Update with latest changes from develop (#246)

- Updating doc examples
- Update plot conditions method
- Fix github action builds

.devcontainer/cpu/devcontainer.json

@@ -0,0 +1,26 @@
+{
+    "name": "EEG-ExPy-CPU",
+    "image": "mcr.microsoft.com/devcontainers/python:3.8",
+
+    "customizations": {
+      "vscode": {
+        "extensions": [
+          "ms-python.python"
+        ],
+        "settings": {
+          "python.pythonPath": "/usr/local/bin/python"
+        }
+      }
+    },
+
+    "forwardPorts": [
+      8000,
+      8888,
+      5000,
+      6000
+    ],
+    // print the python version:
+    "postCreateCommand": "python --version && pip install -r requirements.txt && pip install -e . && echo 'Dependencies installed'",
+    "appPort": 8000
+
+  }

.github/workflows/docs.yml

@@ -8,7 +8,7 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python
@@ -17,17 +17,18 @@ jobs:
         python-version: 3.8
     - name: Install dependencies
       run: |
+        make install-deps-apt
         python -m pip install --upgrade pip wheel
         python -m pip install attrdict
 
-        # Install wxPython wheels since they are distribution-specific and therefore not on PyPI
-        # See: https://wxpython.org/pages/downloads/index.html
-        pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04 wxPython
+        make install-deps-wxpython
+    - name: Build project
+      run: |
+        make build
 
-        pip install .
     - name: Build docs
       run: |
-        cd doc && make html
+        make docs
     - name: Deploy Docs
       uses: peaceiris/actions-gh-pages@v3
       if: github.ref == 'refs/heads/master'  # TODO: Deploy seperate develop-version of docs?

.github/workflows/test.yml

@@ -8,60 +8,53 @@ on:
 
 jobs:
   test:
-    name: ${{ matrix.os }}, py-${{ matrix.python_version }}
+    name: test (${{ matrix.os }}, py-${{ matrix.python_version }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, windows-latest, macOS-latest]
-        python_version: [3.7]
+        os: ['ubuntu-22.04', windows-latest, macOS-latest]
+        python_version: ['3.8']
         include:
-          - os: ubuntu-latest
-            python_version: 3.8
           # Experimental: Python 3.9
           # Works fine, commented out because mostly covered (at least installing/building deps) by the typecheck job
           # See issue: https://github.com/NeuroTechX/eeg-notebooks/issues/50
           #- os: ubuntu-latest
           #  python_version: 3.9
 
+          # Check 3.10 for future-proofing
+          - os: ubuntu-22.04
+            python_version: '3.10'
+
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python_version }}
+
     # Not needed if pywinhook is installed from wheels
     #- name: Install swig
     #  if: "startsWith(runner.os, 'windows')"
     #  run: |
     #    (New-Object System.Net.WebClient).DownloadFile("http://prdownloads.sourceforge.net/swig/swigwin-4.0.1.zip","swigwin-4.0.1.zip");
     #    Expand-Archive .\swigwin-4.0.1.zip .;
     #    echo "$((Get-Item .).FullName)/swigwin-4.0.1" | Out-File -FilePath $env:GITHUB_PATH -Encoding utf8 -Append
+
     - name: Install APT dependencies
       if: "startsWith(runner.os, 'Linux')"
       run: |
-        # update archive links
-        sudo apt-get update
-        # xvfb is a dependency to create a virtual display
-        # libgtk-3-dev is a requirement for wxPython
-        # freeglut3-dev is a requirement for a wxPython dependency
-        sudo apt-get -y install xvfb libgtk-3-dev freeglut3-dev
+        make install-deps-apt
+    - name: Upgrade pip
+      run: |
+        python -m pip install --upgrade pip wheel
     - name: Install Linux dependencies
       if: "startsWith(runner.os, 'Linux')"
       run: |
-        python -m pip install --upgrade pip wheel
-
-        # Install wxPython wheels since they are distribution-specific and therefore not on PyPI
-        # See: https://wxpython.org/pages/downloads/index.html
-        pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-18.04 wxPython
-
-        pip install .
-    - name: Install MacOS/Windows dependencies
+        make install-deps-wxpython
+    - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip wheel
-        pip install .
-        pip install -U psychtoolbox  # JG_ADD
-                                     # EB: needed?
+        make build
     - name: Run eegnb install test
       shell: bash
       run: |
@@ -78,14 +71,15 @@ jobs:
           Xvfb :0 -screen 0 1024x768x24 -ac +extension GLX +render -noreset &> xvfb.log &
           export DISPLAY=:0
         fi
-        pytest
+        make test
 
   typecheck:
+    name: typecheck (${{ matrix.os }}, py-${{ matrix.python_version }})
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest]
+        os: ['ubuntu-22.04']
         python_version: [3.9]
 
