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Load raw suite2p data #81

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wants to merge 332 commits into from
Closed

Load raw suite2p data #81

wants to merge 332 commits into from
This pull request is big! We’re only showing the most recent 250 commits.

Commits on Dec 19, 2022

  1. Apply changes from branch scaffold

    @lauraporta
    lauraporta committed Dec 19, 2022
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  2. Update load_data.py

    @lauraporta
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  3. Merge commit 'ba9904f4769e3214ef3cc736b5244cbc761ad14d' into extract-… 

    …file-names
    @lauraporta
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  4. Merge pull request #8 from neuroinformatics-unit/scaffold 

    Change main structure of the repo
    @lauraporta
    lauraporta authored Dec 19, 2022
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  5. Refactor and goodbye to os module

    @lauraporta
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Commits on Dec 20, 2022

  1. Add logic to load matlab files

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Commits on Jan 6, 2023

  1. Change to h5py

    @lauraporta
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  2. Add style changes

    @lauraporta
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  3. Merge branch 'developement' into load-data

    @lauraporta
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Commits on Jan 9, 2023

  1. Add logic to read HDF5 data, i.e. read 7.3 matlab complex files

    @lauraporta
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  2. Add docstrings

    @lauraporta
    lauraporta committed Jan 9, 2023
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Commits on Jan 10, 2023

  1. Stop tracking config file

    @lauraporta
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  2. Use env variables to store the path of config

    @lauraporta
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  3. Add renaming

    @lauraporta
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  4. Change handling of DataType not found, remove exception

    @lauraporta
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  5. Remove test linked to specific config file

    @lauraporta
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  6. Merge pull request #14 from neuroinformatics-unit/extract-file-names 

    Extract file names
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  7. Merge commit 'd7338f16187d2ab121528255c51128c7042cafed' into load-data

    @lauraporta
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  8. Change how to handle config path

    @lauraporta
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  9. Improvements to DataRaw, logging, classmethods and repr obj

    @lauraporta
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  10. Fix some errors in reading hdf5 files

    @lauraporta
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  11. Add integration test with mock for loading hdf5 data

    @lauraporta
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  12. Add h5py dependency to pyproject.toml

    @lauraporta
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  13. Update doctrings

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Commits on Jan 11, 2023

  1. Add usage of numpy squeeeze

    @lauraporta
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  2. Split tests

    @lauraporta
    lauraporta committed Jan 11, 2023
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  3. Add missing squeeze

    @lauraporta
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Commits on Jan 17, 2023

  1. Add code to reorganize data

    @lauraporta
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Commits on Jan 23, 2023

  1. Add pyproject.toml dependency

    @lauraporta
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  2. Add instructions to handle configs

    @lauraporta
    lauraporta committed Jan 23, 2023
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  3. Add improvements to load data

    @lauraporta
    lauraporta committed Jan 23, 2023
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  4. Add edits to DataRaw according to suggestions

    @lauraporta
    lauraporta committed Jan 23, 2023
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  5. Invert order of methods again

    @lauraporta
    lauraporta committed Jan 23, 2023
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  6. Improve tests

    @lauraporta
    lauraporta committed Jan 23, 2023
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  7. Remove unnecessary tox edit

    @lauraporta
    lauraporta committed Jan 23, 2023
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  8. Add better example explanation

    @lauraporta
    lauraporta committed Jan 23, 2023
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Commits on Jan 24, 2023

  1. Add example in folder name request

    @lauraporta
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Commits on Jan 26, 2023

  1. Merge commit 'c5466481e811324a8f2773d774a8fb9cd10a1533' into reorgani… 

    …ze-data
    @lauraporta
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  2. Fix decouple package name

    @lauraporta
    lauraporta authored Jan 26, 2023
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  3. Remove dot

    @lauraporta
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  4. Merge commit '021d61f76a97308a9678be95404996dadc68049d' into reorgani… 

    …ze-data
    @lauraporta
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  5. Change field name of raw_data

    @lauraporta
    lauraporta committed Jan 26, 2023
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  6. Merge pull request #16 from neuroinformatics-unit/load-data 

