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3D objects in PDFs are cool. My thesis used those in a few places. The PDF would print normally, but you could rotate it when open in Adobe Reader. Getting thi

3D objects in PDFs are cool. My thesis used those in a few places. The PDF would print normally, but you could rotate it when open in Adobe Reader. Getting this to work with Latex was... interesting. I spent a lot of time typesetting as a grad student.

thangngoc89 6y ago
Do you know of any automated way for extracting 3D objects in PDFs? My main profession is a dentist and I worked with various 3D and CAD/CAM system. I have intra-oral scanner that would capture 3D-colour model inside your mouth. The sad thing is the entire system is a walled garden. It uses its own 3D format (.dxd) and would only offer STL as an export format, which doesn’t contain any colors information. I worked around this by first exporting to a 3D PDF file. Then I use Sumatra PDF [1] to MANUALLY extract the 3D model in u3d format. U3D is a very obsolete format that almost no 3D authoring program can read it. So I have to use (yet another) proprietary software [2] to convert it to a common 3D format like PLY or 3DS or even to WebGL [3]. [1]: https://www.sumatrapdfreader.org/free-pdf-reader.html https://www.sumatrapdfreader.org/free-pdf-reader.html [2]: http://www.finalmesh.com/ http://www.finalmesh.com/ [3]: https://khoadabest.surge.sh https://khoadabest.surge.sh
- petters 6y ago
  I don't, sorry. From what you wrote, you definitely seem more knowledgeable than me in this area.
  - thangngoc89 6y ago
    Thank you for your input. I forgot the mention in the original post that there is a tool called pdf-parser.py [1] which claims to be able to do that but it produces a broken output. I don’t know anything about Python or PDF internals to hack on it. Posting it here and hoping that the HN crowds could point me in the correct direction. [1]: https://blog.didierstevens.com/programs/pdf-tools/ https://blog.didierstevens.com/programs/pdf-tools/
    - solresol 6y ago
      I'd like to talk to you about this, but you don't have any contact details in your profile. You can find me email address in my profile.
      - thangngoc89 6y ago
        Thank you very much. I updated my profile with an email address. Nevertheless, I emailed you via the contact details
    - aidos 6y ago
      Top tip: install mutool and run mutool clean -d your.pdf clean.pdf Now open clean.pdf with a text editor.
      - thangngoc89 6y ago
        That's really a top tip! Thank you very much. It looks like the original file is compressed using FlatDecode. Passing through mutool decompresses all streams and let's the parser does its job. Thank you!
        aidos 6y ago
        Great! Glad it worked. Happy to help you unpick things a bit further. When you look inside the pdf file you’ll see that it’s actually a “tree” of “things”. Each one starts with “obj 0 1234” (or something like that). And they reference each other to build the structure. So for example, the document is made of a list of pages. So that’s one object. And each page is another object. And then each page is made of a bunch more stuff and so on. Somewhere in there, no doubt, you’ll find an object that’s your model.
- daeken 6y ago
  Any chance you could get me some dxd files? I'd love to take a stab at reverse-engineering this and writing a direct converter to something standard. Feel free to email them to me (email in bio).
  - thangngoc89 6y ago
    Absolutely yes! I don't have any files that doesn't contains sensitive patient informations on my laptop at the moment but I will create new files when I'm back at work on Monday. I will email you when I have the files.
- thehesiod 6y ago
  I'd look at the 3D JS API via the JS bridge that I helped write: https://www.adobe.com/content/dam/acom/en/devnet/acrobat/pdfs/js_3d_api_reference.pdf https://www.adobe.com/content/dam/acom/en/devnet/acrobat/pdf...
- exikyut 6y ago
  Besides the other ideas in this subthread, the first thing that springs to mind for me is scanning a bunch of random objects, converting the models to as many 3D formats as you reasonably can, and dumping everything on GitHub along with reference photos of the objects. I'm personally idly curious, but have no experience with reverse engineering or 3D or file formats... so the emphasis on my end is idle curiosity :). But it's possible that many such people poking around may still generate interesting leads. Depending on how effectively intraoral scanners can scan things other than teeth, offering to scan random objects people send/bring in, on a best-effort/no-warranty basis, may also generate practical interest. (Also, wow, looks like these things are in the $25k range?)
