d-public] X3D minutes 27 MAR 2020: COVID modeling, Web3D video archives, Tool Updates, compression, spec, CORS
Don Brutzman
brutzman at nps.edu
Fri Mar 27 10:23:13 PDT 2020
X3D Working Group teleconference
1. Usual coordinates for telcon today, appearing near bottom of this message.
Attendees: Anita Havele, Vince Marchetti, Nicholas Polys, Dick Puk, Don Brutzman.
Participant review confirmed that no member-only information is included in these minutes.
Editorial note: these minutes are long because we are doing so much, which is great! We will continue to "divide and conquer" issues through multiple separate email threads on the x3d-public list.
All progress remains welcome and impressive, please keep charging! 8)
Recent meeting minutes:
[1.0] [x3d-public] X3D minutes 20 MAR 2020: COVID, X3D Ontology, PBR, Xj3D, Blender and MeshLab,
CollisionCollection, IFS in CADInterchange, CORS
https://web3d.org/pipermail/x3d-public_web3d.org/2020-March/011913.html
[1.1] [x3d-public] X3D minutes 6 MAR 2020: X3D4 special meeting on PBR, issue progress,
Metadata containerField defaults for XML encoding
https://web3d.org/pipermail/x3d-public_web3d.org/2020-March/thread.html
[1.2] [x3d] X3D WG discussions Feb 28 2020
https://web3d.org/mailman/private/x3d_web3d.org/2020-February/007819.html
[1.3] [x3d-public] X3D agenda 21 FEB 2020: X3Dv4 schedule planning
https://web3d.org/pipermail/x3d-public_web3d.org/2020-February/011791.html
[1.4] [x3d-public] X3D minutes 31 JAN 2020: X3Dv4 issues, XML Metadata containerField, consolidating mismatched field names
https://web3d.org/pipermail/x3d-public_web3d.org/2020-January/011746.html
TODO: prior minutes have a number of pending actions and changes to apply that are only partially complete. Efforts continue.
WARNING: Web3D.org mailman server is still misconfigured and returns http addresses (vice https) by default. Trouble report again submitted. Please be careful to use https wherever possible.
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2. *News and Events*
2.a. *COVID modeling discussion*.
[2.1] [x3d-public] Web3D COVID-19 Update
https://web3d.org/pipermail/x3d-public_web3d.org/2020-March/011900.html
From last week:
> [2.2] COVID
>> https://3dprint.nih.gov/discover?terms=covid&field_model_category_tag_tid%5B%5D=94
>
> [2.3] Corona
>> https://3dprint.nih.gov/discover?terms=corona&field_model_category_tag_tid%5B%5D=94
>
> Am planning to put one or two in X3D Example archives to get alternative encodings including JSON and TTL (Turtle for Semantic Web)
> [...] various opportunities to share current and emerging X3D capabilities for medical visualization and reasoning.
>
> ... perhaps a weekly topic?? continue the journey of 1000 steps...
> ... then convert it to various formats including Turtle for Semantic Web queries
> ... for X3D Semantic Web group, what is roadmap needed for usefulness to medical community?
> ... broader convergence? diverse expertise needed, Semantic Web is always cross disciplinary.
> ... temper expectations. we can't make any major contributions, but perhaps modest progress might help slightly with pandemic crisis.
> ... worth weekly agenda item to note activity. if ready perhaps a breakout meeting at some point.
Further model exploration on X3D Semantic Web call last Monday:
[2.4] X3D Semantic Web Working Group: chapter, talk, Tika and ROBOT tools, *COVID/Coronavirus models*
https://web3d.org/pipermail/x3d-public_web3d.org/2020-March/011920.html
Discussion: we are still looking for appropriate COVID 3D models appropriate for full set of X3D conversions and further work.
Nicholas has several years experience in bioinformatics and helped us understand the problem space better.
Certainly we are not going to "solve" anything major in this domain. We are way out of our depth, other experts and major companies have been working in this domain for decades. Often the papers being written and published are looking at a very specific protein receptor or virus site. Anything we might do would be from a computer science perspective.
