#2 Modify the unit of fluorophore_radius

ecell · Mar 4, 2019 · 6d58add · 6d58add
1 parent 411cada
commit 6d58add
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Showing 5 changed files with 8 additions and 7 deletions.
diff --git a/examples/defaults.ini b/examples/defaults.ini
@@ -10,7 +10,7 @@ dichroic_mirror = 'FF562-Di03-25x36'
 ADConverter_fpn_type = 'none'
 ignore_open_errors = False
 source_depth = 2e-05
-fluorophore_radius = 20
+fluorophore_radius = 20e-9
 detector_pair_pulses = 0.0
 detector_readout_noise = 100
 detector_base_position = (-2.0, 0.5, 0.5)

diff --git a/examples/tirf_script.py b/examples/tirf_script.py
@@ -27,9 +27,9 @@ def test_tirf() :
 
     ## set epifm configurations
     config.set_epifm_shutter(start_time=t0, end_time=t1)
-    config.set_epifm_light_source(source_type='LASER', wave_length=532, flux_density=40, angle=72)
+    config.set_epifm_light_source(source_type='LASER', wave_length=532e-9, flux_density=40, angle=72)
     config.set_epifm_fluorophore(
-        fluorophore_type='Tetramethylrhodamine(TRITC)', normalization=1.0, radius=20)
+        fluorophore_type='Tetramethylrhodamine(TRITC)', normalization=1.0, radius=20e-9)
     config.set_epifm_dichroic_mirror('FF562-Di03-25x36')
     focal_point = numpy.array([lengths[0] * 0.0, lengths[1] * 0.5, lengths[2] * 0.5])
     # config.set_epifm_magnification(magnification=100)

diff --git a/examples/twocolor_script.py b/examples/twocolor_script.py
@@ -30,9 +30,9 @@ def test_tirf() :
 
     ## set epifm configurations
     config.set_epifm_shutter(start_time=t0, end_time=t1)
-    config.set_epifm_light_source(source_type='LASER', wave_length=532, flux_density=40, angle=72)
+    config.set_epifm_light_source(source_type='LASER', wave_length=532e-9, flux_density=40, angle=72)
     config.set_epifm_fluorophore(
-        fluorophore_type='Tetramethylrhodamine(TRITC)', normalization=1.0, radius=20)
+        fluorophore_type='Tetramethylrhodamine(TRITC)', normalization=1.0, radius=20e-9)
     config.set_epifm_dichroic_mirror('FF562-Di03-25x36')
     focal_point = numpy.array([lengths[0] * 0.0, lengths[1] * 0.5, lengths[2] * 0.5])
     config.set_epifm_magnification(magnification=241)

diff --git a/scopyon/defaults.ini b/scopyon/defaults.ini
@@ -19,6 +19,7 @@ shutter_end_time = 0.0
 
 fluorophore_type = 'Gauss'
 fluorophore_lifetime = 10e-9 # sec
+fluorophore_radius = 20e-9 # m
 
 # Fluorophore PSF
 

diff --git a/scopyon/epifm.py b/scopyon/epifm.py
@@ -79,7 +79,7 @@ def initialize(self, config, rng=None):
         _log.info('--- Fluorophore: {} PSF'.format(self.fluorophore_type))
         _log.info('    Wave Length   =  {} m'.format(self.psf_wavelength))
         _log.info('    Normalization =  {}'.format(self.psf_normalization))
-        _log.info('    Fluorophore radius =  {} nm'.format(self.fluorophore_radius))
+        _log.info('    Fluorophore radius =  {} m'.format(self.fluorophore_radius))
         if hasattr(self, 'psf_width'):
             _log.info('    Lateral Width =  {} m'.format(self.psf_width[0]))
             _log.info('    Axial Width =  {} m'.format(self.psf_width[1]))
@@ -1039,7 +1039,7 @@ def __get_emit_photons(self, amplitude, unit_time):
         n_abs = amplitude * x_sec * unit_time
 
         # Beer-Lamberts law: A = log(I0 / I) = abs coef. * concentration * path length ([m2]*[#/m3]*[m])
-        fluorophore_radius = self.configs.fluorophore_radius * 1e-9
+        fluorophore_radius = self.configs.fluorophore_radius
         fluorophore_volume = (4.0 / 3.0) * numpy.pi * numpy.power(fluorophore_radius, 3)
         fluorophore_depth  = 2.0 * fluorophore_radius