    Load data
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Commits on Jan 31, 2023

  1. Add mapping implementation with pandas

    @lauraporta
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  2. Remove reorganize data

    @lauraporta
    lauraporta committed Jan 31, 2023
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  3. Delete tests

    @lauraporta
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  4. Refactor and add documentation

    @lauraporta
    lauraporta committed Jan 31, 2023
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  5. Move attribute

    @lauraporta
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  6. Move logic to PhotonData object as originally meant

    @lauraporta
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Commits on Feb 1, 2023

  1. Small fixes to improve info logged

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Commits on Feb 6, 2023

  1. Add tests

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Commits on Feb 7, 2023

  1. Add setup instruction to help reviewing the code

    @lauraporta
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  2. Test fix pre-commit/virtualenv bug

    @lauraporta
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  3. Test fix 2

    @lauraporta
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  4. Renaming main folder

    @lauraporta
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  5. fixed equality syntax in dependencies

    @niksirbi
    niksirbi committed Feb 7, 2023
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  6. autoupdated pre-commit to latest versions

    @niksirbi
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  7. MANIFEST include py scripts located at the project root

    @niksirbi
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Commits on Feb 13, 2023

  1. Edit config file creation for demo

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Commits on Feb 14, 2023

  1. Refactor and remove redundant objects "options" and "specifications"

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  2. Add stim matrix logic and flake8 adjustments

    @lauraporta
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  3. Add missing tox dependency

    @lauraporta
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  4. Add missing tox dependency

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  5. Edit setup for demo

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  6. Update setup for demo

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Commits on Feb 15, 2023

  1. Improve calculations of response and baseline given a padding

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  2. Update tests/test_integration/test_photon_data.py 

    Co-authored-by: Niko Sirmpilatze <[email protected]>
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Commits on Feb 16, 2023

  1. Add fps to config file

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  2. Add test fixtures in tests for photon data

    @lauraporta
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  3. Update dependencies

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  4. Improve setup for demo

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  5. Merge pull request #19 from neuroinformatics-unit/reorganize-data 

    Implementation of PhotonData class
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Commits on Feb 17, 2023

  1. Renaming the main project folder (#23) 

    * Renaming main folder

* Update pre-commit

* Add missing tox dependency
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Commits on Feb 23, 2023

  1. Fix bugs in photon data and add many checks

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  2. Add tests edits

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  3. Merge commit '97515c608adbd40860ee8680c07a9f5914edd892' into responsi… 

    …veness
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  4. Add usage of config in phton_data for more controls

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  5. Update setup_for_demo

    @lauraporta
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  6. Add logic to calculate mean response and baseline

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  7. Fix test error - silence checks that require real data

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Commits on Feb 28, 2023

  1. Add unique stimuli dict and fix start frames bug in photon_data

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  2. Change logging and error messages

    @lauraporta
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  3. Add imporvements in windows estimation and initial version of statist… 

    …ical calculations (last one stil; buggy)
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  4. Add fixes to anova

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  5. Fix signed rank test

    @lauraporta
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  6. Add magintude calculations and refactoring

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  7. Add calculations for significance

    @lauraporta
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  8. Reorder methods and add docstrings

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Commits on Mar 2, 2023

  1. Refactor and imporve PhotonData, imporve tests

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  2. Change sf_tf class name

    @lauraporta
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  3. Add share pytest.fixture file and sf_tf tests

    @lauraporta
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  4. Add dependencies

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  5. Add data processing description

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  6. Add description of SF TF analysis

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Commits on Mar 6, 2023

  1. Change imports

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Commits on Mar 7, 2023

  1. Change imports

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  2. Add draft dashboard (very ugly)

    @lauraporta
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  3. Add sublots of SF/TF

    @lauraporta
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Commits on Mar 8, 2023

  1. Improve subplots

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Commits on Mar 9, 2023

  1. Add heatmaps with first version of gaussian fit

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Commits on Mar 13, 2023

  1. Update setup_for_demo.py

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Commits on Mar 14, 2023

  1. Add massive refactoring

    @lauraporta
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  2. Add docs to keep track of progress

