ExplorePy Version 3.2.0 (#328)

* change unstable bt threshold to .5s (#295) * Hotfix unstable imp (#296) * change unstable bt threshold to .5s * add hint for disabled BT * Hotfix unstable imp (#297) * change unstable bt threshold to .5s * add hint for disabled BT * apply changes for v3.1.0 * delete redundant files * add shared libraries * add .pyd file * add mac libraries * add files to public repo * fix flake8 error * apply isort * add files to public repo (#311) * add files to public repo * fix flake8 error * apply isort * Bump sentry-sdk from 1.19.1 to 2.8.0 in /docs (#304) Bumps [sentry-sdk](https://github.com/getsentry/sentry-python) from 1.19.1 to 2.8.0. - [Release notes](https://github.com/getsentry/sentry-python/releases) - [Changelog](https://github.com/getsentry/sentry-python/blob/master/CHANGELOG.md) - [Commits](getsentry/sentry-python@1.19.1...2.8.0) --- updated-dependencies: - dependency-name: sentry-sdk dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Salman Rahman <salman2135@gmail.com> * Bump tornado from 6.3.2 to 6.4.1 in /docs (#303) Bumps [tornado](https://github.com/tornadoweb/tornado) from 6.3.2 to 6.4.1. - [Changelog](https://github.com/tornadoweb/tornado/blob/master/docs/releases.rst) - [Commits](tornadoweb/tornado@v6.3.2...v6.4.1) --- updated-dependencies: - dependency-name: tornado dependency-type: direct:production ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Salman Rahman <salman2135@gmail.com> * delete shared lib * add byte calculator * update sentry sdk version to 2.8.0 (#314) * APIS-1081 Added testing for available EEG service in btcpp and unpair for OS other than Mac * APIS-1081 Changed call to get services, removed debug messages * APIS-1081 Removed reconnection attempts (on Maziar's recommendation) * APIS-1081 Removed execution of service discovery for MacOS * APIS-1081 Added async wait and replaced check for Mac with check for Windows * APIS-1081 Added UUID normalization, fixed linter * APIS-1081 Made wait only necessary for Windows, added checks to prevent getting new client and connecting if already done * Froze pylsl version to 1.16.2 (for now) * discard corrupt yaml file on load (#319) * discard corrupt yaml file on load * fix isort error * no reconnect on ble disconnection (#320) * no reconnect on ble disconnect * Set correct log messsage on disconnection callback * APIS-1036 Added Miniconda installation to macOS runner, updated upload action, updated Python version * Apis 930 reconnect problem at higher sampling rates (#317) * break parser loop on usb disconnect * APIS-1115 Replaced function to calculate notch coefficients with iirnotch * change baud rate & do sanity check on usb disconnect * read USB data in chunks * increase usb read timeout * check device name before usb connection (#318) * add comment * fix flake8 error * add whitespace before inline * read all available bytes from serial port in one go * wait 10ms in read method when data is not enough * set bt flag to false on usb * handle value error or recording stop * remove backslash from string * use lower order filter for higher SPS * add lock on data write * fix flake8 error * continue usb connection when name query fails * change core usb buffer to deque, add usb conditional in bt drop calc * restore debug message on usb read * APIS-930 Added catching yaml.parser.ParserError --------- Co-authored-by: SonjaSt <sonja.stefani@tum.de> * Apis 935 explore desktop loses track of impedance mode being enabled disabled (#321) * break parser loop on usb disconnect * APIS-1115 Replaced function to calculate notch coefficients with iirnotch * change baud rate & do sanity check on usb disconnect * read USB data in chunks * increase usb read timeout * check device name before usb connection (#318) * add comment * fix flake8 error * add whitespace before inline * read all available bytes from serial port in one go * wait 10ms in read method when data is not enough * set bt flag to false on usb * handle value error or recording stop * remove backslash from string * use lower order filter for higher SPS * add lock on data write * fix flake8 error * continue usb connection when name query fails * disable imp on fresh connection * check device info with specific key for imp mode * fix isort and flake8 errors --------- Co-authored-by: SonjaSt <sonja.stefani@tum.de> * Apis 1131 fix name connect issue in mac (#323) * stop stream and clear stream buffer before name query * remove unused method and import * remove print statement * isort fix * APIS-1131 Added lock to prevent simultaneous read/write to settings yaml * Linter (E302) settings_manager.py --------- Co-authored-by: SonjaSt <sonja.stefani@tum.de> * Froze bleak version (0.22.3) * Update tools.py (#325) * Bugfix command thread (#327) * move disable imp command on fresh connection to top level file * remove disable imp command from stream processor, update thread variable * separate notch filters for impedance (#326) * simplify-mac-intel-connection * Revert "simplify-mac-intel-connection" This reverts commit f2a1a86. * Remove acquiring serial port instance on BLE connect (#329) * remove acquiring serial port instance on BLE connect * APIS-1193 remove unused import for pr submission * Revert "APIS-1193 remove unused import for pr submission" This reverts commit 845b801. * APIS-1193 remove unused import for pr submission * Merge master into develop (#330) * Release 3.1.0 (#307) * change unstable bt threshold to .5s (#295) * Hotfix unstable imp (#296) * change unstable bt threshold to .5s * add hint for disabled BT * Hotfix unstable imp (#297) * change unstable bt threshold to .5s * add hint for disabled BT * apply changes for v3.1.0 * delete redundant files * add shared libraries * add .pyd file * add mac libraries * Updated the P300 oddball paradigm to work with Explore Pro devices (#310) * delete dynamic lib files --------- Co-authored-by: Kyotikk <63866051+Kyotikk@users.noreply.github.com> * delete dynamic lib files * Removed macOS from unit testing * Update docs (#333) * Added email to authors, removed duplicate section in stallation rst * Updated installation rst * Removed blueutil requirement for Mac * bumpversion minor * add changelog --------- Co-authored-by: Salman Rahman <salman2135@gmail.com> --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Nayan Sharma <51515645+rednayan@users.noreply.github.com> Co-authored-by: SonjaSt <sonja.stefani@tum.de> Co-authored-by: Sonja Stefani <35492857+SonjaSt@users.noreply.github.com> Co-authored-by: Kyotikk <63866051+Kyotikk@users.noreply.github.com>
Mentalab-hub · Jan 31, 2025 · 9f05b8d · 9f05b8d
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diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.1.0
+current_version = 3.2.0
 commit = False
 tag = False
 

diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml
@@ -6,8 +6,8 @@ jobs:
     test:
         strategy:
             matrix:
-                os: [ubuntu-latest, windows-latest, macos-latest]
-                python: [3.9.12]
+                os: [ubuntu-latest, windows-latest]
+                python: [3.12]
         runs-on: ${{ matrix.os }}
         timeout-minutes: 10
         steps:
@@ -21,23 +21,36 @@ jobs:
               run: git checkout ${{ env.BRANCH }}
 
             - name: Install non-python dependencies on Ubuntu
-              if: runner.os == 'Linux'
+              if: matrix.os == 'ubuntu-latest'
               run: |
                 sudo apt-get update -y
                 sudo apt-get install libbluetooth-dev -y
-            - name: Set up Python ${{ matrix.python }}
+            - name: Set up Miniconda for Linux and Windows with ${{ matrix.python }}
+              if: matrix.os == 'ubuntu-latest' || matrix.os == 'windows-latest'
               uses: s-weigand/setup-conda@v1
               with:
                   python-version: ${{ matrix.python }}
                   conda-channels: anaconda, conda-forge
+            - name: Set up Miniconda for macOS with ${{ matrix.python }}
+              if: matrix.os == 'macos-latest'
+              shell: bash
+              run: |
+                  mkdir -p ${{ github.workspace }}/miniconda3
+                  curl "https://repo.anaconda.com/miniconda/Miniconda3-py312_24.9.2-0-MacOSX-arm64.sh" -o "${{ github.workspace }}/miniconda3/miniconda.sh"
+                  bash ${{ github.workspace }}/miniconda3/miniconda.sh -b -u -p ${{ github.workspace }}/miniconda3
+                  rm ${{ github.workspace }}/miniconda3/miniconda.sh
+                  source ${{ github.workspace }}/miniconda3/bin/activate
+                  conda init bash
+                  conda config --prepend channels conda-forge
+                  echo "${{ github.workspace }}/miniconda3/bin/" >> $GITHUB_PATH
             - name: Install liblsl from conda-forge
               run: |
                 conda install -c conda-forge liblsl
                 pip install -e .[test]
                 python -m pytest --import-mode=append --html=pytest_report.html --self-contained-html
             -   name: Archive test results
                 if: success() || failure()
-                uses: actions/upload-artifact@v3
+                uses: actions/upload-artifact@v4
                 with:
-                    name: pytest-results
+                    name: pytest-results-${{ matrix.runs-on }}
                     path: pytest_report.html
diff --git a/AUTHORS.rst b/AUTHORS.rst
@@ -3,9 +3,9 @@ Authors
 =======
 
