def run_benchmark_iter(self,sizes=None):
'''return a table of runtimes for all functions for a range of data sizes'''
group = self.group
if sizes is None:
sizes = group.bench_sizes
rawdata = self.make_data(group.nin,group.itypes,max(sizes))
out = group._prep_testdata(*rawdata)
if isinstance(out,tuple):
alldata,kwargs = out
else:
alldata,kwargs = out,{}
names = [name for (name,func) in self.testfuncs]
perfseen = UniTable(keys=['_n_']+names)
skiplist = []
for i,size in enumerate(sizes):
perf = {'_n_':size}
reference = None
for name,func in self.testfuncs:
if name in skiplist:
perf[name] = self.NA
continue
timings,results = self.run_tests(func,alldata,[size],kwargs=kwargs)
rate = timings[0]
perf[name] = rate
if self.too_long(rate=rate):
skiplist.append(name)
if reference is None:
reference = results
elif results is not None:
self.compare_data(reference,results,name)
perfseen.append(perf)
yield perfseen.copy()
def __init__(self, filename, target, inputs=None, threshold=1.0e-9):
CountsBase.__init__(self, threshold=threshold)
if isinstance(filename, UniTable):
data = filename
else:
data = UniTable().fromfile(filename)
self.model_build(data, target, inputs)
self.verify_result = verify = UniTable()
verify['orig'] = data[self.target]
verify['pred'] = self.model_predict(data)
verify['agree'] = verify['orig'] == verify['pred']
self.accuracy = float(verify['agree'].sum()) / len(data)
def run_benchmark(self,sizes=None):
'''return a table of runtimes for all functions for a range of data sizes'''
group = self.group
if sizes is None:
sizes = group.bench_sizes
performance = UniTable()
performance['_n_'] = sizes
rawdata = self.make_data(group.nin,group.itypes,max(sizes))
out = group._prep_testdata(*rawdata)
if isinstance(out,tuple):
alldata,kwargs = out
else:
alldata,kwargs = out,{}
reference = None
for (name,func) in self.testfuncs:
timings,results = self.run_tests(func,alldata,sizes,kwargs=kwargs)
if len(timings) == len(performance):
performance[name] = timings
else:
missing = len(performance)-len(timings)
performance[name] = list(timings) + [self.NA]*missing
results = list(results) + [None]*missing
if reference is None:
reference = results
elif results is not None:
self.compare_data(reference,results,name)
return performance
def top_ten(filenames):
# track values for each field
seen_fields = {}
total_recs = 0
# read each file in turn
for filename in filenames:
tbl = UniTable()
tbl.fromfile(filename)
keys = tbl.keys()[:]
if '_count_' in keys:
total_recs += tbl['_count_'].sum()
keys.remove('_count_')
else:
total_recs += len(tbl)
tbl['_count_'] = 1
# read each column in turn
for key in keys:
seen_values = seen_fields.setdefault(key, {})
# iterate over counts and values
for cnt, value in izip(tbl['_count_'], tbl[key]):
try:
seen_values[value] += cnt
except KeyError:
seen_values[value] = cnt
# report results
for key, seen_values in seen_fields.items():
# find top ten
top_cnts = sorted(seen_values.values())
cutoff = top_cnts[-10:][0]
tmp = sorted([cnt, value] for (value, cnt) in seen_values.items()
if cnt >= cutoff)
top = reversed(tmp[-10:])
# report
print 'Field:', key
for (cnt, value) in top:
percent = 100.0 * cnt / float(total_recs)
print '\t(%8.5f%%) %r' % (percent, value)
def top_ten(filenames):
# track values for each field
seen_fields = {}
total_recs = 0
# read each file in turn
for filename in filenames:
tbl = UniTable()
tbl.fromfile(filename)
keys = tbl.keys()[:]
if '_count_' in keys:
total_recs += tbl['_count_'].sum()
keys.remove('_count_')
else:
total_recs += len(tbl)
tbl['_count_'] = 1
# read each column in turn
for key in keys:
seen_values = seen_fields.setdefault(key,{})
# iterate over counts and values
for cnt,value in izip(tbl['_count_'],tbl[key]):
try:
seen_values[value] += cnt
except KeyError:
seen_values[value] = cnt
# report results
for key,seen_values in seen_fields.items():
# find top ten
top_cnts = sorted(seen_values.values())
cutoff = top_cnts[-10:][0]
tmp = sorted([cnt,value] for (value,cnt) in seen_values.items() if cnt >= cutoff)
top = reversed(tmp[-10:])
