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from time import perf_counter as clock
import numpy as np
import tables as tb
N = 10_000_000
filters = tb.Filters(9, "blosc2", shuffle=True)
def timed(func, *args, **kwargs):
start = clock()
res = func(*args, **kwargs)
print(f"{clock() - start:.3f}s elapsed.")
return res
def create_table(output_path):
print("creating array...", end=" ")
dt = np.dtype([("field%d" % i, int) for i in range(32)])
a = np.zeros(N, dtype=dt)
print("done.")
output_file = tb.open_file(output_path, mode="w")
table = output_file.create_table("/", "test", dt, filters=filters)
print("appending data...", end=" ")
table.append(a)
print("flushing...", end=" ")
table.flush()
print("done.")
output_file.close()
def copy1(input_path, output_path):
print(f"copying data from {input_path} to {output_path}...")
input_file = tb.open_file(input_path, mode="r")
output_file = tb.open_file(output_path, mode="w")
# copy nodes as a batch
input_file.copy_node(
"/", output_file.root, recursive=True, filters=filters
)
output_file.close()
input_file.close()
def copy2(input_path, output_path):
print(f"copying data from {input_path} to {output_path}...")
input_file = tb.open_file(input_path, mode="r")
input_file.copy_file(output_path, overwrite=True, filters=filters)
input_file.close()
def copy3(input_path, output_path):
print(f"copying data from {input_path} to {output_path}...")
input_file = tb.open_file(input_path, mode="r")
output_file = tb.open_file(output_path, mode="w", filters=filters)
table = input_file.root.test
table.copy(output_file.root)
output_file.close()
input_file.close()
def copy4(input_path, output_path):
print(f"copying data from {input_path} to {output_path}...")
input_file = tb.open_file(input_path, mode="r")
output_file = tb.open_file(output_path, mode="w", filters=filters)
input_table = input_file.root.test
print("reading data...", end=" ")
start = clock()
data = input_file.root.test.read()
print(f"{clock() - start:.3f}s elapsed.")
print("done.")
output_table = output_file.create_table("/", "test", input_table.dtype)
print("appending data...", end=" ")
start = clock()
output_table.append(data)
print("flushing...", end=" ")
output_table.flush()
print(f"{clock() - start:.3f}s elapsed.")
print("done.")
input_file.close()
output_file.close()
def copy5(input_path, output_path):
print(f"copying data from {input_path} to {output_path}...")
input_file = tb.open_file(input_path, mode="r")
output_file = tb.open_file(output_path, mode="w", filters=filters)
input_table = input_file.root.test
output_table = output_file.create_table("/", "test", input_table.dtype)
chunksize = 100_000
rowsleft = len(input_table)
start = 0
for chunk in range(int(len(input_table) / chunksize) + 1):
stop = start + min(chunksize, rowsleft)
data = input_table.read(start, stop)
output_table.append(data)
output_table.flush()
rowsleft -= chunksize
start = stop
input_file.close()
output_file.close()
if __name__ == "__main__":
timed(create_table, "tmp.h5")
timed(copy1, "tmp.h5", "test1.h5")
timed(copy2, "tmp.h5", "test2.h5")
timed(copy3, "tmp.h5", "test3.h5")
timed(copy4, "tmp.h5", "test4.h5")
timed(copy5, "tmp.h5", "test5.h5")
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