 
-* Salman Rahman - mentalab.com
-* Andrea Escartin - mentalab.com
-* Sonja Stefani - mentalab.com
-* Mohamad Atayi - mentalab.com
-* Masoome Fazelian - mentalab.com
-* Alex Platt - mentalab.com
+* Salman Rahman - `salman@mentalab.com <mailto:salman@mentalab.com>`_
+* Andrea Escartin
+* Sonja Stefani -  `sonja@mentalab.com <mailto:sonja@mentalab.com>`_
+* Mohamad Atayi
+* Masoome Fazelian
+* Alex Platt
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -2,22 +2,33 @@
 Changelog
 =========
 
+3.2.0 (31.1.2025)
+------------------
+* Fix critical bug in settings file modification
+* Improve BT communication 
+* Disable impedance on fresh connection
+* Introduce new sampling rates
+
+
 3.1.0 (8.11.2024)
 ------------------
 * Add USB streaming support
 * Improve BT communication
 
+
 3.0.1 (28.08.2024)
 ------------------
 * Improve device connectivity
 * Add text marker support
 
+
 3.0.0 (7.6.2024)
 ------------------
 * Improve Mac OSX support
 * Add Support for Explore Pro
 * Robust data parsing
 
+
 2.0.0 (5.1.2024)
 ------------------
 * Add Mac OSX support
@@ -31,7 +42,6 @@ Changelog
 * Add yaml file for RTD build
 
 
-
 1.8.1 (11.7.2023)
 ------------------
 * Bugfix record data
@@ -50,7 +60,7 @@ Changelog
 
 1.7.0 (21.12.2022)
 ------------------
-* Add suppport for new explore+ 32 ch device
+* Add support for new explore+ 32 ch device
 * Sorted timestamps in CSV
 * Settings file to preserve experiment settings
 

diff --git a/README.rst b/README.rst
@@ -17,9 +17,9 @@
     :target: https://pypi.org/project/explorepy
 
 
-.. |commits-since| image:: https://img.shields.io/github/commits-since/Mentalab-hub/explorepy/v3.1.0.svg
+.. |commits-since| image:: https://img.shields.io/github/commits-since/Mentalab-hub/explorepy/v3.2.0.svg
     :alt: Commits since latest release
-    :target: https://github.com/Mentalab-hub/explorepy/compare/v3.1.0...master
+    :target: https://github.com/Mentalab-hub/explorepy/compare/v3.2.0...master
 
 
 .. |wheel| image:: https://img.shields.io/pypi/wheel/explorepy.svg

diff --git a/docs/conf.py b/docs/conf.py
@@ -29,8 +29,7 @@
 year = '2018-2024'
 author = 'Mentalab GmbH.'
 copyright = '{0}, {1}'.format(year, author)
-version = release = '3.1.0'
-
+version = release = '3.2.0'
 pygments_style = 'trac'
 templates_path = ['.']
 extlinks = {

diff --git a/docs/installation.rst b/docs/installation.rst
@@ -3,73 +3,80 @@ Installation
 ============
 
