Commit 02a4f68a authored by Yaroslav Halchenko's avatar Yaroslav Halchenko
Browse files

New upstream version 0.2.13

parent c702e794

build

+7 −6
Original line number Diff line number Diff line
@@ -221,13 +221,13 @@ except: 






def SVN_last_changed (filename):

def git_last_changed (filename):

  try:

    process = subprocess.Popen ([ 'svn', 'info', filename ], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)

    process = subprocess.Popen ([ 'git', 'log', '--pretty=format:%ad', '--date=short', 

      '-n', '1', 'master', '--',filename ], stdout=subprocess.PIPE, stderr=subprocess.STDOUT)

    if process.wait() != 0: raise 0

    for line in process.stdout:

      if line.startswith ('Text Last Updated:'):

        return line.split(':')[1].split()[0].strip() 

      return as_str(line)

  except:

    return None
@@ -711,15 +711,16 @@ MRtrix version #VERSION#<br> 
def gen_doc ():

  shutil.rmtree (doc_dir, True)

  shutil.copytree (os.path.join (misc_dir, doc_dir), doc_dir)

  os.makedirs (os.path.join (doc_dir, 'commands'));

  gen_command_html_help()

  for root, dirs, files in os.walk (doc_dir):

    for entry in files:

      if entry[0] == '.': continue

      if not entry.endswith ('.html'): continue

      fname = os.path.join (root, entry)

      timestamp = SVN_last_changed (os.path.join (misc_dir, fname))

      timestamp = git_last_changed (os.path.join (misc_dir, fname))

      if not timestamp:

        timestamp = SVN_last_changed (os.path.join (cmd_dir, entry.replace (".html", cpp_suffix)))

        timestamp = git_last_changed (os.path.join (cmd_dir, entry.replace (".html", cpp_suffix)))

      if not timestamp:

        timestamp = '-'

      with fopen(fname, 'r') as fd:

cmd/tracks2prob.cpp

+3 −3
Original line number Diff line number Diff line
@@ -127,9 +127,9 @@ class Voxel 
      z (_z_) { }



    Voxel (const Point& p) :

      x (round (p[0])),

      y (round (p[1])),

      z (round (p[2]))

      x (std::round (p[0])),

      y (std::round (p[1])),

      z (std::round (p[2]))

    { 

      assert (gsl_finite (p[0]) && gsl_finite (p[1]) && gsl_finite (p[2]));

    }

doc/commands/average.html

deleted100644 → 0
+0 −62
Original line number Diff line number Diff line 
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">

<html>

<head>

  <meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">

  <title>MRtrix 0.2.12 documentation</title>

  <link rel="stylesheet" href="../stylesheet.css" type="text/css" media=screen>

</head>



<body>



<table class=nav>

  <tr>

    <td><a href="index.html"><img src="../left.png"></a></td>

    <td><a href="index.html"><img src="../up.png"></a></td>

    <td><a href="../index.html"><img src="../home.png"></a></td>

    <th>average</th>

    <td><a href="cat_tracks.html"><img src="../right.png"></a></td>

  </tr>

</table>



<h2>Description</h2>

<p>

average an image along a specific axis.

</p>

<p class=indented><strong>syntax:</strong> &nbsp; &nbsp; average [ options ] image1 output </p>

<h2>Arguments</h2>

<table class=args>

<tr><td><b>image1</b></td>

<td>the first input image.</td></tr>

<tr><td><b>output</b></td>

<td>the output image.</td></tr>

</table>

<h2>Options</h2>

<table class=args>

<tr><td nowrap><b>-axis</b>&nbsp;<i>axis</i></td>

<td>specify axis along which averaging should be performed. By default, the program will use the last non-singleton axis of the input image.

<table class=opts>

<tr><td><i>axis</i></td>

<td>the concatenation axis</td></tr>

</table></td></tr>

<tr><td nowrap><b>-geometric</b></td>

<td>produce geometric mean. By default, the program will produce the arithmetic mean.</td></tr>

<tr><td nowrap><b>-info</b></td>

<td>display information messages.</td></tr>

<tr><td nowrap><b>-quiet</b></td>

<td>do not display information messages or progress status.</td></tr>

<tr><td nowrap><b>-debug</b></td>

<td>display debugging messages.</td></tr>

<tr><td nowrap><b>-help</b></td>

<td>display this information page and exit.</td></tr>

<tr><td nowrap><b>-version</b></td>

<td>display version information and exit.</td></tr>

</table>



<p class=footer>

Donald Tournier<br>

MRtrix version 0.2.12<br>

Last updated 2014-02-25

</p>



</body>

</html>

doc/commands/cat_tracks.html

deleted100644 → 0
+0 −56
Original line number Diff line number Diff line 
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">

