braindecode 0.1.2__tar.gz → 0.1.3__tar.gz

{Braindecode-0.1.2 → Braindecode-0.1.3}/Braindecode.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: Braindecode
-Version: 0.1.2
+Version: 0.1.3
 Summary: A deep learning for raw time-domain EEG decoding toolbox.
 Home-page: https://github.com/robintibor/braindecode
 Author: Robin Tibor Schirrmeister
@@ -17,7 +17,14 @@ Description: Note: The old braindecode repository has been moved to
         Installation
         ============
         
-        Install pytorch from http://pytorch.org/.
+        First, install pytorch from http://pytorch.org/.
+        
+        Then, install braindecode via pip:
+        
+        .. code-block:: bash
+        
+          pip install braindecode
+        
         
         Documentation
         =============

{Braindecode-0.1.2 → Braindecode-0.1.3}/Braindecode.egg-info/SOURCES.txt

@@ -1,6 +1,6 @@
 LICENSE.txt
 MANIFEST.in
-README.md
+README.rst
 setup.py
 Braindecode.egg-info/PKG-INFO
 Braindecode.egg-info/SOURCES.txt
@@ -9,12 +9,11 @@ Braindecode.egg-info/not-zip-safe
 Braindecode.egg-info/requires.txt
 Braindecode.egg-info/top_level.txt
 braindecode/__init__.py
-braindecode/iterators.py
-braindecode/splitters.py
-braindecode/trial_segment.py
 braindecode/util.py
-braindecode/datasets/__init__.py
-braindecode/datasets/signal_target.py
+braindecode/datautils/__init__.py
+braindecode/datautils/iterators.py
+braindecode/datautils/signal_target.py
+braindecode/datautils/splitters.py
 braindecode/experiments/__init__.py
 braindecode/experiments/experiment.py
 braindecode/experiments/monitors.py
@@ -31,7 +30,7 @@ docs/Makefile
 docs/conf.py
 docs/index.rst
 docs/notebooks/TrialWise_Decoding.ipynb
-docs/source/braindecode.datasets.rst
+docs/source/braindecode.datautils.rst
 docs/source/braindecode.experiments.rst
 docs/source/braindecode.models.rst
 docs/source/braindecode.rst

{Braindecode-0.1.2 → Braindecode-0.1.3}/MANIFEST.in

@@ -1,4 +1,4 @@
-include README.md
+include README.rst
 include LICENSE.txt
 
 recursive-include docs *.ipynb *.rst conf.py Makefile

{Braindecode-0.1.2 → Braindecode-0.1.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 1.1
 Name: Braindecode
-Version: 0.1.2
+Version: 0.1.3
 Summary: A deep learning for raw time-domain EEG decoding toolbox.
 Home-page: https://github.com/robintibor/braindecode
 Author: Robin Tibor Schirrmeister
@@ -17,7 +17,14 @@ Description: Note: The old braindecode repository has been moved to
         Installation
         ============
         
-        Install pytorch from http://pytorch.org/.
+        First, install pytorch from http://pytorch.org/.
+        
+        Then, install braindecode via pip:
+        
+        .. code-block:: bash
+        
+          pip install braindecode
+        
         
         Documentation
         =============

Braindecode-0.1.2/README.md → Braindecode-0.1.3/README.rst

@@ -9,7 +9,14 @@ A deep learning for raw time-domain EEG decoding toolbox.
 Installation
 ============
 
-Install pytorch from http://pytorch.org/.
+First, install pytorch from http://pytorch.org/.
+
+Then, install braindecode via pip:
+
+.. code-block:: bash
+
+  pip install braindecode
+
 
 Documentation
 =============

{Braindecode-0.1.2 → Braindecode-0.1.3}/braindecode/experiments/experiment.py

@@ -1,10 +1,11 @@
-from collections import OrderedDict
 import logging
+import numpy as np
+from collections import OrderedDict
 from copy import deepcopy
+
 import pandas as pd
-import numpy as np
 
