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CHANGELOG.md

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0.18.6 (Sat Jun 01 2024)

🐛 Bug Fix

Authors: 2

0.18.5 (Mon May 20 2024)

🐛 Bug Fix

Authors: 2

0.18.4 (Mon May 20 2024)

🐛 Bug Fix

🏠 Internal

Authors: 3

0.18.3 (Tue Sep 05 2023)

🐛 Bug Fix

  • fix: Make sure butterworth order is given (@smoia)

Authors: 1

0.18.2 (Mon Aug 28 2023)

🐛 Bug Fix

⚠️ Pushed to master

Authors: 1

0.18.1 (Sun Aug 13 2023)

🐛 Bug Fix

⚠️ Pushed to master

  • int: codespell happy (@smoia)
  • Start adding a bunch of tests (@smoia)
  • Wrong library ;) (@smoia)
  • int: Add codespell (@smoia)
  • int: update auto-release environment (@smoia)
  • int: update python-publish environment (@smoia)

🏠 Internal

Authors: 2

0.18.1 (Thu May 11 2023)

⚠️ Pushed to master

  • Start adding a bunch of tests (@smoia)
  • Wrong library ;) (@smoia)
  • int: Add codespell (@smoia)
  • int: update auto-release environment (@smoia)
  • int: update python-publish environment (@smoia)

🏠 Internal

Authors: 2

0.18.0 (Wed Mar 08 2023)

💥 Breaking Change during development

🐛 Bug Fix

  • Improve auto settings to include all labels and plugins #72 (@smoia)

⚠️ Pushed to master

  • int: Fix issue templates (@smoia)

Authors: 2

0.17.2 (Sat Feb 25 2023)

🐛 Bug Fix

⚠️ Pushed to master

  • docs: Update developer installation (@smoia)

🏠 Internal

Authors: 2

0.17.1 (Mon Dec 12 2022)

🐛 Bug Fix

Authors: 1

0.17.0 (Fri Nov 18 2022)

🚀 Enhancement

Authors: 2

0.16.0 (Mon Oct 10 2022)

🚀 Enhancement

  • Add pre-commit and format all code #54 (@smoia)

⚠️ Pushed to master

  • docs: Fix badges and latest DOI (@smoia)

Authors: 1

0.15.3 (Fri Jul 01 2022)

🐛 Bug Fix

  • fix: force mask to be an ndarray of booleans in regression (@smoia)

Authors: 1

0.15.2 (Fri Jul 01 2022)

🐛 Bug Fix

  • fix: Fix plot of xcorr that was called even when skipping xcorr (@smoia)

Authors: 1

0.15.1 (Fri Jun 24 2022)

🐛 Bug Fix

  • Fix dimensionality check for functional images #52 (@smoia)

Authors: 1

0.15.0 (Wed Apr 27 2022)

🚀 Enhancement

  • Add the possibility to skip the cross correlation step when creating lagged regressors #50 (@smoia)

Authors: 1

0.14.1 (Tue Apr 19 2022)

🐛 Bug Fix

  • fix: Fix nifti import and mask creation (@smoia)

Authors: 1

0.14.0 (Tue Apr 19 2022)

🚀 Enhancement

  • Allow confounding matrix and mask to be optional in stats.regression #49 (@smoia)

Authors: 1

0.13.0 (Tue Apr 05 2022)

🚀 Enhancement

  • Enhance cross correlation to allow both regressor and reference to be shifted and consider max abs corr #48 (@smoia)

Authors: 1

0.12.1 (Tue Apr 05 2022)

🐛 Bug Fix

  • Let signal be resampled over any axis of the input timeseries (default to first dimension) #47 (@smoia)

⚠️ Pushed to master

  • docs: fix readme citations (@smoia)
  • docs: update README with installation instruction and badges (@smoia)

Authors: 1

0.12.0 (Tue Mar 22 2022)

💥 Breaking Change during development

  • Change behaviour to create petco2hrf fmri proxy due to the SPC of average signal being more robust than average of SPC #46 ([email protected])

