def test_tirfm(t0, t1) :
# create TIRF Microscopy
tirfm = TIRFMConfigs()
tirfm.set_LightSource(source_type='LASER', wave_mode='TEM00', M2_factor=1.0, wave_length=473, power=10e-3, radius=0.32e-3)
tirfm.set_BeamExpander(expander_type='Keplerian', focal_length1=300e-3, focal_length2=20e-3, pinhole_radius=23e-6)
tirfm.set_Fluorophore(fluorophore_type='Tetramethylrhodamine(TRITC)')
#tirfm.set_Fluorophore(fluorophore_type='Gaussian', wave_length=578, width=(20.0, 140.0))
#tirfm.set_Fluorophore(fluorophore_type='Point-like', wave_length=578)
tirfm.set_EvanescentField(depth=200)
tirfm.set_Objective(NA=1.49, Nm=1.37, focal_length=1.90e-3, efficiency=0.90)
tirfm.set_DichroicMirror('FF562-Di03-25x36')
tirfm.set_EmissionFilter('FF01-593_40-25')
tirfm.set_TubeLens1(focal_length=160e-3)
tirfm.set_ScanLens(focal_length=50e-3)
tirfm.set_TubeLens2(focal_length=200e-3)
tirfm.set_Detector(detector='EMCCD', zoom=1, emgain=150, focal_point=(0.0,0.5,0.5), \
start_time=t0, end_time=t1, fps=1.0/3.3e-3, exposure_time=33e-3)
tirfm.set_Movie(image_file_dir='./images_nishida', movie_filename='./movies/tirfm_movie.mp4')
tirfm.set_DataFile(['./data/lattice/test_model_07.h5'])
# create physical effects
physics = PhysicalEffects()
physics.set_Conversion(ratio=1e-7)
physics.set_Background(mean=0, width=100)
#physics.set_DepthOfFocus(a=0.5, b=0.0)
physics.set_DetectorCrosstalk(width=3.0)
#physics.set_Photobleaching(rate=1/2.00)
#physics.set_Photoblinking(P0=0.5, alpha_on=0.0048, alpha_off=0.0055)
# create image and movie
create = TIRFMVisualizer(configs=tirfm, effects=physics)
#create.get_plots(plot_filename='./plots/tirfm_plots.pdf')
create.output_frames(num_div=16)
def test_tirfm(t0, t1, Molecule) :
# create TIRF Microscopy
tirfm = TIRFMConfigs()
tirfm.set_LightSource(source_type='LASER', wave_mode='TEM00', M2_factor=1.00, wave_length=473, power=1e-3, radius=0.32e-3)
#tirfm.set_BeamExpander(expander_type='Keplerian', focal_length1=300e-3, focal_length2=20e-3, pinhole_radius=23e-6)
#tirfm.set_Fluorophore(fluorophore_type='mCherry')
tirfm.set_Fluorophore(fluorophore_type='EGFP')
#tirfm.set_Fluorophore(fluorophore_type='Gaussian', wave_length=578, width=(70.0, 140.0))
#tirfm.set_Fluorophore(fluorophore_type='Point-like', wave_length=578)
tirfm.set_Objective(NA=1.49, Nm=1.37, focal_length=1.9e-3, efficiency=0.90)
tirfm.set_EvanescentField(depth=200)
tirfm.set_DichroicMirror('FF562-Di03-25x36')
tirfm.set_EmissionFilter('FF01-593_40-25')
tirfm.set_TubeLens1(focal_length=160e-3)
tirfm.set_ScanLens(focal_length=50e-3)
tirfm.set_TubeLens2(focal_length=200e-3)
tirfm.set_Detector(detector='EMCCD', zoom=1, emgain=300, focal_point=(0.0,0.5,0.5), \
start_time=t0, end_time=t1, fps=1/33e-3, exposure_time=33e-3)
tirfm.set_Movie(image_file_dir='./images_egfm_%s' % (Molecule), movie_filename='./movies/egfm_movie.mp4')
tirfm.set_DataFile(['/home/kiwamoto/share/EGF_model_20130603/LogHDF5_Raf_1.h5'], observable=Molecule)
tirfm.set_BCFile(['/home/kiwamoto/share/EGF_model_20130603/LogCoordinate_Shape.csv'])
# create physical effects
physics = PhysicalEffects()
physics.set_Conversion(ratio=1e-6)
#physics.set_Background(mean=30)
#physics.set_DepthOfFocus(a=0.5, b=0.0)
#physics.set_DetectorCrosstalk(width=2.0)
#physics.set_Photobleaching(rate=1/5.0)
#physics.set_Photoblinking(P0=0.5, alpha_on=0.0048, alpha_off=0.0055)
# create image and movie
create = TIRFMVisualizer(configs=tirfm, effects=physics)
#create.get_plots(plot_filename='./plots/tirfm.plots.pdf')
create.output_frames(num_div=16)
def test_tirfm(t0, t1):
# create TIRF Microscopy
tirfm = TIRFMConfigs()
tirfm.set_LightSource(
source_type="LASER", wave_mode="TEM00", M2_factor=1.0, wave_length=473, power=1.0e-3, radius=10e-6
)
tirfm.set_Fluorophore(fluorophore_type="Tetramethylrhodamine(TRITC)")
# tirfm.set_Fluorophore(fluorophore_type='Gaussian', wave_length=578, width=(20.0, 20.0))
# tirfm.set_Fluorophore(fluorophore_type='Point-like', wave_length=578)
tirfm.set_EvanescentField(depth=200)
tirfm.set_Objective(NA=1.49, Nm=1.37, focal_length=1.90e-3, efficiency=0.90)
tirfm.set_TubeLens1(focal_length=160e-3)
tirfm.set_ScanLens(focal_length=50e-3)
tirfm.set_TubeLens2(focal_length=200e-3)
tirfm.set_Detector(
detector="EMCCD",
zoom=1,
emgain=300,
focal_point=(0.0, 0.5, 0.5),
start_time=t0,
end_time=t1,
fps=1.0 / 3.3e-3,
exposure_time=33e-3,
)
tirfm.set_Movie(image_file_dir="./images", movie_filename="./movies/tirfm_movie.mp4")
tirfm.set_DataFile(["./data/lattice/test_model_11.h5"])
# create physical effects
physics = PhysicalEffects()
physics.set_Conversion(ratio=1e-6)
physics.set_DetectorCrosstalk(width=2.00)
# create image and movie
create = TIRFMVisualizer(configs=tirfm, effects=physics)
create.output_frames(num_div=16)
