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)
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')
f.close()
widthEM = imEM0.width
heightEM = imEM0.height
imEM0.close()
f = open(os.path.join(registrationFolder, 'lowResEMBounds'), 'w')
pickle.dump([widthEM, heightEM], f)
f.close()
registrationStatsPath = os.path.join(registrationFolder, 'registrationStats')
registrationStats = []
# create dummy trakem for applying affine and cropping LM in the first registration step
pZ, loaderZ, layersetZ, nLayersZ = fc.getProjectUtils(
fc.initTrakem(temporaryFolder, 1))
layersetZ.setDimensions(0, 0, widthEM * 5, heightEM * 5)
layerZ = layersetZ.getLayers().get(0)
lock = threading.Lock()
# Setting up the parallel threads and starting them
atomicI = AtomicInteger(0)
fc.startThreads(computeRegistration, fractionCores=1, wait=0.5)
fc.closeProject(pZ) # close dummy trakem
# save some stats on the registration
with open(registrationStatsPath, 'w') as f:
pickle.dump(registrationStats, f)
fc.terminatePlugin(namePlugin, MagCFolder)
# fc.shouldRunAgain(namePlugin, currentLayer, nSections, MagCFolder, '', increment = nLayersAtATime)
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, '')
allPatchCoordinates = []
downsampledFolder = os.path.join(MagC_EM_Folder, 'MagC_EM_' + factorString)
IJ.log('downsampledFolder ' + downsampledFolder)
foldersToStitch = [
os.path.join(downsampledFolder, folderName)
for folderName in os.walk(downsampledFolder).next()[1]
]
foldersToStitch = fc.naturalSort(foldersToStitch)
IJ.log('foldersToStitch ------------- ' + str(foldersToStitch))
# stitching should be done in parallel but the stitching plugin does not seem to run in parallel, so fractionCores=0 -> only one core used ...
atom = AtomicInteger(0)
fc.startThreads(parallelStitch,
fractionCores=0,
wait=0,
arguments=(atom, foldersToStitch, allPatchCoordinates))
#for k in range(len(foldersToStitch)):
# sectionFolder = foldersToStitch[k]
# tileConfigurationPath = os.path.join(sectionFolder, 'TileConfiguration_' + str(k).zfill(4) + '.registered.txt')
# stitchCommand = 'type=[Filename defined position] order=[Defined by filename ] grid_size_x=' + str(numTilesX) + ' grid_size_y=' + str(numTilesY) + ' tile_overlap=' + str(100 * (tileOverlapX + tileOverlapY)/2.) + ' first_file_index_x=0 first_file_index_y=0 directory=' + sectionFolder + ' file_names=Tile_{xx}-{yy}_resized_' + factorString + '.tif output_textfile_name=TileConfiguration_' + str(k).zfill(4) +'.txt fusion_method=[Do not fuse images (only write TileConfiguration)] regression_threshold=0.70 max/avg_displacement_threshold=2.50 absolute_displacement_threshold=3.50 compute_overlap subpixel_accuracy computation_parameters=[Save computation time (but use more RAM)] image_output=[Write to disk] output_directory=' + sectionFolder
# IJ.log('stitchCommand ---- ' + stitchCommand)
# IJ.run('Grid/Collection stitching', stitchCommand)
# f = open(tileConfigurationPath, 'r')
# lines = f.readlines()[4:] # trimm the heading
# f.close()
l = atomicI.getAndIncrement()
if l < nLayers:
IJ.log('Stitching layer ' + str(l))
AlignTask().montageLayers(params, layerset.getLayers(l, l), tilesAreInPlaceIn, largestGraphOnlyIn, hideDisconnectedTilesIn, deleteDisconnectedTilesIn)
IJ.log('Blending layer ' + str(l))
Blending.blendLayerWise(layerset.getLayers(l, l), True, None)
if l%10 == 0: # save project every 5 layers
project.save()
namePlugin = 'montage_LM'
MagCFolder = fc.startPlugin(namePlugin)
ControlWindow.setGUIEnabled(False)
# get mosaic size
MagCParameters = fc.readMagCParameters(MagCFolder)
mosaic = MagCParameters[namePlugin]['mosaic'] # e.g. [2,2]
if mosaic !=[1,1]:
projectPath = fc.findFilesFromTags(MagCFolder,['LMProject'])[0]
projectName = os.path.basename(projectPath)
project, loader, layerset, nLayers = fc.openTrakemProject(projectPath)
nLayers = len(layerset.getLayers())
atomicI = AtomicInteger(0)
fc.startThreads(stitchLayers, fractionCores = 0.1)
fc.resizeDisplay(layerset)
project.save()
fc.closeProject(project)
fc.terminatePlugin(namePlugin, MagCFolder)
