In [ ]:

    

from glob import glob
from leicaexperiment import LeicaExperiment
from tifffile import imsave, imshow

experiments = glob('/Users/arve/Dokumenter/TFY4500/comparison/experiment--*')

leica_experiments = []
for e in experiments:
    leica_experiments.append(LeicaExperiment(e))


for experiment in leica_experiments:
    well = experiment.wells[0] # assume only one well
    for channel in range(well.channels):
        for z in range(well.z_stacks):
            print('Merging experiment {} channel {} z-stack {}'.format(experiment.str_time, channel, z))
            img = well.merge(z, channel)
            #filename = (experiment.path.replace('experiment--2014_11_', 'merged/') +
                        #'ch' + str(channel) + 'z' + str(z) + '.tif')
            #imsave(filename, img)

            # invert
            img = 255-img
            filename = (experiment.path.replace('experiment--2014_11_', 'inverted/') +
                        'ch' + str(channel) + 'z' + str(z) + '.compressed.tif')
            imsave(filename, img, compress=1)