def filter_bank(img, coeff_resolution):
"""
Calculates the responses of an image to M filters.
Returns 2-d array of the vectorial responses
"""
h, w = img.shape
im = np.reshape(img, (h*w, 1))
e1 = np.reshape(entropy(img, disk(coeff_resolution*5)), (h*w, 1))
e2 = np.reshape(entropy(img, disk(coeff_resolution*8)), (h*w, 1))
e3 = np.reshape(entropy(img, disk(coeff_resolution*10)), (h*w, 1))
g1 = np.reshape(gradient(img, disk(1)), (h*w, 1))
g2 = np.reshape(gradient(img, disk(coeff_resolution*3)), (h*w, 1))
g3 = np.reshape(gradient(img, disk(coeff_resolution*5)), (h*w, 1))
m1 = np.reshape(ndi.maximum_filter(256-img, size=coeff_resolution*2, mode='constant'), (h*w, 1))
m2 = np.reshape(ndi.maximum_filter(256-img, size=coeff_resolution*4, mode='constant'), (h*w, 1))
m3 = np.reshape(ndi.maximum_filter(256-img, size=coeff_resolution*7, mode='constant'), (h*w, 1))
#c = np.reshape(canny(img), (h*w, 1))
s = np.reshape(sobel(img), (h*w, 1))
return np.column_stack((im, e1, e2, e3, g1, g2, g3, m1, m2, m3, s))
def canny(image, high_threshold, low_threshold):
grad_x = ndimage.sobel(image, 0)
grad_y = ndimage.sobel(image, 1)
grad_mag = numpy.sqrt(grad_x**2+grad_y**2)
grad_angle = numpy.arctan2(grad_y, grad_x)
# next, scale the angles in the range [0, 3] and then round to quantize
quantized_angle = numpy.around(3 * (grad_angle + numpy.pi) / (numpy.pi * 2))
# Non-maximal suppression: an edge pixel is only good if its magnitude is
# greater than its neighbors normal to the edge direction. We quantize
# edge direction into four angles, so we only need to look at four
# sets of neighbors
NE = ndimage.maximum_filter(grad_mag, footprint=_NE)
W = ndimage.maximum_filter(grad_mag, footprint=_W)
NW = ndimage.maximum_filter(grad_mag, footprint=_NW)
N = ndimage.maximum_filter(grad_mag, footprint=_N)
thinned = (((grad_mag > W) & (quantized_angle == _N_d )) |
((grad_mag > N) & (quantized_angle == _W_d )) |
((grad_mag > NW) & (quantized_angle == _NE_d)) |
((grad_mag > NE) & (quantized_angle == _NW_d)) )
thinned_grad = thinned * grad_mag
# Now, hysteresis thresholding: find seeds above a high threshold, then
# expand out until we go below the low threshold
high = thinned_grad > high_threshold
low = thinned_grad > low_threshold
canny_edges = ndimage.binary_dilation(high, structure=numpy.ones((3,3)), iterations=-1, mask=low)
return grad_mag, thinned_grad, canny_edges
def test_multiple_modes():
# Test that the filters with multiple mode cababilities for different
# dimensions give the same result as applying a single mode.
arr = np.array([[1., 0., 0.],
[1., 1., 0.],
[0., 0., 0.]])
mode1 = 'reflect'
mode2 = ['reflect', 'reflect']
assert_equal(sndi.gaussian_filter(arr, 1, mode=mode1),
sndi.gaussian_filter(arr, 1, mode=mode2))
assert_equal(sndi.prewitt(arr, mode=mode1),
sndi.prewitt(arr, mode=mode2))
assert_equal(sndi.sobel(arr, mode=mode1),
sndi.sobel(arr, mode=mode2))
assert_equal(sndi.laplace(arr, mode=mode1),
sndi.laplace(arr, mode=mode2))
assert_equal(sndi.gaussian_laplace(arr, 1, mode=mode1),
sndi.gaussian_laplace(arr, 1, mode=mode2))
assert_equal(sndi.maximum_filter(arr, size=5, mode=mode1),
sndi.maximum_filter(arr, size=5, mode=mode2))
assert_equal(sndi.minimum_filter(arr, size=5, mode=mode1),
sndi.minimum_filter(arr, size=5, mode=mode2))
assert_equal(sndi.gaussian_gradient_magnitude(arr, 1, mode=mode1),
sndi.gaussian_gradient_magnitude(arr, 1, mode=mode2))
assert_equal(sndi.uniform_filter(arr, 5, mode=mode1),
sndi.uniform_filter(arr, 5, mode=mode2))
def LocalMax(self, data, kwidth, scaling, out = None):
assert len(data.shape) == 3, \
"Unsupported shape for input data: %s" % (data.shape,)
kshape = (kwidth, kwidth)
output = np.empty_like(data)
for d, o in zip(data, output):
maximum_filter(d, kshape, output = o)
output_bands = PruneArray(output, kshape, scaling)
if out != None:
out[:] = output_bands.flat
return out
return output_bands
def max_diff(self, spec, pos=False, diff_frames=None, max_bins=None):
"""
Calculates the difference of k-th frequency bin of the magnitude
spectrogram relative to the maximum over m bins (e.g. m=3: k-1, k, k+1)
of the N-th previous frame.
:param spec: the magnitude spectrogram
:param pos: only keep positive values [default=False]
:param diff_frames: calculate the difference to the N-th previous frame [default=None]
:param max_bins: number of bins the maximum is search [default=None]
Note: This method works only properly if the number of bands for the
filterbank is chosen carefully. A values of 24 (i.e. quarter-tone
resolution) usually yields good results.
"""
# import
import scipy.ndimage as sim
# init diff matrix
diff = np.zeros_like(spec)
if diff_frames is None:
diff_frames = self.diff_frames
assert diff_frames >= 1, 'number of diff_frames must be >= 1'
if max_bins is None:
max_bins = self.max_bins
assert max_bins >= 1, 'search range for the maximum filter must be >= 1'
# calculate the diff
diff[diff_frames:] = spec[diff_frames:] - sim.maximum_filter(spec, size=[1, max_bins])[0:-diff_frames]
# keep only positive values
if pos:
diff = diff * (diff > 0)
return diff
def _detect(self,im):
'''
void cvCornerHarris( const CvArr* image, CvArr* harris_responce,
int block_size, int aperture_size=3, double k=0.04 );
'''
gray = im.asOpenCVBW()
#gray = opencv.cvCreateImage( opencv.cvGetSize(cvim), 8, 1 );
corners = cv.CreateImage( cv.GetSize(gray), 32, 1 );
#opencv.cvCvtColor( cvim, gray, opencv.CV_BGR2GRAY );
cv.CornerHarris(gray,corners,self.block_size,self.aperture_size,self.k)
buffer = corners.tostring()
corners = numpy.frombuffer(buffer,numpy.float32).reshape(corners.height,corners.width).transpose()
footprint = ones((3,3))
mx = maximum_filter(corners, footprint = footprint)
local_maxima = (corners == mx) * (corners != zeros(corners.shape)) # make sure to remove completly dark points
points = nonzero(local_maxima)
del local_maxima
points = array([points[0],points[1]]).transpose()
L = []
for each in points:
L.append((corners[each[0],each[1]],each[0],each[1],None))
return L
def detect_peaks(image):
"""Detect peaks in an image using a maximum filter.
Parameters
----------
TODO
Returns
-------
TODO
"""
from scipy.ndimage import maximum_filter
from scipy.ndimage.morphology import binary_erosion
# Set up 3x3 footprint for maximum filter, can also be a different neighborhood if necessary
footprint = np.ones((3, 3))
# Apply maximum filter: All pixel in the neighborhood are set
# to the maximal value. Peaks are where image = maximum_filter(image)
local_maximum = maximum_filter(image, footprint=footprint) == image
# We have false detections, where the image is zero, we call it background.
# Create the mask of the background
zero_background = (image == 0)
# Erode background at the borders, otherwise we would miss the points in the neighborhood
eroded_background = binary_erosion(zero_background, structure=footprint, border_value=1)
# Remove the background from the local_maximum image
detected_peaks = local_maximum - eroded_background
return detected_peaks
def detect_peaks_3D(image):
"""Same functionality as detect_peaks, but works on image cubes.
