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First working implementation of the derotoation package #3

Merged
merged 169 commits into from
Dec 19, 2023
Merged

First working implementation of the derotoation package #3

merged 169 commits into from
Dec 19, 2023

Commits on Jun 20, 2023

  1. Find optimal threshold for frames

    @lauraporta
    lauraporta committed Jun 20, 2023
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  2. Assign correct sign for rotation

    @lauraporta
    lauraporta committed Jun 20, 2023
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  3. Get the rotation angle per tick

    @lauraporta
    lauraporta committed Jun 20, 2023
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  4. Add draft logic to fit the rotation degree changes to curve [not work… 

    …ing]
    @lauraporta
    lauraporta committed Jun 20, 2023
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  5. Linting

    @lauraporta
    lauraporta committed Jun 20, 2023
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Commits on Jun 22, 2023

  1. Add working logic to calculate the rotation degree for each frame

    @lauraporta
    lauraporta committed Jun 22, 2023
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  2. Visualize effects of derotation and correct some errors

    @lauraporta
    lauraporta committed Jun 22, 2023
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Commits on Jun 23, 2023

  1. Add draft pipeline to find centroid

    @lauraporta
    lauraporta committed Jun 23, 2023
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Commits on Jun 26, 2023

  1. Add libraries to pyproject.toml

    @lauraporta
    lauraporta committed Jun 26, 2023
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  2. Clean up

    @lauraporta
    lauraporta committed Jun 26, 2023
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  3. Improve plots

    @lauraporta
    lauraporta committed Jun 26, 2023
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  4. Optimization v1

    @lauraporta
    lauraporta committed Jun 26, 2023
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Commits on Jun 28, 2023

  1. Add changes to gitignore

    @lauraporta
    lauraporta committed Jun 28, 2023
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  2. Add functioning algorithm to optimize rotation degrees

    @lauraporta
    lauraporta committed Jun 28, 2023
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Commits on Jun 29, 2023

  1. Add improvements in the optimization algorithms for centroid location… 

    … and derotation angles
    @lauraporta
    lauraporta committed Jun 29, 2023
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Commits on Jul 10, 2023

  1. Add new plotting of centroids

    @lauraporta
    lauraporta committed Jul 10, 2023
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  2. Move part of the analysis code in methods in other files - analog pre… 

    …processing - extraction of rotation angles
    @lauraporta
    lauraporta committed Jul 10, 2023
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  3. Update pyproject.toml

    @lauraporta
    lauraporta committed Jul 10, 2023
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  4. Refactor plots and other methods

    @lauraporta
    lauraporta committed Jul 10, 2023
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  5. dummy napari plotting widget

    @alessandrofelder
    alessandrofelder committed Jul 10, 2023
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  6. Merge branch 'derotation-01' into napari-matplotlib

    @lauraporta
    lauraporta committed Jul 10, 2023
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  7. make a napari-MPL widget

    @alessandrofelder
    alessandrofelder committed Jul 10, 2023
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  8. Add functioning napari plugin

    @lauraporta
    lauraporta committed Jul 10, 2023
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Commits on Jul 11, 2023

  1. Add dependencies

    @lauraporta
    lauraporta committed Jul 11, 2023
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  2. Use unique configs and make path relative

    @lauraporta
    lauraporta committed Jul 11, 2023
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  3. Big refactoring

    @lauraporta
    lauraporta committed Jul 11, 2023
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  4. Remove curve fitting

    @lauraporta
    lauraporta committed Jul 11, 2023
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  5. Clean up gitignore

    @lauraporta
    lauraporta committed Jul 11, 2023
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  6. Move code to find best centroid

    @lauraporta
    lauraporta committed Jul 11, 2023
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  7. Rename method

    @lauraporta
    lauraporta committed Jul 11, 2023
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  8. Use pipeline in old script

    @lauraporta
    lauraporta committed Jul 11, 2023
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  9. Add new strategy for derotation

    @lauraporta
    lauraporta committed Jul 11, 2023
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  10. Small edits