-from braindecode.splitters import concatenate_sets
+from braindecode.datautils.splitters import concatenate_sets
 from braindecode.experiments.stopcriteria import MaxEpochs, ColumnBelow, Or
 from braindecode.torchext.util import np_to_var, set_random_seeds
 

{Braindecode-0.1.2 → Braindecode-0.1.3}/docs/Makefile

@@ -17,9 +17,6 @@ help:
 apidoc:
 	sphinx-apidoc -o source ../braindecode/
 
-livehtml:
-	sphinx-autobuild -b html  . _build/html
-
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile

{Braindecode-0.1.2 → Braindecode-0.1.3}/docs/conf.py

@@ -45,7 +45,7 @@ extensions = ['sphinx.ext.autodoc',
     'nbsphinx',
 ]
 
-exclude_patterns = ['_build', '**.ipynb_checkpoints']
+exclude_patterns = ['_build', '**.ipynb_checkpoints/**']
  
 napoleon_google_docstring = False
 napoleon_use_param = False

{Braindecode-0.1.2 → Braindecode-0.1.3}/docs/index.rst

@@ -1,19 +1,20 @@
-.. Braindecode documentation master file, created by
-   sphinx-quickstart on Sat Jul  1 01:51:38 2017.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
 Welcome to Braindecode
 =======================================
 
-
-
-Some simple explanation!?!
+**Under construction**
+A deep learning for raw time-domain EEG decoding toolbox.
 
 
 Installation
 =======================================
-Well something how to install it, right?
+
+First, install pytorch from http://pytorch.org/.
+
+Then, install braindecode via pip:
+
+.. code-block:: bash
+
+  pip install braindecode
 
 
 Tutorials

{Braindecode-0.1.2 → Braindecode-0.1.3}/docs/notebooks/TrialWise_Decoding.ipynb

@@ -5,6 +5,8 @@
    "execution_count": 1,
    "metadata": {
     "collapsed": true,
+    "deletable": true,
+    "editable": true,
     "nbsphinx": "hidden"
    },
    "outputs": [],
@@ -17,14 +19,20 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "# Trialwise Decoding"
    ]
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "In this example, we will use a convolutional neural network on the [Physiobank EEG Motor Movement/Imagery Dataset](https://www.physionet.org/physiobank/database/eegmmidb/) to decode two classes:\n",
     "\n",
@@ -50,7 +58,10 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "You can use any way to load your EEG dataset, here we will use the [python-mne](https://www.martinos.org/mne/stable/index.html) library. For a tutorial from mne using Common Spatial Patterns to decode this data, see [here](http://martinos.org/mne/stable/auto_examples/decoding/plot_decoding_csp_eeg.html)."
    ]
@@ -110,14 +121,20 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "## Convert data to Braindecode Format"
    ]
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "Braindecode has a minimalistic ```SignalAndTarget``` class, with attributes `X` for the signal and `y` for the labels. For trialwise decoding, X should have these dimensions: trials x channels x timesteps."
    ]
@@ -141,7 +158,10 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "We use the first 60 trials for training and the last 30 for testing."
    ]
@@ -156,7 +176,7 @@
    },
    "outputs": [],
    "source": [
-    "from braindecode.datasets.signal_target import SignalAndTarget\n",
+    "from braindecode.datautils.signal_target import SignalAndTarget\n",
     "from braindecode.torchext.util import set_random_seeds\n",
     "\n",
     "train_set = SignalAndTarget(X[:60], y=y[:60])\n",
@@ -165,14 +185,20 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "## Create the model"
    ]
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "Braindecode comes with some predefined convolutional neural network architectures for raw time-domain EEG. here, we use the shallow ConvNet model from [Deep learning with convolutional neural networks for brain mapping and decoding of movement-related information from the human EEG](https://arxiv.org/abs/1703.05051)."
    ]
@@ -205,7 +231,10 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "We use [Adam](https://arxiv.org/abs/1412.6980) to optimize the parameters of our network."
    ]
@@ -227,14 +256,20 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "## Training loop"
    ]
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "This is a conventional stochastic gradient descent training loop:\n",
     "1. Get randomly shuffled batches of trials\n",
@@ -411,7 +446,7 @@
    ],
    "source": [
     "from braindecode.torchext.util import np_to_var, var_to_np\n",
-    "from braindecode.iterators import get_balanced_batches\n",
+    "from braindecode.datautils.iterators import get_balanced_batches\n",
     "import torch.nn.functional as F\n",
     "from numpy.random import RandomState\n",
     "rng = RandomState((2017,6,30))\n",
@@ -460,21 +495,30 @@
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "Eventually, we arrive at 63.3% accuracy, so 19 from 30 trials are correctly predicted. See in the next tutorial, how we can achieve better accuracies using cropped training."
    ]
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     "## Dataset References\n"
    ]
   },
   {
    "cell_type": "markdown",
-   "metadata": {},
+   "metadata": {
+    "deletable": true,
+    "editable": true
+   },
    "source": [
     " This dataset was created and contributed to PhysioNet by the developers of the [BCI2000](http://www.schalklab.org/research/bci2000) instrumentation system, which they used in making these recordings. The system is described in:\n",
     " \n",