<html>

<head>

  <meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">

  <title>MRtrix 0.2.12 documentation</title>

  <link rel="stylesheet" href="../stylesheet.css" type="text/css" media=screen>

</head>



<body>



<table class=nav>

  <tr>

    <td><a href="average.html"><img src="../left.png"></a></td>

    <td><a href="index.html"><img src="../up.png"></a></td>

    <td><a href="../index.html"><img src="../home.png"></a></td>

    <th>cat_tracks</th>

    <td><a href="cleanup_ANTS_warp.html"><img src="../right.png"></a></td>

  </tr>

</table>



<h2>Description</h2>

<p>

Concatenate two track files

</p>

<p class=indented><strong>syntax:</strong> &nbsp; &nbsp; cat_tracks [ options ] output track1 track2 [ track2 ... ] </p>

<h2>Arguments</h2>

<table class=args>

<tr><td><b>output</b></td>

<td>the output file containing the tracks.</td></tr>

<tr><td><b>track1</b></td>

<td>the first input tracks file.</td></tr>

<tr><td><b>track2</b> [ multiples allowed ]</td>

<td>the second input tracks file.</td></tr>

</table>

<h2>Options</h2>

<table class=args>

<tr><td nowrap><b>-info</b></td>

<td>display information messages.</td></tr>

<tr><td nowrap><b>-quiet</b></td>

<td>do not display information messages or progress status.</td></tr>

<tr><td nowrap><b>-debug</b></td>

<td>display debugging messages.</td></tr>

<tr><td nowrap><b>-help</b></td>

<td>display this information page and exit.</td></tr>

<tr><td nowrap><b>-version</b></td>

<td>display version information and exit.</td></tr>

</table>



<p class=footer>

Donald Tournier<br>

MRtrix version 0.2.12<br>

Last updated 2014-02-25

</p>



</body>

</html>

doc/commands/cleanup_ANTS_warp.html

deleted100644 → 0
+0 −56
Original line number Diff line number Diff line 
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">

<html>

<head>

  <meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">

  <title>MRtrix 0.2.12 documentation</title>

  <link rel="stylesheet" href="../stylesheet.css" type="text/css" media=screen>

</head>



<body>



<table class=nav>

  <tr>

    <td><a href="cat_tracks.html"><img src="../left.png"></a></td>

    <td><a href="index.html"><img src="../up.png"></a></td>

    <td><a href="../index.html"><img src="../home.png"></a></td>

    <th>cleanup_ANTS_warp</th>

    <td><a href="csdeconv.html"><img src="../right.png"></a></td>

  </tr>

</table>



<h2>Description</h2>

<p>

clean up warp field generated by ANTS (or more specifically, WarpMultiImageTransform, replacing background voxels with NaN when they map to regions outside the original image.

</p>

<p class=indented><strong>syntax:</strong> &nbsp; &nbsp; cleanup_ANTS_warp [ options ] unit_warp ants_warp clean_warp </p>

<h2>Arguments</h2>

<table class=args>

<tr><td><b>unit_warp</b></td>

<td>the original unit warp image</td></tr>

<tr><td><b>ants_warp</b></td>

<td>the warp image as produced by WarpMultiImageTransform.</td></tr>

<tr><td><b>clean_warp</b></td>

<td>the output cleaned-up warp image.</td></tr>

</table>

<h2>Options</h2>

<table class=args>

<tr><td nowrap><b>-info</b></td>

<td>display information messages.</td></tr>

<tr><td nowrap><b>-quiet</b></td>

<td>do not display information messages or progress status.</td></tr>

<tr><td nowrap><b>-debug</b></td>

<td>display debugging messages.</td></tr>

<tr><td nowrap><b>-help</b></td>

<td>display this information page and exit.</td></tr>

<tr><td nowrap><b>-version</b></td>

<td>display version information and exit.</td></tr>

</table>



<p class=footer>

Donald Tournier<br>

MRtrix version 0.2.12<br>

Last updated 2014-02-25

</p>



</body>

</html>