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[WIP] Feature abnormality detection #98

Merged
merged 146 commits into from
Feb 9, 2023
Merged

[WIP] Feature abnormality detection #98

merged 146 commits into from
Feb 9, 2023

Commits on Jul 1, 2022

  1. add SpikeCutout class

    @jihugo
    jihugo committed Jul 1, 2022
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  2. fix Spikecutout initializer

    @jihugo
    jihugo committed Jul 1, 2022
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  3. Merge branch 'GazzolaLab:main' into feature_abnormality_detection

    @jihugo
    jihugo authored Jul 1, 2022
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  4. clean up redundant stuff

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    jihugo committed Jul 1, 2022
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  5. 🚧 Abnormality Detector

    @jihugo
    jihugo committed Jul 1, 2022
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  6. 🚧 add ChannelSpikeCutout class

    @jihugo
    jihugo committed Jul 1, 2022
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  7. 🚧 edit _get_cutouts()

    @jihugo
    jihugo committed Jul 1, 2022
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  8. Merge branch 'feature_abnormality_detection' of https://github.com/ji… 

    …hugo/MiV-OS into feature_abnormality_detection
    @jihugo
    jihugo committed Jul 1, 2022
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  9. 🚧 fix type error

    @jihugo
    jihugo committed Jul 1, 2022
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  10. 🚧 add documentation

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    jihugo committed Jul 1, 2022
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  11. 🚧 update inline doc

    @jihugo
    jihugo committed Jul 1, 2022
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  12. 🚧 add categorize_spontaneous() and inline doc

    @jihugo
    jihugo committed Jul 1, 2022
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  13. 🚧 add categorize()

    @jihugo
    jihugo committed Jul 1, 2022
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  14. 🚧 add get_labeled_cutouts()

    @jihugo
    jihugo committed Jul 1, 2022
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  15. 🚧 add size into return value for get_labeled_cutouts()

    @jihugo
    jihugo committed Jul 1, 2022
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  16. 🚧 add train_model()

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    jihugo committed Jul 1, 2022
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  17. 🚧 correct typing error

    @jihugo
    jihugo committed Jul 1, 2022
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Commits on Jul 2, 2022

  1. 🚧 add get_cutouts_by_component() and inline doc

    @jihugo
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  2. 🚧 add dunder functions

    @jihugo
    jihugo committed Jul 2, 2022
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  3. add plot_waveforms_with_SpikeCutout(...)

    @jihugo
    jihugo committed Jul 2, 2022
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  4. 🚧 fix typing errors

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    jihugo committed Jul 2, 2022
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  5. 🚧 fix typing errors

    @jihugo
    jihugo committed Jul 2, 2022
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  6. include new function in __all__

    @jihugo
    jihugo committed Jul 2, 2022
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  7. 🚧 get rid of misused dunder function

    @jihugo
    jihugo committed Jul 2, 2022
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  8. fix n_spikes in new function

    @jihugo
    jihugo committed Jul 2, 2022
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  9. 🚧 add num_channels variable

    @jihugo
    jihugo committed Jul 2, 2022
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Commits on Jul 4, 2022

  1. 🚧 include empty channels in _get_cutouts(...)

    @jihugo
    jihugo committed Jul 4, 2022
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  2. 🚧 make skipped channels a class variable

    @jihugo
    jihugo committed Jul 4, 2022
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  3. 🚧 fix categorization bug and typos

    @jihugo
    jihugo committed Jul 4, 2022
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Commits on Jul 6, 2022

  1. 🚧 fix error with getting labeled cutouts

    @jihugo
    jihugo committed Jul 6, 2022
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  2. 🚧 change category numbers to have -1 to reflect 'uncategorized'

    @jihugo
    jihugo committed Jul 6, 2022
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  3. 🚧 fix some errors in train_model(...)

    @jihugo
    jihugo committed Jul 6, 2022
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  4. 🚧 minor fixes

    @jihugo
    jihugo committed Jul 6, 2022
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  5. 🚧 change categorized bool from channel level to spike level for bette… 

    …r model accuracy
    @jihugo
    jihugo committed Jul 6, 2022
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  6. 🚧 add get_only_neuronal_spikes(...)

