def remove_space(img,
threshold=40,
kernel_size=3,
keepprop=6,
vborder=3,
resize=False):
# Filter horizontal
imgfilt = ndimage.minimum_filter(img[6:-6].max(2), size=kernel_size)
rows = np.max(imgfilt, 0) > threshold
from_, to_ = np.where(rows)[0][[0, -1]]
keeprand = np.random.choice(range(from_, to_), (to_ - from_) // keepprop,
replace=False)
rows[keeprand] = True
imgout = img[:, rows]
# Filter vertical
h, w, _ = imgout.shape
imgfilt = ndimage.minimum_filter(imgout[:, vborder:-vborder].max(2),
size=kernel_size)
cols = np.where(np.max(imgfilt, 1) > threshold)[0]
from_ = 0 if cols[0] < 2 else cols[0] + vborder
to_ = h if cols[-2] == h - 2 * vborder - 1 else cols[-1]
imgout = imgout[from_:to_]
# rows = np.where(np.max(imgfilt, 0) > threshold)[0]
if resize:
# Rescale to imgin height
scale = h / imgout.shape[0]
imgout = cv2.resize(imgout, (int(round(scale * imgout.shape[1])), h))
return imgout
def fill_gaps(data, mask):
"""Interpolate in the gaps in the data
Parameters
----------
data: np.ndarray
data to have values filled in for
mask: float or nd.ndarray
If an nd.ndarray, it will be assumed to be a mask
with values equal to 1 where they should be interpolated
over. If a float, pixels with that value will be replaced
"""
ys, xs = data.shape
if isinstance(mask, numpy.ndarray):
mask = (mask == 0)
for i in range(ys):
x = numpy.arange(xs)
rdata = data[i, :]
rmask = mask[i, :]
rmask = nd.minimum_filter(rmask, size=3)
rdata = numpy.interp(x, x[rmask], rdata[rmask])
data[i, rmask == 0] = rdata[rmask == 0]
else:
mask = (data != mask)
for i in range(ys):
x = numpy.arange(xs)
rdata = data[i, :]
rmask = mask[i, :]
rmask = nd.minimum_filter(rmask, size=3)
rdata = numpy.interp(x, x[rmask], rdata[rmask])
data[i, rmask == 0] = rdata[rmask == 0]
return data
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 test_locmin(self):
arr = np.ones((9, 12))
arr[4, 3] = -2
arr[4, 7] = -5
filter = ndimage.minimum_filter(arr,
8,
mode='constant',
cval=np.min(arr) - 1)
filter[filter == np.max(arr)] = -999
maxoutt = (arr == filter)
yy, xx = np.where((maxoutt == 1))
assert (yy, xx) == (4, 7)
filter = ndimage.minimum_filter(arr,
3,
mode='constant',
cval=np.min(arr) - 1)
filter[filter == np.max(arr)] = -999
maxoutt = (arr == filter)
yy, xx = np.where((maxoutt == 1))
assert_array_equal(np.array([4, 4]), yy)
assert_array_equal(np.array([3, 7]), xx)
def bf_fluo_correlate(embryo_idx,
bf_image,
fluo_image,
normalized=False,
smoothed=None,
dim=3):
"""Plot correlation between bf/fluo images, pixel-by-pixel or smoothed in tiles."""
norm_str = ('N' if normalized else 'Unn') + 'ormalized'
smooth_str = 'unsmoothed'
if normalized:
bf_image = normalize_img(bf_image)
fluo_image = normalize_img(fluo_image)
if smoothed:
if smoothed == 'avg':
weights = [[1 / (dim**2)] * dim] * dim
bf_image = correlate(bf_image, weights)
fluo_image = correlate(fluo_image, weights)
elif smoothed == 'max':
bf_image = maximum_filter(bf_image, size=dim)
fluo_image = maximum_filter(fluo_image, size=dim)
elif smoothed == 'min':
bf_image = minimum_filter(bf_image, size=dim)
fluo_image = minimum_filter(fluo_image, size=dim)
else:
raise Exception('smoothed can only be avg, max, or min')
smooth_str = 'smoothed by ' + smoothed
plt.scatter(bf_image.flatten(), fluo_image.flatten())
plt.xlabel(f"{norm_str} bf frame val")
plt.ylabel(f"{norm_str} fluo frame val")
plt.title(f"Correlation plot for {smooth_str} embryo {embryo_idx}")
plt.show()
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 quick_bg_fix(raw_data, npix=4112):
left_xx = np.arange(npix/2)
right_xx = np.arange(npix/2, npix)
left_bg = ndimage.minimum_filter(ndimage.gaussian_filter(raw_data[:npix/2],3), size=100)
right_bg = ndimage.minimum_filter(ndimage.gaussian_filter(raw_data[npix/2:],3), size=100)
data = raw_data.copy()
data[left_xx] = raw_data[left_xx] - left_bg
data[right_xx] = raw_data[right_xx] - right_bg
return data
def filtroMin(I): If = I.copy() Ir = If[:,:,0] Iv = If[:,:,1] Ia = If[:,:,2] Ir = ndimage.minimum_filter(Ir, 3) Iv = ndimage.minimum_filter(Iv, 3) Ia = ndimage.minimum_filter(Ia, 3) If[:,:,0] = Ir If[:,:,1] = Iv If[:,:,2] = Ia return If
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 difference_of_gaussians(image, octaves_num=4, σ=1.6, scales_num=3):
differences = []
# computing all differences
for oct in range(octaves_num):
image_zoomed = ndim.zoom(image, 0.5 ** oct)
differences.append(difference_of_gaussians_one_octave(image_zoomed, σ, scales_num))
# find keypoints
# computing maximal values in 3x3 windows from every difference
footprint = np.ones((3,3,3))
footprint[1,1,1] = 0
keypoints_for_octaves = []
for oct in range(octaves_num):
diff = differences[oct]
# computing indices of maximas
maxima_around = ndim.maximum_filter(diff, footprint=footprint)[1:4]
minima_around = ndim.minimum_filter(diff, footprint=footprint)[1:4]
