Refactor lsl stream (#326)

* add first rmap and CEBRA example

* add example cebra

* rm files not available in main

* Minor changes on top of mne_lsl merge

* refactor

* converted lsl example to .py file, shortend lsl tests ,added testing for lsl

* add pypandoc install

* add pypandoc to gitignore

* adjustments in tests and changes in stream naming and stream auto detection

* player not auto creating raw file when running

* changed naming of player stream, debugging

* added test for lsl data

* debug data test

* Cleanup test

* Update nm_stream_offline.py

merge imports

Co-Authored-By: Toni M. Brotons <10654467+toni-neurosc@users.noreply.github.com>

* Update nm_mnelsl_stream.py

Added keyword for LSLStream wait till disconnect

* changes in imports in tests, added docstrings in functions, added channel type as param for player

* fix bug pandoc sphinx build

* embedd html example link

* adapt LSL example

* add sphinx-gallery embedded CEBRA example

* modify path for GH Actions documentation

* delete dead code, change np.array_equal to np.allclose

* fix path issue for running LSL documentation

* change naming in lsl player, fixture for lsl player and lsl test

* add thumbnail dor documentation

* Add sleep command to not hog cpu

* add support for raw files/paths/ data,sfreq in player

* Update nm_IO.py - delete unused params in get bids data

* fix read_BIDS unused parameters

* Update __init__.py - fix matplotlib backend for mac

* Update __init__.py fix import

* fix platform import

* fix platform import

---------

Co-authored-by: timonmerk <timon.merk@charite.de>
Co-authored-by: Antonio Martinez Brotons <10654467+toni-neurosc@users.noreply.github.com>
Co-authored-by: Samed Rouven Vossberg <57455873+MateGram@users.noreply.github.com>
Co-authored-by: timonmerk <timon.merk95@gmail.com>

.gitignore

@@ -149,6 +149,8 @@ docs/source/data/*
 
 examples/data/derivatives/*
 examples/other_examples/*
+examples/plot_7_lsl_example.ipynb
+examples/lange_n8.ipynb
 
 examples/sub/*
 examples/utils/*
@@ -164,6 +166,16 @@ py_neuromodulation/ConnectivityDecoding/connectome_folder/*
 
 plot_0_first_demo.py
 plot_1_example_BIDS.py
+temp_raw.fif
 
 requirements.lock
-requirements-dev.lock
+requirements-dev.lock
+
+docs/source/bin/pandoc
+
+docs/source/sg_execution_times.rst
+
+figures_ucsf/*
+catboost_info/*
+out_per
+.DS_Store

docs/source/api_documentation.rst

@@ -25,7 +25,6 @@ Feature Estimation
 .. toctree::
    :maxdepth: 4
 
-   nm_features_abc
    nm_features
    nm_filter
    nm_oscillatory
@@ -50,5 +49,3 @@ Analysis
    nm_plots
    nm_RMAP
    nm_stats
-   nm_cohortwrapper
-   nm_across_patient_decoding

docs/source/conf.py

@@ -18,7 +18,9 @@
 SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
 if os.path.basename(SCRIPT_DIR) == "source":
     # this check is necessary, so we can also run the script from the root directory
-    SCRIPT_DIR = os.path.join(os.path.dirname(os.path.dirname(SCRIPT_DIR)), "py_neuromodulation")
+    SCRIPT_DIR = os.path.join(
+        os.path.dirname(os.path.dirname(SCRIPT_DIR)), "py_neuromodulation"
+    )
 print(f"Script Directory to add: {SCRIPT_DIR}")
 sys.path.append(SCRIPT_DIR)
 
@@ -29,40 +31,44 @@
 
 
 # -- Project information -----------------------------------------------------
-project = 'py_neuromodulation'
-copyright = '2021, Timon Merk'
-author = 'Timon Merk'
+project = "py_neuromodulation"
+copyright = "2021, Timon Merk"
+author = "Timon Merk"
 
 source_parsers = {
-    '.md': 'recommonmark.parser.CommonMarkParser',
+    ".md": "recommonmark.parser.CommonMarkParser",
 }
 
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.autosectionlabel',
-    'sphinx_gallery.gen_gallery',
-    'sphinx_togglebutton',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.autosectionlabel",
+    "sphinx_gallery.gen_gallery",
+    "sphinx_togglebutton",
+    # "nbsphinx",
 ]
 