    @jihugo
    jihugo committed Jul 6, 2022
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  7. 🚧 fix typing errors

    @jihugo
    jihugo committed Jul 6, 2022
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Commits on Jul 7, 2022

  1. 🚧 fix some errors with get_only_neuronal_spikes(...)

    @jihugo
    jihugo committed Jul 7, 2022
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  2. 🚧 add time to SpikeCutout object as variable

    @jihugo
    jihugo committed Jul 7, 2022
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  3. 🚧 add MockSpikeCutout object

    @jihugo
    jihugo committed Jul 7, 2022
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Commits on Jul 8, 2022

  1. 🚧 test_get_cutouts_by_components

    @jihugo
    jihugo committed Jul 8, 2022
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  2. 🚧 fix: make categorize() change self.categorized to True

    @jihugo
    jihugo committed Jul 8, 2022
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  3. 🚧 add test_categorize() and test_labeled_cutouts()

    @jihugo
    jihugo committed Jul 8, 2022
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  4. add test_len()

    @jihugo
    jihugo committed Jul 8, 2022
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  5. 🚧 add MockAbnormalityDetector and test_categorize_spontaneous()

    @jihugo
    jihugo committed Jul 8, 2022
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Commits on Jul 10, 2022

  1. 🚧 add inline doc and start get_only_neuronal_components

    @jihugo
    jihugo committed Jul 10, 2022
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  2. 🚧 add get_only_neuronal_components

    @jihugo
    jihugo committed Jul 10, 2022
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  3. 🚧 fix typing errors

    @jihugo
    jihugo committed Jul 10, 2022
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  4. 🚧 add test_train_model(), found error with train_model()

    @jihugo
    jihugo committed Jul 10, 2022
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  5. 🚧 add check for model is trained for getting new spiketrains

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    jihugo committed Jul 10, 2022
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Commits on Jul 14, 2022

  1. add KerasModelType

    @jihugo
    jihugo committed Jul 14, 2022
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  2. 🚧 use SpikeFeatureExtractionProtocol instead of PCADecomposition

    @jihugo
    jihugo committed Jul 14, 2022
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  3. add kerasModelType

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  4. 🚧 use spike_feature_extractor instead of specific PCADecomposition ob… 

    …ject
    @jihugo
    jihugo committed Jul 14, 2022
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  5. 🚧 separate evaluate_model(..) from train_model(..)

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    jihugo committed Jul 14, 2022
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Commits on Jul 15, 2022

  1. get rid of KerasModelType

    @jihugo
    jihugo committed Jul 15, 2022
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  2. 🚧 temporarily remove test_train_model()

    @jihugo
    jihugo committed Jul 15, 2022
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  3. 🚧 add SpikeClassificationModelProtocol

    @jihugo
    jihugo committed Jul 15, 2022
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  4. 🚧 add compile(..)

    @jihugo
    jihugo committed Jul 15, 2022
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  5. add project(..) to SpikeFeatureExtractionProtocol

    @jihugo
    jihugo committed Jul 15, 2022
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  6. 🚧 fix some errors

    @jihugo
    jihugo committed Jul 15, 2022
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  7. 🚧 update code after changes in AbnormalityDetector

    @jihugo
    jihugo committed Jul 15, 2022
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  8. 🚧 add test_create_default_model()

    @jihugo
    jihugo committed Jul 15, 2022
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  9. 🚧 add test_create_default_model()

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Commits on Jul 18, 2022

  1. :contruction: add test_evaluate_model()

    @jihugo
    jihugo committed Jul 18, 2022
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  2. 🚧 fix code error

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    jihugo committed Jul 18, 2022
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  3. 🚧 fix some errors

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    jihugo committed Jul 18, 2022
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Commits on Jul 19, 2022

  1. fix issues with categorization

    @jihugo
    jihugo committed Jul 19, 2022
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Commits on Jul 21, 2022

  1. add neuronal_spike_classification

    @jihugo
    jihugo committed Jul 21, 2022
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  2. add inline doc

    @jihugo
    jihugo committed Jul 21, 2022
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  3. add import neuronal_spike_classification

    @jihugo
    jihugo committed Jul 21, 2022
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  4. name change from 'events' to 'classification'

