def _calc_mean(self, axis=None):
if axis is None:
result = self._new(input=self.dag.transform(
lambda x: (x.shape[0] * x.shape[1], np.sum(x, axis=axis)),
[self.input],
))._compute()
total_count = builtins.sum([res[0] for res in result])
mean = np.sum([res[1] for res in result], axis=axis) / total_count
return mean
elif axis == 0: # mean of each column
result = self._new(input=self.dag.transform(
lambda x: (x.shape[0], np.sum(x, axis=axis)),
[self.input]))._compute()
total_count = builtins.sum([res[0] for res in result])
mean = np.sum([res[1] for res in result], axis=axis) / total_count
# new dag
dag = DAG(self.executor)
partitioned_input = [mean]
input = dag.add_input(partitioned_input)
return self._new(
dag=dag,
input=input,
shape=mean.shape,
chunks=mean.shape,
partition_row_counts=mean.shape,
)
return NotImplemented
def _repartition_chunks(self, chunks):
c = chunks[0]
partition_row_ranges, total_rows, new_num_partitions = calculate_partition_boundaries(
chunks, self.partition_row_counts)
# make a new zarr group in the intermediate store with a unique name
root = self.intermediate_group.create_group(str(uuid.uuid4()))
# make a zarr group for each partition
with concurrent.futures.ThreadPoolExecutor(max_workers=64) as executor:
executor.map(lambda index: root.create_group(str(index)),
range(new_num_partitions))
def tmp_store(pairs):
for pair in pairs:
index, offsets, partial_chunk = pair[0], pair[1][0], pair[1][1]
g = root.require_group(str(index))
g.array("%s-%s" % (offsets[0], offsets[1]),
partial_chunk,
chunks=False)
x1 = self.dag.add_input(partition_row_ranges)
x2 = self.dag.transform(
lambda x, y: extract_partial_chunks((x, y), chunks),
[x1, self.input])
x3 = self.dag.transform(tmp_store, [x2])
# run computation to save partial chunks
list(self.dag.compute(x3))
# create a new computation to read and combine partial chunks
def tmp_load(new_index):
# last chunk has fewer than c rows
if new_index == new_num_partitions - 1 and total_rows % c != 0:
last_chunk_rows = total_rows % c
arr = np.zeros((last_chunk_rows, chunks[1]))
else:
arr = np.zeros(chunks)
g = root.require_group(str(new_index))
for (name, partial_chunk) in g.arrays():
new_start_offset, new_end_offset = [
int(n) for n in name.split("-")
]
arr[new_start_offset:new_end_offset] = partial_chunk
return arr
dag = DAG(self.executor)
input = dag.add_input(list(range(new_num_partitions)))
input = dag.transform(tmp_load, [input])
# TODO: delete intermediate store when dag is computed
return ExecutorZappyArray(self.executor, dag, input, self.shape,
chunks, self.dtype)
def ones(cls, executor, shape, chunks, dtype=float, intermediate_store=None):
dag = DAG(executor)
input = dag.add_input(list(get_chunk_sizes(shape, chunks)))
input = dag.transform(lambda chunk: np.ones(chunk, dtype=dtype), [input])
return cls(
executor,
dag,
input,
shape,
chunks,
dtype,
intermediate_store=intermediate_store,
)
def from_ndarray(cls, executor, arr, chunks, intermediate_store=None):
func, chunk_indices = ZappyArray._read_chunks(arr, chunks)
dag = DAG(executor)
# the input is just the chunk indices
input = dag.add_input(chunk_indices)
# add a transform to read chunks
input = dag.transform(func, [input])
return cls(
executor,
dag,
input,
arr.shape,
chunks,
arr.dtype,
intermediate_store=intermediate_store,
)
def _calc_func_axis_distributive(self, func, axis):
per_chunk_result = [func(x, axis=axis) for x in self._compute()]
result = func(per_chunk_result, axis=axis)
if axis is None:
return result
elif axis == 0: # column-wise
# new dag
dag = DAG(self.executor)
partitioned_input = [result]
input = dag.add_input(partitioned_input)
return self._new(
dag=dag,
input=input,
shape=result.shape,
chunks=result.shape,
partition_row_counts=result.shape,
)
return NotImplemented
def test_no_transform():
dag = DAG(concurrent.futures.ThreadPoolExecutor())
output = dag.add_input([2])
assert list(dag.compute(output)) == [2]
def test_incompatible_num_partitions():
dag = DAG(concurrent.futures.ThreadPoolExecutor())
dag.add_input([2])
with pytest.raises(AssertionError):
dag.add_input([1, 5])
def test_dag_multiple_partitions():
dag = DAG(concurrent.futures.ThreadPoolExecutor())
input = dag.add_input([2, 3, 5])
output = dag.transform(add_one, [input])
assert list(dag.compute(output)) == [3, 4, 6]
def test_dag_single_partition_binary_function():
dag = DAG(concurrent.futures.ThreadPoolExecutor())
input1 = dag.add_input([2])
input2 = dag.add_input([3])
output = dag.transform(add, [input1, input2])
assert list(dag.compute(output)) == [5]
def test_dag_single_partition_serial_functions():
dag = DAG(concurrent.futures.ThreadPoolExecutor())
input = dag.add_input([2])
intermediate = dag.transform(add_one, [input])
output = dag.transform(times_two, [intermediate])
assert list(dag.compute(output)) == [6]
def test_dag_multiple_partitions_binary_function():
dag = DAG(concurrent.futures.ThreadPoolExecutor())
input1 = dag.add_input([2, 3, 5])
input2 = dag.add_input([7, 11, 13])
output = dag.transform(add, [input1, input2])
assert list(dag.compute(output)) == [9, 14, 18]