 Minimal Requirements
-------------
-* Python 3.10 to Python 3.12. We recommend Python 3.10.
+--------------------
+* Python 3.10 to Python 3.12. We recommend Python 3.12.
 * Microsoft Build Tools for Visual Studio 2019 (only Windows)
 * 6GB RAM (minimum 1GB *free* RAM during the session)
 * Intel i5 or higher (2x2.5GHz) CPU
 
 Recommended Requirements
-------------
-* Python 3.10
+------------------------
+* Python 3.12
 * Microsoft Build Tools for Visual Studio 2019 (only Windows)
 * 8GB RAM
 * Intel i7 or higher CPU
 
 How to install
 --------------
 
-Windows
-^^^^^^^
-
 Option 1: Installing via installer file (basic)
-""""""""
+"""""""""""""""""""""""""""""""""""""""""""""""
 
-*This option is best for users who only intend to use* ``explorepy`` *via graphical user interface*
+Windows and Mac
+^^^^^^^^^^^^^^^
 
-For example, if you want to quickly visualize and record data, use Option 1.
-If you intend to add ``explorepy`` commands to a Python script
-(e.g. an experiment script), install ``explorepy`` via Anaconda instead.
+*This option is best for users who only intend to use functionalities offered by* ``explorepy`` *via a graphical user interface*
 
-For an overview of ``explorepy`` commands, click `here <https://explorepy.readthedocs.io/en/latest/usage.html#command-line-interface>`_.
+For example, if you want to quickly visualize and record data and don't need the command line interface or to use it in your own Python script, use this option.
 
-On a Windows and Mac operating systems, standalone desktop software ``explorepy-desktop`` can be installed using the .exe installable file uploaded to
-`release page <https://github.com/Mentalab-hub/explore-desktop-release/releases/latest/>`_. Please note that the dependencies will be installed automatically.
+If you intend to call ``explorepy`` from the command line or a Python script (e.g. from an experiment script), install ``explorepy`` via Anaconda/pip instead.
+
+For Windows and Mac, the standalone desktop software ExploreDesktop can be installed using the installer files uploaded to the 
+`release page <https://github.com/Mentalab-hub/explore-desktop-release/releases/latest/>`_. Please note that the dependencies will be installed automatically and bundled locally with the installed software.
 
 
 Option 2: Installing from Python Package Index (PyPI) and pip (advanced)
-""""""""
-*To install explorepy for any python version except 3.10, please contact support@mentalab.com.*
+""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+*To install explorepy for any Python version below 3.10, please contact support@mentalab.com.*
+
+*This option is best for users who intend to include* ``explorepy`` *functionalities in their own Python scripts or use it from the command line.*
+
+For an overview of ``explorepy`` commands, click `here <https://explorepy.readthedocs.io/en/latest/usage.html#command-line-interface>`_.
+
+Windows
+^^^^^^^
 
-*This option is best for users who intend to include* ``explorepy`` *functionalities in their own Python scripts.*
 To install the ``explorepy`` API and all its dependencies using pip on Windows:
 
-1. Install Anaconda (or any other Python distribution; these instructions pertain to Anaconda only). Download and install the `Anaconda Windows installer <https://www.anaconda.com/distribution/#download-section>`_.
+1. Install Anaconda (or any other Python distribution; these instructions pertain to Anaconda only). Download and run the `Anaconda installer for windows <https://www.anaconda.com/download/success>`_.
 2. Install `Microsoft Build Tools for Visual Studio 2019 <https://visualstudio.microsoft.com/thank-you-downloading-visual-studio/?sku=BuildTools&rel=16>`_. Select *Desktop development with C++* in the workloads tab. Make sure that *MSVCv142 - VS 2019 C++ x64/x86 build tools* and the latest version of *Windows 10 SDK* are checked.
-3. Open the Conda command prompt.
-4. We recommend using a virtual environment. To do this:
+3. Open the Anaconda command prompt.
+4. We recommend using a conda environment. To do this:
 
-   a. In Conda command prompt: ``conda create -n myenv python=3.10``
-   b. Activate the virtual environment: ``conda activate myenv``
+   a. In the Anaconda command prompt: ``conda create -n myenv python=3.12``
+   b. Activate the conda environment: ``conda activate myenv``
 
 5. Upgrade your pip: ``python -m pip install --upgrade pip``
-6. Run: ``pip install explorepy``, to install ``explorepy`` from PyPI.
+6. Install liblsl: ``conda install -c conda-forge liblsl``
+7. Run ``pip install explorepy`` to install ``explorepy`` from PyPI.
 
