def denoised(self,
noise_level,
noise_size,
smoothing_size=None,
threshold=None):
image = self.noisy_image(noise_level)
return bandpass(image, noise_size, smoothing_size, threshold)
def preprocess(raw_image, noise_size=None, smoothing_size=None, threshold=None):
if noise_size is not None:
image = bandpass(raw_image, noise_size, smoothing_size, threshold)
# Coerce the image into integer type. Rescale to fill dynamic range.
if np.issubdtype(raw_image.dtype, np.integer):
dtype = raw_image.dtype
else:
dtype = np.uint8
scale_factor = scalefactor_to_gamut(image, dtype)
image = scale_to_gamut(image, dtype, scale_factor)
elif np.issubdtype(raw_image.dtype, np.integer):
# Do nothing when image is already of integer type
scale_factor = 1.
image = raw_image
else:
# Coerce the image into uint8 type. Rescale to fill dynamic range.
scale_factor = scalefactor_to_gamut(raw_image, np.uint8)
image = scale_to_gamut(raw_image, np.uint8, scale_factor)
try:
frame_no = raw_image.frame_no
except AttributeError:
frame_no = None
return Frame(image, frame_no,
metadata=dict(scale_factor=scale_factor))
from __future__ import division
import nose
from numpy.testing.utils import assert_allclose
from trackpy.preprocessing import (bandpass, legacy_bandpass,
legacy_bandpass_fftw)
from trackpy.artificial import gen_nonoverlapping_locations, draw_spots
from trackpy.tests.common import StrictTestCase
pos = gen_nonoverlapping_locations((512, 512), 200, 20)
frame = draw_spots((512, 512), pos, 20, noise_level=100)
margin = 11
bp_scipy = bandpass(frame, 3, 11)[margin:-margin, margin:-margin]
def test_legacy_bandpass():
lbp_numpy = legacy_bandpass(frame, 3, 11)[margin:-margin, margin:-margin]
assert_allclose(lbp_numpy, bp_scipy, atol=1.1)
def test_legacy_bandpass_fftw():
try:
import pyfftw
except ImportError:
raise nose.SkipTest("pyfftw not installed. Skipping.")
lbp_fftw = legacy_bandpass_fftw(frame, 3, 11)[margin:-margin, margin:-margin]
assert_allclose(lbp_fftw, bp_scipy, atol=1.1)
if __name__ == '__main__':
import nose
nose.runmodule(argv=[__file__, '-vvs', '-x', '--pdb', '--pdb-failure'],
def setUp(self):
pos = gen_nonoverlapping_locations((512, 512), 200, 20)
self.frame = draw_spots((512, 512), pos, 20, noise_level=100)
self.margin = 11
self.bp_scipy = bandpass(self.frame, 2, 11)[self.margin:-self.margin,
self.margin:-self.margin]
def locate(raw_image, diameter, minmass=100., maxsize=None, separation=None,
noise_size=1, smoothing_size=None, threshold=1, invert=False,
percentile=64, topn=None, preprocess=True, max_iterations=10,
filter_before=True, filter_after=True,
characterize=True, engine='auto'):
"""Locate Gaussian-like blobs of a given approximate size.
Preprocess the image by performing a band pass and a threshold.
Locate all peaks of brightness, characterize the neighborhoods of the peaks
and take only those with given total brightnesss ("mass"). Finally,
refine the positions of each peak.
Parameters
----------
image : image array (any dimensions)
diameter : feature size in px
minmass : minimum integrated brightness
Default is 100, but a good value is often much higher. This is a
crucial parameter for elminating spurrious features.
maxsize : maximum radius-of-gyration of brightness, default None
separation : feature separation, in pixels
Default is the feature diameter + 1.
noise_size : width of Gaussian blurring kernel, in pixels
Default is 1.
smoothing_size : size of boxcar smoothing, in pixels
Default is the same is feature separation.
threshold : Clip bandpass result below this value.
Default 1; use 8 for 16-bit images.
invert : Set to True if features are darker than background. False by
default.
percentile : Features must have a peak brighter than pixels in this
percentile. This helps eliminate spurrious peaks.
topn : Return only the N brightest features above minmass.
If None (default), return all features above minmass.
