def _test_compare_to_old(self):
"""Good just to compare if I didn't screw up anything... treat
it as a regression test
"""
import mvpa.mappers.wavelet_ as wavelet_
ds = datasets['uni2medium']
d2d = ds.samples
ws = 16 # size of timeline for wavelet
sp = np.arange(ds.nsamples-ws*2) + ws
# create 3D instance (samples x timepoints x channels)
bcm = BoxcarMapper(sp, ws)
d3d = bcm.forward(d2d)
# use wavelet mapper
for wdm, wdm_ in ((WaveletTransformationMapper(),
wavelet_.WaveletTransformationMapper()),
(WaveletPacketMapper(),
wavelet_.WaveletPacketMapper()),):
d3d_wd = wdm(d3d)
d3d_wd_ = wdm_(d3d)
self.failUnless((d3d_wd == d3d_wd_).all(),
msg="We should have got same result with old and new code. "
"Got %s and %s" % (d3d_wd, d3d_wd_))
def test_simple_wdm(self):
"""
"""
ds = datasets['uni2medium']
d2d = ds.samples
ws = 15 # size of timeline for wavelet
sp = np.arange(ds.nsamples-ws*2) + ws
# create 3D instance (samples x timepoints x channels)
bcm = BoxcarMapper(sp, ws)
d3d = bcm.forward(d2d)
# use wavelet mapper
wdm = WaveletTransformationMapper()
d3d_wd = wdm.forward(d3d)
d3d_swap = d3d.swapaxes(1,2)
self.failUnlessRaises(ValueError, WaveletTransformationMapper,
wavelet='bogus')
self.failUnlessRaises(ValueError, WaveletTransformationMapper,
mode='bogus')
# use wavelet mapper
for wdm, wdm_swap in ((WaveletTransformationMapper(),
WaveletTransformationMapper(dim=2)),
(WaveletPacketMapper(),
WaveletPacketMapper(dim=2))):
for dd, dd_swap in ((d3d, d3d_swap),
(d2d, None)):
dd_wd = wdm.forward(dd)
if dd_swap is not None:
dd_wd_swap = wdm_swap.forward(dd_swap)
self.failUnless((dd_wd == dd_wd_swap.swapaxes(1,2)).all(),
msg="We should have got same result with swapped "
"dimensions and explicit mentioining of it. "
"Got %s and %s" % (dd_wd, dd_wd_swap))
# some sanity checks
self.failUnless(dd_wd.shape[0] == dd.shape[0])
if not isinstance(wdm, WaveletPacketMapper):
# we can do reverse only for DWT
dd_rev = wdm.reverse(dd_wd)
# inverse transform might be not exactly as the
# input... but should be very close ;-)
self.failUnlessEqual(dd_rev.shape, dd.shape,
msg="Shape should be the same after iDWT")
diff = np.linalg.norm(dd - dd_rev)
ornorm = np.linalg.norm(dd)
self.failUnless(diff/ornorm < 1e-10)
def test_datasetmapping():
# 6 samples, 4 features
data = np.arange(24).reshape(6,4)
ds = Dataset(data,
sa={'timepoints': np.arange(6),
'multidim': data.copy()},
fa={'fid': np.arange(4)})
# with overlapping and non-overlapping boxcars
startpoints = [0, 1, 4]
boxlength = 2
bm = BoxcarMapper(startpoints, boxlength, inspace='boxy')
# train is critical
bm.train(ds)
mds = bm.forward(ds)
assert_equal(len(mds), len(startpoints))
assert_equal(mds.nfeatures, boxlength)
# all samples attributes remain, but the can rotated/compressed into
# multidimensional attributes
assert_equal(sorted(mds.sa.keys()), ['boxy_onsetidx'] + sorted(ds.sa.keys()))
assert_equal(mds.sa.multidim.shape,
(len(startpoints), boxlength, ds.nfeatures))
assert_equal(mds.sa.timepoints.shape, (len(startpoints), boxlength))
assert_array_equal(mds.sa.timepoints.flatten(),
np.array([(s, s+1) for s in startpoints]).flatten())
assert_array_equal(mds.sa.boxy_onsetidx, startpoints)
# feature attributes also get rotated and broadcasted
assert_array_equal(mds.fa.fid, [ds.fa.fid, ds.fa.fid])
# and finally there is a new one
assert_array_equal(mds.fa.boxy_offsetidx,
np.repeat(np.arange(boxlength), 4).reshape(2,-1))
# now see how it works on reverse()
rds = bm.reverse(mds)
# we got at least something of all original attributes back
assert_equal(sorted(rds.sa.keys()), sorted(ds.sa.keys()))
assert_equal(sorted(rds.fa.keys()), sorted(ds.fa.keys()))
# it is not possible to reconstruct the full samples array
# some samples even might show up multiple times (when there are overlapping
# boxcars
assert_array_equal(rds.samples,
np.array([[ 0, 1, 2, 3],
