Pre-Release API Review #9
Description
The API has been greatly narrowed with #7, and I am currently planning to limit the API further by only exposing top-level packages in #8, but I'd like more eyes on the API before any releases. We should consider:
Whether the API is navigable and self-explanatory
One motivation for #7 was that I found the API to be confusing - similar functionality existed in multiple classes, each in different directories, without sufficient documentation to describe the benefits of the different implementations. I tried making that clearer with docstrings, but I'm not sure whether it is enough. I don't want to bikeshed forever here, but some refactoring with the input of others would be beneficial.
Whether the API is sufficient for our use cases
@ctrueden was kind enough to compile a (mostly correct, by his admission) list of some projects that use imglib2-ij (sorted by number of imports) - we should ensure transition to imglib2-imagej is seamless:
1 3d/sciview-docs
1 clij/clij-custom-convolution-plugin
1 clij/clij-ops
1 clij/clijx
1 clij/clupath
1 fiji/Graph_Cut
1 fiji/Kappa
1 flimlib/flimj-ops
1 imagej/example-android-app
1 imagej/imagej-modelzoo
1 imagej/imagej-notebook
1 knime/knip-stitching
1 mastodon/mastodon-ellipsoid-fitting
1 napari/napari-imagej
1 sj-stuff/bigdataviewer-selector
1 sj-stuff/Hadim_Scripts
1 sj-stuff/ijp-imagetoatlas
1 sj-stuff/imglib2-icy
1 sj-stuff/mars-swing
1 sj-stuff/pendent-drop
1 sj-stuff/stardist-imagej
1 trackmate/TrackMate-Ilastik
1 training/i2k2020-imglib2-advanced
1 training/i2k-2020-pyimagej
2 3d/sciview
2 bigdist/BigDistributor_DesktopApp
2 clearvolume/imglib2-clearvolume
2 clij/clij
2 clij/clij-bdv
2 clij/clij-benchmarking-jmh
2 fiji/Correct_3D_Drift
2 fiji/fiji
2 fiji/fiji.github.io
2 fiji/FilamentDetector
2 fiji/legacy-imglib1
2 imagej/imagej-ui-swing
2 imglib/imglib2-realtransform
2 knime/knip-externals
2 knime/knip-scijava-bundles
2 mastodon/mastodon
2 mastodon/mastodon-collection
2 n5/n5
2 n5/n5-imglib2
2 sj-stuff/deepimagej-plugin
2 sj-stuff/mars-core
2 sj-stuff/mobie-io
2 sj-stuff/PHANTAST-FIJI
2 sj-stuff/SAMJ-IJ
2 trackmate/TrackMate-MorphoLibJ
2 trackmate/TrackMate-Weka
3 bigdist/BigDistributor-core
3 clij/clicy
3 clij/clij2-tests
3 clij/clij-mandelbrot-example
3 clij/clij-notebooks
3 fiji/MaMuT
3 fiji/simplified-io
3 imagej/imagej-common
3 n5/n5-utils
3 n5/n5-viewer
3 openspim/SPIMAcquisition
3 science/bigcat
3 sj-stuff/CircleSkinner
3 sj-stuff/ilastik4ij
3 sj-stuff/ImgLib2Access
3 sj-stuff/Interactive-H-Watershed
3 sj-stuff/LimeSeg
3 sj-stuff/metaseg
3 trackmate/TrackMate-Cellpose
3 trackmate/trackmate-core
3 trackmate/TrackMate-StarDist
3 training/imagej-legacy-course
4 bigdist/Dbio_headless
4 bioimage-io/JDLL
4 clij/clij2-fft
4 fiji/blockmatching
4 fiji/Trainable_Segmentation
4 imagej/imagej-scripting
4 sj-stuff/SAMJ-BDV
4 trackmate/TrackMate-Oneat
4 trackmate/TrackMate-Skeleton
4 trakem2/TrakEM2
5 bdv/bigdataviewer_fiji
5 bdv/bigdataviewer-playground
5 clij/clij-docs
5 ctrueden/sandbox
5 fiji/Image_Expression_Parser
5 imagej/presentations
5 n5/n5-spark
5 sj-stuff/mobie-viewer-fiji
6 clij/clij-boofcv
6 fiji/Colocalisation_Analysis
6 fiji-ext/z-spacing
6 fiji/Stitching
6 imagej/tutorials
6 imglib/imglib2-blk
6 sj-stuff/bigdataviewer-biop-tools
6 sj-stuff/BigTrace
7 3d/bigvolumeviewer-core
7 bdp/bigdataprocessor2
7 clij/clij-core
8 openspim/micro-OpenSPIM
9 3d/scenery
9 imagej/ops-experiments
9 sj-stuff/jipipe
9 sj-stuff/MoMA
9 sj-stuff/multiview-simulation
11 bigdist/BigDistributor
11 imagej/imagej-legacy
11 trackmate/TrackMate
12 imglib/imglib2-algorithm
12 sj-stuff/BigStitcher
12 sj-stuff/imagejfx
12 sj-stuff/JEX
12 sj-stuff/labkit-pixel-classification
14 mia/mia
14 sj-stuff/image-analysis-notebooks
15 imagej/imagej.github.io
16 knime/knip
16 sj-stuff/SNT
18 fiji-ext/bigwarp
18 imglib/imglib2-introductory-workshop
18 imglib/imglib2-www
18 n5/n5-ij
18 sj-stuff/fun.imagej
23 sj-stuff/labkit-ui
24 fiji/SPIM_Registration
26 imglib/imglib2-advanced-workshop
26 sj-stuff/RS-FISH
26 training/learnathon-2019
28 imglib/imglib2
37 imglib/imglib2-tutorials
39 sj-stuff/multiview-reconstruction
46 sj-stuff/hot-knife
60 training/learnathon-2017
63 imglib/imglib2-tests
69 imglib/imglib2-ij
76 sj-stuff/MTrack