-source_suffix = ['.rst', '.md', ]
+source_suffix = [
+    ".rst",
+    ".md",
+]
 
 autosummary_generate = True
 
-PYDEVD_DISABLE_FILE_VALIDATION=1
+PYDEVD_DISABLE_FILE_VALIDATION = 1
 
 sphinx_gallery_conf = {
     "examples_dirs": "../../examples",
     "gallery_dirs": "auto_examples",
-    "within_subsection_order" : sphinx_gallery.sorting.FileNameSortKey,
+    "within_subsection_order": sphinx_gallery.sorting.FileNameSortKey,
 }
 
-#sphinx_gallery_conf = {
+# sphinx_gallery_conf = {
 #    "examples_dirs": "../../examples",
 #    "gallery_dirs": "auto_examples",
 #    #'plot_gallery': True,
@@ -71,14 +77,14 @@
 #    'show_memory': True,
 #    'notebook_images': 'https://py-neuromodulation.readthedocs.io/en/latest/',
 #    'default_thumb_file': os.path.join('_static', 'RMAP_figure.png'),
-#}
+# }
 
 templates_path = ["_templates"]
 exclude_patterns = []
 
 
 html_theme = "pydata_sphinx_theme"
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 html_theme_options = {
     "show_nav_level": 4,
@@ -100,6 +106,5 @@
     "matplotlib": ("https://matplotlib.org/stable", None),
     "numba": ("https://numba.readthedocs.io/en/latest", None),
     "mne": ("https://mne.tools/stable", None),
-    "pandas" : ("https://pandas.pydata.org/docs", None),
+    "pandas": ("https://pandas.pydata.org/docs", None),
 }
-

docs/source/sg_execution_times.rst

@@ -0,0 +1,61 @@
+
+:orphan:
+
+.. _sphx_glr_sg_execution_times:
+
+
+Computation times
+=================
+**00:25.522** total execution time for 9 files **from all galleries**:
+
+.. container::
+
+  .. raw:: html
+
+    <style scoped>
+    <link href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/5.3.0/css/bootstrap.min.css" rel="stylesheet" />
+    <link href="https://cdn.datatables.net/1.13.6/css/dataTables.bootstrap5.min.css" rel="stylesheet" />
+    </style>
+    <script src="https://code.jquery.com/jquery-3.7.0.js"></script>
+    <script src="https://cdn.datatables.net/1.13.6/js/jquery.dataTables.min.js"></script>
+    <script src="https://cdn.datatables.net/1.13.6/js/dataTables.bootstrap5.min.js"></script>
+    <script type="text/javascript" class="init">
+    $(document).ready( function () {
+        $('table.sg-datatable').DataTable({order: [[1, 'desc']]});
+    } );
+    </script>
+
+  .. list-table::
+   :header-rows: 1
+   :class: table table-striped sg-datatable
+
+   * - Example
+     - Time
+     - Mem (MB)
+   * - :ref:`sphx_glr_auto_examples_plot_7_lsl_example.py` (``..\..\examples\plot_7_lsl_example.py``)
+     - 00:25.497
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_plot_8_cebra_example.py` (``..\..\examples\plot_8_cebra_example.py``)
+     - 00:00.025
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_plot_0_first_demo.py` (``..\..\examples\plot_0_first_demo.py``)
+     - 00:00.000
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_plot_1_example_BIDS.py` (``..\..\examples\plot_1_example_BIDS.py``)
+     - 00:00.000
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_plot_2_example_add_feature.py` (``..\..\examples\plot_2_example_add_feature.py``)
+     - 00:00.000
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_plot_3_example_sharpwave_analysis.py` (``..\..\examples\plot_3_example_sharpwave_analysis.py``)
+     - 00:00.000
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_plot_4_example_gridPointProjection.py` (``..\..\examples\plot_4_example_gridPointProjection.py``)
+     - 00:00.000
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_plot_5_example_rmap_computing.py` (``..\..\examples\plot_5_example_rmap_computing.py``)
+     - 00:00.000
+     - 0.0
+   * - :ref:`sphx_glr_auto_examples_plot_6_real_time_demo.py` (``..\..\examples\plot_6_real_time_demo.py``)
+     - 00:00.000
+     - 0.0

examples/README.rst

@@ -2,4 +2,3 @@
 
 Examples
 ========
-