def exportLayer(): while atom.get() < min(nLayers, currentWrittenLayer + nLayersAtATime + 1): k = atom.getAndIncrement() 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])
str(toAlignPatchPath)) aff = AffineTransform( [float(transforms[a]) for a in range(i + 2, i + 8)]) patch = Patch.createPatch(project, toAlignPatchPath) layer = layerset.getLayers().get(l) layer.add(patch) patch.setAffineTransform(aff) patch.updateBucket() time.sleep(1) IJ.log('Readjusting display') fc.resizeDisplay(layerset) IJ.log('Blending all layers') Blending.blendLayerWise(layerset.getLayers(), True, None) IJ.log('Exporting') for scaleFactor in scaleFactors: theBaseName = 'exported_downscaled_' + str(int( 1 / float(scaleFactor))) + '_' + channel outputFolder = fc.mkdir_p( os.path.join(os.path.dirname(transformsPath), theBaseName)) fc.exportFlat(project, outputFolder, scaleFactor, baseName=theBaseName, bitDepth=8, flipX=flipX) fc.closeProject(project) fc.terminatePlugin(namePlugin, MagCFolder)