  - thangngoc89 6y ago
    I think this is a pretty nice ideas. I will let you know once I've setup this. And just FYI, these expensive machines are actually at $50k. $25k range is for the scanner that has no color and requires you to coat the tooth with a layer of powder to prevent reflection from interfering with the scanner.
    - exikyut 6y ago
      Wow, nice :) I can imagine color being incredibly helpful... and not needing powder certainly makes the process more user friendly and less intrusive. Also, a very small extra thought, scanning extremely simple objects like cubes and flat planes may make the analysis process slightly easier because the data in the file will be easier to pars--wait. Okay I have more ideas. Can you convert/import arbitrary 3D data into the proprietary dxd format? If there is any way to do this, there is nothing else that will move the analysis process as far forward as quickly, and offer the best chances of producing the most complete result. This is because a) the data files will have 99% less complexity due to being synthetic and not containing noise associated with real-world data, b) they'll be full of reference points from known 3d models, and c) entirely controllable input data gives the highest chance of figuring out all values/fields in the model files. If this is possible, chances are most imports would be user requests based on the analysis process ("does changing this value alter this byte?"). Initial ideas I can think of would be the 3D Teapot, a single pixel :D, and simple cubes, triangles and planes. Lastly, coordinating a backup installation of the scanning software onto a dedicated machine, or moving the main install onto such a machine, that enterprising reverse-engineers could connect to remotely (ideally at any time of day, and obviously after privately negotiating credentials) and install debugging tools (read: IDA/Ghidra/etc) onto, would likely be extremely helpful, and should provide the best "how we reversed this" narrative with regards to licensing. This would simplify the import request situation too. If importing is not possible, IDA et al may end up being necessary to understand certain complex details or possibly even get started. Solving the "generate interest" problem would naturally be more complex in this scenario though. :/ I think I've really exhausted my knowledge in this area now :), although I do remain interested in knowing how things go.
- namdnay 6y ago
  Interestingly enough one of my early jobs was pretty much the opposite, writing a u3d encoder from spec and then using a commercial c++ pdf manipulation library to inject them into pdf files. I am sure there are libraires un python or JS nowadays, it’s just a question of parsing the tree to find the u3d node and dumping it out, very simple
  - thangngoc89 6y ago
    HN is really the only place that you can ask a question and received answers from someone who actually worked on the problem before. And you're correct that all I need to do is find u3d node and dumping it out. See my response in parent thread about using pdf-parser.py.
abhgh 6y ago
I am considering animations for my thesis. When printing, a designated frame should be used, but inside a reader, the animation should work. I am writing my thesis in LaTeX too. Any pointers?
- thangngoc89 6y ago
  Many 3D authoring program like Blender, Meshmixer can output U3D or RPC that you can use to embed into 3D PDF files. There are just many tools that can read the format. But beware that only Adobe Reader can show the 3D object
  - abhgh 6y ago
    Thank you! Yes, I wasn't thinking about the read-time support.
    - mkl 6y ago
      Note that PDF 3D models have a static image (a bitmap) which readers that don't support 3D (most of them) will show instead. Actually Adobe Reader shows the static image too, until you click on it to activate the 3D rendered version.
- ktpsns 6y ago
  You probably better invest the time in the preparation of a couple of beautiful Jupyter notebooks. That's where people expect interactivity and code to happen, not in PDFs. In my scientific community, virtually nobody uses Adobe Reader (people on Mac use Preview.App, people on Linux use poppler/xpdf/evince, browsers have their own internal readers). Edit/Appendum: Crafting an interactive website (i.e. without the dependency on jupyter) might be more future proof.
  - thangngoc89 6y ago
    Idyll (https://idyll-lang.org/ https://idyll-lang.org/) is a very promising tool in this field.
mkl 6y ago
Getting it to work in Latex is easy if you use Asymptote: https://asymptote.sourceforge.io/ https://asymptote.sourceforge.io/ Back in 2011 I used it to make a whole lot of figures for a multivariable calculus course; they're still in use.

