Merge branch 'dev' into dev-kim-bugfix

.gitattributes

@@ -1 +1,2 @@
-scripts/* linguist-vendored
+scripts/* linguist-vendored
+*.ipynb linguist-language=Python

.github/CONTRIBUTING.rst

@@ -21,6 +21,13 @@ Contributing is the best way to learn programming, to meet new people, to grow y
 
 For instance, authors of significant contributions (features, tough bug fixes etc.) will be listed as official `Contributors <https://neuropsychology.github.io/NeuroKit/authors.html>`_ section of our website. Additionally, frequent contributors that also get involved in general maintaining (e.g,participating in issues, fixing stuff, reviewing PRs, writing docs etc.) might be included in as package maintainers, in which case they'll be expected to be more generally involved in the general development direction. Finally, we expect this project (the development of the package *per se* and all of the discussions/experiments that are around it) to result in several **publications** (could be about some features of the package, but also some tutorial papers, validation studies or whatnot. Obviously, people that contributed and allowed for a paper to be written will be included as authors.
 
+.. tip::
+
+    On top of this, you can add that you are a contributor of NeuroKit to your CV. Since many labs
+    and companies use it, they might be particularly interested in recruiting someone that
+    has a good understanding of NeuroKit, and demonstrated skills in Python and software
+    development.
+
 Long story short, we want this project to be helpful to you, whether you're a user, a contributor, or anything else in between :) And as always, do not hesitate to ask us if you have any questions.
 
 

.github/stale.yml

@@ -1,17 +1,17 @@
-# Number of days of inactivity before an issue becomes stale
-daysUntilStale: 180
-# Number of days of inactivity before a stale issue is closed
-daysUntilClose: 180
-# Issues with these labels will never be considered stale
-exemptLabels:
-  - feature idea 🔥
-  - bug 🐛
-# Label to use when marking an issue as stale
-staleLabel: inactive 👻
-# Comment to post when marking an issue as stale. Set to `false` to disable
-markComment: >
-  This issue has been automatically marked as inactive because it has not had
-  recent activity. It will eventually be closed if no further activity occurs.
-# Comment to post when closing a stale issue. Set to `false` to disable
-closeComment: >
-  This issue has been inactive for a long time. We're closing it (but feel free to reopen it if need be).
+# # Number of days of inactivity before an issue becomes stale
+# daysUntilStale: 180
+# # Number of days of inactivity before a stale issue is closed
+# daysUntilClose: 180
+# # Issues with these labels will never be considered stale
+# exemptLabels:
+#   - feature idea 🔥
+#   - bug 🐛
+# # Label to use when marking an issue as stale
+# staleLabel: inactive 👻
+# # Comment to post when marking an issue as stale. Set to `false` to disable
+# markComment: >
+#   This issue has been automatically marked as inactive because it has not had
+#   recent activity. It will eventually be closed if no further activity occurs.
+# # Comment to post when closing a stale issue. Set to `false` to disable
+# closeComment: >
+#   This issue has been inactive for a long time. We're closing it (but feel free to reopen it if need be).

.github/workflows/style.yml

@@ -4,6 +4,7 @@ on:
   pull_request:
     branches:
       - master
+      - dev
   push:
 
 jobs:

.gitignore

@@ -138,6 +138,8 @@ data/eogdb/eogdb_task2.csv
 data/eogdb/eogdb_task3.csv
 data/eogdb/eogdb_task4.csv
 data/rs_eeg_texas/data/
+data/rebel_eeg_restingstate_fr
+data/rebel_eeg_restingstate_sg
 docs/readme/README_popularity.py
 paper/NeuroKit_Submission/
 data/fantasia/fantasia-database-1.0.0
@@ -147,6 +149,9 @@ data/RealObjectsEEG
 studies/hrv_structure/efa.csv
 studies/hrv_structure/data_stability_1.csv
 studies/hrv_structure/data2.csv
+data/lemon/lemon/*
+data/srm_restingstate_eeg/eeg/
+data/testretest_restingstate_eeg/eeg/
 data/mit_nst/data2.csv
 data/mit_long-term/download_mit_long-term.py
 *.atr
@@ -203,5 +208,7 @@ docs/readme/README_popularity.py
 paper/OHBM2022/OHBM2022_Makowski.mp4
 
