Merge pull request #258 from neuropsychology/dev

0.0.38

.binder/requirements.txt

@@ -2,4 +2,5 @@ neurokit2
 pandas
 matplotlib
 seaborn
-numpy
+numpy
+pywt

.codeclimate.yml

@@ -11,7 +11,6 @@ engines:
       E303:
         enabled: false
 
-
 checks:
   argument-count:
     enabled: false
@@ -32,11 +31,12 @@ checks:
   similar-code:
     enabled: false
   identical-code:
-    enabled: true
+    enabled: false
 
 exclude_patterns:
 - "tests/"
 - "scripts/"
+- "benchmarks/"
 - "data/"
 - "docs/img/"
 - "docs/readme/"

.github/CONTRIBUTING.rst

@@ -41,13 +41,22 @@ Now, navigate to the folder where your script is by typing ``cd C:\the\folder\of
 
     isort myfile.py -l 120  --balanced --multi-line 3 --lines-between-types 1 --lines-after-imports 2 --trailing-comma
     black myfile.py --line-length 120
-    docformatter myfile.py --wrap-summaries 120 --wrap-descriptions 113 --blank  --make-summary-multi-line --in-place
+    docformatter myfile.py --wrap-summaries 120 --wrap-descriptions 113 --blank --in-place
     
     flake8 myfile.py --max-line-length=127 --max-complexity=10 --ignore E303,C901,E203,W503
-    pylint myfile.py --max-line-length=127 --load-plugins=pylint.extensions.docparams --load-plugins=pylint.extensions.docstyle --variable-naming-style=any --argument-naming-style=any --reports=n --suggestion-mode=y --disable=E303 --disable=R0913 --disable=R0801 --disable=C0114 --disable=E203 --disable=E0401 --disable=W9006 --disable=C0330 --disable=R0914 --disable=R0912 --disable=R0915 --disable=W0102 --disable=W0511 --disable=C1801 --disable=C0111 --disable=R1705 --disable=R1720 --disable=C0301 --disable=C0415 --disable=C0103 --disable=C0302 --disable=R1716 --disable=W0632 --disable=E1136
+    pylint myfile.py --max-line-length=127 --load-plugins=pylint.extensions.docparams --load-plugins=pylint.extensions.docstyle --variable-naming-style=any --argument-naming-style=any --reports=n --suggestion-mode=y --disable=E303 --disable=R0913 --disable=R0801 --disable=C0114 --disable=E203 --disable=E0401 --disable=W9006 --disable=C0330 --disable=R0914 --disable=R0912 --disable=R0915 --disable=W0102 --disable=W0511 --disable=C1801 --disable=C0111 --disable=R1705 --disable=R1720 --disable=C0301 --disable=C0415 --disable=C0103 --disable=C0302 --disable=R1716 --disable=W0632 --disable=E1136 --extension-pkg-whitelist=numpy
 The first three commands will make some modifications to your code so that it is nicely formatted, while the two last will run some checks to detect any additional issues. Please try to fix them!
 
-*PS:* If you want to check the whole package, just replace 'myfile.py' by 'neurokit2' and add ``--recursive`` to ``isort`` and ``docformatter``.
+*PS:* If you want to check the whole package (i.e., all the files of the package), run:
+
+.. code-block::
+
+    isort neurokit2 -l 120 --balanced --multi-line 3 --lines-between-types 1 --lines-after-imports 2 --trailing-comma --skip neurokit2/complexity/__init__.py --recursive 
+    black neurokit2 --line-length 120
+    docformatter neurokit2 --wrap-summaries 120 --wrap-descriptions 113 --blank --in-place --recursive
+    
+    flake8 neurokit2 --exclude neurokit2/__init__.py --max-line-length=127 --max-complexity=10 --ignore E303,C901,E203,W503
+    pylint neurokit2 --max-line-length=127 --load-plugins=pylint.extensions.docparams --load-plugins=pylint.extensions.docstyle --variable-naming-style=any --argument-naming-style=any --reports=n --suggestion-mode=y --disable=E303 --disable=R0913 --disable=R0801 --disable=C0114 --disable=E203 --disable=E0401 --disable=W9006 --disable=C0330 --disable=R0914 --disable=R0912 --disable=R0915 --disable=W0102 --disable=W0511 --disable=C1801 --disable=C0111 --disable=R1705 --disable=R1720 --disable=C0301 --disable=C0415 --disable=C0103 --disable=C0302 --disable=R1716 --disable=W0632 --disable=E1136 --extension-pkg-whitelist=numpy --exit-zero
 