maxima_mask = diff[1:4] > maxima_around
minima_mask = diff[1:4] < minima_around
keypoints_candidates = np.argwhere(maxima_mask | minima_mask)
draw_image_with_points('data/Episcopal_Gaudi/EG_2.jpg', np.fliplr(keypoints_candidates[:,1:]), (255,0,0), 'temp.jpg')
# filter keypoints with low contrast
keypoints = []
for s in range(scales_num):
keypoints_after_filtering = filter_low_contrast_keypoints(keypoints_candidates[keypoints_candidates[:,0] == s][:,1:], differences[oct][s:s+3,:,:])
keypoints.append(keypoints_after_filtering)
keypoints_for_octaves.append(np.concatenate(keypoints, axis=0))
return keypoints_for_octaves
def extract_spectral_peaks_2(self, spectrogram):
"""
:param spectrogram:
:return:
"""
# computing local maximum points with the specified maximum filter dimension
local_max_values = maximum_filter(input=spectrogram,
size=(self.maximum_filter_height,
self.maximum_filter_width))
# extracting time and frequency information for local maximum points
j, i = np.where(spectrogram == local_max_values)
peaks = list(zip(i, j))
# computing local minimum points with specified minimum filter dimension
local_min_values = minimum_filter(input=spectrogram,
size=(self.minimum_filter_height,
self.minimum_filter_width))
# extracting time and frequency information for local minimums
k, m = np.where(spectrogram == local_min_values)
lows = list(zip(m, k))
# avoiding spectral points with are both local maximum and local minimum
spectral_peaks = list(set(peaks) - set(lows))
# time and frequency information for extracted spectral peaks
time_indices = [i[0] for i in spectral_peaks]
freq_indices = [i[1] for i in spectral_peaks]
spectral_peaks.sort(key=itemgetter(0))
return spectral_peaks, time_indices, freq_indices
def processImages():
sims = cPickle.load(open('AmuInstSimMats.pkl'))
for i,sim in enumerate(sims):
pyplot.figure(0,(16,9))
pyplot.imshow(sim, vmin = 0, vmax = 1, cmap = pyplot.get_cmap('gray'), aspect = 'auto', origin = 'lower')
pyplot.title('Unfiltered Sim Matrix ' + str(i))
pyplot.savefig('Unfiltered Sim Matrix ' + str(i) + '.jpg')
pyplot.figure(1,(16,9))
pyplot.imshow(filter.tv_denoise(numpy.array(sim,numpy.float64), weight = 1), vmin = 0, vmax = 1, cmap = pyplot.get_cmap('gray'), aspect = 'auto', origin = 'lower')
pyplot.title('TV_Denoise ' + str(i))
pyplot.savefig('TV_Denoise ' + str(i) + '.jpg')
pyplot.figure(2,(16,9))
pyplot.imshow(filter.threshold_adaptive(numpy.array(sim,numpy.float64),21), vmin = 0, vmax = 1, cmap = pyplot.get_cmap('gray'), aspect = 'auto', origin = 'lower')
pyplot.title('Threshold_Adaptive ' + str(i))
pyplot.savefig('Threshold_Adaptive ' + str(i) + '.jpg')
pyplot.figure(3,(16,9))
pyplot.imshow(ndimage.minimum_filter(numpy.array(sim,numpy.float64),size=2), vmin = 0, vmax = 1, cmap = pyplot.get_cmap('gray'), aspect = 'auto', origin = 'lower')
pyplot.title('Local Minimum_Filter ' + str(i))
pyplot.savefig('Local Minimum_Filter ' + str(i) + '.jpg')
pyplot.figure(4,(16,9))
template = numpy.array([[0,1,1,1,1,1,1,1],[1,0,1,1,1,1,1,1],[1,1,0,1,1,1,1,1],[1,1,1,0,1,1,1,1],
[1,1,1,1,0,1,1,1],[1,1,1,1,1,0,1,1],[1,1,1,1,1,1,0,1],[1,1,1,1,1,1,1,0]])
pyplot.imshow(feature.match_template(numpy.array(sim,numpy.float64),template), vmin = 0, vmax = 1, cmap = pyplot.get_cmap('gray'), aspect = 'auto', origin = 'lower')
pyplot.title('Match_Template with my own 8x8 beat diagonal template ' + str(i))
pyplot.savefig('Match_Template with my own 8x8 beat diagonal template ' + str(i) + '.jpg')
sys.exit()
def get_minimums(self, floor):
return minimum_filter(
floor,
footprint=[[0, 1, 0], [1, 0, 1], [0, 1, 0]],
mode='constant',
cval=10,
) > floor
def split_on_dash(img, label, threshold=40, kernel_size=2):
# Filter horizontal
imgfilt = ndimage.minimum_filter(img[6:-6].max(2), size=kernel_size)
# Image.fromarray(imgfilt)
rows = np.where(np.max(imgfilt, 0) > threshold)[0]
diff = rows[1:] - rows[:-1]
try:
nbigcuts = len(np.where(diff >= 15)[0])
minbigcut = min(diff[diff >= 15])
nmdlcuts = len(
np.where((diff < minbigcut) & (diff > (minbigcut - 12)))[0])
if not ((nbigcuts == 4) & (nmdlcuts == 0)):
return None
except:
return None
cuts = ((rows[np.where(diff > 15)[0] + 1] + rows[np.where(diff > 15)[0]]) /
2).astype(np.int16)
if (cuts[0] < 80) or (img.shape[1] - cuts[-1] < 80):
return None
imgl = [img[:, :cuts[0]], img[:, cuts[1]:cuts[2]], img[:, cuts[3]:]]
labl = label.split('-')
if random.choice([True, False]):
for p1, p2 in [(1, 0), (2, 0), (2, 1)]:
imgl.append(
remove_space(np.concatenate((imgl[p1], imgl[p2]), 1),
keepprop=random.randrange(3, 20)))
labl.append(labl[p1] + labl[p2])
outls = [(i, l) for i, l in zip(imgl[3:], labl[3:])]
else:
outls = [(remove_space(i, keepprop=random.randrange(3, 20)), l)
for i, l in zip(imgl, labl)]
return outls
def extract_spectral_peaks(self, spectrogram):
"""
A method to extract spectral peaks given the spectrogram of an audio.
