def test_read_bytes_delimited(s3, blocksize):
_, values = read_bytes(test_bucket_name+'/test/accounts*',
blocksize=blocksize, delimiter=b'\n', s3=s3)
_, values2 = read_bytes(test_bucket_name+'/test/accounts*',
blocksize=blocksize, delimiter=b'foo', s3=s3)
assert ([a.key for a in concat(values)] !=
[b.key for b in concat(values2)])
results = compute(*concat(values))
res = [r for r in results if r]
assert all(r.endswith(b'\n') for r in res)
ourlines = b''.join(res).split(b'\n')
testlines = b"".join(files[k] for k in sorted(files)).split(b'\n')
assert ourlines == testlines
# delimiter not at the end
d = b'}'
_, values = read_bytes(test_bucket_name+'/test/accounts*',
blocksize=blocksize, delimiter=d, s3=s3)
results = compute(*concat(values))
res = [r for r in results if r]
# All should end in } except EOF
assert sum(r.endswith(b'}') for r in res) == len(res) - 2
ours = b"".join(res)
test = b"".join(files[v] for v in sorted(files))
assert ours == test
def compute_up(expr, data, scope=None, **kwargs):
data = lower_column(data)
grouper = compute(
expr.grouper,
scope,
post_compute=False,
return_type='native',
**kwargs
)
app = expr.apply
reductions = [
compute(
val,
data,
post_compute=None,
return_type='native',
).label(name)
for val, name in zip(app.values, app.fields)
]
froms = list(unique(chain(get_all_froms(grouper),
concat(map(get_all_froms, reductions)))))
inner_cols = list(getattr(grouper, 'inner_columns', [grouper]))
grouper_cols = inner_cols[:]
inner_cols.extend(concat(
getattr(getattr(r, 'element', None), 'inner_columns', [r])
for r in reductions
))
wheres = unify_wheres([grouper] + reductions)
sel = unify_froms(sa.select(inner_cols, whereclause=wheres), froms)
return sel.group_by(*grouper_cols)
def test_read_bytes_delimited():
with filetexts(files, mode='b'):
for bs in [5, 15, 45, 1500]:
_, values = read_bytes('.test.accounts*',
blocksize=bs, delimiter=b'\n')
_, values2 = read_bytes('.test.accounts*',
blocksize=bs, delimiter=b'foo')
assert ([a.key for a in concat(values)] !=
[b.key for b in concat(values2)])
results = compute(*concat(values))
res = [r for r in results if r]
assert all(r.endswith(b'\n') for r in res)
ourlines = b''.join(res).split(b'\n')
testlines = b"".join(files[k] for k in sorted(files)).split(b'\n')
assert ourlines == testlines
# delimiter not at the end
d = b'}'
_, values = read_bytes('.test.accounts*', blocksize=bs, delimiter=d)
results = compute(*concat(values))
res = [r for r in results if r]
# All should end in } except EOF
assert sum(r.endswith(b'}') for r in res) == len(res) - 2
ours = b"".join(res)
test = b"".join(files[v] for v in sorted(files))
assert ours == test
def diagnostic_yield(self, metric='completeness', cutoff=1,
superblock_ids=None, group_id=None, sample_ids=None):
"""Calculate diagnostic yield."""
# extract column to filter on
metric_column = getattr(BlockData, metric)
# set up the base query for all blocks
total_query = self.total_count(BlockData)
if superblock_ids:
# apply the superblock filter on the Block class level
total_query = total_query.join(BlockData.parent)\
.filter(Block.superblock_id.in_(superblock_ids))
# extend base query to include only passed blocks
pass_query = total_query.filter(metric_column >= cutoff)
# optionally limit query
queries = [limit_query(query, group=group_id, samples=sample_ids)
for query in (total_query, pass_query)]
# group multiple queries by sample ID (first column)
metrics = groupby(get(0), concat(queries))
# iterate over all values, concat different query results, and keep
# only the unique values (excluding second sample_id)
combined = (unique(concat(values)) for values in itervalues(metrics))
# calculate diagnostic yield by simple division
for sample_id, group_id, total, covered in combined:
yield sample_id, group_id, (covered / total)
def scatter(kd, control, colors=['orange', 'blue'], **kwargs):
"""Show a jittered scatterplot of the measurements.
Parameters
----------
kd : list of list of float
The list of `trf_quantify` results for all AUKB knockdown
images in the dataset. (Each result is itself a list.)
control : list of list of float
The list of `trf_quantify` results for all control images in
the dataset.
colors : list of two matplotlib colorspecs, optional
The colors corresponding to AUKB-KD (0) and control (1) data
points on the scatterplot.
Additional Parameters
---------------------
**kwargs : keyword arguments
Additional keyword arguments passed directly to
``plt.scatter``.
Returns
-------
fig : matplotlib axes
The returned value from the call to ``plt.scatter``.