 Avoid Semantic Errors
 ^^^^^^^^^^^^^^^^^^^^^^
@@ -58,14 +67,6 @@ Most errors detected by our code checks can be easily automated with ``isort``,
 
 - Missing function arguments in ``Parameters`` and ``Returns``. 
 - In internal functions, missing ``Returns`` section detected only if ``Parameters`` is documented but is not followed by returns documentation.
-- Failure to detect parameter/return type documentation when including commas:
-
-.. code-block::
-
-    y_values : list, array or Series
-
-will result in a ``pylint`` error like ``W9015: "y_values" missing in parameter documentation (missing-param-doc)`` so write it as such ``y_values : list or array or Series``.
-
 - Failure to detect documentation of arguments when they are done simultaneously in one line:
 
 .. code-block::

.github/release-drafter-config.yml

@@ -1,8 +1,24 @@
+name-template: '$RESOLVED_VERSION'
+tag-template: 'v$RESOLVED_VERSION'
+
+version-resolver:
+  major:
+    labels:
+      - 'major'
+  minor:
+    labels:
+      - 'minor'
+  patch:
+    labels:
+      - 'patch'
+  default: patch
+
 template: |
   ## 🚀 What’s New
 
   $CHANGES
   
   ## 👏 Thanks to 
   
-  $CONTRIBUTORS
+  $CONTRIBUTORS
+  

.github/workflows/checks.yml

@@ -18,8 +18,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install https://github.com/DominiqueMakowski/popularipy/zipball/master
-        cd $GITHUB_WORKSPACE
-        python setup.py install 
+        cd $GITHUB_WORKSPACE && pip install .[test]
    
     - name: Run README_examples.py
       run: |
@@ -30,4 +29,4 @@ jobs:
       run: |
         python -m pip install --upgrade setuptools pip wheel twine
         python setup.py sdist bdist_wheel
-        python -m twine check dist/*
+        python -m twine check dist/*

.github/workflows/release-drafter.yml

@@ -0,0 +1,18 @@
+name: 🚀 Release Drafter
+
+on:
+  push:
+    branches:
+      - master
+
+jobs:
+  update_release_draft:
+    runs-on: ubuntu-latest
+    steps:
+      # Drafts your next Release notes as Pull Requests are merged into "master"
+      - uses: release-drafter/release-drafter@v5
+        with:
+          # (Optional) specify config name to use, relative to .github/. Default: release-drafter.yml
+          config-name: release-drafter-config.yml
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/style.yml

@@ -20,31 +20,40 @@ jobs:
         python -m pip install tox-gh-actions
         tox
 
-    - name: Check isort (check import calls)
+    - name: Fix code style with isort (import calls)
       run: |
         python -m pip install isort
-        isort neurokit2 --recursive -l 120 --balanced --multi-line 3 --lines-between-types 1 --lines-after-imports 2 --trailing-comma --skip neurokit2/complexity/__init__.py --check --diff
+        isort neurokit2 --recursive -l 120 --balanced --multi-line 3 --lines-between-types 1 --lines-after-imports 2 --trailing-comma --skip neurokit2/complexity/__init__.py --diff
 
-    - name: Detect style errors that can be fixed by running black
+    - name: Fix code style with black (line lengths)
       run: |
         pip install black
         # The GitHub editor is 127 chars wide. See https://black.readthedocs.io/en/stable/installation_and_usage.html
-        black neurokit2 --line-length 120 --check
+        black neurokit2 --line-length 120 .
 
