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# Sphinx build info version 1
# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
config: eae639d6f48449cb996a2fb66279b327
config: 1e96f39d61659b04257a14cd680ab183
tags: 645f666f9bcd5a90fca523b33c5a78b7
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview: module code &#8212; MNE-BIDS 0.17.0.dev19+g41ce36a4 documentation</title>
<title>Overview: module code &#8212; MNE-BIDS 0.17.0.dev20+g18bd9739 documentation</title>



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<link href="../_static/styles/theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
<link href="../_static/styles/pydata-sphinx-theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />

<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=a746c00c" />
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=8f2a1f02" />
<link rel="stylesheet" type="text/css" href="../_static/copybutton.css?v=76b2166b" />
<link rel="stylesheet" type="text/css" href="../_static/sg_gallery.css?v=d2d258e8" />
<link rel="stylesheet" type="text/css" href="../_static/sg_gallery-binder.css?v=f4aeca0c" />
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<link rel="preload" as="script" href="../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
<link rel="preload" as="script" href="../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />

<script src="../_static/documentation_options.js?v=2641d958"></script>
<script src="../_static/documentation_options.js?v=80f87c15"></script>
<script src="../_static/doctools.js?v=9bcbadda"></script>
<script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="../_static/clipboard.min.js?v=a7894cd8"></script>
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<meta name="viewport" content="width=device-width, initial-scale=1"/>
<meta name="docsearch:language" content="en"/>
<meta name="docsearch:version" content="0.17.0.dev19+g41ce36a4" />
<meta name="docsearch:version" content="0.17.0.dev20+g18bd9739" />

</head>

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<p class="title logo__title">MNE-BIDS 0.17.0.dev19+g41ce36a4 documentation</p>
<p class="title logo__title">MNE-BIDS 0.17.0.dev20+g18bd9739 documentation</p>

</a></div>

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<p class="copyright">

© Copyright 2017, The MNE-BIDS developers. Last updated on 2025-01-03.
© Copyright 2017, The MNE-BIDS developers. Last updated on 2025-01-07.
<br/>

</p>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mne_bids.sidecar_updates &#8212; MNE-BIDS 0.17.0.dev19+g41ce36a4 documentation</title>
<title>mne_bids.sidecar_updates &#8212; MNE-BIDS 0.17.0.dev20+g18bd9739 documentation</title>



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<link href="../../_static/styles/theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
<link href="../../_static/styles/pydata-sphinx-theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />

<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=a746c00c" />
<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=8f2a1f02" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
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<link rel="stylesheet" type="text/css" href="../../_static/sg_gallery-binder.css?v=f4aeca0c" />
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<link rel="preload" as="script" href="../../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
<link rel="preload" as="script" href="../../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />

<script src="../../_static/documentation_options.js?v=2641d958"></script>
<script src="../../_static/documentation_options.js?v=80f87c15"></script>
<script src="../../_static/doctools.js?v=9bcbadda"></script>
<script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
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<meta name="viewport" content="width=device-width, initial-scale=1"/>
<meta name="docsearch:language" content="en"/>
<meta name="docsearch:version" content="0.17.0.dev19+g41ce36a4" />
<meta name="docsearch:version" content="0.17.0.dev20+g18bd9739" />

</head>

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<p class="title logo__title">MNE-BIDS 0.17.0.dev19+g41ce36a4 documentation</p>
<p class="title logo__title">MNE-BIDS 0.17.0.dev20+g18bd9739 documentation</p>

</a></div>

Expand Down Expand Up @@ -486,24 +486,24 @@ <h1>Source code for mne_bids.sidecar_updates</h1><div class="highlight"><pre>
<span class="c1"># Authors: The MNE-BIDS developers</span>
<span class="c1"># SPDX-License-Identifier: BSD-3-Clause</span>

<span class="kn">import</span> <span class="nn">json</span>
<span class="kn">from</span> <span class="nn">collections</span> <span class="kn">import</span> <span class="n">OrderedDict</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">json</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">collections</span><span class="w"> </span><span class="kn">import</span> <span class="n">OrderedDict</span>

<span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
<span class="kn">from</span> <span class="nn">mne.channels</span> <span class="kn">import</span> <span class="n">DigMontage</span><span class="p">,</span> <span class="n">make_dig_montage</span>
<span class="kn">from</span> <span class="nn">mne.io</span> <span class="kn">import</span> <span class="n">read_fiducials</span>
<span class="kn">from</span> <span class="nn">mne.io.constants</span> <span class="kn">import</span> <span class="n">FIFF</span>
<span class="kn">from</span> <span class="nn">mne.utils</span> <span class="kn">import</span> <span class="n">_check_on_missing</span><span class="p">,</span> <span class="n">_on_missing</span><span class="p">,</span> <span class="n">_validate_type</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">verbose</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">numpy</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">np</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">mne.channels</span><span class="w"> </span><span class="kn">import</span> <span class="n">DigMontage</span><span class="p">,</span> <span class="n">make_dig_montage</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">mne.io</span><span class="w"> </span><span class="kn">import</span> <span class="n">read_fiducials</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">mne.io.constants</span><span class="w"> </span><span class="kn">import</span> <span class="n">FIFF</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">mne.utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">_check_on_missing</span><span class="p">,</span> <span class="n">_on_missing</span><span class="p">,</span> <span class="n">_validate_type</span><span class="p">,</span> <span class="n">logger</span><span class="p">,</span> <span class="n">verbose</span>

