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DataConversionToNIX
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mnetonix.html

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  1. <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
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  2. <html><head><title>Python: module mnetonix</title>
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  8. <td valign=bottom>&nbsp;<br>
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  9. <font color="#ffffff" face="helvetica, arial">&nbsp;<br><big><big><strong>mnetonix</strong></big></big></font></td
    10. 

  10. ><td align=right valign=bottom
    11. 

  11. ><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:/Users/achilleas/code/pilsen-workshop/DataConversionToNIX/mnetonix.py">/Users/achilleas/code/pilsen-workshop/DataConversionToNIX/mnetonix.py</a></font></td></tr></table>
    12. 

  12.     <p><tt>mnetonix.py<br>
    13. 

  13. &nbsp;<br>
    14. 

  14. Usage:<br>
    15. 

  15. python&nbsp;mnetonix.py&nbsp;&lt;datafile&gt;&nbsp;&lt;montage&gt;<br>
    16. 

  16. &nbsp;<br>
    17. 

  17. -&nbsp;datafile:&nbsp;Either&nbsp;an&nbsp;EDF&nbsp;file&nbsp;or&nbsp;a&nbsp;BrainVision&nbsp;header&nbsp;file&nbsp;(vhdr).<br>
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  18. -&nbsp;montage:&nbsp;Any&nbsp;format&nbsp;montage&nbsp;file&nbsp;supported&nbsp;by&nbsp;MNE.<br>
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  19. &nbsp;<br>
    20. 

  20. (Requires&nbsp;Python&nbsp;3)<br>
    21. 

  21. &nbsp;<br>
    22. 

  22. Command&nbsp;line&nbsp;script&nbsp;for&nbsp;reading&nbsp;EDF&nbsp;and&nbsp;BrainVision&nbsp;files&nbsp;using&nbsp;MNE<br>
    23. 

  23. (mne-python)&nbsp;and&nbsp;storing&nbsp;the&nbsp;data&nbsp;and&nbsp;metadata&nbsp;into&nbsp;a&nbsp;NIX&nbsp;file.&nbsp;&nbsp;Supports<br>
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  24. reading&nbsp;montage&nbsp;files&nbsp;for&nbsp;recording&nbsp;channel&nbsp;locations.<br>
    25. 

  25. &nbsp;<br>
    26. 

  26. NIX&nbsp;Format&nbsp;layout:<br>
    27. 

  27. &nbsp;<br>
    28. 

  28. Data:<br>
    29. 

  29. Raw&nbsp;Data&nbsp;are&nbsp;stored&nbsp;in&nbsp;either&nbsp;a&nbsp;single&nbsp;2-dimensional&nbsp;DataArray&nbsp;or&nbsp;a&nbsp;collection<br>
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  30. of&nbsp;DataArrays&nbsp;(one&nbsp;per&nbsp;recording&nbsp;channel).&nbsp;&nbsp;The&nbsp;latter&nbsp;makes&nbsp;tagging&nbsp;easier<br>
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  31. since&nbsp;MultiTag&nbsp;positions&nbsp;and&nbsp;extents&nbsp;don't&nbsp;need&nbsp;to&nbsp;specify&nbsp;every&nbsp;channel&nbsp;they<br>
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  32. reference.&nbsp;&nbsp;However,&nbsp;creating&nbsp;multiple&nbsp;DataArrays&nbsp;makes&nbsp;file&nbsp;sizes&nbsp;much<br>
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  33. bigger.<br>
    34. 

  34. &nbsp;<br>
    35. 

  35. Stimuli:<br>
    36. 

  36. MNE&nbsp;provides&nbsp;stimulus&nbsp;information&nbsp;through&nbsp;the&nbsp;Raw.annotations&nbsp;dictionary.<br>
    37. 

  37. Onsets&nbsp;correspond&nbsp;to&nbsp;the&nbsp;'positions'&nbsp;array&nbsp;and&nbsp;durations&nbsp;correspond&nbsp;to&nbsp;the<br>
    38. 