Returns
-------
DataFrame([x, y, mass, size, ecc, signal])
where mass means total integrated brightness of the blob,
size means the radius of gyration of its Gaussian-like profile,
and ecc is its eccentricity (1 is circular).
Other Parameters
----------------
preprocess : Set to False to turn out bandpass preprocessing.
max_iterations : integer
max number of loops to refine the center of mass, default 10
filter_before : boolean
Use minmass (and maxsize, if set) to eliminate spurrious features
based on their estimated mass and size before refining position.
True by default for performance.
filter_after : boolean
Use final characterizations of mass and size to elminate spurrious
features. True by default.
characterize : boolean
Compute "extras": eccentricity, signal, ep. True by default.
engine : {'auto', 'python', 'numba'}
See Also
--------
batch : performs location on many images in batch
Notes
-----
This is an implementation of the Crocker-Grier centroid-finding algorithm.
[1]_
References
----------
.. [1] Crocker, J.C., Grier, D.G. http://dx.doi.org/10.1006/jcis.1996.0217
"""
# Validate parameters and set defaults.
if not diameter & 1:
raise ValueError("Feature diameter must be an odd number. Round up.")
if not separation:
separation = int(diameter) + 1
radius = int(diameter)//2
if smoothing_size is None:
smoothing_size = diameter
raw_image = np.squeeze(raw_image)
shape = raw_image.shape
# Check whether the image looks suspiciously like a color image.
if 3 in shape or 4 in shape:
dim = raw_image.ndim
warnings.warn("I am interpreting the image as {0}-dimensional. "
"If it is actually a {1}-dimensional color image, "
"convert it to grayscale first.".format(dim, dim-1))
if preprocess:
if invert:
# It is tempting to do this in place, but if it is called multiple
# times on the same image, chaos reigns.
max_value = np.iinfo(raw_image.dtype).max
raw_image = raw_image ^ max_value
image = bandpass(raw_image, noise_size, smoothing_size, threshold)
else:
image = raw_image.copy()
# Coerce the image into integer type. Rescale to fill dynamic range.
if np.issubdtype(raw_image.dtype, np.integer):
dtype = raw_image.dtype
else:
dtype = np.int8
image = scale_to_gamut(image, dtype)
# Set up a DataFrame for the final results.
if image.ndim < 4:
coord_columns = ['x', 'y', 'z'][:image.ndim]
else:
coord_columns = map(lambda i: 'x' + str(i), range(image.ndim))
char_columns = ['mass']
if characterize:
char_columns += ['size', 'ecc', 'signal']
columns = coord_columns + char_columns
# The 'ep' column is joined on at the end, so we need this...
if characterize:
all_columns = columns + ['ep']
else:
all_columns = columns
# Find local maxima.
coords = local_maxima(image, radius, separation, percentile)
count_maxima = coords.shape[0]
if count_maxima == 0:
return DataFrame(columns=all_columns)
# Proactively filter based on estimated mass/size before
# refining positions.
if filter_before:
approx_mass = np.empty(count_maxima) # initialize to avoid appending
for i in range(count_maxima):
approx_mass[i] = estimate_mass(image, radius, coords[i])
condition = approx_mass > minmass
if maxsize is not None:
approx_size = np.empty(count_maxima)
for i in range(count_maxima):
approx_size[i] = estimate_size(image, radius, coords[i],
approx_mass[i])
condition &= approx_size < maxsize
coords = coords[condition]
count_qualified = coords.shape[0]
if count_qualified == 0:
warnings.warn("No maxima survived mass- and size-based prefiltering.")
return DataFrame(columns=all_columns)
# Refine their locations and characterize mass, size, etc.
refined_coords = refine(raw_image, image, radius, coords, max_iterations,
engine, characterize)
# Filter again, using final ("exact") mass -- and size, if set.
MASS_COLUMN_INDEX = image.ndim
SIZE_COLUMN_INDEX = image.ndim + 1
exact_mass = refined_coords[:, MASS_COLUMN_INDEX]
if filter_after:
condition = exact_mass > minmass
if maxsize is not None:
exact_size = refined_coords[:, SIZE_COLUMN_INDEX]
condition &= exact_size < maxsize
refined_coords = refined_coords[condition]
exact_mass = exact_mass[condition] # used below by topn
count_qualified = refined_coords.shape[0]
if count_qualified == 0:
warnings.warn("No maxima survived mass- and size-based filtering.")