Parameters:
spectrogram (numpy.ndarray): Time-Frequency representation of an audio.
Returns:
List : list of spectral peaks.
"""
# computing local maximum points with the specified maximum filter dimension
local_max_values = maximum_filter(input=spectrogram, size=(self.maximum_filter_height,
self.maximum_filter_width))
# extracting time and frequency information for local maximum points
j, i = np.where(spectrogram == local_max_values)
peaks = list(zip(i, j))
# computing local minimum points with specified minimum filter dimension
local_min_values = minimum_filter(input=spectrogram, size=(self.minimum_filter_height,
self.minimum_filter_width))
# extracting time and frequency information for local minimums
k, m = np.where(spectrogram == local_min_values)
lows = list(zip(m, k))
# avoiding spectral points with are both local maximum and local minimum
spectral_peaks = list(set(peaks) - set(lows))
# time and frequency information for extracted spectral peaks
time_indices = [i[0] for i in spectral_peaks]
freq_indices = [i[1] for i in spectral_peaks]
spectral_peaks.sort(key=itemgetter(0))
return spectral_peaks, time_indices, freq_indices
def clip(a):
#return a
result = ndimage.minimum_filter(gaussian_filter(a, 4), size=130)
#bg = np.percentile(a, 45)
#print(bg)
#return(np.clip(a, -1e9, bg))
return result
def denoise(img):
tmp = ndimage.minimum_filter(img, 3)
tmp = wiener(tmp, 2)
tmp = ndimage.maximum_filter(tmp, 2)
tmp = ndimage.rank_filter(tmp, 2, 2)
tmp = ndimage.gaussian_filter(tmp, 0.5)
return tmp
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 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 _roll_ball(file, DAPI_roi, size=20):
blured = _gaussian_blur(file, DAPI_roi)
result = np.empty(blured.shape)
# Background substraction
background = ndimage.minimum_filter(blured, size=8)
result = blured - background
return (result)
def apply_min_filter(cells, start_pos, min_dist):
from scipy.ndimage import minimum_filter
ncells = cells.copy()
## ncells[ncells == 0] = 2*ncells.max()
ncells = farray(minimum_filter(ncells, size=min_dist))
minima = [
tuple(x) for x in transpose((
logical_and(ncells == cells, ncells != ncells.max())).nonzero())
]
class Duplicate:
pass
while True:
try:
for min1, min2 in combinations(minima, 2):
if (farray(min1) - farray(min2)).norm() < min_dist:
print 'duplicate', min1, min2
raise Duplicate
else:
break
except Duplicate:
d1 = (farray(min1) - farray(start_pos)).norm()
d2 = (farray(min2) - farray(start_pos)).norm()
print d1, d2
if d1 < d2:
print 'removing', min2
minima.remove(min2)
else:
print 'removing', min1
minima.remove(min1)
return minima
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 get_slopes(self, reso, n, fp, normalize=True, intersect=False):
ds = buzz.DataSource()
with ds.open_araster(self.dsm_path(reso, n)).close as r:
if intersect:
fp = r.fp.dilate(fp.rlength // 2) & fp
arr = r.get_data(fp=fp.dilate(1))
nodata_mask = arr == r.nodata
nodata_mask = ndi.binary_dilation(nodata_mask)
kernel = [
[0, 1, 0],
[1, 1, 1],
[0, 1, 0],
]
arru = ndi.maximum_filter(arr, None, kernel) - arr
arru = np.arctan(arru / fp.pxsizex)
arru = arru / np.pi * 180.
arru[nodata_mask] = 0
arru = arru[1:-1, 1:-1]
arrd = arr - ndi.minimum_filter(arr, None, kernel)
arrd = np.arctan(arrd / fp.pxsizex)
arrd = arrd / np.pi * 180.
arrd[nodata_mask] = 0
arrd = arrd[1:-1, 1:-1]
arr = np.dstack([arrd, arru])
if normalize:
arr = arr / 45 - 1
return arr
def sliding_minima(img=None,
weight=1.,
window_size=30,
boundary_condition='reflect'):
'''
Subtracts the minimum calculated within a sliding window from the centre of
the window.
Parameters
----------
img : array_like
Single image as numpy array or multiple images as array-like object
weight : scalar
Fraction of minima to be subtracted from each pixel.
Value of `weight` should be in the interval (0.0,1.0).
window_size : scalar or tuple
Sets the size of the sliding window.
