def __init__(self, period=60, chunks=100, throughput=0):
self.period = period # The time period over which to produce throughput
self.chunks = chunks
self.throughput = AtomicInteger(throughput)
self.throughput_success = AtomicInteger(0)
self.resume = AtomicBoolean(True)
self.curr_tick = AtomicInteger(0)
def onInit():
global eventCounter
# Variables for assertions only
eventCounter = Collections.synchronizedMap(HashMap())
eventCounter.put("blue", AtomicInteger(0))
eventCounter.put("red", AtomicInteger(0))
sponge.setVariable("eventCounter", eventCounter)
def test_number_transform(self):
a = AtomicInteger(0)
b = AtomicInteger(1)
c = AtomicInteger(2)
x = ArrayList()
x.add(a)
x.add(b)
x.add(c)
self.assertEqual(x.get(0).get(), 0)
self.assertEqual(x.get(1).get(), 1)
self.assertEqual(x.get(2).get(), 2)
def onInit():
# Variables for assertions only
sponge.setVariable("onInitCalled", AtomicBoolean(False))
sponge.setVariable("onBeforeLoadCalled", AtomicInteger(0))
sponge.setVariable("onLoadCalled", AtomicInteger(0))
sponge.setVariable("onAfterLoadCalled", AtomicInteger(0))
sponge.setVariable("onStartupCalled", AtomicBoolean(False))
sponge.setVariable("onBeforeReloadCalled", AtomicBoolean(False))
sponge.setVariable("onAfterReloadCalled", AtomicBoolean(False))
sponge.logger.debug("onInit")
sponge.getVariable("onInitCalled").set(True)
class IdFactory:
def __init__(self):
import java.util.concurrent.atomic.AtomicInteger as AtomicInt
self.nextid = AtomicInt()
def next(self):
nextid = self.nextid.getAndIncrement()
return nextid
class IdFactory:
def __init__(self):
import java.util.concurrent.atomic.AtomicInteger as AtomicInt
self.nextid = AtomicInt()
def next(self):
nextid = self.nextid.getAndIncrement()
return nextid
class Counter(object):
def __init__(self, initial=0):
self.atomic = AtomicInteger(initial)
# waiting is important here to ensure that
# defaultdict factories can step on each other
time.sleep(0.001)
def decrementAndGet(self):
return self.atomic.decrementAndGet()
def incrementAndGet(self):
return self.atomic.incrementAndGet()
def get(self):
return self.atomic.get()
def __repr__(self):
return "Counter<%s>" % (self.atomic.get())
class Counter(object):
def __init__(self, initial=0):
self.atomic = AtomicInteger(initial)
# waiting is important here to ensure that
# defaultdict factories can step on each other
time.sleep(0.001)
def decrementAndGet(self):
return self.atomic.decrementAndGet()
def incrementAndGet(self):
return self.atomic.incrementAndGet()
def get(self):
return self.atomic.get()
def __repr__(self):
return "Counter<%s>" % (self.atomic.get())
class ThreadFactorySameGroup(ThreadFactory):
def __init__(self, name):
self.name = name
self.group = Thread.currentThread().getThreadGroup()
self.counter = AtomicInteger(0)
def newThread(self, runnable):
title = "%s-%i" % (self.name, self.counter.incrementAndGet())
t = Thread(self.group, runnable, title)
t.setPriority(Thread.NORM_PRIORITY)
return t
def fetch(self):
""" generated source for method fetch """
totalFetchDataSize = self.calcDataSize(len(self.variables))
if totalFetchDataSize == 0:
raise RuntimeException("no data to fetch")
if totalFetchDataSize > dataSizeLimitForFetch:
raise RuntimeException("exceed the max data limit for fetch")
dataSet = GridDataSet(self.meta)
latch = CountDownLatch(len(self.variables) * self.tRange.getSize() * self.zRange.getSize())
exceptions = ConcurrentLinkedQueue()
counter = AtomicInteger()
taskCount = 0
for variable in variables:
dataSet.addVariable(variable, Grid4D(buffer_, self.meta.getDataType(), self.getOrigin(), self.getShape()))
#
# * not thread-safe
#
while t < tRange.getEnd():
#
# * not thread-safe
#
#
# * not thread-safe
#
while z < zRange.getEnd():
#
# * not thread-safe
#
self.addTask(counter, data, curPos, variable, t, z, latch, exceptions)
curPos += xRange.getSize() * yRange.getSize() * meta.getDataType().getSize()
taskCount += 1
z += 1
t += 1
latch.await()
if not exceptions.isEmpty():