"""
xs = list(tz.concat([i + 0.2 * np.random.randn(n)
for i, n in enumerate(map(len, kd + control))]))
color_vector = ([colors[0]] * sum(map(len, kd)) +
[colors[1]] * sum(map(len, control)))
ys = list(tz.concat(kd + control))
fig = plt.scatter(xs, ys, c=color_vector, **kwargs)
plt.xlim(0, max(xs) + 1)
plt.ylim(0, max(ys) + 1)
return fig
def test_modification_time_read_bytes():
with s3_context('compress', files) as s3:
_, a = read_bytes('compress/test/accounts.*', s3=s3)
_, b = read_bytes('compress/test/accounts.*', s3=s3)
assert [aa._key for aa in concat(a)] == [bb._key for bb in concat(b)]
with s3_context('compress', valmap(double, files)) as s3:
_, c = read_bytes('compress/test/accounts.*', s3=s3)
assert [aa._key for aa in concat(a)] != [cc._key for cc in concat(c)]
def start(self):
self.status = 'running'
logger.debug("Start Progress Plugin")
self._start()
if not self.keys or not any(v for v in self.keys.values()):
self.stop()
elif all(k in self.scheduler.exceptions_blame for k in
concat(self.keys.values())):
key = next(k for k in concat(self.keys.values()) if k in
self.scheduler.exceptions_blame)
self.stop(exception=True, key=key)
def compute_up(expr, args, **kwargs):
from_objs = list(unique(concat(map(get_all_froms, args))))
if len(from_objs) > 1:
# TODO: how do you do this in sql? please send help
raise ValueError('only columns from the same table can be merged')
cols = list(unique(concat(map(get_unsafe_inner_columns, args, expr.args))))
sel = sa.select(cols, from_obj=from_objs[0])
where = unify_wheres(args)
if where is not None:
sel = sel.where(where)
return sel
def render_tabular(api, options=None):
"""Entry point for the tabular reporter interface."""
# determine separator
separator = options.get('report.separator', '\t')
human = options.get('report.human')
panel = options.get('report.panel')
samples = options.get('report.samples')
group = options.get('report.group')
# read gene panel file if it has been set
if panel:
superblock_ids = [line.rstrip() for line in panel]
else:
superblock_ids = None
# get sample ID, group and cutoff from metadata
sample_query = limit_query(api.samples(), group=group, samples=samples)
metadata = ((sample.id, sample.group_id, sample.cutoff)
for sample in sample_query)
# get the data
base_query = limit_query(api.average_metrics(superblock_ids=superblock_ids),
group=group,
samples=samples)
queries = [metadata,
base_query,
api.diagnostic_yield(superblock_ids=superblock_ids,
group_id=group, sample_ids=samples),
api.sex_checker(group_id=group, sample_ids=samples)]
# group multiple queries by sample ID (first column)
key_metrics = groupby(get(0), concat(queries))
# get the column names dynamically from the query
headers = concatv(['sample_id', 'group_id', 'cutoff'],
(column['name'] for column
in base_query.column_descriptions),
['diagnostic yield', 'gender'])
unique_headers = unique(headers)
# iterate over all values, concat different query results, and keep
# only the unique values (excluding second sample_id)
data = (unique(concat(values)) for values in itervalues(key_metrics))
if human:
# export key_metrics in a more human friendly format
return tabulate(data, unique_headers)
# yield headers
return '\n'.join(cons('#' + separator.join(unique_headers),
stringify_list(data, separator=separator)))
def compile_components(summary, schema):
"""Given a ``Summary`` object and a table schema, returning 5 sub-functions.
Parameters
----------
summary : Summary
The expression describing the aggregations to be computed.
Returns
-------
A tuple of the following functions:
``create(shape)``
Takes the aggregate shape, and returns a tuple of initialized numpy
arrays.
``info(df)``
Takes a dataframe, and returns preprocessed 1D numpy arrays of the
needed columns.
``append(i, x, y, *aggs_and_cols)``
Appends the ``i``th row of the table to the ``(x, y)`` bin, given the
base arrays and columns in ``aggs_and_cols``. This does the bulk of the
work.
``combine(base_tuples)``
Combine a list of base tuples into a single base tuple. This forms the
reducing step in a reduction tree.
``finalize(aggs)``
Given a tuple of base numpy arrays, returns the finalized
``dynd`` array.
"""
paths, reds = zip(*preorder_traversal(summary))
# List of base reductions (actually computed)
bases = list(unique(concat(r._bases for r in reds)))
dshapes = [b.out_dshape(schema) for b in bases]
# List of tuples of (append, base, input columns, temps)
calls = [_get_call_tuples(b, d) for (b, d) in zip(bases, dshapes)]
# List of unique column names needed
cols = list(unique(concat(pluck(2, calls))))
# List of temps needed
temps = list(pluck(3, calls))
create = make_create(bases, dshapes)
info = make_info(cols)
append = make_append(bases, cols, calls)
combine = make_combine(bases, dshapes, temps)
finalize = make_finalize(bases, summary, schema)
return create, info, append, combine, finalize
def test_chunk_datetime():
data = [[1, 'Alice', 100, datetime.datetime(2014, 10, 1, 1, 1, 1)],
[2, 'Bob', 200, datetime.datetime(2014, 10, 1, 1, 1, 1)],
[3, 'Alice', -300, datetime.datetime(2014, 10, 1, 1, 1, 1)],
[4, 'Charlie', 400, datetime.datetime(2014, 10, 1, 1, 1, 1)],
[5, 'Edith', 200, datetime.datetime(2014, 10, 1, 1, 1, 1)]]
t = Symbol('t', 'var * {id: int, name: string, amount: int, when: datetime}')
c = ChunkIterable(data, chunksize=2)
assert list(concat(compute(t.when.day, c))) == [1] * 5
assert list(concat(compute(t.when.date, c))) == \
[datetime.date(2014, 10, 1)] * 5
def test_deterministic_key_names(hdfs):
data = b'abc\n' * int(1e3)
fn = '%s/file' % basedir
with hdfs.open(fn, 'wb', replication=1) as fil:
fil.write(data)
_, x = read_bytes('hdfs://%s/*' % basedir, delimiter=b'\n', sample=False)
_, y = read_bytes('hdfs://%s/*' % basedir, delimiter=b'\n', sample=False)
_, z = read_bytes('hdfs://%s/*' % basedir, delimiter=b'c', sample=False)
assert [f.key for f in concat(x)] == [f.key for f in concat(y)]