[ 4, 5, 6, 7],
[ 4, 5, 6, 7],
[ 8, 9, 10, 11],
[16, 17, 18, 19],
[20, 21, 22, 23]]))
assert_array_equal(rds.sa.timepoints, [0, 1, 1, 2, 4, 5])
assert_array_equal(rds.sa.multidim, ds.sa.multidim[rds.sa.timepoints])
# but feature attributes should be fully recovered
assert_array_equal(rds.fa.fid, ds.fa.fid)
def _test_compare_to_old(self):
"""Good just to compare if I didn't screw up anything... treat
it as a regression test
"""
import mvpa.mappers.wavelet_ as wavelet_
ds = datasets['uni2medium']
d2d = ds.samples
ws = 16 # size of timeline for wavelet
sp = np.arange(ds.nsamples - ws * 2) + ws
# create 3D instance (samples x timepoints x channels)
bcm = BoxcarMapper(sp, ws)
d3d = bcm(d2d)
# use wavelet mapper
for wdm, wdm_ in (
(WaveletTransformationMapper(),
wavelet_.WaveletTransformationMapper()),
(WaveletPacketMapper(), wavelet_.WaveletPacketMapper()),
):
d3d_wd = wdm(d3d)
d3d_wd_ = wdm_(d3d)
self.failUnless(
(d3d_wd == d3d_wd_).all(),
msg="We should have got same result with old and new code. "
"Got %s and %s" % (d3d_wd, d3d_wd_))
def test_simple_wdm(self):
"""
"""
ds = datasets['uni2medium']
d2d = ds.samples
ws = 15 # size of timeline for wavelet
sp = np.arange(ds.nsamples - ws * 2) + ws
# create 3D instance (samples x timepoints x channels)
bcm = BoxcarMapper(sp, ws)
d3d = bcm(d2d)
# use wavelet mapper
wdm = WaveletTransformationMapper()
d3d_wd = wdm(d3d)
d3d_swap = d3d.swapaxes(1, 2)
self.failUnlessRaises(ValueError,
WaveletTransformationMapper,
wavelet='bogus')
self.failUnlessRaises(ValueError,
WaveletTransformationMapper,
mode='bogus')
# use wavelet mapper
for wdm, wdm_swap in ((WaveletTransformationMapper(),
WaveletTransformationMapper(dim=2)),
(WaveletPacketMapper(),
WaveletPacketMapper(dim=2))):
for dd, dd_swap in ((d3d, d3d_swap), (d2d, None)):
dd_wd = wdm(dd)
if dd_swap is not None:
dd_wd_swap = wdm_swap(dd_swap)
self.failUnless(
(dd_wd == dd_wd_swap.swapaxes(1, 2)).all(),
msg="We should have got same result with swapped "
"dimensions and explicit mentioining of it. "
"Got %s and %s" % (dd_wd, dd_wd_swap))
# some sanity checks
self.failUnless(dd_wd.shape[0] == dd.shape[0])
if not isinstance(wdm, WaveletPacketMapper):
# we can do reverse only for DWT
dd_rev = wdm.reverse(dd_wd)
# inverse transform might be not exactly as the
# input... but should be very close ;-)
self.failUnlessEqual(
dd_rev.shape,
dd.shape,
msg="Shape should be the same after iDWT")
diff = np.linalg.norm(dd - dd_rev)
ornorm = np.linalg.norm(dd)
self.failUnless(diff / ornorm < 1e-10)
def test_simple_wp1_level(self):
"""
"""
ds = datasets['uni2large']
d2d = ds.samples
ws = 50 # size of timeline for wavelet
sp = (np.arange(ds.nsamples - ws*2) + ws)[:4]
# create 3D instance (samples x timepoints x channels)
bcm = BoxcarMapper(sp, ws)
d3d = bcm.forward(d2d)
# use wavelet mapper
wdm = WaveletPacketMapper(level=2, wavelet='sym2')
d3d_wd = wdm.forward(d3d)
# Check dimensionality
d3d_wds, d3ds = d3d_wd.shape, d3d.shape
self.failUnless(len(d3d_wds) == len(d3ds)+1)
self.failUnless(d3d_wds[1] * d3d_wds[2] >= d3ds[1])
self.failUnless(d3d_wds[0] == d3ds[0])
self.failUnless(d3d_wds[-1] == d3ds[-1])
#print d2d.shape, d3d.shape, d3d_wd.shape
if externals.exists('pywt wp reconstruct'):
# Test reverse -- should be identical
# we can do reverse only for DWT
d3d_rev = wdm.reverse(d3d_wd)
# inverse transform might be not exactly as the
# input... but should be very close ;-)
self.failUnlessEqual(d3d_rev.shape, d3d.shape,
msg="Shape should be the same after iDWT")
diff = np.linalg.norm(d3d - d3d_rev)
ornorm = np.linalg.norm(d3d)
skip_if_no_external('pywt wp reconstruct fixed')
self.failUnless(diff/ornorm < 1e-10)
else:
self.failUnlessRaises(NotImplementedError, wdm.reverse, d3d_wd)
def testIds(self):
data = N.arange(20).reshape( (10,2) )
bcm = BoxcarMapper([1, 4, 6], 3)
trans = bcm(data)
self.failUnlessEqual(bcm.isValidInId( [1] ), True)