    @lauraporta
    lauraporta committed Mar 14, 2023
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  3. Test image rendering

    @lauraporta
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  4. Finalize image view on md file

    @lauraporta
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  5. Move methods in correct modules (more refactoring)

    @lauraporta
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  6. Add fixes for github actions

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Commits on Mar 15, 2023

  1. Begin to work on proper gaussian fit

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Commits on Mar 16, 2023

  1. Add improved version of gaussian fit - has a lot of hardcoded parameters

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  2. Update docs

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  3. Change image width

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  4. Document more: add traces screenshots

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  5. Edit image of matlab gaussian fit

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Commits on Mar 21, 2023

  1. Refactor: move calculations in the analysis part; Add murakami plot

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Commits on Mar 23, 2023

  1. Add more interactions for murakami plot and improve handling of frequ… 

    …encies
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  2. Add tox dependency

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  3. Improve gaussian plots

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  4. Improve line plot of the session

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Commits on Mar 24, 2023

  1. Add cruft link output

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  2. Change repository url

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  3. Change to the correct commit hash

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  4. Add results of cruft check

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  5. Add unrealted black changes

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  6. Add changes to manifest

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Commits on Mar 28, 2023

  1. Improve polar plots

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  2. Add edits of black

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  3. Add controllers to the direction plots

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  4. Add prettier direction controller

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  5. Fix some errors in the x/y labels

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  6. Fix presentation of direction plots

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Commits on Mar 30, 2023

  1. Merge pull request #25 from neuroinformatics-unit/responsiveness 

    Responsiveness logic
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  2. Get rid of hardcoded parameters

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  3. Improve direction controller, clean up

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  4. Clean up callbacks

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Commits on Apr 3, 2023

  1. Add typing

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  2. Fix division by 0 error

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  3. Refactor sf/tf attribute

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  4. Add more types for attributes for PhotonData and make complete list

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  5. Add missing types

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  6. Fix error in test relative to different sf/tf in mock data

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  7. Fixing error in test leads to curious result

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  8. Add tests for gaussian funcions and fitting

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Commits on Apr 4, 2023

  1. Add tests for static methods of sf tf analysis

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Commits on Apr 13, 2023

  1. Add script to store output data of correct analysis pipeline

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Commits on Apr 14, 2023

  1. Improve sf/tf analysis function tests

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Commits on Apr 17, 2023

  1. Add more improvements to tests

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  2. Add some docstrings and improve previous ones

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  3. Add use of poisson distribution in mock data

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  4. First version of statistical test report generator

    @lauraporta
    lauraporta committed Apr 17, 2023
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  5. Clean up

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  6. Fix linting

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  7. Remove changes related to dashboard from this branch

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  8. Merge branch 'developement' into improve-analysis

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  9. Remove images

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  10. Merge commit '26cda761e06bd9d68175e3d9bf9a7d200f18ab64' into improve-… 

    …analysis
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Commits on Apr 19, 2023

  1. Add cruft link output

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  2. Change repository url

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  3. Change to the correct commit hash

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  4. Add results of cruft check

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  5. Add unrealted black changes

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  6. Add changes to manifest

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  7. Delete stats report since it belongs now to a different branch

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  8. Fix pandas and pickle interaction causing tox errors

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  9. Add changes made by ruff

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  10. Try this chatgpt github action workflow

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  11. Fix linting error

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    lauraporta committed Apr 19, 2023
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  12. Add chatgpt reviewer

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  13. Add changes to manifest

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  14. Apply suggested modification to the repo

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Commits on Apr 20, 2023

  1. Merge pull request #47 from neuroinformatics-unit/new-cruft 

    Apply changes generated using cruft
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  2. Change imports

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  3. Change imports

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  4. Add draft dashboard (very ugly)

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  5. Add sublots of SF/TF

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  6. Improve subplots

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  7. Add heatmaps with first version of gaussian fit

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  8. Add massive refactoring

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  9. Add docs to keep track of progress

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  10. Test image rendering

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  11. Finalize image view on md file

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  12. Move methods in correct modules (more refactoring)