assert [f.key for f in concat(x)] != [f.key for f in concat(z)]
def test_join():
cities = TableSymbol('cities', schema='{id: int, city: string}')
j = join(t, cities, 'id')
city_data = [[1, 'NYC'], [1, 'Chicago'], [5, 'Paris']]
assert set(concat(compute(join(cities, t, 'id')[['name', 'city']],
{t: c, cities: city_data}))) == \
set((('Alice', 'NYC'), ('Alice', 'Chicago'), ('Edith', 'Paris')))
assert set(concat(compute(join(t, cities, 'id')[['name', 'city']],
{t: c, cities: city_data}))) == \
set((('Alice', 'NYC'), ('Alice', 'Chicago'), ('Edith', 'Paris')))
def test_join():
cities = symbol('cities', dshape='var * {id: int, city: string}')
j = join(t, cities, 'id')
city_data = [[1, 'NYC'], [1, 'Chicago'], [5, 'Paris']]
assert set(concat(compute(j[['name', 'city']],
{t: c, cities: city_data}))) == \
set((('Alice', 'NYC'), ('Alice', 'Chicago'), ('Edith', 'Paris')))
assert set(concat(compute(j[['name', 'city']],
{t: c, cities: city_data}))) == \
set((('Alice', 'NYC'), ('Alice', 'Chicago'), ('Edith', 'Paris')))
def test_deterministic_key_names(e, s, a, b):
with make_hdfs() as (hdfs, basedir):
data = b'abc\n' * int(1e3)
fn = '%s/file' % basedir
with hdfs.open(fn, 'wb', replication=1) as f:
f.write(data)
_, x = read_bytes('hdfs://%s/*' % basedir, delimiter=b'\n')
_, y = read_bytes('hdfs://%s/*' % basedir, delimiter=b'\n')
_, z = read_bytes('hdfs://%s/*' % basedir, delimiter=b'c')
assert [f.key for f in concat(x)] == [f.key for f in concat(y)]
assert [f.key for f in concat(x)] != [f.key for f in concat(z)]
def deserialize(bytes, dtype, copy=False):
if dtype == 'O':
try:
l = list(concat(map(msgpack.unpackb, framesplit(bytes))))
except:
l = list(concat(map(pickle.loads, framesplit(bytes))))
l = decode(l)
return np.array(l, dtype='O')
else:
result = np.frombuffer(bytes, dtype)
if copy:
result = result.copy()
return result
def test_registered_read_bytes():
from dask.bytes.core import read_bytes
with filetexts(files, mode='b'):
sample, values = read_bytes('.test.accounts.*')
results = compute(*concat(values))
assert set(results) == set(files.values())
def _check_for_problem_somatic_batches(items, config):
"""Identify problem batch setups for somatic calling.
We do not support multiple tumors in a single batch and VarDict(Java) does not
handle pooled calling, only tumor/normal.
"""
to_check = []
for data in items:
data = copy.deepcopy(data)
data["config"] = config_utils.update_w_custom(config, data)
to_check.append(data)
data_by_batches = collections.defaultdict(list)
for data in to_check:
batches = dd.get_batches(data)
if batches:
for batch in batches:
data_by_batches[batch].append(data)
for batch, items in data_by_batches.items():
if vcfutils.get_paired(items):
vcfutils.check_paired_problems(items)
elif len(items) > 1:
vcs = list(set(tz.concat([dd.get_variantcaller(data) or [] for data in items])))
if any(x.lower().startswith("vardict") for x in vcs):
raise ValueError("VarDict does not support pooled non-tumor/normal calling, in batch %s: %s"
% (batch, [dd.get_sample_name(data) for data in items]))
elif any(x.lower() == "mutect" for x in vcs):
raise ValueError("Mutect requires a 'phenotype: tumor' sample for calling, in batch %s: %s"
% (batch, [dd.get_sample_name(data) for data in items]))
def aggregate_shape(leaf, expr, chunk, chunk_expr):
""" The shape of the intermediate aggregate
>>> leaf = Symbol('leaf', '10 * 10 * int')
>>> expr = leaf.sum(axis=0)
>>> chunk = Symbol('chunk', '3 * 3 * int') # 3 does not divide 10
>>> chunk_expr = chunk.sum(axis=0, keepdims=1)
>>> aggregate_shape(leaf, expr, chunk, chunk_expr)
(4, 10)
"""
if datashape.var in concat(map(shape, [leaf, expr, chunk, chunk_expr])):
return (datashape.var, ) * leaf.ndim
numblocks = [int(floor(l / c)) for l, c in zip(leaf.shape, chunk.shape)]
last_chunk_shape = [l % c for l, c in zip(leaf.shape, chunk.shape)]
if builtins.sum(last_chunk_shape) != 0:
last_chunk = Symbol(chunk._name,
DataShape(*(last_chunk_shape + [chunk.dshape.measure])))
last_chunk_expr = chunk_expr._subs({chunk: last_chunk})
last_chunk_shape = shape(last_chunk_expr)
return tuple(int(floor(l / c)) * ce + lce
for l, c, ce, lce
in zip(shape(leaf), shape(chunk), shape(chunk_expr), last_chunk_shape))
def f(c, a, b):
keys = yield _scatter((c.ip, c.port), [1, 2, 3])
assert merge(a.data, b.data) == \
{k: i for k, i in zip(keys, [1, 2, 3])}
assert set(c.who_has) == set(keys)
assert all(len(v) == 1 for v in c.who_has.values())
keys2, who_has, nbytes = yield scatter_to_workers([a.address, b.address],
[4, 5, 6])
m = merge(a.data, b.data)
for k, v in zip(keys2, [4, 5, 6]):
assert m[k] == v
assert isinstance(who_has, dict)
assert set(concat(who_has.values())) == {a.address, b.address}
assert len(who_has) == len(keys2)
assert isinstance(nbytes, dict)
assert set(nbytes) == set(who_has)
assert all(isinstance(v, int) for v in nbytes.values())
result = yield _gather((c.ip, c.port), keys2)
assert result == [4, 5, 6]
def schema(self):
for c in self.children:
if not isinstance(c.schema[0], Record):
raise TypeError("All schemas must have Record shape. Got %s" %
c.schema[0])
return dshape(Record(list(concat(c.schema[0].parameters[0] for c in
self.children))))
def test_current_session(self):
regular_minutes = self.trading_calendar.minutes_for_sessions_in_range(
self.equity_minute_bar_days[0],
self.equity_minute_bar_days[-1]
)
bts_minutes = days_at_time(
self.equity_minute_bar_days,
time(8, 45),
"US/Eastern"
)
# some other non-market-minute
three_oh_six_am_minutes = days_at_time(
self.equity_minute_bar_days,
time(3, 6),
"US/Eastern"
)
all_minutes = [regular_minutes, bts_minutes, three_oh_six_am_minutes]
for minute in list(concat(all_minutes)):
bar_data = self.create_bardata(lambda: minute)
self.assertEqual(
self.trading_calendar.minute_to_session_label(minute),
bar_data.current_session
)
def write_tables(fname, models, year):
"""
Write all tables injected into `models` to a pandas.HDFStore file.
