def setReaderOptions(imagefile, stitchtiles=False,
setflatres=True,
setconcat=False,
openallseries=False,
showomexml=False,
attach=False,
autoscale=True):
czi_options = DynamicMetadataOptions()
czi_options.setBoolean("zeissczi.autostitch", stitchtiles)
czi_options.setBoolean("zeissczi.attachments", attach)
# set the option for the CZIReader
czireader = ImportTools.setCZIReaderOptions(imagefile, czi_options, setflatres=setflatres)
# Set the preferences in the ImageJ plugin
# Note although these preferences are applied, they are not refreshed in the UI
Prefs.set("bioformats.zeissczi.allow.autostitch", str(stitchtiles).lower())
Prefs.set("bioformats.zeissczi.include.attachments", str(attach).lower())
# set the option for the BioFormats import
reader_options = ImporterOptions()
reader_options.setOpenAllSeries(openallseries)
reader_options.setShowOMEXML(showomexml)
reader_options.setConcatenate(setconcat)
reader_options.setAutoscale(autoscale)
reader_options.setStitchTiles(stitchtiles)
reader_options.setId(imagefile)
return reader_options, czireader
def run(imagefile, useBF=True,
series=0,
filtertype='MEDIAN',
filterradius='5'):
#log.log(LogLevel.INFO, 'Image Filename : ' + imagefile)
log.info('Image Filename : ' + imagefile)
# get basic image metainfo
metainfo = get_metadata(imagefile, imageID=series)
for k, v in metainfo.items():
#log.log(LogLevel.INFO, str(k) + ' : ' + str(v))
log.info(str(k) + ' : ' + str(v))
if not useBF:
# using IJ static method
imp = IJ.openImage(imagefile)
if useBF:
# initialize the importer options for BioFormats
options = ImporterOptions()
options.setOpenAllSeries(True)
options.setShowOMEXML(False)
options.setConcatenate(True)
options.setAutoscale(True)
options.setId(imagefile)
options.setStitchTiles(True)
# open the ImgPlus
imps = BF.openImagePlus(options)
imp = imps[series]
# apply the filter
if filtertype != 'NONE':
# apply filter
#log.log(LogLevel.INFO, 'Apply Filter : ' + filtertype)
#log.log(LogLevel.INFO, 'Filter Radius : ' + str(filterradius))
log.info('Apply Filter : ' + filtertype)
log.info('Filter Radius : ' + str(filterradius))
# apply the filter based on the chosen type
imp = apply_filter(imp,
radius=filterradius,
filtertype=filtertype)
if filtertype == 'NONE':
#log.log(LogLevel.INFO, 'No filter selected. Do nothing.')
log.info('No filter selected. Do nothing.')
return imp
def readbf(imagefile, metainfo,
setflatres=False,
readpylevel=0,
setconcat=False,
openallseries=True,
showomexml=False,
autoscale=True,
stitchtiles=True):
# initialize the importer options
options = ImporterOptions()
options.setOpenAllSeries(openallseries)
options.setShowOMEXML(showomexml)
options.setConcatenate(setconcat)
options.setAutoscale(autoscale)
options.setId(imagefile)
options.setStitchTiles(stitchtiles)
# in case of concat=True all series set number of series = 1
# and set pyramidlevel = 0 (1st level) since there will be only one
# unless setflatres = True --> read pyramid levels
series = metainfo['SeriesCount_BF']
if setconcat and setflatres:
series = 1
readpylevel = 0
metainfo['Pyramid Level Output'] = readpylevel
# open the ImgPlus
imps = BF.openImagePlus(options)
# read image data using the specified pyramid level
imp, slices, width, height, pylevel = ImageTools.getImageSeries(imps, series=readpylevel)
metainfo['Output Slices'] = slices
metainfo['Output SizeX'] = width
metainfo['Output SizeY'] = height
return imp, metainfo