def plot_blob_grid(self, window=11, **kwargs):
"""Display a grid of blobs"""
return display_grid(
{
i: self.data[slice_maker((y, x), window)]
for i, (y, x, s, r) in enumerate(self.blobs)
}, **kwargs)
def fit_blobs(self, width=10, **kwargs):
"""Fit blobs to Gaussian funtion."""
# If we don't have blobs, find them.
if self._blobs is None:
self.find_blobs()
# set up the container for our fits
peakfits = []
# iterate through blobs
for y, x, s, r in self.blobs:
# make a fit window
win = slice_maker(int(y), int(x), width)
# make a fit object with a subset of the data
mypeak = Gauss2D(self.data[win])
# optimize params
mypeak.optimize_params(**kwargs)
fit_coefs = mypeak.all_params_dict()
# need to place the fit coefs in the right place
fit_coefs['y0'] += win[0].start
fit_coefs['x0'] += win[1].start
# Calc SNR for each peak
fit_coefs['noise'] = mypeak.noise
fit_coefs['SNR'] = fit_coefs['amp'] / fit_coefs['noise']
# append to peakfits
peakfits.append(fit_coefs)
# construct DataFrame
peakfits_df = pd.DataFrame(peakfits)
# internalize DataFrame
self._fits = peakfits_df
# Return it to user
return peakfits_df
def plot_fits(self, window_width, residuals=False, **kwargs):
"""Generate a plot of the found peaks, individually"""
# check if the fitting has been performed yet, warn user if it hasn't
if self._fits is None:
raise RuntimeError('Blobs have not been fit yet, cannot show fits')
else:
fits = self._fits
# pull the labels and the data from the object
data = self.data
# find objects from labelled data
my_objects = [
slice_maker(center, window_width)
for center in fits[["y0", "x0"]].values
]
# generate a nice layout
nb_labels = len(my_objects)
nrows = int(np.ceil(np.sqrt(nb_labels)))
ncols = int(np.ceil(nb_labels / nrows))
fig, axes = plt.subplots(nrows, ncols, figsize=(3 * ncols, 3 * nrows))
for n, (obj, ax) in enumerate(zip(my_objects, axes.ravel())):
ex = (obj[1].start, obj[1].stop - 1, obj[0].stop - 1, obj[0].start)
ax.set_title(n)
ax.grid("off")
# generate the model fit to display, from parameters.
dict_params = dict(fits.loc[n].dropna())
# recenter
dict_params['x0'] -= obj[1].start
dict_params['y0'] -= obj[0].start
params = Gauss2D.dict_to_params(dict_params)
fake_data = Gauss2D.gen_model(data[obj], *params)
if residuals:
ax.matshow(data[obj] - fake_data, extent=ex, **kwargs)
else:
ax.matshow(data[obj], extent=ex, **kwargs)
ax.contour(fake_data, extent=ex, colors='w', origin='image')
# # Remove empty plots
for ax in axes.ravel():
if not (len(ax.images)) and not (len(ax.lines)):
fig.delaxes(ax)
fig.tight_layout()
# return the fig and axes handles to user for later manipulation.
return fig, axes
def pattern_params(my_pat, size=2):
"""Find stuff"""
# REAL FFT!
# note the limited shifting, we don't want to shift the last axis
my_pat_fft = fftshift(rfftn(ifftshift(my_pat)),
axes=tuple(range(my_pat.ndim))[:-1])
my_abs_pat_fft = abs(my_pat_fft)
# find dc loc, center of FFT after shifting
sizeky, sizekx = my_abs_pat_fft.shape
# remember we didn't shift the last axis!
dc_loc = (sizeky // 2, 0)
# mask data and find next biggest peak
dc_power = my_abs_pat_fft[dc_loc]
my_abs_pat_fft[dc_loc] = 0
max_loc = np.unravel_index(my_abs_pat_fft.argmax(), my_abs_pat_fft.shape)
# pull the 3x3 region around the peak and fit
max_shift = localize_peak(my_abs_pat_fft[slice_maker(max_loc, 3)])
# calculate precise peak relative to dc
peak = np.array(max_loc) + np.array(max_shift) - np.array(dc_loc)
# correct location based on initial data shape
peak_corr = peak / np.array(my_pat.shape)
# calc angle
preciseangle = np.arctan2(*peak_corr)
# calc period
precise_period = 1 / norm(peak_corr)
# calc phase
phase = np.angle(my_pat_fft[max_loc[0], max_loc[1]])
# calc modulation depth
numerator = abs(my_pat_fft[slice_maker(max_loc, size)].sum())
mod = numerator / dc_power
return {"period": precise_period,
"angle": preciseangle,
"phase": phase,
"fft": my_pat_fft,
"mod": mod,
"max_loc": max_loc}
def fit_blobs(self, width=10, poly_coefs_df=None, **kwargs):
"""Fit blobs to Gaussian funtion.
