def collect( self ):
'''collect all data.
Data is stored in a multi-level dictionary (DataTree)
'''
self.data = odict()
self.debug( "%s: collecting data paths." % (self.tracker))
is_function, datapaths = self.getDataPaths(self.tracker)
self.debug( "%s: collected data paths." % (self.tracker))
# if function, no datapaths
if is_function:
d = self.getData( () )
# save in data tree as leaf
DataTree.setLeaf( self.data, ("all",), d )
self.debug( "%s: collecting data finished for function." % (self.tracker))
return
# if no tracks, error
if len(datapaths) == 0 or len(datapaths[0]) == 0:
self.warn( "%s: no tracks found - no output" % self.tracker )
return
self.debug( "%s: filtering data paths." % (self.tracker))
# filter data paths
datapaths = self.filterDataPaths( datapaths )
self.debug( "%s: filtered data paths." % (self.tracker))
# if no tracks, error
if len(datapaths) == 0 or len(datapaths[0]) == 0:
self.warn( "%s: no tracks remain after filtering - no output" % self.tracker )
return
self.debug( "%s: building all_paths" % (self.tracker ) )
if len(datapaths) > MAX_PATH_NESTING:
self.warn( "%s: number of nesting in data paths too large: %i" % (self.tracker, len(all_paths)))
raise ValueError( "%s: number of nesting in data paths too large: %i" % (self.tracker, len(all_paths)))
all_paths = list(itertools.product( *datapaths ))
self.debug( "%s: collecting data started for %i data paths" % (self.tracker,
len( all_paths) ) )
self.data = odict()
for path in all_paths:
d = self.getData( path )
# ignore empty data sets
if d is None: continue
# save in data tree as leaf
DataTree.setLeaf( self.data, path, d )
self.debug( "%s: collecting data finished for %i data paths" % (self.tracker,
len( all_paths) ) )
return self.data
def transform(self, data, path):
debug( "%s: called" % str(self))
vals = data.keys()
new_data = odict()
for x1 in range(len(vals)-1):
n1 = vals[x1]
# find the first field that fits
for field in self.fields:
if field in data[n1]:
d1 = data[n1][field]
break
else:
raise KeyError("could not find any match from '%s' in '%s'" % (str(data[n1].keys()), str(self.fields )))
for x2 in range(x1+1, len(vals)):
n2 = vals[x2]
try:
d2 = data[n2][field]
except KeyErrror:
raise KeyError("no field %s in '%s'" % sttr(data[n2]))
## check if array?
if len(d1) != len(d2):
raise ValueError("length of elements not equal: %i != %i" % (len(d1), len(d2)))
DataTree.setLeaf( new_data, ( ("%s x %s" % (n1, n2) ), n1),
d1 )
DataTree.setLeaf( new_data, ( ("%s x %s" % (n1, n2) ), n2),
d2 )
return new_data
def __call__(self, data ):
if self.nlevels == None: raise NotImplementedError("incomplete implementation of %s" % str(self))
labels = DataTree.getPaths( data )
debug( "transform: started with paths: %s" % labels)
assert len(labels) >= self.nlevels, "expected at least %i levels - got %i" % (self.nlevels, len(labels))
paths = list(itertools.product( *labels[:-self.nlevels] ))
for path in paths:
work = DataTree.getLeaf( data, path )
if not work: continue
new_data = self.transform( work, path )
if new_data:
if path:
DataTree.setLeaf( data, path, new_data )
else:
# set new root
data = new_data
else:
warn( "no data at %s - removing branch" % str(path))
DataTree.removeLeaf( data, path )
debug( "transform: finished with paths: %s" % DataTree.getPaths( data ))
return data
def collect(self):
"""collect all data.
Data is stored in a multi-level dictionary (DataTree)
"""
self.data = odict()
is_function, datapaths = self.getDataPaths(self.tracker)
# if function, no datapaths
if is_function:
d = self.getData(())
# save in data tree as leaf
DataTree.setLeaf(self.data, ("all",), d)
self.debug("%s: collecting data finished for function." % (self.tracker))
return
# if no tracks, error
if len(datapaths) == 0 or len(datapaths[0]) == 0:
self.warn("%s: no tracks found - no output" % self.tracker)
raise ValueError("no tracks found from %s" % self.tracker)
# filter data paths
datapaths = self.filterDataPaths(datapaths)
# if no tracks, error
if len(datapaths) == 0 or len(datapaths[0]) == 0:
self.warn("%s: no tracks remain after filtering - no output" % self.tracker)
raise ValueError("no tracks found from %s" % self.tracker)
all_paths = list(itertools.product(*datapaths))
self.debug("%s: collecting data started for %i data paths" % (self.tracker, len(all_paths)))
self.data = odict()
for path in all_paths:
d = self.getData(path)
# ignore empty data sets
if d == None:
continue
# save in data tree as leaf
DataTree.setLeaf(self.data, path, d)
self.debug("%s: collecting data finished for %i data paths" % (self.tracker, len(all_paths)))
def transform(self,data,path):
from rpy2.robjects import r as R
paths, lengths, values = [],[],[]
labels = DataTree.getPaths(data)
paths = list(itertools.product( *labels[:-1]))
for path in paths:
work = DataTree.getLeaf(data, path)
try:
lengths.append(len(work[self.pval]))
values.extend(work[self.pval])
except TypeError:
lengths.append(0)
values.append(work[self.pval])
padj = R["p.adjust"](values, method = self.method)
padj = [x for x in padj]
for path in paths:
num = lengths.pop(0)
if num > 0:
new_values = padj[0:num]
padj = padj[num:]
else:
new_values = padj[0]
padj = padj[1:]
if path:
work = odict(DataTree.getLeaf(data,path))
work["P-adjust"] = new_values
DataTree.setLeaf(data,path,work)
else:
data["P-adjust"] = new_values
return data