# report
print 'Field:', key
for (cnt,value) in top:
percent = 100.0*cnt/float(total_recs)
print '\t(%8.5f%%) %r' % (percent,value)
def __init__(self,filename=None,keys=[]):
self.keys = keys
self.data = data = {'':0} # try to pre-assign empty string value
self.filename = filename
if filename and os.path.exists(filename):
from augustus.kernel.unitable import UniTable
tbl = UniTable().fromfile(filename)
for i,value in it.izip(tbl['index'],tbl['data']):
data[value] = i
del tbl
def _make_tbl(self, cfunc, ccfunc):
out = UniTable()
ikvlist = list(self.iter_ikv())
out['__fld__'] = [''] + [ikv[0] for ikv in ikvlist]
out['__val__'] = [''] + [ikv[1] for ikv in ikvlist]
for tval in self.all_tval():
value = cfunc(tval)
ikv_vals = [ccfunc(tval, ikey, ival) for (ikey, ival) in ikvlist]
out[str(tval)] = [value] + ikv_vals
return str(out)
def test1(self):
data = {
'a': (1, 2, 3),
'ts': (34567, 35678, 34657),
'values': (5.4, 2.2, 9.9)
}
keyorder = ('a', 'ts', 'values')
t = UniTable(keys=keyorder, **data)
rec = t[0]
assert rec[0] == 1
def receive_unitable(self):
_csvargs = {}
if self.types is not None:
_csvargs['types'] = self.types
try:
if self.header is None:
if self.sep is None:
#No special treatment needed
if ((len(_csvargs) == 0) and (self.ffConvert is None)):
return UniTable().fromfile(self.handle)
elif (self.ffConvert is not None):
# Jonathan's clean solution:
fields = self.ffConvert.fields
return UniTable().from_fixed_width_file(
self.handle, fields)
else:
return UniTable().from_csv_file(
self.handle, **_csvargs)
else:
return UniTable().from_csv_file(self.handle,
insep=self.sep,
**_csvargs)
else:
if self.sep is None:
return UniTable().from_csv_file(self.handle,
header=self.header,
**_csvargs)
else:
return UniTable().from_csv_file(self.handle,
header=self.header,
insep=self.sep,
**_csvargs)
except:
return None
def flush(self):
if self.filename and len(self.data) > 1:
from augustus.kernel.unitable import UniTable
tbl = UniTable(keys=['index','data'])
tmp = self.data.items()
tbl['index'] = [x[1] for x in tmp]
tbl['data'] = [x[0] for x in tmp]
del tmp
tbl.sort_on('index')
tbl.to_csv_file(self.filename)
del tbl
def receive_unitable(self):
_csvargs={}
if self.types is not None:
_csvargs['types'] = self.types
if self.sep is not None:
_csvargs['insep'] = self.sep
if self.header is not None:
_csvargs['header'] = self.header
try:
if self.header is None:
if self.sep is None:
#No special treatment needed
if ((len(_csvargs) == 0) and (self.ffConvert is None)):
u = UniTable()
if self.framing != 'EOF':
#New size-framed stream
u.fromfile(self.handle, bufferFramed=True, chunksize=self.chunksize)
d = u.get_csv_dialect()
self.sep = d.delimiter
self.header = self.sep.join(u.keys())
else:
# Traditional file-framed:
u.fromfile(self.handle, bufferFramed=False, chunksize=self.chunksize)
return u
elif self.ffConvert is not None:
# Jonathan's clean solution:
fields = self.ffConvert.fields
return UniTable().from_fixed_width_file(self.handle, fields)
else:
return UniTable().from_csv_file(self.handle,**_csvargs)
else:
u = UniTable()
if self.framing != 'EOF':
#New size-framed stream
u.fromfile(self.handle, bufferFramed=True, insep = self.sep, chunksize=self.chunksize, **_csvargs)
self.header = self.sep.join(u.keys())
else:
# Traditional file-framed:
u.fromfile(self.handle, insep = self.sep, bufferFramed=False, chunksize=self.chunksize, **_csvargs)
return u
#return UniTable().from_csv_file(self.handle, insep = self.sep, **_csvargs)
else:
if self.framing != 'EOF':
# A header exists so a prior read has been made.
if self.sep is None:
return UniTable().from_csv_file(self.handle, bufferFramed=True, chunksize=self.chunksize, header = self.header, **_csvargs)
else:
return UniTable().from_csv_file(self.handle, bufferFramed=True, chunksize=self.chunksize, header = self.header, insep = self.sep, **_csvargs)
else:
return UniTable().from_csv_file(self.handle, bufferFramed=False, **_csvargs)
except Exception, inst:
#print "Exception is: {0}".format(type(inst))
#print inst.args
#print inst
return None