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from pathlib import Path
from indexed_search import DB
import tables as tb
class PyTablesDB(DB):
def __init__(
self,
nrows,
rng,
userandom,
datadir,
docompress=0,
complib="zlib",
kind="medium",
optlevel=6,
):
DB.__init__(self, nrows, rng, userandom)
self.tprof = []
# Specific part for pytables
self.docompress = docompress
self.complib = complib
# Complete the filename
filename = f"pro-{self.filename.name}-O{optlevel}-{kind}"
if docompress:
filename = f"{filename}-{complib}{docompress}"
self.datadir = Path(datadir)
if not self.datadir.is_dir():
self.datadir.mkdir(parents=True, exist_ok=True)
print(f"Created {self.datadir}.")
self.filename = self.datadir / f"{self.filename}.h5"
# The chosen filters
self.filters = tb.Filters(
complevel=self.docompress, complib=self.complib, shuffle=1
)
print("Processing database:", self.filename)
def open_db(self, remove=0):
if remove and Path(self.filename).is_file():
Path(self.filename).unlink()
con = tb.open_file(self.filename, "a")
return con
def close_db(self, con):
# Remove first the table_cache attribute if it exists
if hasattr(self, "table_cache"):
del self.table_cache
con.close()
def create_table(self, con):
class Record(tb.IsDescription):
col1 = tb.Int32Col()
col2 = tb.Int32Col()
col3 = tb.Float64Col()
col4 = tb.Float64Col()
con.create_table(
con.root,
"table",
Record,
filters=self.filters,
expectedrows=self.nrows,
)
def fill_table(self, con):
"Fills the table"
table = con.root.table
j = 0
for i in range(0, self.nrows, self.step):
stop = (j + 1) * self.step
if stop > self.nrows:
stop = self.nrows
arr_i4, arr_f8 = self.fill_arrays(i, stop)
# recarr = records.fromarrays([arr_i4, arr_i4, arr_f8, arr_f8])
# table.append(recarr)
table.append([arr_i4, arr_i4, arr_f8, arr_f8])
j += 1
table.flush()
def index_col(self, con, column, kind, optlevel, verbose):
col = getattr(con.root.table.cols, column)
tmp_dir = self.datadir / "scratch2"
tmp_dir.mkdir(parents=True, exist_ok=True)
col.create_index(
kind=kind,
optlevel=optlevel,
filters=self.filters,
tmp_dir=tmp_dir,
_verbose=verbose,
_blocksizes=None,
)
# _blocksizes=(2**27, 2**22, 2**15, 2**7))
# _blocksizes=(2**27, 2**22, 2**14, 2**6))
# _blocksizes=(2**27, 2**20, 2**13, 2**5),
# _testmode=True)
def do_query(self, con, column, base, inkernel):
if True:
if not hasattr(self, "table_cache"):
self.table_cache = table = con.root.table
self.colobj = getattr(table.cols, column)
# self.colobj = getattr(table.cols, 'col1')
self.condvars = {
"col": self.colobj,
"col1": table.cols.col1,
"col2": table.cols.col2,
"col3": table.cols.col3,
"col4": table.cols.col4,
}
table = self.table_cache
colobj = self.colobj
else:
table = con.root.table
colobj = getattr(table.cols, column)
self.condvars = {
"col": colobj,
"col1": table.cols.col1,
"col2": table.cols.col2,
"col3": table.cols.col3,
"col4": table.cols.col4,
}
self.condvars["inf"] = self.rng[0] + base
self.condvars["sup"] = self.rng[1] + base
# For queries that can use two indexes instead of just one
d = (self.rng[1] - self.rng[0]) / 2
inf1 = int(self.rng[0] + base)
sup1 = int(self.rng[0] + d + base)
inf2 = self.rng[0] + base * 2
sup2 = self.rng[0] + d + base * 2
self.condvars["inf1"] = inf1
self.condvars["sup1"] = sup1
self.condvars["inf2"] = inf2
self.condvars["sup2"] = sup2
# condition = "(inf == col2)"
# condition = "(inf==col2) & (col4==sup)"
# condition = "(inf==col2) | (col4==sup)"
# condition = "(inf==col2) | (col2==sup)"
# condition = "(inf==col2) & (col3==sup)"
# condition = "((inf==col2) & (sup==col4)) & (col3==sup)"
# condition = "((inf==col1) & (sup==col4)) & (col3==sup)"
# condition = "(inf<=col1) & (col3<sup)"
# condition = "(inf<=col2) & (col4<sup)"
# condition = "(inf<=col4) & (col4<sup)"
# condition = "((inf<=col4) & (col4<sup)) | (col2<3)"
# condition = "((inf<=col4) | (col4<sup)) & (col2<3)"
# condition = "((inf<=col4) | (col4<sup)) & ((inf<col2) & (col2<sup))"
# condition = "((inf<=col4) & (col4<sup)) | ((inf<col2) & (col2<sup))"
# condition = "((inf<=col4) & (col4<sup)) & ((inf<col2) & (col2<sup))"
# condition = "((inf2<=col3) & (col3<sup2)) | ((inf1<col1) & (col1<sup1))"
# print "lims-->", inf1, inf2, sup1, sup2
condition = "((inf2<=col) & (col<sup2)) | ((inf1<col2) & (col2<sup1))"
condition += " & ((col1+3.1*col2+col3*col4) > 3)"
# condition += " & (col2*(col3+3.1)+col3*col4 > col1)"
# condition = "(inf<=col) & (col<=sup) & (col3 >= 0)"
# # condition = "(inf<=col) & (col<=sup)"
# condition = "(%s<=col) & (col<=%s)" % \
# (self.rng[0]+base, self.rng[1]+base)
# condition = "(%s<=col1*col2) & (col3*col4<=%s)" % \
# (self.rng[0]+base, self.rng[1]+base)
# condition = "(col**2.4==%s)" % (self.rng[0]+base)
# condition = "(col==%s)" % (self.rng[0]+base)
# condvars = {"col": colobj}
# c = self.condvars
# print "condvars-->", c['inf'], c['sup'], c['inf2'], c['sup2']
ncoords = 0
if colobj.is_indexed:
results = [
r[column] for r in table.where(condition, self.condvars)
]
# coords = table.get_where_list(condition, self.condvars)
# results = table.read_coordinates(coords, field=column)
# results = table.read_where(condition, self.condvars, field=column)
elif inkernel:
print("Performing in-kernel query")
results = [
r[column] for r in table.where(condition, self.condvars)
]
# coords = [r.nrow for r in table.where(condition, self.condvars)]
# results = table.read_coordinates(coords)
# for r in table.where(condition, self.condvars):
# var = r[column]
# ncoords += 1
else:
# coords = [r.nrow for r in table
# if (self.rng[0]+base <= r[column] <= self.rng[1]+base)]
# results = table.read_coordinates(coords)
print("Performing regular query")
results = [
r[column]
for r in table
if (
((inf2 <= r["col4"]) and (r["col4"] < sup2))
or ((inf1 < r["col2"]) and (r["col2"] < sup1))
and (
(r["col1"] + 3.1 * r["col2"] + r["col3"] * r["col4"])
> 3
)
)
]
ncoords = len(results)
# return coords
# print "results-->", results
# return results
return ncoords
# self.tprof.append( self.colobj.index.tprof )
# return ncoords, self.tprof
|
