def unscramble(num_im, num_slices, input_file_name, output_file_name):
interlaced_image_raw = tif_to_array(input_file_name).astype(np.float64)
##check to make sure I am divisible by num_im
num_columns = interlaced_image_raw.shape[-1]
extra_pixels = num_columns % num_im
if extra_pixels == 0:
interlaced_image = interlaced_image_raw
else:
interlaced_image = interlaced_image_raw[:, :, :num_columns-extra_pixels]
zstacks = num_im * num_slices
yrows = interlaced_image.shape[-2]
xcolumns = (interlaced_image.shape[-1]/num_im)
sorted_image_stack = np.zeros((zstacks, yrows, xcolumns),
dtype= interlaced_image.dtype)
for j in range(num_slices):
##l2r
for i in range(num_im):
sorted_image_stack[(j*num_im) + i, :, :] = interlaced_image[j, :, i::num_im]
##r2l
for i in range(num_im):
sorted_image_stack[(j*num_im) + i, :, :] = interlaced_image[j, :, i::num_im]
array_to_tif(sorted_image_stack.astype(np.float32), output_file_name)
print "Image 1:", sorted_image_stack.shape, sorted_image_stack.dtype
def image_filename_to_array(
image_filename, shape=None, dtype=None,
verbose=True, config=None, master=None):
"""Load tif (.tif, .tiff extension) and raw binary files (.dat,
.raw extension). If raw binary, 'dtype' and 'shape' must be specified."""
if verbose:
print "Loading %s..."%(os.path.split(image_filename)[1])
extension = os.path.splitext(image_filename)[1]
if extension in ('.tif', '.tiff'):
a, info = tif_to_array(image_filename, return_info=True)
info = dict([x.split('=') for x in info['description'].split('\n')
if len(x.split('=')) > 1])
if verbose and int(info.get('channels', 1)) > 1:
print "Image data seems to be an ImageJ hyperstack",
print " with multiple colors."
channels = int(info['channels'])
else:
channels = 1
return a, channels
elif extension in ('.raw', '.dat'):
if (shape is None) or (dtype is None):
info = get_image_info(
image_filename, config=config, master=master)
if info == 'cancelled':
return 'cancelled', None
xy_shape, dtype_name = info
config.set('File', 'last_leftright_shape', repr(xy_shape[1]))
config.set('File', 'last_updown_shape', repr(xy_shape[0]))
config.set('File', 'last_dtype', dtype_name)
save_config(config)
dtype = {
'uint8': numpy.uint8,
'uint16': numpy.uint16,
'uint32': numpy.uint32,
'float32': numpy.float32,
'float64': numpy.float64,
}[dtype_name]
else:
xy_shape = shape[1:]
data = numpy.fromfile(image_filename, dtype=dtype)
try:
data = data.reshape(
(data.size // (xy_shape[0] * xy_shape[1]),) + xy_shape)
except ValueError:
print xy_shape, dtype
raise UserWarning("The given shape and datatype do not match" +
" the size of %s"%(
os.path.split(image_filename)[1]))
return data, 1 #Multi-channel raw is probably to be avoided
else:
raise UserWarning("Extension '%s' not recognized.\n"%(extension) +
"File extension must be one of:\n"
" ('.tif', '.tiff', '.raw', '.dat').")
