major update: merging develop to master (#217)

* example test commit (#182) * example test commit * example edit * ci: run test workflow on develop branch * ci: add develop branch to job triggers * ci: fix syntax issue in workflow * fix: fixed import (brainflow updated API) * build(deps): locked pylsl==1.10.5 (#187) * Experiment Class Refactor (update to #183), converting specific experiments to subclasses (#184) * First commit * Second commit * Modifications * Lol * Lol * Incorporated N170 and p300, looking good for a PR * ssvep update * Implementing subclasses instead of loose functions * fix: fixed import (brainflow updated API) * Playing around still * Fixing import errors * Adding abstractmethod decorators * Still working on the import error * Guess what's finally working * Comments and naming ticks * More comments * Live coding demonstration * ssvep adapted * Adapting Auditory Oddball * changing save_fn to self.save_fun * This maybe the last big change * utils file changed, changes work through cli Co-authored-by: Erik Bjäreholt <erik@bjareho.lt> * Submodule added for gsoc * Adding pipelines for cli analysis (#202) * started pipelines function * almost working simple function equivalents of nb scripts * fix: fixed import (brainflow updated API) * sqc fixes for unicorn (#176) * Ignore pushes * Trying to create a cli * Stepping through the problem * First commit * Fixing pause in signal quality check * Fixing Signal quality check problem * fix the technical debt * Save path done for automated saving pdf * I feel amazing * Almost through * Update eegnb/cli/__main__.py Co-authored-by: Erik Bjäreholt <erik@bjareho.lt> * Trying to create cli but it's being really painful * Extra word cli error * Changed example handling * Pain * Adding whole datapath * Finally fixed cli * hmm * Looking good * added hyperlink * Having some issues with detecting css and image deltetion * Just the css now * Fixed the css linking problem though it's a weird soln * Automated running, still fnames problem * Hahahah embedded images in html * Improving code * Okay now * Look at that * Almost there just the two figures now * Now * Added attrdict to do with cli error Co-authored-by: John Griffiths <j.davidgriffiths@gmail.com> Co-authored-by: Erik Bjäreholt <erik@bjareho.lt> Co-authored-by: John Griffiths <JohnGriffiths@users.noreply.github.com> * added more options for site args; improved function names; removed some redundant lines (#209) * fix subject num parsing bug * analysis report function improvements for openbci cyton and gtec unicorn devices * run exp fix * Update requirements.txt * fixes to get docs building by github action (#210) * fixes to get docs building by github action * reverted some changes * Update 01r__ssvep_viz.py Co-authored-by: John Griffiths <JohnGriffiths@users.noreply.github.com> * Update README.rst small commit to test doc build workflow on this branch * removing gsoc submodule Co-authored-by: Erik Bjäreholt <erik@bjareho.lt> Co-authored-by: Parv Agarwal <65726543+Parvfect@users.noreply.github.com> Co-authored-by: Parvfect <parvagrw02@gmail.com> Co-authored-by: Ben Pettit <pelleter@gmail.com>
NeuroTechX · Jan 19, 2023 · ac1f5fb · ac1f5fb
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diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -2,35 +2,36 @@ name: Docs
 
 on:
   push:
-    branches: [ master, 'dev/*' ]
+    branches: [ master, develop, 'dev/*' ]
   pull_request:
-    branches: [ master ]
+    branches: [ master, develop ]
 
 jobs:
   build:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
-        python-version: 3.7
+        python-version: 3.8
     - name: Install dependencies
       run: |
         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-18.04 wxPython
+        pip install -U -f https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04 wxPython
 
         pip install .
     - name: Build docs
       run: |
         cd doc && make html
     - name: Deploy Docs
       uses: peaceiris/actions-gh-pages@v3
-      if: github.ref == 'refs/heads/master'
+      if: github.ref == 'refs/heads/master'  # TODO: Deploy seperate develop-version of docs?
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: doc/_build/html
- 
+
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -2,9 +2,9 @@ name: Test
 
 on:
   push:
-    branches: [ master ]
+    branches: [ master, develop ]
   pull_request:
-    branches: [ master ]
+    branches: [ master, develop ]
 