If year is not None it will be used to prefix the table names so that
multiple years can go in the same file.
Parameters
----------
fname : str
File name for HDFStore. Will be opened in append mode and closed
at the end of this function.
models : list of str
Models from which to gather injected tables for saving.
year : int or None
If an integer, used as a prefix along with table names for
labeling DataFrames in the HDFStore.
"""
models = (get_model(m) for m in toolz.unique(models))
table_names = toolz.unique(toolz.concat(m._tables_used() for m in models))
tables = (get_table(t) for t in table_names)
key_template = '{}/{{}}'.format(year) if year is not None else '{}'
with pd.get_store(fname, mode='a') as store:
for t in tables:
store[key_template.format(t.name)] = t.to_frame()
def test_repeat():
x = np.random.random((10, 11, 13))
d = da.from_array(x, chunks=(4, 5, 3))
repeats = [1, 2, 5]
axes = [-3, -2, -1, 0, 1, 2]
for r in repeats:
for a in axes:
assert_eq(x.repeat(r, axis=a), d.repeat(r, axis=a))
assert_eq(d.repeat(2, 0), da.repeat(d, 2, 0))
with pytest.raises(NotImplementedError):
da.repeat(d, np.arange(10))
with pytest.raises(NotImplementedError):
da.repeat(d, 2, None)
with pytest.raises(NotImplementedError):
da.repeat(d, 2)
for invalid_axis in [3, -4]:
with pytest.raises(ValueError):
da.repeat(d, 2, axis=invalid_axis)
x = np.arange(5)
d = da.arange(5, chunks=(2,))
assert_eq(x.repeat(3), d.repeat(3))
for r in [1, 2, 3, 4]:
assert all(concat(d.repeat(r).chunks))
def batch(sel, chunksize=10000, bind=None):
"""Execute `sel`, streaming row at a time and fetching from the database in
batches of size `chunksize`.
Parameters
----------
sel : sa.sql.Selectable
Selectable to execute
chunksize : int, optional, default 10000
Number of rows to fetch from the database
"""
def rowterator(sel, chunksize=chunksize):
with getbind(sel, bind).connect() as conn:
result = conn.execute(sel)
yield result.keys()
for rows in iter_except(curry(result.fetchmany, size=chunksize), sa.exc.ResourceClosedError):
if rows:
yield rows
else:
return
terator = rowterator(sel)
return next(terator), concat(terator)
def init_state(self, network):
super(ANRATNode, self).init_state(network)
inits = list(toolz.concat(network.find_hyperparameters(["inits"], [])))
# setting initial lambda to 5 instead of 10, because 10 is too large
# for the default parameters
# TODO might also want to add clipping to cap the value of lambda
initial_lambda = network.find_hyperparameter(["anrat_initial_lambda"], 5)
if ANRAT_USE_LOG_LAMBDA:
initial_lambda = np.log(initial_lambda)
lambda_vw = network.create_vw(
name="lambda",
is_shared=True,
shape=(),
tags={"parameter"},
inits=inits + [treeano.inits.ConstantInit(initial_lambda)],
)
p = network.find_hyperparameter(["nrae_p"], 2)
q = network.find_hyperparameter(["nrae_q"], 2)
r = network.find_hyperparameter(["anrat_r"], 1)
alpha = network.find_hyperparameter(["anrat_alpha", "alpha"], 0.1)
i32_target = network.find_hyperparameter(["i32_target"], False)
lambda_var = lambda_vw.variable
if ANRAT_USE_LOG_LAMBDA:
lambda_var = T.exp(lambda_var)
cost_function = functools.partial(_ANRAT, lambda_=lambda_var, p=p, q=q, r=r, alpha=alpha, i32_target=i32_target)
network.set_hyperparameter(self.name + "_elementwise", "cost_function", cost_function)
def compute_down(expr, data, chunksize=2**20, map=map, **kwargs):
leaf = expr._leaves()[0]
# If the bottom expression is a projection or field then want to do
# compute_up first
children = set(e for e in expr._traverse()
if isinstance(e, Expr)
and any(i is expr._leaves()[0] for i in e._inputs))
if len(children) == 1 and isinstance(first(children), (Field, Projection)):
raise NotImplementedError()
chunk = symbol('chunk', chunksize * leaf.schema)
(chunk, chunk_expr), (agg, agg_expr) = split(leaf, expr, chunk=chunk)
data_parts = partitions(data, chunksize=(chunksize,))
parts = list(map(curry(compute_chunk, data, chunk, chunk_expr),
data_parts))
if isinstance(parts[0], np.ndarray):
intermediate = np.concatenate(parts)
elif isinstance(parts[0], pd.DataFrame):
intermediate = pd.concat(parts)
elif isinstance(parts[0], Iterable):
intermediate = list(concat(parts))
else:
raise TypeError(
"Don't know how to concatenate objects of type %s" % type(parts[0]))
return compute(agg_expr, {agg: intermediate})
def load_adjusted_array(self, columns, dates, assets, mask):
return dict(
concat(map(
partial(self._load_dataset, dates, assets, mask),
itervalues(groupby(getdataset, columns))
))
)
def scatter_to_workers(center, ncores, data, key=None):
""" Scatter data directly to workers
This distributes data in a round-robin fashion to a set of workers based on
how many cores they have. ncores should be a dictionary mapping worker
identities to numbers of cores.
