Changelog

v0.6.7 (2022-06-29)

v0.6.6 (2022-06-29)

Documentation

  • Change codecov settings (fe32513)

  • Change codecov badge to reflect new org name (41d5543)

  • Get rid of docs badge - causing glitch on rtd (d0a65b4)

v0.6.5 (2022-06-29)

Fix

  • Just rerun notebook and comment in the decomposition (9763f79)

v0.6.4 (2022-06-29)

Documentation

  • Fix docs badge (edf26bd)

  • Replace readthedocs latest branch with stable branch (5a1382b)

v0.6.3 (2022-06-29)

v0.6.2 (2022-06-29)

Documentation

  • Use synonyms for affect and reword relearning part (f2ca67e)

  • Make rscript commands copy-pasteable (e189d81)

  • Get rid of double inaccurate (5363fe5)

  • Standardize docstrings (cb4acf9)

  • Update docstrings (27d801a)

  • Add line about running notebook locally (2354f77)

  • Fix toc links (3dc965b)

  • Add project directory: (24357e4)

  • Add overview section (41d8f3c)

  • Add copyright notice (06800c6)

  • Add toc (eeba7b4)

v0.6.1 (2022-06-28)

Documentation

  • Further trim down report (f180279)

v0.6.0 (2022-06-28)

Feature

  • Remove delete peak functions (7246973)

  • For the future. notebook but with remove peak working. (1fbd574)

  • Add the remove false peak feature (52987ce)

Fix

  • Fix data compatibility issues with hug data and peak selection and optimize some code (31a83ce)

  • Fix RMSE broken (cdc976d)

  • Latest notebook (64307b8)

  • Make dashboard nice and streamlined. widgets for everything. Remove Delete Peak from main notebook for now (8eeea97)

  • Method param is now str instead of function to allow for widget selection (e9b504a)

  • Adding code to allow for team and source data to be visualised (bf821eb)

  • Small tweaks to pulse (e726429)

  • Fixing incorrect filtering of dataframe (e6b5d23)

Documentation

  • Further document viz scripts, and couple minor patches (7beb17b)

  • More viz comments (e54660e)

  • Add comments to contrast.py (fda6711)

  • Update comments (fd3fcb0)

  • Update comments (b3cd300)

  • Editing instructions in notebook (de0baaf)

  • Editing instructions within notebook (9a09ad2)

  • Update params in dashboard() function (4b81d70)

v0.5.3 (2022-06-28)

Documentation

v0.5.2 (2022-06-28)

Fix

  • Bring nb up to date before spinning it off to new branch (ce882ce)

  • Viz script had trash on top (f4eee35)

  • Resolve conflict (8d592f6)

Documentation

  • Fix formatting of code chunks (a2a70b0)

  • Add in-depth pdf rendering instructions (53f1cb9)

  • Improved notebook documentation to elaborate that file extension doesnt need to be mat or have SIG (9206266)

  • Add gui plots (dcb0f36)

  • Re-write conclusion (6994e74)

  • Fix grammar and spelling errors, make more abbreviations (e984e3c)

  • Add equations and made revisions (7fc21e9)

  • Add separation and preprocessing figures (6f28822)

  • Change emg hardware img (5c68672)

  • Fix reference formatting in methods (915f733)

  • Name ot bioelletronica software and add references (4d978cb)

  • Add references for motor unit fig and add general EMG tech fig (041183d)

  • Comment and uncomment some cells so it looks nicer (2d43e41)

  • Document the notebook more thoroughly (494fb01)

  • Document the notebook (2847d0e)

  • Document the notebook (33245e4)

  • Document the notebook (29c9b47)

  • Add github link (d26b875)

  • Further revise intro (80b10f0)

  • Revise the summary to include alexi’s suggestions (acf6dee)

  • Add accent to alexis name (c0876ab)

  • Add copyright lines and descriptions of each script (6454fd4)

  • Add link to choosealicense (8f99ff4)

  • Add python version requirement (d1f212a)

  • Incorporating revisions from feedback (46b61f9)

  • Add list to the methods section (ca90736)

v0.5.1 (2022-06-28)

Documentation

v0.5.0 (2022-06-28)