self.failUnlessEqual(bcm.isValidInId( [0,1] ), False)
self.failUnlessEqual(bcm.isValidOutId( [1] ), True)
self.failUnlessEqual(bcm.isValidOutId( [3] ), False)
self.failUnlessEqual(bcm.isValidOutId( [0,1] ), True)
self.failUnlessEqual(bcm.isValidOutId( [0,1,0] ), False)
def test_simple_wp1_level(self):
"""
"""
ds = datasets['uni2large']
d2d = ds.samples
ws = 50 # size of timeline for wavelet
sp = (np.arange(ds.nsamples - ws * 2) + ws)[:4]
# create 3D instance (samples x timepoints x channels)
bcm = BoxcarMapper(sp, ws)
d3d = bcm(d2d)
# use wavelet mapper
wdm = WaveletPacketMapper(level=2, wavelet='sym2')
d3d_wd = wdm(d3d)
# Check dimensionality
d3d_wds, d3ds = d3d_wd.shape, d3d.shape
self.failUnless(len(d3d_wds) == len(d3ds) + 1)
self.failUnless(d3d_wds[1] * d3d_wds[2] >= d3ds[1])
self.failUnless(d3d_wds[0] == d3ds[0])
self.failUnless(d3d_wds[-1] == d3ds[-1])
#print d2d.shape, d3d.shape, d3d_wd.shape
if externals.exists('pywt wp reconstruct'):
# Test reverse -- should be identical
# we can do reverse only for DWT
d3d_rev = wdm.reverse(d3d_wd)
# inverse transform might be not exactly as the
# input... but should be very close ;-)
self.failUnlessEqual(d3d_rev.shape,
d3d.shape,
msg="Shape should be the same after iDWT")
diff = np.linalg.norm(d3d - d3d_rev)
ornorm = np.linalg.norm(d3d)
skip_if_no_external('pywt wp reconstruct fixed')
self.failUnless(diff / ornorm < 1e-10)
else:
self.failUnlessRaises(NotImplementedError, wdm.reverse, d3d_wd)
def test_datasetmapping():
# 6 samples, 4 features
data = np.arange(24).reshape(6, 4)
ds = Dataset(data,
sa={
'timepoints': np.arange(6),
'multidim': data.copy()
},
fa={'fid': np.arange(4)})
# with overlapping and non-overlapping boxcars
startpoints = [0, 1, 4]
boxlength = 2
bm = BoxcarMapper(startpoints, boxlength, inspace='boxy')
# train is critical
bm.train(ds)
mds = bm.forward(ds)
assert_equal(len(mds), len(startpoints))
assert_equal(mds.nfeatures, boxlength)
# all samples attributes remain, but the can rotated/compressed into
# multidimensional attributes
assert_equal(sorted(mds.sa.keys()),
['boxy_onsetidx'] + sorted(ds.sa.keys()))
assert_equal(mds.sa.multidim.shape,
(len(startpoints), boxlength, ds.nfeatures))
assert_equal(mds.sa.timepoints.shape, (len(startpoints), boxlength))
assert_array_equal(mds.sa.timepoints.flatten(),
np.array([(s, s + 1) for s in startpoints]).flatten())
assert_array_equal(mds.sa.boxy_onsetidx, startpoints)
# feature attributes also get rotated and broadcasted
assert_array_equal(mds.fa.fid, [ds.fa.fid, ds.fa.fid])
# and finally there is a new one
assert_array_equal(mds.fa.boxy_offsetidx,
np.repeat(np.arange(boxlength), 4).reshape(2, -1))
# now see how it works on reverse()
rds = bm.reverse(mds)
# we got at least something of all original attributes back
assert_equal(sorted(rds.sa.keys()), sorted(ds.sa.keys()))
assert_equal(sorted(rds.fa.keys()), sorted(ds.fa.keys()))
# it is not possible to reconstruct the full samples array
# some samples even might show up multiple times (when there are overlapping
# boxcars
assert_array_equal(
rds.samples,
np.array([[0, 1, 2, 3], [4, 5, 6, 7], [4, 5, 6, 7], [8, 9, 10, 11],
[16, 17, 18, 19], [20, 21, 22, 23]]))
assert_array_equal(rds.sa.timepoints, [0, 1, 1, 2, 4, 5])
assert_array_equal(rds.sa.multidim, ds.sa.multidim[rds.sa.timepoints])
# but feature attributes should be fully recovered
assert_array_equal(rds.fa.fid, ds.fa.fid)
def plot_erp(data, SR=500, onsets=None,
pre=0.2, pre_onset=None, post=None, pre_mean=None,
color='r', errcolor=None, errtype=None, ax=pl,
ymult=1.0, *args, **kwargs):
"""Plot single ERP on existing canvas
Parameters
----------
data : 1D or 2D ndarray
The data array can either be 1D (samples over time) or 2D
(trials x samples). In the first case a boxcar mapper is used to
extract the respective trial timecourses given a list of trial onsets.
