def reorder_values_array(arr, variables):
for col, var in enumerate(variables):
if getattr(var, "fix_order", False) and len(var.values) < 1000:
new_order = var.ordered_values(var.values)
if new_order == var.values:
continue
arr[:, col] += 1000
for i, val in enumerate(var.values):
bn.replace(arr[:, col], 1000 + i, new_order.index(val))
var.values = new_order
delattr(var, "fix_order")
def test_replace_nan_int():
"Test replace, int array, old=nan, new=0"
a = np.arange(2 * 3 * 4).reshape(2, 3, 4)
actual = a.copy()
bn.replace(actual, np.nan, 0)
desired = a.copy()
msg = 'replace failed on int input looking for nans'
assert_array_equal(actual, desired, err_msg=msg)
actual = a.copy()
bn.slow.replace(actual, np.nan, 0)
msg = 'slow.replace failed on int input looking for nans'
assert_array_equal(actual, desired, err_msg=msg)
def test_replace_nan_int():
"Test replace, int array, old=nan, new=0"
a = np.arange(2*3*4).reshape(2,3,4)
actual = a.copy()
bn.replace(actual, np.nan, 0)
desired = a.copy()
msg = 'replace failed on int input looking for nans'
assert_array_equal(actual, desired, err_msg=msg)
actual = a.copy()
bn.slow.replace(actual, np.nan, 0)
msg = 'slow.replace failed on int input looking for nans'
assert_array_equal(actual, desired, err_msg=msg)
def reorder_values_array(self, arr, variables):
newvars = []
for col, var in enumerate(variables):
if getattr(var, "fix_order", False):
nvar = var.make(var.name, var.values, var.ordered)
nvar.attributes = var.attributes
move = len(var.values)
if nvar.values != var.values:
arr[:, col] += move
for i, val in enumerate(var.values):
bn.replace(arr[:, col], move + i, nvar.values.index(val))
var = nvar
newvars.append(var)
return newvars
def reorder_values_array(self, arr, variables):
newvars = []
for col, var in enumerate(variables):
if getattr(var, "fix_order", False):
nvar = var.make(var.name, var.values, var.ordered)
nvar.attributes = var.attributes
move = len(var.values)
if nvar.values != var.values:
arr[:, col] += move
for i, val in enumerate(var.values):
bn.replace(arr[:, col], move + i,
nvar.values.index(val))
var = nvar
newvars.append(var)
return newvars
def data_table(self, data, headers=None):
"""
Return Orange.data.Table given rows of `headers` (iterable of iterable)
and rows of `data` (iterable of iterable; if ``numpy.ndarray``, might
as well **have it sorted column-major**, e.g. ``order='F'``).
Basically, the idea of subclasses is to produce those two iterables,
however they might.
If `headers` is not provided, the header rows are extracted from `data`,
assuming they precede it.
"""
if not headers:
headers, data = self.parse_headers(data)
# Consider various header types (single-row, two-row, three-row, none)
if 3 == len(headers):
names, types, flags = map(list, headers)
else:
if 1 == len(headers):
HEADER1_FLAG_SEP = '#'
# First row format either:
# 1) delimited column names
# 2) -||- with type and flags prepended, separated by #,
# e.g. d#sex,c#age,cC#IQ
_flags, names = zip(*[
i.split(HEADER1_FLAG_SEP, 1) if HEADER1_FLAG_SEP in i else
('', i) for i in headers[0]
])
names = list(names)
elif 2 == len(headers):
names, _flags = map(list, headers)
else:
# Use heuristics for everything
names, _flags = [], []
types = [
''.join(filter(str.isupper, flag)).lower() for flag in _flags
]
flags = [Flags.join(filter(str.islower, flag)) for flag in _flags]
# Determine maximum row length
rowlen = max(map(len, (names, types, flags)))
def _equal_length(lst):
lst.extend([''] * (rowlen - len(lst)))
return lst
# Ensure all data is of equal width in a column-contiguous array
data = np.array([_equal_length(list(row)) for row in data if any(row)],
copy=False,
dtype=object,
order='F')
# Data may actually be longer than headers were
try:
rowlen = data.shape[1]
except IndexError:
pass
else:
for lst in (names, types, flags):
_equal_length(lst)
NAMEGEN = namegen('Feature ', 1)
Xcols, attrs = [], []
Mcols, metas = [], []
Ycols, clses = [], []
Wcols = []
# Iterate through the columns
for col in range(rowlen):