Feature

  • Remove unfinished peel-off function (33146dd)

v0.4.5 (2022-06-28)

v0.4.4 (2022-06-28)

v0.4.3 (2022-06-28)

Documentation

v0.4.2 (2022-06-24)

v0.4.1 (2022-06-23)

Documentation

v0.4.0 (2022-06-22)

Feature

  • Add functions to and clean up visualization script (a42226e)

Fix

  • Making the notebook tick (ad02d2c)

  • Add bandpass filtering to dashboard and get rid of other bugs (e70a3f5)

  • Add default mu to dashboard func (5d2d39e)

  • Add data massaging into dashboard (ac38fb7)

  • Clean up comments and imports (90ebe54)

Documentation

  • Shorten intro (af41b4d)

  • Add info about results (11a4503)

  • Edit methods (942e74d)

  • Add a little more info to usage (bc6eabc)

  • Fix formatting of some references (a703821)

  • Update references (42a6728)

  • Add final report images (c8a278e)

  • Add summary and conclusions (d21bf5b)

  • Update intro (c778e05)

  • Add intro (b9a909f)

  • Add line about future validation (db3dbf2)

  • Add part about stakeholders (068d470)

  • Update usage section (7d72f0d)

  • Get rid of unnecessary hyphens (9d2d859)

  • Update to reflect new license and all authors (0a528e1)

  • Update package name (e3340c5)

  • Fix formatting in credits (3aa38ee)

  • Change license to gplv3 (a9da174)

  • Update readme credits, description, and usage (0bcb39c)

  • Write data product draft (79bd1fa)

  • Write draft of data science methods section (83dd899)

  • Create final report parent and child documents (6c25266)

v0.3.1 (2022-06-21)

Fix

  • Properly call bandpass args and R arg in decomposition (03be854)

v0.3.0 (2022-06-20)

Feature

  • Add band-pass filter function (6a2fe0b)

  • Add more print statements to refinement (2378e67)

  • Add discard channel argument (532fde3)

  • Update decomposition (3542783)

  • Update refinement (8800cc3)

  • Update separation (aa303a6)

  • Replace initialize_w with initial_w_matrix (b2d4436)

  • Add rada’s peel-off function (fe7d0a2)

  • Add rada’s orthogonalization wrapper (cfca9cb)

  • Create deflate function (2826f25)

  • Create gram-schmidt function (3eccc57)

  • Create pulse to noise ratio function (49515bc)

  • Add page numbers to plots (7e6f0cd)

  • Create MUAP visualization functions (04667f5)

  • Create new silhouette score function (054f0b5)

  • Build initialize() function (c0aec10)

  • New decomposition and initialize_w functions, changes to other functions (80d62ff)

  • Add pulse train save functionality and made code clearer (9fd71c5)

  • Add refinement function draft (83d5174)

  • Create two other options for contrast functions and fix docstring for skew (284fdf6)

  • Add orthogonalize, normalize, apply_contrast_fun_router, skew functions and skeleton of sepatation function (79c0882)

Fix

  • Rounding error in whitening test (0bff4cf)

  • Correct regularization factor in whitening (ea754c5)

  • Init test (fdac487)

  • Import center_matrix (d9fa2a8)

  • Change sil to use peaks and noise clusters instead of cluster a and cluster b (d9fb56d)

  • Correct pnr formula (d47045a)

  • Edit viz function to handle pt < l (5bd542e)

  • Change column number (1877030)

  • Fix pt dimensions and commented out count limitation in muap_plot (1658379)

  • Variable typo (3116cc8)

  • Minor test fix (53114ee)

  • Orthogonalization and peel-off functions notebook (ef05344)

  • Merge conflictuehriuhudviugfuvdbfvd (f65c968)

  • Update interval (9d2c021)

  • Omg comma making formatting funny (4f55ddc)

  • Fix file path (8a7de01)

  • Deleted the cursed doppleganger pnr function. merge my damn pr for love of god (f211af1)

  • Remove incorrectly called function (6f2b4d7)

  • Center firing in middle of signal interval (9e5d39c)

  • Get rid of merge conflict (2afed78)

  • Revert back to old muap interval (3459a83)

  • Muap test interval symmetry (1b68e13)

  • Fix: peak interval symmetry (a26419f)

  • Update import statements (a598132)