Authors: 1

0.11.2 (Tue Mar 22 2022)

🐛 Bug Fix

  • Fix SPC computation by dividing by the transposed mean (not the matrix itself) #45 ([email protected])

Authors: 1

0.11.1 (Mon Mar 07 2022)

🐛 Bug Fix

Authors: 1

0.11.0 (Thu Mar 03 2022)

💥 Breaking Change during development

Authors: 2

0.10.0 (Wed Feb 23 2022)

💥 Breaking Change during development

Authors: 2

0.9.0 (Wed Feb 23 2022)

💥 Breaking Change during development

Authors: 2

0.8.0 (Wed Feb 23 2022)

💥 Breaking Change during development

Authors: 2

0.7.1 (Sun Feb 06 2022)

🐛 Bug Fix

Authors: 2

0.7.0 (Sun Feb 06 2022)

🚀 Enhancement

Authors: 2

0.6.2 (Tue Feb 01 2022)

⚠️ Pushed to master

Authors: 1

0.6.1 (Sat Jan 29 2022)

🎉 This release contains work from a new contributor! 🎉

Thank you, DeepSource Bot (@deepsourcebot), for all your work!

⚠️ Pushed to master

Authors: 1

0.6.0 (Thu Jan 27 2022)

💥 Breaking Change during development

Authors: 2

0.5.1 (Thu Jan 13 2022)

🐛 Bug Fix

  • Fix astype call on physiological indexes array #31 (@smoia)

Authors: 1

0.5.0 (Mon Nov 15 2021)

🚀 Enhancement

  • Add output of all regression results for debug #30 (@smoia)

Authors: 1

0.4.2 (Mon Nov 15 2021)

🐛 Bug Fix

  • Fix scale factor (divide instead of multiply) for bulk shift output #29 (@smoia)

Authors: 1

0.4.1 (Thu Nov 04 2021)

🐛 Bug Fix

Authors: 1

0.4.0 (Wed Nov 03 2021)

💥 Breaking Change during development

  • If scale factor is declared, divide the betas by the scale factor #27 (@smoia)

Authors: 1

0.3.1 (Wed Nov 03 2021)

⚠️ Pushed to master

  • Extension check are case insensitive (@smoia)

Authors: 1

0.3.0 (Sun Oct 31 2021)

💥 Breaking Change during development

  • Allow to provide a mask to exclude voxels from the computations, and a separate ROI to use for Xcorr average signal (and lag correction) #26 (@smoia)

Authors: 1

0.2.4 (Sun Oct 31 2021)

🎉 This release contains work from a new contributor! 🎉

Thank you, Kristina Zvolanek (@kristinazvolanek), for all your work!

🐛 Bug Fix

  • Fixed output regressor to be the optimally shifted version, rather than the original demeaned regressor #25 (@kristinazvolanek)

Authors: 1

0.2.3 (Sat Oct 30 2021)

🐛 Bug Fix

  • Fix denoise_matrix input from CLI that was causing it to be a list of lists #24 (@smoia)

Authors: 1

0.2.2 (Sat Oct 30 2021)

⚠️ Pushed to master

  • Fix check_ext call in generating output name (@smoia)

Authors: 1

0.2.1 (Sat Oct 30 2021)

🐛 Bug Fix

Authors: 1

0.2.0 (Fri Oct 15 2021)

💥 Breaking Change during development

Authors: 1

0.1.1 (Sun Oct 10 2021)

🐛 Bug Fix

Authors: 1

0.1.0 (Sun Oct 10 2021)

💥 Breaking Change during development

  • Fix auto config file #20 (@smoia)
  • Add configuration files for CD, declare licence in all codefiles, update development status #19 (@smoia)

🐛 Bug Fix

Authors: 1

0.0.3 (Sun Oct 10 2021)

🐛 Bug Fix

Authors: 1

0.0.2 (Sat Oct 09 2021)

🐛 Bug Fix

  • Invert CLI behaviour for lagged regressors, improve workflow input parameters definition and check #16 (@smoia)