Trying to associate an X3D representation with a smaller protein-level mode might be more useful. We might try to illustrate the processes being analyzed from a organic biochemistry perspective. Focusing on a specific model and paper might be useful.
Trying to connect geometric aspects of a PDB model to metadata to biochemical-reaction equation relationships might be the path to establishing a useful complement to existing capability. If we found a useful technique it might even be a good practice for some of the modeling-tool exporters.
Tools of interest relevant to Protein Data Base (PDB) which includes data + metadata:
[2.5] Chimera
From X3D Resources:
"Chimera by UCSF is a highly extensible program for interactive visualization and analysis of molecular structures and related data. Chimera exports X3D and VRML97."
[2.6] PMOD https://www.pmod.com
PMOD 3D Imaging Rendering Tool (P3D) enables interactive investigation of volumetric medical data and imagery as part of modeling tool suite.
Our thoughts and prayers are with everyone affected by the pandemic.
Note that NIH 3D Print Exchange ingests PDB models, uses a 3D exporter, and also adds struts for hydrogen bonds to allow printing.
[2.7] NIH 3D Print Exchange: models by Nicholas Polys
https://3dprint.nih.gov/discover?terms=&uid=nicholas+polys&field_model_license_nid=All&sort_by=created&sort_order=DESC&items_per_page=24
[2.8] NIH 3D Print Exchange announcement
"A collection of the latest SARS-CoV-2 viral structures is coming soon."
https://3dprint.nih.gov
Can we create a metadata template for this kind of work? Can we correlate it to the paper describing a protein, using DOI and other references? Many similarities with metadata needs for tool-chain work flows Cultural Heritage, CAD, 3D printing and other problem domains.
Candidate example of interest:
==================================================
[2.9] 6M17 The 2019-nCoV RBD/ACE2-B0AT1 complex
https://3dprint.nih.gov/discover/3DPX-013156
Model ID 3DPX-013156
Category: Proteins, Macromolecules and Viruses
http://www.rcsb.org/structure/6M17
Protein Data Bank ID 6M17
External Derivative Source RCSB PDB
see Literature section:
Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2.
Yan, R., Zhang, Y., Li, Y., Xia, L., Guo, Y., Zhou, Q.
(2020) Science --: --
PubMed: 32132184 Search on PubMed
DOI: 10.1126/science.abb2762
==================================================
Goal for this week:
- put this model in our examples and do conversions
- add inset to web3d.org
- link it to appropriate resource
---
2.b Renewed work on Web3D video archives.
The Web3D Communications Team has been working to add assets to our YouTube sites.
[2.10] Web3D Copnsortium YouTube
https://www.web3d.org/youtube
[2.11] Web3D Conference YouTube
https://www.youtube.com/channel/UCxg1RdwicxPHgRT0QQbuGFQ
[2.12] NIH 3D Print Exchange
https://www.youtube.com/channel/UCNmPN3UVxRrKbgsxSIKFxzQ/videos
Nicholas recent IEEE VR tutorial is online, we are working to also add it to YouTube for long-term stability.
[2.13] X3D Quickstart tutorial at IEEE VR
https://www.web3d.org/event/x3d-quickstart-tutorial-ieee-vr
http://www.ieeevr.org/2020/program/tutorials.html#T3
(see link to current Zoom page, recorded on IEEE VR account)
We discussed how video is being supported by IEEE VR, ACM SIGGRAPH and other organizations. We continue looking ahead at Web3D 2020 alternatives, video is an important part of our preparations.
---
2.c Next week we will review and update
[2.14] X3D Projects Wish List
https://www.web3d.org/projects/wish-list
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3. *Tool Updates*
a. Blender. Continuing bugfix activity noted there. 8)
[3.1] Blender Maniphest issues list: search X3D
https://developer.blender.org/search/query/61qmxOB3yNk4/#R
b. Meshlab. Developer release at
[3.2] MeshLab-2020.03
https://github.com/cnr-isti-vclab/meshlab/releases
[3.3] Meshlab issues list
https://github.com/cnr-isti-vclab/meshlab/issues
c. FreeWRL implementing PBR, has tremendous coverage of X3Dv3.3 already.
d. Castle Game Engine view3dscene continued progress on PBR, many opportunities to review and test and comment.
e. Xj3D rebuilt under OpenJDK 14 but debugging izPack installer upgrade deficiencies.
f. X_ITE X3D Browser, Have you seen this?
