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import sys
import unittest
import os
import copy
import time
import contextlib
import pyopenms
from pyopenms.sysinfo import free_mem
import numpy as np
def show_mem(label):
p = free_mem()
p /= 1024.0 * 1024
print (label+" ").ljust(50, "."), ": %8.2f MB" % p
sys.stdout.flush()
@contextlib.contextmanager
def MemTester(name):
mem_at_start = free_mem()
print
show_mem("start test '%s' with" % name)
yield
missing = mem_at_start - free_mem()
show_mem("end with")
print
assert missing <= 0.1* mem_at_start, "possible mem leak: %s at start, missing %s" % (mem_at_start, missing)
if True or int(os.environ.get("WITH_MEMLEAK_TESTS", 0)):
class TestAll(unittest.TestCase):
def setUp(self):
self.mem_at_start = free_mem()
print
show_mem("AT THE BEGINNING ")
print
dirname = os.path.dirname(os.path.abspath(__file__))
self.testfile = os.path.join(dirname, "../test.mzXML")
def tearDown(self):
time.sleep(3)
print
show_mem("AT THE END ")
print
missing = self.mem_at_start - free_mem()
assert missing <= 0.1* self.mem_at_start, "possible mem leak: %s at start, missing %s" % (self.mem_at_start, missing)
def testAll(self):
with MemTester("specs from experiment"):
self.run_extractSpetraFromMSExperiment()
with MemTester("copy experiment"):
self.run_MSExperiment_copy()
with MemTester("string_conversions1"):
self.run_string_conversions1()
with MemTester("string_conversions2"):
self.run_string_conversions2()
with MemTester("string_lists"):
self.run_string_lists()
with MemTester("list_conversions"):
self.run_list_conversions()
with MemTester("set_spec_peaks"):
self.set_spec_peaks()
with MemTester("set_spec_peaks2"):
self.set_spec_peaks2()
with MemTester("test io"):
self.run_fileformats_io()
def run_string_conversions1(self):
basestr = 200000*" "
li = []
for i in range(1000):
if (i+1)%100 == 0:
show_mem("%4d runs" % i)
dv = pyopenms.DataValue(basestr)
dv = pyopenms.DataValue(basestr)
li.append(dv)
del li
def run_string_conversions2(self):
basestr = 200000*" "
li = []
for i in range(1000):
if (i+1)%100 == 0:
show_mem("%4d runs" % i)
sf = pyopenms.SourceFile()
sf.setNameOfFile(basestr)
sf.setNameOfFile(basestr)
li.append(sf)
del li
def run_string_lists(self):
basestr = 10000*" "
li = []
for i in range(100):
if (i+1)%100 == 0:
show_mem("%4d runs" % i)
sl = pyopenms.DataValue([basestr]*30)
sl = pyopenms.DataValue([basestr]*30)
li.append(sl)
del sl
del li
def run_list_conversions(self):
pc = pyopenms.Precursor()
allpcs = 500*[pc]
li = []
for i in range(500):
if (i+1)%100 == 0:
show_mem("%4d runs" % i)
spec = pyopenms.MSSpectrum()
spec.setPrecursors(allpcs)
spec.setPrecursors(allpcs)
li.append(spec)
del spec
del li
def set_spec_peaks(self):
data = np.zeros((10000,2), dtype=np.float32)
li = []
for i in range(1000):
if (i+1)%100 == 0:
show_mem("%4d specs processed" % i)
spec = pyopenms.MSSpectrum()
spec.set_peaks(data)
spec.set_peaks(data)
spec.set_peaks(data)
li.append(spec)
for spec in li:
del spec
del data
def set_spec_peaks2(self):
data = np.zeros((10000,2), dtype=np.float32)
li = []
for i in range(1000):
if (i+1)%100 == 0:
show_mem("%4d specs processed" % i)
spec = pyopenms.MSSpectrum()
spec.set_peaks(data)
spec.set_peaks(data)
spec.set_peaks(data)
spec.set_peaks(spec.get_peaks())
li.append(spec)
for spec in li:
del spec
del data
def run_extractSpetraFromMSExperiment(self):
p = pyopenms.FileHandler()
e = pyopenms.MSExperiment()
p.loadExperiment(self.testfile, e)
show_mem("data loaded")
li = []
print "please be patient :",
for k in range(5):
sys.stdout.flush()
li.append([ e[i] for i in range(e.size()) ])
li.append([ e[i] for i in range(e.size()) ])
print (20*k+20), "%",
print
show_mem("spectra list generated")
del li
show_mem("spectra list deleted")
del p
del e
def run_MSExperiment_copy(self):
p = pyopenms.FileHandler()
e1 = pyopenms.MSExperiment()
p.loadExperiment(self.testfile, e1)
show_mem("data loaded")
specs = list(e1)
for s in specs:
for _ in range(10):
e1.addSpectrum(s)
li = []
print "please be patient :",
N = 5
for k in range(N):
sys.stdout.flush()
for __ in range(400):
e2 = copy.copy(e1)
li.append(e2)
e1 = copy.copy(e2)
li.append(e1)
print int(100.0*(k+1)/N), "%",
print
show_mem("experiment list generated")
del li
del e1
del e2
del p
show_mem("experiment list deleted")
def run_fileformats_io(self):
p = pyopenms.FileHandler()
e = pyopenms.MSExperiment()
p.loadExperiment(self.testfile, e)
show_mem("after load mzXML")
ct = pyopenms.ChromatogramTools()
ct.convertChromatogramsToSpectra(e)
p.storeExperiment(self.testfile, e)
show_mem("after store mzXML")
p.loadExperiment(self.testfile, e)
show_mem("after load mzXML")
p = pyopenms.FileHandler()
ct.convertSpectraToChromatograms(e, True)
p.storeExperiment("../test.mzML", e)
show_mem("after store mzML")
p.loadExperiment("../test.mzML", e)
show_mem("after load mzML")
p = pyopenms.FileHandler()
ct.convertChromatogramsToSpectra(e)
p.storeExperiment("../test.mzData", e)
show_mem("after store mzData")
p.loadExperiment("../test.mzData", e)
show_mem("after load mzData")
del e
del p
del ct
if __name__ == "__main__":
unittest.main()
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