-    - name: Check docstrings with docformatter
+    - name: Fix code style with docformatter (docstrings)
       run: |
         pip install docformatter
         # See https://github.com/myint/docformatter
-        docformatter neurokit2 --recursive --wrap-summaries 120 --wrap-descriptions 113 --blank --pre-summary-newline --make-summary-multi-line
+        docformatter neurokit2 --wrap-summaries 120 --wrap-descriptions 113 --blank --make-summary-multi-line --recursive
 
-    - name: Detect style errors with flake8
+    - name: Detect remaining style errors with flake8
       run: |
         pip install flake8
         # The GitHub editor is 127 chars wide. See https://flake8.pycqa.org/en/latest/user/configuration.html
         flake8 neurokit2 --exclude neurokit2/__init__.py --max-line-length=127 --max-complexity=10 --ignore E303,C901,E203,W503
 
-    - name: Detect style errors with Pylint (fail under)
+    - name: Detect remaining style errors with Pylint (fail under)
       run: |
         pip install pylint-fail-under
         # See http://pylint.pycqa.org/en/latest/index.html
-        pylint-fail-under neurokit2 --max-line-length=127 --load-plugins=pylint.extensions.docparams --load-plugins=pylint.extensions.docstyle --variable-naming-style=any --argument-naming-style=any --reports=n --suggestion-mode=y --disable=E303 --disable=R0913 --disable=R0801 --disable=C0114 --disable=E203 --disable=E0401 --disable=W9006 --disable=C0330 --disable=R0914 --disable=R0912 --disable=R0915 --disable=W0102 --disable=W0511 --disable=C1801 --disable=C0111 --disable=R1705 --disable=R1720 --disable=C0301 --disable=C0415 --disable=C0103 --disable=C0302 --disable=R1716 --disable=W0632 --disable=E1136 --exit-zero --fail_under 9.97
+        pylint-fail-under neurokit2 --max-line-length=127 --load-plugins=pylint.extensions.docparams --load-plugins=pylint.extensions.docstyle --variable-naming-style=any --argument-naming-style=any --reports=n --suggestion-mode=y --disable=E303 --disable=R0913 --disable=R0801 --disable=C0114 --disable=E203 --disable=E0401 --disable=W9006 --disable=C0330 --disable=R0914 --disable=R0912 --disable=R0915 --disable=W0102 --disable=W0511 --disable=C1801 --disable=C0111 --disable=R1705 --disable=R1720 --disable=C0301 --disable=C0415 --disable=C0103 --disable=C0302 --disable=R1716 --disable=W0632 --disable=E1136 --extension-pkg-whitelist=numpy --exit-zero --fail_under 9.95
+
+    - name: Commit changes
+      uses: EndBug/add-and-commit@v4
+      with:
+        message: "Commit style fixes"
+        add: "*.py"
+        cwd: "./neurokit2/"
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/tests.yml

@@ -1,7 +1,12 @@
 name: 📊 Tests
 
 # on: [push, pull_request]
-on: pull_request
+on:
+  # Trigger the workflow on push to master branch or pull request
+  push:
+    branches:
+      - master
+  pull_request:
 
 jobs:
   build:

.gitignore

@@ -126,3 +126,8 @@ data/ludb/mit-bih-normal-sinus-rhythm-database-1.0.0/*
 data/ludb/ECGs.csv
 data/ludb/Rpeaks.csv
 benchmarks/ecg_preprocessing/make_data.py
+data/eogdb/eogdb.csv
+data/eogdb/eogdb_task1.csv
+data/eogdb/eogdb_task2.csv
+data/eogdb/eogdb_task3.csv
+data/eogdb/eogdb_task4.csv

README.rst

@@ -65,7 +65,7 @@ Contributing
         :target: https://github.com/neuropsychology/NeuroKit/blob/master/LICENSE
         :alt: License
 
-.. image:: https://github.com/neuropsychology/neurokit/workflows/%E2%9C%A8%20Style/badge.svg
+.. image:: https://github.com/neuropsychology/neurokit/workflows/%E2%9C%A8%20Style/badge.svg?branch=master
         :target: https://github.com/neuropsychology/NeuroKit/actions
         :alt: GitHub CI
 
@@ -133,6 +133,8 @@ Examples
 -  `Extract and Visualize Individual Heartbeats <https://neurokit2.readthedocs.io/en/latest/examples/heartbeats.html>`_
 -  `Locate P, Q, S and T waves in ECG <https://neurokit2.readthedocs.io/en/latest/examples/ecg_delineate.html>`_
 -  `Complexity Analysis of Physiological Signals <https://neurokit2.readthedocs.io/en/latest/tutorials/complexity.html>`_
+-  `Analyze Electrooculography EOG data <https://neurokit2.readthedocs.io/en/latest/examples/eog.html>`_
+-  `Fit a function to a signal <https://neurokit2.readthedocs.io/en/latest/tutorials/fit_function.html>`_
 
 *You can try out these examples directly* `in your browser <https://github.com/neuropsychology/NeuroKit/tree/master/docs/examples#cloud-based-interactive-examples>`_.
 