 Ubuntu
 ^^^^^^
-1. From Linux Terminal, run these commands one by one: ``sudo apt-get install libbluetooth-dev`` and ``sudo apt-get install build-essential`` and ``conda install -c conda-forge liblsl``.
+1. From the terminal, run these commands one by one: ``sudo apt-get install libbluetooth-dev`` and ``sudo apt-get install build-essential``.
 2. We recommend installing Anaconda. Download and installer `Anaconda<https://www.anaconda.com/download>`/Miniconda/.
 3. We recommend using a virtual environment in Conda. To do this:
 
-   a. In Conda command prompt: ``conda create -n myenv python=3.10``
-   b. Activate the virtual environment: ``conda activate myenv``
+   a. In the Anaconda command prompt: ``conda create -n myenv python=3.12``
+   b. Activate the conda environment: ``conda activate myenv``
 
 4. Upgrade your pip: ``python -m pip install --upgrade pip``
-5. Run: ``pip install explorepy``, to install ``explorepy`` from PyPI.
-6. From Linux Terminal, run: ``sudo apt install libxcb-cursor0``
+5. Install liblsl: ``conda install -c conda-forge liblsl``
+6. Run ``pip install explorepy`` to install ``explorepy`` from PyPI.
+7. From the terminal, run: ``sudo apt install libxcb-cursor0``
 
 Set up USB streaming in Linux
-"""""""""""""""""""""""""""""
++++++++++++++++++++++++++++++
+
 a. Set up ``udev`` rules for appropiate permission to ``/dev/ttyACM*`` in Linux
 
     *Steps to Execute the Udev Script Manually*
@@ -108,29 +115,33 @@ b. Alternate method: Temporarily granting appropriate permissions to ``/dev/ttyA
     1. Identify the device (ttyACM0, ttyACM1, ttyACM2, etc) in ``/dev`` directory
 
 
-    2. Execute this command in the terminal (replcae * with appropiate id) ::
+    2. Execute this command in the terminal (replace * with appropiate id) ::
 
             chmod 666 /dev/ttyACM*
 
 Mac
 ^^^
 1. Install ``XCode`` from the Mac App store. For this, you may need to upgrade to the latest version of MacOS. For older versions of MacOS, find compatible versions of ``XCode`` `here <https://en.wikipedia.org/wiki/Xcode>`_. All old ``XCode`` versions are available `here <https://developer.apple.com/download/more/>`_.
-2. Accept the license agreement: ``sudo xcodebuild -license``
-3. Download and installer `Anaconda<https://www.anaconda.com/download>`/Miniconda/.
-4. We recommend using a virtual environment in Conda.
+2. Accept the license agreement: ``sudo xcodebuild -license``.
+3. It is best to install Anaconda. Download  and run the `Anaconda installer for Mac <https://www.anaconda.com/download/success>`_. For older versions of MacOS, compatible version of Anaconda can be found in `this table <https://docs.continuum.io/anaconda/install/#old-os>`_ and downloaded `here <https://repo.anaconda.com/archive/index.html>`_.
+4. We recommend using a conda environment.
 
-   a. In Conda command prompt: ``conda create -n myenv python=3.10``
-   b. Activate the virtual environment: ``conda activate myenv``
+   a. In the Anaconda command prompt: ``conda create -n myenv python=3.10``
+   b. Activate the conda environment: ``conda activate myenv``
 
 5. Upgrade your pip: ``python -m pip install --upgrade pip``
-6. Run: ``pip install explorepy``, to install ``explorepy`` from PyPI.
-7. Connect your Explore device from Mac Bluetooth menu and run your Python script.
+6. Install liblsl: ``conda install -c conda-forge liblsl``
+7. Run ``pip install explorepy`` to install ``explorepy`` from PyPI.
+8. Connect your Explore device from the Bluetooth menu and run your Python script.
+
 
