-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathREADME.html
More file actions
651 lines (478 loc) · 27.4 KB
/
README.html
File metadata and controls
651 lines (478 loc) · 27.4 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
<!DOCTYPE html>
<html lang="en" data-content_root="./" >
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Overview — MouseAR Documentation</title>
<script data-cfasync="false">
document.documentElement.dataset.mode = localStorage.getItem("mode") || "";
document.documentElement.dataset.theme = localStorage.getItem("theme") || "";
</script>
<!--
this give us a css class that will be invisible only if js is disabled
-->
<noscript>
<style>
.pst-js-only { display: none !important; }
</style>
</noscript>
<!-- Loaded before other Sphinx assets -->
<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=03e43079" />
<link rel="stylesheet" type="text/css" href="_static/styles/sphinx-book-theme.css?v=3c74b3bc" />
<link rel="stylesheet" type="text/css" href="_static/togglebutton.css?v=9c3e77be" />
<link rel="stylesheet" type="text/css" href="_static/copybutton.css?v=76b2166b" />
<link rel="stylesheet" type="text/css" href="_static/mystnb.11b39860a7a0cbfd473a3ad8a317855267ff0bd372690045ca344a6b62be495e.css" />
<link rel="stylesheet" type="text/css" href="_static/sphinx-thebe.css?v=4fa983c6" />
<link rel="stylesheet" type="text/css" href="_static/sphinx-design.min.css?v=95c83b7e" />
<!-- So that users can add custom icons -->
<script src="_static/scripts/fontawesome.js?digest=8878045cc6db502f8baf"></script>
<!-- Pre-loaded scripts that we'll load fully later -->
<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=9eb32ce0"></script>
<script src="_static/doctools.js?v=9a2dae69"></script>
<script src="_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="_static/clipboard.min.js?v=a7894cd8"></script>
<script src="_static/copybutton.js?v=f281be69"></script>
<script src="_static/scripts/sphinx-book-theme.js?v=fab101a9"></script>
<script>let toggleHintShow = 'Click to show';</script>
<script>let toggleHintHide = 'Click to hide';</script>
<script>let toggleOpenOnPrint = 'true';</script>
<script src="_static/togglebutton.js?v=b8b12719"></script>
<script>var togglebuttonSelector = '.toggle, .admonition.dropdown';</script>
<script src="_static/design-tabs.js?v=f930bc37"></script>
<script>const THEBE_JS_URL = "https://unpkg.com/thebe@0.8.2/lib/index.js"; const thebe_selector = ".thebe,.cell"; const thebe_selector_input = "pre"; const thebe_selector_output = ".output, .cell_output"</script>
<script async="async" src="_static/sphinx-thebe.js?v=c100c467"></script>
<script>var togglebuttonSelector = '.toggle, .admonition.dropdown';</script>
<script>const THEBE_JS_URL = "https://unpkg.com/thebe@0.8.2/lib/index.js"; const thebe_selector = ".thebe,.cell"; const thebe_selector_input = "pre"; const thebe_selector_output = ".output, .cell_output"</script>
<script>DOCUMENTATION_OPTIONS.pagename = 'README';</script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="Python Control System - Overview" href="docs/python/Overview.html" />
<meta name="viewport" content="width=device-width, initial-scale=1"/>
<meta name="docsearch:language" content="en"/>
<meta name="docsearch:version" content="" />
</head>
<body data-bs-spy="scroll" data-bs-target=".bd-toc-nav" data-offset="180" data-bs-root-margin="0px 0px -60%" data-default-mode="">
<div id="pst-skip-link" class="skip-link d-print-none"><a href="#main-content">Skip to main content</a></div>
<div id="pst-scroll-pixel-helper"></div>
<button type="button" class="btn rounded-pill" id="pst-back-to-top">
<i class="fa-solid fa-arrow-up"></i>Back to top</button>
<dialog id="pst-search-dialog">
<form class="bd-search d-flex align-items-center"
action="search.html"
method="get">
<i class="fa-solid fa-magnifying-glass"></i>
<input type="search"
class="form-control"
name="q"
placeholder="Search this book..."