thangngoc89 6y ago

Do you know of any automated way for extracting 3D objects in PDFs? My main profession is a dentist and I worked with various 3D and CAD/CAM system. I have intra-oral scanner that would capture 3D-colour model inside your mouth. The sad thing is the entire system is a walled garden. It uses its own 3D format (.dxd) and would only offer STL as an export format, which doesn’t contain any colors information. I worked around this by first exporting to a 3D PDF file. Then I use Sumatra PDF [1] to MANUALLY extract the 3D model in u3d format. U3D is a very obsolete format that almost no 3D authoring program can read it. So I have to use (yet another) proprietary software [2] to convert it to a common 3D format like PLY or 3DS or even to WebGL [3]. [1]: https://www.sumatrapdfreader.org/free-pdf-reader.html https://www.sumatrapdfreader.org/free-pdf-reader.html [2]: http://www.finalmesh.com/ http://www.finalmesh.com/ [3]: https://khoadabest.surge.sh https://khoadabest.surge.sh

petters 6y ago
I don't, sorry. From what you wrote, you definitely seem more knowledgeable than me in this area.
- thangngoc89 6y ago
  Thank you for your input. I forgot the mention in the original post that there is a tool called pdf-parser.py [1] which claims to be able to do that but it produces a broken output. I don’t know anything about Python or PDF internals to hack on it. Posting it here and hoping that the HN crowds could point me in the correct direction. [1]: https://blog.didierstevens.com/programs/pdf-tools/ https://blog.didierstevens.com/programs/pdf-tools/
  - solresol 6y ago
    I'd like to talk to you about this, but you don't have any contact details in your profile. You can find me email address in my profile.
    - thangngoc89 6y ago
      Thank you very much. I updated my profile with an email address. Nevertheless, I emailed you via the contact details
  - aidos 6y ago
    Top tip: install mutool and run mutool clean -d your.pdf clean.pdf Now open clean.pdf with a text editor.
    - thangngoc89 6y ago
      That's really a top tip! Thank you very much. It looks like the original file is compressed using FlatDecode. Passing through mutool decompresses all streams and let's the parser does its job. Thank you!
      - aidos 6y ago
        Great! Glad it worked. Happy to help you unpick things a bit further. When you look inside the pdf file you’ll see that it’s actually a “tree” of “things”. Each one starts with “obj 0 1234” (or something like that). And they reference each other to build the structure. So for example, the document is made of a list of pages. So that’s one object. And each page is another object. And then each page is made of a bunch more stuff and so on. Somewhere in there, no doubt, you’ll find an object that’s your model.
daeken 6y ago
Any chance you could get me some dxd files? I'd love to take a stab at reverse-engineering this and writing a direct converter to something standard. Feel free to email them to me (email in bio).
- thangngoc89 6y ago
  Absolutely yes! I don't have any files that doesn't contains sensitive patient informations on my laptop at the moment but I will create new files when I'm back at work on Monday. I will email you when I have the files.
thehesiod 6y ago
I'd look at the 3D JS API via the JS bridge that I helped write: https://www.adobe.com/content/dam/acom/en/devnet/acrobat/pdfs/js_3d_api_reference.pdf https://www.adobe.com/content/dam/acom/en/devnet/acrobat/pdf...
exikyut 6y ago
Besides the other ideas in this subthread, the first thing that springs to mind for me is scanning a bunch of random objects, converting the models to as many 3D formats as you reasonably can, and dumping everything on GitHub along with reference photos of the objects. I'm personally idly curious, but have no experience with reverse engineering or 3D or file formats... so the emphasis on my end is idle curiosity :). But it's possible that many such people poking around may still generate interesting leads. Depending on how effectively intraoral scanners can scan things other than teeth, offering to scan random objects people send/bring in, on a best-effort/no-warranty basis, may also generate practical interest. (Also, wow, looks like these things are in the $25k range?)
- thangngoc89 6y ago
  I think this is a pretty nice ideas. I will let you know once I've setup this. And just FYI, these expensive machines are actually at $50k. $25k range is for the scanner that has no color and requires you to coat the tooth with a layer of powder to prevent reflection from interfering with the scanner.
  - exikyut 6y ago
    Wow, nice :) I can imagine color being incredibly helpful... and not needing powder certainly makes the process more user friendly and less intrusive. Also, a very small extra thought, scanning extremely simple objects like cubes and flat planes may make the analysis process slightly easier because the data in the file will be easier to pars--wait. Okay I have more ideas. Can you convert/import arbitrary 3D data into the proprietary dxd format? If there is any way to do this, there is nothing else that will move the analysis process as far forward as quickly, and offer the best chances of producing the most complete result. This is because a) the data files will have 99% less complexity due to being synthetic and not containing noise associated with real-world data, b) they'll be full of reference points from known 3d models, and c) entirely controllable input data gives the highest chance of figuring out all values/fields in the model files. If this is possible, chances are most imports would be user requests based on the analysis process ("does changing this value alter this byte?"). Initial ideas I can think of would be the 3D Teapot, a single pixel :D, and simple cubes, triangles and planes. Lastly, coordinating a backup installation of the scanning software onto a dedicated machine, or moving the main install onto such a machine, that enterprising reverse-engineers could connect to remotely (ideally at any time of day, and obviously after privately negotiating credentials) and install debugging tools (read: IDA/Ghidra/etc) onto, would likely be extremely helpful, and should provide the best "how we reversed this" narrative with regards to licensing. This would simplify the import request situation too. If importing is not possible, IDA et al may end up being necessary to understand certain complex details or possibly even get started. Solving the "generate interest" problem would naturally be more complex in this scenario though. :/ I think I've really exhausted my knowledge in this area now :), although I do remain interested in knowing how things go.
namdnay 6y ago
Interestingly enough one of my early jobs was pretty much the opposite, writing a u3d encoder from spec and then using a commercial c++ pdf manipulation library to inject them into pdf files. I am sure there are libraires un python or JS nowadays, it’s just a question of parsing the tree to find the u3d node and dumping it out, very simple
- thangngoc89 6y ago
  HN is really the only place that you can ask a question and received answers from someone who actually worked on the problem before. And you're correct that all I need to do is find u3d node and dumping it out. See my response in parent thread about using pdf-parser.py.