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  13. Add fixes for github actions

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  14. Begin to work on proper gaussian fit

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  15. Add improved version of gaussian fit - has a lot of hardcoded parameters

    @lauraporta
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  16. Update docs

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  17. Change image width

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  18. Document more: add traces screenshots

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  19. Edit image of matlab gaussian fit

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  20. Refactor: move calculations in the analysis part; Add murakami plot

    @lauraporta
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  21. Add more interactions for murakami plot and improve handling of frequ… 

    …encies
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  22. Add tox dependency

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  23. Improve gaussian plots

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  24. Improve line plot of the session

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  25. Improve polar plots

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  26. Add edits of black

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  27. Add controllers to the direction plots

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  28. Add prettier direction controller

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  29. Fix some errors in the x/y labels

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  30. Fix presentation of direction plots

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  31. Get rid of hardcoded parameters

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  32. Improve direction controller, clean up

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  33. Clean up callbacks

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  34. Add typing

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  35. Fix division by 0 error

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  36. Refactor sf/tf attribute

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  37. Add more types for attributes for PhotonData and make complete list

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  38. Add missing types

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  39. Fix error in test relative to different sf/tf in mock data

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  40. Fixing error in test leads to curious result

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  41. Add tests for gaussian funcions and fitting

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  42. Add tests for static methods of sf tf analysis

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  43. Add script to store output data of correct analysis pipeline

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  44. Improve sf/tf analysis function tests

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  45. Add more improvements to tests

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  46. Add some docstrings and improve previous ones

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  47. Add use of poisson distribution in mock data

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  48. First version of statistical test report generator

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  49. Clean up

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  50. Fix linting

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  51. Remove changes related to dashboard from this branch

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  52. Remove images

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  53. Add changes to manifest

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  54. Delete stats report since it belongs now to a different branch

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  55. Fix pandas and pickle interaction causing tox errors

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  56. Add changes made by ruff

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  57. Merge branch 'improve-analysis' of github.com:neuroinformatics-unit/l… 

    …oad-suite2p into improve-analysis
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    lauraporta committed Apr 20, 2023
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  58. Add typing as suggested by chat-gpt reviewer

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  59. Revert "Add typing as suggested by chat-gpt reviewer" 

    This reverts commit 5e61c49.
    @lauraporta
    lauraporta committed Apr 20, 2023
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  60. Add small explanation

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    lauraporta committed Apr 20, 2023
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  61. Update readme

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    lauraporta committed Apr 20, 2023
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  62. Fix ascii conversion error

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    lauraporta committed Apr 20, 2023
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  63. Fixes and docstring correction

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Commits on May 5, 2023

  1. Merge pull request #49 from neuroinformatics-unit/improve-analysis 

    Improve analysis
    @lauraporta
    lauraporta authored May 5, 2023
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  2. Delete openai workflow

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  3. Merge pull request #52 from neuroinformatics-unit/developement 

    Merge dev into main
    @lauraporta
    lauraporta authored May 5, 2023
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Commits on May 31, 2023

  1. Perform the analysis also by pooling data from all directions (#56) 

    * Add code to pool directions

* Add notes

* Cleanup

* Fix broken tests

* Recalculate outputs

* Update manifest and pyproject

* Fix package name

* Update package links

* Update dependencies

* Add more descriptions

* Edit pyproject file

* Expand readme with more details on the analysis

* Add docstring

* Test if we can see the schema in the readme file

* Update docstring

* Insert correct image

* Linting

* Apply suggestions from code review

Co-authored-by: Niko Sirmpilatze <[email protected]>

* Change prompt message

* Adjust input params of method get_median_subtracted_response_and_params

* Renaming and other small suggested fixes

* Small fixes

* Move out the method to make gaussian matrices

* Clean up

---------

Co-authored-by: Niko Sirmpilatze <[email protected]>
    @lauraporta @niksirbi
    lauraporta and niksirbi authored May 31, 2023
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Commits on Jun 15, 2023