    @lauraporta
    lauraporta committed Jul 11, 2023
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Commits on Jul 13, 2023

  1. Visualize labels

    @lauraporta
    lauraporta committed Jul 13, 2023
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  2. Use pilot data

    @lauraporta
    lauraporta committed Jul 13, 2023
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  3. Fix imports and attributes

    @lauraporta
    lauraporta committed Jul 13, 2023
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Commits on Jul 14, 2023

  1. Add less permissive angle

    @lauraporta
    lauraporta committed Jul 14, 2023
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  2. Rename files

    @lauraporta
    lauraporta committed Jul 14, 2023
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Commits on Aug 1, 2023

  1. Load grid data

    @lauraporta
    lauraporta committed Aug 1, 2023
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  2. More workarounds to play with grid data 🥲

    @lauraporta
    lauraporta committed Aug 1, 2023
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Commits on Aug 2, 2023

  1. Renaming functions to make them generic and add WORKING DEROTATION BY… 

    … LINE 🥳
    @lauraporta
    lauraporta committed Aug 2, 2023
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  2. Further refinement and changes in napari and debugging script

    @lauraporta
    lauraporta committed Aug 2, 2023
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Commits on Aug 3, 2023

  1. Improve the algorithm for end of rotation

    @lauraporta
    lauraporta committed Aug 3, 2023
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  2. Improve naming of conditions

    @lauraporta
    lauraporta committed Aug 3, 2023
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  3. Remove bugs for negative rotations

    @lauraporta
    lauraporta committed Aug 3, 2023
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  4. Handle rotation ticks missing better

    @lauraporta
    lauraporta committed Aug 3, 2023
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  5. Add script to visualize how different params of scipy.rotate affect t… 

    …he image
    @lauraporta
    lauraporta committed Aug 3, 2023
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Commits on Aug 4, 2023

  1. Handle better initialization of original image at the beginning and a… 

    …t the end of the rotation - no interpolation with scipy
    @lauraporta
    lauraporta committed Aug 4, 2023
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  2. Choose data

    @lauraporta
    lauraporta committed Aug 4, 2023
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  3. Improve plotting and image handling in script

    @lauraporta
    lauraporta committed Aug 4, 2023
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Commits on Aug 7, 2023

  1. Add two images regarding scipy rotate params exploration

    @lauraporta
    lauraporta committed Aug 7, 2023
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  2. Fix error in detection of false rotations

    @lauraporta
    lauraporta committed Aug 7, 2023
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  3. Workaround for suboptimal threshold identification

    @lauraporta
    lauraporta committed Aug 7, 2023
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  4. Clean up napari script

    @lauraporta
    lauraporta committed Aug 7, 2023
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  5. Temporary adjustament of rotation algorithm

    @lauraporta
    lauraporta committed Aug 7, 2023
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  6. Include other datasets

    @lauraporta
    lauraporta committed Aug 7, 2023
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  7. Complete pipeline including masking and saving of tif file

    @lauraporta
    lauraporta committed Aug 7, 2023
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Commits on Aug 9, 2023

  1. Renaming file

    @lauraporta
    lauraporta committed Aug 9, 2023
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  2. Refactoring, move modules in different folders

    @lauraporta
    lauraporta committed Aug 9, 2023
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  3. More refactoring and deletion of unused methods

    @lauraporta
    lauraporta committed Aug 9, 2023
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  4. More refactoring

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

  1. More refactoring related to data in input, changes in the config files

    @lauraporta
    lauraporta committed Aug 10, 2023
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  2. Add readme

    @lauraporta
    lauraporta committed Aug 10, 2023
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  3. Renaming

    @lauraporta
    lauraporta committed Aug 10, 2023
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  4. Change dependencies

    @lauraporta
    lauraporta committed Aug 10, 2023
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  5. Add logging

    @lauraporta
    lauraporta committed Aug 10, 2023
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  6. Fix small import bug and change order of rotate method