  • Reorder parameters where refinement is called in decomp function (19a60cf)

  • Catch up decomp function to latest or else ci fails (2de0281)

  • Keep finding small bugs in refine test (34b98fc)

  • Remove unneeded vars, change path (70b921c)

  • Path name again yikes (4cac533)

  • Update path (7036f9d)

  • Change facet variable (e8ab3e1)

  • Add defintion of l in muap_plot() (c882d48)

  • Path name in test_maup_dict() (a6f8f52)

  • Fix file path in test_muap_dict() (179929b)

  • Remove incorrect import statement (a57bfe4)

  • Add emg import statement (13a1ecd)

  • Remove extraneous test (98a10d4)

  • Modify refinement test (ec2b0d1)

  • Don’t update separation vector after cv_curr > cv_prev (e83ca1c)

  • Copy paste error, EOL string (f6d4c17)

  • Add random_seed to kmeans (4f70ec7)

  • Get rid of quotation marks in function arguments (ff70083)

  • Get rid of redundant parameters and update decomposition to include new refinement parameters (b15e5be)

  • For some reason my GLs are named GMs. Fixed path (9fdc54f)

  • Tweak refinement function to allow for random seed for testing (6561667)

  • Change function to average over every MUAP firing instead of every channel (2cc8837)

  • Get rid of double ptl assignment (27702fc)

  • Change silhouette_score function in refinement (4fb0eb4)

  • Fix intra_sums (be163f1)

  • Fix inter_cluster sum and replace silhouette function in refinement (9c8ebc7)

  • Get rid of second kmeans parameter (7a783b1)

  • Correct sklearn inputs and change it to save PT only if source is extracted (0f4c7bb)

  • I edited the wrong test_function lol (0bb15e8)

  • In test_log_cosh(), switch np.isclose to np.allclose [to test array calculations] (97259aa)

  • Forgot to define test_arr for test_apply_contrast (e0266f2)

  • Change np.array_equal() to np.isclose() in test_log_cosh() (43e4c95)

  • Fix initialization of w (a1f6f03)

  • Update variable name in skew() (ab14b92)

  • Correct dimensions of output (9666833)

  • Rewrite child contrast functions and docstrings to do arrays, rewrite parent apply_contrast function docstring accordingly (2bc1fbf)

  • Add regularization step (4225f2d)

  • Correct variable called by preprocessing functions (0ada908)

  • Correct variable called by center_matrix (1ca76f5)

  • Add flatten signal (851bda3)

  • Change back to use real data (45be0f4)

  • Add random state parameter and move W-prev=w_curr to end (7026f25)

  • Fixed inf overflow error for log_cosh function (12db8af)

  • Change x_cent to x (5083274)

  • Correct submodule importation (014c25c)

  • Get rid of centring in whiten function (f113bc0)

  • Correct parameters in refinement function (6b1d198)

  • Rearrange arguments in decomposion(), separation(), refinement() functions (ddad019)

  • Improve skeleton of decomposition() function (76e0f59)

  • Add B as argument to separation() (ba3ba8b)

  • Resolve merge conflict (3331f42)

  • Rearrange functions so referenced functions are before referencering (635b913)

  • Use proper variables in separate function (5a12803)

  • Build upon separation function (ee0a84c)

  • Rewrite helper functions to have option to do derivative or not (b0107ad)

  • Comment out shell of while loop so whole functions file doesn’t appear broken (9d105e6)

Documentation

  • Get rid of redundant argument in refinement docstring (acd43f6)

  • Update returns in docstring (0e76114)

  • Add period to docstring lol (0285f88)

  • Update pnr docstring to include squared source (cbc364c)

  • Get rid of unnecessary while loop comment (8e85e98)

  • Edit docstring to reflect average over firings instead of channels (de27058)

  • Get rid of plural ‘unit tests’ (e358795)

  • Minor formatting changes (cad3338)

  • Correct docstrings (bf901e2)

  • Add correct data citations (ead4b0d)

  • Standardize docstrings and correct examples (99842fe)

  • Update separation function docstring (004e087)

Performance

  • Edit test fx to use fixtures (0fa09c0)

  • Create fixtures for test data (90c57e4)

v0.2.0 (2022-05-19)

Feature

  • Add whiten function to emg-decompy.py (3682a09)