In the latter case, each row of the data array is taken as the EEG
signal timecourse of a particular trial.
onsets : list(int)
List of onsets (in samples not in seconds).
SR : int, optional
Sampling rate (1/s) of the signal.
pre : float, optional
Duration (in seconds) to be plotted prior to onset.
pre_onset : float or None
If data is already in epochs (2D) then pre_onset provides information
on how many seconds pre-stimulus were used to generate them. If None,
then pre_onset = pre
post : float
Duration (in seconds) to be plotted after the onset.
pre_mean : float
Duration (in seconds) at the beginning of the window which is used
for deriving the mean of the signal. If None, pre_mean = pre
errtype : None or 'ste' or 'std' or 'ci95' or list of previous three
Type of error value to be computed per datapoint. 'ste' --
standard error of the mean, 'std' -- standard deviation 'ci95'
-- 95% confidence interval (1.96 * ste), None -- no error margin
is plotted (default)
Optionally, multiple error types can be specified in a list. In that
case all of them will be plotted.
color : matplotlib color code, optional
Color to be used for plotting the mean signal timecourse.
errcolor : matplotlib color code
Color to be used for plotting the error margin. If None, use main color
but with weak alpha level
ax :
Target where to draw.
ymult : float, optional
Multiplier for the values. E.g. if negative-up ERP plot is needed:
provide ymult=-1.0
*args, **kwargs
Additional arguments to `pylab.plot`.
Returns
-------
array
Mean ERP timeseries.
"""
if pre_mean is None:
pre_mean = pre
# set default
pre_discard = 0
if onsets is not None: # if we need to extract ERPs
if post is None:
raise ValueError, \
"Duration post onsets must be provided if onsets are given"
# trial timecourse duration
duration = pre + post
# We are working with a full timeline
bcm = BoxcarMapper(onsets,
boxlength = int(SR * duration),
offset = -int(SR * pre))
erp_data = bcm(data)
# override values since we are using Boxcar
pre_onset = pre
else:
if pre_onset is None:
pre_onset = pre
if pre_onset < pre:
warning("Pre-stimulus interval to plot %g is smaller than provided "
"pre-stimulus captured interval %g, thus plot interval was "
"adjusted" % (pre, pre_onset))
pre = pre_onset
if post is None:
# figure out post
duration = float(data.shape[1]) / SR - pre_discard
post = duration - pre
else:
duration = pre + post
erp_data = data
pre_discard = pre_onset - pre
# Scale the data appropriately
erp_data *= ymult
# validity check -- we should have 2D matrix (trials x samples)
if len(erp_data.shape) != 2:
raise RuntimeError, \
"plot_erp() supports either 1D data with onsets, or 2D data " \
"(trials x sample_points). Shape of the data at the point " \
"is %s" % erp_data.shape
if not (pre_mean == 0 or pre_mean is None):
# mean of pre-onset signal accross trials
erp_baseline = np.mean(
erp_data[:, int((pre_onset-pre_mean)*SR):int(pre_onset*SR)])
# center data on pre-onset mean
# NOTE: make sure that we make a copy of the data to don't
# alter the original. Better be safe than sorry
erp_data = erp_data - erp_baseline
# generate timepoints and error ranges to plot filled error area
# top ->
# bottom <-
time_points = np.arange(erp_data.shape[1]) * 1.0 / SR - pre_onset
# if pre != pre_onset
if pre_discard > 0:
npoints = int(pre_discard * SR)
time_points = time_points[npoints:]
erp_data = erp_data[:, npoints:]
# select only time points of interest (if post is provided)
if post is not None:
npoints = int(duration * SR)
time_points = time_points[:npoints]
erp_data = erp_data[:, :npoints]
# compute mean signal timecourse accross trials
erp_mean = np.mean(erp_data, axis=0)
# give sane default
if errtype is None:
errtype = []
if not isinstance(errtype, list):
errtype = [errtype]
for et in errtype:
# compute error per datapoint
if et in ['ste', 'ci95']:
erp_stderr = erp_data.std(axis=0) / np.sqrt(len(erp_data))
if et == 'ci95':
erp_stderr *= 1.96
elif et == 'std':
erp_stderr = erp_data.std(axis=0)
else:
raise ValueError, "Unknown error type '%s'" % errtype
time_points2w = np.hstack((time_points, time_points[::-1]))
error_top = erp_mean + erp_stderr
error_bottom = erp_mean - erp_stderr
error2w = np.hstack((error_top, error_bottom[::-1]))
if errcolor is None:
errcolor = color
# plot error margin
pfill = ax.fill(time_points2w, error2w,
edgecolor=errcolor, facecolor=errcolor, alpha=0.2,
zorder=3)
# plot mean signal timecourse
ax.plot(time_points, erp_mean, lw=2, color=color, zorder=4,
*args, **kwargs)
# ax.xaxis.set_major_locator(pl.MaxNLocator(4))
return erp_mean
def eventrelated_dataset(ds, events=None, time_attr=None, match="prev", eprefix="event"):
"""Segment a dataset into a set of events.