def initialize_volume(self):
volume_voltages = np.zeros((30000, self.daq.num_mutable_channels),
dtype=np.float64)
##objective starts where it was
objective_voltage = self.daq.default_voltages[-1, n2c['objective']]
volume_voltages[:, n2c['objective']] = objective_voltage
##objective does loaded scan
loaded_signal = tif_to_array(
filename='input_voltage_objective_01.tif').astype(
np.float64).ravel()
loaded_signal += objective_voltage
volume_voltages[:22500, n2c['objective']] = loaded_signal[:]
print "min", oh_snap_voltages[:, n2c['objective']].min()
print "max", oh_snap_voltages[:, n2c['objective']].max()
##excitation galvo starts where it was
galvo_voltage = self.daq.default_voltages[-1, n2c['excitation_scan']]
volume_voltages[:, n2c['excitation_scan']] = galvo_voltage
##excitation galvo scans illumination
galvo_voltage[5000:10000] = np.linspace(
galvo_voltage, galvo_voltage + 0.2, 5000)
galvo_voltage[10000:12500] = galvo_voltage + 0.2
galvo_voltage[12500:17500] = np.linspace(
galvo_voltage + 0.2, galvo_voltage, 5000)
##murrcle stays at what it was
murrcle_voltage = self.daq.default_voltages[-1, n2c['emission_scan']]
oh_snap_voltages[:, n2c['emission_scan']] = murrcle_voltage
#Camera triggers at the start of a write
oh_snap_voltages[:self.daq.write_length//4, n2c['camera']] = 3
#AOTF fires on one perpendicular facet
start_point_laser = (#Integer num of writes plus a perp facet time
self.daq.perpendicular_facet_times[6] + self.illumination_offset+
self.daq.write_length * int(roll_time * 1.0 /
self.daq.write_length))
oh_snap_voltages[start_point_laser:start_point_laser+self.illumination_length, n2c['488']] = 10
oh_snap_voltages[start_point_laser:start_point_laser+self.illumination_length, n2c['blanking']] = 10
## oh_snap_voltages[start_point_laser, n2c['blanking']] = 10
time.sleep(1)
"""
let's test the objective impulse response
"""
## marker = start_point_laser
## scan = np.linspace(5, 6, 5000)
## oh_snap_voltages[marker:(marker+5000), n2c['objective']] = scan
## marker += 5000
## oh_snap_voltages[marker:(
## marker+2500), n2c['objective']] = 6
## marker += 2500
## oh_snap_voltages[marker:(
## marker+5000), n2c['objective']] = np.linspace(6,5,5000)
## marker += 5000
## loaded_signal = tif_to_array(
## filename='input_voltage_objective_00.tif').astype(
## np.float64).ravel()
## loaded_signal += objective_voltage
## oh_snap_voltages[:22500, n2c['objective']] = loaded_signal[:]
## print "min", oh_snap_voltages[:, n2c['objective']].min()
## print "max", oh_snap_voltages[:, n2c['objective']].max()
##
## loaded_desired_signal = tif_to_array(
## filename='desired_result_objective.tif').astype(
## np.float64).ravel()
## loaded_desired_signal += objective_voltage
## loaded_desired_signal[0] += 1
## oh_snap_voltages[:, n2c['561']] = objective_voltage
## oh_snap_voltages[:22500, n2c['561']] = loaded_desired_signal[:]
print oh_snap_voltages.shape
self.daq.send_voltage(oh_snap_voltages, 'snap')
return None
def initialize_characterize(self):
"""
Create the murrrcle signal up here. All we care about is how
many DAQ points long it is.
"""
## impulse_strength = 1
## num_periods = 4
## daq_timepoints_per_period = 1500
## amplitude_volts = 0.1
## murrcle_signal = np.sin(np.linspace(
## 0, 2*np.pi*num_periods, num_periods * daq_timepoints_per_period))
## murrcle_signal[:daq_timepoints_per_period] = 0
## murrcle_signal[-daq_timepoints_per_period:] = 0
murrcle_signal = np.zeros(20000, dtype=np.float64)
default_murrcle = self.daq.default_voltages[-1, n2c['emission_scan']]
murrcle_signal[:] = default_murrcle
## murrcle_signal[1000:1152] = 0.05
## murrcle_signal[1152:-1000] = 0.1
## murrcle_signal[200:204] = default_murrcle + impulse_strength
"""
Read in an arbitrary signal from a tif file
"""
loaded_signal = tif_to_array(
filename='input_voltage_to_mirror_05.tif').astype(np.float64)
## loaded_signal += default_murrcle
## loaded_signal *= 1.75
##
## loaded_signal[loaded_signal < 0] *= 0.45
##
## print "Pre Loaded signal min, max:",
## print loaded_signal.min(), loaded_signal.max()
##
print "Loaded signal min, max:",
print loaded_signal.min(), loaded_signal.max()
print
"""
Put this optimzed waveform into the larger array
"""
murrcle_signal[:loaded_signal.size] = loaded_signal[:, 0, 0]
