def _reassign_bad_bins(classe, x, y):
"""
Implements steps (vi)-(vii) in section 5.1 of Cappellari & Copin (2003)
"""
# Find the centroid of all succesful bins.
# CLASS = 0 are unbinned pixels which are excluded.
#
good = np.unique(classe[classe > 0])
xnode = ndimage.mean(x, labels=classe, index=good)
ynode = ndimage.mean(y, labels=classe, index=good)
# Reassign pixels of bins with S/N < targetSN
# to the closest centroid of a good bin
#
bad = classe == 0
index = np.argmin((x[bad, np.newaxis] - xnode)**2 + (y[bad, np.newaxis] - ynode)**2, axis=1)
classe[bad] = good[index]
# Recompute all centroids of the reassigned bins.
# These will be used as starting points for the CVT.
#
good = np.unique(classe)
xnode = ndimage.mean(x, labels=classe, index=good)
ynode = ndimage.mean(y, labels=classe, index=good)
return xnode, ynode
def ClusterObjects(farn, struct_elem):
magn_img = farn.magnitude_image
dir_img = farn.direction_image
bin_img = np.zeros(shape=(magn_img.shape[0], magn_img.shape[1]), dtype=np.uint8)
bin_img[magn_img < 25] = 0
bin_img[magn_img >= 25] = 1
bin_img = ndimage.binary_dilation(bin_img, structure=struct_elem, iterations=3).astype(bin_img.dtype)
labels, nb_labels = Morphology.ConnenctedComponents(bin_img)
filt_labels, areas, nb_new_labels = Morphology.FilterArea(bin_img, labels, nb_labels, 480)
temp_magn = ndimage.mean(magn_img, filt_labels, range(nb_new_labels + 1))
temp_dir = ndimage.mean(dir_img, filt_labels, range(nb_new_labels + 1))
data = np.concatenate((np.reshape(temp_magn, (-1,1)), np.reshape(temp_dir, (-1,1))), axis=1)
clusters = -1
if nb_new_labels >= 1:
Y = pdist(data, 'euclidean')
agglo = AgglomerativeClustering.Agglomerative(Y, 50.)
agglo.AggloClustering(criterion = 'distance', method = 'single', metric = 'euclidean', normalized = False)
clusters = agglo.clusters
bin_img[filt_labels == 0] = 0
bin_img[filt_labels >= 1] = 1
return bin_img, nb_new_labels, temp_magn, temp_dir, data, clusters
def calculateParticleStackStats(self, imgstackfile, boxedpartdatas):
### read mean and stdev
partmeantree = []
t0 = time.time()
imagicdata = apImagicFile.readImagic(imgstackfile)
apDisplay.printMsg("gathering mean and stdev data")
### loop over the particles and read data
for i in range(len(boxedpartdatas)):
partdata = boxedpartdatas[i]
partarray = imagicdata['images'][i]
### if particle stdev == 0, then it is all constant, i.e., a bad particle
stdev = float(partarray.std())
if stdev < 1.0e-6:
apDisplay.printError("Standard deviation == 0 for particle %d in image %s"%(i,self.shortname))
### skew and kurtosis
partravel = numpy.ravel(partarray)
skew = float(stats.skew(partravel))
kurtosis = float(stats.kurtosis(partravel))
### edge and center stats
edgemean = float(ndimage.mean(partarray, self.edgemap, 1.0))
edgestdev = float(ndimage.standard_deviation(partarray, self.edgemap, 1.0))
centermean = float(ndimage.mean(partarray, self.edgemap, 0.0))
centerstdev = float(ndimage.standard_deviation(partarray, self.edgemap, 0.0))
self.summedParticles += partarray
### take abs of all means, because ctf whole image may become negative
partmeandict = {
'partdata': partdata,
'mean': abs(float(partarray.mean())),
'stdev': stdev,
'min': float(partarray.min()),
'max': float(partarray.max()),
'skew': skew,
'kurtosis': kurtosis,
'edgemean': abs(edgemean),
'edgestdev': edgestdev,
'centermean': abs(centermean),
'centerstdev': centerstdev,
}
### show stats for first particle
"""
if i == 0:
keys = partmeandict.keys()
keys.sort()
mystr = "PART STATS: "
for key in keys:
if isinstance(partmeandict[key], float):
mystr += "%s=%.3f :: "%(key, partmeandict[key])
print mystr
"""
partmeantree.append(partmeandict)
self.meanreadtimes.append(time.time()-t0)
return partmeantree
def compute_resultant_force_directions(nx_arr, ny_arr, nz_arr,
label_im, nb_labels):
nx = ni.mean(nx_arr, label_im, range(1, nb_labels + 1))
ny = ni.mean(ny_arr, label_im, range(1, nb_labels + 1))
nz = ni.mean(nz_arr, label_im, range(1, nb_labels + 1))
if nx.__class__!= list:
nx = [nx]
ny = [ny]
nz = [nz]
return nx, ny, nz
def compute_centers_of_pressure(cx_arr, cy_arr, cz_arr, label_im,
nb_labels):
# for the forearm skin patch, it might be more accurate to perform
# the averaging in cylindrical coordinates (to ensure that the COP
# lies on the surface of the skin), but Advait does not care
# enough.
cx = ni.mean(cx_arr, label_im, range(1, nb_labels + 1))
cy = ni.mean(cy_arr, label_im, range(1, nb_labels + 1))
cz = ni.mean(cz_arr, label_im, range(1, nb_labels + 1))
if cx.__class__!= list:
cx = [cx]
cy = [cy]
cz = [cz]
return cx, cy, cz
def createRaster(self):
"""
from center of image, generate a raster of points
"""
#print "xy raster"
try:
imageshape = self.currentimagedata['image'].shape
except:
imageshape = (512,512)
xspacing = float(self.settings['raster spacing'])
xpoints = int(self.settings['raster limit'])
if self.settings['raster symmetric']:
yspacing = xspacing
ypoints = xpoints
else:
yspacing = float(self.settings['raster spacing asymm'])
ypoints = int(self.settings['raster limit asymm'])
radians = math.pi * self.settings['raster angle'] / 180.0
if self.settings['raster center on image']:
x0 = imageshape[0]/2.0
y0 = imageshape[1]/2.0
else:
x0 = float(self.settings['raster center x'])
y0 = float(self.settings['raster center y'])
points = []
#new stuff
xlist = numpy.asarray(range(xpoints), dtype=numpy.float32)
xlist -= ndimage.mean(xlist)
ylist = numpy.asarray(range(ypoints), dtype=numpy.float32)
ylist -= ndimage.mean(ylist)
for xt in xlist:
xshft = xt * xspacing
for yt in ylist:
yshft = yt * yspacing
xrot = xshft * numpy.cos(radians) - yshft * numpy.sin(radians)
yrot = yshft * numpy.cos(radians) + xshft * numpy.sin(radians)
x = int(xrot + x0)
y = int(yrot + y0)
if x < 0 or x >= imageshape[0]: continue
if y < 0 or y >= imageshape[1]: continue
points.append( (x,y) )
#old stuff
self.setTargets(points, 'Raster')
self.rasterpoints = points
self.logger.info('Full raster has %s points' % (len(points),))
def test_mean03():
labels = np.array([1, 2])
for type in types:
input = np.array([[1, 2], [3, 4]], type)
output = ndimage.mean(input, labels=labels,
index=2)
assert_almost_equal(output, 3.0)
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 interpixel_watershed(img,min_dist=3,max_iter=100000, **filter_args):
##don't work... stop dev at sort_label
img = _filter(img, **filter_args)
# make marker map
size = (2*min_dist+1)
marker = _local_min(-img,footprint=size).astype('int16') # find markers
marker,N = _nd.label(marker, structure=_np.ones(img.ndim*(3,)))
# sort label (marker)
mean = _nd.mean(img,marker,index=_np.arange(1,N+1))
order = _np.argsort(mean)
# here order[i] = position of marker==i+1 in the sorted list of all marker values
#order[marker[marker!=0]-1]
# => knowing that all pixels of a label have same image value
#mask = marker!=0
#label = marker[mask]
#order = _np.argsort(img[mask])
#marker[mask] = label[order]
return marker, N, order
def _estimate_profile(self, image, image_err, mask):
"""
Estimate image profile.