aria-label="Search this book..."
autocomplete="off"
autocorrect="off"
autocapitalize="off"
spellcheck="false"/>
<span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd>K</kbd></span>
</form>
</dialog>
<div class="pst-async-banner-revealer d-none">
<aside id="bd-header-version-warning" class="d-none d-print-none" aria-label="Version warning"></aside>
</div>
<header class="bd-header navbar navbar-expand-lg bd-navbar d-print-none">
</header>
<div class="bd-container">
<div class="bd-container__inner bd-page-width">
<dialog id="pst-primary-sidebar-modal"></dialog>
<div id="pst-primary-sidebar" class="bd-sidebar-primary bd-sidebar">
<div class="sidebar-header-items sidebar-primary__section">
</div>
<div class="sidebar-primary-items__start sidebar-primary__section">
<div class="sidebar-primary-item">
<a class="navbar-brand logo" href="#">
<img src="_static/logo.png" class="logo__image only-light" alt="MouseAR Documentation - Home"/>
<img src="_static/logo.png" class="logo__image only-dark pst-js-only" alt="MouseAR Documentation - Home"/>
</a></div>
<div class="sidebar-primary-item">
<button class="btn search-button-field search-button__button pst-js-only" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
<i class="fa-solid fa-magnifying-glass"></i>
<span class="search-button__default-text">Search</span>
<span class="search-button__kbd-shortcut"><kbd class="kbd-shortcut__modifier">Ctrl</kbd>+<kbd class="kbd-shortcut__modifier">K</kbd></span>
</button></div>
<div class="sidebar-primary-item"><nav class="bd-links bd-docs-nav" aria-label="Main">
<div class="bd-toc-item navbar-nav active">
<ul class="nav bd-sidenav bd-sidenav__home-link">
<li class="toctree-l1 current active">
<a class="reference internal" href="#">
Overview
</a>
</li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Getting Started</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="docs/python/Overview.html">System Overview</a></li>
<li class="toctree-l1"><a class="reference internal" href="docs/Unity/Overview.html">Unity Framework Overview</a></li>
<li class="toctree-l1"><a class="reference internal" href="docs/touchscreen/Overview.html">Touchscreen System Overview</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Unity Game Framework</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="docs/Unity/Architecture.html">Core Architecture</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l2"><a class="reference internal" href="docs/Unity/EpisodeManagement.html">Episode Management</a></li>
<li class="toctree-l2"><a class="reference internal" href="docs/Unity/Spawners.html">Spawners & Object Creation</a></li>
<li class="toctree-l2"><a class="reference internal" href="docs/Unity/Agents.html">ML-Agents Integration</a></li>
<li class="toctree-l2"><a class="reference internal" href="docs/Unity/ParameterSystem.html">Parameter Configuration</a></li>
<li class="toctree-l2"><a class="reference internal" href="docs/Unity/VisualFeedback.html">Visual Feedback & Utilities</a></li>
<li class="toctree-l2"><a class="reference internal" href="docs/Unity/MouseVision.html">Mouse Visual Observations</a></li>
<li class="toctree-l2"><a class="reference internal" href="docs/Unity/HockeyGame.html">Hockey Game</a></li>
</ul>
</details></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Python Control System</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1 has-children"><a class="reference internal" href="docs/python/GUIs.html">Python GUIs</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l2"><a class="reference internal" href="docs/python/DataTransferGUI.html">Data Transfer GUI</a></li>
</ul>
</details></li>
<li class="toctree-l1"><a class="reference internal" href="docs/python/ConfigSystem.html">Configuration System</a></li>
<li class="toctree-l1 has-children"><a class="reference internal" href="docs/python/Tasks.html">Task Controllers</a><details><summary><span class="toctree-toggle" role="presentation"><i class="fa-solid fa-chevron-down"></i></span></summary><ul>
