[DRAFT] Possible implementation of Morphology

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:
+
+            # 

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

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