See scatter for parameter docstring
"""
center = coerce_to_rpc(center)
if key is None:
key = str(uuid.uuid1())
if isinstance(ncores, Iterable) and not isinstance(ncores, dict):
ncores = {worker: 1 for worker in ncores}
workers = list(concat([w] * nc for w, nc in ncores.items()))
if isinstance(data, dict):
names, data = list(zip(*data.items()))
else:
names = ("%s-%d" % (key, i) for i in count(0))
L = list(zip(cycle(workers), names, data))
d = groupby(0, L)
d = {k: {b: c for a, b, c in v} for k, v in d.items()}
yield [rpc(ip=w_ip, port=w_port).update_data(data=v, close=True) for (w_ip, w_port), v in d.items()]
result = [RemoteData(b, center.ip, center.port, result=c) for a, b, c in L]
raise Return(result)
def compute(self, **kwargs):
results = self.get(self.dask, self._keys(), **kwargs)
if isinstance(results[0], Iterable):
results = concat(results)
if not isinstance(results, Iterator):
results = iter(results)
return results
def aconcat(seqs):
"""Like `toolz.concat`, but it returns a array instead of an iterator."""
return np.array(list(toolz.concat(seqs)))
def compute_broadcast(expr, *data, **kwargs):
expr_inds = tuple(range(ndim(expr)))[::-1]
func = get_numba_ufunc(expr)
return atop(func,
expr_inds,
*concat((dat, tuple(range(ndim(dat))[::-1])) for dat in data))
def get_all_froms(function):
return list(unique(concat(map(get_all_froms, function.clauses.clauses))))
def slice_with_bool_dask_array(x, index):
""" Slice x with one or more dask arrays of bools
This is a helper function of `Array.__getitem__`.
Parameters
----------
x: Array
index: tuple with as many elements as x.ndim, among which there are
one or more Array's with dtype=bool
Returns
-------
tuple of (sliced x, new index)
where the new index is the same as the input, but with slice(None)
replaced to the original slicer when a filter has been applied.
Note: The sliced x will have nan chunks on the sliced axes.
"""
from .core import Array, atop, elemwise
out_index = [
slice(None) if isinstance(ind, Array) and ind.dtype == bool else ind
for ind in index
]
if len(index) == 1 and index[0].ndim == x.ndim:
y = elemwise(getitem, x, *index, dtype=x.dtype)
name = 'getitem-' + tokenize(x, index)
dsk = {(name, i): k
for i, k in enumerate(core.flatten(y.__dask_keys__()))}
chunks = ((np.nan, ) * y.npartitions, )
return (Array(sharedict.merge(y.dask, (name, dsk)), name, chunks,
x.dtype), out_index)
if any(
isinstance(ind, Array) and ind.dtype == bool and ind.ndim != 1
for ind in index):
raise NotImplementedError(
"Slicing with dask.array of bools only permitted when "
"the indexer has only one dimension or when "
"it has the same dimension as the sliced "
"array")
indexes = [
ind if isinstance(ind, Array) and ind.dtype == bool else slice(None)
for ind in index
]
arginds = []
i = 0
for ind in indexes:
if isinstance(ind, Array) and ind.dtype == bool:
new = (ind, tuple(range(i, i + ind.ndim)))
i += x.ndim
else:
new = (slice(None), None)
i += 1
arginds.append(new)
arginds = list(concat(arginds))
out = atop(getitem_variadic,
tuple(range(x.ndim)),
x,
tuple(range(x.ndim)),
*arginds,
dtype=x.dtype)
chunks = []
for ind, chunk in zip(index, out.chunks):
if isinstance(ind, Array) and ind.dtype == bool:
chunks.append((np.nan, ) * len(chunk))
else:
chunks.append(chunk)
out._chunks = tuple(chunks)
return out, tuple(out_index)
def assert_balanced(inp, expected, c, s, *workers):
steal = s.extensions["stealing"]
steal._pc.stop()
counter = itertools.count()
tasks = list(concat(inp))
data_seq = itertools.count()
futures = []
for w, ts in zip(workers, inp):
for t in sorted(ts, reverse=True):
if t:
[dat] = yield c.scatter([next(data_seq)], workers=w.address)
ts = s.tasks[dat.key]
# Ensure scheduler state stays consistent
old_nbytes = ts.nbytes
ts.nbytes = s.bandwidth * t
for ws in ts.who_has:
ws.nbytes += ts.nbytes - old_nbytes
else:
dat = 123
s.task_duration[str(int(t))] = 1
i = next(counter)
f = c.submit(
func,
dat,
key="%d-%d" % (int(t), i),
workers=w.address,
allow_other_workers=True,
pure=False,
priority=-i,
)
futures.append(f)
while len(s.rprocessing) < len(futures):
yield gen.sleep(0.001)
for i in range(10):
steal.balance()
while steal.in_flight:
yield gen.sleep(0.001)
result = [
sorted([int(key_split(k)) for k in s.processing[w.address]],
reverse=True) for w in workers
]
result2 = sorted(result, reverse=True)
expected2 = sorted(expected, reverse=True)
if config.get("pdb-on-err"):
if result2 != expected2:
import pdb
pdb.set_trace()
if result2 == expected2:
return
raise Exception("Expected: {}; got: {}".format(str(expected2),
str(result2)))
def everything_but(k, d):
"""
Return iterator of all values in d except the values in k.
