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))
fc.resizeDisplay(layerset)
project.save()
IJ.log('Sleeping in case the saving of the large project takes some time ...')
time.sleep(20)
# save all transforms
transformsPath = os.path.join(os.path.dirname(projectPath) , namePlugin + '_Transforms.txt')
if l.get() > nLayers-1:
fc.writeAllAffineTransforms(project,transformsPath)
fc.shouldRunAgain(namePlugin, currentWrittenLayer, nLayers, MagCFolder, project, increment = nLayersAtATime)
if k < min(nLayers, currentWrittenLayer + nLayersAtATime):
IJ.log('Start exporting layer ' + str(k) + ' currentWrittenLayer - ' + str(currentWrittenLayer))
fc.exportFlat(project, exportFolder, 1/float(downsamplingFactor), baseName = 'stitchedDownsampledEM', bitDepth = 8, layers = [k])
namePlugin = 'export_stitchedEMForAlignment'
MagCFolder = fc.startPlugin(namePlugin)
ControlWindow.setGUIEnabled(False)
MagCParams = fc.readMagCParameters(MagCFolder)
nLayersAtATime = min (MagCParams[namePlugin]['nLayersAtATime'], Runtime.getRuntime().availableProcessors())
nThreads = MagCParams[namePlugin]['nThreads']
# getting downsamplingFactor
downsamplingFactor = MagCParams['downsample_EM']['downsamplingFactor']
projectPath = fc.cleanLinuxPath(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)
fc.resizeDisplay(layerset) # has been done in previous script but in case ...
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 ? To save mipmaps for subsequent faster processing ? Probably not needed ...
time.sleep(3)
fc.shouldRunAgain(namePlugin, currentWrittenLayer, nLayers, MagCFolder, project, increment = nLayersAtATime)