Parameters
----------
TODO
Returns
-------
TODO
"""
from scipy.ndimage import maximum_filter
from scipy.ndimage.morphology import binary_erosion
# Set up 3x3 footprint for maximum filter
footprint = np.ones((3, 3, 3))
# Apply maximum filter: All pixel in the neighborhood are set
# to the maximal value. Peaks are where image = maximum_filter(image)
local_max = maximum_filter(image, footprint=footprint, mode='constant') == image
# We have false detections, where the image is zero, we call it background.
# Create the mask of the background
background = (image == 0)
# Erode background at the borders, otherwise we would miss
eroded_background = binary_erosion(background, structure=footprint, border_value=1)
# Remove the background from the local_max mask
detected_peaks = local_max - eroded_background
return detected_peaks
def extract_local_max(img_gray):
im = img_as_float(img_gray)
# image_max is the dilation of im with a 20*20 structuring element
# It is used within peak_local_max function
image_max = ndimage.maximum_filter(im, size=20, mode='constant')
# Comparison between image_max and im to find the coordinates of local maxima
coordinates = peak_local_max(im, min_distance=20)
# display results
fig, ax = plt.subplots(1, 3, figsize=(8, 3))
ax1, ax2, ax3 = ax.ravel()
ax1.imshow(im, cmap=plt.cm.gray)
ax1.axis('off')
ax1.set_title('Original')
ax2.imshow(image_max, cmap=plt.cm.gray)
ax2.axis('off')
ax2.set_title('Maximum filter')
ax3.imshow(im, cmap=plt.cm.gray)
ax3.autoscale(False)
ax3.plot(coordinates[:, 1], coordinates[:, 0], 'r.')
ax3.axis('off')
ax3.set_title('Peak local max')
fig.subplots_adjust(wspace=0.02, hspace=0.02, top=0.9,
bottom=0.02, left=0.02, right=0.98)
plt.show()
def test_multiple_modes_sequentially():
# Test that the filters with multiple mode cababilities for different
# dimensions give the same result as applying the filters with
# different modes sequentially
arr = np.array([[1., 0., 0.],
[1., 1., 0.],
[0., 0., 0.]])
modes = ['reflect', 'wrap']
expected = sndi.gaussian_filter1d(arr, 1, axis=0, mode=modes[0])
expected = sndi.gaussian_filter1d(expected, 1, axis=1, mode=modes[1])
assert_equal(expected,
sndi.gaussian_filter(arr, 1, mode=modes))
expected = sndi.uniform_filter1d(arr, 5, axis=0, mode=modes[0])
expected = sndi.uniform_filter1d(expected, 5, axis=1, mode=modes[1])
assert_equal(expected,
sndi.uniform_filter(arr, 5, mode=modes))
expected = sndi.maximum_filter1d(arr, size=5, axis=0, mode=modes[0])
expected = sndi.maximum_filter1d(expected, size=5, axis=1, mode=modes[1])
assert_equal(expected,
sndi.maximum_filter(arr, size=5, mode=modes))
expected = sndi.minimum_filter1d(arr, size=5, axis=0, mode=modes[0])
expected = sndi.minimum_filter1d(expected, size=5, axis=1, mode=modes[1])
assert_equal(expected,
sndi.minimum_filter(arr, size=5, mode=modes))
def _count_covertypes_within_window(self, lct, cover_type_list, footprint):
"""Return integer array indicating the number of different covertypes
of interest that are within the moving window (footprint)"""
m = zeros(shape=lct.shape, dtype=int32)
for cover_type in cover_type_list:
m += maximum_filter(equal(lct, cover_type), footprint=footprint)
return m
def k_means_classifier(image):
n_clusters = 8
# blur and take local maxima
blur_image = gaussian(image, sigma=8)
blur_image = ndi.maximum_filter(blur_image, size=3)
# get texture features
feats = local_binary_pattern(blur_image, P=40, R=5, method="uniform")
feats_r = feats.reshape(-1, 1)
# cluster the texture features
km = k_means(n_clusters=n_clusters, batch_size=500)
clus = km.fit(feats_r)
# copy relevant attributes
labels = clus.labels_
clusters = clus.cluster_centers_
# reshape label arrays
labels = labels.reshape(blur_image.shape[0], blur_image.shape[1])
# segment shadow
img = blur_image.ravel()
shadow_seg = img.copy()
for i in range(0, n_clusters):
# set up array of pixel indices matching cluster
mask = np.nonzero((labels.ravel() == i) == True)[0]
if len(mask) > 0:
thresh = threshold_otsu(img[mask])
shadow_seg[mask] = shadow_seg[mask] < thresh
shadow_seg = shadow_seg.reshape(*image.shape)
return shadow_seg
def adjacent_labels(labels):
m1 = nd.maximum_filter(labels, size=3)
m1[m1 == labels] = 0
m2 = nd.minimum_filter(labels, size=3)
m2[m2 == labels] = 0
m1[m2 > 0] = m2[m2 > 0]
return m1
def local_maxima(array, min_distance = 1, periodic=False,
edges_allowed=True):
"""Find all local maxima of the array, separated by at least
min_distance.
adapted from = http://old.nabble.com/Finding-local-minima-of-greater-than-a-given-depth-td18988309.html"""
array = np.asarray(array)
cval = 0
if periodic:
mode = 'wrap'
elif edges_allowed:
mode = 'nearest'
else:
mode = 'constant'
cval = array.max()+1
nbhood=ndimage.morphology.generate_binary_structure(len(array.shape),2)
maxima = array == ndimage.maximum_filter(array, footprint=nbhood, mode=mode, cval=cval)
background = (array==0)
eroded_background = ndimage.morphology.binary_erosion(
background, structure=nbhood, border_value=1)
maxima = maxima - eroded_background
maxpy, maxpx = np.where(maxima)
max_points = [(maxpy[i],maxpx[i]) for i in range(len(maxpy))]
if not type(max_points)==list:
max_points=[max_points]
return max_points
def find_corners(im, name):
coherence, _, _ = structure.orientation_field(im, 11)
pylab.imshow(im, cmap=pylab.cm.gray)
pylab.figure()
pylab.imshow(coherence)
pylab.title('coherence')
pylab.colorbar()
local_mean = nd.filters.gaussian_filter(im.astype(float), 20)
local_variance = nd.filters.gaussian_filter(im.astype(float) ** 2.0, 20) - local_mean ** 2
pylab.figure()
pylab.imshow(np.sqrt(local_variance) / local_mean, cmap=pylab.cm.gray)
pylab.title('std / mean')
pylab.colorbar()
potential_corners = coherence / np.sqrt(local_variance)
pylab.figure()
pylab.imshow(potential_corners, cmap=pylab.cm.gray)
pylab.colorbar()
# find local max with a suppression window of radius 11
pc_max = nd.minimum_filter(potential_corners, (20, 20))
corners = potential_corners == pc_max
print np.sum(corners)
corners = nd.maximum_filter(corners, (5, 5))
pylab.show()
imtmp = np.dstack((im, im, im))
imtmp[:, :, 2][corners] = 255
cv2.imshow(name, imtmp[::2, ::2])
def find_local_maxima(image, min_distance):
"""Find maxima in an image.
Finds the highest-valued points in an image, such that each point is
separted by at least min_distance.
If there are flat regions that are all at a maxima, the enter of mass of
the region is reported. Large flat regions of more than min_distance in
radius will be erroneously returned as maxima even if they are not. Further
filtering should be performed to exclude these if needed.
Returns the position of the maxima and the value at each maximum.