"""
assert k in d
return concat(keyfilter(lambda x: x != k, d).values())
def read_text(urlpath, blocksize=None, compression='infer',
encoding=system_encoding, errors='strict',
linedelimiter=os.linesep, collection=True,
storage_options=None):
""" Read lines from text files
Parameters
----------
urlpath: string or list
Absolute or relative filepath, URL (may include protocols like
``s3://``), globstring, or a list of beforementioned strings.
blocksize: None or int
Size (in bytes) to cut up larger files. Streams by default.
compression: string
Compression format like 'gzip' or 'xz'. Defaults to 'infer'
encoding: string
errors: string
linedelimiter: string
collection: bool, optional
Return dask.bag if True, or list of delayed values if false
storage_options: dict
Extra options that make sense to a particular storage connection, e.g.
host, port, username, password, etc.
Examples
--------
>>> b = read_text('myfiles.1.txt') # doctest: +SKIP
>>> b = read_text('myfiles.*.txt') # doctest: +SKIP
>>> b = read_text('myfiles.*.txt.gz') # doctest: +SKIP
>>> b = read_text('s3://bucket/myfiles.*.txt') # doctest: +SKIP
>>> b = read_text('s3://key:secret@bucket/myfiles.*.txt') # doctest: +SKIP
>>> b = read_text('hdfs://namenode.example.com/myfiles.*.txt') # doctest: +SKIP
Parallelize a large file by providing the number of uncompressed bytes to
load into each partition.
>>> b = read_text('largefile.txt', blocksize=1e7) # doctest: +SKIP
Returns
-------
dask.bag.Bag if collection is True or list of Delayed lists otherwise
See Also
--------
from_sequence: Build bag from Python sequence
"""
if isinstance(urlpath, (tuple, list, set)):
blocks = sum([read_text(fn, blocksize=blocksize,
compression=compression, encoding=encoding, errors=errors,
linedelimiter=linedelimiter, collection=False,
storage_options=storage_options)
for fn in urlpath], [])
else:
if blocksize is None:
files = open_text_files(urlpath, encoding=encoding, errors=errors,
compression=compression,
**(storage_options or {}))
blocks = [delayed(list, pure=True)(delayed(file_to_blocks)(file))
for file in files]
else:
_, blocks = read_bytes(urlpath, delimiter=linedelimiter.encode(),
blocksize=blocksize, sample=False,
compression=compression,
**(storage_options or {}))
if isinstance(blocks[0], (tuple, list)):
blocks = list(concat(blocks))
blocks = [delayed(decode)(b, encoding, errors)
for b in blocks]
if not blocks:
raise ValueError("No files found", urlpath)
if not collection:
return blocks
else:
return from_delayed(blocks)
def physical_tables_join(join):
# Physical roots of Join nodes are the unique physical roots of their
# left and right TableNodes.
func = compose(physical_tables, methodcaller('op'))
return list(unique(concat(map(func, (join.left, join.right)))))
def everything_but(k, d):
"""
Return iterator of all values in d except the values in k.
"""
assert k in d
return concat(itervalues(keyfilter(ne(k), d)))
def physical_tables_node(node):
# Iterative case. Any other Node's physical roots are the unique physical
# roots of that Node's root tables.
tables = toolz.concat(map(physical_tables, node.root_tables()))
return list(toolz.unique(tables, key=id))
def powerset(values):
"""
Return the power set (i.e., the set of all subsets) of entries in `values`.
"""
return concat(combinations(values, i) for i in range(len(values) + 1))
def distinct_roots(*expressions):
# TODO: move to analysis
roots = toolz.concat(expr.op().root_tables() for expr in expressions)
return list(toolz.unique(roots))
def distinct_roots(*expressions):
roots = toolz.concat(expression._root_tables()
for expression in expressions)
return list(toolz.unique(roots, key=id))
def __iter__(self):
return toolz.unique(toolz.concat(self.layers.values()))
def lconcat(seqs):
"""Like `toolz.concat`, but it returns a list instead of an iterator."""
