From af1192badca5c2ee7fb394205fd43862de731cb7 Mon Sep 17 00:00:00 2001 From: young-x-skyee Date: Mon, 8 Jan 2024 13:06:26 +0000 Subject: [PATCH 1/3] Combining EOG and ECG ICA components selection --- kymata/config/dataset4.yaml | 2 +- kymata/preproc/data_cleansing.py | 32 +- poetry.lock | 491 ++++++++++++++++--------------- 3 files changed, 284 insertions(+), 241 deletions(-) diff --git a/kymata/config/dataset4.yaml b/kymata/config/dataset4.yaml index 0532ab0f..d3a9cda4 100644 --- a/kymata/config/dataset4.yaml +++ b/kymata/config/dataset4.yaml @@ -9,7 +9,7 @@ mri_structurals_directory: "raw_mri_structurals" # General information related to the dataset list_of_participants: [ - "participant_08" + "participant_17" ] input_streams: [ "auditory" diff --git a/kymata/preproc/data_cleansing.py b/kymata/preproc/data_cleansing.py index 32c386f5..cfb797b2 100644 --- a/kymata/preproc/data_cleansing.py +++ b/kymata/preproc/data_cleansing.py @@ -217,11 +217,15 @@ def run_second_pass_cleansing_and_EOG_removal(list_of_participants: list[str], ica.exclude = [] - if remove_ecg: - _remove_ecg(filt_raw, ica) + if supress_excessive_plots_and_prompts: + _remove_ecg_eog(filt_raw, ica) - if remove_veoh_and_heog: - _remove_veoh_and_heog(filt_raw, ica) + else: + if remove_ecg: + _remove_ecg(filt_raw, ica) + + if remove_veoh_and_heog: + _remove_veoh_and_heog(filt_raw, ica) ica.apply(raw_fif_data_sss_movecomp_tr) @@ -280,6 +284,26 @@ def _remove_ecg(filt_raw, ica): ica.plot_overlay(filt_raw, exclude=ica.exclude, picks='mag') +def _remove_ecg_eog(filt_raw, ica): + """ + Note: mutates `ica`. + """ + print_with_color(f" Starting ECG and EOG removal...", Fore.GREEN) + + + ecg_indices, ecg_scores = ica.find_bads_ecg(filt_raw) + eog_indices, eog_scores = ica.find_bads_eog(filt_raw) + ica.exclude = ecg_indices + ica.exclude += eog_indices + + + ica.plot_sources(filt_raw, show_scrollbars=True) + ica.plot_scores(ecg_scores) + ica.plot_scores(eog_scores) + + + + def create_trials(dataset_directory_name: str, list_of_participants: list[str], repetitions_per_runs: int, diff --git a/poetry.lock b/poetry.lock index 5c5b8f8e..9653b7d9 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,4 +1,4 @@ -# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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""" print_with_color(f" Starting ECG and EOG removal...", Fore.GREEN) - - ecg_indices, ecg_scores = ica.find_bads_ecg(filt_raw) eog_indices, eog_scores = ica.find_bads_eog(filt_raw) ica.exclude = ecg_indices ica.exclude += eog_indices - - + eog_scores.append(ecg_scores) ica.plot_sources(filt_raw, show_scrollbars=True) - ica.plot_scores(ecg_scores) ica.plot_scores(eog_scores) diff --git a/poetry.lock b/poetry.lock index 9653b7d9..641fd5a4 100644 --- a/poetry.lock +++ b/poetry.lock @@ -712,6 +712,21 @@ files = [ {file = "iniconfig-2.0.0.tar.gz", hash = "sha256:2d91e135bf72d31a410b17c16da610a82cb55f6b0477d1a902134b24a455b8b3"}, ] +[[package]] +name = "ipdb" +version = "0.13.13" +description = "IPython-enabled pdb" +optional = false +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +files = [ + {file = "ipdb-0.13.13-py3-none-any.whl", hash = "sha256:45529994741c4ab6d2388bfa5d7b725c2cf7fe9deffabdb8a6113aa5ed449ed4"}, + {file = "ipdb-0.13.13.tar.gz", hash = "sha256:e3ac6018ef05126d442af680aad863006ec19d02290561ac88b8b1c0b0cfc726"}, +] + +[package.dependencies] +decorator = {version = "*", markers = "python_version >= \"3.11\""} +ipython = {version = ">=7.31.1", markers = "python_version >= \"3.11\""} + [[package]] name = "ipykernel" version = "6.28.0" @@ -3229,4 +3244,4 @@ viz = ["matplotlib", "nc-time-axis", "seaborn"] [metadata] lock-version = "2.0" python-versions = "~3.11" -content-hash = "126306034c10e3925f50ffae936c8d079c2d21d58f756b3f7b30fe49cf09f65c" +content-hash = "940bb8daf43bfdde09e9bcfb99c3cd68386fd39ba5c9f434334f7640bf84ff80" diff --git a/pyproject.toml b/pyproject.toml index bf5b62ae..c24701b6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,6 +29,7 @@ sparse = "^0.14.0" xarray = "^2023.9.0" pyqt6 = "^6.6.1" h5io = "^0.1.9" +ipdb = "^0.13.13" [tool.poetry.dev-dependencies] pytest = "^7.4.2" From 31069326bd9ad13adeb7f9f6da1053c73d03d777 Mon Sep 17 00:00:00 2001 From: young-x-skyee Date: Mon, 8 Jan 2024 16:54:15 +0000 Subject: [PATCH 3/3] Put ipdb under tool.poetry.dev-dependencies --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index c24701b6..3ca09672 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,10 +29,10 @@ sparse = "^0.14.0" xarray = "^2023.9.0" pyqt6 = "^6.6.1" h5io = "^0.1.9" -ipdb = "^0.13.13" [tool.poetry.dev-dependencies] pytest = "^7.4.2" +ipdb = "^0.13.13" [build-system] requires = ["poetry-core>=1.0.0"]