Parameters:
image: image of arbitrary dimensionality
min_distance: maxima found will be at least this many pixels apart
Returns:
centroids: list of centers of each maxima
values: image value at each maxima
"""
image_max = ndimage.maximum_filter(image, size=2*min_distance+1, mode='constant')
peak_mask = (image == image_max)
# NB: some maxima might be marked by multiple contiguous pixels if the image
# has "plateaus". So we need to label the mask and get the centroids
# of each of the labeled regions.
labeled_image, num_regions = ndimage.label(peak_mask)
label_indices = numpy.arange(1, num_regions+1)
centroids = ndimage.center_of_mass(peak_mask, labeled_image, label_indices)
values = ndimage.mean(image, labeled_image, label_indices)
return numpy.array(centroids), values
def find_local_maxima(self):
'''
Find local maxima in each of the detected blobs
'''
ge_labeled_data = self.ge_labeled_data
ge_data = self.ge_data
cfg = self.cfg
logger = self.logger
int_scale_factor = self.int_scale_factor
number_of_labels = self.number_of_labels
min_peak_separation = self.min_peak_separation
blobs = self.blobs
logger.info("Detecting local maxima")
for blob in blobs:
slice_x, slice_y, slice_z = blob.slice_x, blob.slice_y, blob.slice_z
label_num = blob.blob_label
roi = ge_data[slice_x, slice_y, slice_z]
write_image('roi' + str(label_num) + '.png', np.amax(roi, 0), vmin=0)
max_points = roi == ndimage.maximum_filter(roi, min_peak_separation,
mode='nearest', cval=0)
max_points[roi < int_scale_factor*cfg.fit_grains.threshold]
roi[np.logical_not(max_points)] = 0
write_image('roi' + str(label_num) + '_max.png', np.amax(roi, 0), vmin=0)
return blobs
def compute_harris_response(image, eps=1e-6):
""" compute the Harris corner detector response function
for each pixel in the image"""
# derivatives
image = ndimage.gaussian_filter(image, 1)
imx = ndimage.sobel(image, axis=0, mode='constant')
imy = ndimage.sobel(image, axis=1, mode='constant')
Wxx = ndimage.gaussian_filter(imx * imx, 1.5, mode='constant')
Wxy = ndimage.gaussian_filter(imx * imy, 1.5, mode='constant')
Wyy = ndimage.gaussian_filter(imy * imy, 1.5, mode='constant')
# determinant and trace
Wdet = Wxx * Wyy - Wxy ** 2
Wtr = Wxx + Wyy
harris = Wdet / (Wtr + eps)
# Non maximum filter of size 3
harris_max = ndimage.maximum_filter(harris, 3, mode='constant')
harris *= harris == harris_max
# Remove the image corners
harris[:3] = 0
harris[-3:] = 0
harris[:, :3] = 0
harris[:, -3:] = 0
return harris
def nonmax_supress(area_img, angles):
_NE_d = 0
_W_d = 1
_NW_d = 2
_N_d = 3
quantized_angle = np.around(angles) % 4
NE = ndimage.maximum_filter(area_img, footprint=_NE)
W = ndimage.maximum_filter(area_img, footprint=_W)
NW = ndimage.maximum_filter(area_img, footprint=_NW)
N = ndimage.maximum_filter(area_img, footprint=_N)
thinned = (((area_img >= W) & (quantized_angle == _N_d )) |
((area_img >= N) & (quantized_angle == _W_d )) |
((area_img >= NW) & (quantized_angle == _NE_d)) |
((area_img >= NE) & (quantized_angle == _NW_d)) )
thinned_grad = thinned * area_img
return thinned_grad
def dom_get(wseries, tpoint, scales):
values = (np.abs(wseries)) * (np.abs(wseries))
values = values / (scales * scales)
maxoutt = (values == ndimage.maximum_filter(values, 15, mode='reflect'))
try:
x = np.where(
(maxoutt == 1)) # & (np.abs(parr) > scales ** .5)# ((wl >= np.percentile(wl[wl >= 0.5], 90)) &
except IndexError:
return False
try:
ind = (x[0])[0]
except IndexError:
return False
scal = scales[ind]
wavelet_pos_neg = np.real(wseries)[ind]
if (wavelet_pos_neg < 0) : #| (tpoint < -1.)
scal = scal * -1
# if values[ind] < 0.02:
# scal = np.nan
return scal
def non_maximal_edge_suppresion(mag, orient, minEdgeRadius=20, maxEdgeRadius=None):
"""
Non Maximal suppression of gradient magnitude and orientation.
"""
t0 = time.time()
## bin orientations into 4 discrete directions
abin = ((orient + math.pi) * 4 / math.pi + 0.5).astype('int') % 4
radialsq, angles = getRadialAndAngles(mag.shape)
### create circular mask
if maxEdgeRadius is None:
maxEdgeRadiusSq = radialsq[mag.shape[0]/2,mag.shape[0]/10]
else:
maxEdgeRadiusSq = maxEdgeRadius**2
outermask = numpy.where(radialsq > maxEdgeRadiusSq, False, True)
## probably a bad idea here
innermask = numpy.where(radialsq < minEdgeRadius**2, False, True)
### create directional filters to go with offsets
horz = numpy.where(numpy.abs(angles) < 3*math.pi/4., numpy.abs(angles), 0)
horz = numpy.where(horz > math.pi/4., True, False)
vert = -horz
upright = numpy.where(angles < math.pi/2, False, True)
upleft = numpy.flipud(upright)
upleft = numpy.fliplr(upleft)
upright = numpy.logical_or(upright, upleft)
upleft = -upright
# for rotational edges
filters = [horz, upleft, vert, upright]
# for radial edges
#filters = [vert, upright, horz, upleft]
offsets = ((1,0), (1,1), (0,1), (-1,1))
edge_map = numpy.zeros(mag.shape, dtype='bool')
for a in range(4):
di, dj = offsets[a]
footprint = numpy.zeros((3,3), dtype="int")
footprint[1,1] = 0
footprint[1+di,1+dj] = 1
footprint[1-di,1-dj] = 1
## get adjacent maximums
maxfilt = ndimage.maximum_filter(mag, footprint=footprint)
## select points larger than adjacent maximums
newedge_map = numpy.where(mag>maxfilt, True, False)
## filter by edge orientation
newedge_map = numpy.where(abin==a, newedge_map, False)
## filter by location
newedge_map = numpy.where(filters[a], newedge_map, False)
## add to main map
edge_map = numpy.where(newedge_map, True, edge_map)
## remove corner edges
edge_map = numpy.where(outermask, edge_map, False)
edge_map = numpy.where(innermask, edge_map, False)
#print time.time() - t0
return edge_map
def on_image_image(self, image_id):
#def on_image_image(self, request, image_id):
result = self.work.get_image(image_id).copy()
seg = self.work.get_segmentation(image_id)
border = ndimage.maximum_filter(seg.labels,size=(3,3)) != ndimage.minimum_filter(seg.labels,size=(3,3))
result[border] = 0.0
return image_response(result)
def apply(array, **kwargs):
"""
Apply a set of standard filter to array data:
Call: apply(array-data, <list of key=value arguments>)
The list of key-value define the filtering to be done and should be given in
the order to be process. Possible key-value are:
* smooth: gaussian filtering, value is the sigma parameter (scalar or tuple)
* uniform: uniform filtering (2)
* max: maximum filtering (1)
* min: minimum filtering (1)
* median: median filtering (1)
* dilate: grey dilatation (1)
* erode: grey erosion (1)
* close: grey closing (1)
* open: grey opening (1)
* linear_map: call linear_map(), value is the tuple (min,max) (3)
* normalize: call normalize(), value is the method (3)
* adaptive: call adaptive(), value is the sigma (3)
* adaptive_: call adaptive(), with uniform kernel (3)
The filtering is done using standard scipy.ndimage functions.
