import random as random_mod
import sys, os, pickle


__parallel_loaded__ = False
_cpu_count = 1

try:
    import multiprocessing as processing
    __parallel_loaded__ = True
    _cpu_count = processing.cpu_count
except:
    try:
        import processing
        __parallel_loaded__ = True
        _cpu_count = processing.cpuCount()
    except:
        #print 'processing not installed no parallel processing possible'
        pass
    

import model

from lib.Simplex import Simplex

# Add current path to the system paths
# just in case some user make a directory change
sys.path.append(os.getcwd())

#==============================================================================
# class: DiffEv
Beispiel #2
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        queue.task_done()


if __name__ == '__main__':
    start = time.time()
    src_path = "/media/tx-eva-data/NAS/基础数据库/华中科技大学同济医学院附属同济医院/2017_07_13_abnormal"
    dec_path = "/media/tx-eva-data/NAS/原始数据库/华中科技大学同济医学院附属同济医院"

    queue = multiprocessing.JoinableQueue()
    list_p = []
    for i in range(multiprocessing.cpu_count() - 2):
        process = multiprocessing.Process(target=Worker, args=(queue, ))
        process.daemon = True
        process.start()
        list_p.append(process)

    for dirpath, dirnames, filenames in os.walk(src_path):
        for file in filenames:
            dcm_path = os.path.join(dirpath, file)
            queue.put([dcm_path, dec_path])

    queue.join()

    for i in range(multiprocessing.cpuCount() - 2):
        queue.put(None)

    for p in list_p:
        p.join()

    elapsed = time.time() - start
    print('main end! %f' % elapsed)
Beispiel #3
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# USER-SPECIFIC PATHS AND VALUES
# We'll be using SWarp. Define the proper bin executable here. This is
# particularly important if you have different installations and want to use a
# specific version in the reduction. Also, note that the SWarp packaged with
# Scisoft probably won't work properly on Intel 64-bit Macs. It is strongly
# advised that you recompile and install SWarp from source if SWarp's coadd
# mosaics are null images.
swarp_bin = "/Applications/scisoft//i386/bin/swarp"
# We'll also be using some WCSTools. There should be no problem with the Scisoft
# version of thses.
sethead_bin = "/Applications/scisoft//i386/bin/sethead"
# For parallel processing we need the number of available CPUs. You could hard-
# code this value to something else, but it would result in non-optimal
# performance.
if doparallel == 1:
    numprocessors = cpuCount()
else:
    numprocessors = 1
# Debugging mode outputs intermediate image files to help track down problems.
# It requires more time to run because of the additional hard disk reads/writes.
DEBUG = False


#-------------------------------------------------------------------------------
# FUNCTION DEFINITIONS
# Simple function allowing parallelization of mosaicing with SWarp.
def run_swarp(command):
    system(command)
    return

Beispiel #4
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# advised that you recompile and install SWarp from source if SWarp's coadd 
# mosaics are null images.
swarp_bin = "swarp"
# We'll also be using some WCSTools. There should be no problem with the Scisoft
# version of thses.
sethead_bin = "sethead"
# For parallel processing we need the number of available CPUs. You could hard-
# code this value to something else, but it would result in non-optimal 
# performance.

# AMORGAN ADDS for WCS FITTING  Change if your python version is different.
# Will want to avoid having to load this in future versions.
pypath = ""

if doparallel == 1:
    numprocessors = cpuCount()
else:
    numprocessors = 1
# Debugging mode outputs intermediate image files to help track down problems.
# It requires more time to run because of the additional hard disk reads/writes.
DEBUG = False
#-------------------------------------------------------------------------------
# FUNCTION DEFINITIONS
# Simple function allowing parallelization of mosaicing with SWarp.
def run_swarp(command):
    system(command)
    return
#-------------------------------------------------------------------------------
# BEGIN MAIN PROGRAM

if not os.environ.has_key("Q_DIR"):
import version
__version__ = version.version

def complement(s, _comp=string.maketrans('ATCG', 'TAGC')):
    return s.translate(_comp)
def revcomp(s, _comp=string.maketrans('ATCG', 'TAGC')):
    return s.translate(_comp)[::-1]

CPU_COUNT = 4
try:
    import multiprocessing as processing
    CPU_COUNT = processing.cpu_count()
except ImportError:
    import processing
    CPU_COUNT = processing.cpuCount()

def write_c2t(fasta_name, unconverted, colorspace=False):
    """
    given a fasta file, write a new file:
        `some.fr.c2t.fasta` which contains:
          + the same headers prefixed with 'f' with all C's converted to T
          + headers prefixed with 'r' reverse complemented with
                                 all C's converted to T.

    if unconverted is false, then also save a file with the forward and reverse
    without conversion.
    """
    d = op.join(op.dirname(fasta_name), "bowtie_index")
    if colorspace: d += "_colorspace"
    if not op.exists(d): os.mkdir(d)
Beispiel #6
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import test
# from test import pystone
import multiprocessing
import time

STONES_PER_PROCESS = 10 * test.pystone.LOOPS


def f(q):
    t = test.pystone.pystones(STONES_PER_PROCESS)
    q.put(t, block=True)


if __name__ == '__main__':
    print 'multiprocessing test.pystones() benchmark'
    print 'You have ' + str(multiprocessing.cpuCount()) + ' CPU(s)'
    print 'Processes\tPystones\tWall time\tpystones/s'

    results = multiprocessing.Queue()
    for N in range(1, multiprocessing.cpuCount() + 3):
        p = []
        q = multiprocessing.Queue()
        results = []

        for m in range(1, N + 1):
            p.append(multiprocessing.Process(target=f, args=(q, )))

        start = time.time()
        for pr in p:
            pr.start()
        for r in p:
Beispiel #7
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def complement(s, _comp=string.maketrans('ATCG', 'TAGC')):
    return s.translate(_comp)


def revcomp(s, _comp=string.maketrans('ATCG', 'TAGC')):
    return s.translate(_comp)[::-1]


CPU_COUNT = 4
try:
    import multiprocessing as processing
    CPU_COUNT = processing.cpu_count()
except ImportError:
    import processing
    CPU_COUNT = processing.cpuCount()


def write_c2t(fasta_name, unconverted, colorspace=False):
    """
    given a fasta file, write a new file:
        `some.fr.c2t.fasta` which contains:
          + the same headers prefixed with 'f' with all C's converted to T
          + headers prefixed with 'r' reverse complemented with
                                 all C's converted to T.

    if unconverted is false, then also save a file with the forward and reverse
    without conversion.
    """
    d = op.join(op.dirname(fasta_name), "bowtie_index")
    if colorspace: d += "_colorspace"