Parameters
----------
width : int
The size of the fitting window in pixels
**kwargs is for Gauss2D optimize_params
"""
# If we don't have blobs, find them.
if self._blobs is None:
self.find_blobs()
@dask.delayed
def fitfunc(win, sub_data):
# fit the data as we should
if poly_coefs_df is None:
mypeak = Gauss2D(sub_data)
else:
mypeak = Gauss2Dz(sub_data, poly_coefs_df)
# optimize params
mypeak.optimize_params(**kwargs)
fit_coefs = mypeak.all_params_dict()
# need to place the fit coefs in the right place
fit_coefs['y0'] += win[0].start
fit_coefs['x0'] += win[1].start
# Calc SNR for each peak
fit_coefs['noise'] = mypeak.noise
fit_coefs['SNR'] = fit_coefs['amp'] / fit_coefs['noise']
return fit_coefs
# iterate through blobs
windows = [
slice_maker((int(y), int(x)), width) for y, x, s, r in self.blobs
]
data_to_fit = [self.data[win] for win in tqdm.tqdm_notebook(windows)]
peakfits = dask.delayed([
fitfunc(win, sub_data)
for win, sub_data in zip(windows, data_to_fit)
])
# construct DataFrame
with ProgressBar():
peakfits_df = pd.DataFrame(peakfits.compute(scheduler="processes"))
# internalize DataFrame
self._fits = peakfits_df
# Return it to user
return peakfits_df
def prep_data_for_PR(data, xysize=None, multiplier=1.5):
"""A utility to prepare data for phase retrieval
Will pad or crop to xysize and remove mode times multiplier
Parameters
----------
data : ndarray
The PSF data to prepare for phase retrieval
xysize : int
Size to pad or crop `data` to along the y, x dimensions
multiplier : float
The amount to by which to multiply the mode before subtracting
Returns
-------
prepped_data : ndarray
The data that has been prepped for phase retrieval.
"""
# pull shape
nz, ny, nx = data.shape
# remove background
data_without_bg = remove_bg(data, multiplier)
# figure out padding or cropping
if xysize is None:
xysize = max(ny, nx)
if xysize == ny == nx:
pad_data = data_without_bg
elif xysize >= max(ny, nx):
pad_data = fft_pad(data_without_bg, (nz, xysize, xysize),
mode="constant")
else:
# if need to crop, crop and center and return
my_slice = slice_maker(((ny + 1) // 2, (nx + 1) // 2), xysize)
return center_data(data_without_bg)[[Ellipsis] + my_slice]
# return centered data
return center_data(pad_data)
def _fitPeaks_sim(fitwidth, blob, stack, **kwargs):
"""
A sub function that can be dispatched to multiple cores for processing
This function is specific to analyzing SIM data and is designed to fit
substacks _without_ moving the fit window (i.e. it is assumed that
drift is minimal).
Parameters
----------
fitwidth : int
size of fitting window
blob : list [int]
a blob as returned by the find peak function
Returns
-------
df : DataFrame
A pandas DataFrame that contains all the fit parameters for a full
stack.
"""
# fix stack
if stack is None:
# if stack is None we know we've been decorated
stack = _fitPeaks_sim.stack
# pull parameters from the blob
y, x, w, amp = blob
# generate a slice
myslice = slice_maker(y, x, fitwidth)
# save the upper left coordinates for later use
ystart = myslice[0].start
xstart = myslice[1].start
# insert the equivalent of `:` at the beginning
myslice.insert(0, slice(None, None, None))
# pull the substack
substack = stack[myslice]
# fit the max projection for a good initial guess
max_z = Gauss2D(substack.max(0))
max_z.optimize_params(**kwargs)
# save the initial guess for later use
guess_params = max_z.opt_params
# check to see if initial fit was successful, if so proceed
if np.isfinite(guess_params).all():
def get_params(myslice):
"""
A helper function for the list comprehension below
Takes a slice and fits a gaussian to it, makes sure to update
fit window coordinates to full ROI coordinates
"""
# set up the fit object
fit = Gauss2D(myslice)
# do the fit, using the guess_parameters
fit.optimize_params(guess_params=guess_params, **kwargs)
# get the optimized parameters as a dict
opt = fit.all_params_dict()
# update coordinates
opt['x0'] += xstart
opt['y0'] += ystart
# add an estimate of the noise
opt['noise'] = (myslice - fit.fit_model).std()
# return updated coordinates
return opt
# prep our container
peakfits = [get_params(myslice) for myslice in substack]