(1) The value given (to the key) is the width of the the filter:
the distance from the center pixel (the size of the filter is thus 2*value+1)
The neighborhood is an (approximated) boolean circle (up to discretization)
(2) Same as (*) but the neighborhood is a complete square
(3) See doc of respective function
"""
for key in kwargs:
value = kwargs[key]
if key not in ('smooth','uniform'):
fp = _kernel.distance(array.ndim*(2*value+1,))<=value # circular filter
if key=='smooth' : array = _nd.gaussian_filter(array, sigma=value)
elif key=='uniform': array = _nd.uniform_filter( array, size=2*value+1)
elif key=='max' : array = _nd.maximum_filter( array, footprint=fp)
elif key=='min' : array = _nd.minimum_filter( array, footprint=fp)
elif key=='median' : array = _nd.median_filter( array, footprint=fp)
elif key=='dilate' : array = _nd.grey_dilation( array, footprint=fp)
elif key=='erode' : array = _nd.grey_erosion( array, footprint=fp)
elif key=='open' : array = _nd.grey_opening( array, footprint=fp)
elif key=='close' : array = _nd.grey_closing( array, footprint=fp)
elif key=='linear_map': array = linear_map(array, min=value[0], max=value[1])
elif key=='normalize' : array = normalize( array, method = value)
elif key=='adaptive' : array = adaptive( array, sigma = value, kernel='gaussian')
elif key=='adaptive_' : array = adaptive( array, sigma = value, kernel='uniform')
else:
print '\033[031mUnrecognized filter :', key
return array
def LocalMax(self, data, kwidth, scaling, out = None):
"""Convolve maps with local 2-D max filter.
data -- (3-D) array of input data
kwidth -- (positive int) kernel width
scaling -- (positive int) subsampling factor
out -- (2-D) array in which to store result
"""
assert len(data.shape) == 3, \
"Unsupported shape for input data: %s" % (data.shape,)
kshape = (kwidth, kwidth)
output = np.empty_like(data)
for d, o in zip(data, output):
maximum_filter(d, kshape, output = o)
output_bands = PruneArray(output, kshape, scaling)
if out != None:
out[:] = output_bands.flat
return out
return output_bands
def select_region_slices(sci_data, badpix_mask, box_size=256, num_boxes=10):
"""
Find the optimal regions for calculating the noise autocorrelation (areas
with the fewest objects/least signal)
:param sci_data: Science image data array
:param badpix_mask: Boolean array that is True for bad pixels
:param box_size: Size of the (square) boxes to select
:param num_boxes: Number of boxes to select. If insufficient good pixels can
be found, will return as many boxes as possible
:return: List of 2D slices, tuples of (slice_y, slice_x)
"""
# TODO: For large images this is pretty slow, due to 3 full-size filters
img_boxcar = ndimg.uniform_filter(sci_data, size=box_size)
# Smooth over mask with min filter, to ignore small areas of bad pixels
# One tenth of box size in each dimension means ignoring bad pixel regions
# comprising <1% of total box pixels
smooth_size = box_size // 10
badpix_mask = ndimg.minimum_filter(badpix_mask, size=smooth_size,
mode='constant', cval=False)
# Expand zone of avoidance of bad pixels, so we don't pick boxes that
# contain them. mode=constant, cval=True means treat all borders as
# if they were masked-out pixels
badpix_mask = ndimg.maximum_filter(badpix_mask, size=smooth_size + box_size,
mode='constant', cval=True)
img_boxcar = np.ma.array(img_boxcar, mask=badpix_mask)
box_slices = []
for box in range(num_boxes):
# Find the location of the minimum value of the boxcar image, excluding
# masked areas. This will be a pixel with few nearby sources within one
# box width
min_loc = img_boxcar.argmin()
min_loc = np.unravel_index(min_loc, img_boxcar.shape)
lower_left = tuple(int(x - box_size / 2) for x in min_loc)
# Negative values of lower_left mean argmin ran out of unmasked pixels
if lower_left[0] < 0 or lower_left[1] < 0:
warn('Ran out of good pixels when placing RMS calculation regions '
'for file {}. Only {:d} boxes selected.'.format(sci_data, box))
break
min_slice = tuple(slice(x, x + box_size) for x in lower_left)
box_slices += [min_slice]
# Zone of avoidance (for center) is twice as big, since we are picking
# box centers. Use clip to ensure avoidance slice stays within array
# bounds
lower_left = tuple(int(x - box_size) for x in min_loc)
avoid_slice = tuple(slice(np.clip(x, 0, extent),
np.clip(x + 2 * box_size, 0, extent))
for x, extent in zip(lower_left, img_boxcar.shape))
# Add this box to the mask
img_boxcar[avoid_slice] = np.ma.masked
return box_slices
def _detect(self,image):
# Asssumes a two dimensional array
A = None
if isinstance(image,Image):
A = image.asMatrix2D()
elif isinstance(image,array) and len(image.shape)==2:
A = image
else:
raise TypeError("ERROR Unknown Type (%s) - Only arrays and pyvision images supported."%type(image))
filter = array(self.filter)
assert len(filter.shape) == 2
#feature window calculation
del_A_1 = conv2(A,filter)
del_A_2 = conv2(A,filter.transpose())
del_A_1_1 = del_A_1 * del_A_1
matrix_1_1 = gaussian_filter(del_A_1_1, self.sigma)
del del_A_1_1
del_A_2_2 = del_A_2 * del_A_2
matrix_2_2 = gaussian_filter(del_A_2_2, self.sigma)
del del_A_2_2
del_A_1_2 = del_A_1 * del_A_2
matrix_1_2 = gaussian_filter(del_A_1_2, self.sigma)
del del_A_1_2
del del_A_1,del_A_2
dM = matrix_1_1*matrix_2_2 - matrix_1_2*matrix_1_2
tM = matrix_1_1+matrix_2_2
del matrix_1_1 , matrix_1_2, matrix_2_2
R = dM-self.k*pow(tM,2)
footprint = ones((self.radius,self.radius))
mx = maximum_filter(R, footprint = footprint)
local_maxima = (R == mx) * (R != zeros(R.shape)) # make sure to remove completly dark points
del mx
points = nonzero(local_maxima)
del local_maxima
points = array([points[0],points[1]]).transpose()
L = []
for each in points:
L.append((R[each[0],each[1]],each[0],each[1],None))
del R
return L
def geodesic_dilation(marker,mask):
""" Perform geodesic dilation based on algorithm
on p. 185 of Soille (2002).
"""
# Compute the size for the filter based on the shape
# of the marker array
mshape = len(marker.shape)
msize = (3,) * mshape
marker_dilation = ndimage.maximum_filter(marker, size=msize)
return np.where(mask <= marker_dilation, mask, marker_dilation)
def detect_peaks(img, include_plateaus=True):
"""
Takes an image and detect the peaks using the local maximum filter.
Returns a boolean mask of the peaks (i.e. 1 when the pixel's value is the
neighborhood maximum, 0 otherwise)
Code taken from http://stackoverflow.com/a/3689710/932593
"""
# define an 8-connected neighborhood
neighborhood = ndimage.generate_binary_structure(2, 2)
if include_plateaus:
#apply the local maximum filter; all pixel of maximal value
#in their neighborhood are set to 1
img_max = ndimage.maximum_filter(img, footprint=neighborhood)
local_max = (img == img_max)
#local_max is a mask that contains the peaks we are
#looking for, but also the background.
#In order to isolate the peaks we must remove the background from the mask.
