Eyepy

Feature

* feat(io.__init__.py): adds support for topcon fda files (12)

* NF: add basic support for fda files

* refactor(main-and-io-module-__init__-files): specify topcon as vendor in fda import function

* feat(io.__init__.py): add bscan metadata to returned eye volume

before the fda reader only parsed bscans and segmentation. These changes incorporate scaling and bscan position in fundus images.

* feat(io.__init__.py): add fundus image to eyevolume

the changes allow to create a full EyeVolume with fundus image and metadata

* style(io.__init__.py): remove double quotes

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Co-authored-by: Olivier Morelle <Oli4users.noreply.github.com> ([`53f2908`](https://github.com/MedVisBonn/eyepy/commit/53f2908f95556c2be7a3259bfd5653208188ff71))

Ci

* ci(.github): add pre-commit checking to quality workflow and call quality workflow for pull requests ([`9e47a09`](https://github.com/MedVisBonn/eyepy/commit/9e47a09248a29f36525aa7e406bb478ef8bcdf09))

Documentation

* docs(core.annotations): adds docstrings ([`236c074`](https://github.com/MedVisBonn/eyepy/commit/236c074e8e28eb4ccb5a1e0538237fcec5dff415))

Feature

* feat(core.plotting): adds a scale bar and a watermark to Bscan and Fundus visualizations ([`0e3eaa0`](https://github.com/MedVisBonn/eyepy/commit/0e3eaa0be4420c0d8ba4cbc53381fc36da2cdc81))

Fix

* fix(eyepy.core): fixes bscan_region and bscan_position plotting when plotting only a part of the fundus

also adds new header_gif to the README ([`2c88074`](https://github.com/MedVisBonn/eyepy/commit/2c880743b6329cf24e74f7019035ad455800e89a))

* fix(core.grids.py): fixes error related to python 3.8 not supporting new type annotation Dict-dict List-list ([`3c6ba41`](https://github.com/MedVisBonn/eyepy/commit/3c6ba41133215bc64efb48f432cb0be78b627b2c))

Style

* style(eyepy): applys improved pre-commit style guides

adds dostrings formatting via docformatter \n unifies single/double quotes \n upgrades type hints to be pep585 compliant ([`28b1b4c`](https://github.com/MedVisBonn/eyepy/commit/28b1b4c4767c686541eca7b069c6238d11191dd5))

Documentation

* docs(eyepy.core): adds type annotations to all objects in the core subpackage ([`ea1cb4c`](https://github.com/MedVisBonn/eyepy/commit/ea1cb4c415604a97d1e7ef64998b1743e7c5fe75))

* docs(annotations.py): adds type annotations to all objects in this module ([`986f9bc`](https://github.com/MedVisBonn/eyepy/commit/986f9bc6347227311725d31726ea38741e582d75))

Fix

* fix(e2e_reader.py): makes exception formatting compatible with python < 3.10 ([`2c4cbb0`](https://github.com/MedVisBonn/eyepy/commit/2c4cbb0c2a91c47d951945aa75145dd1e34e5c4e))

Ci

* ci(ci.yaml): set python version to 3.10 for building and deploying documentation ([`b6feb0d`](https://github.com/MedVisBonn/eyepy/commit/b6feb0d63dc47b732a354ac8b4b58fcc9809a203))

Documentation

* docs(README.md): clarify that the localizer is a fundus image ([`4e41acd`](https://github.com/MedVisBonn/eyepy/commit/4e41acd3660f3a07abed11464bdcacba81bda984))

Fix

* fix(e2e_reader.py): extract number of Bscans more reliably by using the number of slice substructures; Skip localizer affine transformation for now, because slodata is not always available; support reading single B-scan data ([`1287a24`](https://github.com/MedVisBonn/eyepy/commit/1287a24d40907085d33e867b35f458078faa6b75))

* fix(e2e_format.py): change the name of E2EFile to E2EFormat to avoid confustion with E2EFileStructure in e2e_reader.py ([`01be6a0`](https://github.com/MedVisBonn/eyepy/commit/01be6a0a6ce4e80491871800a970b7f75eb8c86d))

Breaking

* feat(HeE2EReader): switch to construct_typed for describing structures; create file hierarchy when parsing the E2E file; add search functions to the HeE2eReader

BREAKING CHANGE: ([`45578a5`](https://github.com/MedVisBonn/eyepy/commit/45578a5a9949a2722a03c1fe4bdef228c3a980c0))

Documentation

* docs(documentation): improve documentation; rename Voxel/Area Annotation to PixelAnnotation for consistency ([`ab38837`](https://github.com/MedVisBonn/eyepy/commit/ab388378522f4be7f1fc55725a101a6483c1893b))

Feature

* feat(eyepy.io.utils.py): add functions to search for integer/float values in binary data; set relative tolerance for Bscan distance to 4% (fixes sample data warning) ([`96fd58b`](https://github.com/MedVisBonn/eyepy/commit/96fd58bf1146b6f9b60d63cdb8abbbc8704f6bde))

Fix

* fix(HeE2eReader): fix issues with inspect after renaming classes ([`891c79c`](https://github.com/MedVisBonn/eyepy/commit/891c79ceb2f0417c5b1b003fa1332ce1d4572b1b))

* fix(__init__.py): exclude __init__.py from isort to prevent circular import ([`9254231`](https://github.com/MedVisBonn/eyepy/commit/92542318b23098323855abf410c5c294ff956466))

* fix(pyproject.toml): add imageio as dependency and umpgrade imagecodecs to latest version ([`bef44a0`](https://github.com/MedVisBonn/eyepy/commit/bef44a0cca752e280f5a405a9b9c4e4d0590f292))

Fix

* fix(pyproject.toml): increase allowed version range for numpy (fixes 10) ([`c66f6f6`](https://github.com/MedVisBonn/eyepy/commit/c66f6f65909aef7b086b62f66d6ce55f0b04220e))