Specifying `window_size=3` is equivalent to `window_size=(3,3)`.
boundary_condition : {'reflect', 'constant', 'nearest', 'mirror', 'wrap'}
Mode of handling array borders.
'''
img_out = img - weight * nd.minimum_filter(
img, size=window_size, mode=boundary_condition)
return img_out
def find_v_cut(cut):
overlap_x = cut.shape[1]
if overlap_x < 3: return None
w1height = cut.shape[0]
min_vals = np.empty_like(cut)
min_vals[0] = cut[0]
for i in range(1, w1height, 1):
min_vals[i] = cut[i] + ndimage.minimum_filter(min_vals[i - 1:i + 1],
footprint=[[1, 1, 1],
[0, 0, 0]],
mode='constant')[1]
min_vals[i,
0] = cut[i, 0] + min(min_vals[i - 1, 0], min_vals[i - 1, 1])
min_vals[i, -1] = cut[i, -1] + min(min_vals[i - 1, -1],
min_vals[-i - 1, -1])
res = np.empty(w1height)
res[-1] = np.argmin(min_vals[-1])
for i in range(w1height - 2, -1, -1):
res[i] = res[i + 1] + np.argmin(min_vals[
i, max(res[i + 1] - 1, 0):min(overlap_x, res[i + 1] +
2)]) - 1 + int(res[i + 1] - 1 < 0)
return res
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 pointFinder(image, seeing_pix, threshold):
"""Take an image file and identify where point sources are. This is done by utilizing
Scipy maximum and minimum filters.
Inputs:
image: an array of the image
seeing_pix: a guess of the seeing size in pixel used to define the size of max/min filters
threshold: a threshold (in counts) used to determine a detection from noise fluctuation
Output:
cutouts: list of cutouts of sources found in this image."""
#First, find maxima in the image
#peaks = maximum_filter(image, footprint = pattern)#size = seeing_pix) #filter to find max
peaks = maximum_filter(image, size=0.1 * seeing_pix)
maxima = (peaks == image
) #booleen array indicating locations of the maxima
#now, compute the minimum for background subtraction. This will get rid of
#"maxima" that are really just noise
troughs = minimum_filter(
image,
size=4 * seeing_pix) #to find min. make sure we erase the traces
#now make sure that the real maxima are large enough from the backfround
diff = (peaks - troughs) > threshold
#label this such that every clump of '1's are labelled. Scipy magic!
labeled, num_obj = label(diff) #, structure = pattern)
cutouts = find_objects(labeled) #get cutouts of area with objects
return cutouts
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")
maximg = ndimage.maximum_filter(harrisImage, [7, 7])
minimg = ndimage.minimum_filter(harrisImage, [7, 7])
height, width = harrisImage.shape[:2]
for i in range(0, height):
for j in range(0, width):
destImage[i, j] = (maximg[i, j] == harrisImage[i, j]) and (
maximg[i, j] != minimg[i, j])
#destImage[i, j] = (maximg[i, j] == harrisImage[i, j])
# TODO-BLOCK-END
return destImage
def find_peaks_minmax(z, distance=5., threshold=10.):
"""Method to locate the positive peaks in an image by comparing maximum
and minimum filtered images.
Parameters
----------
z : numpy.ndarray
Matrix of image intensities.
distance : float
Expected distance between peaks.
threshold : float
Minimum difference between maximum and minimum filtered images.
Returns
-------
peaks : :py:class:`numpy.ndarray` of shape (n_peaks, 2)
Peak pixel coordinates.
"""
data_max = ndi.maximum_filter(z, distance)
maxima = (z == data_max)
data_min = ndi.minimum_filter(z, distance)
diff = ((data_max - data_min) > threshold)
maxima[diff == 0] = 0
labeled, num_objects = ndi.label(maxima)
peaks = np.array(ndi.center_of_mass(z, labeled, range(1, num_objects + 1)))
return clean_peaks(np.round(peaks).astype(int))
def new_id_slits(flat):
ncols = flat.shape[1]
midtrace = flat[:, ncols / 2].astype(scipy.float64)
midtrace[midtrace <= 0.] = 1.
laplace = scipy.array([-1., -1., -1., 1., 1., 1.])
deriv = signal.convolve(midtrace, laplace, mode='same') / midtrace
d2 = abs(signal.convolve(midtrace, [-1., 1.], mode='same'))
deriv = ndimage.gaussian_filter1d(deriv, 1)
deriv[:5] = 0.
deriv[-5:] = 0.
