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
params.bmSearchRadius = 50
params.bmBlockRadius = 50
params.bmMinR = 0.1
params.bmMaxCurvatureR = 100
params.bmRodR = 1
params.bmUseLocalSmoothnessFilter = True
regParams, use_shrinking_constraint)
time.sleep(2)
# IJ.getImage().close()
WindowManager.closeAllWindows()
IJ.log('Rigid Alignment done')
else:
IJ.log('Rigid alignment already performed - skipping')
################################################
###########################################
IJ.log('Aligning the lowEM with the new rigid transforms')
projectPath = fc.cleanLinuxPath(
fc.findFilesFromTags(MagCFolder,
['EMProject_'])[0]) # this is the low res EM
project, loader, layerset, nLayers = fc.openTrakemProject(
projectPath) # the low res EM
for l, layer in enumerate(layerset.getLayers()):
transformPath = os.path.join(
resultRigidAlignmentFolder,
'stitchedDownsampledEM_' + str(l).zfill(4) + '.xml')
theList = ArrayList(HashSet())
aff = fc.getAffFromRVSTransformPath(transformPath)
for patch in layer.getDisplayables(Patch):
patch.setLocation(
patch.getX(),
patch.getY()) # compensate for the extracted bounding box
currentAff = patch.getAffineTransform()
currentAff.preConcatenate(aff)
patch.setAffineTransform(currentAff)