raise exceptions.peek()
if counter.get() != taskCount:
raise RuntimeException("not all task success")
return dataSet
def onInit():
global eventCounter
# Variables for assertions only
eventCounter = Collections.synchronizedMap(HashMap())
eventCounter.put("Trigger1, file1", AtomicInteger(0))
eventCounter.put("Trigger2, file1", AtomicInteger(0))
eventCounter.put("Trigger1, file2", AtomicInteger(0))
eventCounter.put("Trigger2, file2", AtomicInteger(0))
eventCounter.put("Trigger1, file3", AtomicInteger(0))
eventCounter.put("Trigger3, file3", AtomicInteger(0))
sponge.setVariable("eventCounter", eventCounter)
def __init__(self, user, node, streaminguri):
super(NsServerNumConcurrentRequests, self).__init__(user, node)
self.nconns = [] # Belongs exclusively to poll method
self.thread = None
self.httprq = get_http_request(self.node.ip, streaminguri,
self.node.rest_username,
self.node.rest_password)
self.no_of_connections = AtomicInteger(0)
self.no_of_open_connections = AtomicInteger(0)
self.no_of_throughput_updates = AtomicInteger(0)
self.rest = RestConnection(self.node)
class Library:
def __init__(self):
self.books = CopyOnWriteArrayList()
self.currentId = AtomicInteger(0)
self.readOnly = False
def addBook(self, author, title, cover=None, force=False):
if list(
filter(
lambda book: book.author == author and book.title == title,
self.books)):
raise Exception("This book has already been added to the library")
if not self.readOnly or force:
self.books.add(
Book(self.currentId.incrementAndGet(), author, title, cover))
def getBook(self, bookId):
return filter(lambda book: book.id == bookId, self.books)[0]
def updateBook(self, bookId, author, title, cover=None):
book = self.getBook(bookId)
if not self.readOnly:
book.author = author
book.title = title
if cover:
book.cover = cover
def removeBook(self, bookId):
if not self.readOnly:
self.books.removeIf(PyPredicate(lambda book: book.id == bookId))
def findBooks(self, searchString):
return list(filter(lambda book: searchString is None or re.search(searchString.upper(), book.author.upper())\
or re.search(searchString.upper(), book.title.upper()), self.books))
def getAuthors(self):
return sorted(list(set(list(map(lambda book: book.author,
self.books)))),
key=lambda author: author.lower())
def __init__(self, initial=0):
self.atomic = AtomicInteger(initial)
# waiting is important here to ensure that
# defaultdict factories can step on each other
time.sleep(0.001)
def __init__(self, name):
self.name = name
self.group = Thread.currentThread().getThreadGroup()
self.counter = AtomicInteger(0)
if k < min(nLayers, currentWrittenLayer + nLayersAtATime):
IJ.log('Start exporting layer ' + str(k) + ' currentWrittenLayer - ' + str(currentWrittenLayer))
fc.exportFlat(project, exportFolder, 1/float(LMEMFactor), baseName = 'alignedDownsampledEM', bitDepth = 8, layers = [k])
namePlugin = 'export_alignedEMForRegistration'
MagCFolder = fc.startPlugin(namePlugin)
ControlWindow.setGUIEnabled(False)
MagCParams = fc.readMagCParameters(MagCFolder)
nLayersAtATime = MagCParams[namePlugin]['nLayersAtATime']
nThreads = MagCParams[namePlugin]['nThreads']
LMEMFactor = fc.getLMEMFactor(MagCFolder)
IJ.log('Exporting with LMEMFactor = ' + str(LMEMFactor))
projectPath = fc.findFilesFromTags(MagCFolder,['EM', 'Project'])[0]
exportFolder = fc.mkdir_p(os.path.join(os.path.dirname(projectPath), namePlugin))
project, loader, layerset, nLayers = fc.openTrakemProject(projectPath)
temporaryFolder = fc.mkdir_p(os.path.join(os.path.dirname(projectPath), 'temporary_LMEMRegistration')) # to save contrasted images
# currentLayerPath stores in a file the current layer being processed by the script which is run several times
currentLayerPath = os.path.join(os.path.dirname(projectPath), 'currentLayer_' + namePlugin + '.txt')
currentWrittenLayer = fc.incrementCounter(currentLayerPath, increment = nLayersAtATime)
atom = AtomicInteger(currentWrittenLayer)
fc.startThreads(exportLayer, wait = 0, nThreads = nThreads)