"""
from scipy import ndimage
p = self.parameters
labels = self._label_image(image, mask)
profile_err = None
index = np.arange(1, len(self._get_x_edges(image)))
if p['method'] == 'sum':
profile = ndimage.sum(image.data, labels.data, index)
if image.unit.is_equivalent('counts'):
profile_err = np.sqrt(profile)
elif image_err:
# gaussian error propagation
err_sum = ndimage.sum(image_err.data ** 2, labels.data, index)
profile_err = np.sqrt(err_sum)
elif p['method'] == 'mean':
# gaussian error propagation
profile = ndimage.mean(image.data, labels.data, index)
if image_err:
N = ndimage.sum(~np.isnan(image_err.data), labels.data, index)
err_sum = ndimage.sum(image_err.data ** 2, labels.data, index)
profile_err = np.sqrt(err_sum) / N
return profile, profile_err
def test_mean01():
"mean 1"
labels = np.array([1, 0], bool)
for type in types:
input = np.array([[1, 2], [3, 4]], type)
output = ndimage.mean(input, labels=labels)
assert_almost_equal(output, 2.0)
def compute(self, dataset_pool):
persons = dataset_pool.get_dataset('person')
hhs = self.get_dataset()
where_adult = where(persons.get_attribute('is_adult'))[0]
age = persons.get_attribute('age')
return array(ndimage.mean(age[where_adult], labels=persons.get_attribute('household_id')[where_adult],
index=hhs.get_id_attribute()))
def getRealLabeledMeanStdev(image,labeled_image,indices,info):
print "Getting real mean and stdev"
mean=nd.mean(image,labels=labeled_image,index=indices)
stdev=nd.standard_deviation(image,labels=labeled_image,index=indices)
ll=0
try:
len(mean)
except:
mean=[mean]
stdev=[stdev]
try:
len(indices)
except:
indices=[indices]
try:
info.keys()
except:
offset=1
else:
offset=0
for l in indices:
info[l-offset][1]=mean[ll]
info[l-offset][2]=stdev[ll]
ll += 1
return info
def binarization(image):
"""
Binarize the image to improve contrast. Makes image black and white only.
:param image: 256x256 numpy array of fingerprint
:param window_size: Size of the window. It is recommended that this be set to 32.
:return: 256x256 numpy array of enhanced fingerprint
"""
(w,h) = image.shape
size = 16 #Window Size
(w,h) = image.shape
w1 = np.floor(w/size)*size
h1 = np.floor(h/size)*size
ft_output = np.zeros((w1,h1),dtype=np.double)
"Running same window as FFT.... eventually we should just have one loop"
for i in range(0,int(w1)-1,size):
for j in range(0,int(h1)-1,size):
#Create window sizes
a = size+i
b = size+j
#Get windowed mean
mean = ndimage.mean(image[i:a,j:b])
#If pixel is greater than mean, 1, O.W. 0
image[i:a,j:b] = np.where(image[i:a,j:b] > mean, 1, 0)
return image
def normalizeImage(a): """ Normalizes numarray to fit into an image format that is values between 0 and 255. """ #Minimum image value, i.e. how black the image can get minlevel = 0.0 #Maximum image value, i.e. how white the image can get maxlevel = 235.0 #Maximum standard deviations to include, i.e. pixel > N*stdev --> white devlimit=5.0 imrange = maxlevel - minlevel avg1=ndimage.mean(a) stdev1=ndimage.standard_deviation(a) min1=ndimage.minimum(a) if(min1 < avg1-devlimit*stdev1): min1 = avg1-devlimit*stdev1 max1=ndimage.maximum(a) if(max1 > avg1+devlimit*stdev1): max1 = avg1+devlimit*stdev1 a = (a - min1)/(max1 - min1)*imrange + minlevel a = numarray.where(a > maxlevel,255.0,a) a = numarray.where(a < minlevel,0.0,a) return a
def phase_correlate(image, template): #CALCULATE BIGGER MAP SIZE shape = image.shape kshape = template.shape oversized = (numarray.array(shape) + numarray.array(kshape)) #EXPAND IMAGE TO BIGGER SIZE avg=ndimage.mean(image) image2 = convolve.iraf_frame.frame(image, oversized, mode="wrap", cval=avg) #CALCULATE FOURIER TRANSFORMS imagefft = fft.real_fft2d(image2, s=oversized) templatefft = fft.real_fft2d(template, s=oversized) #imagefft = fft.fft2d(image2, s=oversized) #templatefft = fft.fft2d(template, s=oversized) #MULTIPLY FFTs TOGETHER newfft = (templatefft * numarray.conjugate(imagefft)).copy() del templatefft #NORMALIZE CC TO GET PC print "d" phasefft = newfft / numarray.absolute(newfft) del newfft print "d" #INVERSE TRANSFORM TO GET RESULT correlation = fft.inverse_real_fft2d(phasefft, s=oversized) #correlation = fft.inverse_fft2d(phasefft, s=oversized) del phasefft #RETURN CENTRAL PART OF IMAGE (SIDES ARE JUNK) return correlation[ kshape[0]/2-1:shape[0]+kshape[0]/2-1, kshape[1]/2-1:shape[1]+kshape[1]/2-1 ]
def labelmeanfilter(y, x): # requires integer labels # from mailing list scipy-user 2009-02-11 labelsunique = np.arange(np.max(y)+1) labelmeans = np.array(ndimage.mean(x, labels=y, index=labelsunique)) # returns label means for each original observation return labelmeans[y]
def labelmeanfilter_str(ys, x):
# works also for string labels in ys, but requires 1D
# from mailing list scipy-user 2009-02-11
unil, unilinv = np.unique1d(ys, return_index=False, return_inverse=True)
labelmeans = np.array(ndimage.mean(x, labels=unilinv, index=np.arange(np.max(unil)+1)))
arr3 = labelmeans[unilinv]
return arr3
def block_mean(ar, fact):
assert isinstance(fact, int), type(fact)
sx, sy = ar.shape
X, Y = numpy.ogrid[0:sx, 0:sy]
regions = sy/fact * (X/fact) + Y/fact
res = ndimage.mean(ar, labels=regions, index=numpy.arange(regions.max() + 1))
res.shape = (sx/fact, sy/fact)
return res
def avg_school_score(fazes, schools):
"""
Computes the average of the school's total score over FAZes, where missing values are removed
from the computation. Missing values are those that are less or equal zero.
