def set(self, address):
"""
This parameter stores a biovars.Address object.
"""
if isinstance(address, basestring):
address = self._p._dataset.experiment.variables.get(address)
if address is None or isaddress(address):
Param.set(self, address)
else:
Param.set(self, asaddress(address))
def initWithSegments_over_(self, segments, over, exclude=None,
func=None, mp=False, **kwargs):
"""
kwargs:
func=None: is initially applied to the whole data cube; can be string
'phase'--> x/abs(x)
else: eval
mp=True: use multiprocessing
v=False verbose mode
"""
raise NotImplementedError("TODO: get this method out of here!")
# interpret func
if func == None:
def func(x):
return x
elif func=='phase':
def func(x):
return x/abs(x)
elif type(func)==str:
func = eval(func)
#logging.debug( 'func'+str(func) )
# start
t0 = time.time()
self._properties.update(kwargs)
kwargs['out']='data'
if exclude:
over = over!=exclude
else:
over = asaddress(over)
segs_sorted = over.sort(segments)
slist = segs_sorted.keys()
slist.sort()
self._properties.update({'slist':slist,
'svar':over,
'avars': '???',
'address': '???'})
# determine shape
seg1 = segs_sorted[slist[0]][0]
data1 = seg1.subdata(**kwargs)
shape = data1.shape
# create empty array
self._data = np.empty(shape + (len(slist),))
# collect data
for i, s in enumerate(slist):
segs = segs_sorted[s]
assert len(segs) > 0, "No data for %s"%str(s)
data = np.empty(shape + (len(segs),))
for j, seg in enumerate(segs):
segdata = seg.subdata(**kwargs)
if shape == segdata.shape:
data[...,j] = segdata
else:
msg = "'{n}' shape {s1} does not match the shape {s}"
msg.format(n=seg.name, s1=segdata.shape, s=shape)
raise ValueError(msg)
self._data[...,i] = data.mean(-1)
# info
#segInfo = ' '.join(['%s:%s'%(k, str(len(v)).rjust(3)) for k,v in segments.iteritems()])
print ' '.join([self.name[:10], 'over', over.name[:10],
": time %.1f s"%(time.time()-t0)])
return self
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 set_cov(self, covs):
"list of variables"
if covs:
self._covs = _vars.asaddress(covs).keys()
else:
self._covs = []