     steps:
@@ -97,27 +91,17 @@ jobs:
     - name: Install APT dependencies
       if: "startsWith(runner.os, 'Linux')"
       run: |
-        # update archive links
-        sudo apt-get update
-        # xvfb is a dependency to create a virtual display
-        # libgtk-3-dev is a requirement for wxPython
-        # freeglut3-dev is a requirement for a wxPython dependency
-        sudo apt-get -y install xvfb libgtk-3-dev freeglut3-dev
+        make install-deps-apt
+    - name: Upgrade pip
+      run: |
+        python -m pip install --upgrade pip wheel
     - name: Install Linux dependencies
       if: "startsWith(runner.os, 'Linux')"
       run: |
-        python -m pip install --upgrade pip wheel
-
-        # Install wxPython wheels since they are distribution-specific and therefore not on PyPI
-        # See: https://wxpython.org/pages/downloads/index.html
-        pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-18.04 wxPython
-
-        pip install .
-    - name: Install MacOS/Windows dependencies
+        make install-deps-wxpython
+    - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip wheel
-        pip install .
+        make build
     - name: Typecheck
       run: |
-        # Exclude visual_cueing due to errors
-        python -m mypy --exclude 'examples/visual_cueing'
+        make typecheck

Makefile

@@ -0,0 +1,40 @@
+build:
+	# Use pep517 to install pygatt==4.0.5(deprecated setuptools/egg installer) on macos
+	pip install --use-pep517 .
+
+test:
+	pytest
+
+typecheck:
+	# Exclude visual_cueing due to errors
+	python -m mypy --exclude 'examples/visual_cueing'
+
+docs:
+	cd doc && make html
+
+clean:
+	cd doc && make clean
+
+install-deps-apt:
+	sudo apt-get update  # update archive links
+
+	# xvfb is a dependency to create a virtual display
+	# libgtk-3-dev is a requirement for wxPython
+	# freeglut3-dev is a requirement for a wxPython dependency
+	# portaudio19-dev *might* be required to import psychopy on Ubuntu
+	# pulseaudio *might* be required to actually run the tests (on PsychoPy import)
+	# libpulse-dev required to build pocketsphinx (speech recognition dependency of psychopy)
+	# libsdl2-dev required by psychopy
+	# libnotify4 is so we can have the libnotify.so module used in wxPython working
+	sudo apt-get -y install xvfb libgtk-3-dev freeglut3-dev portaudio19-dev libpulse-dev pulseaudio libsdl2-dev libnotify4
+
+	# configure dynamic links
+	sudo ldconfig
+
+	UPDATED_LIBPATH=$(sudo find / -name libnotify.so)
+	LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$UPDATED_LIBPATH
+
+install-deps-wxpython:
+	# Install wxPython wheels since they are distribution-specific and therefore not on PyPI
+	# See: https://wxpython.org/pages/downloads/index.html
+	pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-22.04 wxPython

doc/conf.py

@@ -284,7 +284,7 @@ def setup(app):
     'backreferences_dir': 'generated',   # Where to drop linking files between examples & API
     'doc_module': ('eeg-notebooks',),
     'reference_url': {'eeg-notebooksS': None},
-    'remove_conffig_comments': True,
+    'remove_config_comments': True,
 }
 
 """

eegnb/analysis/utils.py

@@ -2,12 +2,11 @@
 from copy import deepcopy
 import math
 import logging
+import sys
 from collections import OrderedDict
 from glob import glob
-from typing import Union, List, Dict
-from collections import Iterable
+from typing import Union, List
 from time import sleep, time
-from numpy.core.fromnumeric import std
 import keyboard
 import os
 
@@ -20,6 +19,8 @@
 from mne.channels import make_standard_montage
 from mne.filter import create_filter
 from matplotlib import pyplot as plt
+from matplotlib import lines as mlines
+from scipy import stats
 from scipy.signal import lfilter, lfilter_zi
 
 from eegnb import _get_recording_dir
@@ -221,7 +222,8 @@ def plot_conditions(
     ylim=(-6, 6),
     diff_waveform=(1, 2),
     channel_count=4,
-    channel_order=None):
+    channel_order=None,
+):
     """Plot ERP conditions.
     Args:
         epochs (mne.epochs): EEG epochs
@@ -247,20 +249,19 @@ def plot_conditions(
     """
 
     if channel_order:
-      channel_order = np.array(channel_order)
+        channel_order = np.array(channel_order)
     else:
-      channel_order = np.array(range(channel_count))
-
+        channel_order = np.array(range(channel_count))
+    channel_names = np.array(epochs.ch_names)[channel_order]
 
     if isinstance(conditions, dict):
         conditions = OrderedDict(conditions)
 
     if palette is None:
         palette = sns.color_palette("hls", len(conditions) + 1)
 
