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#!/usr/bin/env python
#
# __init__.py -
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
import io
import os
import sys
import time
import gzip
import shutil
import tempfile
import threading
import subprocess as sp
import multiprocessing as mp
import numpy as np
def tempdir():
"""Returns a context manager which creates and returns a temporary
directory, and then deletes it on exit.
"""
class ctx(object):
def __enter__(self):
self.prevdir = os.getcwd()
self.tempdir = tempfile.mkdtemp()
os.chdir(self.tempdir)
return self.tempdir
def __exit__(self, *a, **kwa):
os.chdir(self.prevdir)
time.sleep(0.25)
shutil.rmtree(self.tempdir)
return ctx()
def touch(path):
"""Create an empty file."""
with open(path, 'wt') as f:
pass
def poll(until):
"""Waits until ``until`` returns ``True``, printing out a message every
minute.
"""
start = time.time()
while not until():
time.sleep(0.5)
cur = time.time()
elapsed = int(round(cur - start))
if int(elapsed) % 60 == 0:
print('Waiting ({:0.2f} minutes)'.format(elapsed / 60.0))
def compress(infile, outfile, buflen=-1):
"""Use gzip to compress the data in infile, saving it to outfile.
If buflen == -1, we compress all of the data at once. Otherwise we
compress chunks, creating a concatenated gzip stream.
"""
def compress_with_gzip_module():
print('Compressing data using python gzip module ...', outfile)
with open(infile, 'rb') as inf:
while True:
data = inf.read(buflen)
if len(data) == 0:
break
with open(outfile, 'ab') as outf:
gzip.GzipFile(fileobj=outf, mode='ab').write(data)
def compress_with_gzip_command():
with open(infile, 'rb') as inf, open(outfile, 'wb') as outf:
# If buflen == -1, do a single call
if buflen == -1:
print('Compressing data with a single '
'call to gzip ...', outfile)
sp.Popen(['gzip', '-c'], stdin=inf, stdout=outf).wait()
# Otherwise chunk the call
else:
print('Compressing data with multiple '
'calls to gzip ...', outfile)
nbytes = 0
chunk = inf.read(buflen)
while len(chunk) != 0:
proc = sp.Popen(['gzip', '-c'], stdin=sp.PIPE, stdout=outf)
proc.communicate(chunk)
nbytes += len(chunk)
if (nbytes / buflen) % 10 == 0:
print('Compressed to {}...'.format(nbytes))
chunk = inf.read(buflen)
# Use python gzip module on windows,
# can't assume gzip exists
if sys.platform.startswith("win"):
target = compress_with_gzip_module
# If not windows, assume that gzip command
# exists, and use it, because the python
# gzip module is super-slow.
else:
target = compress_with_gzip_command
cmpThread = threading.Thread(target=target)
cmpThread.start()
poll(lambda : not cmpThread.is_alive())
def compress_inmem(data, concat):
"""Compress the given data (assumed to be bytes) and return a bytearray
containing the compressed data (including gzip header and footer).
Also returns offsets for the end of each separate stream.
"""
f = io.BytesIO()
if concat: chunksize = len(data) // 10
else: chunksize = len(data)
offsets = []
compressed = 0
print('Generating compressed data {}, concat: {})'.format(
len(data), concat))
while compressed < len(data):
start = len(f.getvalue())
chunk = data[compressed:compressed + chunksize]
with gzip.GzipFile(mode='ab', fileobj=f) as gzf:
gzf.write(chunk)
end = len(f.getvalue())
print(' Wrote stream to {} - {} [{} bytes] ...'.format(
start, end, end - start))
offsets.append(end)
compressed += chunksize
print(' Final size: {}'.format(len(f.getvalue())))
f.seek(0)
return bytearray(f.read()), offsets
def gen_test_data(filename, nelems, concat):
"""Make some data to test with. """
start = time.time()
# The file just contains a sequentially
# increasing list of numbers
print('Generating test data ({} elems, {} bytes -> {})'.format(
nelems,
nelems * 8,
filename))
# Generate the data as a numpy memmap array.
# Allocate at most 128MB at a time
toWrite = nelems
offset = 0
writeBlockSize = min(16777216, nelems)
datafile = '{}_temp'.format(filename)
open(datafile, 'wb+').close()
data = np.memmap(datafile, dtype=np.uint64, shape=nelems)
idx = 0
while toWrite > 0:
if idx % 10 == 0:
print('Generated to {}...'.format(offset))
thisWrite = min(writeBlockSize, toWrite)
vals = np.arange(offset, offset + thisWrite, dtype=np.uint64)
data[offset:offset + thisWrite] = vals
toWrite -= thisWrite
offset += thisWrite
idx += 1
data.flush()
if not concat: maxBufSize = -1
else: maxBufSize = 8 * min(16777216, nelems // 50)
compress(datafile, filename, maxBufSize)
end = time.time()
del data
os.remove(datafile)
print('Done in {:0.2f} seconds'.format(end - start))
def _check_chunk(args):
s, e, test_data = args
valid = np.arange(s, e, dtype=np.uint64)
return np.all(test_data == valid)
def check_data_valid(data, startval, endval=None):
if endval is None:
endval = len(data)
chunksize = 10000000
startval = int(startval)
endval = int(endval)
offsets = np.arange(0, len(data), chunksize)
args = []
result = True
for offset in offsets:
s = startval + offset
e = min(s + chunksize, endval)
nelems = e - s
test_chunk = data[offset:offset + nelems]
args.append((s, e, test_chunk))
pool = mp.Pool()
result = all(pool.map(_check_chunk, args))
pool.terminate()
return result
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