def copy_table(tbl, start=0, stop=None, blen=None, storage=None,
create='table', **kwargs):
"""Copy `tbl` block-wise into a new table."""
# setup
names, columns = _util.check_table_like(tbl)
storage = _util.get_storage(storage)
blen = _util.get_blen_table(tbl, blen)
if stop is None:
stop = len(columns[0])
else:
stop = min(stop, len(columns[0]))
length = stop - start
if length < 0:
raise ValueError('invalid stop/start')
# copy block-wise
out = None
for i in range(start, stop, blen):
j = min(i+blen, stop)
res = [np.asanyarray(c[i:j]) for c in columns]
if out is None:
out = getattr(storage, create)(res, names=names,
expectedlen=length, **kwargs)
else:
out.append(res)
return out
def compress_table(tbl, condition, blen=None, storage=None, create='table',
**kwargs):
"""Return selected rows of a table."""
# setup
storage = _util.get_storage(storage)
names, columns = _util.check_table_like(tbl)
blen = _util.get_blen_table(tbl, blen)
_util.check_equal_length(columns[0], condition)
length = len(columns[0])
nnz = count_nonzero(condition)
# block iteration
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
bcond = np.asanyarray(condition[i:j])
# don't access any data unless we have to
if np.any(bcond):
bcolumns = [np.asanyarray(c[i:j]) for c in columns]
res = [np.compress(bcond, c, axis=0) for c in bcolumns]
if out is None:
out = getattr(storage, create)(res, names=names,
expectedlen=nnz, **kwargs)
else:
out.append(res)
return out
def concatenate_table(tup, blen=None, storage=None, create='table', **kwargs):
"""Stack tables in sequence vertically (row-wise)."""
# setup
storage = _util.get_storage(storage)
if not isinstance(tup, (tuple, list)):
raise ValueError('expected tuple or list, found %r' % tup)
if len(tup) < 2:
raise ValueError('expected two or more tables to stack')
# build output
expectedlen = sum(len(t) for t in tup)
out = None
tnames = None
for tdata in tup:
tblen = _util.get_blen_table(tdata, blen)
tnames, tcolumns = _util.check_table_like(tdata, names=tnames)
tlen = len(tcolumns[0])
for i in range(0, tlen, tblen):
j = min(i + tblen, tlen)
bcolumns = [c[i:j] for c in tcolumns]
if out is None:
out = getattr(storage, create)(bcolumns,
names=tnames,
expectedlen=expectedlen,
**kwargs)
else:
out.append(bcolumns)
return out
def compress_table(tbl, condition, blen=None, storage=None, create='table',
**kwargs):
"""Return selected rows of a table."""
# setup
storage = _util.get_storage(storage)
names, columns = _util.check_table_like(tbl)
blen = _util.get_blen_table(tbl, blen)
_util.check_equal_length(columns[0], condition)
length = len(columns[0])
nnz = count_nonzero(condition)
# block iteration
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
bcond = np.asanyarray(condition[i:j])
# don't access any data unless we have to
if np.any(bcond):
bcolumns = [np.asanyarray(c[i:j]) for c in columns]
res = [np.compress(bcond, c, axis=0) for c in bcolumns]
if out is None:
out = getattr(storage, create)(res, names=names,
expectedlen=nnz, **kwargs)
else:
out.append(res)
return out
def table(self, data, names=None, expectedlen=None, **kwargs):
# setup
names, columns = _util.check_table_like(data, names=names)
# obtain group
h5g = kwargs.pop('group', None)
if h5g is None:
# open file, use root group
h5g, kwargs = self.open_file(**kwargs)
# create columns
for n, c in zip(names, columns):
self.create_dataset(h5g,
data=c,
name=n,
expectedlen=expectedlen,
**kwargs)
# patch in append method
h5g.append = MethodType(_table_append, h5g)
# patch in names attribute
h5g.names = names
return h5g
def copy_table(tbl,
start=0,
stop=None,
blen=None,
storage=None,
create='table',
**kwargs):
"""Copy `tbl` block-wise into a new table."""
