ReSurfEMG

Commits

• 6604a47: added periodogram and welch method (ElineOppersma) #316
• 1257aa5: rostack to vstack (deprecated) (ElineOppersma) #316
• b6a906e: ros_stack to vstack (deprecated) (ElineOppersma) #316
• b2cb994: row_stack to vstack (deprecated) (ElineOppersma) #316
• 267a987: added tests and changes for review (ElineOppersma) #316
• e617e42: added patch for mock plot in testing suite (ElineOppersma) #316
• 00d287f: removed plottitle (ElineOppersma) #316
• 01622e4: plot title to general code (ElineOppersma) #316
• 711408a: Tests for time_product and area under the baseline (rspwarnaarUT) #323
• 1f3b088: Implement test for percentage_aub quality criterium (rspwarnaarUT) #323
• 6e919a6: Fix deprecation errors (rspwarnaarUT) #323
• e4e671e: Fix deprecation warnings (rspwarnaarUT) #323
• af6335d: Fix deprecation warnings (rspwarnaarUT) #323
• 74c4c90: Eoppersma/interpeak (#322) (ElineOppersma) #322
• 2816afa: WIP time series plotting (rspwarnaarUT) #325
• 9bfe01f: TimeSeriesData class, including plotting function (rspwarnaarUT) #325
• e2b82d6: Clean pipelines imports and visualization (rspwarnaarUT) #325
• f115b0b: fix np.NaN deprecation (rspwarnaarUT) #325
• 1fb3de4: Clean out notebook (rspwarnaarUT) #325
• 08a84bc: Provide data_classes with docstring (rspwarnaarUT) #325
• 30d32ca: Fix linting (rspwarnaarUT) #325
• 6524532: Split TimeSeries per channel. Include VentilatorDataGroup as child-class (rspwarnaarUT) #325
• 1d634ea: Add marker plotting to full window plot (rspwarnaarUT) #325
• 33cca36: Plot library: Plot individual peaks (rspwarnaarUT) #325
• 0290b6c: Plot markers for full time plot and subplot per peak (rspwarnaarUT) #325
• e122a9c: Move snr_pseudo to quality assessment (rspwarnaarUT) #323
• 4c317ce: Implement test for pseudo_snr (rspwarnaarUT) #323
• 4e9855f: Fix pseudo_snr import in postprocessing test (rspwarnaarUT) #323
• 6c2ae16: Add reference to synthetic data (rspwarnaarUT) #323
• 574bc70: WIP Pocc quality evaluation method (rspwarnaarUT) #323
• 87f7d77: Bug fix in pocc_quality (rspwarnaarUT) #323
• e4dca51: Implement tests for pocc_quality (rspwarnaarUT) #323
• 292db53: Fix naming convention in pocc_quality (rspwarnaarUT) #323
• Time product and area under baseline features #323 (rspwarnaarUT)
• 9507d7b: Time product and AUB: Write docstrings, fix linting (rspwarnaarUT) #323
• ff46f30: Tests for time_product and area under the baseline (rspwarnaarUT) #323
• 9d721f6: Implement test for percentage_aub quality criterium (rspwarnaarUT) #323
• 17eba89: Fix deprecation errors (rspwarnaarUT) #323
• 3c0ccaa: Fix deprecation warnings (rspwarnaarUT) #323
• 948e1a1: Fix deprecation warnings (rspwarnaarUT) #323
• e7ec25e: Eoppersma/interpeak (#322) (ElineOppersma) #323
• 37f6ca4: Move Pocc detection method to event_detection submodule (rspwarnaarUT) #325
• 0726ae9: Implement test for find_occluded_breaths method (rspwarnaarUT) #325
• 222910b: Update exemplary notebooks with new code (rspwarnaarUT) #325
• 1f5d898: Fix docstrings (rspwarnaarUT) #325
• 0a92a71: Implement test for plot_peaks and plot_markers. (rspwarnaarUT) #325
• 71dd2e7: Merge branch 'release_0_3_2' into feature/plotting_library (rspwarnaarUT) #325
• 5cf36f0: Merge branch 'release_0_3_2' into feature/plotting_library (rspwarnaarUT) #325