This function can be used to extract event-related samples from any
time-series based dataset (actually, it don't have to be time series, but
could also be any other type of ordered samples). Boxcar-shaped event
samples, potentially spanning multiple input samples can be automatically
extracted using :class:`~mvpa.misc.support.Event` definition lists. For
each event all samples covering that particular event are used to form the
corresponding sample.
An event definition is a dictionary that contains ``onset`` (as sample index
in the input dataset), ``duration`` (as number of consecutive samples after
the onset), as well as an arbitrary number of additonal attributes.
Alternatively, ``onset`` and ``duration`` may also be given as real time
stamps (or durations). In this case a to be specified samples attribute in
the input dataset will be used to convert these into sample indices.
Parameters
----------
ds : Dataset
The samples of this input dataset have to be in whatever ascending order.
events : list
Each event definition has to specify ``onset`` and ``duration``. All other
attributes will be passed on to the sample attributes collection of the
returned dataset.
time_attr : str or None
If not None, the ``onset`` and ``duration`` specs from the event list will
be converted using information from this sample attribute. Its values will
be treated as in-the-same-unit and are used to determine corresponding
samples from real-value onset and duration definitions.
match : {'prev', 'next', 'closest'}
Strategy used to match real-value onsets to sample indices. 'prev' chooses
the closes preceding samples, 'next' the closest following sample and
'closest' to absolute closest sample.
eprefix : str or None
If not None, this prefix is used to name additional attributes generated
by the underlying `~mvpa.mappers.boxcar.BoxcarMapper`. If it is set to
None, no additional attributes will be created.
Returns
-------
Dataset
The returned dataset has one sample per each event definition that has
been passed to the function.
Examples
--------
The documentation also contains an :ref:`example script
<example_eventrelated>` showing a spatio-temporal analysis of fMRI data
that involves this function.
>>> from mvpa.datasets import Dataset
>>> ds = Dataset(np.random.randn(10, 25))
>>> events = [{'onset': 2, 'duration': 4},
... {'onset': 4, 'duration': 4}]
>>> eds = eventrelated_dataset(ds, events)
>>> len(eds)
2
>>> eds.nfeatures == ds.nfeatures * 4
True
>>> 'mapper' in ds.a
False
>>> print eds.a.mapper
<ChainMapper: <Boxcar: bl=4>-<Flatten>>
And now the same conversion, but with events specified as real time. This is
on possible if the input dataset contains a sample attribute with the
necessary information about the input samples.
>>> ds.sa['record_time'] = np.linspace(0, 5, len(ds))
>>> rt_events = [{'onset': 1.05, 'duration': 2.2},
... {'onset': 2.3, 'duration': 2.12}]
>>> rt_eds = eventrelated_dataset(ds, rt_events, time_attr='record_time',
... match='closest')
>>> np.all(eds.samples == rt_eds.samples)
True
>>> # returned dataset e.g. has info from original samples
>>> rt_eds.sa.record_time
array([[ 1.11111111, 1.66666667, 2.22222222, 2.77777778],
[ 2.22222222, 2.77777778, 3.33333333, 3.88888889]])
"""
# relabel argument
conv_strategy = {"prev": "floor", "next": "ceil", "closest": "round"}[match]
if not time_attr is None:
tvec = ds.sa[time_attr].value
# we are asked to convert onset time into sample ids
descr_events = []
for ev in events:
# do not mess with the input data
ev = copy.deepcopy(ev)
# best matching sample
idx = value2idx(ev["onset"], tvec, conv_strategy)
# store offset of sample time and real onset
ev["orig_offset"] = ev["onset"] - tvec[idx]
# rescue the real onset into a new attribute
ev["orig_onset"] = ev["onset"]
ev["orig_duration"] = ev["duration"]
# figure out how many sample we need
ev["duration"] = len(tvec[idx:][tvec[idx:] < ev["onset"] + ev["duration"]])
# new onset is sample index
ev["onset"] = idx
descr_events.append(ev)
else:
descr_events = events
# convert the event specs into the format expected by BoxcarMapper
# take the first event as an example of contained keys
evvars = {}
for k in descr_events[0]:
try:
evvars[k] = [e[k] for e in descr_events]
except KeyError:
raise ValueError("Each event property must be present for all " "events (could not find '%s')" % k)
# checks
for p in ["onset", "duration"]:
if not p in evvars:
raise ValueError("'%s' is a required property for all events." % p)
boxlength = max(evvars["duration"])
if __debug__:
if not max(evvars["duration"]) == min(evvars["duration"]):
warning("Boxcar mapper will use maximum boxlength (%i) of all " "provided Events." % boxlength)
# finally create, train und use the boxcar mapper
bcm = BoxcarMapper(evvars["onset"], boxlength, inspace=eprefix)
bcm.train(ds)
ds = ds.get_mapped(bcm)
