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Move files and deprecate print without parentheses
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kaizu committed Mar 14, 2018
1 parent e449549 commit 5c36fee
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Showing 1,397 changed files with 320 additions and 320 deletions.
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Empty file added bioimaging/__init__.py
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Expand Up @@ -40,7 +40,7 @@ def get_auto_corr(I0, It) :

C_auto= get_auto_corr(I0, It)

print It[i,0], It[i,2], C_auto
print(It[i,0], It[i,2], C_auto)



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Expand Up @@ -126,7 +126,7 @@ def convert(file_in, file_out, index=None) :
dev2 = (signal - s_avg)**2
err_s = numpy.sqrt(dev2.sum()/length)

print 210, s_avg, err_s, b_avg, err_b
print(210, s_avg, err_s, b_avg, err_b)

# 8-bit data format (for making movie)
#toimage(image, cmin=100, cmax=1000).save(file_out + '/image_summed.png')
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2 changes: 1 addition & 1 deletion analyses_palm_data.py → bioimaging/analyses_palm_data.py
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Expand Up @@ -55,7 +55,7 @@ def convert(file_in, file_out, index=None) :
amin = numpy.amin(image)
amax = numpy.amax(image)

print amin, amax
print(amin, amax)

# 16-bit data format
#image_array.astype('uint16')
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Expand Up @@ -83,7 +83,7 @@ def convert(file_in, file_out) :
errorfunction = lambda p : numpy.ravel(gaussian(*p)(*numpy.indices(image0.shape)) - image0)
p, success = optimize.leastsq(errorfunction, params)

print intensity, x_px-(x-8), y_px-(y-8), I_sum, p[2], p[1], B_avg, B_dev
print(intensity, x_px-(x-8), y_px-(y-8), I_sum, p[2], p[1], B_avg, B_dev)
#print intensity, x_px-(x-8), y_px-(y-8), p, success, B_avg, B_dev


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4 changes: 2 additions & 2 deletions blinking_script.py → bioimaging/blinking_script.py
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Expand Up @@ -46,10 +46,10 @@ def test_palm(t0, t1) :
budget = physics.fluorescence_budget[0]
state = physics.fluorescence_state[0]

print '#', budget, 'photons', (budget/n_emit0)*dt, 'sec'
print('#', budget, 'photons', (budget/n_emit0)*dt, 'sec')

for i in range(len(state)) :
print dt*i, state[i], budget
print(dt*i, state[i], budget)

if (state[i] > 0) :
budget = budget - n_emit0
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32 changes: 16 additions & 16 deletions camera_handler.py → bioimaging/camera_handler.py
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Expand Up @@ -43,7 +43,7 @@ def __init__(self, user_configs_dict = None):
# user setting
if user_configs_dict is not None:
if type(user_configs_dict) != type({}):
print 'Illegal argument type for constructor of Configs class'
print('Illegal argument type for constructor of Configs class')
sys.exit()
configs_dict.update(user_configs_dict)

Expand Down Expand Up @@ -89,16 +89,16 @@ def set_Detector(self, detector = None,
self._set_data('detector_dark_count', dark_count)
self._set_data('detector_emgain', emgain)

print '--- Detector : ', self.detector_type
print '\tImage Size = ', self.detector_image_size[0], 'x', self.detector_image_size[1]
print '\tPixel Size = ', self.detector_pixel_length, 'm/pixel'
print '\tFocal Point = ', self.detector_focal_point
print '\tPosition = ', self.detector_base_position
print '\tExposure Time = ', self.detector_exposure_time, 'sec'
print '\tQuantum Efficiency = ', 100*self.detector_qeff, '%'
print '\tReadout Noise = ', self.detector_readout_noise, 'electron'
print '\tDark Count = ', self.detector_dark_count, 'electron/sec'
print '\tEM gain = ', 'x', self.detector_emgain
print('--- Detector : ', self.detector_type)
print('\tImage Size = ', self.detector_image_size[0], 'x', self.detector_image_size[1])
print('\tPixel Size = ', self.detector_pixel_length, 'm/pixel')
print('\tFocal Point = ', self.detector_focal_point)
print('\tPosition = ', self.detector_base_position)
print('\tExposure Time = ', self.detector_exposure_time, 'sec')
print('\tQuantum Efficiency = ', 100*self.detector_qeff, '%')
print('\tReadout Noise = ', self.detector_readout_noise, 'electron')
print('\tDark Count = ', self.detector_dark_count, 'electron/sec')
print('\tEM gain = ', 'x', self.detector_emgain)



Expand All @@ -116,11 +116,11 @@ def set_ADConverter(self, bit = None,
self._set_data('ADConverter_fpn_type', fpn_type)
self._set_data('ADConverter_fpn_count', fpn_count)

print '--- A/D Converter : %d-bit' % (self.ADConverter_bit)
print '\tGain = %.3f count/electron' % (self.ADConverter_gain)
print '\tOffset = ', self.ADConverter_offset, 'count'
print '\tFullwell = ', self.ADConverter_fullwell, 'electron'
print '\t%s-Fixed Pattern Noise :' % (self.ADConverter_fpn_type), self.ADConverter_fpn_count, 'count'
print('--- A/D Converter : %d-bit' % (self.ADConverter_bit))
print('\tGain = %.3f count/electron' % (self.ADConverter_gain))
print('\tOffset = ', self.ADConverter_offset, 'count')
print('\tFullwell = ', self.ADConverter_fullwell, 'electron')
print('\t%s-Fixed Pattern Noise :' % (self.ADConverter_fpn_type), self.ADConverter_fpn_count, 'count')

# image pixel-size
Nw_pixel = self.detector_image_size[0]
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