def iterateLif(filename,impProcessor):
"""
Iterate over all series in a LIF file and process them.
Arguments:
filename: LIF filename
impProcessor: processor object, implements method process(ImagePlus).
"""
opts = ImporterOptions()
opts.setId(filename)
opts.setUngroupFiles(True)
# set up import process
process = ImportProcess(opts)
process.execute()
nseries = process.getSeriesCount()
# reader belonging to the import process
reader = process.getReader()
# reader external to the import process
impReader = ImagePlusReader(process)
for i in range(0, nseries):
print "iterateLif: %d/%d %s" % (i+1, nseries, process.getSeriesLabel(i))
# activate series (same as checkbox in GUI)
opts.setSeriesOn(i,True)
# point import process reader to this series
reader.setSeries(i)
# read and process all images in series
imps = impReader.openImagePlus()
for imp in imps:
imp.setTitle("%s_%d_%d" % (imp.getTitle(),i+1,nseries))
print "iterateLif: " + imp.getTitle()
try:
impProcessor.process(imp)
finally:
imp.close()
# deactivate series (otherwise next iteration will have +1 active series)
opts.setSeriesOn(i, False)
# Initialize variables for Saving
name = ['File']
layer = ['Layer']
results = ['Slice,Count,Total Area,Average Size,%Area']
summary = {"Top": [], "Middle": [], "Bottom": []}
# Check if folders are there or not
if not os.path.exists(saveDir):
os.mkdir(saveDir)
# set up options for import
opts = ImporterOptions()
opts.setId(filename)
opts.setUngroupFiles(True)
# set up import process
process = ImportProcess(opts)
process.execute()
nseries = process.getSeriesCount()
# Channel Splitter Definition
splitter = ChannelSplitter()
# reader belonging to the import process
reader = process.getReader()
# reader external to the import process
impReader = ImagePlusReader(process)