tmp = deriv.copy()
tmp.sort()
std = tmp[tmp.size * 0.01:tmp.size * 0.99].std()
peaks = ndimage.maximum_filter(deriv, 9)
right = scipy.where((peaks == deriv) & (peaks > std))[0]
peaks = ndimage.minimum_filter(deriv, 9)
left = scipy.where((peaks == deriv) & (peaks < -1. * std))[0]
orders = []
stars = []
for i in range(len(left)):
thresh = stats.stats.std(midtrace[left[i] + 3:right[i] - 3])
good = scipy.where(d2[left[i]:right[i]] < thresh)[0] + left[i]
orders.append([good[0], good[-1]])
if deriv[right[i]] > 3. * std:
stars.append([good[0], good[-1]])
print orders
print stars
return orders
def get_csf(image, x, y, params):
res_image, mean_intensity, mean_x, mean_y, abs_steps, angle_steps, xs_AB, ys_AB, cols_AB = lib.make_preobr(
image, x, y, params)
maxes = ndimage.maximum_filter(res_image, size=wind4csf, mode="wrap")
mines = ndimage.minimum_filter(res_image, size=wind4csf, mode="wrap")
michelson_contrast = (maxes - mines) / (maxes + mines)
fig, ax = plt.subplots(nrows=1, ncols=4) # , figsize=(15, 15)
ax[0].imshow(image, cmap='gray', vmin=0, vmax=255)
ax[1].imshow(res_image, cmap='gray', vmin=0, vmax=255)
ax[2].imshow(michelson_contrast, cmap='gray', vmin=0, vmax=1)
center_line = michelson_contrast[Len_x // 2, Len_y // 2:]
# wind = signal.parzen(35)
# center_line = np.convolve(center_line, wind, "same")
ax[3].plot(center_line)
fig.savefig(params["outfile"] + ".png", dpi=200)
plt.close('all')
return center_line
def compute_data(compute_fp, input_data, input_fps, selfraster):
"""
computes up and down slopes
"""
arr = input_data[0]
assert arr.shape == tuple(compute_fp.dilate(1).shape)
nodata_mask = arr == nodata
nodata_mask = ndi.binary_dilation(nodata_mask)
kernel = [
[0, 1, 0],
[1, 1, 1],
[0, 1, 0],
]
arru = ndi.maximum_filter(arr, None, kernel) - arr
arru = np.arctan(arru / full_fp.pxsizex)
arru = arru / np.pi * 180.
arru[nodata_mask] = 0
arru = arru[1:-1, 1:-1]
arrd = arr - ndi.minimum_filter(arr, None, kernel)
arrd = np.arctan(arrd / full_fp.pxsizex)
arrd = arrd / np.pi * 180.
arrd[nodata_mask] = 0
arrd = arrd[1:-1, 1:-1]
arr = np.dstack([arrd, arru])
return arr
def regional_minima(a, connectivity=1):
"""Find the regional minima in an ndarray."""
values = unique(a)
delta = (values - minimum_filter(values, footprint=ones(3)))[1:].min()
marker = complement(a)
mask = marker + delta
return marker == morphological_reconstruction(marker, mask, connectivity)
def depth_discont_sobel(di, tol=0.5):
import scipy.ndimage as ndimage
dx = ndimage.convolve(di, [[-1, 0, 1], [-2, 0, 2], [-1, 0, 1]])
dy = ndimage.convolve(di, [[-1, -2, -1], [0, 0, 0], [1, 2, 1]])
diff_im = np.sqrt(dx**2 + dy**2)
diff_im[diff_im < tol] = 0
#import pydb; pydb.set_trace()
di_diff = np.zeros(di.shape)
di_diff[diff_im > 0] = di[diff_im > 0]
#import pdb;pdb.set_trace()
#import pylab
#pylab.ion()
di_diff = ndimage.minimum_filter(di_diff, size=(2, 2))
#for i in range(di_diff.shape[0]):
# for j in range(di_diff.shape[1]-1):
# p1 = di_diff[i,j]
# p2 = di_diff[i,j+1]
# if p1 == 0 or p2 == 0:
# continue
# if p1 > p2:
# p1 = 0
# elif p2 > p1:
# p2 = 0
# di_diff[i,j] = p1
# di_diff[i,j+1] = p2
#import pdb;pdb.set_trace()
#pylab.imshow(di_diff)
return di_diff
def regional_minima(a, connectivity=1):
"""Find the regional minima in an ndarray."""
values = unique(a)
delta = (values - minimum_filter(values, footprint=ones(3)))[1:].min()
marker = complement(a)
mask = marker+delta
return marker == morphological_reconstruction(marker, mask, connectivity)
def find_h_cut(cut):
overlap_y = cut.shape[0]
if overlap_y < 3: return None # overlap too small
w1width = cut.shape[1]
min_vals = np.empty_like(cut)
min_vals[:, 0] = cut[:, 0]
for i in range(1, w1width, 1):
min_vals[:, i] = cut[:, i] + ndimage.minimum_filter(
min_vals[:, i - 1:i + 1],
footprint=[[1, 0], [1, 0], [1, 0]],
mode='constant')[:, 1]
min_vals[0,
i] = cut[0, i] + min(min_vals[0, i - 1], min_vals[1, i - 1])
min_vals[-1, i] = cut[-1, i] + min(min_vals[-1, i - 1],
min_vals[-1, i - 1])
res = np.empty(w1width)
res[-1] = np.argmin(min_vals[:, -1])
for i in range(w1width - 2, -1, -1):
res[i] = res[i + 1] + np.argmin(
min_vals[max(0, res[i + 1] - 1):min(overlap_y, res[i + 1] + 2),
i]) - 1 + int(res[i + 1] - 1 < 0)
return res
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 argmax_translation(array, filter_pcorr, constraints=None, reports=None):
if constraints is None:
constraints = dict(tx=(0, None), ty=(0, None))
# We want to keep the original and here is obvious that
# it won't get changed inadvertently
array_orig = array.copy()
if filter_pcorr > 0:
array = ndi.minimum_filter(array, filter_pcorr)
ashape = np.array(array.shape, int)
mask = np.ones(ashape, float)
# first goes Y, then X
for dim, key in enumerate(("ty", "tx")):
if constraints.get(key, (0, None))[1] is None:
continue
pos, sigma = constraints[key]
alen = ashape[dim]
dom = np.linspace(-alen // 2, -alen // 2 + alen, alen, False)
if sigma == 0:
# generate a binary array closest to the position
idx = np.argmin(np.abs(dom - pos))
vals = np.zeros(dom.size)
vals[idx] = 1.0
else:
vals = np.exp(-(dom - pos)**2 / sigma**2)
if dim == 0:
mask *= vals[:, np.newaxis]
else:
mask *= vals[np.newaxis, :]