• b33a222: Fix merge error (rspwarnaarUT) #325
• d321246: Add gating pipeline and ECG peak detection methods (rspwarnaarUT) #328
• 675baa4: Fix linting (rspwarnaarUT) #328
• 3e6b888: Add synthetic eeot manoeuvre data to test_data (rspwarnaarUT) #328
• d5079e4: Implement tests for detect_ecg_peaks ecg_removal_gating (rspwarnaarUT) #328
• cb6d6c1: Add filtering and gating methods to data_classes (rspwarnaarUT) #328
• a287d20: Feature/plotting library (#325) (rspwarnaarUT) #325
• 989c512: consecutive manoeuvres check function and test (#324) (ElineOppersma) #324
• 33f91a8: arv function (ElineOppersma) #327
• bb311a0: Add exemplary ARV notebook (rspwarnaarUT) #327
• df748f2: Get ARV its own test class (rspwarnaarUT) #327
• 343d464: Rename pocc test data to _quiet_breathing (rspwarnaarUT) #328
• 0f6266c: Rename ventilator test data tot quiet breathing (rspwarnaarUT) #328
• 19205ac: Add synthetic Pocc data to test_dat (rspwarnaarUT) #328
• f29e915: Fix indexing errors for single channel plots (rspwarnaarUT) #328
• 279b9db: Add ARV method to envelope options (rspwarnaarUT) #328
• f0af6f5: Merge branch 'release_0_3_2' into feature/pipelines_2 (rspwarnaarUT) #328
• ae2e9f5: link peak function: peak_set 1 to peak_set 2 (rspwarnaarUT) #328
• cf3656e: Automatic EMG quality assessment and peak validity evaluation in TimeSeries object (rspwarnaarUT) #328
• 09dfc40: Implement time_product, and automated Pocc quality_assessment in TimeSeries (rspwarnaarUT) #328
• 10bf85e: Convert PeaksSet items to dataframe (rspwarnaarUT) #328
• 533f54f: Update tests for data_classess (Rob Warnaar) #328
• 104a610: Implement test + minor improvent for event_deteciton.find_linked_peaks (rspwarnaarUT) #328
• ae9b17f: Clean imports in post_processing_test (rspwarnaarUT) #328
• 6861ac8: Implement test for event_detection.detect_emg_breaths (rspwarnaarUT) #328
• 607118d: Last tests for data_classes (rspwarnaarUT) #328
• 75a850a: Remove ML outputs from repo (rspwarnaarUT) #330
• 117b80b: Move dev notebooks to notebooks/dev (rspwarnaarUT) #330
• a8e90be: Sort open_work folder (rspwarnaarUT) #330
• 41ece2e: Clean researcher_interface (rspwarnaarUT) #330
• 3b37596: Delete ML models (rspwarnaarUT) #330
• 29a6e81: Delete notebooks archive (rspwarnaarUT) #330
• da94224: Move entropy functions to legacy (rspwarnaarUT) #330
• a6d42dd: Clean out rudementary functions (rspwarnaarUT) #330
• 8996b00: Delete commented functions, update changelog (rspwarnaarUT) #330
• 65856b5: Farnaz/bell (#329) (FarSoleimani) #329
• 3936ce1: Merge branch 'release_0_3_2' into maintaince/clean_functions_notebooks (rspwarnaarUT) #330
• 8b69cc2: Add curve-fit to data_class (rspwarnaarUT) #330
• 3ff4998: Naming convention: _sampling_rate converted to _fs (rspwarnaarUT) #330
• 75d5254: start_s --> start_idx (rspwarnaarUT) #330
• ae340f9: starts_s --> start_idxs (rspwarnaarUT) #330
• 6f2bfb2: peaks_s --> peak_idxs (rspwarnaarUT) #330
• 8b8981a: peak_s --> peak_idx (rspwarnaarUT) #330
• 3fd99ee: ends_s --> end_idxs (rspwarnaarUT) #330
• 7069d0c: end_s --> end_idx (rspwarnaarUT) #330
• 632d3bd: draeger --> vent (rspwarnaarUT) #330
• 9cf7e91: Tidy up (rspwarnaarUT) #330
• f9b7651: Fix import errors in notebooks (rspwarnaarUT) #330