<span class="kn">from</span> <span class="nn">mne_bids</span> <span class="kn">import</span> <span class="n">BIDSPath</span>
<span class="kn">from</span> <span class="nn">mne_bids.utils</span> <span class="kn">import</span> <span class="n">_write_json</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">mne_bids</span><span class="w"> </span><span class="kn">import</span> <span class="n">BIDSPath</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">mne_bids.utils</span><span class="w"> </span><span class="kn">import</span> <span class="n">_write_json</span>


<span class="c1"># TODO: add support for tsv files</span>
<div class="viewcode-block" id="update_sidecar_json">
<a class="viewcode-back" href="../../generated/mne_bids.update_sidecar_json.html#mne_bids.update_sidecar_json">[docs]</a>
<span class="nd">@verbose</span>
<span class="k">def</span> <span class="nf">update_sidecar_json</span><span class="p">(</span><span class="n">bids_path</span><span class="p">,</span> <span class="n">entries</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="k">def</span><span class="w"> </span><span class="nf">update_sidecar_json</span><span class="p">(</span><span class="n">bids_path</span><span class="p">,</span> <span class="n">entries</span><span class="p">,</span> <span class="n">verbose</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Update sidecar files using a dictionary or JSON file.</span>

<span class="sd"> Will update metadata fields inside the path defined by</span>
Expand Down Expand Up @@ -606,7 +606,7 @@ <h1>Source code for mne_bids.sidecar_updates</h1><div class="highlight"><pre>



<span class="k">def</span> <span class="nf">_update_sidecar</span><span class="p">(</span><span class="n">sidecar_fname</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">val</span><span class="p">):</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_update_sidecar</span><span class="p">(</span><span class="n">sidecar_fname</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">val</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Update a sidecar JSON file with a given key/value pair.</span>

<span class="sd"> Parameters</span>
Expand All @@ -627,7 +627,7 @@ <h1>Source code for mne_bids.sidecar_updates</h1><div class="highlight"><pre>
<div class="viewcode-block" id="update_anat_landmarks">
<a class="viewcode-back" href="../../generated/mne_bids.update_anat_landmarks.html#mne_bids.update_anat_landmarks">[docs]</a>
<span class="nd">@verbose</span>
<span class="k">def</span> <span class="nf">update_anat_landmarks</span><span class="p">(</span>
<span class="k">def</span><span class="w"> </span><span class="nf">update_anat_landmarks</span><span class="p">(</span>
<span class="n">bids_path</span><span class="p">,</span>
<span class="n">landmarks</span><span class="p">,</span>
<span class="o">*</span><span class="p">,</span>
Expand Down Expand Up @@ -826,12 +826,12 @@ <h1>Source code for mne_bids.sidecar_updates</h1><div class="highlight"><pre>



<span class="k">def</span> <span class="nf">_get_landmarks_from_fiducials_file</span><span class="p">(</span>
<span class="k">def</span><span class="w"> </span><span class="nf">_get_landmarks_from_fiducials_file</span><span class="p">(</span>
<span class="o">*</span><span class="p">,</span> <span class="n">bids_path</span><span class="p">,</span> <span class="n">fname</span><span class="p">,</span> <span class="n">fs_subject</span><span class="p">,</span> <span class="n">fs_subjects_dir</span>
<span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Get anatomical landmarks from fiducials file, in MRI voxel space.&quot;&quot;&quot;</span>
<span class="c1"># avoid dicrular imports</span>
<span class="kn">from</span> <span class="nn">mne_bids.write</span> <span class="kn">import</span> <span class="p">(</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">mne_bids.write</span><span class="w"> </span><span class="kn">import</span> <span class="p">(</span>
<span class="n">_get_fid_coords</span><span class="p">,</span>
<span class="n">_get_t1w_mgh</span><span class="p">,</span>
<span class="n">_mri_landmarks_to_mri_voxels</span><span class="p">,</span>
Expand Down Expand Up @@ -914,7 +914,7 @@ <h1>Source code for mne_bids.sidecar_updates</h1><div class="highlight"><pre>

<p class="copyright">

© Copyright 2017, The MNE-BIDS developers. Last updated on 2025-01-03.
© Copyright 2017, The MNE-BIDS developers. Last updated on 2025-01-07.
<br/>

</p>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>mne_bids.stats &#8212; MNE-BIDS 0.17.0.dev19+g41ce36a4 documentation</title>
<title>mne_bids.stats &#8212; MNE-BIDS 0.17.0.dev20+g18bd9739 documentation</title>