    @jihugo
    jihugo committed Jul 21, 2022
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  5. rewrite __init__ and _get_all_cutouts

    @jihugo
    jihugo committed Jul 21, 2022
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  6. change categorize_spontaneous to use np.ndarray

    @jihugo
    jihugo committed Jul 21, 2022
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  7. make get_labeled_cutouts return labels and cutouts in np.ndarray inst… 

    …ead of list
    @jihugo
    jihugo committed Jul 21, 2022
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  8. minor name change for get_labeled_cutouts()['cutouts']

    @jihugo
    jihugo committed Jul 21, 2022
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  9. minor name change for get_labeled_cutouts()['cutouts']

    @jihugo
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  10. rewrite train_model into init_classifier and train_classifier_model t… 

    …o integrate with NeuronalSpikeClassifier
    @jihugo
    jihugo committed Jul 21, 2022
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  11. name change

    @jihugo
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  12. get rid of create default model function

    @jihugo
    jihugo committed Jul 21, 2022
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  13. get rid of old __init__

    @jihugo
    jihugo committed Jul 21, 2022
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  14. organize directory

    @jihugo
    jihugo committed Jul 21, 2022
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  15. get rid of redundant test cases

    @jihugo
    jihugo committed Jul 21, 2022
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  16. add _check_categorized()

    @jihugo
    jihugo committed Jul 21, 2022
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  17. minor fixes

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    jihugo committed Jul 21, 2022
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Commits on Jul 22, 2022

  1. change import directory after organization

    @jihugo
    jihugo committed Jul 22, 2022
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  2. update key name for get_labeled_cutouts return value

    @jihugo
    jihugo committed Jul 22, 2022
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  3. add default_model() test case and fix some errors

    @jihugo
    jihugo committed Jul 22, 2022
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  4. fix typing errors

    @jihugo
    jihugo committed Jul 22, 2022
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  5. fix typing errors

    @jihugo
    jihugo committed Jul 22, 2022
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  6. add AdvancedMockData

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    jihugo committed Jul 22, 2022
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Commits on Jul 24, 2022

  1. fix errors with **kwargs

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Commits on Jul 26, 2022

  1. reorganize and add notebook, will run later since it may take some hours

    @jihugo
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  2. add train data file

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    jihugo committed Jul 26, 2022
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  3. reveal best combination

    @jihugo
    jihugo committed Jul 26, 2022
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  4. change default compile parameters after result from comparison

    @jihugo
    jihugo committed Jul 26, 2022
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  5. fix typo

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    jihugo committed Jul 26, 2022
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  6. Add EarlyStopping callback to fit function and update best combination

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Commits on Jul 27, 2022

  1. add default_init_and_train_model function

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    jihugo committed Jul 27, 2022
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  2. Add EarlyStopping callback and change loss to BinaryCrossentropy

    @jihugo
    jihugo committed Jul 27, 2022
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  3. 🚧 add test_predict_categories()

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    jihugo committed Jul 27, 2022
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Commits on Jul 29, 2022

  1. correct output layer

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    jihugo committed Jul 29, 2022
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  2. match new function argument format for create_default_model

    @jihugo
    jihugo committed Jul 29, 2022
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  3. change prediction function and test to use sigmoid output

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    jihugo committed Jul 29, 2022
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  4. add test_confusion_matrix and fix error in get_confusion_matrix

    @jihugo
    jihugo committed Jul 29, 2022
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  5. Merge branch 'main' of https://github.com/GazzolaLab/MiV-OS into feat… 

    …ure_abnormality_detection
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  6. formatting

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  7. fix AdvancedMockData

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    jihugo committed Jul 29, 2022
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  8. fix AdvancedMockData error with signal shape

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    jihugo committed Jul 29, 2022
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  9. add test_get_all_cutouts and edit typing

    @jihugo
    jihugo committed Jul 29, 2022
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Commits on Jul 30, 2022

  1. add test_categorize_spontaneous and fix error with categorize_spontan… 

    …eous
    @jihugo
    jihugo committed Jul 30, 2022
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Commits on Aug 3, 2022

  1. fix error with train_model()

    @jihugo
    jihugo committed Aug 3, 2022
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  2. fix typing errors