  • Create functions script, debug extension functions, write docstrings (af7e346)

Fix

  • Correct package name (233aac0)

  • Incorrectly called create_emg_data() (fe93f12)

  • Rearrange functions so create_emg_data() defined before called in test functions (7a6c50b)

  • Tweak create_emg_data to use np.empty so that shape is consistent with real data (97d67c9)

  • Tweak test_flatten_signal to test for empty arrays pre-flatten (a7c0da4)

  • Small change to create_emg_data() function to not allow 1 dimensional arrays to be created (e744a7c)

  • Change output dimensions so there are no ‘channels’ (3cacf69)

  • Add reg factor to whiten but leave commented out (7491d10)

  • Fix transpose error (265592e)

  • Correct test name for extend_all_channels (8f787ec)

  • Import linalg from scipy (0ad2d15)

  • Properly call center_matrix function (db209b3)

  • Output correct dimensions for extend_all_channels() (deba7a4)

  • Get rid of codecov because repo is private (dd2bb66)

  • Extend() function now outputs what we agreed upon (98cfa16)

  • Figures were all showing weird, adding fig.pos=’h’ fixed it (db47734)

  • Correct package name (f4bf67f)

  • Correct package name (76ae9fb)

  • Import packages, reference package name in functions (62d839a)

  • Remove packages line (1d0a6be)

  • Correct package name (0163446)

  • Fix merge conflict and import emgdecompy (0005d9f)

  • Changing file name to new package (a8c18d5)

  • Changing package name in all documents (22f3129)

  • Put vector extension tests within functions (9b2fd18)

Documentation

  • Update creator names (42f581e)

  • Add codecov badge (a778710)

  • Update package name in test_extend_input_by_R (f3022da)

  • Minor docstring inconsistencies in extend_all_channels() (ce5fdd8)

  • Add clarification comment to test_flatten() according to Jasmine’s feedback (bcc735c)

  • Fix doc string for test_extend_by_R() (79490f4)

  • Fix reference on page 2 (ee57a46)

  • Make docstrings simpler and improve code commenting (5b397c0)

  • Correct format of examples in center_matrix and make it simpler (200bd66)

  • Correct docstring for extend_input_by_R (3e8e9df)

  • Fix grammar in docstrings (1190161)

  • Correct examples line in docstrings (9a4441a)

  • Correct spelling of fibre in summary (ea95835)

  • Bold figure cross-references’ (45a361f)

  • Made corrections to wordings, citations, figure locations (9c48f68)

  • Replace emg hardware image (dc33fae)

  • Replace ot screenshot with higher quality one (ab702a6)

  • Replace ot screenshot with higher quality one (80cfd4b)

  • Add visual of algorithm (e88f15d)

  • Edit Timeline (c4b210b)

  • Add more citations and figures (80de991)

  • Update timeline (afd53d2)

  • Add raw EMG image (b638e46)

  • Fix Tools sections based on Alexi’s feedback (6f64943)

  • Fix package name (eb2b26a)

  • Add Alexi’s corrections (5317c70)

  • Fix badge formatting (f4aa37d)

  • Add ci-cd badge (1d3cbf9)

  • Change package description (16bf912)

  • Bottleneck is spelled with an e lol (9fb41bc)

  • Improve docstring based on Daniel’s advice (7848f49)

  • Add proposal section to README (89618b6)

  • Create layout of proposal and render to pdf (423d6b3)

  • Make corrections (adaa064)

  • Add bibtex references (b299959)

  • Fix section on the interactive learning component (e8fc753)

  • Make some edits and add bibtex (6b79ea7)

  • Remove obsolete citations file (1483e64)

  • Fix line breaks (a1707a6)

  • Make corrections to techniques section and add bibtex (d4af629)

  • Remove html output (9107441)

  • Move titles from child docs to parent doc (0abf1d6)

  • Create bibtex file (f5c6920)

  • Add title to data science technique section (f3ff884)

  • Add yaml metadata (0a625c1)

  • Add proposal intro rmd (472635a)

  • Rewrite tools section to use sentenses instead of bullet points (503a4c2)

  • Create proposal folder and components (042a808)

  • Create teamwork contract (272638c)

v0.1.0 (03/05/2022)

  • First release of emgdecompy!