def kit2fiff(meg_sdir=None, sfreq=250, aligntol=25, **more_kwargs):
"""
Reads multiple input files and combines them into a fiff file that can be
used with mne. Implemented after Gwyneth's Manual
Arguments:
sfreq : scalar
samplingrate of the data
meg_sdir : path(str)
Path to the subjects's meg directory. If ``None``, a file dialog is
displayed to ask for the directory.
more_kwargs :
more keyword arguments (see MNE manual p. 224) e.g., ``lowpass``
"""
if meg_sdir is None:
msg = "Select Subject's Meg Directory"
meg_sdir = ui.ask_dir(msg, msg, True)
param_dir = os.path.join(meg_sdir, 'parameters')
assert os.path.exists(param_dir)
subject = os.path.basename(meg_sdir)
mapath = os.path.join(param_dir, '%s_eref3_markers_average.txt' % subject)
mafile = marker_avg_file(mapath)
elp_file = os.path.join(param_dir, '%s_eref3_electrodes.elp' % subject)
hsp_file = os.path.join(param_dir, '%s_eref3_headshape.hsp' % subject)
hpi_file = mafile.path
sns_file = '~/Documents/Eclipse/Eelbrain\ Reloaded/aux_files/sns.txt'
data_file = '~/Documents/Data/eref/meg/R0368/data/%s_eref3_exported.txt' % subject
out_file = os.path.join(meg_sdir, 'myfif', '%s_raw.fif' % subject)
kwargs = {'elp': elp_file,
'hsp': hsp_file,
'sns': sns_file,
'hpi': hpi_file,
'raw': data_file,
'out': out_file,
'stim': '161:162:163:164:165:166:167:168',
'sfreq': sfreq,
'aligntol': aligntol}
kwargs.update(more_kwargs)
_run('mne_kit2fiff', kwargs)
def _export(self, address, format='txt', sensors=slice(None)):
"""
.. WARNING::
METHOD NOT MAINTAINED
Possible values for format:
'txt': export tsv files to folder (ask)
'names': print a list of filenames ordered for 2 vars in address
"""
segDict = address.dict( self.segments )
dictKey = address.keys()
if format == 'txt':
folder = ui.ask_dir('target dir: ')
if folder == False:
raise IOError("no valid target directory")
for index, segments in segDict.iteritems():
data = np.vstack([s.data for s in segments])
name = '_'.join([ var.name+'-'+var[v] for var,v in zip(dictKey,
index) ])
filename = folder + name +'.txt'
np.savetxt(filename, data, delimiter='\t')
elif format == 'names':
if len(dictKey)!=2:
raise NotImplementedError
d0=[]; d1=[]; names={}
for index in segDict.keys():
if index[0] not in d0:
d0.append(index[0])
if index[1] not in d1:
d1.append(index[1])
if index not in names:
names[index]= '_'.join([var.name+'-'+var[v] for var,v in \
zip(dictKey, index)]+['.txt'])
txt=['\t']
for i1 in d1:
txt.append( dictKey[1][i1]+'\t' )
for i0 in d0:
txt.append('\n'+dictKey[0][i0]+'\t')
for i1 in d1:
txt.append(names[(i0,i1)]+'\t')
print ''.join(txt)
def set(self, path=None):
"""
path can be file or directory
if path==None: a dialog will be displayed to select a directory
(use .set_ext('ext') method to modify file extension)
"""
if path is None:
path = ui.ask_dir()
if not path:
return
if isinstance(path, basestring):
if os.path.isdir(path):
self._value['d'].append(path)
elif os.path.exists(path):
self._value['f'].append(path)
else:
raise IOError("%s does not exists"%path)
self._changed()
else:
raise ValueError("must be string")
def OnInsertPath(self, event, t=None):
if t is None:
t = event.GetSelection()
# get
if t == 0: # File
filenames = ui.ask_file(mult=True)
elif t == 1: # Dir
filenames = ui.ask_dir()
elif t == 2: # New
filenames = ui.ask_saveas(title = "Get New File Name",
message = "Please Pick a File Name",
ext = None)
# put to terminal
if filenames:
if len(filenames) == 1:
filenames = '"'+filenames[0]+'"'
else:
filenames = '"'+str(filenames)+'"'
if 'wxMSW' in wx.PlatformInfo:
filenames = 'r'+filenames
self.InsertStr(filenames)
def set_bin_dir(package):
"""
Change the location from which binaries are used.
package : str
Binary package for which to set the directory. One from:
``['mne', 'freesurfer', 'edfapi']``
"""
have_valid_path = False
while not have_valid_path:
title = "Select %r bin Directory" % package
message = ("Please select the directory containing the binaries for "
"the %r package." % package)
answer = ui.ask_dir(title, message, must_exist=True)
if answer:
if _is_bin_path(package, answer):
_bin_dirs[package] = answer
pickle.dump(_bin_dirs, open(_cfg_path, 'w'))
_set_bin_dirs(**{package: answer})
have_valid_path = True
else:
raise IOError("%r bin directory not set" % package)