return list(toolz.concat(seqs))
def elemwise_array(expr, *data, **kwargs):
leaves = expr._inputs
expr_inds = tuple(range(ndim(expr)))[::-1]
return atop(curry(compute_it, expr, leaves, **kwargs),
expr_inds,
*concat((dat, tuple(range(ndim(dat))[::-1])) for dat in data))
def morph_counts_fastest_version(self, words):
# Word List to list of all morphisms
word_counts = Counter(
word for word in toolz.concat(map(self.word_tokenizer, words)))
#print("words_counts: ")
#print(word_counts)
print("")
print("Unique number words: " + str(len(set(words))))
print("Total number of words: " + str(len(words)))
print("")
unique_words_set = set(words)
unique_words = list(unique_words_set)
frog = Frog(
FrogOptions(tok=True,
lemma=True,
morph=True,
daringmorph=False,
mwu=False,
chunking=False,
ner=False,
parser=False))
batch_size = 400
morphisms = []
print_batch_number = 1
start_time = time.time()
total_batch_number = math.ceil(len(unique_words) / batch_size)
total_process_time = 0
total_getting_morphisms_time = 0
for i in range(0, len(unique_words), batch_size):
t0 = time.time()
words_batch = unique_words[i:i + batch_size]
words_batch_string = ' '.join(words_batch)
output = frog.process(words_batch_string)
process_time = time.time() - t0
t1 = time.time()
for j in range(0, len(words_batch) - 1):
current_word = output[j].get("text")
morphisms_word = output[j].get("morph")
morphisms_word_list = morphisms_word.replace('[',
'').split(']')
current_word_count = word_counts[current_word]
# Momenteel GEEN GEHELE WOORDEN IN COUNT
if len(morphisms_word_list) > 2:
morphisms += morphisms_word_list * current_word_count
total_batch_length = len(words_batch)
print("batch" + " (" + str(batch_size) + " words): " +
str(print_batch_number) + " of " + str(total_batch_number))
print_batch_number += 1
getting_morphisms_time = time.time() - t1
total_process_time += process_time
total_getting_morphisms_time += getting_morphisms_time
print("")
print("Total number of words: ")
print(len(words))
print("")
print("Unique number words: ")
print(len(set(words)))
print("")
print("Total Process Time:")
print(self.format_time(total_process_time))
print("")
print("Total Getting Morphisms Time: ")
print(self.format_time(total_getting_morphisms_time))
print("")
print("Total Time:")
print(self.format_time(time.time() - start_time))
print("")
# Remove the empty strings
morphisms = list(filter(None, morphisms))
#Make a counter of all morphisms
morph_counts = Counter(morphisms)
with open('Old/morph_counts.pickle', 'wb') as outputfile:
pickle.dump(morph_counts, outputfile)
return morph_counts
def test_default_calendars(self):
# concat 连接迭代
for name in concat(
[_default_calendar_factories, _default_calendar_aliases]):
self.assertIsNotNone(get_calendar(name),
"get_calendar(%r) returned None" % name)
def get_assets(self):
assets = [directory.walk() for directory in self._root_dirs]
self.assets = sorted(toolz.unique(toolz.concat(assets)))
return self
def atop(func, out_ind, *args, **kwargs):
""" Tensor operation: Generalized inner and outer products
A broad class of blocked algorithms and patterns can be specified with a
concise multi-index notation. The ``atop`` function applies an in-memory
function across multiple blocks of multiple inputs in a variety of ways.
Many dask.array operations are special cases of atop including elementwise,
broadcasting, reductions, tensordot, and transpose.
Parameters
----------
func : callable
Function to apply to individual tuples of blocks
out_ind : iterable
Block pattern of the output, something like 'ijk' or (1, 2, 3)
*args : sequence of Array, index pairs
Sequence like (x, 'ij', y, 'jk', z, 'i')
**kwargs : dict
Extra keyword arguments to pass to function
dtype : np.dtype
Datatype of resulting array.
concatenate : bool, keyword only
If true concatenate arrays along dummy indices, else provide lists
adjust_chunks : dict
Dictionary mapping index to function to be applied to chunk sizes
new_axes : dict, keyword only
New indexes and their dimension lengths
Examples
--------
2D embarrassingly parallel operation from two arrays, x, and y.
>>> z = atop(operator.add, 'ij', x, 'ij', y, 'ij', dtype='f8') # z = x + y # doctest: +SKIP
Outer product multiplying x by y, two 1-d vectors
>>> z = atop(operator.mul, 'ij', x, 'i', y, 'j', dtype='f8') # doctest: +SKIP
z = x.T
>>> z = atop(np.transpose, 'ji', x, 'ij', dtype=x.dtype) # doctest: +SKIP
The transpose case above is illustrative because it does same transposition
both on each in-memory block by calling ``np.transpose`` and on the order
of the blocks themselves, by switching the order of the index ``ij -> ji``.
We can compose these same patterns with more variables and more complex
in-memory functions
z = X + Y.T
>>> z = atop(lambda x, y: x + y.T, 'ij', x, 'ij', y, 'ji', dtype='f8') # doctest: +SKIP
Any index, like ``i`` missing from the output index is interpreted as a
contraction (note that this differs from Einstein convention; repeated
indices do not imply contraction.) In the case of a contraction the passed
function should expect an iterable of blocks on any array that holds that
index. To receive arrays concatenated along contracted dimensions instead
pass ``concatenate=True``.
Inner product multiplying x by y, two 1-d vectors
>>> def sequence_dot(x_blocks, y_blocks):
... result = 0
... for x, y in zip(x_blocks, y_blocks):
... result += x.dot(y)
... return result
>>> z = atop(sequence_dot, '', x, 'i', y, 'i', dtype='f8') # doctest: +SKIP
Add new single-chunk dimensions with the ``new_axes=`` keyword, including
the length of the new dimension. New dimensions will always be in a single
chunk.
>>> def f(x):
... return x[:, None] * np.ones((1, 5))
>>> z = atop(f, 'az', x, 'a', new_axes={'z': 5}, dtype=x.dtype) # doctest: +SKIP
If the applied function changes the size of each chunk you can specify this
with a ``adjust_chunks={...}`` dictionary holding a function for each index
that modifies the dimension size in that index.