# project.save() # why do I save the project here ?
time.sleep(3)
fc.shouldRunAgain(namePlugin, currentWrittenLayer, nLayers, MagCFolder, project, increment = nLayersAtATime)
def onInit():
sponge.setVariable("sentEvents", AtomicInteger(100))
sponge.setVariable("finishedEvents", AtomicInteger(0))
contrastedChannel = 'contrasted' + refChannel
channels.append(contrastedChannel)
toContrastPaths = []
for (dirpath, dirnames, filenames) in os.walk(LMDataFolder):
for filename in filenames:
IJ.log('ToContrast: ' + str(filename))
if (os.path.splitext(filename)[1] == '.tif') and (refChannel
in filename):
imagePath = os.path.join(dirpath, filename)
contrastedPath = os.path.join(
dirpath, filename.replace(refChannel, contrastedChannel))
toContrastPaths.append([imagePath, contrastedPath])
IJ.log('toContrastPaths : ' + str(toContrastPaths))
nPaths = len(toContrastPaths)
atomicI = AtomicInteger(0)
fc.startThreads(contrastImage)
# Update metadata with the new contrasted channel
f = open(LMMetadataPath, 'r')
lines = f.readlines()
for idLine, line in enumerate(lines):
if 'nChannels' in line:
lines[idLine] = 'nChannels = ' + str(nChannels + 1)
if 'channels' in line:
lines[idLine] = 'channels = [' + ','.join(
map(lambda x: "'" + x + "'", channels)) + ']'
f.close()
f = open(LMMetadataPath, 'w')
for line in lines:
f.write(line + '\n')
def onInit():
# Variables for assertions only
sponge.setVariable("receivedCamelMessages", AtomicInteger(0))
def onInit():
# Variables for assertions only
sponge.setVariable("nameCount", AtomicInteger(0))
sponge.setVariable("patternCount", AtomicInteger(0))
def __init__(self, initial=0):
self.atomic = AtomicInteger(initial)
# waiting is important here to ensure that
# defaultdict factories can step on each other
time.sleep(0.001)
def __init__(self):
import java.util.concurrent.atomic.AtomicInteger as AtomicInt
self.nextid = AtomicInt()
def onInit():
# Variables for assertions only
sponge.setVariable("countA", AtomicInteger(0))
sponge.setVariable("countB", AtomicInteger(0))
sponge.setVariable("listC", ArrayList())
def onInit():
global eventEntry, eventCounter
eventEntry = None
eventCounter = AtomicInteger(0)
sponge.setVariable("eventCounter", eventCounter)
sponge.setVariable("allowNumber", 2)
def __init__(self):
self.nextid = AtomicInt()
TEST_NAME = 'http_get_test'
# 设置时间格式为yyyy-mm-dd hh24:mi:ss
ISOTIMEFORMAT = '%Y-%m-%d %X'
# 根据实际情况选择方案1或2，可以重复利用的测试数据可以选择1或者2，不可重复利用的测试数据选择2。
# 方案1
random = Random()
# 方案2
# processNum = int(grinder.getProperties().get('grinder.processes'))
# threadNum = int(grinder.getProperties().get('grinder.threads'))
# 一般无需修改
ERR_LOG = 'err.log'
logfile = open(ERR_LOG, 'w')
is_open = AtomicInteger(int(grinder.getProperties().get('grinder.threads')))
# 需要修改列表名称
param_file = "http_get_test.txt"
infile = open(param_file, 'r')
keyword_list = []
for line in infile.readlines():
keyword_list.append(line.strip())
infile.close()
# 可能需要修改url和headers等值
url = 'https://www.baidu.com'
headers = [
NVPair(
'User-Agent',
'Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/50.0.2661.102 Safari/537.36'
def onInit():
# Variables for assertions only
sponge.setVariable("receivedRssCount", AtomicInteger(0))
def onInit():