array *= mask
# WE ARE FFTSHIFTED already.
# ban translations that are too big
thresh = ashape // 6
mask2 = np.zeros(ashape, int)
mask2[thresh[0]:-thresh[0], thresh[1]:-thresh[1]] = 1
array *= mask2
# Find what we look for
tvec = _argmax_ext(array, 'inf')
tvec = _interpolate(array_orig, tvec)
if 0:
print("tvec: %s" % tvec)
import pylab as pyl
pyl.figure()
pyl.imshow(array, cmap=pyl.cm.gray, interpolation='nearest')
pyl.colorbar()
# pyl.show()
# If we use constraints or min filter,
# array_orig[tvec] may not be the maximum
success = _get_success(array_orig, tuple(tvec), 2)
if reports is not None:
reports["amt-orig"] = array_orig.copy()
reports["amt-postproc"] = array.copy()
return tvec, success
def fill_simple_depressions(values):
""" Fill simple depressions in-place. """
footprint = np.array([(1, 1, 1),
(1, 0, 1),
(1, 1, 1)], dtype='b1')
edge = ndimage.minimum_filter(values, footprint=footprint)
locs = edge > values
values[locs] = edge[locs]
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 minfilt_thresh(array, t, rad):
"""
Applies a minimum filter to the input array and returns an array
thresholded to the specified value.
"""
marray = ndi.minimum_filter(array, footprint=circlemask(rad))
thrarr = where(marray < t, 1, 0)
return thrarr
def complex_flux(spectrogram, diff_frames=None, diff_max_bins=3,
temporal_filter=3, temporal_origin=0):
"""
Complex Flux with a local group delay based tremolo suppression.
:param spectrogram: Spectrogram instance
:param diff_frames: number of frames to calculate the diff to [int]
:param diff_max_bins: number of bins used for maximum filter [int]
:param temporal_filter: temporal maximum filtering of the local group delay
:param temporal_origin: origin of the temporal maximum filter
:return: complex flux onset detection function
"Local group delay based vibrato and tremolo suppression for onset
detection"
Sebastian Böck and Gerhard Widmer.
Proceedings of the 13th International Society for Music Information
Retrieval Conference (ISMIR), 2013.
"""
# create a mask based on the local group delay information
from scipy.ndimage import maximum_filter, minimum_filter
# take only absolute values of the local group delay and normalize them
lgd = np.abs(spectrogram.stft.phase().lgd()) / np.pi
# maximum filter along the temporal axis
# TODO: use HPSS instead of simple temporal filtering
if temporal_filter > 0:
lgd = maximum_filter(lgd, size=[temporal_filter, 1],
origin=temporal_origin)
# lgd = uniform_filter(lgd, size=[1, 3]) # better for percussive onsets
# create the weighting mask
try:
# if the magnitude spectrogram was filtered, use the minimum local
# group delay value of each filterbank (expanded by one frequency
# bin in both directions) as the mask
mask = np.zeros_like(spectrogram)
num_bins = lgd.shape[1]
for b in range(mask.shape[1]):
# determine the corner bins for the mask
corner_bins = np.nonzero(spectrogram.filterbank[:, b])[0]
# always expand to the next neighbour
start_bin = corner_bins[0] - 1
stop_bin = corner_bins[-1] + 2
# constrain the range
if start_bin < 0:
start_bin = 0
if stop_bin > num_bins:
stop_bin = num_bins
# set mask
mask[:, b] = np.amin(lgd[:, start_bin: stop_bin], axis=1)
except AttributeError:
# if the spectrogram is not filtered, use a simple minimum filter
# covering only the current bin and its neighbours
mask = minimum_filter(lgd, size=[1, 3])
# sum all positive 1st order max. filtered and weighted differences
return np.sum(spectrogram.diff(diff_frames=diff_frames,
diff_max_bins=diff_max_bins,
positive_diffs=True) * mask, axis=1)
def __local_minima_fancy__(self,fits, window=50):
from scipy.ndimage import minimum_filter
fits = numpy.asarray(fits)
minfits = minimum_filter(fits, size=window, mode="wrap")
minima_mask = fits == minfits
good_indices = numpy.arange(len(fits))[minima_mask]
good_fits = fits[minima_mask]
order = good_fits.argsort()
return good_indices[order], good_fits[order]
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 _lgd_mask(spec, lgd, filterbank=None, temporal_filter=0,
temporal_origin=0):
"""
Calculates a weighting mask for the magnitude spectrogram based on the
local group delay.
:param spec: the magnitude spectrogram
:param lgd: local group delay of the spectrogram
:param filterbank: filterbank used for dimensionality reduction of
the magnitude spectrogram
:param temporal_filter: temporal maximum filtering of the local group
delay
:param temporal_origin: origin of the temporal maximum filter
"Local group delay based vibrato and tremolo suppression for onset
detection"
Sebastian Böck and Gerhard Widmer.
Proceedings of the 13th International Society for Music Information
Retrieval Conference (ISMIR), 2013.