>>> def double(x):
... return np.concatenate([x, x])
>>> y = atop(double, 'ij', x, 'ij',
... adjust_chunks={'i': lambda n: 2 * n}, dtype=x.dtype) # doctest: +SKIP
Include literals by indexing with None
>>> y = atop(add, 'ij', x, 'ij', 1234, None, dtype=x.dtype) # doctest: +SKIP
See Also
--------
top - dict formulation of this function, contains most logic
"""
out = kwargs.pop('name', None) # May be None at this point
token = kwargs.pop('token', None)
dtype = kwargs.pop('dtype', None)
adjust_chunks = kwargs.pop('adjust_chunks', None)
new_axes = kwargs.get('new_axes', {})
from .core import Array, unify_chunks, normalize_arg
if dtype is None:
raise ValueError("Must specify dtype of output array")
chunkss, arrays = unify_chunks(*args)
for k, v in new_axes.items():
chunkss[k] = (v, )
arginds = list(zip(arrays, args[1::2]))
for arg, ind in arginds:
if hasattr(arg, 'ndim') and hasattr(
ind, '__len__') and arg.ndim != len(ind):
raise ValueError(
"Index string %s does not match array dimension %d" %
(ind, arg.ndim))
numblocks = {a.name: a.numblocks for a, ind in arginds if ind is not None}
argindsstr = list(
toolz.concat([(normalize_arg(a) if ind is None else a.name, ind)
for a, ind in arginds]))
# Finish up the name
if not out:
out = '%s-%s' % (token or utils.funcname(func).strip('_'),
base.tokenize(func, out_ind, argindsstr, dtype, **
kwargs))
kwargs2 = {k: normalize_arg(v) for k, v in kwargs.items()}
dsk = _top(func, out, out_ind, *argindsstr, numblocks=numblocks, **kwargs2)
dsks = [a.dask for a, ind in arginds if ind is not None]
chunks = [chunkss[i] for i in out_ind]
if adjust_chunks:
for i, ind in enumerate(out_ind):
if ind in adjust_chunks:
if callable(adjust_chunks[ind]):
chunks[i] = tuple(map(adjust_chunks[ind], chunks[i]))
elif isinstance(adjust_chunks[ind], numbers.Integral):
chunks[i] = tuple(adjust_chunks[ind] for _ in chunks[i])
elif isinstance(adjust_chunks[ind], (tuple, list)):
chunks[i] = tuple(adjust_chunks[ind])
else:
raise NotImplementedError(
"adjust_chunks values must be callable, int, or tuple")
chunks = tuple(chunks)
return Array(sharedict.merge(
(out, dsk),
*dsks,
dependencies={out: {a.name
for a, ind in arginds if ind is not None}}),
out,
chunks,
dtype=dtype)
def _():
return concat(
convert(chunks(pd.DataFrame), csv, **kwargs) for csv in csvs)
def get_unsafe_inner_columns(f):
unique_columns = unique(concat(map(get_unsafe_inner_columns, f.clauses)))
lowered = [x.label(getattr(x, 'name', None)) for x in unique_columns]
return [getattr(sa.func, f.name)(*lowered)]
def test_registered(s3):
sample, values = read_bytes('s3://%s/test/accounts.*.json' %
test_bucket_name)
results = compute(*concat(values))
assert set(results) == set(files.values())
def get_all_froms(colelement):
return list(unique(concat(map(get_all_froms, colelement.get_children()))))
def inputs(self):
return tuple(unique(concat(v.inputs for v in self.values)))
def __init__(self,
host='127.0.0.1',
http_port=9786,
bokeh_port=8787,
scheduler_address='tcp://127.0.0.1:8786',
bokeh_whitelist=[],
log_level=logging_level,
show=False,
prefix=None,
use_xheaders=False,
quiet=True):
self.port = bokeh_port
ip = socket.gethostbyname(host)
hosts = ['localhost', '127.0.0.1', ip, host]
with ignoring(Exception):
hosts.append(socket.gethostbyname(ip))
with ignoring(Exception):
hosts.append(socket.gethostbyname(socket.gethostname()))
hosts = ['%s:%d' % (h, bokeh_port) for h in hosts]
hosts.append("*")
hosts.extend(map(str, bokeh_whitelist))
args = ([sys.executable, '-m', 'bokeh', 'serve'] + paths + [
'--check-unused-sessions=50', '--unused-session-lifetime=1',
'--allow-websocket-origin=*', '--port',
str(bokeh_port)
])
if bokeh.__version__ <= '0.12.4':
args += sum([['--host', h] for h in hosts], [])
if prefix:
args.extend(['--prefix', prefix])
if show:
args.append('--show')
if use_xheaders:
args.append('--use-xheaders')
if log_level in ('debug', 'info', 'warning', 'error', 'critical'):
args.extend(['--log-level', log_level])
bokeh_options = {
'host': host,
'http-port': http_port,
'scheduler-address': scheduler_address,
'bokeh-port': bokeh_port
}
args.extend(['--args'] + list(map(str, concat(bokeh_options.items()))))
import subprocess
process = subprocess.Popen(args)
self.process = process
@atexit.register
def cleanup_process():
try:
process.terminate()
except OSError:
pass
if not quiet:
logger.info("Web UI: http://%s:%d/status/" % (ip, bokeh_port))
plt.show()
###########################################################################
# Calculating variances
# array of features
xa = np.vstack([list(toolz.pluck('x', ep)) for ep in episodes])
# get array of returns
ga = np.hstack([episode_return(ep) for ep in episodes])
# returns multiplied by feature vector
gx = xa.T * ga
# per-feature variance (is this right?)
va = np.var(gx, axis=1)
# Delta squared for variance
deltas = np.array(list(toolz.pluck('delta', toolz.concat(episodes))))
dsqa = deltas**2
# delta-squared return
dsqret = calculate_return(dsqa, lpluck('gm', concat(episodes)))
# multiplying by features
dsqrx = xa.T * dsqret
# averaging for per-feature delta-squared return (is this right?)
dsvar_w = np.mean(dsqrx, axis=1)
# least squares solution (this appears to have some sort of issue)
# dsvar_w, res, *_ = np.linalg.lstsq(xa, dsqret)
# make heatmap
traj = np.array(list(toolz.pluck('obs', episodes[-1])))
def sumDigits(ints: PVector[int]) -> int:
return last(accumulate(add, concat(map(lambda c: toDigits(c), ints))))
def physical_tables_node(node):
# Iterative case. Any other Node's physical roots are the unique physical
# roots of that Node's root tables.
return list(unique(concat(map(physical_tables, node.root_tables()))))
def subterms(expr):
return concat([[expr], concat(map(subterms, expr._inputs))])