Umami merge requestshttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests2021-10-19T14:05:21+02:00https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/194Merging Preprocessing-Remake in Master2021-10-19T14:05:21+02:00Alexander FrochMerging Preprocessing-Remake in MasterPreprocessing rewriteAlexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/170Removing hard-coded labels from evaluation tools2021-09-15T16:27:48+02:00Alexander FrochRemoving hard-coded labels from evaluation toolsThis MR removes the hard-coded labels from the evaluation tools and cleans up the code concerning the evaluation.
Unit tests for the new/rewritten functions are provided.
Also, I tried running the integration tests for the preproce...This MR removes the hard-coded labels from the evaluation tools and cleans up the code concerning the evaluation.
Unit tests for the new/rewritten functions are provided.
Also, I tried running the integration tests for the preprocessing and the training. I updated the concerning test files according to the new behavior of the functions and calls.
In addition to the callbacks, the training metrics are now saved in an extra json file in the corresponding model folder with the name `history.json`. The handling of this file, when it comes to plotting, is providedPreprocessing rewriteAlexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/164Remove hardcoded labels from input vars tools2021-08-25T16:57:05+02:00Alexander FrochRemove hardcoded labels from input vars toolsThis MR removes the hard-coded labels from the input variable plotting tools and update them. I cannot add a MR dependency here, but the changes from !161 are already implemented here. Merge !161 first.
This MR is related to &1This MR removes the hard-coded labels from the input variable plotting tools and update them. I cannot add a MR dependency here, but the changes from !161 are already implemented here. Merge !161 first.
This MR is related to &1Preprocessing rewriteAlexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/161Removing hard-coded labels from train_tools for UMAMI and DL1r2021-08-24T15:12:27+02:00Alexander FrochRemoving hard-coded labels from train_tools for UMAMI and DL1rThis MR adds removes the hard-coded labels completely now from the `train_tools` also from UMAMI and DL1r. Unit tests are provided. MR is related to &1.
a step towards #58This MR adds removes the hard-coded labels completely now from the `train_tools` also from UMAMI and DL1r. Unit tests are provided. MR is related to &1.
a step towards #58Preprocessing rewriteAlexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/155Remove hard-coded labels for DIPS2021-08-17T18:03:22+02:00Alexander FrochRemove hard-coded labels for DIPSThis MR will remove the hard-coded labels in the training process for DIPS. I did this only for DIPS in one go, because the MR is already very large (Sorry for that...) but I wasn't able to make it smaller. But the next MRs concerning th...This MR will remove the hard-coded labels in the training process for DIPS. I did this only for DIPS in one go, because the MR is already very large (Sorry for that...) but I wasn't able to make it smaller. But the next MRs concerning the rewriting of the DL1r and UMAMI tools should be less.Preprocessing rewriteAlexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/639Fix error calculation in ROC plots2022-09-16T09:15:41+02:00Joschka BirkFix error calculation in ROC plots## Summary
This MR introduces the following changes
* In the `evaluate_model.py` script: save the `n_jets_<flavour>` attribute for each dataset
--> Fixes wrong error calculation in ROC curves when using `plotting_umami.py`
## Conf...## Summary
This MR introduces the following changes
* In the `evaluate_model.py` script: save the `n_jets_<flavour>` attribute for each dataset
--> Fixes wrong error calculation in ROC curves when using `plotting_umami.py`
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] ~~[Documentation](https://umami-docs.web.cern.ch)~~
- [x] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [x] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/618Adding truth label to results file + Fix flavour retrieval in plotting2022-08-16T13:33:43+02:00Alexander FrochAdding truth label to results file + Fix flavour retrieval in plotting## Summary
This MR introduces the following changes
* **Note:** Unit test files changed! No pipeline will success until this is merged!
* Adding the jet truth labels to the results file produced by `evaluate_model.py` (Like `HadronCone...## Summary
This MR introduces the following changes
* **Note:** Unit test files changed! No pipeline will success until this is merged!
* Adding the jet truth labels to the results file produced by `evaluate_model.py` (Like `HadronConeExclTruthLablID`)
* Removing error prone flavour retrieval from plotting code. This was based on the order of `class_labels` (which needed to be similar to the ones in the preprocess/train config, otherwise this would lead to wrong flavour retrieval). Now it is based on the truth labels which are stored in the results file.
* Adding dummy empty `label` values for plotting. If you only want to plot one model without a model `label` and only the flavour names, this would produce (at the moment) an error. When no `label` is given for the model, an empty string is added to the `model_labels` list to keep the lists dimensionality correct.
