def test_kinesin():
# create Confocal Microscopy for off-lattice model (Kinesin)
confm = KinesinConfigs()
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="PMT",
zoom=2,
emgain=1e7,
focal_point=(0.5, 0.5, 0.5),
start_time=0,
end_time=30,
fps=1 / 30e-3,
exposure_time=30e-3,
)
confm.set_Movie(image_file_dir="./images_kinesin", movie_filename="./movies/kinesin_m100_movie.mp4")
# confm.set_DataFile(['./data/lattice/satyaKinesinVisualLog.csv'])
confm.set_DataFile(["./data/lattice/CoordinateLog_act0.15_m100.csv"])
# create image and movie
create = KinesinVisualizer(configs=confm)
# create.get_plots(plot_filename='./plots/kinesin_plots.pdf')
# create.output_frames(num_div=16)
create.output_movie(num_div=16)
def test_b3c(t0, t1) :
# create EPIF Microscopy
epifm = KinesinConfigs()
epifm.set_LightSource(source_type='LASER', wave_mode='TEM00', M2_factor=1.00, wave_length=473, power=10e-3, radius=0.32e-3)
epifm.set_BeamExpander(expander_type='Keplerian', focal_length1=300e-3, focal_length2=20e-3, pinhole_radius=23e-6)
#epifm.set_Fluorophore(fluorophore_type='Tetramethylrhodamine(TRITC)')
epifm.set_Fluorophore(fluorophore_type='Gaussian', wave_length=578, width=(10.0, 20.0))
#epifm.set_Fluorophore(fluorophore_type='Point-like', wave_length=578)
epifm.set_Objective(NA=1.49, Nm=1.37, focal_length=1.9e-3, efficiency=0.90)
#epifm.set_DichroicMirror('FF562-Di03-25x36')
#epifm.set_EmissionFilter('FF01-593_40-25')
epifm.set_TubeLens1(focal_length=160e-3)
epifm.set_ScanLens(focal_length=50e-3)
epifm.set_TubeLens2(focal_length=200e-3)
epifm.set_Detector(detector='EMCCD', zoom=1, emgain=100, pixel_length=0.16e-6, focal_point=(0.0,0.5,0.5), \
start_time=t0, end_time=t1, fps=1, exposure_time=1)
epifm.set_Movie(image_file_dir='./images_b3c', movie_filename='./movies/band3_cluster.mp4')
epifm.set_DataFile(['./data/lattice/band3_cluster.csv'])
# create image and movie
create = KinesinVisualizer(configs=epifm)
#create.get_plots(plot_filename='./plots/epifm_plots.pdf')
create.output_frames(num_div=16)