print "Loaded signal size", loaded_signal.size
## """
## Smoothly drop the voltage to default; hopefully this reduces ringing.
## """
## murrcle_signal[loaded_signal.size:2*(loaded_signal.size)
## ] = np.linspace(
## loaded_signal[-1, 0, 0],
## default_murrcle,
## loaded_signal.size)
## print "last value for signal" , loaded_signal[-1, 0 , 0]
## print murrcle_signal[loaded_signal.size * 1.5] #Remove this soon
##
self.characterization_points = murrcle_signal.size
delay_points = max(#Figure out the limiting factor
murrcle_signal.size,
1e-6 * self.get_camera_rolling_time_microseconds() * self.daq.rate)
start_point_laser = (#Integer num of writes plus a perp facet time
self.daq.perpendicular_facet_times[0] +
self.daq.write_length * int(np.ceil(delay_points * 1.0 /
self.daq.write_length)))
assert (self.exposure_time_microseconds * 1e6 >=
start_point_laser * 1.0 / self.daq.rate)
voltage = np.zeros(((start_point_laser + murrcle_signal.shape[0]),
self.daq.num_mutable_channels),
dtype=np.float64)
"""
Trigger the camera
"""
voltage[:self.daq.write_length//4, n2c['camera']] = 3
"""
Trigger the laser
"""
voltage[start_point_laser, n2c['488']] = 10
voltage[start_point_laser, n2c['blanking']] = 10
"""
Wiggle the murrrrcle
"""
print "murrcle_Signal[0]", murrcle_signal[0]
print "murrcle_Signal[-1]", murrcle_signal[-1]
print "default murrcle", default_murrcle
## assert murrcle_signal[0] == default_murrcle
assert murrcle_signal[-1] == default_murrcle
voltage[:, n2c['emission_scan']] = default_murrcle
voltage[-murrcle_signal.size:, n2c['emission_scan']] = murrcle_signal
print "Impulse starts at DAQ pixel:",
print voltage.size - murrcle_signal.size + 250
"""
Objective stays at what it was
"""
objective_voltage = self.daq.default_voltages[-1, n2c['objective']]
voltage[:, n2c['objective']] = objective_voltage
"""
Excitation Galvo stays at what it was
"""
galvo_voltage = self.daq.default_voltages[-1, n2c['excitation_scan']]
voltage[:, n2c['excitation_scan']] = galvo_voltage
self.daq.send_voltage(voltage, 'characterize')
return None
for s, sig in enumerate(sigmas):
density += gaussian_filter(multiview_data[s, :, :], sigma=sig)
density *= 1.0 / len(sigmas)
return density
def multiview_data_to_visualization(multiview_data, outfile=None):
if outfile is not None:
array_to_tif(multiview_data.astype(np.float32), outfile)
return multiview_data
"""
Load and truncate the object
"""
print "Loading resolution_target.tif..."
actual_object = tif_to_array('resolution_target.tif'
)[0, :, :].astype(np.float64)
print "Done loading."
print "Apodizing resolution target..."
mask = np.zeros_like(actual_object)
trim_size = 40
blur_size = 10
mask[trim_size:-trim_size, trim_size:-trim_size] = 1
gaussian_filter(mask, sigma=blur_size, output=mask)
array_to_tif(
mask.reshape((1,)+mask.shape).astype(np.float32), outfile='mask.tif')
np.multiply(actual_object, mask, out=actual_object)
print "Done apodizing."
"""
Generate noiseless data
"""
for m in range(msim_data.shape[2]):
for n in range(msim_data.shape[3]):
interpolation.shift(
input=msim_data[:, :, m, n],
shift=(0.5*(m - 0.5*msim_data.shape[2]),
0.5*(n - 0.5*msim_data.shape[3])),
output=shifted_msim_data[:, :, m, n],
order=3)
shifted_msim_data[shifted_msim_data < 0] = 0 #Interpolation can produce zeros
return shifted_msim_data
"""
Load and truncate the object
"""
print "Loading resolution_target.tif..."
actual_object = tif_to_array('ladder_complete.tif'
)[0, :, :].astype(np.float64)
print "Done loading."
print "Apodizing resolution target..."
mask = np.zeros_like(actual_object)
trim_size = 20#40
blur_size = 2#10
mask[trim_size:-trim_size, trim_size:-trim_size] = 1
gaussian_filter(mask, sigma=blur_size, output=mask)
array_to_tif(
mask.reshape((1,)+mask.shape).astype(np.float32), outfile='mask.tif')
np.multiply(actual_object, mask, out=actual_object)
print "Done apodizing."