<li class="toctree-l2"><a class="reference internal" href="docs/python/DLCProcessors.html">DLC Processors</a></li>
<li class="toctree-l2"><a class="reference internal" href="docs/python/DLCProcessor_recording_ctrl.html">Recording Control</a></li>
<li class="toctree-l2"><a class="reference internal" href="docs/python/DLCClient.html">DLC Client</a></li>
</ul>
</details></li>
<li class="toctree-l1"><a class="reference internal" href="docs/python/TouchClient.html">Touchscreen Client</a></li>
<li class="toctree-l1"><a class="reference internal" href="docs/python/Teensy.html">Teensy Hardware Control</a></li>
<li class="toctree-l1"><a class="reference internal" href="docs/python/TTLGenerator.html">TTL Signal Generation</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Touchscreen Interface</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="docs/touchscreen/TouchscreenArchitecture.html">Architecture & Implementation</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Hardware</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="docs/hardware/Teensy.html">Teensy Microcontroller</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">Reinforcement Learning</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="docs/RL/GYMNASIUM_WRAPPERS.html">Gymnasium Wrappers</a></li>
</ul>
<p aria-level="2" class="caption" role="heading"><span class="caption-text">DataJoint Pipeline</span></p>
<ul class="nav bd-sidenav">
<li class="toctree-l1"><a class="reference internal" href="docs/datajoint/Overview.html">Pipeline Overview</a></li>
<li class="toctree-l1"><a class="reference internal" href="docs/datajoint/Connections.html">Database Connections</a></li>
<li class="toctree-l1"><a class="reference internal" href="docs/datajoint/Population.html">Populating the Pipeline</a></li>
<li class="toctree-l1"><a class="reference internal" href="docs/datajoint/Infrastructure.html">Infrastructure (Docker & MySQL)</a></li>
<li class="toctree-l1"><a class="reference internal" href="docs/datajoint/Schema_Dataset.html">Schema - Dataset</a></li>
<li class="toctree-l1"><a class="reference internal" href="docs/datajoint/Schema_Behavior.html">Schema - Behavior</a></li>
<li class="toctree-l1"><a class="reference internal" href="docs/datajoint/Schema_Video.html">Schema - Video</a></li>
<li class="toctree-l1"><a class="reference internal" href="docs/datajoint/Schema_DLCLive.html">Schema - DLC Live</a></li>
<li class="toctree-l1"><a class="reference internal" href="docs/datajoint/Schema_ScreenSync.html">Schema - Screen Sync</a></li>
</ul>
</div>
</nav></div>
</div>
<div class="sidebar-primary-items__end sidebar-primary__section">
<div class="sidebar-primary-item">
<div id="ethical-ad-placement"
class="flat"
data-ea-publisher="readthedocs"
data-ea-type="readthedocs-sidebar"
data-ea-manual="true">
</div></div>
</div>
</div>
<main id="main-content" class="bd-main" role="main">
<div class="sbt-scroll-pixel-helper"></div>
<div class="bd-content">
<div class="bd-article-container">
<div class="bd-header-article d-print-none">
<div class="header-article-items header-article__inner">
<div class="header-article-items__start">
<div class="header-article-item"><button class="sidebar-toggle primary-toggle btn btn-sm" title="Toggle primary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
<span class="fa-solid fa-bars"></span>
</button></div>
</div>
<div class="header-article-items__end">
<div class="header-article-item">
<div class="article-header-buttons">
<div class="dropdown dropdown-source-buttons">
<button class="btn dropdown-toggle" type="button" data-bs-toggle="dropdown" aria-expanded="false" aria-label="Source repositories">
<i class="fab fa-github"></i>
</button>
<ul class="dropdown-menu">
<li><a href="https://github.com/SCENE-Collaboration/SCENE_MouseAR" target="_blank"