We note with pleasure that X_ITE v4.6.10 has quietly added 7 example models demonstrating X3D Volume Component (look near the bottom of many linked tiles). Cool! 8)
[3.4] X_ITE Examples
https://create3000.de/x_ite/getting-started/#x3d-examples
g. X3DOM? Others?
h. As ever, unit testing and regression checks continuing.
[3.5] X3D Resources, Examples: Scene Archives for X3D
https://www.web3d.org/x3d/content/examples/X3dResources.html#Examples
[3.6] X3D Validator
https://savage.nps.edu/X3dValidator
[3.7] X3D Resources, Examples: Quality Assurance (QA)
https://www.web3d.org/x3d/content/examples/X3dResources.html#QualityAssurance
Data point for today: complete build of X3D ConformanceNist suite took 1,387 minutes (~23 hours) of dedicated laptop time. Now uploaded.
Recent build logs: the following language-based regression tests are recent, in version control (to track progress) and linked at
https://www.web3d.org/x3d/content/examples/X3dResources.html#QualityAssurance
* https://www.web3d.org/x3d/content/examples/build.java.all.log.txt
* https://www.web3d.org/x3d/content/examples/build.json.all.log.txt
* https://www.web3d.org/x3d/content/examples/build.python.all.log.txt
TODO: will similarly add and list the following individual project build logs.
* https://x3dgraphics.com/examples/X3dForWebAuthors/build.log.txt
* https://x3dgraphics.com/examples/X3dForAdvancedModeling/build.log.txt
* https://www.web3d.org/x3d/content/examples/ConformanceNist/build.log.txt
* https://www.web3d.org/x3d/content/examples/Vrml2Sourcebook/build.log.txt
Vince noted that the ISO TC184 SC4 working group 12 (STEP product representations and geometry ontology) has been referring to the STEP examples added by the CAD Design Printing Scanning working group. The combination of formats (including Turtle .ttl) is useful.
[3.8] ConformanceNist X3D Examples Archive: STEP
https://www.web3d.org/x3d/content/examples/ConformanceNist/#STEP
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4. Binary geometric compression issues.
Web3D members in (CAD) Design Printing Scanning group have begun reexamining compression issues, especially in light of recent progress by multiple large-scale applications applying POP and SRC techniques. Interesting.
Membership has value. This topic has general interest, more to follow.
[4.0] Design Printing and Scanning Working Group
https://www.web3d.org/working-groups/design-printing-and-scanning
"The Design Printing and Scanning Working Group develops and demonstrates best practices for X3D support of Computer-Aided Design, 3D Printing, and 3D Scanning applications."
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5. Recent topic: CollisionCollection/RigidBody and X3DBoundedObject interface
Can we finish describing choices and rationales? I am not clear on rationale for not doing this.
> Nicholas mentioned slides by a student in Athanasios Malamos' multimedia group in TEI Crete during past Web3D Symposium that include these capabilities. He is reviewing and re-implementing them. There are three example scenes, deserves further interest.
>
>> http://medialab.teicrete.gr/minipages/H-Anim/
>> http://medialab.teicrete.gr/minipages/H-Anim/X3DOM_Physics.pdf
>> THANKS TO http://www.medialab.teicrete.gr
>
> See prior minutes for details on topic issue. Thought since last time: if we don't implement this interface, it is hard to explain consistently with other X3D design principles.
>
>> [6] [x3d-public] CollisionCollection implement X3DBoundedObject
>> https://web3d.org/pipermail/x3d-public_web3d.org/2020-February/011751.html
>>
>> [6.1] Mantis issue 1275: whether CollisionCollection and RigidBody implement X3DBoundedObject node
>> https://www.web3d.org/member-only/mantis/view.php?id=1275
>>
>> Seems simple, a parent node containing nodes with bbox fields should itself contain bbox fields. Let's review.