"""
Generate noiseless data
"""
for m in range(msim_data.shape[2]):
for n in range(msim_data.shape[3]):
interpolation.shift(
input=msim_data[:, :, m, n],
shift=(0.5*(m - 0.5*msim_data.shape[2]),
0.5*(n - 0.5*msim_data.shape[3])),
output=shifted_msim_data[:, :, m, n],
order=3)
shifted_msim_data[shifted_msim_data < 0] = 0 #Interpolation can produce zeros
return shifted_msim_data
"""
Load and truncate the object
"""
print "Loading resolution_target.tif..."
actual_object = tif_to_array('lena_gray.tif'
)[0, :, :].astype(np.float64)
print "Done loading."
print "Apodizing resolution target..."
mask = np.zeros_like(actual_object)
trim_size = 40
blur_size = 10
mask[trim_size:-trim_size, trim_size:-trim_size] = 1
gaussian_filter(mask, sigma=blur_size, output=mask)
array_to_tif(
mask.reshape((1,)+mask.shape).astype(np.float32), outfile='mask.tif')
np.multiply(actual_object, mask, out=actual_object)
print "Done apodizing."
"""
Generate noiseless data
"""
def result_optimization_units_to_mirror_units(er):
return (er * 155.0) * scale + shift - 46.0 # Watch out for DC drift here
def result_mirror_units_to_optimization_units(er):
return (((er - shift + 46.0) * 1.0 / scale)) / 155.0
assert (
result_mirror_units_to_optimization_units(result_optimization_units_to_mirror_units(1)) == 1.0
) # Careful! Floats!
if __name__ == "__main__":
input_voltage = simple_tif.tif_to_array("input_voltage.tif").astype(np.float64)
expected_result = simple_tif.tif_to_array("expected_result.tif").astype(np.float64)
simple_tif.array_to_tif(
voltage_optimization_units_to_mirror_units(input_voltage).astype(np.float32), "input_voltage_to_mirror.tif"
)
simple_tif.array_to_tif(
result_optimization_units_to_mirror_units(expected_result).astype(np.float32), "expected_result_from_chip.tif"
)
plt.figure()
plt.subplot(2, 1, 1)
plt.plot(voltage_optimization_units_to_mirror_units(input_voltage).ravel(), label="Voltage to mirror")
plt.grid("on")
plt.legend()
plt.subplot(2, 1, 2)
input_voltage_cursor += len_ramp
##plt.figure()
##plt.plot(input_voltage_sample)
##plt.plot(time, desired_result_sample, '.')
##plt.plot(time, H(input_voltage_sample), '.')
##plt.plot(input_voltage_camera)
##plt.plot(time, desired_result_camera, '.')
##plt.plot(time, H(input_voltage_camera), '.')
##plt.show()
naive_input_voltage_sample = input_voltage_sample.copy()
naive_input_voltage_camera = input_voltage_camera.copy()
print "Loading 'input_voltage_sample.tif' and 'input_voltage_camera.tif'..."
try:
input_voltage_sample = simple_tif.tif_to_array('input_voltage_sample.tif'
).ravel().astype(np.float64)
input_voltage_camera = simple_tif.tif_to_array('input_voltage_camera.tif'
).ravel().astype(np.float64)
print "Initial guess loaded"
except IOError:
print "Loading failed. Using naive input voltages as initial guess."
iterations = 1000000
regularization = 0.1
plt.close('all')
plt.figure()
for i in range(iterations):
print 'Iteration', i
expected_result_sample = H(input_voltage_sample)
expected_result_camera = H(input_voltage_camera)
if not os.path.exists(previous_result_filename):
raise UserWarning("Result data not found")
break
print iteration
print "Previous:"
print ' ', previous_input_voltage_filename
print ' ', previous_result_filename
print 'Creating:'
print ' ', new_input_voltage_filename
"""
Load everything in optimization units
"""
previous_input_voltage = simple_tif.tif_to_array(
previous_input_voltage_filename).ravel().astype(np.float64)
previous_input_voltage = (
convert_units.voltage_mirror_units_to_optimization_units(
previous_input_voltage))
if iteration == 0:
"""
The pre-optimizer isn't allowed to write voltages during the
linker; this optimizer is. Pad with zeros.