 
-studies/complexity_benchmark/README_cache/
-studies/complexity_benchmark/manuscript_cache/
+studies/complexity_structure/README_cache/
+studies/complexity_structure/manuscript_cache/
+studies/complexity_eeg/data_attractor.csv
+studies/complexity_eeg/data_delay.csv

AUTHORS.rst

@@ -4,8 +4,10 @@ Authors
 .. hint::
    Want to be a part of the project? Read how to `contribute and join us <https://neuropsychology.github.io/NeuroKit/resources/contributing.html>`_!
 
-Maintainers
------------
+The full log of contributors is available on `GitHub <https://github.com/neuropsychology/NeuroKit/graphs/contributors>`_.
+
+Current maintainers
+-------------------
 
 * `Dominique Makowski <https://github.com/DominiqueMakowski>`_ *(Nanyang Technological University, Singapore)*
 * `An Shu Te <https://github.com/anshu-97>`_ *(Nanyang Technological University, Singapore)*
@@ -21,12 +23,13 @@ Core contributors
 * `François Lespinasse <https://github.com/sangfrois>`_ *(Université de Montréal, Canada)*
 
 .. note::
-   We might sometimes update the authors page categories, order of display, etc., and we won't necessarily notify each contributor every time. However, if you are for any reasons unsatisfied with the list, or your position in it, please do let us know!
+   We might sometimes update the categories, order of display, etc., and we won't necessarily notify each contributor every time. However, if you are for any reasons unsatisfied with the list, or your position in it, please do let us know!
 
 
 Contributors
 -------------
 
+* `Danielle Benesch <https://github.com/danibene>`_ *(École de technologie supérieure, Canada)*
 * `Hung Pham <https://github.com/hungpham2511>`_ *(Eureka Robotics, Singapore)*
 * `Christopher Schölzel <https://github.com/CSchoel>`_ *(THM University of Applied Sciences, Germany)*
 * `Duy Le <https://github.com/duylp>`_ *(Hubble, Singapore)*
@@ -46,6 +49,7 @@ Contributors
 * `Jacob Epifano <https://github.com/jrepifano>`_ *(Rowan University - Children's Hospital of Philadelphia, USA)*
 * `Patryk Wielopolski <https://github.com/pfilo8>`_ *(Wrocław University of Science and Technology, Poland)*
 * `Danielle Benesch <https://github.com/danibene>`_ *(École de technologie supérieure, Canada)*
+* `Jannik Gut <https://github.com/rostro36>`_
 * `Nattapong Thammasan <https://github.com/Nattapong-OnePlanet>`_ *(OnePlanet, Netherlands)*
 
 

NEWS.rst

@@ -2,6 +2,32 @@ News
 =====
 
 
+
+
+
+0.2.1
+-------------------
+New Features
++++++++++++++
+
+* Allow for input with NaNs and extrapolation in `signal_interpolate()`
+* Add argument `method` in `find_outliers()`
+
+
+
+
+
+0.2.0
+-------------------
+New Features
++++++++++++++
+
+* Add new time-domain measures in `hrv_time()`: `Prc20NN`, `Prc80NN`, `MinNN`, and `MaxNN`
+
+
+
+
+
 0.1.6
 -------------------
 
@@ -15,6 +41,7 @@ New Features
 +++++++++++++
 
 * Add new time-domain measures in `hrv_time()`: `Prc20NN`, `Prc80NN`, `MinNN`, and `MaxNN`
+* Allow `fix_peaks()` to account for larger intervals
 