flag = Flags(Flags.split(flags[col]))
if flag.i: continue
type_flag = types and types[col].strip()
try:
orig_values = [
np.nan if i in MISSING_VALUES else i
for i in (i.strip() for i in data[:, col])
]
except IndexError:
# No data instances leads here
orig_values = []
# In this case, coltype could be anything. It's set as-is
# only to satisfy test_table.TableTestCase.test_append
coltype = DiscreteVariable
coltype_kwargs = {}
valuemap = []
values = orig_values
if type_flag in StringVariable.TYPE_HEADERS:
coltype = StringVariable
elif type_flag in ContinuousVariable.TYPE_HEADERS:
coltype = ContinuousVariable
try:
values = [float(i) for i in orig_values]
except ValueError:
for row, num in enumerate(orig_values):
try:
float(num)
except ValueError:
break
raise ValueError('Non-continuous value in (1-based) '
'line {}, column {}'.format(
row + len(headers) + 1, col + 1))
elif type_flag in TimeVariable.TYPE_HEADERS:
coltype = TimeVariable
elif (type_flag in DiscreteVariable.TYPE_HEADERS
or _RE_DISCRETE_LIST.match(type_flag)):
if _RE_DISCRETE_LIST.match(type_flag):
valuemap = Flags.split(type_flag)
coltype_kwargs.update(ordered=True)
else:
valuemap = sorted(set(orig_values) - {np.nan})
else:
# No known type specified, use heuristics
is_discrete = is_discrete_values(orig_values)
if is_discrete:
valuemap = sorted(is_discrete)
else:
try:
values = [float(i) for i in orig_values]
except ValueError:
tvar = TimeVariable('_')
try:
values = [tvar.parse(i) for i in orig_values]
except ValueError:
coltype = StringVariable
else:
coltype = TimeVariable
else:
coltype = ContinuousVariable
if valuemap:
# Map discrete data to ints
def valuemap_index(val):
try:
return valuemap.index(val)
except ValueError:
return np.nan
values = np.vectorize(valuemap_index,
otypes=[float])(orig_values)
coltype = DiscreteVariable
coltype_kwargs.update(values=valuemap)
if coltype is StringVariable:
values = ['' if i is np.nan else i for i in orig_values]
if flag.m or coltype is StringVariable:
append_to = (Mcols, metas)
elif flag.w:
append_to = (Wcols, None)
elif flag.c:
append_to = (Ycols, clses)
else:
append_to = (Xcols, attrs)
cols, domain_vars = append_to
cols.append(col)
if domain_vars is not None:
if names and names[col]:
# Use existing variable if available
var = coltype.make(names[col].strip(), **coltype_kwargs)
else:
# Never use existing for un-named variables
var = coltype(next(NAMEGEN), **coltype_kwargs)
var.attributes.update(flag.attributes)
domain_vars.append(var)
# Reorder discrete values to match existing variable
if var.is_discrete and not var.ordered:
new_order, old_order = var.values, coltype_kwargs.get(
'values', var.values)
if new_order != old_order:
offset = len(new_order)
column = values if data.ndim > 1 else data
column += offset
for i, val in enumerate(var.values):
try:
oldval = old_order.index(val)
except ValueError:
continue
bn.replace(column, offset + oldval,
new_order.index(val))
if coltype is TimeVariable:
# Re-parse the values because only now after coltype.make call
# above, variable var is the correct one
values = [var.parse(i) for i in orig_values]
# Write back the changed data. This is needeed to pass the
# correct, converted values into Table.from_numpy below
try:
data[:, col] = values
except IndexError:
pass
domain = Domain(attrs, clses, metas)
if not data.size:
return Table.from_domain(domain, 0)
table = Table.from_numpy(domain, data[:, Xcols].astype(float,
order='C'),
data[:, Ycols].astype(float, order='C'),
data[:, Mcols].astype(object, order='C'),
data[:, Wcols].astype(float, order='C'))
return table
def data_table(self, data, headers=None):
"""
Return Orange.data.Table given rows of `headers` (iterable of iterable)
and rows of `data` (iterable of iterable; if ``numpy.ndarray``, might
as well **have it sorted column-major**, e.g. ``order='F'``).
Basically, the idea of subclasses is to produce those two iterables,
however they might.
If `headers` is not provided, the header rows are extracted from `data`,
assuming they precede it.