 jobs:
   test:
@@ -60,13 +60,13 @@ jobs:
       run: |
         python -m pip install --upgrade pip wheel
         pip install .
+        pip install -U psychtoolbox  # JG_ADD
+                                     # EB: needed?
     - name: Run eegnb install test
-      shell: bash  
-        pip install -U psychtoolbox # JG_ADD
+      shell: bash
       run: |
         if [ "$RUNNER_OS" == "Linux" ]; then
           Xvfb :0 -screen 0 1024x768x24 -ac +extension GLX +render -noreset &> xvfb.log &
-          /
           export DISPLAY=:0
         fi
         eegnb --help

diff --git a/.gitignore b/.gitignore
@@ -14,3 +14,6 @@ examples/visual_cueing/*.csv
 .coverage
 coverage.xml
 htmlcov
+
+# PyCharm
+.idea/
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "GSOC-eeg-notebooks"]
+	path = GSOC-eeg-notebooks
+	url = https://github.com/Parvfect/GSOC-eeg-notebooks
diff --git a/README.rst b/README.rst
@@ -17,7 +17,7 @@ EEG-Notebooks
 
 EEG-Notebooks is a collection of classic EEG experiments, implemented in Python 3 and Jupyter notebooks. The experimental protocols and analyses are quite generic, but are primarily taylored for low-budget / consumer EEG hardware such as the InteraXon MUSE and OpenBCI Cyton. The goal is to make cognitive neuroscience and neurotechnology more accessible, affordable, and scalable. 
 
-- **For an intro talk on the eeg-notebooks project see:** `JG's Brainhack Ontario 2020 presentation <https://www.crowdcast.io/e/brainhack-ontario/7>`_.  
+- **For an intro talk on the eeg-notebooks project see:** `JG's Brainhack Ontario presentation <https://www.crowdcast.io/e/brainhack-ontario/7>`_.  
 - **For documentation see:** `documentation site <https://neurotechx.github.io/eeg-notebooks/index.html>`_.
 - **For code see:** `github site <https://github.com/neurotechx/eeg-notebooks>`_.
 - **For instructions on running experiments see:** `running experiments <https://neurotechx.github.io/eeg-notebooks/getting_started/running_experiments.html>`_.