class="btn btn-sm btn-source-repository-button dropdown-item"
title="Source repository"
data-bs-placement="left" data-bs-toggle="tooltip"
>
<span class="btn__icon-container">
<i class="fab fa-github"></i>
</span>
<span class="btn__text-container">Repository</span>
</a>
</li>
<li><a href="https://github.com/SCENE-Collaboration/SCENE_MouseAR/issues/new?title=Issue%20on%20page%20%2FREADME.html&body=Your%20issue%20content%20here." target="_blank"
class="btn btn-sm btn-source-issues-button dropdown-item"
title="Open an issue"
data-bs-placement="left" data-bs-toggle="tooltip"
>
<span class="btn__icon-container">
<i class="fas fa-lightbulb"></i>
</span>
<span class="btn__text-container">Open issue</span>
</a>
</li>
</ul>
</div>
<div class="dropdown dropdown-download-buttons">
<button class="btn dropdown-toggle" type="button" data-bs-toggle="dropdown" aria-expanded="false" aria-label="Download this page">
<i class="fas fa-download"></i>
</button>
<ul class="dropdown-menu">
<li><a href="_sources/README.md" target="_blank"
class="btn btn-sm btn-download-source-button dropdown-item"
title="Download source file"
data-bs-placement="left" data-bs-toggle="tooltip"
>
<span class="btn__icon-container">
<i class="fas fa-file"></i>
</span>
<span class="btn__text-container">.md</span>
</a>
</li>
<li>
<button onclick="window.print()"
class="btn btn-sm btn-download-pdf-button dropdown-item"
title="Print to PDF"
data-bs-placement="left" data-bs-toggle="tooltip"
>
<span class="btn__icon-container">
<i class="fas fa-file-pdf"></i>
</span>
<span class="btn__text-container">.pdf</span>
</button>
</li>
</ul>
</div>
<button onclick="toggleFullScreen()"
class="btn btn-sm btn-fullscreen-button pst-navbar-icon"
title="Fullscreen mode"
data-bs-placement="bottom" data-bs-toggle="tooltip"
>
<span class="btn__icon-container">
<i class="fas fa-expand"></i>
</span>
</button>
<button class="btn btn-sm nav-link pst-navbar-icon theme-switch-button pst-js-only" aria-label="Color mode" data-bs-title="Color mode" data-bs-placement="bottom" data-bs-toggle="tooltip">
<i class="theme-switch fa-solid fa-sun fa-lg" data-mode="light" title="Light"></i>
<i class="theme-switch fa-solid fa-moon fa-lg" data-mode="dark" title="Dark"></i>
<i class="theme-switch fa-solid fa-circle-half-stroke fa-lg" data-mode="auto" title="System Settings"></i>
</button>
<button class="btn btn-sm pst-navbar-icon search-button search-button__button pst-js-only" title="Search" aria-label="Search" data-bs-placement="bottom" data-bs-toggle="tooltip">
<i class="fa-solid fa-magnifying-glass fa-lg"></i>
</button>
<button class="sidebar-toggle secondary-toggle btn btn-sm pst-navbar-icon" title="Toggle secondary sidebar" data-bs-placement="bottom" data-bs-toggle="tooltip">
<span class="fa-solid fa-list"></span>
</button>
</div></div>
</div>
</div>
</div>
<div id="jb-print-docs-body" class="onlyprint">
<h1>Overview</h1>
<!-- Table of contents -->
<div id="print-main-content">
<div id="jb-print-toc">
<div>
<h2> Contents </h2>
</div>
<nav aria-label="Page">
<ul class="visible nav section-nav flex-column">
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#organization">Organization</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#installation">Installation</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#documentation">Documentation</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#code-formatting-linting">Code Formatting & Linting</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#acknowledgement">Acknowledgement</a></li>
</ul>
</nav>
</div>
</div>
</div>
<div id="searchbox"></div>
<article class="bd-article">
<section class="tex2jax_ignore mathjax_ignore" id="overview">
<h1>Overview<a class="headerlink" href="#overview" title="Link to this heading">#</a></h1>
<p>This repository is a work-in-progress for SCENE - mice affordance tasks using Augmented Reality(AR) in Unity.