Braindecode-0.1.3/docs/source/braindecode.datautils.rst

@@ -0,0 +1,38 @@
+braindecode\.datautils package
+==============================
+
+Submodules
+----------
+
+braindecode\.datautils\.iterators module
+----------------------------------------
+
+.. automodule:: braindecode.datautils.iterators
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+braindecode\.datautils\.signal\_target module
+---------------------------------------------
+
+.. automodule:: braindecode.datautils.signal_target
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+braindecode\.datautils\.splitters module
+----------------------------------------
+
+.. automodule:: braindecode.datautils.splitters
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: braindecode.datautils
+    :members:
+    :undoc-members:
+    :show-inheritance:

Braindecode-0.1.3/docs/source/braindecode.rst

@@ -0,0 +1,32 @@
+braindecode package
+===================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    braindecode.datautils
+    braindecode.experiments
+    braindecode.models
+    braindecode.torchext
+
+Submodules
+----------
+
+braindecode\.util module
+------------------------
+
+.. automodule:: braindecode.util
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: braindecode
+    :members:
+    :undoc-members:
+    :show-inheritance:

{Braindecode-0.1.2 → Braindecode-0.1.3}/setup.py

@@ -5,7 +5,7 @@ from os import path
 here = path.abspath(path.dirname(__file__))
 
 # Get the long description from the relevant file
-with open(path.join(here, 'README.md'), encoding='utf-8') as f:
+with open(path.join(here, 'README.rst'), encoding='utf-8') as f:
     long_description = f.read()
 
 
@@ -15,7 +15,7 @@ setup(
     # Versions should comply with PEP440.  For a discussion on single-sourcing
     # the version across setup.py and the project code, see
     # http://packaging.python.org/en/latest/tutorial.html#version
-    version='0.1.2',
+    version='0.1.3',
 
     description='A deep learning for raw time-domain EEG decoding toolbox.',
     long_description=long_description,  #this is the