* Fixing working point values in the discriminant plots. The x-value was given as label to `puma` which lead to wrong numbers above the vertical lines.
* Sorting the working points which are to be plotted in the discriminant plot in decreasing order so they are correctly printed when `same_height_WP` is `False`.
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/585Fixing track masking for the input variable plots2022-07-23T01:32:14+02:00Alexander FrochFixing track masking for the input variable plots## Summary
This MR introduces the following changes
* Adding `valid` as the default track mask variable. If `valid` is not available, `ptfrac` will be used instead.
* Adding new unit test R22 test file (with `tracks_loose` and `valid` ...## Summary
This MR introduces the following changes
* Adding `valid` as the default track mask variable. If `valid` is not available, `ptfrac` will be used instead.
* Adding new unit test R22 test file (with `tracks_loose` and `valid` flag present) (**Will be added when this MR is approved, otherwise all other pipelines will fail.**)
Relates to the following issues
* Closes #196
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/746Update paper branch2023-11-22T10:04:08+01:00Philipp GadowUpdate paper branch## Summary
This MR introduces the following changes
* adds a "how to contribute" section to the documentation
* adds a tutorial based on the JetClass dataset
Relates to the following issues
* https://github.com/umami-hep/umami/issues...## Summary
This MR introduces the following changes
* adds a "how to contribute" section to the documentation
* adds a tutorial based on the JetClass dataset
Relates to the following issues
* https://github.com/umami-hep/umami/issues/4
* https://github.com/umami-hep/umami/issues/2
* https://github.com/umami-hep/umami/issues/1
## Conformity
- [ ] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation](https://umami-docs.web.cern.ch)
- [x] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [x] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Philipp GadowPhilipp Gadowhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/741Black mismatch2023-10-16T18:55:41+02:00Ivan OleksiyukBlack mismatch## Summary
This MR introduces the following changes
* Changes to black==23.3 in CI as it is stated in dev-requirements
## Conformity
- [ ] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/ma...## Summary
This MR introduces the following changes
* Changes to black==23.3 in CI as it is stated in dev-requirements
## Conformity
- [ ] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation](https://umami-docs.web.cern.ch)
- [x] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [x] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Ivan OleksiyukIvan Oleksiyukhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/739Change truth label names2023-10-30T15:37:02+01:00Philipp GadowChange truth label names## Summary
This MR introduces the following changes
* Change truth label names to account for changes in DAODs (see salt MR here: https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/salt/-/merge_requests/142/diffs)
## Conform...## Summary
This MR introduces the following changes
* Change truth label names to account for changes in DAODs (see salt MR here: https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/salt/-/merge_requests/142/diffs)
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation](https://umami-docs.web.cern.ch)
- [x] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [x] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Philipp GadowPhilipp Gadowhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/722Adding plot_type to Preprocessing configs2023-04-17T13:17:25+02:00Alexander FrochAdding plot_type to Preprocessing configs## Summary
This MR introduces the following changes
* Adding the option `plot_type` to the preprocessing config which sets the plot type of all plots which are created during preprocessing. This is optional and backward compatible. The...## Summary
This MR introduces the following changes
* Adding the option `plot_type` to the preprocessing config which sets the plot type of all plots which are created during preprocessing. This is optional and backward compatible. The default (if `plot_type` is not given in the config) is pdf.
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/714Adding duplicated jets plot to after resampling plots2023-03-28T15:33:04+02:00Alexander FrochAdding duplicated jets plot to after resampling plots## Summary
This MR introduces the following changes
* Adding a histogram how often a jet is duplicated (Duplicated_jet_multiplicity.pdf)
* Fixing preprocessing plots for hybrid resampling (plots are overwritten when the hybrid resampli...## Summary
This MR introduces the following changes
* Adding a histogram how often a jet is duplicated (Duplicated_jet_multiplicity.pdf)
* Fixing preprocessing plots for hybrid resampling (plots are overwritten when the hybrid resampling starts, this is fixed now)
The new plots look like this:
<img src="/uploads/a7804c5f0ceda3e80f6feea4d02d4240/Duplicated_jet_multiplicity.png" width="600" height="450">
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/692Adding figsize argument to train configuration2023-01-26T12:05:50+01:00Alexander FrochAdding figsize argument to train configuration## Summary
This MR introduces the following changes
* Adding `figsize` argument to the `train_config` configuration file to adapt the figure size for the training validation plots.
