wip

move settings dataclasses into separate file;
add SemiUnitaryLayer;
clean up model response plotting code;
cnt hyperparameter search

.gitattributes

@@ -1,4 +1,5 @@
 data/**/* filter=lfs diff=lfs merge=lfs -text
+data/*.db filter=lfs diff=lfs merge=lfs -text
 data/*.ini filter=lfs diff=lfs merge=lfs text
 
 ## lfs setup

.gitignore

@@ -1,8 +1,5 @@
-pypho
+src/**/*.ini
-
+.*
-
-# VSCode
-.vscode
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
@@ -166,3 +163,5 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+tolerance_results/*
+data/*

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "pypho"]
+	path = pypho
+	url = git@gitlab.lrz.de:000000003B9B3E61/pypho.git
+	branch = main

LICENSE

@@ -0,0 +1,290 @@
+# EUROPEAN UNION PUBLIC LICENCE v. 1.2
+
+> EUPL © the European Union 2007, 2016
+
+This European Union Public Licence (the 'EUPL') applies to the Work (as defined
+below) which is provided under the terms of this Licence. Any use of the Work,
+other than as authorised under this Licence is prohibited (to the extent such
+use is covered by a right of the copyright holder of the Work).
+
+The Work is provided under the terms of this Licence when the Licensor (as
+defined below) has placed the following notice immediately following the
+copyright notice for the Work:
+
+```raw
+Licensed under the EUPL
+```
+
+or has expressed by any other means his willingness to license under the EUPL.
+
+## 1. Definitions
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+In this Licence, the following terms have the following meaning:
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+
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+Copyleft clause: If the Licensee distributes or communicates copies of the
+Original Works or Derivative Works, this Distribution or Communication will be
+done under the terms of this Licence or of a later version of this Licence
+unless the Original Work is expressly distributed only under this version of the
+Licence — for example by communicating 'EUPL v. 1.2 only'. The Licensee
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+
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+
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+
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+conditions by exercising any rights granted to You by Article 2 of this Licence,
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+Distribution or Communication by You of the Work or copies thereof.
+
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+
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+communication by You (for example, by offering to download the Work from a
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+
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+
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+have identical value. Parties can take advantage of the linguistic version of
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+
+## 14. Jurisdiction
+
+Without prejudice to specific agreement between parties,
+
+- any litigation resulting from the interpretation of this License, arising
+  between the European Union institutions, bodies, offices or agencies, as a
+  Licensor, and any Licensee, will be subject to the jurisdiction of the Court
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+
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+  interpretation of this License, will be subject to the exclusive jurisdiction
+  of the competent court where the Licensor resides or conducts its primary
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+
+## 15. Applicable Law
+
+Without prejudice to specific agreement between parties,
+
+- this Licence shall be governed by the law of the European Union Member State
+  where the Licensor has his seat, resides or has his registered office,
+
+- this licence shall be governed by Belgian law if the Licensor has no seat,
+  residence or registered office inside a European Union Member State.
+
+## Appendix
+
+'Compatible Licences' according to Article 5 EUPL are:
+
+- GNU General Public License (GPL) v. 2, v. 3
+- GNU Affero General Public License (AGPL) v. 3
+- Open Software License (OSL) v. 2.1, v. 3.0
+- Eclipse Public License (EPL) v. 1.0
+- CeCILL v. 2.0, v. 2.1
+- Mozilla Public Licence (MPL) v. 2
+- GNU Lesser General Public Licence (LGPL) v. 2.1, v. 3
+- Creative Commons Attribution-ShareAlike v. 3.0 Unported (CC BY-SA 3.0) for
+  works other than software
+- European Union Public Licence (EUPL) v. 1.1, v. 1.2
+- Québec Free and Open-Source Licence — Reciprocity (LiLiQ-R) or Strong
+  Reciprocity (LiLiQ-R+).
+
+The European Commission may update this Appendix to later versions of the above
+licences without producing a new version of the EUPL, as long as they provide
+the rights granted in Article 2 of this Licence and protect the covered Source
+Code from exclusive appropriation.
+
+All other changes or additions to this Appendix require the production of a new
+EUPL version.

README.md

@@ -1,93 +1,33 @@
+<!--
+README.md
+
+This file is part of the repo "optical-regeneration"
+https://git.suuppl.dev/seppl/optical-regeneration.git
+
+Joseph Hopfmüller
+Copyright 2024
+Licensed under the EUPL
+
+Full license text in LICENSE file
+-->
+
 # optical-regeneration
 
+## Notes on cloning
 
+- `pypho` is added as a submodule -> `--recurse-submodules`
+- This repo has about 7.5GB of datasets in it. The `git lfs fetch` step will take a while.
 
-## Getting started
+```bash
-
+apt install git-lfs
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
+# only necessary once per user account
-
+git lfs install
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
-
-## Add your files
-
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
 
+git clone --recurse-submodules https://git.suuppl.dev/seppl/optical-regeneration.git && cd optical-regeneration
+git lfs fetch
+git lfs checkout
 ```
-cd existing_repo
-git remote add origin https://gitlab.lrz.de/000000003B9B3E61/optical-regeneration.git
-git branch -M main
-git push -uf origin main
-```
-
-## Integrate with your tools
-
-- [ ] [Set up project integrations](https://gitlab.lrz.de/000000003B9B3E61/optical-regeneration/-/settings/integrations)
-
-## Collaborate with your team
-
-- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
-- [ ] [Set auto-merge](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
-
-## Test and Deploy
-
-Use the built-in continuous integration in GitLab.
-
-- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing (SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
-
-***
-
-# Editing this README
-
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
-
-## Suggestions for a good README
-
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
-
-## Name
-Choose a self-explaining name for your project.
-
-## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
-
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
-
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
-
-## Installation
-Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
-
-## Usage
-Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
-
-## Support
-Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
-
-## Roadmap
-If you have ideas for releases in the future, it is a good idea to list them in the README.
-
-## Contributing
-State if you are open to contributions and what your requirements are for accepting them.
-
-For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
-
-You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
-
-## Authors and acknowledgment
-Show your appreciation to those who have contributed to the project.
 
 ## License
-For open source projects, say how it is licensed.
 
-## Project status
+This project is licensed under EUPL-1.2.
-If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.

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