    @jihugo
    jihugo committed Aug 3, 2022
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  3. add evaluate_model()

    @jihugo
    jihugo committed Aug 3, 2022
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  4. check classifier

    @jihugo
    jihugo committed Aug 3, 2022
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  5. add compile functions

    @jihugo
    jihugo committed Aug 3, 2022
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  6. 🚧 add test case and fix errors with evaluate_model and other functions

    @jihugo
    jihugo committed Aug 3, 2022
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Commits on Aug 6, 2022

  1. Delete redundant imports and fix error with _get_all_cutouts()

    @jihugo
    jihugo committed Aug 6, 2022
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  2. make get_ctuouts_by_component() return raw spikes instead of SpikeCut… 

    …out objects
    @jihugo
    jihugo committed Aug 6, 2022
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  3. add get_spontaneous_cutouts_by_component()

    @jihugo
    jihugo committed Aug 6, 2022
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Commits on Aug 11, 2022

  1. update test cases

    @jihugo
    jihugo committed Aug 11, 2022
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  2. rename and restructure for new class of detector

    @jihugo
    jihugo committed Aug 11, 2022
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  3. add DetectorWithTrainData

    @jihugo
    jihugo committed Aug 11, 2022
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  4. 🚧 add new functions

    @jihugo
    jihugo committed Aug 11, 2022
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  5. add default_compile_and_train()

    @jihugo
    jihugo committed Aug 11, 2022
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  6. add keep_only_neuronal_spikes()

    @jihugo
    jihugo committed Aug 11, 2022
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  7. fix typing errors

    @jihugo
    jihugo committed Aug 11, 2022
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  8. fix conflicts

    @jihugo
    jihugo committed Aug 11, 2022
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  9. add classifer demo

    @jihugo
    jihugo committed Aug 11, 2022
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  10. merge from head

    @jihugo
    jihugo committed Aug 11, 2022
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  11. resolve conflicts

    @jihugo
    jihugo committed Aug 11, 2022
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Commits on Aug 17, 2022

  1. add keep_only_neuronal_spikes_from_data

    @jihugo
    jihugo committed Aug 17, 2022
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  2. change return type for keep_only_neuronal_spikes_from_data

    @jihugo
    jihugo committed Aug 17, 2022
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  3. fix some typing errors

    @jihugo
    jihugo committed Aug 17, 2022
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Commits on Aug 21, 2022

  1. 🚧 add train_model()

    @jihugo
    jihugo committed Aug 21, 2022
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Commits on Aug 22, 2022

  1. 🚧 fix keep_only_neuronal_spikes_from_data()

    @jihugo
    jihugo committed Aug 22, 2022
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  2. 🚧 add pre and post values for extract_waveforms in keep_only_neuronal… 

    …_spikes_from_data()
    @jihugo
    jihugo committed Aug 22, 2022
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  3. 🚧 change keep_only_neuronal_spikes_from_data to use the boolean predi… 

    …ction function from classifier
    @jihugo
    jihugo committed Aug 22, 2022
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  4. fix some errors

    @jihugo
    jihugo committed Aug 22, 2022
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  5. add auto_masking_with_classification_demo notebook

    @jihugo
    jihugo committed Aug 22, 2022
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  6. Merge branch 'GazzolaLab:main' into feature_abnormality_detection

    @jihugo
    jihugo authored Aug 22, 2022
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  7. fix merge conflict

    @jihugo
    jihugo committed Aug 22, 2022
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  8. Merge branch 'feature_abnormality_detection' of https://github.com/ji… 

    …hugo/MiV-OS into feature_abnormality_detection
    @jihugo
    jihugo committed Aug 22, 2022
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  9. added some sentence

    @jihugo
    jihugo committed Aug 22, 2022
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Commits on Dec 20, 2022

  1. Merge branch 'update-0.2.3' into feature_abnormality_detection

    @skim0119
    skim0119 authored Dec 20, 2022
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Commits on Feb 9, 2023

  1. feat: add window view

    @skim0119
    skim0119 committed Feb 9, 2023
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  2. Merge remote-tracking branch 'public/update-0.2.4' into feature_abnor… 

    …mality_detection
    @skim0119
    skim0119 committed Feb 9, 2023
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