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Port FlimJ-Ops to SciJava Ops #125

Merged
merged 13 commits into from
Apr 10, 2024
Merged

Port FlimJ-Ops to SciJava Ops #125

merged 13 commits into from
Apr 10, 2024

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gselzer
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@gselzer gselzer commented Feb 9, 2024

This PR adds a new module, SciJava Ops Flim, which ports the (ImageJ) Ops from FlimJ Ops.

TODO:

  • I had an issue encapsulating the SciJava Ops Flim code within a module, which I believe stems from native code access. Currently, the module info exists but is disabled through renaming, however we should either restore it or delete it (in its own commit, so we can find it again if necessary).
  • I removed parallel computation from AbstractSingleFitWorker because the routine depends on the Chunk class, which is internal to SciJava Ops Image. Do we care to add parallel computation back in? Should we add a compile-time dependency on SciJava Ops Image to enable us to depend on Chunk, or do something else? EDIT: I filed Parallelize SciJava Ops FLIM Ops scijava#205 for this.
  • I did not port this notebook describing FlimJ Ops access from Python, as those mechanisms are not yet set in stone. Maybe we should file a Paper 3 issue to port that notebook? EDIT: I filed Port flimj-ops Python notebook to SciJava Ops FLIM scijava#206 for this.
  • I cannot reproduce this image, using either the groovy script in the FlimJ Ops README, or with the new script in the updated README in this PR. Should we update the image below, which I observe running both scripts? EDIT: I incorrectly contrasted the image, thanks to @elevans for figuring that out. Added a note in the readme that hopefully prevents others from encountering this issue.
    image

@gselzer gselzer added documentation Improvements or additions to documentation enhancement New feature or request labels Feb 9, 2024
@gselzer gselzer requested a review from hinerm February 9, 2024 21:06
@gselzer gselzer self-assigned this Feb 9, 2024
@hinerm hinerm force-pushed the scijava-ops-flimlib/init branch 2 times, most recently from f719719 to 6d16edf Compare March 6, 2024 21:07
@gselzer gselzer force-pushed the scijava-ops-flimlib/init branch 4 times, most recently from b8d1226 to 62c551c Compare April 2, 2024 16:37
@gselzer gselzer force-pushed the scijava-ops-flimlib/init branch 9 times, most recently from b053728 to b8c5dee Compare April 2, 2024 23:35
@gselzer gselzer force-pushed the scijava-ops-flimlib/init branch from c58e7d7 to e9adfad Compare April 2, 2024 23:48
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gselzer commented Apr 2, 2024

Closes scijava/scijava#205

@gselzer gselzer linked an issue Apr 2, 2024 that may be closed by this pull request
@gselzer gselzer force-pushed the scijava-ops-flimlib/init branch 4 times, most recently from 4b22615 to d11b8d5 Compare April 9, 2024 16:29
@gselzer gselzer force-pushed the scijava-ops-flimlib/init branch from 58b43cd to bef2239 Compare April 10, 2024 14:03
gselzer added 4 commits April 10, 2024 17:52
Hopefully others find it easier to understand now that there's some
explanation
@gselzer gselzer force-pushed the scijava-ops-flimlib/init branch from 5335221 to d0af4b2 Compare April 10, 2024 22:58
@gselzer gselzer marked this pull request as ready for review April 10, 2024 23:03
@gselzer gselzer merged commit d25c6e4 into main Apr 10, 2024
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@gselzer gselzer deleted the scijava-ops-flimlib/init branch April 10, 2024 23:09
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Parallelize SciJava Ops FLIM Ops
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