def open_from_lif_series(fpath, i): options = ImporterOptions() options.setId(fpath) options.clearSeries() options.setSeriesOn(i, True) imps = BF.openImagePlus(options) return imps[0]
reader.setId(sipmm_inputFile.getAbsolutePath())
seriesCount = reader.getSeriesCount()
reader.close()
log('Found {} series'.format(seriesCount))
outfile = os.path.join(outdir,'results.csv')
h = 'Name,path,Rarea,Rmean,Rstd,Garea,Gmean,Gstd,GQarea,GQmean,GQintden,GQstd,nPunctae,RMregions,maxp,extravar'
with open(outfile,'a') as of:
of.write(h+'\n')
for impi in range(seriesCount):
log('Analyzing series {}/{}...'.format(impi+1,seriesCount))
options = ImporterOptions()
options.setId(sipmm_inputFile.getAbsolutePath())
options.clearSeries()
options.setSeriesOn(impi,True)
imp, = BF.openImagePlus(options)
#Separate Green, Red
chans = ChannelSplitter.split(imp)
if two_channels:
if len(chans)!=2:
log('ERROR! Expecting a 2-channel images and got {}'.format(len(chans)))
green, red = chans
else:
if len(chans)!=3:
log('ERROR! Expecting a 3-channel images and got {}'.format(len(chans)))
green, red, nuc = chans