# turn everything into a data frame for easy manipulation.
peakfits_df = pd.DataFrame(peakfits)
# convert sigmas to positive values
peakfits_df[['sigma_x', 'sigma_y']] =\
abs(peakfits_df[['sigma_x', 'sigma_y']])
peakfits_df.index.name = 'slice'
return peakfits_df
else:
# initial fit failed, return None
return None
def _fitPeaks_psf(fitwidth, blob, stack, **kwargs):
"""Fitting subfucntion for PSFStackAnalyzer"""
# check if we're being dispatched from the multiprocessing pool
if stack is None:
stack = _fitPeaks_psf.stack
# unpack peak variables
y, x, w, amp = blob
# make the slice around the blob
myslice = slice_maker(y, x, fitwidth)
# find the start
ystart = myslice[0].start
xstart = myslice[1].start
# insert the equivalent of `:` at the beginning
myslice.insert(0, slice(None, None, None))
# make the substack
substack = stack[myslice]
# we could do median filtering on the substack before attempting to
# find the max slice!
# this could still get messed up by salt and pepper noise.
# my_max = np.unravel_index(substack.argmax(), substack.shape)
# use the sum of each z-slice
my_max = substack.sum((1, 2)).argmax()
# now change my slice to be that zslice
myslice[0] = my_max
substack = stack[myslice]
# prep our container
peakfits = []
# initial fit
max_z = Gauss2D(substack)
max_z.optimize_params(**kwargs)
if np.isfinite(max_z.opt_params).all():
# recenter the coordinates and add a slice variable
opt_params = max_z.all_params_dict()
opt_params['slice'] = my_max
opt_params['x0'] += xstart
opt_params['y0'] += ystart
# append to our list
peakfits.append(opt_params.copy())
# pop the slice parameters
opt_params.pop('slice')
forwardrange = range(my_max + 1, stack.shape[0])
backwardrange = reversed(range(0, my_max))
peakfits += fitPeak(
stack, forwardrange, fitwidth, opt_params.copy(), quiet=True)
peakfits += fitPeak(
stack, backwardrange, fitwidth, opt_params.copy(), quiet=True)
# turn everything into a data frame for easy manipulation.
peakfits_df = pd.DataFrame(peakfits)
# convert sigmas to positive values
peakfits_df[['sigma_x', 'sigma_y']] =\
abs(peakfits_df[['sigma_x', 'sigma_y']])
return peakfits_df.set_index('slice').sort_index()
else:
print('blob {} is unfittable'.format(blob))
return None
def fitPeak(stack, slices, width, startingfit, **kwargs):
"""
Method to fit a peak through the stack.
The method will track the peak through the stack, assuming that moves
are relatively small from one slice to the next
Parameters
----------
slices : iterator
an iterator which dictates which slices to fit, should yeild
integers only
width : integer
width of fitting window
startingfit : dict
fit coefficients
Returns
-------
list : list of dicts
A list of dictionaries containing the best fits. Easy to turn into
a DataFrame
"""
# set up our variable to return
toreturn = []
# grab the starting fit parameters
popt_d = startingfit.copy()
y0 = int(round(popt_d['y0']))
x0 = int(round(popt_d['x0']))
if len(popt_d) == 6 * 2:
modeltype = 'norot'
elif len(popt_d) == 5 * 2:
modeltype = 'sym'
elif len(popt_d) == 7 * 2:
modeltype = 'full'
else:
raise ValueError("Dictionary is too big {}".format(popt_d))
for s in slices:
# make the slice
try:
myslice = slice_maker(y0, x0, width)
except RuntimeError as e:
print('Fit window moved to edge of ROI')
break
else:
# pull the starting values from it
ystart = myslice[0].start
xstart = myslice[1].start
# insert the z-slice number
myslice.insert(0, s)
# set up the fit and perform it using last best params
sub_stack = stack[myslice]
fit = Gauss2D(sub_stack)
# move our guess coefs back into the window
popt_d['x0'] -= xstart
popt_d['y0'] -= ystart
# leave this in for now for easier debugging in future.
try:
fit.optimize_params(popt_d, **kwargs)
except TypeError as e:
print(repr(myslice))
raise e
# if there was an error performing the fit, try again without
# a guess
if fit.error:
fit.optimize_params(modeltype=modeltype, **kwargs)
# if there's not an error update center of fitting window and
# move on to the next fit
if not fit.error:
popt_d = fit.all_params_dict()
popt_d['x0'] += xstart
popt_d['y0'] += ystart
popt_d['slice'] = s
# calculate the apparent noise as the standard deviation
# of what's the residuals of the fit
popt_d['noise'] = (sub_stack - fit.fit_model).std()
toreturn.append(popt_d.copy())
y0 = int(round(popt_d['y0']))
x0 = int(round(popt_d['x0']))
else:
# if the fit fails, make sure to _not_ update positions.
bad_fit = fit.all_params_dict()
bad_fit['slice'] = s
# noise of a failed fit is not really useful
popt_d['noise'] = np.nan
toreturn.append(bad_fit.copy())
return toreturn