"""
valid_idx = schools.total_score > 0
res = ndi.mean(schools.total_score.values[valid_idx.values], labels=schools.faz_id.values[valid_idx.values], index=fazes.index)
return pd.Series(res, index=fazes.index).fillna(0)
def repairPicks(a1, a2, rmsd): """ Attempts to repair lists a1 and a2 that have become shifted out of frame with minimal damage """ maxdev = ndimage.mean(rmsd[:5]) avgdev = 3*ndimage.mean(rmsd) x0 = [ maxdev, avgdev, 0.25*len(rmsd), 0.75*len(rmsd) ] print x0 solved = optimize.fmin(_rsmdStep, x0, args=([rmsd]), xtol=1e-4, ftol=1e-4, maxiter=500, maxfun=500, disp=0, full_output=1) upstep = int(math.floor(solved[0][2])) print solved a1b = numpyPop2d(a1, upstep) a2b = numpyPop2d(a2, upstep) return a1b, a2b
def downsample_pattern(image, factor):
"""Image shape must be exact multiples of downsample factor"""
from scipy import ndimage
size_y, size_x = image.shape
y_2d, x_2d = _numpy.ogrid[:size_y, :size_x]
regions = size_x/factor * (y_2d/factor) + x_2d/factor
result = ndimage.mean(image, labels=regions,
index=_numpy.arange(regions.max()+1))
result.shape = (size_y/factor, size_x/factor)
def test_mean04():
"mean 4"
labels = np.array([[1, 2], [2, 4]], np.int8)
for type in types:
input = np.array([[1, 2], [3, 4]], type)
output = ndimage.mean(input, labels=labels,
index=[4, 8, 2])
assert_array_almost_equal(output[[0,2]], [4.0, 2.5])
assert_(np.isnan(output[1]))
def analyzeList(self, mylist, myrange=(0,1,1), filename=None):
"""
histogram2(a, bins) -- Compute histogram of a using divisions in bins
Description:
Count the number of times values from array a fall into
numerical ranges defined by bins. Range x is given by
bins[x] <= range_x < bins[x+1] where x =0,N and N is the
length of the bins array. The last range is given by
bins[N] <= range_N < infinity. Values less than bins[0] are
not included in the histogram.
Arguments:
a -- 1D array. The array of values to be divied into bins
bins -- 1D array. Defines the ranges of values to use during
histogramming.
Returns:
1D array. Each value represents the occurences for a given
bin (range) of values.
"""
#hist,bmin,minw,err = stats.histogram(mynumpy, numbins=36)
#print hist,bmin,minw,err,"\n"
if len(mylist) < 2:
apDisplay.printWarning("Did not write file not enough rows ("+str(filename)+")")
return
if myrange[0] is None:
mymin = float(math.floor(ndimage.minimum(mylist)))
else:
mymin = float(myrange[0])
if myrange[1] is None:
mymax = float(math.ceil(ndimage.maximum(mylist)))
else:
mymax = float(myrange[1])
mystep = float(myrange[2])
mynumpy = numpy.asarray(mylist, dtype=numpy.float32)
print "range=",round(ndimage.minimum(mynumpy),2)," <> ",round(ndimage.maximum(mynumpy),2)
print " mean=",round(ndimage.mean(mynumpy),2)," +- ",round(ndimage.standard_deviation(mynumpy),2)
#histogram
bins = []
mybin = mymin
while mybin <= mymax:
bins.append(mybin)
mybin += mystep
bins = numpy.asarray(bins, dtype=numpy.float32)
apDisplay.printMsg("Creating histogram with "+str(len(bins))+" bins")
hist = stats.histogram2(mynumpy, bins=bins)
#print bins
#print hist
if filename is not None:
f = open(filename, "w")
for i in range(len(bins)):
out = ("%3.4f %d\n" % (bins[i] + mystep/2.0, hist[i]) )
f.write(out)
f.write("&\n")
def __init__(self, name):
self.name = name
self.labels = workspace.object_set.get_objects(name).segmented
self.nobjects = np.max(self.labels)
if self.nobjects != 0:
self.range = np.arange(1, np.max(self.labels) + 1)
self.labels = self.labels.copy()
self.labels[~im.mask] = 0
self.current_mean = fix(scind.mean(im.pixel_data, self.labels, self.range))
self.start_mean = np.maximum(self.current_mean, np.finfo(float).eps)
def _rsmdStep(x1, rmsd): mean1 = x1[0] mean2 = x1[1] upstep = int(x1[2]) dnstep = int(x1[3]) fit = numpy.ones((len(rmsd)))*mean1 fit[upstep:dnstep] += mean2 error = ndimage.mean((rmsd-fit)**2/fit) return error
def getImageInfo(im):
"""
prints out image information good for debugging
"""
avg1=ndimage.mean(im)
stdev1=ndimage.standard_deviation(im)
min1=ndimage.minimum(im)
max1=ndimage.maximum(im)
return avg1,stdev1,min1,max1
def calcImageFft(image, oversized):
# EXPAND IMAGE TO BIGGER SIZE
avg = nd_image.mean(image)
image2 = convolve.iraf_frame.frame(image, oversized, mode="constant", cval=avg)
# CALCULATE FOURIER TRANSFORMS
imagefft = fft.real_fft2d(image2, s=oversized)
# imagefft = fft.fft2d(image2, s=oversized)
del image2
return imagefft
def block_mean(ar, fact):
# function to downsample inputs by a factor of two
assert isinstance(fact, int), type(fact)
sx, sy = ar.shape
X, Y = np.ogrid[0:sx, 0:sy]
regions = sy/fact * (X/fact) + Y/fact
res = ndimage.mean(ar, labels=regions, index=np.arange(regions.max() + 1))
res.shape = (sx/fact, sy/fact)
return res
def run(self, workspace):
parents = workspace.object_set.get_objects(self.parent_name.value)
children = workspace.object_set.get_objects(self.sub_object_name.value)
child_count, parents_of = parents.relate_children(children)
m = workspace.measurements
if self.wants_per_parent_means.value:
parent_indexes = np.arange(np.max(parents.segmented))+1
for feature_name in m.get_feature_names(self.sub_object_name.value):
if not self.should_aggregate_feature(feature_name):
continue
data = m.get_current_measurement(self.sub_object_name.value,
feature_name)
if data is not None:
if len(parents_of) > 0:
means = fix(scind.mean(data.astype(float),
parents_of, parent_indexes))
else:
means = np.zeros((0,))
