def test_image():
# create TIRF Microscopy
tirfm = TIRFMSettings()
# Spectral Arrangement
#tirfm.set_Fluorophore(fluorophore='Tetramethylrhodamine(TRITC)')
tirfm.set_GaussPSF(intensity=1.0, gauss_sigma=200e-9)
tirfm.set_IncidentBeam(wlength=561,
power=10,
radius=3.0,
position=0.7,
excitation=None)
tirfm.set_Objective(mag=60, NA=1.49, Nm=1.37, efficiency=0.90)
tirfm.set_DichroicMirror('FF562-Di03-25x36')
tirfm.set_EmissionFilter('FF01-593_40-25')
tirfm.set_TubeLens(mag=4, wl_range=(350, 750), efficiency=0.9987)
tirfm.set_camera(image_size=(512, 512),
pixel_length=16e-6,
zoom=0.1,
focal_point=(0.0, 0.5, 0.5))
tirfm.set_movie(frame_interval=0.033,
exposure_time=0.0033,
frame_end_time=1.00)
#tirfm.get_SpectrumPlot(plot_filename='./plots/spectrum_plots.pdf')
# create image and movie
image = TIRFMVisualizer(['./data/lattice/test_model_volume.h5'],
movie_filename='./test_model.mp4',
settings=tirfm)
image.output_movie(num_div=16)
def test_tirfm(t0, t1, index=None) :
# create TIRF Microscopy
tirfm = TIRFMConfigs()
tirfm.set_LightSource(source_type='LASER', wave_length=532, flux_density=10, angle=65.7)
tirfm.set_Fluorophore(fluorophore_type='Tetramethylrhodamine(TRITC)')
#tirfm.set_Fluorophore(fluorophore_type='EGFP')
#tirfm.set_Fluorophore(fluorophore_type='Gaussian', wave_length=532, intensity=0.55, width=(200,400))
tirfm.set_DichroicMirror('FF562-Di03-25x36')
tirfm.set_EmissionFilter('FF01-593_40-25')
tirfm.set_Magnification(Mag=198)
# Detector : CMOS Camera
# tirfm.set_Detector(detector='CMOS', image_size=(600,600), pixel_length=6.5e-6, \
# focal_point=(0.0,0.5,0.5), exposure_time=30e-3, QE=0.73)
# tirfm.set_ADConverter(bit=16, offset=100, fullwell=30000)
# Detector : EMCCD Camera
tirfm.set_Detector(detector='EMCCD', image_size=(512,512), pixel_length=16e-6, \
focal_point=(0.0,0.5,0.5), exposure_time=30e-3, QE=0.92, readout_noise=50, emgain=300)
tirfm.set_ADConverter(bit=14, offset=200, fullwell=800000)
### Output data
tirfm.set_OutputData(image_file_dir='./images')
### Input data
tirfm.set_InputData('./data/tmr_tirfm', start=t0, end=t1, observable="A")
# create physical effects
physics = PhysicalEffects()
physics.set_Conversion(ratio=1e-6)
physics.set_Background(mean=10)
# create image and movie
create = TIRFMVisualizer(configs=tirfm, effects=physics)
create.output_frames(num_div=16)
