Merge pull request #705 from neuropsychology/dev

0.2.2

.github/stale.yml

@@ -1,7 +1,7 @@
 # # 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
+# daysUntilClose: 360
 # # Issues with these labels will never be considered stale
 # exemptLabels:
 #   - feature idea 🔥
@@ -14,4 +14,4 @@
 #   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).
+#   This issue has been inactive for a long time. We're closing it (but feel free to reopen it if need be).

.github/workflows/docs-build.yml

@@ -42,6 +42,7 @@ jobs:
                   pip install seaborn
                   pip install EMD-signal
                   pip install cvxopt
+                  pip install ts2vg
                   pip install https://github.com/neuropsychology/neurokit/zipball/dev
 
             - name: Build documentation 📜

.github/workflows/docs-check.yml

@@ -36,6 +36,7 @@ jobs:
                   pip install seaborn
                   pip install EMD-signal
                   pip install cvxopt
+                  pip install ts2vg
                   pip install https://github.com/neuropsychology/neurokit/zipball/dev
 
             - name: Build documentation 📜

.github/workflows/tests.yml

@@ -22,7 +22,7 @@ jobs:
                 python-version: ["3.7", "3.8", "3.9", "3.10"]
 
         steps:
-            - uses: actions/checkout@master
+            - uses: actions/checkout@v3
 
             - name: Set up Python ${{ matrix.python-version }}
               uses: actions/setup-python@v4
@@ -39,4 +39,4 @@ jobs:
                   cd $GITHUB_WORKSPACE && python -m tox -e py
 
             - name: Upload coverage to Codecov
-              uses: codecov/codecov-action@v2
+              uses: codecov/codecov-action@v3

.gitignore

@@ -97,6 +97,9 @@ ENV/
 # vscode stuff
 .vscode/
 
+# PyCharm stuff
+.idea/
+
 # Rope project settings
 .ropeproject
 

AUTHORS.rst

@@ -50,6 +50,7 @@ Contributors
 * `Patryk Wielopolski <https://github.com/pfilo8>`_ *(Wrocław University of Science and Technology, Poland)*
 * `Jannik Gut <https://github.com/rostro36>`_
 * `Nattapong Thammasan <https://github.com/Nattapong-OnePlanet>`_ *(OnePlanet, Netherlands)*
+* `Marek Sokol <https://github.com/sokolmarek>`_ *(Faculty of Biomedical Engineering of the CTU in Prague, Czech Republic)*
 
 
 Thanks also to `Gansheng Tan <https://github.com/GanshengT>`_, `Chuan-Peng Hu <https://github.com/hcp4715>`_, `@ucohen <https://github.com/ucohen>`_, `Anthony Gatti <https://github.com/gattia>`_, `Julien Lamour <https://github.com/lamourj>`_, `@renatosc <https://github.com/renatosc>`_, `Nicolas Beaudoin-Gagnon <https://github.com/Fegalf>`_ and `@rubinovitz <https://github.com/rubinovitz>`_ for their contribution in `NeuroKit 1 <https://github.com/neuropsychology/NeuroKit.py>`_.

README.rst

@@ -512,7 +512,7 @@ Complexity (Entropy, Fractal Dimensions, ...)
 .. code-block:: python
 
     # Generate signal
-    signal = nk.signal_simulate(frequency=[1, 3], noise=0.01, sampling_rate=100)
+    signal = nk.signal_simulate(frequency=[1, 3], noise=0.01, sampling_rate=200)
 
     # Find optimal time delay, embedding dimension and r
     parameters = nk.complexity_optimize(signal, show=True)

data/eeg_1min_200hz.py

@@ -0,0 +1,20 @@
+import pickle
+
+import mne
+
+raw = mne.io.read_raw_fif(
+    mne.datasets.sample.data_path() / "MEG/sample/sample_audvis_raw.fif",
+    preload=True,
+    verbose=False,
+)
+raw = raw.pick(["eeg", "eog", "stim"], verbose=False)
+raw = raw.crop(0, 60)
+raw = raw.resample(200)
+
+# raw.ch_names
+
+# raw.info["sfreq"]
+
+# Store data (serialize)
+with open("eeg_1min_200hz.pickle", "wb") as handle:
+    pickle.dump(raw, handle, protocol=pickle.HIGHEST_PROTOCOL)

data/eeg_resting_8min.py

@@ -4,13 +4,15 @@
 
 import neurokit2 as nk
 
+# EDF TO FIF
+# ==========
 # Read original file (too big to be uploaded on github)
 raw = mne.io.read_raw_edf("eeg_restingstate_3000hz.edf", preload=True)
 
