diff --git a/tests/conftest.py b/mne_hfo/conftest.py similarity index 100% rename from tests/conftest.py rename to mne_hfo/conftest.py diff --git a/tests/__init__.py b/mne_hfo/tests/__init__.py similarity index 100% rename from tests/__init__.py rename to mne_hfo/tests/__init__.py diff --git a/tests/test_compare.py b/mne_hfo/tests/test_compare.py similarity index 100% rename from tests/test_compare.py rename to mne_hfo/tests/test_compare.py diff --git a/tests/test_detect.py b/mne_hfo/tests/test_detect.py similarity index 100% rename from tests/test_detect.py rename to mne_hfo/tests/test_detect.py diff --git a/tests/test_io.py b/mne_hfo/tests/test_io.py similarity index 100% rename from tests/test_io.py rename to mne_hfo/tests/test_io.py diff --git a/tests/test_posthoc.py b/mne_hfo/tests/test_posthoc.py similarity index 100% rename from tests/test_posthoc.py rename to mne_hfo/tests/test_posthoc.py diff --git a/tests/test_score.py b/mne_hfo/tests/test_score.py similarity index 100% rename from tests/test_score.py rename to mne_hfo/tests/test_score.py diff --git a/tests/test_simulation.py b/mne_hfo/tests/test_simulation.py similarity index 100% rename from tests/test_simulation.py rename to mne_hfo/tests/test_simulation.py diff --git a/tests/test_utils.py b/mne_hfo/tests/test_utils.py similarity index 100% rename from tests/test_utils.py rename to mne_hfo/tests/test_utils.py diff --git a/publication/hfo_analysis_publication.py b/publication/hfo_analysis_publication.py new file mode 100644 index 0000000..7df4147 --- /dev/null +++ b/publication/hfo_analysis_publication.py @@ -0,0 +1,33 @@ +from pathlib import Path +from mne.filter import _overlap_add_filter + +import numpy as np +import pandas as pd +from mne_bids import read_raw_bids, get_entity_vals + +from mne_hfo import (RMSDetector, compute_chs_hfo_rates, + events_to_annotations) +from mne_hfo.simulate import simulate_hfo + + +def analyze_zurich(): + root = Path('/Users/adam2392/OneDrive - Johns Hopkins/ds003498') + + # get all subjects + subjects = get_entity_vals(root, 'subject') + + # get outcomes + part_df = pd.read_csv(root / 'participants.tsv', sep='\t') + + for subject in subjects: + subj_dir = root / f'sub-{subject}' + + outcome = part_df[part_df['participant_id'] == f'sub-{subject}']['outcome'] + + # get all file paths + fpaths = [] + + # loop through each file path and compute HFOs + for fpath in fpaths: + + # \ No newline at end of file diff --git a/requirements.txt b/requirements.txt index fc67e2e..80029bc 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,38 +1,11 @@ -appnope==0.1.2; sys_platform == "darwin" and platform_system == "Darwin" -backcall==0.2.0 -cycler==0.10.0 -decorator==5.0.5; python_version >= "3.5" -ipykernel==5.5.3 -ipython==7.22.0; python_version >= "3.7" -ipython-genutils==0.2.0 -jedi==0.18.0; python_version >= "3.6" -joblib==1.0.1 -jupyter-client==6.1.12; python_version >= "3.5" -jupyter-core==4.7.1; python_version >= "3.6" -kiwisolver==1.3.1; python_version >= "3.6" -matplotlib==3.4.1 -mne==0.22.1 -mne-bids==0.7 -numpy==1.20.2 -pandas==1.2.3 -parso==0.8.2; python_version >= "3.6" -pexpect==4.8.0; sys_platform != "win32" -pickleshare==0.7.5 -pillow==8.2.0; python_version >= "3.6" -prompt-toolkit==3.0.18; python_full_version >= "3.6.1" -ptyprocess==0.7.0 -pydocstyle==6.0.0 -pygments==2.8.1; python_version >= "3.5" -pyparsing==2.4.7; python_version >= "2.6" and python_version not in "3.0, 3.1, 3.2, 3.3" -python-dateutil==2.8.1; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3" -pytz==2021.1 -pyzmq==22.0.3; python_version >= "3.6" -scikit-learn==0.24.1 -scipy==1.6.2 -six==1.15.0; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3" -snowballstemmer==2.1.0 -threadpoolctl==2.1.0; python_version >= "3.5" -tornado==6.1; python_version >= "3.5" -tqdm==4.59.0 -traitlets==5.0.5; python_version >= "3.7" -wcwidth==0.2.5 +# requirements for full MNE-Python functionality (other than raw/epochs export) +numpy>=1.15.4 +scipy>=1.1.0 +mne>=0.23 +scikit-learn +pandas +joblib +psutil +xlrd +tqdm +pooch \ No newline at end of file diff --git a/test_requirements.txt b/test_requirements.txt index af2a96d..b54f776 100644 --- a/test_requirements.txt +++ b/test_requirements.txt @@ -1,103 +1,24 @@ -aiofiles==0.6.0 -alabaster==0.7.12 -appnope==0.1.2; sys_platform == "darwin" and platform_system == "Darwin" -async-generator==1.10; python_version >= "3.5" -attrs==20.3.0; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3" -babel==2.9.0; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3" -backcall==0.2.0 -beautifulsoup4==4.9.3 -bleach==3.3.0; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3, 3.4" -build==0.3.1.post1; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3, 3.4" -certifi==2020.12.5 -chardet==4.0.0; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3, 3.4" -check-manifest==0.46 -click==7.1.2; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3, 3.4" -codespell==2.0.0 -coverage==5.5; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3, 3.4" and python_version < "4" -decorator==5.0.5; python_version >= "3.5" -defusedxml==0.7.1; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3, 3.4" -docutils==0.17; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3, 3.4" -entrypoints==0.3; python_version >= "2.7" -flake8==3.9.0 -idna==2.10; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3" -imagesize==1.2.0; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3" -importlib-metadata==3.10.0; python_version < "3.8" -iniconfig==1.1.1 -ipykernel==5.5.3 -ipython==7.22.0; python_version >= "3.7" -ipython-genutils==0.2.0 -jedi==0.18.0; python_version >= "3.6" -jinja2==2.11.3; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3, 3.4" -jsonschema==3.2.0 -jupyter-client==6.1.12; python_version >= "3.5" -jupyter-core==4.7.1; python_version >= "3.6" -jupyterlab-pygments==0.1.2 -markupsafe==1.1.1; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3" -mccabe==0.6.1 -mistune==0.8.4 -mypy==0.812 -mypy-extensions==0.4.3 -nbclient==0.5.3; python_full_version >= "3.6.1" -nbconvert==6.0.7; python_version >= "3.6" -nbformat==5.1.3; python_version >= "3.5" -nbsphinx==0.8.2 -nest-asyncio==1.5.1; python_version >= "3.5" -numpydoc==1.1.0 -openneuro-py==2021.2 -packaging==20.9; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3" -pandoc==1.0.2 -pandocfilters==1.4.3 -parso==0.8.2; python_version >= "3.6" -pep517==0.10.0 -pexpect==4.8.0; sys_platform != "win32" -pickleshare==0.7.5 -pipfile-requirements==0.3.0 -pluggy==0.13.1; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3" -ply==3.11 -prompt-toolkit==3.0.18; python_full_version >= "3.6.1" -ptyprocess==0.7.0 -py==1.10.0; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3" -py-cpuinfo==7.0.0 -pycodestyle==2.7.0; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3" -pydata-sphinx-theme==0.5.2 -pydocstyle==6.0.0 -pyflakes==2.3.1; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3" -pygments==2.8.1; python_version >= "3.5" -pyparsing==2.4.7; python_version >= "2.6" and python_version not in "3.0, 3.1, 3.2, 3.3" -pyrsistent==0.17.3; python_version >= "3.5" -pytest==6.2.3 -pytest-benchmark==3.2.3 -pytest-cov==2.11.1 -pytest-sugar==0.9.4 -python-dateutil==2.8.1; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3" -pytz==2021.1 -pyzmq==22.0.3; python_version >= "3.6" -requests==2.25.1; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3, 3.4" -rfc3986[idna2008]==1.4.0 -six==1.15.0; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3" -sniffio==1.2.0; python_version >= "3.5" -snowballstemmer==2.1.0 -soupsieve==2.2.1; python_version >= "3.0" -sphinx==3.5.3 -sphinx-autodoc-typehints==1.11.1 -sphinx-bootstrap-theme==0.7.1 -sphinx-copybutton==0.3.1 -sphinx-gallery==0.8.2 -sphinxcontrib-applehelp==1.0.2; python_version >= "3.5" -sphinxcontrib-devhelp==1.0.2; python_version >= "3.5" -sphinxcontrib-htmlhelp==1.0.3; python_version >= "3.5" -sphinxcontrib-jsmath==1.0.1; python_version >= "3.5" -sphinxcontrib-qthelp==1.0.3; python_version >= "3.5" -sphinxcontrib-serializinghtml==1.1.4; python_version >= "3.5" -termcolor==1.1.0 -testpath==0.4.4 -toml==0.10.2; python_version >= "2.6" and python_version not in "3.0, 3.1, 3.2, 3.3" -tornado==6.1; python_version >= "3.5" -tqdm==4.59.0 -traitlets==5.0.5; python_version >= "3.7" -typed-ast==1.4.2 -typing-extensions==3.7.4.3 -urllib3==1.26.4; python_version >= "2.7" and python_version not in "3.0, 3.1, 3.2, 3.3, 3.4" and python_version < "4" -wcwidth==0.2.5 -webencodings==0.5.1 -zipp==3.4.1; python_version < "3.8" +# requirements for running tests (on top of environment.yml/requirements.txt) +pytest!=4.6.0 +pytest-cov +pytest-timeout +pytest-harvest +flake8 +flake8-array-spacing +numpydoc +codespell +pydocstyle +check-manifest +twine +wheel +pooch + +# requirements for building docs +sphinx!=4.1.0 +https://github.com/numpy/numpydoc/archive/main.zip +pydata-sphinx-theme>=0.6.3 +https://github.com/sphinx-gallery/sphinx-gallery/archive/master.zip +sphinxcontrib-bibtex>=2.1.2 +seaborn!=0.11.2 +sphinx_copybutton +https://github.com/mne-tools/mne-bids/archive/main.zip