• b061e6f: WIP Update read-me (rspwarnaarUT) #330
• 9169501: Get rid of sys.path.insert. Local install (pip install -e .[dev]) will do (rspwarnaarUT) #330
• 43f37c0: Eliminate sys.path.insert from Sphinx conf.py + minor fixes in docs (rspwarnaarUT) #330
• bd5b2a4: Auto documentation updated (rspwarnaarUT) #330
• 857913f: Get tests to run on test data included in the repo (rspwarnaarUT) #330
• c0ac7e1: Run tests with repo test data (rspwarnaarUT) #330
• 9c6be81: Fix .[tests] install (rspwarnaarUT) #330
• e6b2c91: Fix pytest command (rspwarnaarUT) #330
• a8f89a2: np.trapz deprecated (rspwarnaarUT) #330
• f0df70f: Update readme (rspwarnaarUT) #330
• de6d3eb: Update test data in readme (rspwarnaarUT) #330
• baceb14: Update Notebook guide (rspwarnaarUT) #330
• f95b5ec: Provide basic EMG pipeline examplary annotated notebook (rspwarnaarUT) #330
• 2003ff6: Fully annotated example pipeline (rspwarnaarUT) #330
• 032f3f1: Merge branch 'release_0_3_2' into feature/pipelines_2 (rspwarnaarUT) #328
• 13d14c8: Merge branch 'release_0_3_2' into maintaince/clean_functions_notebooks (rspwarnaarUT) #330
• e26d2cc: Add plot_aub method to TimeSeries object (rspwarnaarUT) #333
• 02fd2e1: Add plot_aub method to TimeSeries object (rspwarnaarUT) #333
• d956c50: Standardize docstring layout, and arguments (rspwarnaarUT) #334
• 6ad24ab: Merge branch 'release_0_3_2' into maintenance/variable_names (rspwarnaarUT) #334
• 1a0ba37: WIP Software paper notebook (rspwarnaarUT) #335
• ff658af: WIP Software paper notebook (rspwarnaarUT) #335
• 609b850: Merge branch 'release_2_0_0/paper_notebook' of https://github.com/ReSurfEMG/ReSurfEMG into release_2_0_0/paper_notebook (rspwarnaarUT) #335
• a11eec6: Softwarepaper notebook wip (rspwarnaarUT) #335
• 2f3df95: Fix envelope start-up artifacts (rspwarnaarUT) #335
• f95d443: Debug RMS startup artifact (rspwarnaarUT) #335
• d61f021: Fix linting (rspwarnaarUT) #335
• ad8c818: Fix RMS and ARV handling of NaNs (rspwarnaarUT) #335
• ce58121: file_finder function design (rspwarnaarUT) #335
• bf9df15: Maintenance/variable names (#334) (rspwarnaarUT) #334
• 763d22f: File and folder discovery functions (rspwarnaarUT) #335
• 4e2a510: ipywidget for file selection (rspwarnaarUT) #335
• 2c28a45: Update toml file with ipywidgets (rspwarnaarUT) #335
• 1440620: Fix TestIpyWidgets (rspwarnaarUT) #335
• b204be2: Fix np.trapz deprecation (rspwarnaarUT) #335
• ad10b57: Update notebooks with file_discovery functionality (rspwarnaarUT) #335
• 6655869: Merge branch 'release_0_3_2' into release_2_0_0/paper_notebook (rspwarnaarUT) #335
• 8c0d6c6: Reorganize submodules (rspwarnaarUT) #336
• f62a5da: Split config test (rspwarnaarUT) #336
• 30a2255: Remove config submodule (rspwarnaarUT) #336
• 3669a42: Fix naming conventions (rspwarnaarUT) #336
• 9f13d50: Add wavelet denoising (rspwarnaarUT) #336
• 57628e5: WIP Fix file_select widget (rspwarnaarUT) #336
• 859fc3d: Update tests (rspwarnaarUT) #336
• fbb2417: Refactor tests in subfolders (rspwarnaarUT) #336
• 9434cf4: Split postprocessing tests (rspwarnaarUT) #336
• 9c7fab3: Restructure preprocessing and math operationstests (rspwarnaarUT) #336
• 39ba7ec: Release 2 0 0/paper notebook (#335) (rspwarnaarUT) #335
• 368ea8f: Implement standard load_file function (rspwarnaarUT) #336