# at last reflatten the dataset
# could we add some meaningful attribute during this mapping, i.e. would
# assigning 'inspace' do something good?
ds = ds.get_mapped(FlattenMapper(shape=ds.samples.shape[1:]))
# add samples attributes for the events, simply dump everything as a samples
# attribute
for a in evvars:
if not eprefix is None and a in ds.sa:
# if there is already a samples attribute like this, it got mapped
# by BoxcarMapper (i.e. is multi-dimensional). We move it aside
# under new `eprefix` name
ds.sa[eprefix + "_" + a] = ds.sa[a]
if a in ["onset", "duration"]:
# special case: we want the non-descrete, original onset and
# duration
if not time_attr is None:
# but only if there was a conversion happining, since otherwise
# we get the same info from BoxcarMapper
ds.sa[a] = [e[a] for e in events]
else:
ds.sa[a] = evvars[a]
return ds
def test_simpleboxcar():
data = np.atleast_2d(np.arange(10)).T
sp = np.arange(10)
# check if stupid thing don't work
assert_raises(ValueError, BoxcarMapper, sp, 0)
# now do an identity transformation
bcm = BoxcarMapper(sp, 1)
trans = bcm.forward(data)
# ,0 is a feature below, so we get explicit 2D out of 1D
assert_array_equal(trans[:,0], data)
# now check for illegal boxes
if __debug__:
# condition is checked only in __debug__
assert_raises(ValueError, BoxcarMapper(sp, 2).train, data)
# now something that should work
nbox = 9
boxlength = 2
sp = np.arange(nbox)
bcm = BoxcarMapper(sp, boxlength)
trans = bcm(data)
# check that is properly upcasts the dimensionality
assert_equal(trans.shape, (nbox, boxlength) + data.shape[1:])
# check actual values, squeezing the last dim for simplicity
assert_array_equal(trans.squeeze(), np.vstack((np.arange(9), np.arange(9)+1)).T)
# now test for proper data shape
data = np.ones((10,3,4,2))
sp = [ 2, 4, 3, 5 ]
trans = BoxcarMapper(sp, 4)(data)
assert_equal(trans.shape, (4,4,3,4,2))
# test reverse
data = np.arange(240).reshape(10, 3, 4, 2)
sp = [ 2, 4, 3, 5 ]
boxlength = 2
m = BoxcarMapper(sp, boxlength)
m.train(data)
mp = m.forward(data)
assert_equal(mp.shape, (4, 2, 3, 4, 2))
# try full reconstruct
mr = m.reverse(mp)
# shape has to match
assert_equal(mr.shape, (len(sp) * boxlength,) + data.shape[1:])
# only known samples are part of the results
assert_true((mr >= 24).all())
assert_true((mr < 168).all())
# check proper reconstruction of non-conflicting sample
assert_array_equal(mr[0].ravel(), np.arange(48, 72))
# check proper reconstruction of samples being part of multiple
# mapped samples
assert_array_equal(mr[1].ravel(), np.arange(72, 96))
# test reverse of a single sample
singlesample = np.arange(48).reshape(2, 3, 4, 2)
assert_array_equal(singlesample, m.reverse1(singlesample))
# should not work for shape mismatch, but it does work and is useful when
# reverse mapping sample attributes
#assert_raises(ValueError, m.reverse, singlesample[0])
# check broadcasting of 'raw' samples into proper boxcars on forward()
bc = m.forward1(np.arange(24).reshape(3, 4, 2))
assert_array_equal(bc, np.array(2 * [np.arange(24).reshape(3, 4, 2)]))
def test_simpleboxcar():
data = np.atleast_2d(np.arange(10)).T
sp = np.arange(10)
# check if stupid thing don't work
assert_raises(ValueError, BoxcarMapper, sp, 0)
# now do an identity transformation
bcm = BoxcarMapper(sp, 1)
trans = bcm.forward(data)
# ,0 is a feature below, so we get explicit 2D out of 1D
assert_array_equal(trans[:, 0], data)
# now check for illegal boxes
if __debug__:
# condition is checked only in __debug__
assert_raises(ValueError, BoxcarMapper(sp, 2).train, data)
# now something that should work
nbox = 9
boxlength = 2
sp = np.arange(nbox)
bcm = BoxcarMapper(sp, boxlength)
trans = bcm(data)
# check that is properly upcasts the dimensionality
assert_equal(trans.shape, (nbox, boxlength) + data.shape[1:])
# check actual values, squeezing the last dim for simplicity
assert_array_equal(trans.squeeze(),
np.vstack((np.arange(9), np.arange(9) + 1)).T)
# now test for proper data shape
data = np.ones((10, 3, 4, 2))
sp = [2, 4, 3, 5]
trans = BoxcarMapper(sp, 4)(data)
assert_equal(trans.shape, (4, 4, 3, 4, 2))
# test reverse
data = np.arange(240).reshape(10, 3, 4, 2)
