def fitPeaks(self, peaks):
# Adjust to z starting position.
z_index = utilC.getZCenterIndex()
peaks[:,z_index] = peaks[:,z_index] * float(self.mfitter.getSplineSize())
if False:
print("Before fitting")
for i in range(5):
print(" ", peaks[i,0], peaks[i,1], peaks[i,3], peaks[i,5], peaks[i,6], peaks[i,7])
print("")
# Fit to update peak locations.
fit_peaks = self.mfitter.doFit(peaks)
fit_peaks = self.mfitter.getGoodPeaks(fit_peaks, min_height = 0.9 * self.threshold)
# Remove peaks that are too close to each other & refit.
fit_peaks = utilC.removeClosePeaks(fit_peaks, self.sigma, self.fit_neighborhood)
# Redo the fit for the remaining peaks.
fit_peaks = self.mfitter.doFit(fit_peaks)
fit_peaks = self.mfitter.getGoodPeaks(fit_peaks, min_height = 0.9*self.threshold)
residual = self.mfitter.getResidual()
if False:
print("After fitting")
for i in range(5):
print(" ", fit_peaks[i,0], fit_peaks[i,1], fit_peaks[i,3], fit_peaks[i,5], fit_peaks[i,6], fit_peaks[i,7])
print("")
return [fit_peaks, residual]
def fitPeaks(self, peaks):
# Fit to update peak locations.
[fit_peaks, residual] = self.peakFitter(peaks)
fit_peaks = self.mfitter.getGoodPeaks(fit_peaks,
min_height = 0.9*self.threshold)
# Remove peaks that are too close to each other & refit.
fit_peaks = utilC.removeClosePeaks(fit_peaks, self.sigma, self.neighborhood)
[fit_peaks, residual] = self.peakFitter(fit_peaks)
fit_peaks = self.mfitter.getGoodPeaks(fit_peaks,
min_height = 0.9*self.threshold)
return [fit_peaks, residual]
def fitPeaks(self, peaks):
# Fit to update peak locations.
[fit_peaks, residual] = self.peakFitter(peaks)
fit_peaks = self.mfitter.getGoodPeaks(fit_peaks,
min_height = 0.9*self.threshold)
# Remove peaks that are too close to each other & refit.
fit_peaks = utilC.removeClosePeaks(fit_peaks, self.sigma, self.neighborhood)
[fit_peaks, residual] = self.peakFitter(fit_peaks)
fit_peaks = self.mfitter.getGoodPeaks(fit_peaks,
min_height = 0.9*self.threshold)
return [fit_peaks, residual]
def fitPeaks(self, peaks):
# Fit to update peak locations.
[fit_peaks, residual, iterations] = self.peakFitter(peaks)
fit_peaks = multi_c.getGoodPeaks(fit_peaks, 0.9 * self.threshold,
0.5 * self.sigma)
# Remove peaks that are too close to each other & refit.
fit_peaks = util_c.removeClosePeaks(fit_peaks, self.sigma,
self.neighborhood)
[fit_peaks, residual, iterations] = self.peakFitter(fit_peaks)
fit_peaks = multi_c.getGoodPeaks(fit_peaks, 0.9 * self.threshold,
0.5 * self.sigma)
return [fit_peaks, residual]
def fitPeaks(self, peaks):
"""
Performs a single iteration of peak fitting.
peaks - A numpy array of peaks to fit.
return - [updated peaks, updated residual]
"""
# Fit to update peak locations.
[fit_peaks, residual] = self.peakFitter(peaks)
fit_peaks = self.mfitter.getGoodPeaks(fit_peaks, 0.9 * self.threshold,
0.5 * self.sigma)
# Remove peaks that are too close to each other & refit.
fit_peaks = utilC.removeClosePeaks(fit_peaks, self.sigma,
self.neighborhood)
[fit_peaks, residual] = self.peakFitter(fit_peaks)
fit_peaks = self.mfitter.getGoodPeaks(fit_peaks, 0.9 * self.threshold,
0.5 * self.sigma)
return [fit_peaks, residual]
def fitPeaks(self, peaks):
