Eyepy

Build

* build(pyproject.toml): add itk as optional dependency to read RETOUCH data and pygifsicle as dev dependency to optimize the header.gif ([`ccf0d8e`](https://github.com/MedVisBonn/eyepy/commit/ccf0d8e941b728190c93dc23608e68a45a448533))

Documentation

* docs(README.md-/-Cookbook): Add header image to README ([`7501dde`](https://github.com/MedVisBonn/eyepy/commit/7501dde6dabc48ccf6b905985888fa06ca34d6da))

* docs(README-and-Cookbook): fix import of load function in examples ([`e623c4b`](https://github.com/MedVisBonn/eyepy/commit/e623c4bed6f586c3c11ceba0801d4727da08cff8))

Feature

* feat(eyepy.core): reflect plotted region in x and y axis for both localizer and B-scan; check if bscan_region bscan position indicators are in plotting region ([`2842424`](https://github.com/MedVisBonn/eyepy/commit/284242439163a0148d144938674fe98f10413fa9))

* feat(eyepy.io): fix imagio warnings; raise ValueError for scan-pattern 2 and 5 instead of warning; set maxint to NAN when reading XML layers; fix bscan order in layer data (vol_reader) ([`c4a88e7`](https://github.com/MedVisBonn/eyepy/commit/c4a88e7f390f10000e190c5345a5b465d0def7d2))

Fix

* fix(src/eyepy/io): convert very large layer heights indicating no valid layer to np.nan ([`352a984`](https://github.com/MedVisBonn/eyepy/commit/352a98425dfa327d3fba7821986673bbd90802c6))

* fix(eyepy.core): make sure ticklabels match plotted image region for EyeEnfac ande EyeBscan plots ([`f389f47`](https://github.com/MedVisBonn/eyepy/commit/f389f476018db51ceb0554c23d9f9af94393a85c))

* fix(eyepy.core.utils.py): ignore nans in layers when computing drusen from layer heights ([`3c4efcd`](https://github.com/MedVisBonn/eyepy/commit/3c4efcdd30bbe491cf0f323be7359257ba8ce263))

* fix(eyepy.core): set axis in all layer height maps to (n_bscans, width)

Layer in the sample were not correctly oriented due to a different axis order in the HeXMLReader ([`3493b0e`](https://github.com/MedVisBonn/eyepy/commit/3493b0e259a18435b8c537839a359cb1c03e2d66))

Style

* style(eyepy/config.py): change default color of bscan region and bscan position indicators from green to limegreen because of better visibility ([`3658a11`](https://github.com/MedVisBonn/eyepy/commit/3658a1111243b89f3fbcddf328cf67ad89962c9c))

Test

* test(test_eyevolume.py): correct indexing of layer data

The first axis (bscan axis) of the layer data was flipped to reflect B-scan indexing. Therefore layers have to be flipped now when computing drusen and projecting on the localizer. ([`d186317`](https://github.com/MedVisBonn/eyepy/commit/d186317b403c254c84cb5aba014b3c018e0445fe))

Breaking

* refactor(eyepy): work in progress

BREAKING CHANGE: ([`c942c6b`](https://github.com/MedVisBonn/eyepy/commit/c942c6b1b65a9deef07e7e2bd6d10cc96e2b6059))

Ci

* ci(pyproject.yaml): fix semantic release ([`daaea19`](https://github.com/MedVisBonn/eyepy/commit/daaea194e868f277ab8518fac8ff6dae470cfc84))

* ci(ci.yaml): fix syntax ([`c2647c6`](https://github.com/MedVisBonn/eyepy/commit/c2647c631f02d644b6b633388785847b4461d581))

* ci(ci.yaml): fix dependencies ([`7d4eb5f`](https://github.com/MedVisBonn/eyepy/commit/7d4eb5feb59ff87b82b1da65360c6d43e720de53))

* ci(ci.yaml): fix mkdocs deployment dependencies ([`a70a216`](https://github.com/MedVisBonn/eyepy/commit/a70a21608e4252de014da84e2712c5d69c5c2d55))

* ci(quality-check): upgrade poetry version ([`aedd680`](https://github.com/MedVisBonn/eyepy/commit/aedd6808f0e599dfe91c469826125b94116241ef))

Documentation

* docs(README-and-Cookbook): clean up ([`183b317`](https://github.com/MedVisBonn/eyepy/commit/183b317dee559a2da8cc0aec2f0df4b237d7d605))

* docs(eyepy): add docstrings and cookbook examples ([`3b6ce5d`](https://github.com/MedVisBonn/eyepy/commit/3b6ce5d711f79794ffc1db91e1060a3a301bff40))

* docs(formats): e2e documentation ([`059d67b`](https://github.com/MedVisBonn/eyepy/commit/059d67b0d335e3b82c1d631c2be24176c4fa2435))

Feature

* feat(HeE2eReader): read E2E volumes ([`9094890`](https://github.com/MedVisBonn/eyepy/commit/9094890a5fd69335b741d238c1fa8661f83941c0))

Fix

* fix(eyepy): do not use list and tuple for type annotations python 3.8 only supports List / Tuple ([`cc6dfee`](https://github.com/MedVisBonn/eyepy/commit/cc6dfee1098f6e962c2d5c09e33d5c82883000bf))

* fix(region-plotting): remove EllipsisType from allowed types for the region parameter since its not supported in python 3.8 ([`fac7849`](https://github.com/MedVisBonn/eyepy/commit/fac78498c233f765eb06d5bc71b3d71a125626ae))

Refactor

* refactor(eyepy): Use isort with google style for imports and yapf for code formating ([`47f9330`](https://github.com/MedVisBonn/eyepy/commit/47f9330483b5c2ecc6f3ee2830fa1091cb863861))

Test

* test(eyevolume): skip save load test for now ([`bd58274`](https://github.com/MedVisBonn/eyepy/commit/bd582745fd3d09ea7767e27d25b21309e14e1e40))

* test(test_eyevolume): change delete to remove in function names ([`4804dc9`](https://github.com/MedVisBonn/eyepy/commit/4804dc9c8e1ebc660843bf69dd2f2a20976452fe))

* test(eyevolume): skip Vol writing for now ([`cbdc97e`](https://github.com/MedVisBonn/eyepy/commit/cbdc97eabc4e86efd2a97fe87ee5dec249aab7ba))

Fix

* fix(eyepy): update pre-commit; remove itk from dependencies

itk was used to read the RETOUCH dataset and might be added as an extra dependency ([`0339fb6`](https://github.com/MedVisBonn/eyepy/commit/0339fb6f08aefd63027fb8213fc5da526a6890a7))

Refactor

* refactor(EyeVolumeVoxelAnnotation): simplify code for plotting ([`355e7f6`](https://github.com/MedVisBonn/eyepy/commit/355e7f67fbd082abb54b4b76c30eae7040a66ffa))

Fix

* fix(eyevolume.py): remove reformating of knot data in load - eyelab now does it if needed ([`35060ab`](https://github.com/MedVisBonn/eyepy/commit/35060ab079fd52a415cbe61f833622a73d4a4736))

Fix

* fix(eyevolume): auto convert old layer curves ([`7842120`](https://github.com/MedVisBonn/eyepy/commit/78421205c3cd4ddf4f9ff9700bf36dd9515bc4ab))

Fix

* fix(io/utils.py): check for parallel and equal distance B-scans ([`c5d68d2`](https://github.com/MedVisBonn/eyepy/commit/c5d68d23370a314714e4d0a798336ccb6a60f032))