bob.bio.base merge requestshttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests2020-11-11T11:09:14Zhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/205Fix annotators kwargs2020-11-11T11:09:14ZYannick DAYERFix annotators kwargsThe kwargs were not passed correctly in the FailSafe annotator.
Removed the shutdown of dask clients in the `annotate` commands.The kwargs were not passed correctly in the FailSafe annotator.
Removed the shutdown of dask clients in the `annotate` commands.Bob 9.0.0Yannick DAYERYannick DAYERhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/204Remove stackable preprocessors and extractors2020-11-10T15:21:54ZAmir MOHAMMADIRemove stackable preprocessors and extractorsNow that we have standardized on scikit-learn transformers,
scikit-learn alternatives such as FunctionTransformer, Pipeline,
and FeatureUnion should be usedNow that we have standardized on scikit-learn transformers,
scikit-learn alternatives such as FunctionTransformer, Pipeline,
and FeatureUnion should be usedBob 9.0.0Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/203Fix Dask shutting down automatically when calling from a script2020-11-05T13:03:09ZYannick DAYERFix Dask shutting down automatically when calling from a scriptDefers the shutdown task to the user by putting the execution of Vanilla-Biometrics in its own function.
The `bob bio pipelines vanilla-biometrics` command calls this function.Defers the shutdown task to the user by putting the execution of Vanilla-Biometrics in its own function.
The `bob bio pipelines vanilla-biometrics` command calls this function.Bob 9.0.0Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/202Dask annotators2020-11-10T15:33:49ZAmir MOHAMMADIDask annotatorsBob 9.0.0Yannick DAYERYannick DAYERhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/201Correct the chain loading and click implementation2020-10-13T13:20:31ZAmir MOHAMMADICorrect the chain loading and click implementationThe vanilla biometrics script was not using our click API correctly,
this fixes that. Please refer to bob.extension's docs for more info.The vanilla biometrics script was not using our click API correctly,
this fixes that. Please refer to bob.extension's docs for more info.Bob 9.0.0Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/200Database interface2020-10-08T11:26:20ZTiago de Freitas PereiraDatabase interfaceImplemented a simple filelist database interface for the VanillaBiometrics based on CSVFiles.
The `CSVDatasetDevEval` needs to have the following format:
```text
my_dataset/
my_dataset/my_protocol/
my_datase...Implemented a simple filelist database interface for the VanillaBiometrics based on CSVFiles.
The `CSVDatasetDevEval` needs to have the following format:
```text
my_dataset/
my_dataset/my_protocol/
my_dataset/my_protocol/train.csv
my_dataset/my_protocol/train.csv/dev_enroll.csv
my_dataset/my_protocol/train.csv/dev_probe.csv
my_dataset/my_protocol/train.csv/eval_enroll.csv
my_dataset/my_protocol/train.csv/eval_probe.csv
...
```
where each CSV file needs to have the following format:
```text
PATH,SUBJECT
path_1,subject_1
path_2,subject_2
path_i,subject_j
```
This formart allows the usage of metadata by following the pattern below:
```text
PATH,SUBJECT,METADATA_1,METADATA_2,METADATA_k
path_1,subject_1,A,B,C
path_2,subject_2,A,B,1
path_i,subject_j,2,3,4
```
We can imagine other implementations of this.
For instance, `CSVDatasetCrossValidation` that given a csv file, it splits "on-the-fly" several data for enrolling, probing and training.
Or `CSVDatasetWithEyesAnnotation`, that handles annotations for Face Rec pipelines.
I still need to implement a mechanism that takes `zip` files as input to `CSVDatasetDevEval`.
That way we can ship databases as simple zip files
ping @ydayer @amohammadi
I'll merge this tomorrow.
I need this to support the efforts on `bob.bio.vein`.Bob 9.0.0https://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/199Merge 'fix-gen' (already applied on 'master') onto 'dask-pipelines'2020-09-30T08:21:35ZYannick DAYERMerge 'fix-gen' (already applied on 'master') onto 'dask-pipelines'Fixes and features addition for the synthetic scores generator.Fixes and features addition for the synthetic scores generator.https://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/198Fixing and adding features to the scores generation script2020-09-16T10:06:20ZYannick DAYERFixing and adding features to the scores generation scriptI was using the score 'gen' script, but needed some features.
Added:
- A way of specifying how the number of scores is defined (number of subjects and probes, or manually specified);
- A way to generate different scores for dev and eval...I was using the score 'gen' script, but needed some features.
Added:
- A way of specifying how the number of scores is defined (number of subjects and probes, or manually specified);
- A way to generate different scores for dev and eval;
- Tests for the gen script.
Changed:
- The way the scores are generated (each probe against each reference model, instead of randomly).