    @lauraporta
    lauraporta committed Aug 10, 2023
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  7. Upadate readme

    @lauraporta
    lauraporta committed Aug 10, 2023
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  8. Fix wrong log name

    @lauraporta
    lauraporta committed Aug 10, 2023
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  9. Edits to the readme

    @lauraporta
    lauraporta committed Aug 10, 2023
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Commits on Sep 10, 2023

  1. Add extra method (draft)

    @lauraporta
    lauraporta committed Sep 10, 2023
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  2. Add script to saved tifs for unique rotations

    @lauraporta
    lauraporta committed Sep 10, 2023
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Commits on Oct 4, 2023

  1. Add script to correct an artefact

    @lauraporta
    lauraporta committed Oct 4, 2023
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  2. Add script to remove rotations for completed tif file

    @lauraporta
    lauraporta committed Oct 4, 2023
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  3. Move script to isolate rotations

    @lauraporta
    lauraporta committed Oct 4, 2023
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Commits on Oct 10, 2023

  1. Add other plotting scripts

    @lauraporta
    lauraporta committed Oct 10, 2023
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  2. Get data retreives file name

    @lauraporta
    lauraporta committed Oct 10, 2023
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  3. Plots are not saved here anymore

    @lauraporta
    lauraporta committed Oct 10, 2023
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  4. Improve rotation by line and add fileter for incremental rotation

    @lauraporta
    lauraporta committed Oct 10, 2023
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  5. Delete older plots

    @lauraporta
    lauraporta committed Oct 10, 2023
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Commits on Oct 13, 2023

  1. Load data refactoring

    @lauraporta
    lauraporta committed Oct 13, 2023
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  2. Load data refactoring

    @lauraporta
    lauraporta committed Oct 13, 2023
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  3. Merge commit 'ca0b046c3c9df1f65318cacf0256cc96231a053d' into code-cle… 

    …anup
    @lauraporta
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  4. Remove hard coded values

    @lauraporta
    lauraporta committed Oct 13, 2023
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Commits on Oct 17, 2023

  1. Add improvements to analog signals processing and a test

    @lauraporta
    lauraporta committed Oct 17, 2023
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Commits on Oct 23, 2023

  1. Add debugging plots, more logging and reformatting of checks

    @lauraporta
    lauraporta committed Oct 23, 2023
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  2. Remove method with bisect

    @lauraporta
    lauraporta committed Oct 23, 2023
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  3. Change method signature

    @lauraporta
    lauraporta committed Oct 23, 2023
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  4. Rearrange checks logic

    @lauraporta
    lauraporta committed Oct 23, 2023
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  5. Add useful counts

    @lauraporta
    lauraporta committed Oct 23, 2023
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  6. Extend adjust rotation increment

    @lauraporta
    lauraporta committed Oct 23, 2023
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  7. Remove obsolete method

    @lauraporta
    lauraporta committed Oct 23, 2023
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  8. Add further method to correct ticks number

    @lauraporta
    lauraporta committed Oct 23, 2023
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  9. Add better angle interpolation method

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    lauraporta committed Oct 23, 2023
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Commits on Oct 24, 2023

  1. Use new interpolation method

    @lauraporta
    lauraporta committed Oct 24, 2023
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  2. Change order of methods

    @lauraporta
    lauraporta committed Oct 24, 2023
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  3. Improve mask generation

    @lauraporta
    lauraporta committed Oct 24, 2023
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  4. Read speed info as well

    @lauraporta
    lauraporta committed Oct 24, 2023
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  5. Fix interpolation bugs

    @lauraporta
    lauraporta committed Oct 24, 2023
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  6. Add converters

    @lauraporta
    lauraporta committed Oct 24, 2023
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  7. Add more debugging plots

    @lauraporta
    lauraporta committed Oct 24, 2023
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  8. Reordering methods

    @lauraporta
    lauraporta committed Oct 24, 2023
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  9. Improve calculation of rotation increments

    @lauraporta
    lauraporta committed Oct 24, 2023
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  10. Add typing and docstrings