>>
>> We agreed that 37.4.10 RigidBody should implement X3DBoundedObject.
>>
>> Argument was made via various use cases that CollisionCollection might or might not need to be used for bounding box detections. Alternative might be to DEF/USE anything with a bounding box and let a corresponding Group or Transform hold those values... but that in turn would likely require a Switch whichChoice="-1" to avoid duplicate rendering.
>>
>> Use cares working around the hiding of bounding boxes within CollisionCollection are welcome.
>>
>> We haven't reached consensus yet... Pretty confusing for an author to construct all that, not yet clear what an effective design pattern would look like, and of note is that the primary purpose of CollisionCollection node is to hold "a collection of objects in the collidables field that can be managed as a single entity for resolution of inter-object collisions with other groups of collidable objects." So it already has direct knowledge of all bounding box computations and thus could efficiently compose them into an outer bounding box.
Rationales for not having bounding box:
- possible burden on implementers if they don't see benefit of this.
- others?
Also worth resolving:
> Another issue, but we didn't have time to discuss today. TODO further specification review and X3D unified object model checks.
>
>> [7] [x3d-public] X3DBoundedObject always X3DChildNode ?
>> https://web3d.org/pipermail/x3d-public_web3d.org/2020-February/011787.html
>>
>> "Ignoring for second the exception, I think that means there is a opportunity for simplification of the hierarchy by requiring X3DBoundedObject to implement X3DChildNode."
>>
>> Thanks Andreas!
>>
>> More there, certainly seems worth following up. We agreed it was worth further consideration, might possibly also resolve issue 1275.
>>
>> [7.1] Mantis 1282: is X3DBoundedObject always X3DChildNode ?
>> https://www.web3d.org/member-only/mantis/view.php?id=1282
Next step: Don attempts implementing these in X3DUOM and see if first and second issues actually work at simplifying the hierarchy.
With those results, if we are simplifying the hierarchy, then we will accept it. If not, not. Onward...
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6. X_ITE and CORS on local host
What additional material is needed to get the necessary information online?
> First, for conversions of X3D Example Archives to X_ITE presentation, just fixed encoding mismatch with X_ITE recommendations.
>
> prior:
> <X3DCanvas url='"BlenderDefaultBox.x3d"'>
>
> corrected, url changed to src and double-quotes removed:
>
> <X3DCanvas src='BlenderDefaultBox.x3d'>
> <p><b>Display error: X3D model not shown.</b></p>
> <p>Your HTML browser does not appear to support all features required by the
> <a href="http://create3000.de/x_ite" target="_blank">X_ITE</a> X3D player!</p>
> </X3DCanvas>
>
> All examples updated and deployed. This correction works on website, for example
>
> * https://x3dgraphics.com/examples/X3dForAdvancedModeling/Conversions/BlenderDefaultBoxX_ITE.html
>
> but dragging local file into browser gets a CORS error, apparently because it is treated as file:///
>
> Nicholas reports that running on localhost is handled differently because no local web server is present. His tutorial for IEEE VR has a few slides on this.
>
> Different servers are available for running locally...
> - atom text editor with http extension;
> - python -m SimpleHTTPServer
> (built in, must run in current directly)
> - others etc.
>
> Implications: authors deploying HTML/X3D for local usage need to have a localhost http server.
>
> Seems strange that local files can't run, but this is a long-running decision by browsers. Good to finally have an idea what the heck is happening!
>
> We do need to document CORS requirements and this deployment issue better. Perhaps X3D Scene Authoring Hints or another dedicated page, X3D Deployment Hints perhaps? Whatever works. TODO need to expose this knowledge.
We will start a dedicated thread to discuss this deployment issue. (Am also hoping to deconflict possible issues with HTML5/DOM, if any.)
Shouldn't need to be a big issue for our shared X3D4 development focus going forward after that.
