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import sys
from time import perf_counter as clock
from pathlib import Path
import numpy as np
import tables as tb
niter = 3
dirname = "/tmp/blosc-data/"
# expression = "a**2 + b**3 + 2*a*b + 3"
# expression = "a+b"
# expression = "a**2 + 2*a/b + 3"
# expression = "(a+b)**2 - (a**2 + b**2 + 2*a*b) + 1.1"
expression = "3*a-2*b+1.1"
shuffle = True
def create_file(kind, prec, synth):
prefix_orig = "cellzome/cellzome-"
iname = dirname + prefix_orig + "none-" + prec + ".h5"
f = tb.open_file(iname, "r")
if prec == "single":
type_ = tb.Float32Atom()
else:
type_ = tb.Float64Atom()
if synth:
prefix = "synth/synth-"
else:
prefix = "cellzome/cellzome-"
for clevel in range(10):
oname = "%s/%s-%s%d-%s.h5" % (dirname, prefix, kind, clevel, prec)
# print "creating...", iname
f2 = tb.open_file(oname, "w")
if kind in ["none", "numpy"]:
filters = None
else:
filters = tb.Filters(
complib=kind, complevel=clevel, shuffle=shuffle
)
for name in ["maxarea", "mascotscore"]:
col = f.get_node("/", name)
r = f2.create_carray("/", name, type_, col.shape, filters=filters)
if synth:
r[:] = np.arange(col.nrows, dtype=type_.dtype)
else:
r[:] = col[:]
f2.close()
if clevel == 0:
size = 1.5 * Path(oname).stat().st_size
f.close()
return size
def create_synth(kind, prec):
prefix_orig = "cellzome/cellzome-"
iname = dirname + prefix_orig + "none-" + prec + ".h5"
f = tb.open_file(iname, "r")
if prec == "single":
type_ = tb.Float32Atom()
else:
type_ = tb.Float64Atom()
prefix = "synth/synth-"
for clevel in range(10):
oname = "%s/%s-%s%d-%s.h5" % (dirname, prefix, kind, clevel, prec)
# print "creating...", iname
f2 = tb.open_file(oname, "w")
if kind in ["none", "numpy"]:
filters = None
else:
filters = tb.Filters(
complib=kind, complevel=clevel, shuffle=shuffle
)
for name in ["maxarea", "mascotscore"]:
col = f.get_node("/", name)
r = f2.create_carray("/", name, type_, col.shape, filters=filters)
if name == "maxarea":
r[:] = np.arange(col.nrows, dtype=type_.dtype)
else:
r[:] = np.arange(col.nrows, 0, dtype=type_.dtype)
f2.close()
if clevel == 0:
size = 1.5 * Path(oname).stat().st_size
f.close()
return size
def process_file(kind, prec, clevel, synth):
if kind == "numpy":
lib = "none"
else:
lib = kind
if synth:
prefix = "synth/synth-"
else:
prefix = "cellzome/cellzome-"
iname = "%s/%s-%s%d-%s.h5" % (dirname, prefix, kind, clevel, prec)
f = tb.open_file(iname, "r")
a_ = f.root.maxarea
b_ = f.root.mascotscore
oname = "%s/%s-%s%d-%s-r.h5" % (dirname, prefix, kind, clevel, prec)
f2 = tb.open_file(oname, "w")
if lib == "none":
filters = None
else:
filters = tb.Filters(complib=lib, complevel=clevel, shuffle=shuffle)
if prec == "single":
type_ = tb.Float32Atom()
else:
type_ = tb.Float64Atom()
r = f2.create_carray("/", "r", type_, a_.shape, filters=filters)
if kind == "numpy":
a2, b2 = a_[:], b_[:]
t0 = clock()
r = eval(expression, {"a": a2, "b": b2})
print(f"{clock() - t0:5.2f}")
else:
expr = tb.Expr(expression, {"a": a_, "b": b_})
expr.set_output(r)
expr.eval()
f.close()
f2.close()
size = Path(iname).stat().st_size + Path(oname).stat().st_size
return size
if __name__ == "__main__":
if len(sys.argv) > 3:
kind = sys.argv[1]
prec = sys.argv[2]
if sys.argv[3] == "synth":
synth = True
else:
synth = False
else:
print("3 parameters required")
sys.exit(1)
# print "kind, precision, synth:", kind, prec, synth
# print "Creating input files..."
size_orig = create_file(kind, prec, synth)
# print "Processing files for compression levels in range(10)..."
for clevel in range(10):
t0 = clock()
ts = []
for i in range(niter):
size = process_file(kind, prec, clevel, synth)
ts.append(clock() - t0)
t0 = clock()
ratio = size_orig / size
print(f"{min(ts):5.2f}, {ratio:5.2f}")
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