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
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
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()
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()
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')
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)")