@@ -301,19 +303,41 @@ Photoplethysmography (PPG/BVP)
     # Generate 15 seconds of PPG signal (recorded at 250 samples / second)
     ppg = nk.ppg_simulate(duration=15, sampling_rate=250, heart_rate=70)
 
+    # Process it
+    signals, info = nk.ppg_process(ppg, sampling_rate=250)
 
+    # Visualize the processing
+    nk.ppg_plot(signals, sampling_rate=250)
 
-Electrogastrography (EGG)
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Consider `helping us develop it <https://neurokit2.readthedocs.io/en/latest/tutorials/contributing.html>`_!
+.. image:: https://raw.github.com/neuropsychology/NeuroKit/master/docs/readme/README_ppg.png
 
 
 Electrooculography (EOG)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+.. code-block:: python
+    
+    # Import EOG data
+    eog_signal = nk.data("eog_100hz")
+
+    # Process it
+    signals, info = nk.eog_process(eog_signal, sampling_rate=100)
+
+    # Plot
+    plot = nk.eog_plot(signals, sampling_rate=100)
+
+
+.. image:: https://raw.github.com/neuropsychology/NeuroKit/master/docs/readme/README_eog.png
+
+
+
+Electrogastrography (EGG)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
 Consider `helping us develop it <https://neurokit2.readthedocs.io/en/latest/tutorials/contributing.html>`_!
 
+
 Physiological Data Analysis
 ----------------------------
 
@@ -390,6 +414,30 @@ Heart Rate Variability (HRV)
 .. image:: https://raw.github.com/neuropsychology/NeuroKit/master/docs/readme/README_hrv.png
 
 
+ECG Delineation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+- Delineate the QRS complex of an electrocardiac signal (ECG) including P-peaks, T-peaks, as well as their onsets and offsets.
+
+
+.. code-block:: python
+
+
+    # Download data
+    ecg_signal = nk.data(dataset="ecg_3000hz")['ECG']
+
+    # Extract R-peaks locations
+    _, rpeaks = nk.ecg_peaks(ecg_signal, sampling_rate=3000)
+
+    # Delineate
+    signal, waves = nk.ecg_delineate(ecg_signal, rpeaks, sampling_rate=3000, method="dwt", show=True, show_type='all')
+
+
+
+.. image:: https://raw.github.com/neuropsychology/NeuroKit/master/docs/readme/README_delineation.png
+       :target: https://neurokit2.readthedocs.io/en/latest/examples/ecg_delineate.html
+
+
 
 Signal Processing
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -424,6 +472,7 @@ Signal Processing
 
 .. image:: https://raw.github.com/neuropsychology/NeuroKit/master/docs/readme/README_signalprocessing.png
 
+
 Complexity (Entropy, Fractal Dimensions, ...)
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -456,6 +505,65 @@ Complexity (Entropy, Fractal Dimensions, ...)
     nk.entropy_approximate(signal)
 