"""
from scipy.ndimage import maximum_filter, minimum_filter
# take only absolute values of the local group delay
lgd = np.abs(lgd)
# maximum filter along the temporal axis
if temporal_filter > 0:
lgd = maximum_filter(lgd, size=[temporal_filter, 1],
origin=temporal_origin)
# lgd = uniform_filter(lgd, size=[1, 3]) # better for percussive onsets
# create the weighting mask
if filterbank is not None:
# if the magnitude spectrogram was filtered, use the minimum local
# group delay value of each filterbank (expanded by one frequency
# bin in both directions) as the mask
mask = np.zeros_like(spec)
num_bins = lgd.shape[1]
for b in range(mask.shape[1]):
# determine the corner bins for the mask
corner_bins = np.nonzero(filterbank[:, b])[0]
# always expand to the next neighbour
start_bin = corner_bins[0] - 1
stop_bin = corner_bins[-1] + 2
# constrain the range
if start_bin < 0:
start_bin = 0
if stop_bin > num_bins:
stop_bin = num_bins
# set mask
mask[:, b] = np.amin(lgd[:, start_bin: stop_bin], axis=1)
else:
# if the spectrogram is not filtered, use a simple minimum filter
# covering only the current bin and its neighbours
mask = minimum_filter(lgd, size=[1, 3])
# return the normalized mask
return mask / np.pi
def balanceimage(img, r, R):
"""Balance the brightness of an image by leveling.
This is achieved here by applying a minimum filter over radius r
and a uniform filter over radius R, and substracting the minimum
of the two from the original image."""
img_min = ndimage.minimum_filter(img, r)
img_uni = ndimage.uniform_filter(img, R)
return img - numpy.minimum(img_min, img_uni)
def test_locmin(self):
arr = np.ones((9, 12))
arr[4, 3] = -2
arr[4, 7] = -5
filter = ndimage.minimum_filter(arr, 8, mode='constant', cval=np.min(arr) - 1)
filter[filter==np.max(arr)] = -999
maxoutt = (arr==filter)
yy, xx = np.where((maxoutt == 1))
assert (yy, xx) == (4, 7)
filter = ndimage.minimum_filter(arr, 3, mode='constant', cval=np.min(arr) - 1)
filter[filter == np.max(arr)] = -999
maxoutt = (arr == filter)
yy, xx = np.where((maxoutt == 1))
assert_array_equal(np.array([4,4]),yy)
assert_array_equal(np.array([3, 7]), xx)
def local_minima(fits, window=15):
"""fm Zachary Pinkus"""
from scipy.ndimage import minimum_filter
fits = np.asarray(fits)
minfits = minimum_filter(fits, size=window, mode="wrap")
minima_mask = fits == minfits
good_indices = np.arange(len(fits))[minima_mask]
good_fits = fits[minima_mask]
order = good_fits.argsort()
return good_indices[order], good_fits[order]
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 getCutoffCriteria(self, errorArray): #do a small minimum filter to get rid of outliers size = int(len(errorArray)**0.3)+1 errorArray2 = ndimage.minimum_filter(errorArray, size=size, mode='wrap') mean = ndimage.mean(errorArray2) stdev = ndimage.standard_deviation(errorArray2) ### this is so arbitrary cut = mean + 5.0 * stdev + 2.0 ### anything bigger than 20 pixels is too big if cut > self.data['pixdiam']: cut = self.data['pixdiam'] return cut
def argmax_translation(array, filter_pcorr, constraints=None, reports=None):
if constraints is None:
constraints = dict(tx=(0, None), ty=(0, None))
# We want to keep the original and here is obvious that
# it won't get changed inadvertently
array_orig = array.copy()
if filter_pcorr > 0:
array = ndi.minimum_filter(array, filter_pcorr)
ashape = np.array(array.shape, int)
mask = np.ones(ashape, float)
# first goes Y, then X
for dim, key in enumerate(("ty", "tx")):
if constraints.get(key, (0, None))[1] is None:
continue
pos, sigma = constraints[key]
alen = ashape[dim]
dom = np.linspace(-alen // 2, -alen // 2 + alen, alen, False)
if sigma == 0:
# generate a binary array closest to the position
idx = np.argmin(np.abs(dom - pos))
vals = np.zeros(dom.size)
vals[idx] = 1.0
else:
vals = np.exp(- (dom - pos) ** 2 / sigma ** 2)
if dim == 0:
mask *= vals[:, np.newaxis]
else:
mask *= vals[np.newaxis, :]
array *= mask
# WE ARE FFTSHIFTED already.
# ban translations that are too big
aporad = (ashape // 6).min()
mask2 = get_apofield(ashape, aporad)
array *= mask2
# Find what we look for
tvec = _argmax_ext(array, 'inf')
tvec = _interpolate(array_orig, tvec)
# If we use constraints or min filter,
# array_orig[tvec] may not be the maximum
success = _get_success(array_orig, tuple(tvec), 2)
if reports is not None and reports.show("translation"):
reports["amt-orig"] = array_orig.copy()
reports["amt-postproc"] = array.copy()
return tvec, success
def cleanspectra(w, f, e=None, dw=2, grow=6, neg=False):
"""Remove possible bad pixels"""
if e is None: e = f*0.0+f.std()
m = (w>0)
#set a few unreliable sky lines to zero
for l in [5577, 6300, 6364]:
m[abs(w-l)<dw]=0
if neg: m = m * (f>0)
#remove and grow the bad areas
m = nd.minimum_filter(m, size=grow)
return w[m],f[m],e[m]
def local_maxima(data, span=10, sign=1):
from scipy.ndimage import minimum_filter
from scipy.ndimage import maximum_filter
data = numpy.asarray(data)
print 'data size: ', data.shape
if sign <= 0: # look for minima
maxfits = minimum_filter(data, size=span, mode="wrap")
else:
maxfits = maximum_filter(data, size=span, mode="wrap")
print 'maxfits shape: ', maxfits.shape
maxima_mask = numpy.where(data == maxfits)
good_indices = numpy.arange(len(data))[maxima_mask]
print 'len good index: ', len(good_indices)
good_fits = data[maxima_mask]
order = good_fits.argsort()
return good_indices[order], good_fits[order]
def rolling_minimum_background(img, size=(31, 51), kernel=None,
geometry='rectangular', topography='flat',
percentile=0):
"""
Instead of calculating the resulting image, just calculate the background and apply with
img -= rolling_minimum_background(img)
That way you can apply any amount of pre-filters without complex logic:
img -= rolling_minimum_background(gaussian_filter(img, sigma=2))
Notes:
This doesn't work well with images with sharp boundaries, e.g. the edge of a gel.
