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Feature request: Tubular geodesics #194
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Hi @fethallah , I was able to get the multiscale filtering to work on Linux (OpenSUSE Tumbleweed) with the latest Fiji 2.14.0. To reproduce:
However, when I try to load the saved .oof image as a secondary layer using the "From File...", the auto-tracing mode switches to Fast Marching, as expected, but the secondary layer checkbox does not activate, and attempting to select points for tracing fails without an exception. I can look into why this is failing. |
HI @fethallah , But I am a bit confused about the error you are getting:
My understanding is that all of those
with
@carshadi if you are looking into the GUI failure, perhaps I can look into this refractioning. But @fethallah, how do you feel about Tubular Geodesics being ported into Java? Imglib2 and scijava -- that we use for other filtering -- have gone a long way and I'm wondering if direct porting wouldn't be the easiest at this point., as there are still deprecated dependencies being used by |
Thank you @tferr and @carshadi for your prompt responses :-) Why not porting to java. but have no idea how much effort it would take. I need to give myself a refresher, and rebuild a diagram of the components. Happy to take a call (ideally mornings CET time). |
I was able to get past the GUI failure in 7381363 , but there is second point of failure when calling the ITK code:
It appears to reference the old I was trying to test it myself but ran into an issue compiling ITK 4.1 . It appears to require gcc < 5, and it is not straightforward to install super old gcc versions on my system, so I gave up. @fethallah do you think ITK >= 5.0 would work? Or would you have the bandwidth to try building it? On porting to imglib2, that could allow it to run on images much larger than can fit in RAM. It feels like getting the current implementation working again should be fairly quick though. |
@carshadi, this is great. I remade PathResult public with 45764a7. @fethallah, I forked the project here and added minimum tweaks to have it compatible with the current fixes in SNT. I don't know how you guys were managing dependencies at the time (we use maven), but I did not want to make too many changes to your project in case I would break the C++ plus part). Here is what I did:
With these changes, I no longer get compilation warnings (Eclipse and Java 11 -- I assume Mark was using Eclipse at the time, so I also committed Eclipse project files in the fork --), but similarly to @carshadi, I was not able to compile the entire thing. Maybe you can give this a go and see if it works for you? |
Hi @tferr and @carshadi , thanks for moving forward . I just created a draft pull request and added you to the repo. A few things to consider if we decide to keep the C++ dependencies:
Referring to a previous question, bandwidth is a challenge. But if I understood well, I mainly need to focus on the 2 tasks above. @tferr and @carshadi , what would be your preferred route ?
|
@fethallah, I'd love to have this working 'properly' in Java, but I won't be able to commit to this in the near future. Unless @carshadi, has the bandwidth, I'd propose we try to go the ITK route. If those two items above (FFTW and ITK5) become too involved for you, we could re-assess. |
@bogovicj just mentioned that there has been work on IJ/ITK integration here: https://github.com/imagej/imagej-itk |
Is your feature request related to a problem? Please describe.
Hi SNT dev team, really great to see this project still alive. Having contributed to the tubular geodesics plugins, I have just tested it to first generate the multi-scale filtered images, with OOF: Optimally Oriented Flux ) and had the error below (see additional context). I would love to get them back to life (could be helpful for a side project). It seems that the plugins are integrated with the latest version of SNT (under
Fast Marching
), but the multi-scale filtering is an essential step and it's not working.Did anyone managed to execute these plugins recently ?
Describe the solution you'd like
If installing an older version of ImgeJ/Fiji would work, I'd be happy with it, but I couldn't easily find the release history (and java versions dependencies).
Describe alternatives you've considered
I could make a bit of time to help with a merge request if needed.
Additional context
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