The code and task design is based on the previous development in the Mathis Lab - <a class="github reference external" href="https://github.com/SCENE-Collaboration/FreelyMovingVR4Mice">SCENE-Collaboration/FreelyMovingVR4Mice</a>.</p>
<section id="organization">
<h2>Organization<a class="headerlink" href="#organization" title="Link to this heading">#</a></h2>
<ul class="simple">
<li><p><code class="docutils literal notranslate"><span class="pre">mouse_ar/</span></code> - the main python module for the mice AR tasks.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">touchscreen/</span></code> - code for the touchscreen interface.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">UnityAR/</span></code> - Unity project files for the AR environment.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">rl/</span></code> - reinforcement learning related code.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">tests/</span></code> - unit tests for the codebase.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">docs/</span></code> - documentation files.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">dj_pipeline/</span></code> - DataJoint pipeline for data management and transfer, including a GUI for data transfer.</p></li>
</ul>
</section>
<section id="installation">
<h2>Installation<a class="headerlink" href="#installation" title="Link to this heading">#</a></h2>
<p>Clone the repository:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span><repository-url>
</pre></div>
</div>
<p>plain installation:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>-e<span class="w"> </span>.
</pre></div>
</div>
<p>to be able to build docs:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>-e<span class="w"> </span>.<span class="o">[</span>docs<span class="o">]</span>
</pre></div>
</div>
<p>Development Setup</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>-e<span class="w"> </span>.<span class="o">[</span>dev,docs<span class="o">]</span>
</pre></div>
</div>
</section>
<section id="documentation">
<h2>Documentation<a class="headerlink" href="#documentation" title="Link to this heading">#</a></h2>
<p>Documentation can be found at <a class="reference external" href="https://scene-collaboration.github.io/SCENE_MouseAR_Docs/">SCENE_MouseAR_Docs</a>.</p>
<p>To locally build the documentation, run:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>jupyter-book<span class="w"> </span>build<span class="w"> </span>.
</pre></div>
</div>
<p>Then open the generated HTML files in <code class="docutils literal notranslate"><span class="pre">_build/html/</span></code> with your web browser.</p>
<p>Suggested reading flow:</p>
<ol class="arabic simple">
<li><p><a class="reference internal" href="docs/python/Overview.html"><span class="std std-doc">System Overview</span></a></p></li>
<li><p><a class="reference internal" href="docs/Unity/Overview.html"><span class="std std-doc">Unity Framework Overview</span></a></p></li>
<li><p><a class="reference internal" href="docs/touchscreen/Overview.html"><span class="std std-doc">Touchscreen Overview</span></a></p></li>
<li><p><a class="reference internal" href="docs/python/GUIs.html"><span class="std std-doc">Python GUIs</span></a></p></li>
<li><p><a class="reference internal" href="docs/python/DataTransferGUI.html"><span class="std std-doc">Data Transfer GUI</span></a></p></li>
<li><p><a class="reference internal" href="docs/python/Tasks.html"><span class="std std-doc">Task Controllers</span></a></p></li>
</ol>
</section>
<section id="code-formatting-linting">
<h2>Code Formatting & Linting<a class="headerlink" href="#code-formatting-linting" title="Link to this heading">#</a></h2>
<ul class="simple">
<li><p>Formatted code makes your life and those who use/review your code easier. Standardized formatting with tools like <code class="docutils literal notranslate"><span class="pre">black</span></code> and <code class="docutils literal notranslate"><span class="pre">isort</span></code> (see the provided <code class="docutils literal notranslate"><span class="pre">.pre-commit-config.yaml</span></code>).</p></li>