diff --git a/eegnb/analysis/analysis_report.html b/eegnb/analysis/analysis_report.html
@@ -0,0 +1,39 @@
+<!DOCTYPE html>
+<html>
+  <head>
+    <link href="styling.css" rel="stylesheet" />
+    <title>Analysis Report</title>
+  </head>
+  <body>
+    <div class="topnav">
+      <a href="#Description">Description</a>
+      <a href="#Raw Epoch">Raw Epoch</a>
+      <a href="#Stimulus Response">Stimulus Response</a>
+    </div>
+    <div id="Description">
+      <h1>Analysis Report</h1>
+      <p>
+        <b></b>Experiment Name: {} <br>
+        Subject Id: {} <br>
+        Session Id: {} <br>
+        EEG Device: {} <br>
+        Drop Percentage: {} <br> <br>
+        This is an analysis report for the experiment. <br> For more information about the experiment, please visit the <a href="https://neurotechx.github.io/eeg-notebooks/">documentation</a>
+      </p>
+    </div>
+    <div id="Raw Epoch">
+      <h2>Raw Epoch</h2>
+      <p>
+        The raw epoch is shown below. The raw epoch is the data that is recorded from the EEG headset. The raw epoch is then processed to remove noise and artifacts.
+      </p>
+      <img src="power_spectrum.png" alt="Raw Epoch" />
+    </div>
+    <div id="Stimulus Response">
+      <h2>Stimulus Response</h2>
+      <p>
+        The stimulus response is shown below. The stimulus response is the data that is recorded from the EEG headset after removing noise and artifacts.
+      </p>
+      <img src="erp_plot.png" alt="Stimulus Response" />
+    </div>
+  </body>
+</html>
diff --git a/eegnb/analysis/analysis_report.py b/eegnb/analysis/analysis_report.py
@@ -0,0 +1,95 @@
+
+# Generating html using Python
+
+from airium import Airium
+from typing import Dict
+import os
+import eegnb
+import base64
+
+a = Airium()
+
+def get_experiment_information(experiment:str):
+    analysis_save_path = os.path.join(os.path.dirname(eegnb.__file__), "analysis")
+    file_path = os.path.join(analysis_save_path, "experiment_descriptions")
+
+    with open(os.path.join(file_path, experiment + ".txt"), 'r') as f:
+        experiment_text = f.readlines()
+
+    return experiment_text
+
+def get_img_string(image_save_path):
+    """ Returns image as string to embed into the html report """
+    return base64.b64encode(open(image_save_path, "rb").read()).decode()
+
+def get_html(experimental_parameters: Dict):
+
+    # add variable to store the link
+    analysis_save_path = os.path.join(os.path.dirname(eegnb.__file__), "analysis")
+    css_path = os.path.join(analysis_save_path, "styling.css")
+    eeg_device, experiment, subject, session, example, drop_percentage, epochs_chosen = experimental_parameters.values()
+
+    erp_image_path = os.path.join(os.getcwd(), "erp_plot.png")
+    pos_image_path = os.path.join(os.getcwd(), "power_spectrum.png")
+
+    experiment_text = get_experiment_information(experiment)
+
+
+    """ Possibility of unique experiment text - decision to be made """
+    #experiment_text = ""
+    #with open('experiment_descriptions/{}.txt'.format(experiment), 'r') as f:
+     #   experiment_text = f.readlines()
+
+    a('<!DOCTYPE html>')
+    with a.html():
+        with a.head():
+            a.link(href=css_path, rel='stylesheet', type="text/css")
+            a.title(_t="Analysis Report")
+
+        with a.body():
+
+            # Navigation bar
+            with a.div(klass="topnav"):
+                a.a(_t="Description", href="#Description")
+                a.a(_t="Raw Epoch", href="#Raw Epoch")
+                a.a(_t="Stimulus Response", href="#Stimulus Response")
+
+            # Description
+            with a.div(id="Description"):
+                a.h1(_t="Analysis Report")
+                with a.p():
+                    a("Experiment Name: {} <br>".format(experiment))
+
+                    if example:
+                        a("Example File <br>")
+                    else:
+                        a("Subject Id: {} <br>".format(subject))
+                        a("Session Id: {} <br>".format(session))
+
+                    a("EEG Device: {} <br>".format(eeg_device))
+                    a('This is an analysis report for the experiment. <br> For more information about the experiment, please visit the <a href="https://neurotechx.github.io/eeg-notebooks/">documentation</a><br><br>')
+                    a("{}<br>".format(experiment_text[0]))
+                    a("{}<br>".format(experiment_text[1]))
+
+            # Raw Epoch
+            with a.div(id="Raw Epoch"):
+                a.h2(_t="Raw Epoch")
+                with a.p():
+                    a("The power spectrum of the raw epoch is displayed below. The raw epoch is then processed to remove noise and artifacts.")
+                a.img(src="data:image/png;base64, {}".format(get_img_string(pos_image_path)), alt="Raw Epoch")
+
+            # Stimulus Response
+            with a.div(id="Stimulus Response"):
+                a.h2(_t="Stimulus Response")
+                with a.p():
+                    a("The stimulus response is shown below. The stimulus response is the amplitude response at the specific timescales where the response to the stimulus can be detected. <br>")
+                    a("Epochs chosen: {} <br>".format(epochs_chosen))
+                    a("Drop Percentage: {} %<br> <br>".format(round(drop_percentage,2)))
+                a.img(src="data:image/png;base64, {}".format(get_img_string(erp_image_path)), alt="Stimulus Response")
+
+    # Delete the images
+    os.remove(erp_image_path)
+    os.remove(pos_image_path)
+
+    # Return the html
+    return str(a)
diff --git a/eegnb/analysis/experiment_descriptions/visual-N170.txt b/eegnb/analysis/experiment_descriptions/visual-N170.txt
@@ -0,0 +1,2 @@
+The N170 is a large negative event-related potential (ERP) component that occurs after the detection of faces, but not objects, scrambled faces, or other body parts such as hands. 
+In the experiment we aim to detect the N170 using faces and houses as our stimuli. 
diff --git a/eegnb/analysis/experiment_descriptions/visual-P300.txt b/eegnb/analysis/experiment_descriptions/visual-P300.txt
@@ -0,0 +1,2 @@
+The P300 is a positive event-related potential (ERP) that occurs around 300ms after perceiving a novel or unexpected stimulus. It is most commonly elicited through ‘oddball’ experimental paradigms, where a certain subtype of stimulus is presented rarely amidst a background of another more common type of stimulus. 
+In the experiment, we aimed to elicit P300 response using a visual oddball stimulation.