コード例 #1
0
ファイル: _basic_ops_.py プロジェクト: teonbrooks/Eelbrain
def add_ext(path, ext, multiple=False, ask_overwrite=True):
    """
    Adds ext to path;

    kwargs
    -----
    multiple=False:
        =False: if path has an extension, nothing will be done
        ='r', 'replace': existing extension will be replaced.
        ='a', 'add': extension will be added independent of existing extension
    """
    name, old_ext = os.path.splitext(path)
    # remove leading dots
    old_ext = old_ext.lstrip(os.path.extsep)
    ext = ext.lstrip(os.path.extsep)
    # modify
    if old_ext:
        if multiple in ['r', 'replace']:
            pass
        elif  (multiple in ['a', 'add'])  and  (old_ext != ext):
            ext = os.path.extsep.join([old_ext, ext])
        else:
            ext = old_ext

    path = os.path.extsep.join([name, ext])
    if ask_overwrite:
        if os.path.exists(path):
            if not ui.ask(title="Overwrite File?",
                          message="The File '%s' already exists. Overwrite the existing file?" % path):
                return None
    return path
コード例 #2
0
ファイル: shell.py プロジェクト: kriek197/Eelbrain
 def attach(self, dictionary):
     """
     Adds a dictionary to the globals and keeps track of the items so that 
     they can be removed safely with the detach function.
     
     """
     # self._attached_items = {id(dict_like) -> {key -> value}}
     present = []
     for k in dictionary:
         if k in self.global_namespace:
             if id(self.global_namespace[k]) != id(dictionary[k]):
                 present.append(k)
     if present:
         title = "Overwrite Items?"
         message = ("The following items are associated with different "
                    "objects in global namespace. Should we replace them?"
                    + os.linesep)
         message = os.linesep.join((message, ', '.join(repr(k) for k in present)))
         answer = ui.ask(title, message, True)
         if answer is None:
             return
         elif answer:
             attach = dictionary
         else:
             attach = dict((k,v) for k,v in dictionary.iteritems() if k not in present)
     else:
         attach = dictionary
     
     self.global_namespace.update(attach)
     
     items = self._attached_items.setdefault(id(dictionary), {})
     items.update(attach)
     
     msg = "attached: %s" % str(attach.keys())
     print msg
コード例 #3
0
ファイル: MEG.py プロジェクト: teonbrooks/Eelbrain
    def OnRemove(self, event):
        target = None
        rm = sorted(self._rm_comp)
        while not target:
            dlg = wx.TextEntryDialog(self, "What name should the new ndvar be assigned in the dataset?",
                                     "Choose Name for New Variable", "%s" % self._Y.name)
            if dlg.ShowModal() == wx.ID_OK:
                newname = str(dlg.GetValue())
                if newname in self._dataset:
                    msg = ("The dataset already contains an item named %r. "
                           "Should it be replaced? The item is:\n\n%r" %
                            (newname, self._dataset[newname]))
                    answer = ui.ask("Replace %r?" % newname, msg)
                    if answer is True:
                        target = newname
                    elif answer is None:
                        pass
                    else:
                        return
                else:
                    target = newname
            else:
                return

        # if we made it down here, remove the component:
        self._dataset[target] = self.pca.subtract(rm, name=target)

        self.Close()
コード例 #4
0
ファイル: datasets_base.py プロジェクト: teonbrooks/Eelbrain
    def collectstats(self, cells, over, mask=None, mp=False, pool=None, 
                     save='ask', **kwargs):
        """
        cells: address; statistics are extracted for each valid combination of
               values in this address
        over: variable specifying the cases within the cells (usually subject)
        
        - adds statistics segment for all values of cells in address to self.stats
        - forwards statsForAddress_over_ kwargs
        
        kwargs:
        mp  False
            'outer' Spawn one process for each StatsSegment 
            True    do statsSegments serially but use multiple processes in
                    StatsSegment.initWithSegments_over_
                    