## Conformity
- [x] [Changelog entry](https://gitlab...## Summary
This MR introduces the following changes
* Adding `figsize` argument to the `train_config` configuration file to adapt the figure size for the training validation plots.
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/675Rewriting train config Configuration2022-12-06T17:03:27+01:00Alexander FrochRewriting train config Configuration## Summary
This MR introduces the following changes
* Adding dataclasses for the train_config.
Relates to the following issues
* Closes #208
* #181 for the train configs
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch...## Summary
This MR introduces the following changes
* Adding dataclasses for the train_config.
Relates to the following issues
* Closes #208
* #181 for the train configs
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/673Moving/adding checks for options to train_config configuration2022-11-23T15:11:58+01:00Alexander FrochMoving/adding checks for options to train_config configuration## Summary
This MR introduces the following changes
* Moving check for `working_point` and `n_jets` to train_config configuration for validation/evaluation with a freshly trained tagger.
* Adding check for `frac_values` to train_config...## Summary
This MR introduces the following changes
* Moving check for `working_point` and `n_jets` to train_config configuration for validation/evaluation with a freshly trained tagger.
* Adding check for `frac_values` to train_config configuration for validation/evaluation with a freshly trained tagger.
* Adding checks for `tagger` and `frac_values_comp` to the train_config configuration for the validation/evaluation without a freshly trained tagger.
* Removing unused checks in various places for the moved/added checks.
* Adding unit tests for the configuration for the new checks
Relates to the following issues
* Closing #208
## Conformity
- [X] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/669Fixing pylint invalid-name errors2022-11-14T16:43:06+01:00Manuel GuthFixing pylint invalid-name errors## Summary
This MR introduces the following changes
* Fixes the `invalid-name` errors of pylint
Relates to the following issues
* https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/issues/194
* closes https://gitlab...## Summary
This MR introduces the following changes
* Fixes the `invalid-name` errors of pylint
Relates to the following issues
* https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/issues/194
* closes https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/issues/167
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/666Allow for cuts when plotting input variables2022-12-15T12:13:22+01:00Philipp GadowAllow for cuts when plotting input variables## Summary
This MR introduces the following changes
* a `cut_vars_dict` needs to be supplemented when plotting the input variables of jets, tracks, and the track multiplicity
* documentation and example files are modified accordingly
...## Summary
This MR introduces the following changes
* a `cut_vars_dict` needs to be supplemented when plotting the input variables of jets, tracks, and the track multiplicity
* documentation and example files are modified accordingly
## Conformity
- [x] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [x] [Documentation](https://umami-docs.web.cern.ch)
- [x] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [x] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Philipp GadowPhilipp Gadowhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/658Adding support for combining track/jet inputs in input var plotting2022-10-31T17:59:53+01:00Alexander FrochAdding support for combining track/jet inputs in input var plotting## Summary
This MR introduces the following changes
* Enables the possibility to combine two track variables (or two jet variables) with each other and plot it then (for example, adding nPixHits and nSCTHits).
* Removing the need for a...## Summary
This MR introduces the following changes
* Enables the possibility to combine two track variables (or two jet variables) with each other and plot it then (for example, adding nPixHits and nSCTHits).
* Removing the need for a variable dict from the input variable plotting.
* Documentation is added.
* Example combination is added for both jets and tracks.
Tagging @vdao
## Conformity
- [X] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Frochhttps://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/merge_requests/655Fixing issue in the try except blocks of the preprocessing plots2022-10-21T14:56:39+02:00Alexander FrochFixing issue in the try except blocks of the preprocessing plots## Summary
This MR introduces the following changes
* Fixing an issue in the try except blocks of the preprocessing plots. The plots were not correctly made. This is fixed now
## Conformity
- [X] [Changelog entry](https://gitlab.cern....## Summary
This MR introduces the following changes
* Fixing an issue in the try except blocks of the preprocessing plots. The plots were not correctly made. This is fixed now
## Conformity
- [X] [Changelog entry](https://gitlab.cern.ch/atlas-flavor-tagging-tools/algorithms/umami/-/blob/master/changelog.md)
- [X] [Documentation](https://umami-docs.web.cern.ch)
- [X] [Development guidelines](https://umami-docs.web.cern.ch/setup/development/)
- [X] [Style guides](https://umami-docs.web.cern.ch/setup/development/good-practices/)Alexander FrochAlexander Froch