# setup
names, columns = _util.check_table_like(tbl)
storage = _util.get_storage(storage)
blen = _util.get_blen_table(tbl, blen)
if stop is None:
stop = len(columns[0])
else:
stop = min(stop, len(columns[0]))
length = stop - start
if length < 0:
raise ValueError('invalid stop/start')
# copy block-wise
out = None
for i in range(start, stop, blen):
j = min(i + blen, stop)
res = [c[i:j] for c in columns]
if out is None:
out = getattr(storage, create)(res,
names=names,
expectedlen=length,
**kwargs)
else:
out.append(res)
return out
def __init__(self, data, names=None):
names, columns = _util.check_table_like(data, names=names)
# skip super-class constructor because we are more flexible about type of values here
self._values = data
self._names = names
self._columns = columns
self.rowcls = namedtuple('row', names)
def vstack_table(tup, blen=None, storage=None, create='table', **kwargs):
"""Stack tables in sequence vertically (row-wise)."""
# setup
storage = _util.get_storage(storage)
if not isinstance(tup, (tuple, list)):
raise ValueError('expected tuple or list, found %r' % tup)
if len(tup) < 2:
raise ValueError('expected two or more tables to stack')
# build output
expectedlen = sum(len(t) for t in tup)
out = None
tnames = None
for tdata in tup:
tblen = _util.get_blen_table(tdata, blen)
tnames, tcolumns = _util.check_table_like(tdata, names=tnames)
tlen = len(tcolumns[0])
for i in range(0, tlen, tblen):
j = min(i+tblen, tlen)
bcolumns = [np.asanyarray(c[i:j]) for c in tcolumns]
if out is None:
out = getattr(storage, create)(bcolumns, names=tnames,
expectedlen=expectedlen,
**kwargs)
else:
out.append(bcolumns)
return out
def table(self, data, names=None, expectedlen=None, **kwargs):
# setup
names, columns = _util.check_table_like(data, names=names)
kwargs = self._set_defaults(kwargs)
chunks = kwargs.pop('chunks', None)
g = zarr.group(**kwargs)
# create columns
for n, c in zip(names, columns):
if chunks is None:
chunks = default_chunks(c, expectedlen)
if c.dtype == object:
# peek at first value
peek = c[0]
if isinstance(peek, bytes):
object_codec = numcodecs.VLenBytes()
elif isinstance(peek, str):
object_codec = numcodecs.VLenUTF8()
else:
object_codec = numcodecs.MsgPack()
else:
object_codec = None
g.array(name=n, data=c, chunks=chunks, object_codec=object_codec)
# create table
ztbl = ZarrTable(g, names=names)
return ztbl
def table(self, data, names=None, expectedlen=None, **kwargs):
names, columns = _util.check_table_like(data, names=names)
kwargs = self._set_defaults(kwargs)
ctbl = bcolz.ctable(columns, names=names, expectedlen=expectedlen,
**kwargs)
# patch append method
ctbl.append_original = ctbl.append
ctbl.append = MethodType(_table_append, ctbl)
return ctbl
def table(self, data, names=None, expectedlen=None, **kwargs):
names, columns = _util.check_table_like(data, names=names)
kwargs = self._set_defaults(kwargs)
ctbl = bcolz.ctable(columns,
names=names,
expectedlen=expectedlen,
**kwargs)
# patch append method
ctbl.append_original = ctbl.append
ctbl.append = MethodType(_table_append, ctbl)
return ctbl
def eval_table(tbl,
expression,
vm='python',
blen=None,
storage=None,
create='array',
vm_kwargs=None,
**kwargs):
"""Evaluate `expression` against columns of a table."""