For best result, apply AFTER opening() and col+row leveling.
Args:
img:
size: int or 2-tuple with (height, width),
should be higher than the thickest band and wider than the widest smear. Square is usually OK.
kernel: specify kernel / footprint / structuring element manually.
geometry:
topography:
percentile: Use percentile_filter with this percentile instead of minimum_filter (equivalent to percentile=0)
Returns:
background image
"""
if kernel is None:
if isinstance(size, int):
size = (size, size)
if geometry in ('round', 'disk', 'ellipse'):
# multiply with round binary kernel with ones round/elliptical shape.
kernel = ellipse_binary(size)
elif geometry == 'rectangular' or geometry is None:
kernel = np.ones(size)
if topography == 'ball':
# topography generally doesn't work because ndimage filters takes boolean footprints.
# I could probalby do it with a generic filter, or by some other means.
pass
if percentile:
# percentile_filter; footprint must be boolean array; size=(n,m) is equivalent to footprint=np.ones((n,m))
background = percentile_filter(img, percentile=percentile, footprint=kernel)
else:
background = minimum_filter(img, footprint=kernel)
return background
def non_extrema_suppression(features, size=None, output=None):
"""Set non-extrema to nan"""
# Find maxima
maxima = ndimage.maximum_filter(features, size) == features
# Find minima
minima = ndimage.minimum_filter(features, size) == features
extrema = np.logical_xor(maxima, minima)
if output is None:
output = np.zeros_like(features)
output[extrema] = features[extrema]
output[np.logical_not(extrema)] = np.nan
return output
def find_h_cut(cut):
overlap_y = cut.shape[0]
if overlap_y < 3: return None # overlap too small
w1width = cut.shape[1]
min_vals = np.empty_like(cut)
min_vals[:, 0] = cut[:, 0]
for i in range(1, w1width, 1):
min_vals[:, i] = cut[:, i] + ndimage.minimum_filter(min_vals[:,i-1:i+1], footprint = [[1,0], [1,0], [1,0]], mode = 'constant')[:,1]
min_vals[0, i] = cut[0, i] + min (min_vals[0, i-1], min_vals[1, i-1])
min_vals[-1, i] = cut[-1, i] + min (min_vals[-1, i-1], min_vals[-1, i-1])
res = np.empty(w1width)
res[-1] = np.argmin(min_vals[:,-1])
for i in range(w1width-2, -1, -1):
res[i] = res[i+1] + np.argmin(min_vals[max(0,res[i+1]-1): min(overlap_y,res[i+1]+2), i]) - 1 + int(res[i+1]-1 < 0)
return res
def find_v_cut(cut):
overlap_x = cut.shape[1]
if overlap_x < 3: return None
w1height = cut.shape[0]
min_vals = np.empty_like(cut)
min_vals[0] = cut[0]
for i in range(1, w1height, 1):
min_vals[i] = cut[i] + ndimage.minimum_filter(min_vals[i-1:i+1], footprint = [[1,1,1], [0, 0, 0]], mode = 'constant')[1]
min_vals[i, 0] = cut[i, 0] + min (min_vals[i-1, 0], min_vals[i-1, 1])
min_vals[i, -1] = cut[i, -1] + min (min_vals[i-1, -1], min_vals[-i-1, -1])
res = np.empty(w1height)
res[-1] = np.argmin(min_vals[-1])
for i in range(w1height-2, -1, -1):
res[i] = res[i+1] + np.argmin(min_vals[i, max(res[i+1]-1, 0): min(overlap_x,res[i+1]+2)]) - 1 + int(res[i+1]-1 < 0)
return res
def find_all_nthres_fast(data, thres, msep, find_segs=False):
"""
Fast version of find_all_nthres_fast. 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
mn = ndimage.minimum_filter(data, size=wsize, mode='constant') == data
# find positive threshold mask
nthres = np.ma.less(data, thres)
# peaks are bitwise and of maximum mask and threshold mask
locations = np.transpose(np.nonzero(np.bitwise_and(nthres, mn)))
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
def sliding_minima(img=None, weight=1., window_size=30,
boundary_condition='reflect'):
'''
Subtracts the minimum calculated within a sliding window from the centre of
the window.
Parameters
----------
img : array_like
Single image as numpy array or multiple images as array-like object
weight : scalar
Fraction of minima to be subtracted from each pixel.
Value of `weight` should be in the interval (0.0,1.0).
window_size : scalar or tuple
Sets the size of the sliding window.
Specifying `window_size=3` is equivalent to `window_size=(3,3)`.
boundary_condition : {'reflect', 'constant', 'nearest', 'mirror', 'wrap'}
Mode of handling array borders.
'''
img_out = img - weight * nd.minimum_filter(img,
size=window_size,
mode=boundary_condition)
return img_out
def binaryContour(A): x3d = numpy.zeros([3,3,3]) x3d[1,1,:] = 1 x3d[:,1,1] = 1 x3d[1,:,1] = 1 return A-ndimage.minimum_filter(A,footprint=x3d).astype(numpy.uint8)