mean_feature_name = FF_MEAN%(self.sub_object_name.value,
feature_name)
m.add_measurement(self.parent_name.value, mean_feature_name,
means)
m.add_measurement(self.sub_object_name.value,
FF_PARENT%(self.parent_name.value),
parents_of)
m.add_measurement(self.parent_name.value,
FF_CHILDREN_COUNT%(self.sub_object_name.value),
child_count)
parent_names = self.get_parent_names()
for parent_name in parent_names:
if self.find_parent_child_distances in (D_BOTH, D_CENTROID):
self.calculate_centroid_distances(workspace, parent_name)
if self.find_parent_child_distances in (D_BOTH, D_MINIMUM):
self.calculate_minimum_distances(workspace, parent_name)
if workspace.frame is not None:
figure = workspace.create_or_find_figure(title="RelateObjects, image cycle #%d"%(
workspace.measurements.image_set_number),subplots=(2,2))
figure.subplot_imshow_labels(0,0,parents.segmented,
title = self.parent_name.value)
figure.subplot_imshow_labels(1,0,children.segmented,
title = self.sub_object_name.value,
sharex = figure.subplot(0,0),
sharey = figure.subplot(0,0))
parent_labeled_children = np.zeros(children.segmented.shape, int)
parent_labeled_children[children.segmented > 0] = \
parents_of[children.segmented[children.segmented > 0]-1]
figure.subplot_imshow_labels(0,1,parent_labeled_children,
"%s labeled by %s"%
(self.sub_object_name.value,
self.parent_name.value),
sharex = figure.subplot(0,0),
sharey = figure.subplot(0,0))
### File description
# The file contains classical algorithms for sharpness calculation
### Packages import
from scipy import ndimage
from skimage import morphology
import numpy as np
def edge_sharpness(image):
"""
Edge enhancement method
"""
img_dilat = morphology.dilation(image)
img_result = img_dilat - image
return ndimage.sum(img_result)
def variance_sharpness(image):
"""
Variance-based method
"""
return ndimage.variance(image)
def variance_normal_sharpness(image):
"""
Variance-based method with normalization
"""
H, W = image.shape
int_mean = ndimage.mean(image)
return (ndimage.variance(image)/(H*W*int_mean))
import numpy as np
import scipy
from scipy import ndimage
import matplotlib.pyplot as plt
l = scipy.lena()
sx, sy = l.shape
X, Y = np.ogrid[0:sx, 0:sy]
regions = sy/6 * (X/4) + Y/6
block_mean = ndimage.mean(l, labels=regions, index=np.arange(1, regions.max() +1))
block_mean.shape = (sx/4, sy/6)
plt.figure(figsize=(5,5))
plt.imshow(block_mean, cmap=plt.cm.gray)
plt.axis('off')
def run_on_image_setting(self, workspace, image):
assert isinstance(workspace, cpw.Workspace)
image_set = workspace.image_set
assert isinstance(image_set, cpi.ImageSet)
measurements = workspace.measurements
im = image_set.get_image(image.image_name.value,
must_be_grayscale=True)
#
# Downsample the image and mask
#
new_shape = np.array(im.pixel_data.shape)
if image.subsample_size.value < 1:
new_shape = new_shape * image.subsample_size.value
i, j = (np.mgrid[0:new_shape[0], 0:new_shape[1]].astype(float) /
image.subsample_size.value)
pixels = scind.map_coordinates(im.pixel_data, (i, j), order=1)
mask = scind.map_coordinates(im.mask.astype(float), (i, j)) > .9
else:
pixels = im.pixel_data
mask = im.mask
#
# Remove background pixels using a greyscale tophat filter
#
if image.image_sample_size.value < 1:
back_shape = new_shape * image.image_sample_size.value
i, j = (np.mgrid[0:back_shape[0], 0:back_shape[1]].astype(float) /
image.image_sample_size.value)
back_pixels = scind.map_coordinates(pixels, (i, j), order=1)
back_mask = scind.map_coordinates(mask.astype(float), (i, j)) > .9
else:
back_pixels = pixels
back_mask = mask
radius = image.element_size.value
back_pixels = morph.grey_erosion(back_pixels, radius, back_mask)
back_pixels = morph.grey_dilation(back_pixels, radius, back_mask)
if image.image_sample_size.value < 1:
i, j = np.mgrid[0:new_shape[0], 0:new_shape[1]].astype(float)
#
# Make sure the mapping only references the index range of
# back_pixels.
#
i *= float(back_shape[0] - 1) / float(new_shape[0] - 1)
j *= float(back_shape[1] - 1) / float(new_shape[1] - 1)
back_pixels = scind.map_coordinates(back_pixels, (i, j), order=1)
pixels -= back_pixels
pixels[pixels < 0] = 0
#
# For each object, build a little record
#
class ObjectRecord(object):
def __init__(self, name):
self.name = name
self.labels = workspace.object_set.get_objects(name).segmented
self.nobjects = np.max(self.labels)
if self.nobjects != 0:
self.range = np.arange(1, np.max(self.labels) + 1)
self.labels = self.labels.copy()
self.labels[~im.mask] = 0
self.current_mean = fix(
scind.mean(im.pixel_data, self.labels, self.range))
self.start_mean = np.maximum(self.current_mean,
np.finfo(float).eps)
object_records = [
ObjectRecord(ob.objects_name.value) for ob in image.objects
]
#
# Transcribed from the Matlab module: granspectr function
#
# CALCULATES GRANULAR SPECTRUM, ALSO KNOWN AS SIZE DISTRIBUTION,
# GRANULOMETRY, AND PATTERN SPECTRUM, SEE REF.:
# J.Serra, Image Analysis and Mathematical Morphology, Vol. 1. Academic Press, London, 1989
# Maragos,P. "Pattern spectrum and multiscale shape representation", IEEE Transactions on Pattern Analysis and Machine Intelligence, 11, N 7, pp. 701-716, 1989
# L.Vincent "Granulometries and Opening Trees", Fundamenta Informaticae, 41, No. 1-2, pp. 57-90, IOS Press, 2000.
# L.Vincent "Morphological Area Opening and Closing for Grayscale Images", Proc. NATO Shape in Picture Workshop, Driebergen, The Netherlands, pp. 197-208, 1992.