 Fixes
 +++++++++++++

data/lemon/download_lemon.py

@@ -0,0 +1,95 @@
+# -*- coding: utf-8 -*-
+"""Script for formatting the LEMON EEG dataset
+
+https://ftp.gwdg.de/pub/misc/MPI-Leipzig_Mind-Brain-Body-LEMON/EEG_MPILMBB_LEMON/EEG_Preprocessed_BIDS_ID/EEG_Preprocessed/
+
+Steps:
+    1. Download the ZIP database from https://physionet.org/content/nstdb/1.0.0/
+    2. Open it with a zip-opener (WinZip, 7zip).
+    3. Extract the folder of the same name (named 'mit-bih-noise-stress-test-database-1.0.0') to the same folder as this script.
+    4. Run this script.
+
+Credits:
+    pycrostates package by Mathieu Scheltienne and Victor Férat
+"""
+import os
+
+import mne
+import numpy as np
+import pooch
+
+# Path of the database
+path = "https://ftp.gwdg.de/pub/misc/MPI-Leipzig_Mind-Brain-Body-LEMON/EEG_MPILMBB_LEMON/EEG_Preprocessed_BIDS_ID/EEG_Preprocessed/"
+
+# Create a registry with the file names
+files = {
+    f"sub-01{i:04d}_{j}.{k}": None
+    for i in range(2, 319)
+    for j in ["EC", "EO"]
+    for k in ["fdt", "set"]
+}
+
+# Create fetcher
+fetcher = pooch.create(
+    path="lemon/",
+    base_url=path,
+    registry=files,
+)
+
+# Download the files
+for sub in files.keys():
+    try:
+        _ = fetcher.fetch(sub)
+    except:
+        pass
+
+print("Finished downloading!")
+
+# Preprocessing
+
+# fmt: off
+standard_channels = [
+        "Fp1", "Fp2", "F7", "F3", "Fz", "F4", "F8", "FC5",
+        "FC1", "FC2", "FC6", "T7", "C3", "Cz", "C4", "T8",
+        "CP5", "CP1", "CP2", "CP6", "AFz", "P7", "P3", "Pz",
+        "P4", "P8", "PO9", "O1", "Oz", "O2", "PO10", "AF7",
+        "AF3", "AF4", "AF8", "F5", "F1", "F2", "F6", "FT7",
+        "FC3", "FC4", "FT8", "C5", "C1", "C2", "C6", "TP7",
+        "CP3", "CPz", "CP4", "TP8", "P5", "P1", "P2", "P6",
+        "PO7", "PO3", "POz", "PO4", "PO8",
+    ]
+# fmt: on
+
+for sub in os.listdir("lemon/"):
+    if sub.endswith("fdt") is True or sub.endswith("fif") or "sub" not in sub:
+        continue
+    raw = mne.io.read_raw_eeglab("lemon/" + sub, preload=True)
+
+    missing_channels = list(set(standard_channels) - set(raw.info["ch_names"]))
+
+    if len(missing_channels) != 0:
+        # add the missing channels as bads (array of zeros)
+        missing_data = np.zeros((len(missing_channels), raw.n_times))
+        data = np.vstack([raw.get_data(), missing_data])
+        ch_names = raw.info["ch_names"] + missing_channels
+        ch_types = raw.get_channel_types() + ["eeg"] * len(missing_channels)
+        info = mne.create_info(ch_names=ch_names, ch_types=ch_types, sfreq=raw.info["sfreq"])
+        raw = mne.io.RawArray(data=data, info=info)
+        raw.info["bads"].extend(missing_channels)
+
+    raw = raw.add_reference_channels("FCz")
+    raw = raw.reorder_channels(standard_channels)
+    raw = raw.set_montage("standard_1005")
+    raw = raw.interpolate_bads()
+    raw = raw.set_eeg_reference("average").apply_proj()
+
+    raw.save("lemon/" + sub.replace(".set", "") + "_raw.fif", overwrite=True)
+
+
+# Clean-up
+for sub in os.listdir("lemon/"):
+    if sub.endswith("fif"):
+        continue
+    os.remove(f"lemon/{sub}")
+
+print("FINISHED.")

