Source Code for Module mvpa.misc.fsl.base

  1  #emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*- 
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  4  # 
  5  #   See COPYING file distributed along with the PyMVPA package for the 
  6  #   copyright and license terms. 
  7  # 
  8  ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ## 
  9  """Tiny snippets to interface with FSL easily.""" 
 10   
 11  __docformat__ = 'restructuredtext' 
 12   
 13  from mvpa.misc.io import ColumnData 
 14  from mvpa.misc.support import Event 
 15   
 16  if __debug__: 
 17      from mvpa.base import debug 
 18   
 19   
 20 -class FslEV3(ColumnData): 
 21      """IO helper to read FSL's EV3 files. 
 22   
 23      This is a three-column textfile format that is used to specify stimulation 
 24      protocols for fMRI data analysis in FSL's FEAT module. 
 25   
 26      Data is always read as `float`. 
 27      """ 
 28 -    def __init__(self, source): 
 29          """Read and write FSL EV3 files. 
 30   
 31          :Parameter: 
 32            source: filename of an EV3 file 
 33          """ 
 34          # init data from known format 
 35          ColumnData.__init__(self, source, 
 36                              header=['onsets', 'durations', 'intensities'], 
 37                              sep=None, dtype=float) 
 38   
 39   
 40 -    def getNEVs(self): 
 41          """Returns the number of EVs in the file. 
 42          """ 
 43          return self.getNRows() 
 44   
 45   
 46 -    def getEV(self, evid): 
 47          """Returns a tuple of (onset time, simulus duration, intensity) for a 
 48          certain EV. 
 49          """ 
 50          return (self['onsets'][evid], 
 51                  self['durations'][evid], 
 52                  self['intensities'][evid]) 
 53   
 54   
 55 -    def tofile(self, filename): 
 56          """Write data to a FSL EV3 file. 
 57          """ 
 58          ColumnData.tofile(self, filename, 
 59                            header=False, 
 60                            header_order=['onsets', 'durations', 'intensities'], 
 61                            sep=' ') 
 62   
 63   
 64 -    def toEvents(self, **kwargs): 
 65          """Convert into a list of `Event` instances. 
 66   
 67          :Parameters: 
 68            kwargs 
 69              Any keyword arugment provided would be replicated, through all 
 70              the entries. Useful to specify label or even a chunk 
 71          """ 
 72          return \ 
 73              [Event(onset=self['onsets'][i], 
 74                     duration=self['durations'][i], 
 75                     features=[self['intensities'][i]], 
 76                     **kwargs) 
 77               for i in xrange(self.nevs)] 
 78   
 79   
 80      onsets = property(fget=lambda self: self['onsets']) 
 81      durations = property(fget=lambda self: self['durations']) 
 82      intensities = property(fget=lambda self: self['intensities']) 
 83      nevs = property(fget=getNEVs) 
 84   
 85   
 86   
 87 -class McFlirtParams(ColumnData): 
 88      """Read and write McFlirt's motion estimation parameters from and to text 
 89      files. 
 90      """ 
 91      header_def = ['rot1', 'rot2', 'rot3', 'x', 'y', 'z'] 
 92   
 93 -    def __init__(self, source): 
 94          """ 
 95          :Parameter: 
 96   
 97              source: str 
 98                  Filename of a parameter file. 
 99          """ 
100          ColumnData.__init__(self, source, 
101                              header=McFlirtParams.header_def, 
102                              sep=None, dtype=float) 
103   
104   
105 -    def tofile(self, filename): 
106          """Write motion parameters to file. 
107          """ 
108          ColumnData.tofile(self, filename, 
109                            header=False, 
110                            header_order=McFlirtParams.header_def, 
111                            sep=' ') 
112   
113   
114 -    def plot(self): 
115          """Produce a simple plot of the estimated translation and rotation 
116          parameters using. 
117   
118          You still need to can pylab.show() or pylab.savefig() if you want to 
119          see/get anything. 
120          """ 
121          # import internally as it takes some time and might not be needed most 
122          # of the time 
123          import pylab as P 
124   
125          # translations subplot 
126          P.subplot(211) 
127          P.plot(self.x) 
128          P.plot(self.y) 
129          P.plot(self.z) 
130          P.ylabel('Translations in mm') 
131          P.legend(('x', 'y', 'z'), loc=0) 
132   
133          # rotations subplot 
134          P.subplot(212) 
135          P.plot(self.rot1) 
136          P.plot(self.rot2) 
137          P.plot(self.rot3) 
138          P.ylabel('Rotations in rad') 
139          P.legend(('rot1', 'rot2', 'rot3'), loc=0) 
140   
141   
142 -    def toarray(self): 
143          """Returns the data as an array with six columns (same order as in file). 
144          """ 
145          import numpy as N 
146   
147          # return as array with time axis first 
148          return N.array([self[i] for i in McFlirtParams.header_def], 
149                         dtype='float').T 
150