 
+Signal Decomposition
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. code-block:: python
+
+    # Create complex signal
+    signal = nk.signal_simulate(duration=10, frequency=1)  # High freq
+    signal += 3 * nk.signal_simulate(duration=10, frequency=3)  # Higher freq
+    signal += 3 * np.linspace(0, 2, len(signal))  # Add baseline and linear trend
+    signal += 2 * nk.signal_simulate(duration=10, frequency=0.1, noise=0)  # Non-linear trend
+    signal += np.random.normal(0, 0.02, len(signal))  # Add noise
+
+    # Decompose signal using Empirical Mode Decomposition (EMD)
+    components = nk.signal_decompose(signal, method='emd')
+    nk.signal_plot(components)  # Visualize components
+
+    # Recompose merging correlated components
+    recomposed = nk.signal_recompose(components, threshold=0.99)
+    nk.signal_plot(recomposed)  # Visualize components
+
+.. image:: https://raw.github.com/neuropsychology/NeuroKit/master/docs/readme/README_decomposition.png
+        :target: https://neurokit2.readthedocs.io/en/latest/
+
+Signal Power Spectrum Density (PSD)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+.. code-block:: python
+
+    # Generate signal with frequencies of 5, 20 and 30
+	signal = nk.signal_simulate(frequency=5) + 0.5*nk.signal_simulate(frequency=20) + nk.signal_simulate(frequency=30)
+	
+	# Find Power Spectrum Density with different methods
+	# Mutlitaper
+	multitaper = nk.signal_psd(signal, method="multitapers", show=False, max_frequency=100)
+	# Welch
+	welch = nk.signal_psd(signal, method="welch", min_frequency=1, show=False, max_frequency=100)
+	# Burg
+	burg = nk.signal_psd(signal, method="burg", min_frequency=1, show=False, ar_order=15, max_frequency=100)
+
+	# Visualize the different methods together
+	fig, ax = plt.subplots()
+
+	ax.plot(welch["Frequency"], welch["Power"], label="Welch", color="#CFD8DC", linewidth=2)
+	ax.plot(multitaper["Frequency"], multitaper["Power"], label="Multitaper", color="#00695C", linewidth=2)
+	ax.plot(burg["Frequency"], burg["Power"], label="Burg", color="#0097AC", linewidth=2)
+
+	ax.set_title("Power Spectrum Density (PSD)")
+	ax.set_yscale('log')
+	ax.set_xlabel("Frequency (Hz)")
+	ax.set_ylabel("PSD (ms^2/Hz)")
+	ax.legend(loc="upper right")
+
+	# Plot 3 frequencies of generated signal
+	ax.axvline(5, color="#689F38", linewidth=3, ymax=0.95, linestyle="--")
+	ax.axvline(20, color="#689F38", linewidth=3, ymax=0.95, linestyle="--")
+	ax.axvline(30, color="#689F38", linewidth=3, ymax=0.95, linestyle="--")
+
+.. image:: https://raw.github.com/neuropsychology/NeuroKit/master/docs/readme/README_psd.png
+        :target: https://neurokit2.readthedocs.io/en/latest/
+
 Statistics
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

benchmarks/ecg_preprocessing/README.Rmd

@@ -37,6 +37,11 @@ matplotlib$use("Agg", force = TRUE)
 
 # Benchmarking of ECG Preprocessing Methods
 
+*This study can be referenced by* [*citing the package*](https://github.com/neuropsychology/NeuroKit#citation).
+
+**We'd like to publish this study, but unfortunately we currently don't have the time. If you want to help to make it happen, please contact us!**
+
+## Introduction
 
 This work is a replication and extension of the work by @porr2019r, that compared the performance of different popular R-peak detectors.
 
@@ -180,9 +185,7 @@ library(easystats)
 library(lme4)
 
 data <- read.csv("data_detectors.csv", stringsAsFactors = FALSE) %>% 
-  mutate(Database = ifelse(str_detect(Database, "GUDB"), paste0(str_replace(Database, "GUDB_", "GUDB ("), ")"), Database),
-         Method = fct_relevel(Method, "neurokit", "pantompkins1985", "hamilton2002", "martinez2003", "christov2004", "gamboa2008", "elgendi2010", "engzeemod2012", "kalidas2017", "rodrigues2020"),
-         Participant = paste0(Database, Participant))
+  mutate(Method = fct_relevel(Method, "neurokit", "pantompkins1985", "hamilton2002", "martinez2003", "christov2004", "gamboa2008", "elgendi2010", "engzeemod2012", "kalidas2017", "rodrigues2020"))
 
 colors <- c("neurokit"="#E91E63", "pantompkins1985"="#f44336", "hamilton2002"="#FF5722", "martinez2003"="#FF9800", "christov2004"="#FFC107", "gamboa2008"="#4CAF50", "elgendi2010"="#009688", "engzeemod2012"="#2196F3", "kalidas2017"="#3F51B5", "rodrigues2020"="#9C27B0") 
 ```