"""
previous_input_voltage = np.concatenate((previous_input_voltage,
np.zeros(len_linker)))
desired_result = simple_tif.tif_to_array('expected_result.tif'
).ravel().astype(np.float64)
desired_result = np.concatenate((desired_result,
np.zeros(len_deadzone, dtype=np.float64)))
assert desired_result.size == previous_input_voltage.size + len_deadzone
def initialize_characterize(self):
"""
Create the murrrcle signal up here. All we care about is how
many DAQ points long it is.
"""
## impulse_strength = 1
## num_periods = 4
## daq_timepoints_per_period = 1500
## amplitude_volts = 0.1
## murrcle_signal = np.sin(np.linspace(
## 0, 2*np.pi*num_periods, num_periods * daq_timepoints_per_period))
## murrcle_signal[:daq_timepoints_per_period] = 0
## murrcle_signal[-daq_timepoints_per_period:] = 0
murrcle_signal = np.zeros(20000, dtype=np.float64)
default_murrcle = self.daq.default_voltages[-1, n2c['emission_scan']]
murrcle_signal[:] = default_murrcle
## murrcle_signal[1000:1152] = 0.05
## murrcle_signal[1152:-1000] = 0.1
## murrcle_signal[200:204] = default_murrcle + impulse_strength
"""
Read in an arbitrary signal from a tif file
"""
loaded_signal = tif_to_array(
filename='input_voltage_to_mirror_05.tif').astype(np.float64)
## loaded_signal += default_murrcle
## loaded_signal *= 1.75
##
## loaded_signal[loaded_signal < 0] *= 0.45
##
## print "Pre Loaded signal min, max:",
## print loaded_signal.min(), loaded_signal.max()
##
print "Loaded signal min, max:",
print loaded_signal.min(), loaded_signal.max()
print
"""
Put this optimzed waveform into the larger array
"""
murrcle_signal[:loaded_signal.size] = loaded_signal[:, 0, 0]
print "Loaded signal size", loaded_signal.size
## """
## Smoothly drop the voltage to default; hopefully this reduces ringing.
## """
## murrcle_signal[loaded_signal.size:2*(loaded_signal.size)
## ] = np.linspace(
## loaded_signal[-1, 0, 0],
## default_murrcle,
## loaded_signal.size)
## print "last value for signal" , loaded_signal[-1, 0 , 0]
## print murrcle_signal[loaded_signal.size * 1.5] #Remove this soon
##
self.characterization_points = murrcle_signal.size
delay_points = max( #Figure out the limiting factor
murrcle_signal.size,
1e-6 * self.get_camera_rolling_time_microseconds() * self.daq.rate)
start_point_laser = ( #Integer num of writes plus a perp facet time
self.daq.perpendicular_facet_times[0] + self.daq.write_length *
int(np.ceil(delay_points * 1.0 / self.daq.write_length)))
assert (self.exposure_time_microseconds * 1e6 >=
start_point_laser * 1.0 / self.daq.rate)
voltage = np.zeros(((start_point_laser + murrcle_signal.shape[0]),
self.daq.num_mutable_channels),
dtype=np.float64)
"""
Trigger the camera
"""
voltage[:self.daq.write_length // 4, n2c['camera']] = 3
"""
Trigger the laser
"""
voltage[start_point_laser, n2c['488']] = 10
voltage[start_point_laser, n2c['blanking']] = 10
"""
Wiggle the murrrrcle
"""
print "murrcle_Signal[0]", murrcle_signal[0]
print "murrcle_Signal[-1]", murrcle_signal[-1]
print "default murrcle", default_murrcle
## assert murrcle_signal[0] == default_murrcle
assert murrcle_signal[-1] == default_murrcle
voltage[:, n2c['emission_scan']] = default_murrcle
voltage[-murrcle_signal.size:, n2c['emission_scan']] = murrcle_signal
print "Impulse starts at DAQ pixel:",
print voltage.size - murrcle_signal.size + 250
"""
Objective stays at what it was
"""
objective_voltage = self.daq.default_voltages[-1, n2c['objective']]
voltage[:, n2c['objective']] = objective_voltage
"""
Excitation Galvo stays at what it was
"""
galvo_voltage = self.daq.default_voltages[-1, n2c['excitation_scan']]
voltage[:, n2c['excitation_scan']] = galvo_voltage
self.daq.send_voltage(voltage, 'characterize')
return None