# I.Ravkin, V.Temov "Bit representation techniques and image processing", Applied Informatics, v.14, pp. 41-90, Finances and Statistics, Moskow, 1988 (in Russian)
# THIS IMPLEMENTATION INSTEAD OF OPENING USES EROSION FOLLOWED BY RECONSTRUCTION
#
ng = image.granular_spectrum_length.value
startmean = np.mean(pixels[mask])
ero = pixels.copy()
# Mask the test image so that masked pixels will have no effect
# during reconstruction
#
ero[~mask] = 0
currentmean = startmean
startmean = max(startmean, np.finfo(float).eps)
footprint = np.array([[False, True, False], [True, True, True],
[False, True, False]])
statistics = [image.image_name.value]
for i in range(1, ng + 1):
prevmean = currentmean
ero = morph.grey_erosion(ero, mask=mask, footprint=footprint)
rec = morph.grey_reconstruction(ero, pixels, footprint)
currentmean = np.mean(rec[mask])
gs = (prevmean - currentmean) * 100 / startmean
statistics += ["%.2f" % gs]
feature = image.granularity_feature(i)
measurements.add_image_measurement(feature, gs)
#
# Restore the reconstructed image to the shape of the
# original image so we can match against object labels
#
orig_shape = im.pixel_data.shape
i, j = np.mgrid[0:orig_shape[0], 0:orig_shape[1]].astype(float)
#
# Make sure the mapping only references the index range of
# back_pixels.
#
i *= float(new_shape[0] - 1) / float(orig_shape[0] - 1)
j *= float(new_shape[1] - 1) / float(orig_shape[1] - 1)
rec = scind.map_coordinates(rec, (i, j), order=1)
#
# Calculate the means for the objects
#
for object_record in object_records:
assert isinstance(object_record, ObjectRecord)
if object_record.nobjects > 0:
new_mean = fix(
scind.mean(rec, object_record.labels,
object_record.range))
gss = ((object_record.current_mean - new_mean) * 100 /
object_record.start_mean)
object_record.current_mean = new_mean
else:
gss = np.zeros((0, ))
measurements.add_measurement(object_record.name, feature, gss)
return statistics
def run_on_objects(self,object_name, workspace):
"""Run, computing the area measurements for a single map of objects"""
objects = workspace.get_objects(object_name)
assert isinstance(objects, cpo.Objects)
#
# Do the ellipse-related measurements
#
i, j, l = objects.ijv.transpose()
centers, eccentricity, major_axis_length, minor_axis_length, \
theta, compactness =\
ellipse_from_second_moments_ijv(i, j, 1, l, objects.indices, True)
del i
del j
del l
self.record_measurement(workspace, object_name,
F_ECCENTRICITY, eccentricity)
self.record_measurement(workspace, object_name,
F_MAJOR_AXIS_LENGTH, major_axis_length)
self.record_measurement(workspace, object_name,
F_MINOR_AXIS_LENGTH, minor_axis_length)
self.record_measurement(workspace, object_name, F_ORIENTATION,
theta * 180 / np.pi)
self.record_measurement(workspace, object_name, F_COMPACTNESS,
compactness)
is_first = False
if len(objects.indices) == 0:
nobjects = 0
else:
nobjects = np.max(objects.indices)
mcenter_x = np.zeros(nobjects)
mcenter_y = np.zeros(nobjects)
mextent = np.zeros(nobjects)
mperimeters = np.zeros(nobjects)
msolidity = np.zeros(nobjects)
euler = np.zeros(nobjects)
max_radius = np.zeros(nobjects)
median_radius = np.zeros(nobjects)
mean_radius = np.zeros(nobjects)
min_feret_diameter = np.zeros(nobjects)
max_feret_diameter = np.zeros(nobjects)
zernike_numbers = self.get_zernike_numbers()
zf = {}
for n,m in zernike_numbers:
zf[(n,m)] = np.zeros(nobjects)
if nobjects > 0:
chulls, chull_counts = convex_hull_ijv(objects.ijv, objects.indices)
for labels, indices in objects.get_labels():
to_indices = indices-1
distances = distance_to_edge(labels)
mcenter_y[to_indices], mcenter_x[to_indices] =\
maximum_position_of_labels(distances, labels, indices)
max_radius[to_indices] = fix(scind.maximum(
distances, labels, indices))
mean_radius[to_indices] = fix(scind.mean(
distances, labels, indices))
median_radius[to_indices] = median_of_labels(
distances, labels, indices)
#
# The extent (area / bounding box area)
#
mextent[to_indices] = calculate_extents(labels, indices)
#
# The perimeter distance
#
mperimeters[to_indices] = calculate_perimeters(labels, indices)
#
# Solidity
#
msolidity[to_indices] = calculate_solidity(labels, indices)
#
# Euler number
#
euler[to_indices] = euler_number(labels, indices)
#
# Zernike features
#
zf_l = cpmz.zernike(zernike_numbers, labels, indices)
for (n,m), z in zip(zernike_numbers, zf_l.transpose()):
zf[(n,m)][to_indices] = z
#
# Form factor
#
ff = 4.0 * np.pi * objects.areas / mperimeters**2
#
# Feret diameter
#
min_feret_diameter, max_feret_diameter = \
feret_diameter(chulls, chull_counts, objects.indices)
else:
ff = np.zeros(0)
for f, m in ([(F_AREA, objects.areas),
(F_CENTER_X, mcenter_x),
(F_CENTER_Y, mcenter_y),
(F_EXTENT, mextent),
(F_PERIMETER, mperimeters),
(F_SOLIDITY, msolidity),
(F_FORM_FACTOR, ff),
(F_EULER_NUMBER, euler),
(F_MAXIMUM_RADIUS, max_radius),
(F_MEAN_RADIUS, mean_radius),
(F_MEDIAN_RADIUS, median_radius),
(F_MIN_FERET_DIAMETER, min_feret_diameter),
(F_MAX_FERET_DIAMETER, max_feret_diameter)] +
[(self.get_zernike_name((n,m)), zf[(n,m)])
for n,m in zernike_numbers]):
self.record_measurement(workspace, object_name, f, m)
def run_image_pair_objects(self, workspace, first_image_name,
second_image_name, object_name):
'''Calculate per-object correlations between intensities in two images'''
first_image = workspace.image_set.get_image(first_image_name,
must_be_grayscale=True)
second_image = workspace.image_set.get_image(second_image_name,
must_be_grayscale=True)
objects = workspace.object_set.get_objects(object_name)
#
# Crop both images to the size of the labels matrix
#
labels = objects.segmented
try:
first_pixels = objects.crop_image_similarly(first_image.pixel_data)
first_mask = objects.crop_image_similarly(first_image.mask)
except ValueError:
first_pixels, m1 = cpo.size_similarly(labels,
first_image.pixel_data)
first_mask, m1 = cpo.size_similarly(labels, first_image.mask)
first_mask[~m1] = False
try:
second_pixels = objects.crop_image_similarly(
second_image.pixel_data)
second_mask = objects.crop_image_similarly(second_image.mask)
except ValueError:
second_pixels, m1 = cpo.size_similarly(labels,
second_image.pixel_data)
second_mask, m1 = cpo.size_similarly(labels, second_image.mask)
second_mask[~m1] = False
mask = ((labels > 0) & first_mask & second_mask)
first_pixels = first_pixels[mask]
second_pixels = second_pixels[mask]
labels = labels[mask]
result = []
first_pixel_data = first_image.pixel_data
first_mask = first_image.mask
first_pixel_count = np.product(first_pixel_data.shape)
second_pixel_data = second_image.pixel_data
second_mask = second_image.mask
second_pixel_count = np.product(second_pixel_data.shape)
#
# Crop the larger image similarly to the smaller one
#
if first_pixel_count < second_pixel_count:
second_pixel_data = first_image.crop_image_similarly(
second_pixel_data)
second_mask = first_image.crop_image_similarly(second_mask)
elif second_pixel_count < first_pixel_count:
first_pixel_data = second_image.crop_image_similarly(
first_pixel_data)
first_mask = second_image.crop_image_similarly(first_mask)
mask = (first_mask & second_mask & (~np.isnan(first_pixel_data)) &
(~np.isnan(second_pixel_data)))
if np.any(mask):
#
# Perform the correlation, which returns:
# [ [ii, ij],
# [ji, jj] ]
#
fi = first_pixel_data[mask]
si = second_pixel_data[mask]
n_objects = objects.count
# Handle case when both images for the correlation are completely masked out
if n_objects == 0:
corr = np.zeros((0, ))
overlap = np.zeros((0, ))
K1 = np.zeros((0, ))
K2 = np.zeros((0, ))
M1 = np.zeros((0, ))
M2 = np.zeros((0, ))
RWC1 = np.zeros((0, ))
RWC2 = np.zeros((0, ))
C1 = np.zeros((0, ))
C2 = np.zeros((0, ))
elif np.where(mask)[0].__len__() == 0:
corr = np.zeros((n_objects, ))
corr[:] = np.NaN
overlap = K1 = K2 = M1 = M2 = RWC1 = RWC2 = C1 = C2 = corr
else:
#
# The correlation is sum((x-mean(x))(y-mean(y)) /
# ((n-1) * std(x) *std(y)))
#
lrange = np.arange(n_objects, dtype=np.int32) + 1
area = fix(scind.sum(np.ones_like(labels), labels, lrange))
mean1 = fix(scind.mean(first_pixels, labels, lrange))
mean2 = fix(scind.mean(second_pixels, labels, lrange))
#
# Calculate the standard deviation times the population.
#
std1 = np.sqrt(
fix(
scind.sum((first_pixels - mean1[labels - 1])**2, labels,
lrange)))
std2 = np.sqrt(
fix(
scind.sum((second_pixels - mean2[labels - 1])**2, labels,
lrange)))
x = first_pixels - mean1[labels - 1] # x - mean(x)
y = second_pixels - mean2[labels - 1] # y - mean(y)
corr = fix(
scind.sum(x * y / (std1[labels - 1] * std2[labels - 1]),
labels, lrange))
# Explicitly set the correlation to NaN for masked objects
corr[scind.sum(1, labels, lrange) == 0] = np.NaN
result += [[
first_image_name, second_image_name, object_name,
"Mean Correlation coeff",
"%.3f" % np.mean(corr)
],
[
first_image_name, second_image_name, object_name,
"Median Correlation coeff",
"%.3f" % np.median(corr)
],
[
first_image_name, second_image_name, object_name,
"Min Correlation coeff",
"%.3f" % np.min(corr)
],
[
first_image_name, second_image_name, object_name,
"Max Correlation coeff",
"%.3f" % np.max(corr)
]]
# Threshold as percentage of maximum intensity of objects in each channel
tff = (self.thr.value / 100) * fix(
scind.maximum(first_pixels, labels, lrange))
tss = (self.thr.value / 100) * fix(
scind.maximum(second_pixels, labels, lrange))
combined_thresh = (first_pixels >= tff[labels - 1]) & (
second_pixels >= tss[labels - 1])
fi_thresh = first_pixels[combined_thresh]
si_thresh = second_pixels[combined_thresh]
tot_fi_thr = scind.sum(
first_pixels[first_pixels >= tff[labels - 1]],
labels[first_pixels >= tff[labels - 1]], lrange)
tot_si_thr = scind.sum(
second_pixels[second_pixels >= tss[labels - 1]],
labels[second_pixels >= tss[labels - 1]], lrange)
nonZero = (fi > 0) | (si > 0)
xvar = np.var(fi[nonZero], axis=0, ddof=1)
yvar = np.var(si[nonZero], axis=0, ddof=1)
xmean = np.mean(fi[nonZero], axis=0)
ymean = np.mean(si[nonZero], axis=0)
z = fi[nonZero] + si[nonZero]
zvar = np.var(z, axis=0, ddof=1)
covar = 0.5 * (zvar - (xvar + yvar))
denom = 2 * covar
num = (yvar - xvar) + np.sqrt((yvar - xvar) * (yvar - xvar) + 4 *
(covar * covar))
a = (num / denom)
b = (ymean - a * xmean)
i = 1
while i > 0.003921568627:
thr_fi_c = i
thr_si_c = (a * i) + b
combt = (fi < thr_fi_c) | (si < thr_si_c)
costReg = scistat.pearsonr(fi[combt], si[combt])
if costReg[0] <= 0:
break
i = i - 0.003921568627
# Costes' thershold for entire image is applied to each object
fi_above_thr = first_pixels > thr_fi_c
si_above_thr = second_pixels > thr_si_c
combined_thresh_c = fi_above_thr & si_above_thr
fi_thresh_c = first_pixels[combined_thresh_c]
si_thresh_c = second_pixels[combined_thresh_c]
if np.any(fi_above_thr):
tot_fi_thr_c = scind.sum(
first_pixels[first_pixels >= thr_fi_c],
labels[first_pixels >= thr_fi_c], lrange)
else:
tot_fi_thr_c = np.zeros(len(lrange))
if np.any(si_above_thr):
tot_si_thr_c = scind.sum(
second_pixels[second_pixels >= thr_si_c],
labels[second_pixels >= thr_si_c], lrange)
else:
tot_si_thr_c = np.zeros(len(lrange))
# Manders Coefficient
M1 = np.zeros(len(lrange))
M2 = np.zeros(len(lrange))
if np.any(combined_thresh):
M1 = np.array(
scind.sum(fi_thresh, labels[combined_thresh],
lrange)) / np.array(tot_fi_thr)
M2 = np.array(
scind.sum(si_thresh, labels[combined_thresh],
lrange)) / np.array(tot_si_thr)
result += [[
first_image_name, second_image_name, object_name,
"Mean Manders coeff",
"%.3f" % np.mean(M1)
],
[
first_image_name, second_image_name, object_name,
"Median Manders coeff",
"%.3f" % np.median(M1)
],
[
first_image_name, second_image_name, object_name,
"Min Manders coeff",
"%.3f" % np.min(M1)
],
[
first_image_name, second_image_name, object_name,
"Max Manders coeff",
"%.3f" % np.max(M1)
]]
result += [[
second_image_name, first_image_name, object_name,
"Mean Manders coeff",
"%.3f" % np.mean(M2)
],
[
second_image_name, first_image_name, object_name,
"Median Manders coeff",
"%.3f" % np.median(M2)
],
[
second_image_name, first_image_name, object_name,
"Min Manders coeff",
"%.3f" % np.min(M2)
],
[
second_image_name, first_image_name, object_name,
"Max Manders coeff",
"%.3f" % np.max(M2)
]]
# RWC Coefficient
RWC1 = np.zeros(len(lrange))