Authors: 1

0.0.1 (Sat Oct 09 2021)

🐛 Bug Fix

⚠️ Pushed to master

  • Add workflows and templates (@smoia)
  • Parser options all there. (@smoia)
  • lag_step becomes 0.3 (@smoia)
  • Rename lag variables (@smoia)
  • Rename maxlag for coherence (@smoia)
  • Force run_regression to be true if lagged_regression is! (@smoia)
  • Remove unused parameter (@smoia)
  • Start working that parser (@smoia)
  • Fix relative lag background (@smoia)
  • Minor text correction and transform comments into issues (@smoia)
  • Signal percentage change the data outside of regression (@smoia)
  • When co2 signal is not provided, force skip convolution (@smoia)
  • Add relative lag export (@smoia)
  • Reduce butter order to 1 (@smoia)
  • Improve empty array creation, change lag variable names, change take command due to heavy memory load (@smoia)
  • Fix f string (@smoia)
  • Remove breakpoints (@smoia)
  • Fix beta and tstat assignment (@smoia)
  • Invert regr shift call and fix assignment of volumes after regression (@smoia)
  • Close those plot (@smoia)
  • Skip hrf plot (@smoia)
  • Better try than have the doubt (@smoia)
  • Fine shifts exist only if they exist (@smoia)
  • Fix lagged regressor matrices shape (@smoia)
  • Fix step (@smoia)
  • Move output to right folder (@smoia)
  • stats should be debugged. (@smoia)
  • Correct regressors hstack (@smoia)
  • Also say the right matrix! (@smoia)
  • read denoising matrix, not its name (@smoia)
  • Invert petco2hrf shifts matrix orientation (@smoia)
  • Remember to add a plot of the xcorr with both xcorrs if two were used (@smoia)
  • Shorter tp assignment (@smoia)
  • join comes from paths... (@smoia)
  • Fix func import (@smoia)
  • Fix mask import and average of functional signal (@smoia)
  • Boolean input variables as booleans rather than empty (@smoia)
  • Fix general pre-installation stuff (@smoia)
  • Fix authors (@smoia)
  • DEBUG (@smoia)
  • Add multiple denoise matrices (@smoia)
  • If user specifies lag map, use it! (@smoia)
  • stats.regression returns all lagged regressors in memory (@smoia)
  • Update comments (@smoia)
  • If no outdir is specified, make one in the functional input folder (@smoia)
  • Log to log folder (skip code folder) (@smoia)
  • Simplify input (@smoia)
  • Update inputs accordingly (@smoia)
  • Check dimension of confounders input (@smoia)
  • Add R square computation (@smoia)
  • Add possibility to skip convolution (e.g. if input is already petco2hrf) (@smoia)
  • Add legendre and OLS regression (@smoia)
  • Move everything related to statistical models to stats module (@smoia)
  • Move signal related functions to signal module (@smoia)
  • Move io function to their own module (@smoia)
  • Remove extra main (@smoia)
  • Remove nilearn and fix imports (@smoia)
  • Start adding lagged regression - but it's totally untested. (@smoia)
  • Update necessary libraries and import OLSModel (@smoia)
  • Read phys files from peakdet! (@smoia)
  • Remove save call from main workflow (@smoia)
  • Less variables, more understanding (@smoia)
  • Add support for gzipped tsv (@smoia)
  • Load phys files (@smoia)
  • Fix check extension (@smoia)
  • Continue file import, add TR reading, Add filter application (@smoia)
  • Start working on get_regressor (@smoia)
  • Add a filter signal function (@smoia)
  • Save bash call as a function not in main workflow (@smoia)
  • Change scipy import (@smoia)
  • Change author (@smoia)
  • Add most of file import (@smoia)
  • Clear up package (@smoia)
  • Update contributors (@smoia)
  • Add physiopy logo (@smoia)
  • Add parser and main workflow (@smoia)
  • Correct development status (@smoia)
  • Add infra files (@smoia)
  • Initial commit (@smoia)

📝 Documentation

Authors: 1