Braindecode-0.1.2/braindecode/trial_segment.py

@@ -1,198 +0,0 @@
-import logging
-import numpy as np
-import xarray as xr
-
-log = logging.getLogger(__name__)
-
-
-def create_target_series(cnt, marker_def, ival):
-    """
-    Compute one-hot encoded target series.
-    Parameters
-    ----------
-    cnt : DateArray
-    marker_def: OrderedDict (str -> list int)
-        Dictionary mapping class names -> list of marker codes. Order of keys
-         is used to determine indices of classes in one-hot encoded result. 
-    ival : (number, number) tuple
-        Segmentation interval for each trial.
-    Returns
-    -------
-    2darray
-        One-hot encoded target series.
-
-    """
-    assert 'fs' in cnt.attrs
-    assert 'events' in cnt.attrs
-    assert ival[0] < ival[1]
-    sample_ival = cnt.attrs['fs'] * np.array(ival) / 1000.0
-    sample_ival = np.int32(np.round(sample_ival))
-    assert sample_ival[0] < sample_ival[1]
-
-
-    class_names = marker_def.keys()
-    targets = np.zeros((len(cnt.data), len(class_names)), dtype=np.int32)
-    for i_sample, m in cnt.attrs['events']:
-        for class_idx, classname in enumerate(class_names):
-            if m in marker_def[classname]:
-                start_index = i_sample + sample_ival[0]
-                stop_index = i_sample + sample_ival[1]
-                assert stop_index > start_index
-                if start_index >= 0 and stop_index <= len(cnt.coords['time']):
-                    targets[start_index:stop_index, class_idx] = 1
-                elif start_index < 0:
-                    log.warn("Ignoring trial, start index < 0: {:d}".format(
-                        start_index))
-                else:
-                    assert stop_index > len(cnt.coords['time'])
-                    log.warn("Ignoring trial, start index > n_samples:"
-                        "{:d} > {:d} ".format(
-                        stop_index, len(cnt.coords['time'])))
-    return targets
-
-
-def compute_trial_start_stop_samples(y, check_trial_lengths_equal=True,
-                                    input_time_length=None):
-    """Computes trial start and end samples (end is inclusive) from
-    one-hot encoded y-matrix.
-    Specify input time length to kick out trials that are too short after
-    signal start.
-
-    Parameters
-    ----------
-    y : 2darray
-    check_trial_lengths_equal : bool
-         (Default value = True)
-    input_time_length : int, optional
-         (Default value = None)
-
-    Returns
-    -------
-
-    """
-    #TODO: change to start stop
-    trial_part = np.sum(y, 1) == 1
-    boundaries = np.diff(trial_part.astype(np.int32))
-    i_trial_starts = np.flatnonzero(boundaries == 1) + 1
-    i_trial_stops = np.flatnonzero(boundaries == -1) + 1
-    # it can happen that a trial is only partially there since the
-    # cnt signal was split in the middle of a trial
-    # for now just remove these
-    # use that start marker should always be before or equal to end marker
-    if i_trial_starts[0] >= i_trial_stops[0]:
-        # cut out first trial which only has end marker
-        i_trial_stops = i_trial_stops[1:]
-    if i_trial_starts[-1] >= i_trial_stops[-1]:
-        # cut out last trial which only has start marker
-        i_trial_starts = i_trial_starts[:-1]
-
-    assert (len(i_trial_starts) == len(i_trial_stops))
-    assert (np.all(i_trial_starts < i_trial_stops))
-    # possibly remove first trials if they are too early
-    if input_time_length is not None:
-        while i_trial_starts[0] < (input_time_length - 1):
-            i_trial_starts = i_trial_starts[1:]
-            i_trial_stops = i_trial_stops[1:]
-    if check_trial_lengths_equal:
-        # just checking that all trial lengths are equal
-        all_trial_lens = np.array(i_trial_stops) - np.array(i_trial_starts)
-        assert all(all_trial_lens == all_trial_lens[0]), (
-            "All trial lengths should be equal...")
-    return i_trial_starts, i_trial_stops
-
-
-def segment_dat(cnt, marker_def, ival):
-    """Convert a continuous data object to an epoched one.
-
-    Given a continuous data object, a definition of classes, and an
-    interval, this method looks for markers as defined in ``marker_def``
-    and slices the dat according to the time interval given with
-    ``ival`` along the ``timeaxis``. The returned ``dat`` object stores
-    those slices and the class each slice belongs to.
-
-    Epochs that are too close to the borders and thus too short are
-    ignored.
-