 Quick test
 ----------
 
-* Open the Conda command prompt (if you used pip) or Windows command prompt (if you used the installable file).
-* Activate the virtual environment (this step is only necessary in the Conda command prompt): ``conda activate myenv``
+*Note: If you installed the graphical user interface ExploreDesktop as outlined above, explorepy won't be available from the command line.*
+
+* Open the Anaconda command prompt.
+* Activate the virtual environment that you made before installing explorepy: ``conda activate myenv``
 * Run ``explorepy acquire -n DEVICE-NAME``
 * To stop the command execution, press ``Ctrl+C``
 

diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -8,6 +8,7 @@ pylsl==1.16.1
 PyYAML==6.0.1
 PyYAML==6.0.1
 scipy==1.11.1
-sentry_sdk==1.19.1
+tornado==6.4.1
+sentry_sdk==2.8.0
 sphinx-rtd-theme==1.3.0
 sphinx==7.2.4
diff --git a/examples/marker_example.py b/examples/marker_example.py
@@ -17,7 +17,7 @@ def main():
     interval = 2
 
     for i in range(n_markers):
-        explore.set_marker(code=i)
+        explore.set_marker(str(i))
         time.sleep(interval)
 
     explore.stop_recording()

diff --git a/examples/markers_examples/send_8_bit_marker_during_connection_example.py b/examples/markers_examples/send_8_bit_marker_during_connection_example.py
@@ -0,0 +1,15 @@
+import explorepy
+import time
+
+# at first, set correct bt interface! Possible interface options are 'ble' and 'usb'
+explorepy.set_bt_interface('ble')
+
+exp_device = explorepy.Explore()
+exp_device.connect('Explore_AAAC')
+exp_device.record_data(file_name='AAAC', duration=30, file_type='csv')
+n_markers = 20
+interval = 2
+for i in range(n_markers):
+        exp_device.send_8_bit_trigger(i)
+        time.sleep(2)
+
diff --git a/examples/markers_examples/send_8_bit_marker_independently.py b/examples/markers_examples/send_8_bit_marker_independently.py
@@ -0,0 +1,12 @@
+import explorepy
+import time
+
+# for independent markers to be stored only in binary file, we only need to instantiate Explore class!
+exp_device = explorepy.Explore()
+
+n_markers = 20
+interval = 2
+for i in range(n_markers):
+        exp_device.send_8_bit_trigger(i)
+        time.sleep(2)
+
diff --git a/examples/mne_raw_format_from_csv.py b/examples/mne_raw_format_from_csv.py
@@ -0,0 +1,34 @@
+import pandas as pd
+import mne
+import matplotlib.pyplot as plt
+from mne import export
+
+
+def create_mne_raw_format(file_name, channel_number):
+    file_name_root = file_name.split('.')[0][:-4]
+
+    sampling_freq = pd.read_csv(file_name_root + '_Meta.csv', delimiter=',')['sr'][0]
+
+    # Create some dummy metadata
+    n_channels = channel_number
+    ch_types = ["eeg"] * n_channels
+    info = mne.create_info(len(ch_types), sfreq=sampling_freq, ch_types=ch_types)
+
+    data_frame = pd.read_csv(file_name, delimiter=',')
+    data_frame = data_frame.drop('TimeStamp', axis = 1)
+    # convert to volt, because MNE expects data in Volt unit
+    data_frame = data_frame.div(1e6)
+    data_frame = data_frame.transpose()
+    raw_data = mne.io.RawArray(data_frame, info).notch_filter(freqs=50)
+    raw_data.plot(show_scrollbars=True, show_scalebars=True, remove_dc=True, highpass=1, lowpass=40)
+    plt.show()
+    return raw_data
+
+def explort_eeglab_format(raw_input_df, output_file_name):
+    export.export_raw(output_file_name, raw_input_df,
+                      fmt='eeglab',
+                      overwrite=True, physical_range=[-400000, 400000])
+
+
+raw_df = create_mne_raw_format(file_name='chr180924_ExG.csv', channel_number=8)
+explort_eeglab_format(output_file_name='output_edf.edf', raw_input_df=raw_df)