#we create the mask of the background
background = (img == 0)
#a little technicality: we must erode the background in order to
#successfully subtract it form local_max, otherwise a line will
#appear along the background border (artifact of the local maximum filter)
eroded_background = ndimage.binary_erosion(background,
structure=neighborhood,
border_value=1)
#we obtain the final mask, containing only peaks,
#by removing the background from the local_max mask
detected_peaks = local_max - eroded_background
else:
neighborhood[1, 1] = 0
img_max = ndimage.maximum_filter(img, footprint=neighborhood)
detected_peaks = (img > img_max)
return detected_peaks
def file_loop(f):
print('Doing file: ' + f)
dic = xr.open_dataset(f)
res = []
outt = dic['t_lag0'].values
outp = dic['p'].values
for nb in range(5):
boole = np.isnan(outp)
outp[boole] = -1000
gg = np.gradient(outp)
outp[boole] = np.nan
outp[abs(gg[1]) > 300] = np.nan
outp[abs(gg[0]) > 300] = np.nan
gradi = np.gradient(outt)
grad = gradi[1]
maxoutt = (outt == ndimage.minimum_filter(outt, 20, mode='constant', cval=np.amin(outt) - 1))
maxoutt = maxoutt.astype(int)
yt, xt = np.where((maxoutt == 1) & (outt < -50))
tstr = ['t'] * len(yt)
maxoutp = (outp == ndimage.maximum_filter(outp, 20, mode='constant', cval=np.amax(outp) + 1))
maxoutp = maxoutp.astype(int)
yp, xp = np.where((maxoutp == 1) & (outp > 10))
maxoutg = (grad == ndimage.minimum_filter(grad, 20, mode='constant', cval=np.amin(grad) - 1))
maxoutg = maxoutg.astype(int)
yg, xg = np.where((maxoutg == 1) & (grad < -10))
gstr = ['g'] * len(yg)
tstr.extend(gstr)
tglist = tstr
tgx = [xt, xg]
tgx = [item for sublist in tgx for item in sublist]
tgy = [yt, yg]
tgy = [item for sublist in tgy for item in sublist]
points = np.array(list(zip(tgy, tgx)))
for point in zip(yp, xp):
try:
pos = ua.closest_point(point, points)
except ValueError:
continue
if tglist[pos] == 't':
res.append((tglist[pos], outt[tuple(points[pos])], outp[point]))
if tglist[pos] == 'g':
res.append((tglist[pos], grad[tuple(points[pos])], outp[point]))
dic.close()
return res
def canny(image, high_threshold, low_threshold):
grad_x = sobel(image, 0)
grad_y = sobel(image, 1)
grad_mag = sqrt(grad_x**2+grad_y**2)
grad_angle = arctan2(grad_y, grad_x)
# next, scale the angles in the range [0, 3] and then round to quantize
quantized_angle = around(3 * (grad_angle + pi) / (pi * 2))
NE = maximum_filter(grad_mag, footprint=_NE)
W = maximum_filter(grad_mag, footprint=_W)
NW = maximum_filter(grad_mag, footprint=_NW)
N = maximum_filter(grad_mag, footprint=_N)
thinned = (((grad_mag > W) & (quantized_angle == _N_d )) |
((grad_mag > N) & (quantized_angle == _W_d )) |
((grad_mag > NW) & (quantized_angle == _NE_d)) |
((grad_mag > NE) & (quantized_angle == _NW_d)) )
thinned_grad = thinned * grad_mag
# Now, hysteresis thresholding: find seeds above a high threshold, then
# expand out until we go below the low threshold
high = thinned_grad > high_threshold
low = thinned_grad > low_threshold
canny_edges = binary_dilation(high, iterations=-1, mask=low)
return grad_mag, thinned_grad, canny_edges
def build_part_with_score_fast(score_threshold, local_max_radius, scores):
parts = []
num_keypoints = scores.shape[2]
lmd = 2 * local_max_radius + 1
# NOTE it seems faster to iterate over the keypoints and perform maximum_filter
# on each subarray vs doing the op on the full score array with size=(lmd, lmd, 1)
for keypoint_id in range(num_keypoints):
kp_scores = scores[:, :, keypoint_id].copy()
kp_scores[kp_scores < score_threshold] = 0.
max_vals = ndi.maximum_filter(kp_scores, size=lmd, mode='constant')
max_loc = np.logical_and(kp_scores == max_vals, kp_scores > 0)
max_loc_idx = max_loc.nonzero()
for y, x in zip(*max_loc_idx):
parts.append((scores[y, x,
keypoint_id], keypoint_id, np.array((y, x))))
return parts
def test_indices_with_labels(self):
image = np.random.uniform(size=(40, 60))
i, j = np.mgrid[0:40, 0:60]
labels = 1 + (i >= 20) + (j >= 30) * 2
i, j = np.mgrid[-3:4, -3:4]
footprint = (i * i + j * j <= 9)
expected = np.zeros(image.shape, float)
for imin, imax in ((0, 20), (20, 40)):
for jmin, jmax in ((0, 30), (30, 60)):
expected[imin:imax, jmin:jmax] = ndi.maximum_filter(
image[imin:imax, jmin:jmax], footprint=footprint)
expected = np.stack(np.nonzero(expected == image), axis=-1)
expected = expected[np.argsort(image[tuple(expected.T)])[::-1]]
result = peak.peak_local_max(image, labels=labels, min_distance=1,
threshold_rel=0, footprint=footprint,
exclude_border=False)
result = result[np.argsort(image[tuple(result.T)])[::-1]]
assert (result == expected).all()
def test_reorder_labels(self):
image = np.random.uniform(size=(40, 60))
i, j = np.mgrid[0:40, 0:60]
labels = 1 + (i >= 20) + (j >= 30) * 2
labels[labels == 4] = 5
i, j = np.mgrid[-3:4, -3:4]
footprint = (i * i + j * j <= 9)
expected = np.zeros(image.shape, float)
for imin, imax in ((0, 20), (20, 40)):
for jmin, jmax in ((0, 30), (30, 60)):
expected[imin:imax, jmin:jmax] = ndi.maximum_filter(
image[imin:imax, jmin:jmax], footprint=footprint)
expected = (expected == image)
with expected_warnings(["indices argument is deprecated"]):
result = peak.peak_local_max(image, labels=labels, min_distance=1,
threshold_rel=0, footprint=footprint,
indices=False, exclude_border=False)
assert (result == expected).all()
def normalize_spec(w, f, w0, f0, ferr0, \
medfilt_width = 10, maxfilt_width = 5, order = 4):
# w, f : arrays used to define a continuum function
# w0, f0, ferr0: target flux to be normalized
# Median filter
f_medfilt = ndimage.median_filter(f, size=medfilt_width)
# Maximum filter
f_maxfilt = ndimage.maximum_filter(f_medfilt, size=maxfilt_width)
z = np.polyfit(w, f_maxfilt, order)
p = np.poly1d(z)
f_norm = f0 / p(w0)
ferr_norm = ferr0 / p(w0)
return (f_norm, ferr_norm)
def mask_post_processing(thresh_image,
kernel_size=5,
min_obj_size=100,
max_dist=20):
'''Post-process a thresholded mask to remove small objects and apply watershed.