# Adjust to z starting position.
z_index = utilC.getZCenterIndex()
peaks[:, z_index] = peaks[:, z_index] * float(
self.mfitter.getSplineSize())
if False:
print("Before fitting")
for i in range(5):
print(" ", peaks[i, 0], peaks[i, 1], peaks[i, 3], peaks[i, 5],
peaks[i, 6], peaks[i, 7])
print("")
# Fit to update peak locations.
fit_peaks = self.mfitter.doFit(peaks)
fit_peaks = self.mfitter.getGoodPeaks(fit_peaks,
min_height=0.9 * self.threshold)
# Remove peaks that are too close to each other & refit.
fit_peaks = utilC.removeClosePeaks(fit_peaks, self.sigma,
self.fit_neighborhood)
# Redo the fit for the remaining peaks.
fit_peaks = self.mfitter.doFit(fit_peaks)
fit_peaks = self.mfitter.getGoodPeaks(fit_peaks,
min_height=0.9 * self.threshold)
residual = self.mfitter.getResidual()
if False:
print("After fitting")
for i in range(5):
print(" ", fit_peaks[i, 0], fit_peaks[i, 1], fit_peaks[i, 3],
fit_peaks[i, 5], fit_peaks[i, 6], fit_peaks[i, 7])
print("")
return [fit_peaks, residual]
def peakFinder(self, no_bg_image):
all_new_peaks = None
save_convolution = False
if save_convolution:
print("making image")
tif = tifffile.TiffWriter("image.tif")
tif.save(self.image.astype(numpy.uint16) + 100)
tif.save(no_bg_image.astype(numpy.uint16) + 100)
tif.save(self.background.astype(numpy.uint16) + 100)
#
# Find peaks in image convolved with the PSF at different z values.
#
for i in range(len(self.mfilter)):
height_rescale = self.height_rescale[i]
mfilter = self.mfilter[i]
taken = self.taken[i]
z_value = self.z_value[i]
# Smooth image with gaussian filter.
smooth_image = mfilter.convolve(no_bg_image)
if save_convolution:
tif.save(smooth_image.astype(numpy.uint16) + 100)
# Mask the image so that peaks are only found in the AOI.
masked_image = smooth_image * self.peak_mask
# Identify local maxima in the masked image.
[new_peaks, taken] = utilC.findLocalMaxima(masked_image,
taken,
self.cur_threshold,
self.find_max_radius,
self.margin)
#
# Fill in initial values for peak height, background and sigma.
#
# FIXME: We just add the smoothed image and the background together
# as a hack so that we can still use the initializePeaks()
# function.
#
new_peaks = utilC.initializePeaks(new_peaks, # The new peaks.
smooth_image + self.background, # Smooth image + background.
self.background, # The current estimate of the background.
self.sigma, # The starting sigma value.
z_value) # The starting z value.
# Correct initial peak heights.
h_index = utilC.getHeightIndex()
new_peaks[:,h_index] = new_peaks[:,h_index] * height_rescale
if all_new_peaks is None:
all_new_peaks = new_peaks
else:
all_new_peaks = numpy.append(all_new_peaks, new_peaks, axis = 0)
if save_convolution:
tif.close()
#
# Remove the dimmer of two peaks with similar x,y values but different z values.
#
if (len(self.mfilter) > 1):
if False:
print("before", all_new_peaks.shape)
for i in range(all_new_peaks.shape[0]):
print(all_new_peaks[i,:])
print("")
all_new_peaks = utilC.removeClosePeaks(all_new_peaks,
self.find_max_radius,
self.find_max_radius)
if False:
print("after", all_new_peaks.shape)
for i in range(all_new_peaks.shape[0]):
print(all_new_peaks[i,:])
print("")
return all_new_peaks
def peakFinder(self, no_bg_image):
all_new_peaks = None
save_convolution = False
if save_convolution:
print("making image")
tif = tifffile.TiffWriter("image.tif")
tif.save(self.image.astype(numpy.uint16) + 100)
tif.save(no_bg_image.astype(numpy.uint16) + 100)
tif.save(self.background.astype(numpy.uint16) + 100)
