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