Keyword arguments:
thresh image -- thresholded mask
kernel_size -- size of the kernel to adopt for opening operation
min_obj_size -- minimum are accepted, smaller objects are removed
max_dist -- size parameter for ndimage.maximum_filter function
Return:
thresh_image -- post-processed mask (uint8)
'''
# post-processing to remove holes and small objects
kernel = np.ones((kernel_size, kernel_size), np.uint8)
opening = cv2.morphologyEx(thresh_image, cv2.MORPH_OPEN, kernel)
opening = opening.astype("bool")
thresh_image = remove_small_objects(opening,
min_size=min_obj_size,
connectivity=1,
in_place=False)
# apply watershed to separate cells better
distance = ndimage.distance_transform_edt(thresh_image)
maxi = ndimage.maximum_filter(distance, size=max_dist, mode='constant')
local_maxi = peak_local_max(maxi,
indices=False,
footprint=np.ones((3, 3)),
labels=thresh_image)
markers = ndimage.label(local_maxi)[0]
thresh_image = watershed(-distance,
markers,
mask=thresh_image,
watershed_line=True)
thresh_image = thresh_image.astype("bool")
thresh_image = remove_small_objects(thresh_image,
min_size=20,
connectivity=1,
in_place=False)
return (thresh_image.astype("uint8") * 255)
def grow_segmentation_map(seg_file='MACS1149-IR_drz_seg.fits', cat_file='MACS1149-IR.cat', size=30, mag=20):
import scipy.ndimage as nd
import pyregion
import os
#import stsci.convolve
#seg_file='MACS1149-IR_drz_seg.fits'; cat_file='MACS1149-IR.cat'; size=30; mag=20.5
seg_im = pyfits.open(seg_file)
seg = seg_im[0].data*1
cat = threedhst.catIO.Table(cat_file)
ok = cat['MAG_APER'] < mag
so = np.argsort(cat['MAG_APER'][ok])
idx = np.arange(len(cat))[ok][so]
print 'Grow masks:'
for i in idx:
id = cat['NUMBER'][i]
print '%5d (%.2f)' %(id, cat['MAG_APER'][i])
mask = (seg == id)*1
grow_mask = nd.maximum_filter(mask, size=size*2)
#grow_mask = nd.convolve(mask, np.ones((size, size)))
#grow_mask = stsci.convolve.convolve2d(mask, np.ones((size, size)), output=None, mode='nearest', cval=0.0, fft=1)
seg[seg == 0] += grow_mask[seg == 0]*id
reg_file = seg_file.replace('.fits', '_mask.reg')
if os.path.exists(reg_file):
print 'Region mask: %s' %(reg_file)
reg = pyregion.open(reg_file).as_imagecoord(seg_im[0].header)
N = len(reg)
for i in range(N):
if 'text=' not in reg[i].comment:
continue
id = int(reg[i].comment.strip('text={')[:-1])
print '%4d' %(id)
mask = reg[i:i+1].get_mask(seg_im[0])
seg[seg == 0] += mask[seg == 0]*id
pyfits.writeto(seg_file.replace('seg.fits','seg_grow.fits'), data=seg, header=seg_im[0].header, clobber=True)
# End
def peak_local_max_wrap(
image,
min_distance=1,
threshold_abs=None,
threshold_rel=None,
num_peaks=np.inf,
):
""" adapted from skimage to support theta wrap """
if np.all(image == image.flat[0]):
return np.empty((0, 2), np.int)
# Non maximum filter
# if footprint is not None:
# image_max = ndi.maximum_filter(image, footprint=footprint,
# mode='wrap')
# else:
# size = 2 * min_distance + 1
# image_max = ndi.maximum_filter(image, size=size, mode='wrap')
# maximum filter with gaussian kernel
ker = cv2.getGaussianKernel(U.rint(2 * min_distance + 1), sigma=2.0)
ker = ker * ker.T
image_max = ndi.maximum_filter(image, footprint=ker, mode='wrap')
# alternatively,
# size = 2 * min_distance + 1
# image_max = ndi.maximum_filter(image, size=size, mode='wrap')
mask = image == image_max
# find top peak candidates above a threshold
thresholds = []
if threshold_abs is None:
threshold_abs = image.min()
thresholds.append(threshold_abs)
if threshold_rel is not None:
thresholds.append(threshold_rel * image.max())
if thresholds:
mask &= image > max(thresholds)
# Select highest intensities (num_peaks)
coordinates = _get_high_intensity_peaks(image, mask, num_peaks)
return coordinates
def getPPH(dfTors,method='daily',res=10):
r"""
Calculate PPH density from tornado dataframe
Parameters
----------
dfTors : dataframe
method : 'total' or 'daily'
"""
# set up ~80km grid over CONUS
latgrid = np.arange(20,55,res/111)
longrid = np.arange(-130,-65,res/111/np.cos(35*np.pi/180))
interval = int(80/res)
disk = circle_filter(interval)
dfTors['SPC_time'] = dfTors['UTC_time'] - timedelta(hours=12)
dfTors = dfTors.set_index(['SPC_time'])
groups = dfTors.groupby(pd.Grouper(freq="D"))
aggregate_grid = []
for group in groups:
slon,slat = group[1]['slon'].values,group[1]['slat'].values
elon,elat = group[1]['elon'].values,group[1]['elat'].values
torlons = [i for x1,x2 in zip(slon,elon) for i in np.linspace(x1,x2, 10)]
torlats = [i for y1,y2 in zip(slat,elat) for i in np.linspace(y1,y2, 10)]
# get grid count
grid, _, _ = np.histogram2d(torlats,torlons, bins=[latgrid,longrid])
grid = (grid>0)*1.0
grid = maximum_filter(grid,footprint=disk)
aggregate_grid.append(grid)
if method == 'daily':
grid = np.mean(aggregate_grid,axis=0)
PPH = gfilt(grid,sigma=1.5*interval)*100
if method == 'total':
grid = np.sum(aggregate_grid,axis=0)
PPH = gfilt((grid>=1)*1.0,sigma=1.5*interval)*100
return PPH,.5*(longrid[:len(longrid)-1]+longrid[1:]),.5*(latgrid[:len(latgrid)-1]+latgrid[1:])
def nms(image,rad=3,thresh=0):
image = copy.copy(image)
roi = rad
size = 2 * roi + 1
image_max = ndimage.maximum_filter(image, size=size, mode='constant')
mask = (image == image_max)
imin = image.min()
image[np.logical_not(mask)] = imin
# Optionally find peaks above some threshold
image[:roi,:] = imin
image[-roi:,:] = imin
image[:, :roi] = imin
image[:, -roi:] = imin
image_t = (image > thresh) * 1
# get coordinates of peaks
return np.transpose(image_t.nonzero())
def crFind(img, var, nsig=10., sigfrac=0.3):
simg = img / var**0.5
deriv = ndimage.sobel(simg)
deriv = ndimage.sobel(deriv)
mean, std = clip(deriv[deriv != 0.])
crmask = numpy.where(abs(deriv) > 15 * std, 1, 0)
return crmask
thresh = nsig * var**0.5
n = 5
blkimg = img.repeat(n, 0).repeat(n, 1)
deriv = ndimage.laplace(blkimg) * -1.
deriv[deriv < 0] = 0.
d = iT.resamp(deriv, n)
m = numpy.where((d > thresh) & (img > thresh), 1, 0)
bmap = ndimage.maximum_filter(m, 5)
cond = (bmap == 1) & (d > thresh * sigfrac) & (img > thresh * sigfrac)
m[cond] = 1
return m
def get_peak(hms):
coords = {}
for k in range(hms.shape[0]):
hm = hms[k]
mx = maximum_filter(hm, size=5)
idx = zip(*np.where((mx == hm) * (hm > 0.1)))
candidate_points = []
for (y, x) in idx:
candidate_points.append([x, y, hm[y][x]])
if len(candidate_points) == 0:
preds, maxvals = get_max_pred(hm[None, :])
candidate_points.append([preds[0, 0], preds[0, 1], maxvals[0, 0]])
candidate_points = np.array(candidate_points)
candidate_points = candidate_points[np.lexsort(-candidate_points.T)]
candidate_points = torch.Tensor(candidate_points)
coords[k] = candidate_points
return coords
def findKvecsAuto(self):
maxFiltFFT = sciim.maximum_filter(self.rawImageFFT, size=10)
locMaxMask = (self.rawImageFFT==maxFiltFFT)
maxInds = np.argsort(self.rawImageFFT, axis=None)
maxInds = maxInds[::-1]
# find four nonzero k-vectors
nMaxFound = 0
i = 0
kvecList = np.zeros((2,2))
while nMaxFound < 2:
maxCoords = np.unravel_index(maxInds[i], self.rawImageFFT.shape)
kvec = np.array([self.rawImageFreqs[0][maxCoords[0]], self.rawImageFreqs[1][maxCoords[1]]])
if locMaxMask[maxCoords]==1 and (kvec[0]**2+kvec[1]**2)>0.05:
if nMaxFound == 0:
kvecList[0] = kvec
nMaxFound += 1
else:
if np.abs(np.dot(kvecList[0], kvec)) < 0.05*np.linalg.norm(kvec)**2:
kvecList[1] = kvec
nMaxFound += 1
i += 1
xKvecInd = np.argmax(np.abs(kvecList[:,0]))
yKvecInd = np.argmax(np.abs(kvecList[:,1]))
assert xKvecInd!=yKvecInd, 'x and y kvecs are the same!'