#
# Find peaks in image convolved with the PSF at different z values.
#
for i in range(len(self.mfilter)):
height_rescale = self.height_rescale[i]
mfilter = self.mfilter[i]
taken = self.taken[i]
z_value = self.z_value[i]
# Smooth image with gaussian filter.
smooth_image = mfilter.convolve(no_bg_image)
if save_convolution:
tif.save(smooth_image.astype(numpy.uint16) + 100)
# Mask the image so that peaks are only found in the AOI.
masked_image = smooth_image * self.peak_mask
# Identify local maxima in the masked image.
[new_peaks, taken] = utilC.findLocalMaxima(masked_image,
taken,
self.cur_threshold,
self.find_max_radius,
self.margin)
#
# Fill in initial values for peak height, background and sigma.
#
# FIXME: We just add the smoothed image and the background together
# as a hack so that we can still use the initializePeaks()
# function.
#
new_peaks = utilC.initializePeaks(new_peaks, # The new peaks.
smooth_image + self.background, # Smooth image + background.
self.background, # The current estimate of the background.
self.sigma, # The starting sigma value.
z_value) # The starting z value.
# Correct initial peak heights.
h_index = utilC.getHeightIndex()
new_peaks[:,h_index] = new_peaks[:,h_index] * height_rescale
if all_new_peaks is None:
all_new_peaks = new_peaks
else:
all_new_peaks = numpy.append(all_new_peaks, new_peaks, axis = 0)
if save_convolution:
tif.close()
#
# Remove the dimmer of two peaks with similar x,y values but different z values.
#
if (len(self.mfilter) > 1):
if False:
print("before", all_new_peaks.shape)
for i in range(all_new_peaks.shape[0]):
print(all_new_peaks[i,:])
print("")
all_new_peaks = utilC.removeClosePeaks(all_new_peaks,
self.find_max_radius,
self.find_max_radius)
if False:
print("after", all_new_peaks.shape)
for i in range(all_new_peaks.shape[0]):
print(all_new_peaks[i,:])
print("")
return all_new_peaks
def peakFinder(self, fit_images):
"""
This method does the actual peak finding.
We are assuming that Poisson statistics applies, so if we have
a good estimate of the background and foreground then we can
predict the significance of a foreground value with reasonable
accuracy.
"""
#
# Calculate (estimated) background variance for each plane.
#
# The estimated background and variance should both be > 0.0,
# or there is going to be trouble.
#
bg_variances = []
# Save fit images for debugging purposes.
if self.check_mode:
with tifffile.TiffWriter("fit_images.tif") as tf:
for fi in fit_images:
tf.save(numpy.transpose(fi.astype(numpy.float32)))
# Iterate over z values.
for i in range(len(self.vfilters)):
bg_variance = numpy.zeros(fit_images[0].shape)
# Iterate over channels / planes.
for j in range(len(self.vfilters[i])):
# Convolve fit image + background with the appropriate variance filter.
#
# I believe that this is correct, the variance of the weighted average
# of a (independent) Poisson processes is calculated using the square of
# the weights.
#
conv_var = self.vfilters[i][j].convolve(fit_images[j] +
self.backgrounds[j])
# Transform variance to the channel 0 frame.
if self.atrans[j] is None:
bg_variance += conv_var
else:
bg_variance += self.atrans[j].transform(conv_var)
bg_variances.append(bg_variance + self.variances[i])
# Check for problematic values.
if self.check_mode:
for bg in bg_variances:
mask = (bg <= 0.0)
if (numpy.sum(mask) > 0):
print(
"Warning! 0.0 / negative values detected in background variance."
)
# Save results if needed for debugging purposes.
if self.check_mode:
with tifffile.TiffWriter("variances.tif") as tf:
for bg in bg_variances:
tf.save(numpy.transpose(bg.astype(numpy.float32)))
#
# Calculate foreground for each z plane.
#
fg_averages = [
] # This is the average foreground across all the planes for each z value.
foregrounds = [] # This is the foreground for each plane and z value.