 # Find event onset and cut
 event = nk.events_find(raw.copy().pick_channels(["Foto"]).to_data_frame()["Foto"])
 tmin = event["onset"][0] / 3000
-raw = raw.crop(tmin=tmin, tmax=tmin+8*60)
+raw = raw.crop(tmin=tmin, tmax=tmin + 8 * 60)
 
 
 # EOG
@@ -21,21 +23,23 @@
 
 
 # Montage
-mne.rename_channels(raw.info, dict(zip(raw.info["ch_names"], TruScanEEGpy.convert_to_tenfive(raw.info["ch_names"]))))
+mne.rename_channels(
+    raw.info, dict(zip(raw.info["ch_names"], TruScanEEGpy.convert_to_tenfive(raw.info["ch_names"])))
+)
 montage = TruScanEEGpy.montage_mne_128(TruScanEEGpy.layout_128(names="10-5"))
-extra_channels = np.array(raw.info["ch_names"])[np.array([i not in montage.ch_names for i in raw.info["ch_names"]])]
+extra_channels = np.array(raw.info["ch_names"])[
+    np.array([i not in montage.ch_names for i in raw.info["ch_names"]])
+]
 raw = raw.drop_channels(extra_channels[np.array([i not in ["EOG"] for i in extra_channels])])
 raw = raw.set_montage(montage)
 
 
-
 # Save
 raw = raw.resample(300)
 raw.save("eeg_restingstate_300hz.fif", overwrite=True)
 
 
-
 ## Convert to df
-#df = pd.DataFrame(raw.get_data().T)
-#df.columns = raw.info["ch_names"]
-#df.to_csv("eeg_restingstate_300hz.csv")
+# df = pd.DataFrame(raw.get_data().T)
+# df.columns = raw.info["ch_names"]
+# df.to_csv("eeg_restingstate_300hz.csv")

docs/examples/bio_custom/bio_custom.ipynb

@@ -25,19 +25,23 @@
                 "# Load NeuroKit and other useful packages\n",
                 "import neurokit2 as nk\n",
                 "import numpy as np\n",
-                "import matplotlib.pyplot as plt\n",
                 "import pandas as pd"
             ]
         },
         {
             "cell_type": "code",
-            "execution_count": 2,
-            "metadata": {},
+            "execution_count": null,
+            "metadata": {
+                "tags": [
+                    "remove-input"
+                ]
+            },
             "outputs": [],
             "source": [
-                "# This \"decorative\" cell should be hidden from the docs once this is implemented:\n",
-                "# https://github.com/microsoft/vscode-jupyter/issues/1182 \n",
-                "plt.rcParams['figure.figsize'] = [15, 5]  # Bigger images\n",
+                "# Note: this cell is hidden using the \"remove-input\" tag\n",
+                "# Make bigger images\n",
+                "import matplotlib.pyplot as plt\n",
+                "plt.rcParams['figure.figsize'] = [15, 5]  \n",
                 "plt.rcParams['font.size']= 14"
             ]
         },
@@ -318,7 +322,7 @@
     ],
     "metadata": {
         "kernelspec": {
-            "display_name": "Python 3",
+            "display_name": "Python 3.9.7 64-bit",
             "language": "python",
             "name": "python3"
         },
@@ -332,9 +336,14 @@
             "name": "python",
             "nbconvert_exporter": "python",
             "pygments_lexer": "ipython3",
-            "version": "3.8.5"
+            "version": "3.9.7"
+        },
+        "vscode": {
+            "interpreter": {
+                "hash": "11938c6bc6919ae2720b4d5011047913343b08a43b18698fd82dedb0d4417594"
+            }
         }
     },
     "nbformat": 4,
     "nbformat_minor": 2
-}
+}