-    If the segmentation does not result in any epochs (i.e. the markers
-    in ``marker_def`` could not be found in ``dat``, the resulting
-    epo.data will be an empty array.
-
-    This method is also suitable for **online processing**, please read
-    the documentation for the ``newsamples`` parameter and have a look
-    at the Examples below.
-
-    Parameters
-    ----------
-    dat : Data
-        the data object to be segmented
-    marker_def : dict
-        The keys are class names, the values are lists of markers
-    ival : [int, int]
-        The interval in milliseconds to cut around the markers. I.e. to
-        get the interval starting with the marker plus the remaining
-        100ms define the interval like [0, 100]. The start point is
-        included, the endpoint is not (like: ``[start, end)``).  To get
-        200ms before the marker until 100ms after the marker do:
-        ``[-200, 100]`` Only negative or positive values are possible
-        (i.e. ``[-500, -100]``)
-
-    Returns
-    -------
-    epo : Data
-        a copy of the resulting epoched data.
-
-    Raises
-    ------
-    AssertionError
-        * if ``dat`` has not ``.fs`` or ``.markers`` attribute or if
-          ``ival[0] > ival[1]``.
-
-    Examples
-    --------
-
-    Offline Experiment
-
-    >>> # Define the markers belonging to class 1 and 2
-    >>> md = {'class 1': ['S1', 'S2'],
-    ...       'class 2': ['S3', 'S4']
-    ...      }
-    >>> # Epoch the data -500ms and +700ms around the markers defined in
-    >>> # md
-    >>> epo = segment_dat(cnt, md, [-500, 700])
-
-    """
-
-    assert 'fs' in cnt.attrs
-    assert 'events' in cnt.attrs
-    y = create_target_series(cnt, marker_def, ival=ival)
-    # Create classes per trial
-    # and sample inds per trial from the target series
-    starts, stops = compute_trial_start_stop_samples(y)
-    classes = [np.argmax(y[i_s]) for i_s in starts]
-    sample_inds_per_trial = [list(range(i_start, i_stop))
-                             for (i_start, i_stop) in zip(starts, stops)]
-
-    if len(sample_inds_per_trial) == 0:
-        assert "No epochs not tested yet"
-        data = np.array([])
-    else:
-        timeaxis = list(cnt.dims).index('time')
-        # np.take inserts a new dimension at `axis`...
-        data = cnt.data.take(sample_inds_per_trial, axis=timeaxis)
-        # we want that new dimension at axis 0 so we have to swap it.
-        # before that we have to convert the negative axis indices to
-        # their equivalent positive one, otherwise swapaxis will be one
-        # off.
-        data = data.swapaxes(0, timeaxis)
-    time = np.linspace(ival[0], ival[1],
-                       data.shape[1], # assume timeaxis now on 1
-                       endpoint=False)
-    epo = xr.DataArray(data,
-                       coords={'trials': classes, 'time': time,
-                               'channels': cnt.channels,},
-                       dims=('trials', 'time','channels',))
-    epo.attrs = cnt.attrs.copy()
-    # remove events part
-    epo.attrs.pop('events')
-    return epo
-

Braindecode-0.1.2/docs/source/braindecode.datasets.rst

@@ -1,22 +0,0 @@
-braindecode\.datasets package
-=============================
-
-Submodules
-----------
-
-braindecode\.datasets\.signal\_target module
---------------------------------------------
-
-.. automodule:: braindecode.datasets.signal_target
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: braindecode.datasets
-    :members:
-    :undoc-members:
-    :show-inheritance:

Braindecode-0.1.2/docs/source/braindecode.rst

@@ -1,56 +0,0 @@
-braindecode package
-===================
-
-Subpackages
------------
-
-.. toctree::
-
-    braindecode.datasets
-    braindecode.experiments
-    braindecode.models
-    braindecode.torchext
-
-Submodules
-----------
-
-braindecode\.iterators module
------------------------------
-
-.. automodule:: braindecode.iterators
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-braindecode\.splitters module
------------------------------
-
-.. automodule:: braindecode.splitters
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-braindecode\.trial\_segment module
-----------------------------------
-
-.. automodule:: braindecode.trial_segment
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-braindecode\.util module
-------------------------
-
-.. automodule:: braindecode.util
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: braindecode
-    :members:
-    :undoc-members:
-    :show-inheritance: