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<section id="module-wonambi.trans.select">
<span id="wonambi-trans-select-module"></span><h1>wonambi.trans.select module<a class="headerlink" href="#module-wonambi.trans.select" title="Permalink to this heading"></a></h1>
<p>Module to select periods of interest, based on number of trials or any of
the axes.</p>
<p>There is some overlap between Select and the Data.__call__(). The main
difference is that Select takes an instance of Data as input and returns
another instance of Data as output, whil Data.__call__() returns the actual
content of the data.</p>
<p>Select should be as flexible as possible. There are quite a few cases, which
will be added as we need them.</p>
<dl class="py class">
<dt class="sig sig-object py" id="wonambi.trans.select.Segments">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">wonambi.trans.select.</span></span><span class="sig-name descname"><span class="pre">Segments</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/trans/select.html#Segments"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.trans.select.Segments" title="Permalink to this definition">��</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Class containing a set of data segments for analysis, with metadata.
Only contains metadata until .read_data is called.</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="wonambi.trans.select.Segments.dataset">
<span class="sig-name descname"><span class="pre">dataset</span></span><a class="headerlink" href="#wonambi.trans.select.Segments.dataset" title="Permalink to this definition"></a></dt>
<dd><p>metadata for the associated record</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>instance of wonambi.dataset</p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="wonambi.trans.select.Segments.segments">
<span class="sig-name descname"><span class="pre">segments</span></span><a class="headerlink" href="#wonambi.trans.select.Segments.segments" title="Permalink to this definition"></a></dt>
<dd><p>chronological list of segment metadata. Each segment dict contains info
about start and end times, stage, cycle, channel and event name, if
applicable. Once read_data is called, the signal data are added to each
segment dictionary under ‘data’.</p>
<dl class="field-list simple">
<dt class="field-odd">Type<span class="colon">:</span></dt>
<dd class="field-odd"><p>list of dict</p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="wonambi.trans.select.Segments.read_data">
<span class="sig-name descname"><span class="pre">read_data</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">chan</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_chan</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">[]</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">grp_name</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">concat_chan</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">average_channels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_s_freq</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">30000</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">parent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/trans/select.html#Segments.read_data"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.trans.select.Segments.read_data" title="Permalink to this definition"></a></dt>
<dd><p>Read data for analysis. Adds data as ‘data’ in each dict.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>chan</strong> (<em>list</em><em> of </em><em>str</em>) – active channel names as they appear in record, without ref or group
If given an empty list, the channel specified in seg[‘chan’] will
be read for each segment</p></li>
<li><p><strong>ref_chan</strong> (<em>list</em><em> of </em><em>str</em>) – reference channel names as they appear in record, without group</p></li>
<li><p><strong>grp_name</strong> (<em>str</em>) – name of the channel group, required in GUI</p></li>
<li><p><strong>concat_chan</strong> (<em>bool</em>) – if True, data from all channels will be concatenated</p></li>
<li><p><strong>average_channels</strong> (<em>bool</em>) – if True, all channels will be averaged into a single virtual
channel with label ‘avg_chan’</p></li>
<li><p><strong>max_s_freq</strong> (<em>: int</em>) – maximum sampling frequency</p></li>
<li><p><strong>parent</strong> (<em>QWidget</em>) – for GUI only. Identifies parent widget for display of progress
dialog.</p></li>
</ul>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="wonambi.trans.select.fetch">
<span class="sig-prename descclassname"><span class="pre">wonambi.trans.select.</span></span><span class="sig-name descname"><span class="pre">fetch</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">annot</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cat</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">(0,</span> <span class="pre">0,</span> <span class="pre">0,</span> <span class="pre">0)</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evt_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stage</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cycle</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chan_full</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">epoch</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">epoch_dur</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">30</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">epoch_overlap</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">epoch_step</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reject_epoch</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reject_artf</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">min_dur</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">buffer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/trans/select.html#fetch"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.trans.select.fetch" title="Permalink to this definition"></a></dt>
<dd><p>Create instance of Segments for analysis, complete with info about
stage, cycle, channel, event type. Segments contains only metadata until
.read_data is called.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>dataset</strong> (<em>instance</em><em> of </em><a class="reference internal" href="wonambi.dataset.html#wonambi.dataset.Dataset" title="wonambi.dataset.Dataset"><em>Dataset</em></a>) – info about record</p></li>
<li><p><strong>annot</strong> (<em>instance</em><em> of </em><a class="reference internal" href="wonambi.attr.annotations.html#wonambi.attr.annotations.Annotations" title="wonambi.attr.annotations.Annotations"><em>Annotations</em></a>) – scoring info</p></li>
<li><p><strong>cat</strong> (<em>tuple</em><em> of </em><em>int</em>) – Determines where the signal is concatenated.
If cat[0] is 1, cycles will be concatenated.
If cat[1] is 1, different stages will be concatenated.
If cat[2] is 1, discontinuous signal within a same condition
(stage, cycle, event type) will be concatenated.
If cat[3] is 1, events of different types will be concatenated.
0 in any position indicates no concatenation.</p></li>
<li><p><strong>evt_type</strong> (<em>list</em><em> of </em><em>str</em><em>, </em><em>optional</em>) – Enter a list of event types to get events; otherwise, epochs will
be returned.</p></li>
<li><p><strong>stage</strong> (<em>list</em><em> of </em><em>str</em><em>, </em><em>optional</em>) – Stage(s) of interest. If None, stage is ignored.</p></li>
<li><p><strong>cycle</strong> (<em>list</em><em> of </em><em>tuple</em><em> of </em><em>two float</em><em>, </em><em>optional</em>) – Cycle(s) of interest, as start and end times in seconds from record
start. If None, cycles are ignored.</p></li>
<li><p><strong>chan_full</strong> (<em>list</em><em> of </em><em>str</em><em> or </em><em>None</em>) – Channel(s) of interest, only used for events (epochs have no
channel). Channel format is ‘chan_name (group_name)’.
If used for epochs, separate segments will be returned for each
channel; this is necessary for channel-specific artefact removal (see
reject_artf below). If None, channel is ignored.</p></li>
<li><p><strong>epoch</strong> (<em>str</em><em>, </em><em>optional</em>) – If ‘locked’, returns epochs locked to staging. If ‘unlocked’, divides
signal (with specified concatenation) into epochs of duration epoch_dur
starting at first sample of every segment and discarding any remainder.
If None, longest run of signal is returned.</p></li>
<li><p><strong>epoch_dur</strong> (<em>float</em>) – only for epoch=’unlocked’. Duration of epochs returned, in seconds.</p></li>
<li><p><strong>epoch_overlap</strong> (<em>float</em>) – only for epoch=’unlocked’. Ratio of overlap between two consecutive
segments. Value between 0 and 1. Overriden by step.</p></li>
<li><p><strong>epoch_step</strong> (<em>float</em>) – only for epoch=’unlocked’. Time between consecutive epoch starts, in
seconds. Overrides epoch_overlap/</p></li>
<li><p><strong>reject_epoch</strong> (<em>bool</em>) – If True, epochs marked as ‘Poor’ quality or staged as ‘Artefact’ will
be rejected (and the signal segmented in consequence). Has no effect on
event selection.</p></li>
<li><p><strong>reject_artf</strong> (<em>bool</em><em> or </em><em>str</em><em> or </em><em>list</em><em> of </em><em>str</em>) – If True, excludes events marked as ‘Artefact’. If chan_full is
specified, only artefacts marked on a given channel are removed from
that channel. Signal is segmented in consequence.
If None, Artefact events are ignored.
If str or list of str, will reject the specified event types only.</p></li>
<li><p><strong>min_dur</strong> (<em>float</em>) – Minimum duration of segments returned, in seconds.</p></li>
<li><p><strong>buffer</strong> (<em>float</em>) – adds this many seconds of signal before and after each segment</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><em>instance of Segments</em> – metadata for all analysis segments</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="wonambi.trans.select.get_times">
<span class="sig-prename descclassname"><span class="pre">wonambi.trans.select.</span></span><span class="sig-name descname"><span class="pre">get_times</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">annot</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">evt_type</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">stage</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cycle</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">chan</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exclude</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">buffer</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/trans/select.html#get_times"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.trans.select.get_times" title="Permalink to this definition"></a></dt>
<dd><p>Get start and end times for selected segments of data, bundled
together with info.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>annot</strong> (<em>instance</em><em> of </em><a class="reference internal" href="wonambi.attr.annotations.html#wonambi.attr.annotations.Annotations" title="wonambi.attr.annotations.Annotations"><em>Annotations</em></a>) – The annotation file containing events and epochs</p></li>
<li><p><strong>evt_type</strong> (<em>list</em><em> of </em><em>str</em><em>, </em><em>optional</em>) – Enter a list of event types to get events; otherwise, epochs will
be returned.</p></li>
<li><p><strong>stage</strong> (<em>list</em><em> of </em><em>str</em><em>, </em><em>optional</em>) – Stage(s) of interest. If None, stage is ignored.</p></li>
<li><p><strong>cycle</strong> (<em>list</em><em> of </em><em>tuple</em><em> of </em><em>two float</em><em>, </em><em>optional</em>) – Cycle(s) of interest, as start and end times in seconds from record
start. If None, cycles are ignored.</p></li>
<li><p><strong>chan</strong> (<em>list</em><em> of </em><em>str</em><em> or </em><em>tuple</em><em> of </em><em>None</em>) – Channel(s) of interest. Channel format is ‘chan_name (group_name)’.
If None, channel is ignored.</p></li>
<li><p><strong>exclude</strong> (<em>bool</em>) – Exclude epochs by quality. If True, epochs marked as ‘Poor’ quality
or staged as ‘Artefact’ will be rejected (and the signal segmented
in consequence). Has no effect on event selection.</p></li>
<li><p><strong>buffer</strong> (<em>float</em>) – adds this many seconds of signal before and after each segment</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><em>list of dict</em> – Each dict has times (the start and end times of each segment, as
list of tuple of float), stage, cycle, chan, name (event type,
if applicable)</p>
</dd>
</dl>
<p class="rubric">Notes</p>
<p>This function returns epoch or event start and end times, bundled
together according to the specified parameters.
Presently, setting exclude to True does not exclude events found in Poor
signal epochs. The rationale is that events would never be marked in Poor
signal epochs. If they were automatically detected, these epochs would
have been left out during detection. If they were manually marked, then
it must have been Good signal. At the moment, in the GUI, the exclude epoch
option is disabled when analyzing events, but we could fix the code if we
find a use case for rejecting events based on the quality of the epoch
signal.</p>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="wonambi.trans.select.resample">
<span class="sig-prename descclassname"><span class="pre">wonambi.trans.select.</span></span><span class="sig-name descname"><span class="pre">resample</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">s_freq</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">axis</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'time'</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/trans/select.html#resample"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.trans.select.resample" title="Permalink to this definition"></a></dt>
<dd><p>Downsample the data after applying a filter.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>data</strong> (<em>instance</em><em> of </em><a class="reference internal" href="wonambi.datatype.html#wonambi.datatype.Data" title="wonambi.datatype.Data"><em>Data</em></a>) – data to downsample</p></li>
<li><p><strong>s_freq</strong> (<em>int</em><em> or </em><em>float</em>) – desired sampling frequency</p></li>
<li><p><strong>axis</strong> (<em>str</em>) – axis you want to apply downsample on (most likely ‘time’)</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><em>instance of Data</em> – downsampled data</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="wonambi.trans.select.select">
<span class="sig-prename descclassname"><span class="pre">wonambi.trans.select.</span></span><span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">data</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">trial</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">invert</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">axes_to_select</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/trans/select.html#select"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.trans.select.select" title="Permalink to this definition"></a></dt>
<dd><p>Define the selection of trials, using ranges or actual values.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters<span class="colon">:</span></dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>data</strong> (<em>instance</em><em> of </em><a class="reference internal" href="wonambi.datatype.html#wonambi.datatype.Data" title="wonambi.datatype.Data"><em>Data</em></a>) – data to select from.</p></li>
<li><p><strong>trial</strong> (<em>list</em><em> of </em><em>int</em><em> or </em><em>ndarray</em><em> (</em><em>dtype='i'</em><em>)</em><em>, </em><em>optional</em>) – index of trials of interest</p></li>
<li><p><strong>**axes_to_select</strong> – Values need to be tuple or list. If the values in one axis are string,
then you need to specify all the strings that you want. If the values
are numeric, then you should specify the range. To select only up to one
point, you can use (None, value_of_interest). To select multiple
values, you can pass a numpy array with dtype bool</p></li>
<li><p><strong>optional</strong> – Values need to be tuple or list. If the values in one axis are string,
then you need to specify all the strings that you want. If the values
are numeric, then you should specify the range. To select only up to one
point, you can use (None, value_of_interest). To select multiple
values, you can pass a numpy array with dtype bool</p></li>
<li><p><strong>invert</strong> (<em>bool</em>) – take the opposite selection</p></li>
</ul>
</dd>
<dt class="field-even">Returns<span class="colon">:</span></dt>
<dd class="field-even"><p><em>instance, same class as input</em> – data where selection has been applied.</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="wonambi.trans.select.smart_chan">
<span class="sig-prename descclassname"><span class="pre">wonambi.trans.select.</span></span><span class="sig-name descname"><span class="pre">smart_chan</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dataset</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simple_chan_name</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">test_chan</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/wonambi/trans/select.html#smart_chan"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#wonambi.trans.select.smart_chan" title="Permalink to this definition"></a></dt>
<dd><p>From a list of simple channel names, attempts to find the corresponding
channel names in the dataset and returns a list (with same order).
:param dataset: info about record
:type dataset: instance of Dataset
:param simple_chan_name: simple names for channels, e.g. [‘F3’, ‘Fp2’, ‘ECG’]
:type simple_chan_name: list of str</p>
<dl class="field-list simple">
<dt class="field-odd">Returns<span class="colon">:</span></dt>
<dd class="field-odd"><p><em>list</em> – corresponding channel labels as they appear in dataset</p>
</dd>
</dl>
</dd></dl>
</section>
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