• d127aaf: Eliminate ICA (rspwarnaarUT) #336
• 980eac3: Merge branch 'release_0_3_2' into release_2_0_0/wavelet_denoising (rspwarnaarUT) #336
• f7e4aa5: Fix merge of tests (rspwarnaarUT) #336
• 4c239b1: Move running smoother to math operations (rspwarnaarUT) #336
• 23f929d: Update naming conventions (rspwarnaarUT) #336
• e60aa52: Fix naming errors (rspwarnaarUT) #336
• 9d5cd13: Wip rr estimation (rspwarnaarUT) #336
• 22aa345: RR estimation (Rob Warnaar) #336
• 95074e1: Fix linting (rspwarnaarUT) #336
• ee09a34: Implement test for respiratory rate detection (rspwarnaarUT) #336
• 7a83cf7: Implement quality assessment for respiratory rate evaluation (rspwarnaarUT) #336
• 89e3c1d: Quality assessment for local high baseline (rspwarnaarUT) #336
• 4ac2db0: Quality assessment extreme time product check (rspwarnaarUT) #336
• c33b975: Fix linting (rspwarnaarUT) #336
• 9bd5187: Amplitude feature (Rob Warnaar) #336
• 0287c78: Fix linting (Rob Warnaar) #336
• 55a3155: Standardise naming conventions (Rob Warnaar) #336
• 42d6d5f: Quality assessment event timing evaluation (rspwarnaarUT) #336
• e753c49: Merge branch 'release_2_0_0/wavelet_denoising' of https://github.com/ReSurfEMG/ReSurfEMG into release_2_0_0/wavelet_denoising (rspwarnaarUT) #336
• fde761d: Fix linting (rspwarnaarUT) #336
• 9adced8: Restructure and clean filtering module (rspwarnaarUT) #336
• 938249c: Implement quick_look pipeline (excluding test) (rspwarnaarUT) #336
• 96e303b: Updated quick_look notebook (rspwarnaarUT) #336
• bc64559: Fix conversion to scalar warning in filtering (rspwarnaarUT) #336
• a641cec: WIP Sanitize synthetic EMG (rspwarnaarUT) #350
• c3e9f66: WIP Split simulation functions (Rob Warnaar) #350
• 60eaa28: Clean out synthetic EMG and ventilator data functions (Rob Warnaar) #350
• 3712673: WIP fix CLI (Rob Warnaar) #350
• 22d6482: Fix CLI (Rob Warnaar) #350
• f4ab867: Fix tests (Rob Warnaar) #350
• 1166057: Add new EMG quality assessment to data_classes (rspwarnaarUT) #350
• 10a8d4b: Split data_classes in smaller helper_function files (rspwarnaarUT) #350
• cabd008: Add new functions to data_class (rspwarnaarUT) #350
• dc5bb35: Fix data_class tests (rspwarnaarUT) #350
• 6fb9ce0: Add wavelet denoising to data_class (rspwarnaarUT) #350
• 96c80fd: Make clean basic_emg_pipeline and annotated one (rspwarnaarUT) #350
• acd7abf: Move config to data_connector (rspwarnaarUT) #350
• f835c3c: Update config paths (rspwarnaarUT) #350
• ea0bf5b: Rename synthetic ECG maker to EMG maker (rspwarnaarUT) #350
• a8ac26d: WIP Fix config folder depth independency (rspwarnaarUT) #350
• c53d734: Make Config work independent of directory depth (Rob Warnaar) #350
• c152cee: Clean and refactor CLI (Rob Warnaar) #350
• 17f2e2e: Fix CLI (Rob Warnaar) #350
• f789dbe: Update documentation CLI and config (Rob Warnaar) #350
• 9ee7226: Standardise naming of sampling rate (Rob Warnaar) #350
• b6e81f8: Number of samples per second to sampling rate (Rob Warnaar) #350
• 408c217: Update data_classes documentation (Rob Warnaar) #350
• b192623: Fix file_discovery documentation (Rob Warnaar) #350
• c89a1a4: Update peakset documentation (Rob Warnaar) #350
• 7483697: Update synthetic data documentation (Rob Warnaar) #350
• 6fa17a6: TMSIsdk_lite update documentation (Rob Warnaar) #350