sp = [2, 4, 3, 5]
boxlength = 2
m = BoxcarMapper(sp, boxlength)
m.train(data)
mp = m.forward(data)
assert_equal(mp.shape, (4, 2, 3, 4, 2))
# try full reconstruct
mr = m.reverse(mp)
# shape has to match
assert_equal(mr.shape, (len(sp) * boxlength, ) + data.shape[1:])
# only known samples are part of the results
assert_true((mr >= 24).all())
assert_true((mr < 168).all())
# check proper reconstruction of non-conflicting sample
assert_array_equal(mr[0].ravel(), np.arange(48, 72))
# check proper reconstruction of samples being part of multiple
# mapped samples
assert_array_equal(mr[1].ravel(), np.arange(72, 96))
# test reverse of a single sample
singlesample = np.arange(48).reshape(2, 3, 4, 2)
assert_array_equal(singlesample, m.reverse1(singlesample))
# should not work for shape mismatch, but it does work and is useful when
# reverse mapping sample attributes
#assert_raises(ValueError, m.reverse, singlesample[0])
# check broadcasting of 'raw' samples into proper boxcars on forward()
bc = m.forward1(np.arange(24).reshape(3, 4, 2))
assert_array_equal(bc, np.array(2 * [np.arange(24).reshape(3, 4, 2)]))
def testSimple(self):
"""Just the same tests as for transformWithBoxcar.
Mention that BoxcarMapper doesn't apply function with each boxcar
"""
data = N.arange(10)
sp = N.arange(10)
# check if stupid thing don't work
self.failUnlessRaises(ValueError,
BoxcarMapper,
sp,
0 )
# now do an identity transformation
bcm = BoxcarMapper(sp, 1)
trans = bcm(data)
# ,0 is a feature below, so we get explicit 2D out of 1D
self.failUnless( (trans[:,0] == data).all() )
# now check for illegal boxes
self.failUnlessRaises(ValueError,
BoxcarMapper(sp, 2),
data)
# now something that should work
sp = N.arange(9)
bcm = BoxcarMapper(sp,2)
trans = bcm(data)
self.failUnless( (trans == N.vstack((N.arange(9),
N.arange(9)+1)).T ).all() )
# now test for proper data shape
data = N.ones((10,3,4,2))
sp = [ 2, 4, 3, 5 ]
trans = BoxcarMapper(sp, 4)(data)
self.failUnless( trans.shape == (4,4,3,4,2) )
# test reverse
data = N.arange(240).reshape(10, 3, 4, 2)
sp = [ 2, 4, 3, 5 ]
m = BoxcarMapper(sp, 2)
mp = m.forward(data)
self.failUnless(mp.shape == (4, 2, 3, 4, 2))
# try full reconstruct
mr = m.reverse(mp)
# shape has to match
self.failUnless(mr.shape == data.shape)
# first two samples where not in any of the boxcars and cannot be
# reconstructed
self.failUnless(N.sum(mr[:2]) == 0)
# same for the last ones
self.failUnless(N.sum(mr[7:]) == 0)
# check proper reconstruction of non-conflicting sample
self.failUnless((mr[2].ravel() == N.arange(48, 72)).all())
# check proper reconstruction of samples being part of multiple
# mapped samples
self.failUnless((mr[3].ravel() == N.arange(72, 96)).all())
# test reverse of a single sample
singlesample = N.arange(48).reshape(2, 3, 4, 2)
self.failUnless((singlesample == m.reverse(singlesample)).all())
# should not work for shape mismatch
self.failUnlessRaises(ValueError, m.reverse, singlesample[0])
# check broadcasting of 'raw' samples into proper boxcars on forward()
bc = m.forward(N.arange(24).reshape(3, 4, 2))
self.failUnless((bc ==
N.array(2 * [N.arange(24).reshape(3, 4, 2)])).all())
def eventrelated_dataset(ds,
events=None,
time_attr=None,
match='prev',
eprefix='event'):
"""Segment a dataset into a set of events.
This function can be used to extract event-related samples from any
time-series based dataset (actually, it don't have to be time series, but
could also be any other type of ordered samples). Boxcar-shaped event
samples, potentially spanning multiple input samples can be automatically
extracted using :class:`~mvpa.misc.support.Event` definition lists. For
each event all samples covering that particular event are used to form the
corresponding sample.
An event definition is a dictionary that contains ``onset`` (as sample index
in the input dataset), ``duration`` (as number of consecutive samples after
the onset), as well as an arbitrary number of additonal attributes.
Alternatively, ``onset`` and ``duration`` may also be given as real time
stamps (or durations). In this case a to be specified samples attribute in
the input dataset will be used to convert these into sample indices.
