Codebase

The code is in OOP style divided into two parts, radiantkit which contain the core functionality and radiantkit.scripts which contain the command line tools.

The main entry point can be found in run.py which is also called from __main__.py.

Class inheritance

BinarizerSettings -> Binarizer
BoundingElement
ChannelList
CziFile -> CziFile2
Enum -> CenterType
Enum -> DistanceType
Enum -> LaminaDistanceType
Enum -> MidsectionType
Enum -> ProjectionType
Enum -> RootType
Enum -> SegmentationType
Enum -> ShellType
ImageBase -> Image -> ImageBinary
ImageBase -> Image -> ImageBinary -> ParticleBase -> Particle -> Nucleus
ImageBase -> Image -> ImageGrayScale
ImageBase -> Image -> ImageLabeled
MultiRange
ND2Reader -> ND2Reader2
NucleiList
OutputDirectories -> Output
OutputDirectories -> ReportBase
OutputDirectories -> ReportMaker
OutputReader
ParticleFinder
ProfileMultiConditionNorm
ProfileSingleCondition
RadialDistanceCalculator
ReportPage
SeriesList
string.Template -> TIFFNameTemplate
TIFFNameTemplateFields

The call stacks are somewhat deep and can be hard to understand

where
/home/erikw/.local/bin/radiantkit(8)<module>()
-> sys.exit(radiant())
/home/erikw/.local/share/pipx/venvs/radiantkit/lib/python3.12/site-packages/radiantkit/run.py(74)radiant()
-> args.run(args)
/home/erikw/.local/share/pipx/venvs/radiantkit/lib/python3.12/site-packages/radiantkit/scripts/radial_population.py(380)run()
-> profiles = series_list.get_radial_profiles(
/home/erikw/.local/share/pipx/venvs/radiantkit/lib/python3.12/site-packages/radiantkit/series.py(582)get_radial_profiles()
-> self.__prep_single_channel_profile(
/home/erikw/.local/share/pipx/venvs/radiantkit/lib/python3.12/site-packages/radiantkit/series.py(506)__prep_single_channel_profile()
-> channel_intensity_data = self.__retrieve_channel_intensity_at_distance(
/home/erikw/.local/share/pipx/venvs/radiantkit/lib/python3.12/site-packages/radiantkit/series.py(469)__retrieve_channel_intensity_at_distance()
-> s.init_particles_distances(rdc, reInit)
/home/erikw/.local/share/pipx/venvs/radiantkit/lib/python3.12/site-packages/radiantkit/series.py(155)init_particles_distances()
-> particle.init_distances(rdc, C)
/home/erikw/.local/share/pipx/venvs/radiantkit/lib/python3.12/site-packages/radiantkit/particle.py(168)init_distances()
-> distances = rdc.calc(self, C)
> /home/erikw/.local/share/pipx/venvs/radiantkit/lib/python3.12/site-packages/radiantkit/distance.py(159)calc()
-> return (contour_dist.pixels, center_dist.pixels)