• ff90113: Fix data_classes_quality_assesment docs (Rob Warnaar) #350
• 80b4233: Fix docs math_operations (Rob Warnaar) #350
• 09a27c9: Update visualization docs (Rob Warnaar) #350
• ae6f41b: Fix pipelines docs (Rob Warnaar) #350
• 009765d: Eliminate in dict.keys() (Rob Warnaar) #350
• 73217ec: Update preprocessing docs (Rob Warnaar) #350
• 2f50393: Update docs for preprocessing submodule (Rob Warnaar) #350
• ec611c2: Standardize return formatting (Rob Warnaar) #350
• 5557a92: Update changelog (Rob Warnaar) #350
• 093022e: Fix fs_nq error in filtering (Rob Warnaar) #350
• 8b24e06: Add Farnaz as author (Rob Warnaar) #350
• a602f11: Update readme, notebook guide. Remove redundant notebooks (Rob Warnaar) #350
• 432fc3d: Auto generate rst documentation (Rob Warnaar) #350
• b19346a: Fix Sphinx DOC (Rob Warnaar) #351
• a56b4e3: Test Sphinx DOC when making PR to main (Rob Warnaar) #351
• 3e9ee5f: Fix test-sphinx (Rob Warnaar) #351
• 7dcb4cd: Fix Test_Sphinx (Rob Warnaar) #351
• 645334e: Fix Test-Sphinx try 3 (Rob Warnaar) #351
• f6c10c2: Fix Test-Sphinx on push to PR (Rob Warnaar) #351
• c884728: WIP Fix Test-Sphinx (Rob Warnaar) #351
• f1abdd5: WIP Test-Sphinx (Rob Warnaar) #351
• 44e19a9: WIP Test-Sphinx (Rob Warnaar) #351
• ed87dea: Fix deployability tests (Rob Warnaar) #351
• bd2898b: Fix Deployability tests (Rob Warnaar) #351
• 3f8d181: WIP PR to main tests (Rob Warnaar) #351
• 37e1a2c: Fix documentation for Sphinx (Rob Warnaar) #351
• 9f62859: Add 'ipywidgets' to docs dependencies (Rob Warnaar) #351
• 0aac22c: Update Github actions to most recent (Rob Warnaar) #351
• b7f523c: Add confidence interval functions for RMS and ARV calculations in EMG preprocessing (Rob Warnaar) #353
• 61a06b2: Refactor confidence interval calculations in envelope_error_bars notebook (Rob Warnaar) #353
• d9cf6a2: Refactor data_classes (rspwarnaarUT) #353
• 7adf3bc: Elimitate redundancy in data processing functions (rspwarnaarUT) #353
• d7eb155: Refactor data_classes to be more compact (rspwarnaarUT) #353
• 968c7ab: Update config to provide feedback for get_directory (rspwarnaarUT) #353
• 9174067: Refactor annotated basic pipeline (rspwarnaarUT) #353
• c9b2906: Fix config errors (rspwarnaarUT) #353
• 86fdc37: Fix margin_s = 0 in TimeSeries.plot_peaks (rspwarnaarUT) #353
• 781ee6b: Fix sphinx docs (rspwarnaarUT) #353
• 38d1119: Add env confidence intervals to dataclass (rspwarnaarUT) #353
• a250ff7: Compact TimeSeriesGroup plot functions (rspwarnaarUT) #353
• 215623f: Update software and annoated basic emg pipelines (rspwarnaarUT) #353
• 3f6f5f2: Update docs to support up to python 3.12 (rspwarnaarUT) #353
• 803f9ea: Minor bug fixes, update default window_length for envelope to 250 ms (rspwarnaarUT) #353
• e5f50fa: Fix config to not overwrite existing config files (rspwarnaarUT) #353
• 227308e: Update notebooks to paper versions (rspwarnaarUT) #353
• 4004235: changed ecg peak detection to 95-5 percentile (ElineOppersma) #354
• 97858bf: changed peak_fraction to 0.4 (ElineOppersma) #354
• 8877ac8: Fix config to generate ./not_pushed if auto-generating config file (rspwarnaarUT) #352
• 705f936: Merge branch 'main' into release_1_0_0/env_error_bars (rspwarnaarUT) #353
• 34c2738: updated git actions (ElineOppersma) #355