  38. 'extents'&nbsp;array&nbsp;of&nbsp;the&nbsp;"Stimuli"&nbsp;MultiTag.<br>
    39. 

  39. &nbsp;<br>
    40. 

  40. Metadata:<br>
    41. 

  41. MNE&nbsp;collects&nbsp;metadata&nbsp;into&nbsp;a&nbsp;(nested)&nbsp;dictionary&nbsp;(Raw.info).&nbsp;&nbsp;All&nbsp;non-empty<br>
    42. 

  42. keys&nbsp;are&nbsp;converted&nbsp;into&nbsp;Properties&nbsp;in&nbsp;NIX.&nbsp;&nbsp;The&nbsp;nested&nbsp;structure&nbsp;of&nbsp;the<br>
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  43. dictionary&nbsp;is&nbsp;replicated&nbsp;in&nbsp;NIX&nbsp;by&nbsp;creating&nbsp;child&nbsp;Sections,&nbsp;starting&nbsp;with&nbsp;one<br>
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  44. root&nbsp;section&nbsp;with&nbsp;name&nbsp;"Info".</tt></p>
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  45. <p>
    46. 

  46. <table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
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  47. <tr bgcolor="#aa55cc">
    48. 

  48. <td colspan=3 valign=bottom>&nbsp;<br>
    49. 

  49. <font color="#ffffff" face="helvetica, arial"><big><strong>Modules</strong></big></font></td></tr>
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  50.     
    51. 

  51. <tr><td bgcolor="#aa55cc"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
    52. 

  52. <td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="mne.html">mne</a><br>
    53. 

  53. <a href="nixio.html">nixio</a><br>
    54. 

  54. </td><td width="25%" valign=top><a href="numpy.html">numpy</a><br>
    55. 

  55. <a href="os.html">os</a><br>
    56. 

  56. </td><td width="25%" valign=top><a href="matplotlib.pyplot.html">matplotlib.pyplot</a><br>
    57. 

  57. <a href="sys.html">sys</a><br>
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  58. </td><td width="25%" valign=top></td></tr></table></td></tr></table><p>
    59. 

  59. <table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
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  60. <tr bgcolor="#eeaa77">
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  61. <td colspan=3 valign=bottom>&nbsp;<br>
    62. 

  62. <font color="#ffffff" face="helvetica, arial"><big><strong>Functions</strong></big></font></td></tr>
    63. 

  63.     
    64. 

  64. <tr><td bgcolor="#eeaa77"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
    65. 

  65. <td width="100%"><dl><dt><a name="-create_md_tree"><strong>create_md_tree</strong></a>(section, values)</dt></dl>
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  66.  <dl><dt><a name="-main"><strong>main</strong></a>()</dt></dl>
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  67.  <dl><dt><a name="-plot_channel"><strong>plot_channel</strong></a>(data_array, index)</dt></dl>
    68. 

  68.  <dl><dt><a name="-write_multi_da"><strong>write_multi_da</strong></a>(mneraw, block)</dt></dl>
    69. 

  69.  <dl><dt><a name="-write_raw_mne"><strong>write_raw_mne</strong></a>(nfname, mneraw, split_data_channels=True)</dt></dl>
    70. 

  70.  <dl><dt><a name="-write_single_da"><strong>write_single_da</strong></a>(mneraw, block)</dt></dl>
    71. 

  71.  <dl><dt><a name="-write_stim_tags"><strong>write_stim_tags</strong></a>(mneraw, block)</dt></dl>
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  72. </td></tr></table><p>
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  73. <table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
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  74. <tr bgcolor="#55aa55">
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  75. <td colspan=3 valign=bottom>&nbsp;<br>
    76. 

  76. <font color="#ffffff" face="helvetica, arial"><big><strong>Data</strong></big></font></td></tr>
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  77.     
    78. 

  78. <tr><td bgcolor="#55aa55"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
    79. 

  79. <td width="100%"><strong>RAW_DATA_TYPE</strong> = 'Raw Data'</td></tr></table>
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  80. </body></html>
    81.