        **kwargs: 
                    
        """
        t0=time.time()
        msg = "--> Collecting Statistics for {0} over {1}, mp={2}"
        print msg.format(cells.name, over.name, str(mp))
        
        if len(self.stats) > 0:
            msg = "self.stats currently contains the following statistics: %s"%str(self.stats.keys())
            if ui.ask(title="Clear existing statistics?",
                      message=msg):
                self.stats = {}
        
        cells = biovars.asaddress(cells)
        if mask == None:
            all_segments = self.segments
        else:
            all_segments = mask.filter(self.segments)
        segs_sorted = cells.sort(all_segments)
        
        # progress bar
#        n = len(segs_sorted)
#        i = 0
#        prog_ttl = "Collecting statistics for {n} cells".format(n=n)
#        prog_msg = "{name} ({i} of {n}) done...".format(name='{name}', n=n, i='{i}')
#        prog = ui.progress(i_max=n,
#                           title=prog_ttl,
#                           message=prog_msg.format(name='', i=0))
        
        label_dic = cells.short_labels()
        
        for address, segs in segs_sorted.iteritems():
            label = label_dic[address]
#            color = cells.color_for_value(key)
            s = StatsSegment(self.properties, name=label)#, color=color)
            s.initWithSegments_over_(segs, over, **kwargs)

            # make sure label is a valid name
            if label[0].isalpha():
                valid_label = label
            else:
                valid_label = 'c' + label
            
            self.stats[valid_label] = s
            
            # close all files
            self._store.close()
        
#        # progress bar
#            if prog:
#                i += 1
#                prog.advance(prog_msg.format(name=valid_label, i=i))
#        if prog:
#            prog.terminate()


#        if mp=='outer':
#            for key, label in cells.dictionary.iteritems():
#                self.stats[label] = self.stats[label].recv()
        print '\n'.join(["---",
                         "Finished after %s"%(time.time()-t0),
                         "Dataset now contains stats: %s"%self.stats.keys()])
        
        # save the experiment
        if save == 'ask':
            msg = "Save Experiment with newly added statistics segments?"
            save = ui.ask(title="Save Experiment?", message=msg)
        if save:
            self.experiment.save()
コード例 #5
0
ファイル: design.py プロジェクト: teonbrooks/Eelbrain
def export_mat(dataset, values=None, destination=None):
    """
    Usage::
    
        >>> export_mat(dataset, 
        ...            values={varname -> {cellname -> value}},
        ...            destination='/path/to/file.mat')
    
    
    Arguments
    ---------
    
    dataset : dataset
        dataset containing the trial list
    
    values : `None` or `{varname -> {cellname -> value}}`
        additional values that should be stored, where: `varname` is the 
        variable name by which the struct will be available in matlab; 
        `cellname` is the name of the struct's field, and `value` is the value
        of that field.
    
    destination : None or str
        Path where the mat file should be saved. If `None`, the ui will ask 
        for a location.
    
    """
    # Make sure we have a valid destination 
    if destination is None:
        print_path = True
        destination = ui.ask_saveas("Mat destination", 
                                    "Where do you want to save the mat file?", 
                                    ext=[('mat', "Matlab File")])
        if not destination:
            print "aborted"
            return
    else:
        print_path = False
    
    if not isinstance(destination, basestring):
        raise ValueError("destination is not a string")
    
    dirname = os.path.dirname(destination)
    if not os.path.exists(dirname):
        if ui.ask("Create %r?" % dirname, "No folder named %r exists. Should "
                  "it be created?" % dirname):
            os.mkdir(dirname)
        else:
            print "aborted"
            return
    
    if not destination.endswith('mat'):
        os.path.extsep.join(destination, 'mat')
    
    # assemble the mat file contents
    mat = {'trials': list(dataset.itercases())}
    if values:
        mat.update(values)
    
    if print_path:
        print 'Saving: %r' % destination
    scipy.io.savemat(destination, mat, do_compression=True, oned_as='row')
コード例 #6
0
ファイル: subp.py プロジェクト: teonbrooks/Eelbrain
def kit2fiff(paths=dict(mrk=None,
                        elp=None,
                        hsp=None,
                        rawtxt=None,
                        rawfif=None),
             sns='NYU-nellab-2010',
             sfreq=1000, lowpass=100, highpass=0,
             stim=xrange(168, 160, -1), stimthresh=2.5, add=None,  # (188, 190), #xrange()
             aligntol=5, overwrite=False):
    """
    Calls the ``mne_kit2fiff`` binary which reads multiple input files and
    combines them into a fiff file. Implemented after Gwyneth's Manual; for
    more information see the mne manual (p. 222).

    **Arguments:**

    paths : dict
        Dictionary containing paths to input and output files.
        Needs the folowing keys:
        'mrk', 'elp', 'hsp', 'sns', 'rawtxt', 'outfif'

    experiment : str
        The experiment name as it appears in file names.

    highpass : scalar
        The highpass filter corner frequency (only for file info, does not
        filter the data). 0 Hz for DC recording.

    lowpass : scalar
        like highpass

    meg_sdir : str or tuple (see above)
        Path to the subjects's meg directory. If ``None``, a file dialog is
        displayed to ask for the directory.

    sfreq : scalar
        samplingrate of the data

    stimthresh : scalar
        The threshold value used when synthesizing the digital trigger channel

    add : sequence of int | None
        channels to include in addition to the 157 default MEG channels and the
        digital trigger channel. These numbers refer to the scanning order
        channels as listed in the sns file, starting from one.

    stim : iterable over ints
        trigger channels that are used to reconstruct the event cue value from
        the separate trigger channels. The default ``xrange(168, 160, -1)``
        reconstructs the values sent through psychtoolbox.

    aligntol : scalar
        Alignment tolerance for coregistration [mm]

    overwrite : bool
        Automatically overwrite the target fiff file if it already exists.

    """
    # get all the paths
    mrk_path = paths.get('mrk')
    elp_file = paths.get('elp')
    hsp_file = paths.get('hsp')
    raw_file = paths.get('rawtxt')
    out_file = paths.get('rawfif')

    if sns in _sns_files:
        sns_file = _sns_files[sns]
    elif os.path.exists(sns):
        sns_file = sns
    else:
        err = ("sns needs to the be the name of a buit-in sns file (%s) or a path"
               "to an existing sns file" % ', '.join(map(repr, _sns_files)))
        raise IOError(err)

    # convert the marker file
    mrk_file = MarkerFile(mrk_path)
    hpi_file = mrk_file.path

    # make sure target path exists
    out_dir = os.path.dirname(out_file)
    if not os.path.exists(out_dir):
        os.mkdir(out_dir)
    elif not overwrite and os.path.exists(out_file):
        if not ui.ask("Overwrite?", "Target File Already Exists at: %r. Should "
                      "it be replaced?" % out_file):
            return

    cmd = [get_bin('mne', 'mne_kit2fiff'),
           '--elp', elp_file,
           '--hsp', hsp_file,
           '--sns', sns_file,
           '--hpi', hpi_file,
           '--raw', raw_file,
           '--out', out_file,
           '--stim', ':'.join(map(str, stim)),  # '161:162:163:164:165:166:167:168'
           '--sfreq', sfreq,
           '--aligntol', aligntol,
           '--lowpass', lowpass,
           '--highpass', highpass,
           '--stimthresh', stimthresh,
           ]

    if add:
        cmd.extend(('--add', ':'.join(map(str, add))))

    _run(cmd)

    # TODO: rename additional channels
    # how do I know their names?? ~/Desktop/test/EOG  has MISC 28 and MISC 30
#    if add:
#        cmd = [os.path.join(mne_dir, 'bin', 'mne_rename_channels'),
#               '--fif', out_file,
#               ]

    if not os.path.exists(out_file):
        raise RuntimeError("kit2fiff failed (see above)")