  1. Analyse data from experiments run on multiple days (#57) 

    * Add code to pool directions

* Add notes

* Cleanup

* Fix broken tests

* Recalculate outputs

* Update manifest and pyproject

* Fix package name

* Update package links

* Update dependencies

* Add more descriptions

* Edit pyproject file

* Expand readme with more details on the analysis

* Add docstring

* Test if we can see the schema in the readme file

* Add handling of multiple days

* Improve performance to deal with very large files, from O(n ^2) to O(1)

* Delete commented code

* Handle fit fails

* Save the data in a given folder

* Skip ROIs that do not fit

* Add missing fit handling in sftf analysis

* Regenerate mock data according to new "day" values

* Update docstring

* Remove big chunk of duplicated code

* Test image in readme file

* Remove image

* Apply suggestions from code review

Co-authored-by: Niko Sirmpilatze <[email protected]>

* Change prompt message

* Adjust input params of method get_median_subtracted_response_and_params

* Renaming and other small suggested fixes

* Renaming 2

* Small fixes

* Move out the method to make gaussian matrices

* Clean up

* Add tests for multiple days and add more structure and comments regarding creation of mock data

* Update readme

* Small updates in the docs

* Simplify fitting methods according to discussion

* Improve description on dataset creation optimization

* Remove unused config

* Rearrange methods in generate mock data

* Renaming ad adding new fixture

* Add missing n_roi fixture calls

* Renaming and folder reorganization

* Remove try-catch construct

* Linting

* Add missing adjustments

* Add readme file with a description of the regression tests

* Add more descriptions / docs

* Revert readme change

* Fix usage of conftest

* Linting

---------

Co-authored-by: Niko Sirmpilatze <[email protected]>
    @lauraporta @niksirbi
    lauraporta and niksirbi authored Jun 15, 2023
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Commits on Jul 4, 2023

  1. Saving analysis outputs in folders according to SWC-Blueprint (#60) 

    Co-authored-by: Niko Sirmpilatze <[email protected]>
    @lauraporta @niksirbi
    lauraporta and niksirbi authored Jul 4, 2023
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Commits on Jul 19, 2023

  1. Dashboard version 1.0, datatable and murakami plot (#61) 

    Co-authored-by: Niko Sirmpilatze <[email protected]>
Co-authored-by: Joe Ziminski <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    @lauraporta @niksirbi
    @JoeZiminski @pre-commit-ci
    4 people authored Jul 19, 2023
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Commits on Jul 21, 2023

  1. Test new cookiecutter (#66) 

    * Change commit hash

* Revert "Change commit hash"

This reverts commit b1aa762.

* Add changes introduced by cruft

* Getting rid of the docs for now

* Remove sphinx docs action for now

* Include coverage for codecov action

* Test fixing check-manifest error
    @lauraporta
    lauraporta authored Jul 21, 2023
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Commits on Aug 4, 2023

  1. More plots in the dashboard, focus on single ROI (#63) 

    Co-authored-by: Niko Sirmpilatze <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
    @lauraporta @niksirbi @pre-commit-ci
    3 people authored Aug 4, 2023
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Commits on Aug 7, 2023

  1. Renaming of parameter

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    lauraporta committed Aug 7, 2023
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  2. Add new loading methods

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    lauraporta committed Aug 7, 2023
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  3. [pre-commit.ci] auto fixes from pre-commit.com hooks 

    for more information, see https://pre-commit.ci
    @pre-commit-ci
    pre-commit-ci[bot] committed Aug 7, 2023
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  4. Linting

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    lauraporta committed Aug 7, 2023
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  5. Merge branch 'load-raw-suite2p-data' of github.com:neuroinformatics-u… 

    …nit/load-suite2p into load-raw-suite2p-data
    @lauraporta
    lauraporta committed Aug 7, 2023
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  6. Add logic to handle neuropil subtraction

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    lauraporta committed Aug 7, 2023
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  7. Rename config file key

    @lauraporta
    lauraporta committed Aug 7, 2023
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  8. Remove unused attribute

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    lauraporta committed Aug 7, 2023
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  9. Move analysis to pre-process data file

    @lauraporta
    lauraporta committed Aug 7, 2023
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