xKvec = kvecList[xKvecInd]
yKvec = kvecList[yKvecInd]
if xKvec[0]<0:
xKvec *= -1
if yKvec[1]<0:
yKvec *= -1
self.xKvec = xKvec
self.yKvec = yKvec
def v2_chaos_orig(iso_img, n_levels=30):
# GCOVR_EXCL_START # Disable code coverage for this function as it's not prod code
"""Reimplementation of the chaos metric. I didn't manage to get it to exactly match the original
implementation. This one seems to have significantly better dynamic range - it often produces
values like 0.6 when the original implementation rarely produces values below 0.95
Original implementation:
https://github.com/alexandrovteam/ims-cpp/blob/dcc12b4c50dbfdcde3f765af85fb8b3bb5cd7ec3/ims/image_measures.cpp#L89
Old way: level-thresholding -> dilation -> erosion -> connected component count
New way: "dilation" via maximum-filter -> "erosion" via minimum-filter -> level-thresholding
-> connected component count
"""
# Local import of image_manip because numba isn't included in the Lithops Docker image
# as it adds ~25MB. If this metric is ever used again, numba will need to be added to the image.
# pylint: disable=import-outside-toplevel # Avoid pulling numba into lithops
from sm.engine.annotation.image_manip import count_connected_components
dilated = maximum_filter(iso_img,
footprint=np.array([[0, 1, 0], [1, 1, 1],
[0, 1, 0]]))
# Old way: mode='nearest', new way: mode='constant'
iso_img = minimum_filter(dilated, size=(3, 3), mode='nearest')
if not iso_img.any():
# Old way - detect this case when the return value is exactly 1.0
return 0.0
# Old way: np.linspace(0, max_ints, n_levels)
mask = np.empty(iso_img.shape, dtype='bool')
thresholds = np.linspace(0, np.max(iso_img), n_levels)
pixel_counts = np.ones(len(thresholds), 'i')
component_counts = np.zeros(len(thresholds), 'i')
for i, threshold in enumerate(thresholds):
np.greater(iso_img, threshold, out=mask)
if mask.any():
pixel_counts[i] = np.count_nonzero(mask)
component_counts[i] = count_connected_components(mask)
mean_count = 1 - np.mean(component_counts) / np.count_nonzero(iso_img)
return mean_count
def extract_masked(image, linedesc, pad=5, expand=0, background=None):
"""Extract a subimage from the image using the line descriptor.
A line descriptor consists of bounds and a mask."""
assert amin(image) >= 0 and amax(image) <= 1
if background is None or background=="min":
background = amin(image)
elif background =="max":
background = amax(image)
y0,x0,y1,x1 = [int(x) for x in [linedesc.bounds[0].start,linedesc.bounds[1].start, \
linedesc.bounds[0].stop,linedesc.bounds[1].stop]]
if pad > 0:
mask = pad_image(linedesc.mask, pad, cval=0)
else:
mask = linedesc.mask
line = extract(image, y0 - pad, x0 - pad, y1 + pad, x1 + pad)
if expand > 0:
mask = ndi.maximum_filter(mask, (expand, expand))
line = where(mask, line, background)
return line
def computeLocalMaxima(self, harrisImage):
'''
Input:
harrisImage -- numpy array containing the Harris score at
each pixel.
Output:
destImage -- numpy array containing True/False at
each pixel, depending on whether
the pixel value is the local maxima in
its 7x7 neighborhood.
'''
destImage = np.zeros_like(harrisImage, np.bool)
maxArr = ndimage.maximum_filter(harrisImage, size=7)
for i in range(harrisImage.shape[0]):
for j in range(harrisImage.shape[1]):
destImage[i, j] = maxArr[i, j] == harrisImage[i, j]
return destImage
def circMaxCFAR(self, diff, nGuard=5, nNoise=2):
'''
Tries to highlight spots
:param nGuard: radius in pixels of spot
:param nNoise: width in pixels of ring where to collect noise beyond spot
:returns: diff-filtered
'''
# build circular footprint mask
size = 2*(nGuard+nNoise)+1
mask = np.zeros((size, size), dtype=bool)
v = np.arange(size)-size//2
xx, yy = np.meshgrid(v, v)
dist2 = xx**2+yy**2
mask[dist2 > nGuard**2] = True
mask[dist2 > (nGuard+nNoise)**2] = False
# apply footprint
filtered = ndimage.maximum_filter(diff, footprint=mask)
return diff-filtered
def computeLocalMaxima(self, harrisImage):
'''
Input:
harrisImage -- numpy array containing the Harris score at
each pixel.
Output:
destImage -- numpy array containing True/False at
each pixel, depending on whether
the pixel value is the local maxima in
its 7x7 neighborhood.
'''
destImage = np.zeros_like(harrisImage, np.bool)
# TODO 2: Compute the local maxima image
# TODO-BLOCK-BEGIN
maxes = ndimage.maximum_filter(harrisImage, 7, mode='nearest')
destImage = np.equal(harrisImage, maxes)
# TODO-BLOCK-END
return destImage
def computeLocalMaxima(self, harrisImage):
'''
Input:
harrisImage -- numpy array containing the Harris score at
each pixel.
Output:
destImage -- numpy array containing True/False at
each pixel, depending on whether
the pixel value is the local maxima in
its 7x7 neighborhood.
'''
destImage = np.zeros_like(harrisImage, np.bool)
# TODO 2: Compute the local maxima image
# TODO-BLOCK-BEGIN
local_max_array = maximum_filter(harrisImage, size = 7, mode = 'reflect')
destImage = (harrisImage == local_max_array)
# TODO-BLOCK-END
return destImage
def get_maxima(image, size, threshold='mean'):
"""
Find local intensity maxima inside an image. There is no sub-pixel accuracy.
Args:
image (np.ndarray): a n-dimensional image
size (int): the radius of the local region
threshold (float or str): the maxima whose intensity is smaller
than the threshold will be discarded.
Return:
np.ndarray: the coordinates of local intensity maxima, shape (dimension, n)
"""
maxima_img = ndimage.maximum_filter(image, size) == image
if threshold == 'mean':
maxima_img[image < image[image > 0].mean()] = 0
else:
maxima_img[image < threshold] = 0
local_maxima = np.array(np.where(maxima_img > 0))
return local_maxima
def test_four_quadrants(self):
image = np.random.uniform(size=(20, 30))
i, j = np.mgrid[0:20, 0:30]
labels = 1 + (i >= 10) + (j >= 15) * 2
i, j = np.mgrid[-3:4, -3:4]
footprint = (i * i + j * j <= 9)
expected = np.zeros(image.shape, float)
for imin, imax in ((0, 10), (10, 20)):
for jmin, jmax in ((0, 15), (15, 30)):
expected[imin:imax, jmin:jmax] = ndi.maximum_filter(
image[imin:imax, jmin:jmax], footprint=footprint)
expected = (expected == image)
with expected_warnings(["indices argument is deprecated"]):
result = peak.peak_local_max(image, labels=labels,
footprint=footprint,
min_distance=1,
threshold_rel=0,
indices=False,
exclude_border=False)
assert np.all(result == expected)
def computeLocalMaxima(self, harrisImage):
'''
Input:
harrisImage -- numpy array containing the Harris score at
each pixel.
Output:
destImage -- numpy array containing True/False at
each pixel, depending on whether
the pixel value is the local maxima in
its 7x7 neighborhood.
'''
destImage = np.zeros_like(harrisImage, np.bool)
# TODO 2: Compute the local maxima image
# TODO-BLOCK-BEGIN
# raise Exception("TODO in features.py not implemented")
destImage = ndimage.maximum_filter(harrisImage, size=7) == harrisImage
# TODO-BLOCK-END
return destImage
def getCenterline(mask, smoothing):
labels = measure.label(mask)
# assume at least 1 CC
assert( labels.max() != 0 )
# Find largest connected component
bins = np.bincount(labels.flat)[1:]
cc = labels == np.argmax(np.bincount(labels.flat)[1:])+1
filt = ndimage.maximum_filter(cc, size=smoothing)
# Find skeletonized centerline
# cc = morphology.binary_closing(cc)
# cc = morphology.binary_erosion(cc)
# cc = morphology.binary_dilation(cc)
skeleton = skeletonize(filt, method='lee')
# skeleton = medial_axis(cc)
skeleton = thin(skeleton)
return skeleton
def GapFil(input_tif, footprint, output_folder, method='max'):
"""
Gapfil a raster by filling with the minimum, maximum or median of nearby pixels.