-    X = epochs.get_data() * 1e6
-
-    X = X[:,channel_order]
+    dfX = epochs.to_data_frame() 
+    dfX[channel_names] *= 1e6
 
     times = epochs.times
     y = pd.Series(epochs.events[:, -1])
@@ -275,43 +276,45 @@ def plot_conditions(
             plot_axes.append(axes[axis_x, axis_y])
     axes = plot_axes
 
-    for ch in range(channel_count):
-        for cond, color in zip(conditions.values(), palette):
-            sns.tsplot(
-                X[y.isin(cond), ch],
-                time=times,
+    for ch,ch_name in enumerate(channel_names):
+        for cond,cond_name, color in zip(conditions.values(),conditions.keys(), palette):
+            dfXc = dfX[dfX.condition.isin(conditions[cond_name])]
+            sns.lineplot(
+                data=dfXc,
+                x="time",
+                y=ch_name,
                 color=color,
                 n_boot=n_boot,
-                ci=ci,
                 ax=axes[ch],
+                errorbar=('ci',ci)
             )
+        axes[ch].set(xlabel='Time (s)', ylabel='Amplitude (uV)', title=epochs.ch_names[channel_order[ch]])
 
         if diff_waveform:
-            diff = np.nanmean(X[y == diff_waveform[1], ch], axis=0) - np.nanmean(
-                X[y == diff_waveform[0], ch], axis=0
-            )
+            dfXc1 = dfX[dfX.condition.isin(conditions[diff_waveform[1]])]
+            dfXc2 = dfX[dfX.condition.isin(conditions[diff_waveform[0]])]
+            dfXc1_mn = dfXc1.set_index(['time', 'epoch'])[ch_name].unstack('epoch').mean(axis=1)
+            dfXc2_mn = dfXc2.set_index(['time', 'epoch'])[ch_name].unstack('epoch').mean(axis=1)
+            diff = (dfXc1_mn - dfXc2_mn).values
             axes[ch].plot(times, diff, color="k", lw=1)
 
-        axes[ch].set_title(epochs.ch_names[channel_order[ch]])
+        axes[ch].set_title(ch_name)
         axes[ch].set_ylim(ylim)
         axes[ch].axvline(
             x=0, ymin=ylim[0], ymax=ylim[1], color="k", lw=1, label="_nolegend_"
         )
 
-    axes[0].set_xlabel("Time (s)")
-    axes[0].set_ylabel("Amplitude (uV)")
-    axes[-1].set_xlabel("Time (s)")
-    axes[1].set_ylabel("Amplitude (uV)")
-
+    legs = []
+    for cond,cond_name,color in zip(conditions.values(),conditions.keys(), palette):
+        lh = mlines.Line2D([], [], color=color, marker='', ls='-', label=cond_name)
+        legs.append(lh)
     if diff_waveform:
-        legend = ["{} - {}".format(diff_waveform[1], diff_waveform[0])] + list(
-            conditions.keys()
-        )
-    else:
-        legend = conditions.keys()
-    axes[-1].legend(
-        legend, bbox_to_anchor=(1.05, 1), loc="upper left", borderaxespad=0.0
-    )
+        lh = mlines.Line2D([], [], color="k", marker='', ls='-', 
+                          label = "{} - {}".format(diff_waveform[1], diff_waveform[0]))
+        legs.append(lh)
+
+    axes[-1].legend(handles=legs,  
+                    bbox_to_anchor=(1.05, 1), loc="upper left", borderaxespad=0.0)
     sns.despine()
     plt.tight_layout()
 
@@ -331,6 +334,9 @@ def plot_highlight_regions(
     Args:
         x (array_like): x coordinates
         y (array_like): y values of same shape as `x`
+    Keyword Args:
+        hue (array_like): values to be plotted as hue based on `hue_thresh`.
+            Must be of the same shape as `x` and `y`.
     Keyword Args:
         hue (array_like): values to be plotted as hue based on `hue_thresh`.
             Must be of the same shape as `x` and `y`.
@@ -456,12 +462,9 @@ def check_report(eeg: EEG, n_times: int=60, pause_time=5, thres_std_low=None, th
     Usage:
     ------
     from eegnb.devices.eeg import EEG
-    from eegnb.analysis.utils import check_report
-    eeg = EEG(device='museS')
-    check_report(eeg)
+    standard deviation for a quality recording.
 
-    The thres_std_low & thres_std_high values are the 
-    lower and  upper bound of accepted
+    thresholds = {
     standard deviation for a quality recording.
 
     thresholds = {