# setup
storage = _util.get_storage(storage)
names, columns = _util.check_table_like(tbl)
length = len(columns[0])
if vm_kwargs is None:
vm_kwargs = dict()
# setup vm
if vm == 'numexpr':
import numexpr
evaluate = numexpr.evaluate
elif vm == 'python':
# noinspection PyUnusedLocal
def evaluate(expr, local_dict=None, **kw):
# takes no keyword arguments
return eval(expr, dict(), local_dict)
else:
raise ValueError('expected vm either "numexpr" or "python"')
# compile expression and get required columns
variables = _get_expression_variables(expression, vm)
required_columns = {v: columns[names.index(v)] for v in variables}
# determine block size for evaluation
blen = _util.get_blen_table(required_columns, blen=blen)
# build output
out = None
for i in range(0, length, blen):
j = min(i + blen, length)
blocals = {v: c[i:j] for v, c in required_columns.items()}
res = evaluate(expression, local_dict=blocals, **vm_kwargs)
if out is None:
out = getattr(storage, create)(res, expectedlen=length, **kwargs)
else:
out.append(res)
return out
def table(self, data, names=None, expectedlen=None, **kwargs):
# setup
names, columns = _util.check_table_like(data, names=names)
kwargs = self._set_defaults(kwargs)
g = zarr.group(**kwargs)
# create columns
chunks = kwargs.get('chunks', None)
for n, c in zip(names, columns):
if chunks is None:
chunks = default_chunks(c, expectedlen)
g.array(name=n, data=c, chunks=chunks)
# create table
ztbl = ZarrTable(g, names=names)
return ztbl
def eval_table(tbl, expression, vm='python', blen=None, storage=None,
create='array', vm_kwargs=None, **kwargs):
"""Evaluate `expression` against columns of a table."""
# setup
storage = _util.get_storage(storage)
names, columns = _util.check_table_like(tbl)
length = len(columns[0])
if vm_kwargs is None:
vm_kwargs = dict()
# setup vm
if vm == 'numexpr':
import numexpr
evaluate = numexpr.evaluate
elif vm == 'python':
# noinspection PyUnusedLocal
def evaluate(expr, local_dict=None, **kw):
# takes no keyword arguments
return eval(expr, dict(), local_dict)
else:
raise ValueError('expected vm either "numexpr" or "python"')
# compile expression and get required columns
variables = _get_expression_variables(expression, vm)
required_columns = {v: columns[names.index(v)] for v in variables}
# determine block size for evaluation
blen = _util.get_blen_table(required_columns, blen=blen)
# build output
out = None
for i in range(0, length, blen):
j = min(i+blen, length)
blocals = {v: c[i:j] for v, c in required_columns.items()}
res = evaluate(expression, local_dict=blocals, **vm_kwargs)
if out is None:
out = getattr(storage, create)(res, expectedlen=length, **kwargs)
else:
out.append(res)
return out
def table(self, data, names=None, expectedlen=None, **kwargs):
# ignore expectedlen
# setup
names, columns = _util.check_table_like(data, names=names)
kwargs = self._set_defaults(kwargs)
path = kwargs.get('path', None)
zcols = list()
# create columns
for n, c in zip(names, columns):
col_kwargs = kwargs.copy()
if path:
col_kwargs['path'] = os.path.join(path, n)
zcol = self._create_array(c, **col_kwargs)
zcols.append(zcol)
# create table
ztbl = ZarrTable(names, zcols)
return ztbl
def take_table(tbl, indices, blen=None, storage=None, create='table',
**kwargs):
"""Return selected rows of a table."""
# setup
names, columns = _util.check_table_like(tbl)
length = len(columns[0])
# check that indices are strictly increasing
indices = np.asanyarray(indices)
if np.any(indices[1:] <= indices[:-1]):
raise NotImplementedError(
'indices must be strictly increasing'
)
# implement via compress()
condition = np.zeros((length,), dtype=bool)
condition[indices] = True
return compress_table(tbl, condition, blen=blen, storage=storage,
create=create, **kwargs)
def take_table(tbl, indices, blen=None, storage=None, create='table',
**kwargs):
"""Return selected rows of a table."""