    @lauraporta
    lauraporta committed Oct 24, 2023
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  11. Add first working test

    @lauraporta
    lauraporta committed Oct 24, 2023
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  12. Add test on correction of start and end times

    @lauraporta
    lauraporta committed Oct 24, 2023
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  13. Add test for the creation of the signed rotation array

    @lauraporta
    lauraporta committed Oct 24, 2023
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  14. Make drop ticks method static and create related test

    @lauraporta
    lauraporta committed Oct 24, 2023
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  15. Update manifest file

    @lauraporta
    lauraporta committed Oct 24, 2023
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Commits on Oct 25, 2023

  1. Update docstring

    @lauraporta
    lauraporta committed Oct 25, 2023
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  2. Fix random seed bug

    @lauraporta
    lauraporta committed Oct 25, 2023
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  3. Make adjust rotation increment static and add test

    @lauraporta
    lauraporta committed Oct 25, 2023
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  4. Remove over-use of static methods, just one was useful

    @lauraporta
    lauraporta committed Oct 25, 2023
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  5. Fix tick drop bug and add more tests

    @lauraporta
    lauraporta committed Oct 25, 2023
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  6. Add test for angles

    @lauraporta
    lauraporta committed Oct 25, 2023
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  7. Add new visualization and clean up

    @lauraporta
    lauraporta committed Oct 25, 2023
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  8. Add more docs and edit config

    @lauraporta
    lauraporta committed Oct 25, 2023
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  9. Add more docs

    @lauraporta
    lauraporta committed Oct 25, 2023
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Commits on Oct 26, 2023

  1. Refactor and clean up

    @lauraporta
    lauraporta committed Oct 26, 2023
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  2. Add working pipeline for incremental rotations

    @lauraporta
    lauraporta committed Oct 26, 2023
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Commits on Oct 27, 2023

  1. Add saving of angle table, BUT there is a bug in the derotation, solu… 

    …tion not found yet
    @lauraporta
    lauraporta committed Oct 27, 2023
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  2. Add working derotation of incremental images

    @lauraporta
    lauraporta committed Oct 27, 2023
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  3. Add script to identify the displacement of the frames during rotation

    @lauraporta
    lauraporta committed Oct 27, 2023
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Commits on Oct 30, 2023

  1. Finish up script to test incremental derotation registration

    @lauraporta
    lauraporta committed Oct 30, 2023
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  2. Add incremental derotation registration to the pipeline

    @lauraporta
    lauraporta committed Oct 30, 2023
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  3. Allow to change diameter of circular mask

    @lauraporta
    lauraporta committed Oct 30, 2023
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Commits on Nov 1, 2023

  1. Fix derotation by line bug

    @lauraporta
    lauraporta committed Nov 1, 2023
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Commits on Nov 2, 2023

  1. Delete all exploration plots

    @lauraporta
    lauraporta committed Nov 2, 2023
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  2. Delete napari related files

    @lauraporta
    lauraporta committed Nov 2, 2023
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  3. Add typing and docstrings

    @lauraporta
    lauraporta committed Nov 2, 2023
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  4. Move scripts in a dedicated folder

    @lauraporta
    lauraporta committed Nov 2, 2023
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  5. Remove leftover from napari plugin

    @lauraporta
    lauraporta committed Nov 2, 2023
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  6. Fix error in installation of dependencies

    @lauraporta
    lauraporta committed Nov 2, 2023
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Commits on Nov 3, 2023

  1. Simplify derotation by line

    @lauraporta
    lauraporta committed Nov 3, 2023
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  2. Add regression tests for image rotation

    @lauraporta
    lauraporta committed Nov 3, 2023
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  3. Update readme file

    @lauraporta
    lauraporta committed Nov 3, 2023
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  4. Expand readme

    @lauraporta
    lauraporta committed Nov 3, 2023
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  5. Add generic paths to config files

    @lauraporta
    lauraporta committed Nov 3, 2023
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  6. Remove not so useful comments