Parameters
----------
input_tif : str
Raster to be filled.
footprint : ndarray
Boolean array describing the area in which to look for the filling value.
output_folder : str
Folder to store gapfilled map.
method : str, optional
Method to use for gapfilling, options are 'max', 'min' or 'median'. Default is 'max'.
Returns
-------
fh : str
Location of the gapfilled map.
"""
driver, NDV, xsize, ysize, GeoT, Projection = GetGeoInfo(input_tif)
population = OpenAsArray(input_tif, nan_values=True)
if method == 'median':
population_gaps = ndimage.median_filter(population,
footprint=footprint)
if method == 'max':
population_gaps = ndimage.maximum_filter(population,
footprint=footprint)
if method == 'min':
population_gaps = ndimage.minimum_filter(population,
footprint=footprint)
population[np.isnan(population)] = population_gaps[np.isnan(population)]
fn = os.path.split(input_tif)[1].replace('.tif', '_gapfilled.tif')
fh = os.path.join(output_folder, fn)
CreateGeoTiff(fh, population, driver, NDV, xsize, ysize, GeoT, Projection)
return fh
def detect_peaks(image, detection_area = 2):
"""
Takes an image and detects the peaks using a local maximum filter.
Returns a boolean mask of the peaks (i.e. 1 when the pixel's value is a
local maximum, 0 otherwise)
Parameters
----------
image: 2D marray
the data of one FITS image.
detection_area: integer, optional
optional argument. The local maxima are found in asquare neighborhood
with size (2*detection_area+1)*(2*detection_area+1).
Default value is detection_area = 2.
Returns
-------
detected_peaks: 2D array
Numpy array with same size as the input image, with 1 at the image
local maxima, 0 otherwise.
"""
# define an 8-connected neighborhood --> image dimensionality is 2 + there are 8 neighbors for a single pixel
neighborhood = np.ones((1+2*detection_area,1+2*detection_area))
# apply the local maximum filter; all pixel of maximal value in their
# neighborhood are set to 1
local_max = sn.maximum_filter(image, footprint=neighborhood)==image
# local_max is a mask that contains the peaks we are looking for, but also
# the background. In order to isolate the peaks we must remove the
# background from the mask. We create the mask of the background
background = (image==0)
# a little technicality: we must erode the background in order to
# successfully subtract it from local_max, otherwise a line will appear
# along the background border (artifact of the local maximum filter)
eroded_background = sn.binary_erosion(background, structure=neighborhood, border_value=1)
# we obtain the final mask, containing only peaks, by removing the
# background from the local_max mask
detected_peaks = local_max - eroded_background
return detected_peaks
def lidarCB(self, msg):
'''
This callback is called everytime the laserscanner sends us data.
This is about 40hz. The message received is a laserscan message
'''
#Might want to consider checking what highlevel mux is sending and updating changing looking angle and acceptible distance
# this is not implemented yet
increment = msg.angle_increment
middle = int((-msg.angle_min)/increment) #This is the index in ranges of the laser scan pointing forward
start = middle - int(math.radians(self.LOOKING_RANGE)/increment) #index of the scan pointing Looking_Range to right
end = middle + int(math.radians(self.LOOKING_RANGE)/increment) #index of the scan pointing Looking_Range to left
ranges30 = msg.ranges[start:end] #Only look at ranges in our range
#may want to consider making things that are at more of an angle farther away so if we are
#kinds off to an angle of something we dont just stop but has not been added
#remove any readings that are out of range
ranges30 = filter(lambda x: x>msg.range_min and x<msg.range_max,ranges30)
#using max filter
FILTER_WIDTH = 5
ranges30 = sc.maximum_filter(ranges30,FILTER_WIDTH)
ranges30 = ranges30[FILTER_WIDTH/2:-FILTER_WIDTH/2:FILTER_WIDTH/2] #DownSampling
#Find the closest object
closest = min(ranges30)
#If TOO CLOSE STOP
if closest < self.DANGER_DISTANCE:
stop_msg = AckermannDriveStamped()
stop_msg.drive.speed = 0.0
self.pub.publish(stop_msg)
#IF CLOSEISH SLOW DOWN
elif closest < self.CAUTION_DISTANCE:
stop_msg = AckermannDriveStamped()
stop_msg.drive.speed = self.SPEED*(closest-self.DANGER_DISTANCE)/(self.CAUTION_DISTANCE-self.DANGER_DISTANCE)
stop_msg.drive.steering_angle = self.ANGLE
self.pub.publish(stop_msg)
def detect_peaks(image):
"""Detect peaks in an image using a maximum filter"""
#Set up 3x3 footprint for maximum filter
footprint = np.ones((3, 3))
#Apply maximum filter: All pixel in the neighborhood are set
#to the maximal value. Peaks are where image = maximum_filter(image)
local_maximum = maximum_filter(image, footprint=footprint) == image
#We have false detections, where the image is zero, we call it background.
#Create the mask of the background
background = (image == 0)
#Erode background at the borders, otherwise we would miss
eroded_background = binary_erosion(background,
structure=footprint,
border_value=1)
#Remove the background from the local_maximum image
detected_peaks = local_maximum - eroded_background
return detected_peaks
def process(data, size=None):
if data is None or size is None or "values" not in data:
return data
radius = int(size // 2)
footprint = get_footprint(size)[np.newaxis]
# put absolute minimum on no data pixels
array = data["values"].copy()
minimum = get_dtype_min(array.dtype)
no_data_mask = array == data["no_data_value"]
array[no_data_mask] = minimum
# apply maximum filter
filtered = ndimage.maximum_filter(array, footprint=footprint)
# replace absolute minimum with original fillvalue
filtered[(filtered == minimum) & no_data_mask] = data["no_data_value"]
# cut out the result
filtered = filtered[:, radius:-radius, radius:-radius]
return {"values": filtered, "no_data_value": data["no_data_value"]}
def cell_max(values):
r"""
Find pairwise max of consecutive elements across all axes of an array.
Parameters
----------
values : :class:`numpy.ndarray`
An input array of :math:`n` dimensions,
:math:`(m_0, m_1, \dots, m_{n-1})`.
Returns
-------
maxima : :class:`numpy.ndarray`
An input array of :math:`n` dimensions, each with a length 1 less than
the input array,
:math:`(m_0 - 1, m_1 - 1, \dots, m_{n-1} - 1)`.
"""
maxima = maximum_filter(values, size=2, mode='constant')
indices = (slice(1, None), ) * np.ndim(values)
return maxima[indices]
def process(self, batch, request: BatchRequest):
data = batch[self.array].data
if self.threshold is None:
data_min = np.min(data)
data_med = np.median(data)
threshold = (data_min + data_med) / 2
else:
threshold = self.threshold
voxel_size = batch[self.array].spec.voxel_size
window_size = self.window_size / voxel_size
window_size = (1,) * (len(data.shape) - len(window_size)) + window_size
max_filter = maximum_filter(data, window_size)
local_maxima = np.logical_and(max_filter == data, data > threshold)
spec = batch[self.array].spec.copy()
spec.dtype = bool
batch.arrays[self.maxima] = Array(local_maxima, spec)
def find_all_thres_fast(data, thres, msep, find_segs=False):
"""
Fast version of find_all_thres. See :py:func:`find_all_thres`.
"""
wsize = tuple([2 * i + 1 for i in msep]) # window size is 2*seperation+1
# find local maxima mask
mx = ndimage.maximum_filter(data, size=wsize, mode='constant') == data
# find positive threshold mask
pthres = np.ma.greater(data, thres)
# peaks are bitwise and of maximum mask and threshold mask
locations = np.transpose(np.nonzero(np.bitwise_and(pthres, mx)))
locations = [tuple(i) for i in locations]
if find_segs:
seg_slices = [find_pseg_slice(data, l, thres) for l in locations]
return locations, seg_slices
else:
return locations