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Upcoming meeting topics:
-Spatial Audio and Sound (after spec editors review Efi's PR pull request)
Regular updates:
- Blender, Meshlab, tools, projects wish list, and Quality Assurance (QA)
- COVID activity
Focus:
- Continued X3D4 issue review and resolution
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7. *X3Dv4 Background Information*
Major pieces of work in progress and highly mature include:
a. glTF lighting and physically based rendering, Michalis Kamburelis
b. X3D Sound Component and HTML Audio, Athanasios Malamos and Efi Lakka (in a few more weeks, hopefully)
c. Projective Texture Mapping (PTM), Kwan Hee Yoo
d. Many specification improvements and additions.
Key references:
[1] X3D Version 4 Overview
https://www.web3d.org/x3dv4
[2] X3Dv4 Highlights
httpss://www.web3d.org/x3dv4-highlights
[3] X3Dv4 Implementations Status
https://www.web3d.org/x3dv4-implementations
[4] Draft X3Dv4 specification from SIGGRAPH, August 2019
https://www.web3d.org/news-story/x3dv4-draft-specification-available-public-now
[5] X3D Specifications: Schema and DOCTYPE Validation
https://www.web3d.org/specifications
[6] Mantis Issue Tracker (requires multiple sets of member login)
https://www.web3d.org/member-only/mantis/view_all_bug_page.php
Web3D Consortium members can quickly see all X3Dv4 issues (with tag V4.0) by selecting the filter "X3Dv4" within mantis.
As specified in the reference pages, our next steps of implement/evaluate over the next quarter include
- finished specification prose in github,
- addressing all mantis issues,
- proper example X3D models available for each node/field,
- validation tools confirming examples are satisfactory,
- two or more implementations (X3DOM and X_ITE, FreeWrl and Castle Game Engine view3dscene),
- consensus by working group, approval by Web3D Consortium, submission to ISO.
Here are refined milestones from X3Dv4 Implementations Status page:
_Milestones Timeline_
* /26-31 July 2019/. Publish draft specification plus examples and implementation updates at Web3D2019/SIGGRAPH 2019 conferences.
* /16 December 2019/. Working group accepts X3Dv4 new-technology submissions, with rich capability set publicized for implementation work.
* /31 January 2020/. Specification Editors provide ISO Working Draft on github for use and confirmation by Web3D Consortium members.
* /First quarter 2020/. Implement new components in X3D players, evaluate scene examples for conformance. Publish weekly progress updates.
* /When completed/. Completed ISO Working Draft submitted to X3D Community, Web3D Consortium members, Web3D Board of Directors.
* /BoD approval/. Working Draft upgraded to Committee Draft and submitted with NWIP to ISO.
* /Sequential updates/. Specification updates for 19775-2 Scene Access Interface (SAI), file encodings (XML, ClassicVRML, JSON etc.) and language bindings (JavaScript, Java, Python), and X3D Semantic Web (possibly 19775-3).
A draft schedule update appears ready, based on member discussions, but we are still watching world events and conference delays/cancellations closely. More to follow when Board of Directors is ready - perhaps after the upcoming election. Meanwhile much necessary work continues apace.
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8. *Teleconference Information*
We are using the Web3D Consortium Zoom channel, to good effect. It allows use of internet audio, screen sharing and chat with links.
We meet regularly on Fridays 0800-0930 pacific. To join the teleconference:
Join URL https://zoom.us/j/148206572 for X3D Working Group
One tap mobile
* US (New York) +19292056099,,148206572 #
* US (San Jose) +16699006833,,148206572 #
Dial by your location, using (nine-digit number from Join URL above)
* US (New York) +1 929 205 6099
* US (San Jose) +1 669 900 6833
Additional information
Web3D Teleconference
http://www.web3d.org/member/teleconference-information
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Wow. Another major week with many people making progress in many ways.
Membership has value, steadily more than ever before. Please join and support and participate.
[99] Join the Web3D Consortium
https://www.web3d.org/join
Steady progress throughout. *Thanks 1M* for all efforts and stay safe out there.
Have fun with X3D! 8)
all the best, Don
--
Don Brutzman Naval Postgraduate School, Code USW/Br brutzman at nps.edu
Watkins 270, MOVES Institute, Monterey CA 93943-5000 USA +1.831.656.2149
X3D graphics, virtual worlds, navy robotics http://faculty.nps.edu/brutzman
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