Parameters
----------
ds : Dataset
The samples of this input dataset have to be in whatever ascending order.
events : list
Each event definition has to specify ``onset`` and ``duration``. All other
attributes will be passed on to the sample attributes collection of the
returned dataset.
time_attr : str or None
If not None, the ``onset`` and ``duration`` specs from the event list will
be converted using information from this sample attribute. Its values will
be treated as in-the-same-unit and are used to determine corresponding
samples from real-value onset and duration definitions.
match : {'prev', 'next', 'closest'}
Strategy used to match real-value onsets to sample indices. 'prev' chooses
the closes preceding samples, 'next' the closest following sample and
'closest' to absolute closest sample.
eprefix : str or None
If not None, this prefix is used to name additional attributes generated
by the underlying `~mvpa.mappers.boxcar.BoxcarMapper`. If it is set to
None, no additional attributes will be created.
Returns
-------
Dataset
The returned dataset has one sample per each event definition that has
been passed to the function.
Examples
--------
The documentation also contains an :ref:`example script
<example_eventrelated>` showing a spatio-temporal analysis of fMRI data
that involves this function.
>>> from mvpa.datasets import Dataset
>>> ds = Dataset(np.random.randn(10, 25))
>>> events = [{'onset': 2, 'duration': 4},
... {'onset': 4, 'duration': 4}]
>>> eds = eventrelated_dataset(ds, events)
>>> len(eds)
2
>>> eds.nfeatures == ds.nfeatures * 4
True
>>> 'mapper' in ds.a
False
>>> print eds.a.mapper
<ChainMapper: <Boxcar: bl=4>-<Flatten>>
And now the same conversion, but with events specified as real time. This is
on possible if the input dataset contains a sample attribute with the
necessary information about the input samples.
>>> ds.sa['record_time'] = np.linspace(0, 5, len(ds))
>>> rt_events = [{'onset': 1.05, 'duration': 2.2},
... {'onset': 2.3, 'duration': 2.12}]
>>> rt_eds = eventrelated_dataset(ds, rt_events, time_attr='record_time',
... match='closest')
>>> np.all(eds.samples == rt_eds.samples)
True
>>> # returned dataset e.g. has info from original samples
>>> rt_eds.sa.record_time
array([[ 1.11111111, 1.66666667, 2.22222222, 2.77777778],
[ 2.22222222, 2.77777778, 3.33333333, 3.88888889]])
"""
# relabel argument
conv_strategy = {
'prev': 'floor',
'next': 'ceil',
'closest': 'round'
}[match]
if not time_attr is None:
tvec = ds.sa[time_attr].value
# we are asked to convert onset time into sample ids
descr_events = []
for ev in events:
# do not mess with the input data
ev = copy.deepcopy(ev)
# best matching sample
idx = value2idx(ev['onset'], tvec, conv_strategy)
# store offset of sample time and real onset
ev['orig_offset'] = ev['onset'] - tvec[idx]
# rescue the real onset into a new attribute
ev['orig_onset'] = ev['onset']
ev['orig_duration'] = ev['duration']
# figure out how many sample we need
ev['duration'] = \
len(tvec[idx:][tvec[idx:] < ev['onset'] + ev['duration']])
# new onset is sample index
ev['onset'] = idx
descr_events.append(ev)
else:
descr_events = events
# convert the event specs into the format expected by BoxcarMapper
# take the first event as an example of contained keys
evvars = {}
for k in descr_events[0]:
try:
evvars[k] = [e[k] for e in descr_events]
except KeyError:
raise ValueError("Each event property must be present for all "
"events (could not find '%s')" % k)
# checks
for p in ['onset', 'duration']:
if not p in evvars:
raise ValueError("'%s' is a required property for all events." % p)
boxlength = max(evvars['duration'])
if __debug__:
if not max(evvars['duration']) == min(evvars['duration']):
warning('Boxcar mapper will use maximum boxlength (%i) of all '
'provided Events.' % boxlength)
# finally create, train und use the boxcar mapper
bcm = BoxcarMapper(evvars['onset'], boxlength, inspace=eprefix)
bcm.train(ds)
ds = ds.get_mapped(bcm)
# at last reflatten the dataset
# could we add some meaningful attribute during this mapping, i.e. would
# assigning 'inspace' do something good?
ds = ds.get_mapped(FlattenMapper(shape=ds.samples.shape[1:]))
# add samples attributes for the events, simply dump everything as a samples
# attribute
for a in evvars:
if not eprefix is None and a in ds.sa:
# if there is already a samples attribute like this, it got mapped
# by BoxcarMapper (i.e. is multi-dimensional). We move it aside
# under new `eprefix` name
ds.sa[eprefix + '_' + a] = ds.sa[a]
if a in ['onset', 'duration']:
# special case: we want the non-descrete, original onset and
# duration
if not time_attr is None:
# but only if there was a conversion happining, since otherwise
# we get the same info from BoxcarMapper
ds.sa[a] = [e[a] for e in events]
else:
ds.sa[a] = evvars[a]
return ds