# setup
names, columns = _util.check_table_like(tbl)
length = len(columns[0])
# check that indices are strictly increasing
indices = np.asanyarray(indices)
if np.any(indices[1:] <= indices[:-1]):
raise NotImplementedError(
'indices must be strictly increasing'
)
# implement via compress()
condition = np.zeros((length,), dtype=bool)
condition[indices] = True
return compress_table(tbl, condition, blen=blen, storage=storage,
create=create, **kwargs)
def compress_table(condition,
tbl,
axis=None,
out=None,
blen=None,
storage=None,
create='table',
**kwargs):
"""Return selected rows of a table."""
# setup
if axis is not None and axis != 0:
raise NotImplementedError('only axis 0 is supported')
if out is not None:
# argument is only there for numpy API compatibility
raise NotImplementedError('out argument is not supported')
storage = _util.get_storage(storage)
names, columns = _util.check_table_like(tbl)
blen = _util.get_blen_table(tbl, blen)
_util.check_equal_length(columns[0], condition)
length = len(columns[0])
nnz = count_nonzero(condition)
# block iteration
out = None
for i in range(0, length, blen):
j = min(i + blen, length)
bcond = condition[i:j]
# don't access any data unless we have to
if np.any(bcond):
bcolumns = [c[i:j] for c in columns]
res = [np.compress(bcond, c, axis=0) for c in bcolumns]
if out is None:
out = getattr(storage, create)(res,
names=names,
expectedlen=nnz,
**kwargs)
else:
out.append(res)
return out
def table(self, data, names=None, expectedlen=None, **kwargs):
# ignore expectedlen for now
# setup
names, columns = _util.check_table_like(data, names=names)
# obtain group
h5g = kwargs.pop("group", None)
if h5g is None:
# open file, use root group
h5g, kwargs = self.open_file(**kwargs)
# create columns
for n, c in zip(names, columns):
self.create_dataset(h5g, data=c, name=n, **kwargs)
# patch in append method
h5g.append = MethodType(_table_append, h5g)
# patch in names attribute
h5g.names = names
return h5g
def take_table(tbl,
indices,
axis=None,
out=None,
mode='raise',
blen=None,
storage=None,
create='table',
**kwargs):
"""Return selected rows of a table."""
# setup
if axis is not None and axis != 0:
raise NotImplementedError('only axis 0 is supported')
if out is not None:
# argument is only there for numpy API compatibility
raise NotImplementedError('out argument is not supported')
if mode is not None and mode != 'raise':
raise NotImplementedError('only mode=raise is supported')
names, columns = _util.check_table_like(tbl)
length = len(columns[0])
# check that indices are strictly increasing
indices = np.asanyarray(indices)
if np.any(indices[1:] <= indices[:-1]):
raise NotImplementedError('indices must be strictly increasing')
# implement via compress()
condition = np.zeros((length, ), dtype=bool)
condition[indices] = True
return compress_table(condition,
tbl,
blen=blen,
storage=storage,
create=create,
**kwargs)
def __init__(self, data, names=None):
names, columns = _util.check_table_like(data, names=names)
self.data = data
self.names = names
self.columns = columns
self.rowcls = namedtuple('row', names)
def append(self, data):
_, columns = _util.check_table_like(data, names=self.names)
for co, cn in zip(self.columns, columns):
co.append(cn)
def _table_append(h5g, data):
names, columns = _util.check_table_like(data, names=h5g.names)
for n, c in zip(names, columns):
h5d = h5g[n]
_dataset_append(h5d, c)
def _table_append(h5g, data):
names, columns = _util.check_table_like(data, names=h5g.names)
for n, c in zip(names, columns):
h5d = h5g[n]
_dataset_append(h5d, c)
def __init__(self, data, names=None):
names, columns = _util.check_table_like(data, names=names)
self.data = data
self.names = names
self.columns = columns
self.rowcls = namedtuple('row', names)
def append(self, data):
names, columns = _util.check_table_like(data, names=self.names)
for n, c in zip(names, columns):
self.grp[n].append(c)