return DataFrame(columns=all_columns)
if topn is not None and count_qualified > topn:
if topn == 1:
# special case for high performance and correct shape
refined_coords = refined_coords[np.argmax(exact_mass)]
refined_coords = refined_coords.reshape(1, -1)
else:
refined_coords = refined_coords[np.argsort(exact_mass)][-topn:]
f = DataFrame(refined_coords, columns=columns)
# Estimate the uncertainty in position using signal (measured in refine)
# and noise (measured here below).
if characterize:
black_level, noise = uncertainty.measure_noise(
raw_image, diameter, threshold)
f['signal'] -= black_level
ep = uncertainty.static_error(f, noise, diameter, noise_size)
f = f.join(ep)
# If this is a pims Frame object, it has a frame number.
# Tag it on; this is helpful for parallelization.
if hasattr(raw_image, 'frame_no') and raw_image.frame_no is not None:
f['frame'] = raw_image.frame_no
return f
def denoised(self, noise_level, noise_size, smoothing_size=None,
threshold=None):
image = self.noisy_image(noise_level)
return bandpass(image, noise_size, smoothing_size, threshold)
def locate(raw_image,
diameter,
minmass=100.,
maxsize=None,
separation=None,
noise_size=1,
smoothing_size=None,
threshold=None,
invert=False,
percentile=64,
topn=None,
preprocess=True,
max_iterations=10,
filter_before=True,
filter_after=True,
characterize=True,
engine='auto'):
"""Locate Gaussian-like blobs of a given approximate size.
Preprocess the image by performing a band pass and a threshold.
Locate all peaks of brightness, characterize the neighborhoods of the peaks
and take only those with given total brightnesss ("mass"). Finally,
refine the positions of each peak.
Parameters
----------
image : image array (any dimensions)
diameter : feature size in px
minmass : minimum integrated brightness
Default is 100, but a good value is often much higher. This is a
crucial parameter for elminating spurrious features.
maxsize : maximum radius-of-gyration of brightness, default None
separation : feature separation, in pixels
Default is the feature diameter + 1.
noise_size : width of Gaussian blurring kernel, in pixels
Default is 1.
smoothing_size : size of boxcar smoothing, in pixels
Default is the same is feature separation.
threshold : Clip bandpass result below this value.
Default None, passed through to bandpass.
invert : Set to True if features are darker than background. False by
default.
percentile : Features must have a peak brighter than pixels in this
percentile. This helps eliminate spurrious peaks.
topn : Return only the N brightest features above minmass.
If None (default), return all features above minmass.
Returns
-------
DataFrame([x, y, mass, size, ecc, signal])
where mass means total integrated brightness of the blob,
size means the radius of gyration of its Gaussian-like profile,
and ecc is its eccentricity (1 is circular).
Other Parameters
----------------
preprocess : Set to False to turn out bandpass preprocessing.
max_iterations : integer
max number of loops to refine the center of mass, default 10
filter_before : boolean
Use minmass (and maxsize, if set) to eliminate spurrious features
based on their estimated mass and size before refining position.
True by default for performance.
filter_after : boolean
Use final characterizations of mass and size to elminate spurrious
features. True by default.
characterize : boolean
Compute "extras": eccentricity, signal, ep. True by default.
engine : {'auto', 'python', 'numba'}
See Also
--------
batch : performs location on many images in batch
Notes
-----
This is an implementation of the Crocker-Grier centroid-finding algorithm.