abhgh 6y ago

I am considering animations for my thesis. When printing, a designated frame should be used, but inside a reader, the animation should work. I am writing my thesis in LaTeX too. Any pointers?

thangngoc89 6y ago
Many 3D authoring program like Blender, Meshmixer can output U3D or RPC that you can use to embed into 3D PDF files. There are just many tools that can read the format. But beware that only Adobe Reader can show the 3D object
- abhgh 6y ago
  Thank you! Yes, I wasn't thinking about the read-time support.
  - mkl 6y ago
    Note that PDF 3D models have a static image (a bitmap) which readers that don't support 3D (most of them) will show instead. Actually Adobe Reader shows the static image too, until you click on it to activate the 3D rendered version.
ktpsns 6y ago
You probably better invest the time in the preparation of a couple of beautiful Jupyter notebooks. That's where people expect interactivity and code to happen, not in PDFs. In my scientific community, virtually nobody uses Adobe Reader (people on Mac use Preview.App, people on Linux use poppler/xpdf/evince, browsers have their own internal readers). Edit/Appendum: Crafting an interactive website (i.e. without the dependency on jupyter) might be more future proof.
- thangngoc89 6y ago
  Idyll (https://idyll-lang.org/ https://idyll-lang.org/) is a very promising tool in this field.

mkl 6y ago

Getting it to work in Latex is easy if you use Asymptote: https://asymptote.sourceforge.io/ https://asymptote.sourceforge.io/ Back in 2011 I used it to make a whole lot of figures for a multivariable calculus course; they're still in use.