def initTrakem(path, nbLayers, mipmaps = False): #initialize a project
path = cleanLinuxPath(path)
ControlWindow.setGUIEnabled(False)
project = Project.newFSProject("blank", None, path)
project.getLoader().setMipMapsRegeneration(mipmaps)
layerset = project.getRootLayerSet()
for i in range(nbLayers): # create the layers
layerset.getLayer(i, 1, True)
project.getLayerTree().updateList(layerset) #update the LayerTree
Display.updateLayerScroller(layerset) # update the display slider
IJ.log('TrakEM project initialized with ' + str(nbLayers) + ' layers and stored in ' + path + ' (but not saved yet)')
return project
from java.lang import Runtime, Thread
from java.util.concurrent.atomic import AtomicInteger
def elasticMontage():
IJ.log('Thread called **************************')
while l.get() < min(nLayers, currentWrittenLayer + nLayersAtATime + 1) :
k = l.getAndIncrement()
if k < min(nLayers, currentWrittenLayer + nLayersAtATime):
IJ.log('Start montaging elastically layer ' + str(k))
if layerset.getLayers().get(k).getNDisplayables() > 1: # some EM projects have a single large tile
AlignTask().montageLayers(params, layerset.getLayers(k, k))
namePlugin = 'montage_ElasticEM'
MagCFolder = fc.startPlugin(namePlugin)
ControlWindow.setGUIEnabled(False)
MagCParams = fc.readMagCParameters(MagCFolder)
nLayersAtATime = MagCParams[namePlugin]['nLayersAtATime']
nThreads = MagCParams[namePlugin]['nThreads']
projectPath = fc.cleanLinuxPath(fc.findFilesFromTags(MagCFolder,['EM', 'Project'])[0])
project, loader, layerset, nLayers = fc.openTrakemProject(projectPath)
IJ.log('Sleeping in case the opening of the large project takes some time ...')
time.sleep(20)
# parameters for elastic montage
params = ElasticMontage.Param().clone()
params.bmScale = 0.5