# Iterate over z values.
for i in range(len(self.mfilters)):
foreground = numpy.zeros(fit_images[0].shape)
foregrounds.append([])
# Iterate over channels / planes.
for j in range(len(self.mfilters[i])):
# Convolve image / background with the appropriate PSF.
conv_fg = self.mfilters[i][j].convolve(self.images[j] -
fit_images[j] -
self.backgrounds[j])
# Store convolved image in foregrounds.
foregrounds[i].append(conv_fg)
# Transform image to the channel 0 frame.
if self.atrans[j] is None:
foreground += conv_fg
else:
foreground += self.atrans[j].transform(conv_fg)
fg_averages.append(foreground)
# Normalize average foreground by background standard deviation.
fg_bg_ratios = []
for i in range(len(fg_averages)):
fg_bg_ratios.append(fg_averages[i] / numpy.sqrt(bg_variances[i]))
# Save results if needed for debugging purposes.
if self.check_mode:
with tifffile.TiffWriter("foregrounds.tif") as tf:
for fg in fg_averages:
tf.save(numpy.transpose(fg.astype(numpy.float32)))
with tifffile.TiffWriter("fg_bg_ratio.tif") as tf:
for fg_bg_ratio in fg_bg_ratios:
tf.save(numpy.transpose(fg_bg_ratio.astype(numpy.float32)))
#
# At each z value, find peaks in foreground image normalized
# by the background standard deviation.
#
all_new_peaks = None
zero_array = numpy.zeros(fg_bg_ratios[0].shape)
for i in range(len(self.mfilters)):
#
# Mask the image so that peaks are only found in the AOI. Ideally the
# this mask should probably be adjusted to limit analysis to only
# the regions of the image where there is data from every channel / plane.
#
masked_image = fg_bg_ratios[i] * self.peak_mask
# Identify local maxima in the masked image.
[new_peaks,
taken] = utilC.findLocalMaxima(masked_image, self.taken[i],
self.cur_threshold,
self.find_max_radius, self.margin)
#
# Initialize peaks with normalized height value. We'll split these
# later into peaks for each plane, and at that point the height,
# background and z values will be corrected.
#
# Note: Sigma is irrelevant for fitting, but it needs to be some non-zero number.
#
new_peaks = utilC.initializePeaks(
new_peaks, # The new peaks.
masked_image, # Use SNR as height, corrected later for fitting.
zero_array, # Zero for now, corrected later for fitting.
self.sigma, # The starting sigma value.
i) # Index of the z-plane, the actual z value is added later.
# Add to all peaks accumulator.
if all_new_peaks is None:
all_new_peaks = new_peaks
else:
all_new_peaks = numpy.append(all_new_peaks, new_peaks, axis=0)
#
# If there are multiple peaks with similar x,y but in different
# planes, use the one with the highest normalized value.
#
# FIXME: If the planes are far enough apart in z we should allow
# peaks with a similar x,y.
#
if (len(self.mfilters) > 1):
all_new_peaks = utilC.removeClosePeaks(all_new_peaks,
self.find_max_radius,
self.find_max_radius)
#
# Split into a peak/localization for each image plane.
#
# Note that the peaks array is expected to have all the peaks
# for the first plane first, then all the peaks for the second
# plane, etc.. With the same number of peaks per plane.
#
# This is how you would access the same peak in different channels:
#
# ch0) all_new_peaks[0 * n_peaks + peak_number]
# ch1) all_new_peaks[1 * n_peaks + peak_number]
# etc..
#
all_new_peaks = self.mpu.splitPeaks(all_new_peaks)
#
# Remove peaks with members in one or more channels that are
# outside of the image.
#
all_new_peaks = self.mpu.filterPeaks(
all_new_peaks, self.mpu.badPeakMask(all_new_peaks))
# Initialize background values.
mpUtilC.initializeBackground(all_new_peaks, self.backgrounds)
# Need to do this before z initialization as we are using the
# z value to index into the foregrounds array.
mpUtilC.initializeHeight(all_new_peaks, foregrounds,
self.height_rescale)
# Replace z index with the z value used as the initial guess
# for fitting.
mpUtilC.initializeZ(all_new_peaks, self.z_values)
if False:
pp = 3
if (all_new_peaks.shape[0] > pp):
for i in range(pp):
print("Peak", i)
self.mpu.prettyPrintPeak(all_new_peaks, i)
print("")
return all_new_peaks