RWC2 = np.zeros(len(lrange))
[Rank1] = np.lexsort(([labels], [first_pixels]))
[Rank2] = np.lexsort(([labels], [second_pixels]))
Rank1_U = np.hstack(
[[False], first_pixels[Rank1[:-1]] != first_pixels[Rank1[1:]]])
Rank2_U = np.hstack(
[[False],
second_pixels[Rank2[:-1]] != second_pixels[Rank2[1:]]])
Rank1_S = np.cumsum(Rank1_U)
Rank2_S = np.cumsum(Rank2_U)
Rank_im1 = np.zeros(first_pixels.shape, dtype=int)
Rank_im2 = np.zeros(second_pixels.shape, dtype=int)
Rank_im1[Rank1] = Rank1_S
Rank_im2[Rank2] = Rank2_S
R = max(Rank_im1.max(), Rank_im2.max()) + 1
Di = abs(Rank_im1 - Rank_im2)
weight = (R - Di) * 1.0 / R
weight_thresh = weight[combined_thresh]
if np.any(combined_thresh):
RWC1 = np.array(
scind.sum(fi_thresh * weight_thresh,
labels[combined_thresh],
lrange)) / np.array(tot_fi_thr)
RWC2 = np.array(
scind.sum(si_thresh * weight_thresh,
labels[combined_thresh],
lrange)) / np.array(tot_si_thr)
result += [[
first_image_name, second_image_name, object_name,
"Mean RWC coeff",
"%.3f" % np.mean(RWC1)
],
[
first_image_name, second_image_name, object_name,
"Median RWC coeff",
"%.3f" % np.median(RWC1)
],
[
first_image_name, second_image_name, object_name,
"Min RWC coeff",
"%.3f" % np.min(RWC1)
],
[
first_image_name, second_image_name, object_name,
"Max RWC coeff",
"%.3f" % np.max(RWC1)
]]
result += [[
second_image_name, first_image_name, object_name,
"Mean RWC coeff",
"%.3f" % np.mean(RWC2)
],
[
second_image_name, first_image_name, object_name,
"Median RWC coeff",
"%.3f" % np.median(RWC2)
],
[
second_image_name, first_image_name, object_name,
"Min RWC coeff",
"%.3f" % np.min(RWC2)
],
[
second_image_name, first_image_name, object_name,
"Max RWC coeff",
"%.3f" % np.max(RWC2)
]]
# Costes Automated Threshold
C1 = np.zeros(len(lrange))
C2 = np.zeros(len(lrange))
if np.any(combined_thresh_c):
C1 = np.array(
scind.sum(fi_thresh_c, labels[combined_thresh_c],
lrange)) / np.array(tot_fi_thr_c)
C2 = np.array(
scind.sum(si_thresh_c, labels[combined_thresh_c],
lrange)) / np.array(tot_si_thr_c)
result += [[
first_image_name, second_image_name, object_name,
"Mean Manders coeff (Costes)",
"%.3f" % np.mean(C1)
],
[
first_image_name, second_image_name, object_name,
"Median Manders coeff (Costes)",
"%.3f" % np.median(C1)
],
[
first_image_name, second_image_name, object_name,
"Min Manders coeff (Costes)",
"%.3f" % np.min(C1)
],
[
first_image_name, second_image_name, object_name,
"Max Manders coeff (Costes)",
"%.3f" % np.max(C1)
]]
result += [[
second_image_name, first_image_name, object_name,
"Mean Manders coeff (Costes)",
"%.3f" % np.mean(C2)
],
[
second_image_name, first_image_name, object_name,
"Median Manders coeff (Costes)",
"%.3f" % np.median(C2)
],
[
second_image_name, first_image_name, object_name,
"Min Manders coeff (Costes)",
"%.3f" % np.min(C2)
],
[
second_image_name, first_image_name, object_name,
"Max Manders coeff (Costes)",
"%.3f" % np.max(C2)
]]
# Overlap Coefficient
if np.any(combined_thresh):
fpsq = scind.sum(first_pixels[combined_thresh]**2,
labels[combined_thresh], lrange)
spsq = scind.sum(second_pixels[combined_thresh]**2,
labels[combined_thresh], lrange)
pdt = np.sqrt(np.array(fpsq) * np.array(spsq))
overlap = fix(
scind.sum(
first_pixels[combined_thresh] *
second_pixels[combined_thresh],
labels[combined_thresh], lrange) / pdt)
K1 = fix((scind.sum(
first_pixels[combined_thresh] *
second_pixels[combined_thresh], labels[combined_thresh],
lrange)) / (np.array(fpsq)))
K2 = fix(
scind.sum(
first_pixels[combined_thresh] *
second_pixels[combined_thresh],
labels[combined_thresh], lrange) / np.array(spsq))
else:
overlap = K1 = K2 = np.zeros(len(lrange))
result += [[
first_image_name, second_image_name, object_name,
"Mean Overlap coeff",
"%.3f" % np.mean(overlap)
],
[
first_image_name, second_image_name, object_name,
"Median Overlap coeff",
"%.3f" % np.median(overlap)
],
[
first_image_name, second_image_name, object_name,
"Min Overlap coeff",
"%.3f" % np.min(overlap)
],
[
first_image_name, second_image_name, object_name,
"Max Overlap coeff",
"%.3f" % np.max(overlap)
]]
measurement = ("Correlation_Correlation_%s_%s" %
(first_image_name, second_image_name))
overlap_measurement = (F_OVERLAP_FORMAT %
(first_image_name, second_image_name))
k_measurement_1 = (F_K_FORMAT % (first_image_name, second_image_name))
k_measurement_2 = (F_K_FORMAT % (second_image_name, first_image_name))
manders_measurement_1 = (F_MANDERS_FORMAT %
(first_image_name, second_image_name))
manders_measurement_2 = (F_MANDERS_FORMAT %
(second_image_name, first_image_name))
rwc_measurement_1 = (F_RWC_FORMAT %
(first_image_name, second_image_name))
rwc_measurement_2 = (F_RWC_FORMAT %
(second_image_name, first_image_name))
costes_measurement_1 = (F_COSTES_FORMAT %
(first_image_name, second_image_name))
costes_measurement_2 = (F_COSTES_FORMAT %
(second_image_name, first_image_name))
workspace.measurements.add_measurement(object_name, measurement, corr)
workspace.measurements.add_measurement(object_name,
overlap_measurement, overlap)
workspace.measurements.add_measurement(object_name, k_measurement_1,
K1)
workspace.measurements.add_measurement(object_name, k_measurement_2,
K2)
workspace.measurements.add_measurement(object_name,
manders_measurement_1, M1)
workspace.measurements.add_measurement(object_name,
manders_measurement_2, M2)
workspace.measurements.add_measurement(object_name, rwc_measurement_1,
RWC1)
workspace.measurements.add_measurement(object_name, rwc_measurement_2,
RWC2)
workspace.measurements.add_measurement(object_name,
costes_measurement_1, C1)
workspace.measurements.add_measurement(object_name,
costes_measurement_2, C2)
if n_objects == 0:
return [[
first_image_name, second_image_name, object_name,
"Mean correlation", "-"
],
[
first_image_name, second_image_name, object_name,
"Median correlation", "-"
],
[
first_image_name, second_image_name, object_name,
"Min correlation", "-"
],
[
first_image_name, second_image_name, object_name,
"Max correlation", "-"
]]
else:
return result
def MaximaFind(image, qty, len_object=18):
"""
Find the centers coordinates of maximum spots in an image.