Expand All @@ -29,7 +29,7 @@
<link href="../../_static/styles/theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />
<link href="../../_static/styles/pydata-sphinx-theme.css?digest=8878045cc6db502f8baf" rel="stylesheet" />

<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=a746c00c" />
<link rel="stylesheet" type="text/css" href="../../_static/pygments.css?v=8f2a1f02" />
<link rel="stylesheet" type="text/css" href="../../_static/copybutton.css?v=76b2166b" />
<link rel="stylesheet" type="text/css" href="../../_static/sg_gallery.css?v=d2d258e8" />
<link rel="stylesheet" type="text/css" href="../../_static/sg_gallery-binder.css?v=f4aeca0c" />
Expand All @@ -43,7 +43,7 @@
<link rel="preload" as="script" href="../../_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf" />
<link rel="preload" as="script" href="../../_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf" />

<script src="../../_static/documentation_options.js?v=2641d958"></script>
<script src="../../_static/documentation_options.js?v=80f87c15"></script>
<script src="../../_static/doctools.js?v=9bcbadda"></script>
<script src="../../_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="../../_static/clipboard.min.js?v=a7894cd8"></script>
Expand Down Expand Up @@ -77,7 +77,7 @@

<meta name="viewport" content="width=device-width, initial-scale=1"/>
<meta name="docsearch:language" content="en"/>
<meta name="docsearch:version" content="0.17.0.dev19+g41ce36a4" />
<meta name="docsearch:version" content="0.17.0.dev20+g18bd9739" />

</head>

Expand Down Expand Up @@ -140,7 +140,7 @@



<p class="title logo__title">MNE-BIDS 0.17.0.dev19+g41ce36a4 documentation</p>
<p class="title logo__title">MNE-BIDS 0.17.0.dev20+g18bd9739 documentation</p>

</a></div>

Expand Down Expand Up @@ -486,13 +486,13 @@ <h1>Source code for mne_bids.stats</h1><div class="highlight"><pre>
<span class="c1"># Authors: The MNE-BIDS developers</span>
<span class="c1"># SPDX-License-Identifier: BSD-3-Clause</span>

<span class="kn">from</span> <span class="nn">mne_bids</span> <span class="kn">import</span> <span class="n">BIDSPath</span><span class="p">,</span> <span class="n">get_datatypes</span>
<span class="kn">from</span> <span class="nn">mne_bids.config</span> <span class="kn">import</span> <span class="n">EPHY_ALLOWED_DATATYPES</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">mne_bids</span><span class="w"> </span><span class="kn">import</span> <span class="n">BIDSPath</span><span class="p">,</span> <span class="n">get_datatypes</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">mne_bids.config</span><span class="w"> </span><span class="kn">import</span> <span class="n">EPHY_ALLOWED_DATATYPES</span>


<div class="viewcode-block" id="count_events">
<a class="viewcode-back" href="../../generated/mne_bids.stats.count_events.html#mne_bids.stats.count_events">[docs]</a>
<span class="k">def</span> <span class="nf">count_events</span><span class="p">(</span><span class="n">root_or_path</span><span class="p">,</span> <span class="n">datatype</span><span class="o">=</span><span class="s2">&quot;auto&quot;</span><span class="p">):</span>
<span class="k">def</span><span class="w"> </span><span class="nf">count_events</span><span class="p">(</span><span class="n">root_or_path</span><span class="p">,</span> <span class="n">datatype</span><span class="o">=</span><span class="s2">&quot;auto&quot;</span><span class="p">):</span>
<span class="w"> </span><span class="sd">&quot;&quot;&quot;Count events present in dataset.</span>

<span class="sd"> Parameters</span>
Expand Down Expand Up @@ -522,7 +522,7 @@ <h1>Source code for mne_bids.stats</h1><div class="highlight"><pre>
<span class="sd"> Table values were changed from floats (with NaN for missing values)</span>
<span class="sd"> to Pandas nullable integer arrays.</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="kn">import</span> <span class="nn">pandas</span> <span class="k">as</span> <span class="nn">pd</span>
<span class="kn">import</span><span class="w"> </span><span class="nn">pandas</span><span class="w"> </span><span class="k">as</span><span class="w"> </span><span class="nn">pd</span>

<span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">root_or_path</span><span class="p">,</span> <span class="n">BIDSPath</span><span class="p">):</span>
<span class="n">bids_path</span> <span class="o">=</span> <span class="n">BIDSPath</span><span class="p">(</span><span class="n">root</span><span class="o">=</span><span class="n">root_or_path</span><span class="p">)</span>
Expand Down Expand Up @@ -654,7 +654,7 @@ <h1>Source code for mne_bids.stats</h1><div class="highlight"><pre>

<p class="copyright">

© Copyright 2017, The MNE-BIDS developers. Last updated on 2025-01-03.
© Copyright 2017, The MNE-BIDS developers. Last updated on 2025-01-07.
<br/>

</p>
Expand Down
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