    @lauraporta
    lauraporta committed Nov 3, 2023
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  7. Update .gitignore and MANIFEST.in

    @lauraporta
    lauraporta committed Nov 3, 2023
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Commits on Nov 6, 2023

  1. Adapt sphinx docs and improve some docstrings

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    lauraporta committed Nov 6, 2023
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Commits on Nov 10, 2023

  1. Renaming

    @lauraporta
    lauraporta committed Nov 10, 2023
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  2. Move the main method, derotate by line, out of the pipeline

    @lauraporta
    lauraporta committed Nov 10, 2023
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  3. Add more examples in the readme

    @lauraporta
    lauraporta committed Nov 10, 2023
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  4. Fix used dog image

    @lauraporta
    lauraporta committed Nov 10, 2023
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Commits on Nov 27, 2023

  1. Add script to correct csv

    @lauraporta
    lauraporta committed Nov 27, 2023
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Commits on Nov 28, 2023

  1. Move the logic to generate a better csv inside the class

    @lauraporta
    lauraporta committed Nov 28, 2023
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  2. Fixed manifest

    @lauraporta
    lauraporta committed Nov 28, 2023
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  3. Fix docs building bug (missing imports)

    @lauraporta
    lauraporta committed Nov 28, 2023
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Commits on Dec 11, 2023

  1. Add script to run derotation in the cluster

    @lauraporta
    lauraporta committed Dec 11, 2023
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Commits on Dec 12, 2023

  1. Add the dogs 🐕

    @lauraporta
    lauraporta committed Dec 12, 2023
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  2. Merge commit '7cade60719eb972594b2ea0644a9667cb8c1ad2f' into code-cle… 

    …anup
    @lauraporta
    lauraporta committed Dec 12, 2023
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  3. Fix image naming mistake

    @lauraporta
    lauraporta committed Dec 12, 2023
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  4. Fix bug in angle interpolation

    @lauraporta
    lauraporta committed Dec 12, 2023
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  5. Include contrast enhancment

    @lauraporta
    lauraporta committed Dec 12, 2023
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  6. Move threshold and contrast values to config file

    @lauraporta
    lauraporta committed Dec 12, 2023
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  7. Use the image offset to fill in the blank pixels

    @lauraporta
    lauraporta committed Dec 12, 2023
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  8. Fix typo

    @lauraporta
    lauraporta committed Dec 12, 2023
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  9. Use the same diameter for masking when doing derotations one after th… 

    …e other
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    lauraporta committed Dec 12, 2023
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Commits on Dec 14, 2023

  1. Update derotation/analysis/full_rotation_pipeline.py 

    Co-authored-by: Niko Sirmpilatze <[email protected]>
    @lauraporta @niksirbi
    lauraporta and niksirbi committed Dec 14, 2023
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  2. Update derotation/analysis/full_rotation_pipeline.py 

    Co-authored-by: Niko Sirmpilatze <[email protected]>
    @lauraporta @niksirbi
    lauraporta and niksirbi committed Dec 14, 2023
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Commits on Dec 19, 2023

  1. Refactor example

    @lauraporta
    lauraporta committed Dec 19, 2023
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  2. Improve usage of custom methods with docstrings and typing

    @lauraporta
    lauraporta committed Dec 19, 2023
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  3. Substitute np.where with np.nonzero when only the condition is presen… 

    …t (S6729)
    @lauraporta
    lauraporta committed Dec 19, 2023
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  4. Fix bugs found in the incremental rotation pipeline

    @lauraporta
    lauraporta committed Dec 19, 2023
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  5. Fix typo

    @lauraporta
    lauraporta committed Dec 19, 2023
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  6. Fix creation of dataframe

    @lauraporta
    lauraporta committed Dec 19, 2023
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  7. Rename variable k

    @lauraporta
    lauraporta committed Dec 19, 2023
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  8. Add missing dependencies

    @lauraporta
    lauraporta committed Dec 19, 2023
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