[1]_
References
----------
.. [1] Crocker, J.C., Grier, D.G. http://dx.doi.org/10.1006/jcis.1996.0217
"""
# Validate parameters and set defaults.
if not diameter & 1:
raise ValueError("Feature diameter must be an odd number. Round up.")
if not separation:
separation = int(diameter) + 1
radius = int(diameter) // 2
if smoothing_size is None:
smoothing_size = diameter
raw_image = np.squeeze(raw_image)
shape = raw_image.shape
# Check whether the image looks suspiciously like a color image.
if 3 in shape or 4 in shape:
dim = raw_image.ndim
warnings.warn("I am interpreting the image as {0}-dimensional. "
"If it is actually a {1}-dimensional color image, "
"convert it to grayscale first.".format(dim, dim - 1))
if preprocess:
if invert:
# It is tempting to do this in place, but if it is called multiple
# times on the same image, chaos reigns.
if np.issubdtype(raw_image.dtype, np.integer):
max_value = np.iinfo(raw_image.dtype).max
raw_image = raw_image ^ max_value
else:
# To avoid degrading performance, assume gamut is zero to one.
# Have you ever encountered an image of unnormalized floats?
raw_image = 1 - raw_image
image = bandpass(raw_image, noise_size, smoothing_size, threshold)
else:
image = raw_image.copy()
# Coerce the image into integer type. Rescale to fill dynamic range.
if np.issubdtype(raw_image.dtype, np.integer):
dtype = raw_image.dtype
else:
dtype = np.int8
image = scale_to_gamut(image, dtype)
# Set up a DataFrame for the final results.
if image.ndim < 4:
coord_columns = ['x', 'y', 'z'][:image.ndim]
else:
coord_columns = map(lambda i: 'x' + str(i), range(image.ndim))
char_columns = ['mass']
if characterize:
char_columns += ['size', 'ecc', 'signal']
columns = coord_columns + char_columns
# The 'ep' column is joined on at the end, so we need this...
if characterize:
all_columns = columns + ['ep']
else:
all_columns = columns
# Find local maxima.
coords = local_maxima(image, radius, separation, percentile)
count_maxima = coords.shape[0]
if count_maxima == 0:
return DataFrame(columns=all_columns)
# Proactively filter based on estimated mass/size before
# refining positions.
if filter_before:
approx_mass = np.empty(count_maxima) # initialize to avoid appending
for i in range(count_maxima):
approx_mass[i] = estimate_mass(image, radius, coords[i])
condition = approx_mass > minmass
if maxsize is not None:
approx_size = np.empty(count_maxima)
for i in range(count_maxima):
approx_size[i] = estimate_size(image, radius, coords[i],
approx_mass[i])
condition &= approx_size < maxsize
coords = coords[condition]
count_qualified = coords.shape[0]
if count_qualified == 0:
warnings.warn("No maxima survived mass- and size-based prefiltering.")
return DataFrame(columns=all_columns)
# Refine their locations and characterize mass, size, etc.
refined_coords = refine(raw_image, image, radius, coords, max_iterations,
engine, characterize)
# Filter again, using final ("exact") mass -- and size, if set.
MASS_COLUMN_INDEX = image.ndim
SIZE_COLUMN_INDEX = image.ndim + 1
exact_mass = refined_coords[:, MASS_COLUMN_INDEX]
if filter_after:
condition = exact_mass > minmass
if maxsize is not None:
exact_size = refined_coords[:, SIZE_COLUMN_INDEX]
condition &= exact_size < maxsize
refined_coords = refined_coords[condition]
exact_mass = exact_mass[condition] # used below by topn
count_qualified = refined_coords.shape[0]
if count_qualified == 0:
warnings.warn("No maxima survived mass- and size-based filtering.")
return DataFrame(columns=all_columns)
if topn is not None and count_qualified > topn:
if topn == 1:
# special case for high performance and correct shape
refined_coords = refined_coords[np.argmax(exact_mass)]
refined_coords = refined_coords.reshape(1, -1)
else:
refined_coords = refined_coords[np.argsort(exact_mass)][-topn:]
f = DataFrame(refined_coords, columns=columns)
# Estimate the uncertainty in position using signal (measured in refine)
# and noise (measured here below).
if characterize:
black_level, noise = uncertainty.measure_noise(raw_image, diameter,
threshold)
f['signal'] -= black_level
ep = uncertainty.static_error(f, noise, diameter, noise_size)
f = f.join(ep)
# If this is a pims Frame object, it has a frame number.
# Tag it on; this is helpful for parallelization.
if hasattr(raw_image, 'frame_no') and raw_image.frame_no is not None:
f['frame'] = raw_image.frame_no
return f