"""
if not headers:
headers, data = self.parse_headers(data)
# Consider various header types (single-row, two-row, three-row, none)
if 3 == len(headers):
names, types, flags = map(list, headers)
else:
if 1 == len(headers):
HEADER1_FLAG_SEP = '#'
# First row format either:
# 1) delimited column names
# 2) -||- with type and flags prepended, separated by #,
# e.g. d#sex,c#age,cC#IQ
_flags, names = zip(*[i.split(HEADER1_FLAG_SEP, 1) if HEADER1_FLAG_SEP in i else ('', i)
for i in headers[0]])
names = list(names)
elif 2 == len(headers):
names, _flags = map(list, headers)
else:
# Use heuristics for everything
names, _flags = [], []
types = [''.join(filter(str.isupper, flag)).lower() for flag in _flags]
flags = [Flags.join(filter(str.islower, flag)) for flag in _flags]
# Determine maximum row length
rowlen = max(map(len, (names, types, flags)))
def _equal_length(lst):
lst.extend(['']*(rowlen - len(lst)))
return lst
# Ensure all data is of equal width in a column-contiguous array
data = np.array([_equal_length(list(row)) for row in data if any(row)],
copy=False, dtype=object, order='F')
# Data may actually be longer than headers were
try: rowlen = data.shape[1]
except IndexError: pass
else:
for lst in (names, types, flags):
_equal_length(lst)
NAMEGEN = namegen('Feature ', 1)
Xcols, attrs = [], []
Mcols, metas = [], []
Ycols, clses = [], []
Wcols = []
# Iterate through the columns
for col in range(rowlen):
flag = Flags(Flags.split(flags[col]))
if flag.i: continue
type_flag = types and types[col].strip()
try:
orig_values = [np.nan if i in MISSING_VALUES else i
for i in (i.strip() for i in data[:, col])]
except IndexError:
# No data instances leads here
orig_values = []
# In this case, coltype could be anything. It's set as-is
# only to satisfy test_table.TableTestCase.test_append
coltype = DiscreteVariable
coltype_kwargs = {}
valuemap = []
values = orig_values
if type_flag in StringVariable.TYPE_HEADERS:
coltype = StringVariable
elif type_flag in ContinuousVariable.TYPE_HEADERS:
coltype = ContinuousVariable
try:
values = [float(i) for i in orig_values]
except ValueError:
for row, num in enumerate(orig_values):
try: float(num)
except ValueError: break
raise ValueError('Non-continuous value in (1-based) '
'line {}, column {}'.format(row + len(headers) + 1,
col + 1))
elif type_flag in TimeVariable.TYPE_HEADERS:
coltype = TimeVariable
elif (type_flag in DiscreteVariable.TYPE_HEADERS or
_RE_DISCRETE_LIST.match(type_flag)):
if _RE_DISCRETE_LIST.match(type_flag):
valuemap = Flags.split(type_flag)
coltype_kwargs.update(ordered=True)
else:
valuemap = sorted(set(orig_values) - {np.nan})
else:
# No known type specified, use heuristics
is_discrete = is_discrete_values(orig_values)
if is_discrete:
valuemap = sorted(is_discrete)
else:
try: values = [float(i) for i in orig_values]
except ValueError:
tvar = TimeVariable('_')
try: values = [tvar.parse(i) for i in orig_values]
except ValueError:
coltype = StringVariable
else:
coltype = TimeVariable
else:
coltype = ContinuousVariable
if valuemap:
# Map discrete data to ints
def valuemap_index(val):
try: return valuemap.index(val)
except ValueError: return np.nan
values = np.vectorize(valuemap_index, otypes=[float])(orig_values)
coltype = DiscreteVariable
coltype_kwargs.update(values=valuemap)
if coltype is StringVariable:
values = ['' if i is np.nan else i
for i in orig_values]
if flag.m or coltype is StringVariable:
append_to = (Mcols, metas)
elif flag.w:
append_to = (Wcols, None)
elif flag.c:
append_to = (Ycols, clses)
else:
append_to = (Xcols, attrs)
cols, domain_vars = append_to
cols.append(col)
if domain_vars is not None:
if names and names[col]:
# Use existing variable if available
var = coltype.make(names[col].strip(), **coltype_kwargs)
else:
# Never use existing for un-named variables
var = coltype(next(NAMEGEN), **coltype_kwargs)
var.attributes.update(flag.attributes)
domain_vars.append(var)
# Reorder discrete values to match existing variable
if var.is_discrete and not var.ordered:
new_order, old_order = var.values, coltype_kwargs.get('values', var.values)
if new_order != old_order:
offset = len(new_order)
column = values if data.ndim > 1 else data
column += offset
for i, val in enumerate(var.values):
try: oldval = old_order.index(val)
except ValueError: continue
bn.replace(column, offset + oldval, new_order.index(val))
if coltype is TimeVariable:
# Re-parse the values because only now after coltype.make call
# above, variable var is the correct one
values = [var.parse(i) for i in orig_values]
# Write back the changed data. This is needeed to pass the
# correct, converted values into Table.from_numpy below
try: data[:, col] = values
except IndexError: pass
from Orange.data import Table, Domain
domain = Domain(attrs, clses, metas)
if not data.size:
return Table.from_domain(domain, 0)
table = Table.from_numpy(domain,
data[:, Xcols].astype(float, order='C'),
data[:, Ycols].astype(float, order='C'),
data[:, Mcols].astype(object, order='C'),
data[:, Wcols].astype(float, order='C'))
return table