<li><p><a class="reference external" href="https://pre-commit.com/">Pre-commit hooks</a> to automate checks before pushing code! Follow their quick Guide to do this, but in short:</p></li>
</ul>
<p>(1) install it in your dev env</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pip<span class="w"> </span>install<span class="w"> </span>pre-commit
</pre></div>
</div>
<p>(2) install the git hooks:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pre-commit<span class="w"> </span>install
</pre></div>
</div>
<p>(3) Just run it on your code BEFORE you git push:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pre-commit<span class="w"> </span>run<span class="w"> </span>--all-files
</pre></div>
</div>
</section>
<section id="acknowledgement">
<h2>Acknowledgement<a class="headerlink" href="#acknowledgement" title="Link to this heading">#</a></h2>
<p>Some items in this repo are adapted from <a class="reference external" href="https://github.com/DeepLabCut/DeepLabCut">DeepLabCut</a>, <a class="reference external" href="https://cebra.ai/">CEBRA</a>, <a class="reference external" href="https://github.com/SCENE-Collaboration/FreelyMovingVR4Mice">FreelyMovingVR4Mice</a> and the <a class="reference external" href="https://github.com/orgs/AdaptiveMotorControlLab">Mathis Lab of Adaptive Intelligence</a>. It is under an Apache 2.0 License.</p>
</section>
<div class="toctree-wrapper compound">
</div>
<div class="toctree-wrapper compound">
</div>
<div class="toctree-wrapper compound">
</div>
<div class="toctree-wrapper compound">
</div>
<div class="toctree-wrapper compound">
</div>
<div class="toctree-wrapper compound">
</div>
<div class="toctree-wrapper compound">
</div>
</section>
<script type="text/x-thebe-config">
{
requestKernel: true,
binderOptions: {
repo: "binder-examples/jupyter-stacks-datascience",
ref: "master",
},
codeMirrorConfig: {
theme: "abcdef",
mode: "python"
},
kernelOptions: {
name: "python3",
path: "./."
},
predefinedOutput: true
}
</script>
<script>kernelName = 'python3'</script>
</article>
<footer class="prev-next-footer d-print-none">
<div class="prev-next-area">
<a class="right-next"
href="docs/python/Overview.html"
title="next page">
<div class="prev-next-info">
<p class="prev-next-subtitle">next</p>
<p class="prev-next-title">Python Control System - Overview</p>
</div>
<i class="fa-solid fa-angle-right"></i>
</a>
</div>
</footer>
</div>
<dialog id="pst-secondary-sidebar-modal"></dialog>
<div id="pst-secondary-sidebar" class="bd-sidebar-secondary bd-toc"><div class="sidebar-secondary-items sidebar-secondary__inner">
<div class="sidebar-secondary-item"><div
id="pst-page-navigation-heading-2"
class="page-toc tocsection onthispage">
<i class="fa-solid fa-list"></i> Contents
</div>
<nav id="pst-page-toc-nav" class="page-toc" aria-labelledby="pst-page-navigation-heading-2">
<ul class="visible nav section-nav flex-column">
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#organization">Organization</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#installation">Installation</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#documentation">Documentation</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#code-formatting-linting">Code Formatting & Linting</a></li>
<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#acknowledgement">Acknowledgement</a></li>
</ul>
</nav></div>
</div></div>
</div>
<footer class="bd-footer-content">
<div class="bd-footer-content__inner container">
<div class="footer-item">
<p class="component-author">
By M Lab of Adaptive Intelligence
</p>
</div>
<div class="footer-item">
<p class="copyright">
© Copyright 2023.
<br/>
</p>
</div>
<div class="footer-item">
</div>
<div class="footer-item">
<div class="extra_footer">
<div>Powered by <a href="https://jupyterbook.org/">Jupyter Book</a>.</div>
</div>
</div>
</div>
</footer>
</main>
</div>
</div>
<!-- Scripts loaded after <body> so the DOM is not blocked -->
<script defer src="_static/scripts/bootstrap.js?digest=8878045cc6db502f8baf"></script>
<script defer src="_static/scripts/pydata-sphinx-theme.js?digest=8878045cc6db502f8baf"></script>
<footer class="bd-footer">
</footer>
</body>
</html>