def test_confm(t0, t1, Molecule) :
# create Confocal Microscopy
confm = FCSConfigs()
confm.set_LightSource(source_type='LASER', wave_mode='TEM00', M2_factor=1.00, wave_length=473, power=500e-6, radius=0.32e-3)
confm.set_BeamExpander(expander_type='Keplerian', focal_length1=30e-3, focal_length2=20e-3, pinhole_radius=13e-6)
confm.set_Fluorophore(fluorophore_type='EGFP')
#confm.set_Fluorophore(fluorophore_type='Gaussian', wave_length=508, width=(70.0, 140.0))
#confm.set_Fluorophore(fluorophore_type='Point-like', wave_length=508)
confm.set_Objective(NA=1.20, Nm=1.37, focal_length=1.9e-3, efficiency=0.90)
confm.set_TubeLens1(focal_length=160e-3)
confm.set_ScanLens(focal_length=50e-3)
confm.set_PinholeLens(focal_length=200e-3, radius=13e-6)
confm.set_Detector(detector='EMCCD', zoom=1, emgain=5, focal_point=(0.5,0.5,0.5), \
start_time=t0, end_time=t1, fps=1, exposure_time=1)
confm.set_Movie(image_file_dir='./images_egfm_%s' % (Molecule), movie_filename='./movies/egfm_movie.mp4')
confm.set_DataFile(['/home/kiwamoto/share/EGF_model_20130603/LogHDF5_ERK_1.h5'], observable=Molecule)
# create image and movie
create = FCSVisualizer(configs=confm)
#create.get_plots(plot_filename='./plots/epifm.plots.pdf')
create.output_frames(num_div=16)
def test_fcs(t0, t1) : # create TIRF Microscopy fcs = FCSConfigs() fcs.set_LightSource(source_type='LASER', wave_mode='TEM00', M2_factor=1.00, wave_length=473, power=500e-6, radius=0.32e-3) #fcs.set_BeamExpander(expander_type='Keplerian', focal_length1=30e-3, focal_length2=20e-3, pinhole_radius=13e-6) fcs.set_Fluorophore(fluorophore_type='Qdot 605') #fcs.set_Fluorophore(fluorophore_type='Gaussian', wave_length=605, width=(100.0, 200.0)) fcs.set_Objective(NA=1.20, Nm=1.37, focal_length=1.9e-3, efficiency=0.90) fcs.set_TubeLens1(focal_length=160e-3) fcs.set_ScanLens(focal_length=50e-3) fcs.set_PinholeLens(focal_length=200e-3, radius=13e-6) fcs.set_Detector(detector='PMT', zoom=1, emgain=1e+6, focal_point=(0.5,0.5,0.5), \ start_time=t0, end_time=t1, fps=1/10e-5, exposure_time=10e-5) fcs.set_Movie(image_file_dir='./images_fcs_0100', movie_filename='./movies/fcs_movie.mp4') fcs.set_Output(output_file_dir='./output_fcs_0100') fcs.set_DataFile(['./data/lattice/test_fcs_0100.h5']) # create image and movie create = FCSVisualizer(configs=fcs) #create.get_plots(plot_filename='./plots/fcs_airy.pdf') create.output_frames(num_div=1)