data/srm_restingstate_eeg/download_script.py

@@ -0,0 +1,44 @@
+"""
+https://openneuro.org/datasets/ds003775/versions/1.0.0
+"""
+import os
+import shutil
+
+import mne
+import numpy as np
+import openneuro as on
+
+import neurokit2 as nk
+
+# Download cleaned data (takes some time)
+on.download(
+    dataset="ds003775",
+    target_dir="eeg/raw",
+    include="sub-*",
+    exclude="derivatives/cleaned_data",
+)
+
+# Convert to MNE
+path = "eeg/raw/"
+for sub in os.listdir(path):
+    if "sub" not in sub:
+        continue
+    print(f"Participant: {sub}")
+    file = [f for f in os.listdir(path + sub + "/ses-t1/eeg/") if ".edf" in f][0]
+    raw = mne.io.read_raw_edf(path + sub + "/ses-t1/eeg/" + file, preload=True, verbose=False)
+    raw = raw.set_montage("biosemi64")
+
+    # Clean
+    raw = raw.notch_filter(freqs=np.arange(50, 501, 50), verbose=False)
+    raw.info["bads"], _ = nk.eeg_badchannels(
+        raw, bad_threshold=0.33, distance_threshold=0.99, show=False
+    )
+    print("Bad channels: " + str(len(raw.info['bads'])))
+    raw = raw.interpolate_bads()
+
+    raw.save("eeg/" + sub + "_raw.fif", overwrite=True)
+
+print("FINISHED.")
+
+# Clean-up
+shutil.rmtree("eeg/raw/")

data/testretest_restingstate_eeg/download_script.py

@@ -0,0 +1,61 @@
+"""
+https://openneuro.org/datasets/ds003685/
+"""
+import os
+import re
+import shutil
+
+import mne
+import numpy as np
+import openneuro as on
+
+import neurokit2 as nk
+
+# Download cleaned data (takes some time)
+on.download(
+    dataset="ds003685",
+    target_dir="eeg/raw",
+    include="sub-*/ses-session1/*eyes*",
+)
+
+# Convert to MNE
+path = "eeg/raw/"
+for sub in os.listdir(path):
+    if "sub" not in sub or "sub-60" in sub:
+        continue
+    print(f"Participant: {sub}")
+    newpath = path + sub + "/ses-session1/eeg/"
+
+    # The header file is broken as the name in it is incorrect
+    # -------------------------------------------------------------------------
+    for file in [f for f in os.listdir(newpath) if ".vmrk" in f]:
+        with open(newpath + file, "r+") as f:
+            text = f.read()  # read everything in the file
+            pattern = re.search("DataFile=.*\\n", text).group(0)
+            text = text.replace(pattern, pattern.replace(" ", ""))
+        with open(newpath + file, "r+") as f:
+            f.write(text)
+
+    for file in [f for f in os.listdir(newpath) if ".vhdr" in f]:
+
+        with open(newpath + file, "r+") as f:
+            text = f.read()  # read everything in the file
+            pattern = re.search("DataFile=.*\\n", text).group(0)
+            text = text.replace(pattern, pattern.replace(" ", ""))
+            pattern = re.search("MarkerFile=.*\\n", text).group(0)
+            text = text.replace(pattern, pattern.replace(" ", ""))
+        with open(newpath + file, "r+") as f:
+            f.write(text)
+        # -------------------------------------------------------------------------
+
+        raw = mne.io.read_raw_brainvision(newpath + file, preload=True, verbose=False)
+        raw = raw.set_eeg_reference("average")
+        # raw = raw.set_montage("biosemi64")
+        if "eyesopen" in file:
+            raw.save("eeg/" + sub + "_eyesopen_raw.fif", overwrite=True)
+        else:
+            raw.save("eeg/" + sub + "_eyesclosed_raw.fif", overwrite=True)
+
+print("FINISHED.")
+# Clean-up
+shutil.rmtree("eeg/raw/")