# Variables for assertions only
sponge.setVariable("alarms", AtomicInteger(0))
sponge.setVariable("notifications", AtomicInteger(0))
def onInit():
# Variables for assertions only
sponge.setVariable("hardwareFailureScriptCount", AtomicInteger(0))
sponge.setVariable("sameSourceFirstFireCount", AtomicInteger(0))
def onInit():
# Variables for assertions only
sponge.setVariable("receivedEventA1", AtomicInteger(0))
sponge.setVariable("receivedEventA2", AtomicInteger(0))
sponge.setVariable("functionA1", AtomicInteger(0))
sponge.setVariable("functionA2", AtomicInteger(0))
def onInit():
# Variables for assertions only
sponge.setVariable("receivedEventA", AtomicBoolean(False))
sponge.setVariable("receivedEventBCount", AtomicInteger(0))
class IdFactory:
def __init__(self):
self.nextid = AtomicInt()
def next(self):
nextid = self.nextid.getAndIncrement()
return nextid
def __init__(self):
import java.util.concurrent.atomic.AtomicInteger as AtomicInt
self.nextid = AtomicInt()
filePaths.append(imPath)
with open(filePathsPath,'w') as f:
for path in filePaths:
f.write(path + '\n')
# pickle.dump(filePaths,f)
else:
filePaths = []
with open(filePathsPath,'r') as f:
lines = f.readlines()
for line in lines:
filePaths.append(line.replace('\n', ''))
# filePaths = pickle.load(f)
#Create all the subfolders
downSampledEMFolder = fc.mkdir_p(os.path.join(MagCEMFolder, 'MagC_EM_' + factorString, ''))
for sectionFolderName in os.walk(EMDataFolder).next()[1]:
fc.mkdir_p(os.path.join(downSampledEMFolder, sectionFolderName))
normLocalContrastSize = MagCParameters[namePlugin]['normLocalContrastSize']
# downsample in parallel
threads = []
currentLayerPath = os.path.join(MagCEMFolder, 'currentLayer_' + namePlugin + '.txt')
currentWrittenLayer = fc.incrementCounter(currentLayerPath, increment = nTilesAtATime)
IJ.log(namePlugin + ' layer ' + str(currentWrittenLayer))
atomicI = AtomicInteger(currentWrittenLayer)
fc.startThreads(resizeAndSave, fractionCores = 0.9, wait = 0, arguments = (filePaths, atomicI))
# terminate or rerun if more tiles to be processed
time.sleep(1)
fc.shouldRunAgain(namePlugin, atomicI.get(), len(filePaths), MagCFolder, '')
params.tilesAreInPlace = True params.springLengthSpringMesh = 100 params.stiffnessSpringMesh = 0.1 params.maxStretchSpringMesh = 2000 params.maxIterationsSpringMesh = 1000 params.maxPlateauwidthSpringMesh = 200 params.useLegacyOptimizer = True # params.dampSpringMesh # params.maxNumThreads # params.visualize currentLayerPath = os.path.join(os.path.dirname(projectPath), 'currentLayer_' + namePlugin + '.txt') currentWrittenLayer = fc.incrementCounter(currentLayerPath, increment = nLayersAtATime) l = AtomicInteger(currentWrittenLayer) # fc.startThreads(elasticMontage(), wait = 1, nThreads = nThreads) /!\ it does not work I do not understand why. Probably a java6 issue because it works in other scripts in java8 ... threads = [] for p in range(nThreads): thread = Thread(elasticMontage) threads.append(thread) thread.start() time.sleep(0.5) for thread in threads: thread.join() IJ.log( namePlugin + ' layer ' + str(currentWrittenLayer))
def onInit():
# Variables for assertions only
sponge.setVariable("eventCounter", AtomicInteger(0))