Fixed:
- Duplicate click options (-p);
- 'positive scores' were generated with a 'negative scores' variable.Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/197Fixed baselines whose uses estimator.fit2020-08-28T14:42:26ZTiago de Freitas PereiraFixed baselines whose uses estimator.fitFor some reason, the possibility to train an estimator was removed from this package.
It was also fixed the function score_multiple_modelsFor some reason, the possibility to train an estimator was removed from this package.
It was also fixed the function score_multiple_modelshttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/196Fix checkpoint2020-08-28T08:58:25ZTiago de Freitas PereiraFix checkpointRemoved `-T` hackRemoved `-T` hackhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/195Advancements on documentation - Biometrics chapter2020-08-19T14:15:34ZYannick DAYERAdvancements on documentation - Biometrics chapterProgress on the documentation.
Improved the Introduction to Biometrics.Progress on the documentation.
Improved the Introduction to Biometrics.Yannick DAYERYannick DAYERhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/194New documentation bob.bio.base2020-10-14T12:00:53ZTiago de Freitas PereiraNew documentation bob.bio.baseRedoing bob.bio.base documentation
We might rebrand this package to `scikit-biometrics`Redoing bob.bio.base documentation
We might rebrand this package to `scikit-biometrics`Bob 9.0.0https://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/193Some directions to the new documentation2020-08-18T08:25:00ZTiago de Freitas PereiraSome directions to the new documentationHey @ydayer,
Follow the stuff we've discussed.
I'll finish this organization by tomorrow and merge
ThanksHey @ydayer,
Follow the stuff we've discussed.
I'll finish this organization by tomorrow and merge
Thankshttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/192Redoing baselines2020-06-19T13:55:04ZTiago de Freitas PereiraRedoing baselineshttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/191Resolve "`check_existence` flag incorrectly handled in filelistdatabase query"2020-06-03T08:58:06ZManuel Günthersiebenkopf@googlemail.comResolve "`check_existence` flag incorrectly handled in filelistdatabase query"Closes #134Closes #134Amir MOHAMMADIAmir MOHAMMADIhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/190Implementation of S-norm2020-06-12T09:26:13ZTiago de Freitas PereiraImplementation of S-normImplementation of S-Norm in the same fashion as in "Analysis of Score Normalization in Multilingual Speaker Recognition" paper from the following link: https://www.isca-speech.org/archive/Interspeech_2017/pdfs/0803.PDFImplementation of S-Norm in the same fashion as in "Analysis of Score Normalization in Multilingual Speaker Recognition" paper from the following link: https://www.isca-speech.org/archive/Interspeech_2017/pdfs/0803.PDFhttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/189Adding missing argument in preprocessor wrapper2020-11-05T12:59:59ZYannick DAYERAdding missing argument in preprocessor wrapperThe transform_extra_arguments parameter was not transmitted trough the wrappers for preprocessing. Default arguments ("annotations":"annotations") in deeper functions made it work until now. However, RFW samples have no "annotations" (ey...The transform_extra_arguments parameter was not transmitted trough the wrappers for preprocessing. Default arguments ("annotations":"annotations") in deeper functions made it work until now. However, RFW samples have no "annotations" (eyes positions are constant) and could not work like that.Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/188Score normalizations2020-05-25T16:21:55ZTiago de Freitas PereiraScore normalizationsThis is a long MR with the following features:
- [ ] Proper checkpointing of scores (BioAlgCheckpointWrapper). Still in pickle, though
- [ ] Moved the score-writer outside of the VanillaBiometricsPipeline
- [ ] Simplified the sco...This is a long MR with the following features:
- [ ] Proper checkpointing of scores (BioAlgCheckpointWrapper). Still in pickle, though
- [ ] Moved the score-writer outside of the VanillaBiometricsPipeline
- [ ] Simplified the scoring by `BioAlgorithm`. Also made once SampleSet, dump one score.
- [ ] Implemented a new pipeline that does Z, T and ZT score normalizations. Also created wrappers for Checkpointing and Dask this pipeline. Such pipeline has to wrap a VanillaBiometricsPipeline to work.
- [ ] Adapted the CLI command, `bob pipelines vanilla-biometrics` to work with ZNorm. Now, if you want to ztnorm a pipeline, just do `bob pipelines vanilla-biometrics --ztnorm`
Don't know if someone is willing to review this one.
Tiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/187Remove vstack_features -> use the one in bob.pipelines2020-05-12T10:20:49ZAmir MOHAMMADIRemove vstack_features -> use the one in bob.pipelinesTiago de Freitas PereiraTiago de Freitas Pereirahttps://gitlab.idiap.ch/bob/bob.bio.base/-/merge_requests/186Some fixes to wrapper API2020-05-04T14:02:46ZAmir MOHAMMADISome fixes to wrapper APITiago de Freitas PereiraTiago de Freitas Pereira