Parameters
----------
image : array like
Data array containing the greyscale image.
qty : int
The amount of maxima you want to find.
len_object : int
A length in pixels somewhat larger than a typical object.
Returns
-------
refined_position : array like
A 2D array of shape (N, 2) containing the coordinates of the maxima.
"""
filtered = BandPassFilter(image, 1, len_object)
# dilation
structure = _CreateSEDisk(len_object // 2)
dilated = cv2.dilate(filtered, structure, iterations=1)
# find local maxima
binary = (filtered == dilated)
# thresholding
qradius = max(len_object // 4, 1)
structure = _CreateSEDisk(qradius)
BWdil = cv2.dilate(numpy.array(binary).astype(numpy.uint8), structure)
labels, num_features = ndimage.label(BWdil)
index = numpy.arange(1, num_features + 1)
mean = ndimage.mean(filtered, labels=labels, index=index)
si = numpy.argsort(mean)[::-1][:qty]
# estimate spot center position
pos = numpy.array(
ndimage.center_of_mass(filtered, labels=labels,
index=index[si]))[:, ::-1]
if numpy.any(numpy.isnan(pos)):
pos = pos[numpy.any(~numpy.isnan(pos), axis=1)]
logging.debug("Only %d maxima found, while expected %d", len(pos), qty)
# improve center estimate using radial symmetry method
w = len_object // 2
refined_center = numpy.zeros_like(pos)
pos = numpy.rint(pos).astype(numpy.int16)
y_max, x_max = image.shape
for idx, xy in enumerate(pos):
x_start, y_start = xy - w + 1
x_end, y_end = xy + w
# If the spot is near the edge of the image, crop so it is still in the center of the sub-image. Subtract the
# value of x/y_start from x/y_end to keep the spot in the center when x/y_start is set to 0. Add the difference
# between x/y_end and x/y_max to x/y_start to keep the spot in the center when x/y_end is set to x/y_max.
if x_start < 0:
x_end += x_start
x_start = 0
elif x_end > x_max:
x_start += x_end - x_max
x_end = x_max
if y_start < 0:
y_end += y_start
y_start = 0
elif y_end > y_max:
y_start += y_end - y_max
y_end = y_max
spot = filtered[y_start:y_end, x_start:x_end]
refined_center[idx] = numpy.array(FindCenterCoordinates(spot))
refined_position = pos + refined_center
return refined_position
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
# vim: set ts=4 sw=4 et sts=4 ai:
import numpy as np
import scipy
from scipy import ndimage
from scipy.misc import imsave
h = 720
w = 1280
f = np.zeros((h, w), dtype=np.uint32)
for s in [1, 4, 16, 32, 64]:
sx, sy = f.shape
X, Y = np.ogrid[0:sx, 0:sy]
r = np.hypot(X - sx / 2, Y - sy / 2)
n = round(w / 2 / s)
rbin = (n * r / r.max()).astype(np.int)
radial_mean = ndimage.mean(f,
labels=rbin,
index=np.arange(1,
rbin.max() + 1))
imsave('input/circles-{0:02}px.png'.format(s), rbin)
def block_downsample(arr):
res = ndimage.mean(arr, labels=regions, index=indices)
res.shape = (sx / factor, sy / factor)
return res
def segment_layer(filename, params):
'''
Segment one layer in a stack
'''
start = time.time()
#extract pixel size in xy and z
xsize, zsize = extract_zoom(params.folder)
#load image
img = tifffile.imread(params.inputfolder + params.folder + filename)
#normalize image
img = ndimage.median_filter(img, 3)
img = img * 255. / img.max()
##segment kidney tissue
sizefactor = 10.
small = ndimage.interpolation.zoom(
img, 1. / sizefactor) #scale the image to a smaller size
imgf = ndimage.gaussian_filter(small, 3. / xsize) #Gaussian filter
median = np.percentile(imgf, 40) #40-th percentile for thresholding
kmask = imgf > median * 1.5 #thresholding
kmask = mahotas.dilate(kmask, mahotas.disk(5))
kmask = mahotas.close_holes(kmask) #closing holes
kmask = mahotas.erode(kmask, mahotas.disk(5)) * 255
#remove objects that are darker than 2*percentile
l, n = ndimage.label(kmask)
llist = np.unique(l)
if len(llist) > 2:
means = ndimage.mean(imgf, l, llist)
bv = llist[np.where(means < median * 2)]
ix = np.in1d(l.ravel(), bv).reshape(l.shape)
kmask[ix] = 0
kmask = ndimage.interpolation.zoom(kmask,
sizefactor) #scale back to normal size
kmask = normalize(kmask)
kmask = (kmask > mahotas.otsu(kmask.astype(
np.uint8))) * 255. #remove artifacts of interpolation
#save indices of the kidney mask
ind = np.where(kmask > 0)
ind = np.array(ind)
np.save(
params.inputfolder + '../segmented/masks/kidney/' + params.folder +
filename[:-4] + '.npy', ind)
skimage.io.imsave(
params.inputfolder + '../segmented/masks/kidney/' + params.folder +
filename[:-4] + '.tif', (kmask > 0).astype(np.uint8) * 255)
#segment glomeruli, if there is a kidney tissue
if kmask.max() > 0:
#remove all intensity variations larger than maximum radius of a glomerulus
d = mahotas.disk(int(float(params.maxrad) / xsize))
img = img - mahotas.open(img.astype(np.uint8), d)
img = img * 255. / img.max()
ch = img[np.where(kmask > 0)]
#segment glomeruli by otsu thresholding only if this threshold is higher than the 75-th percentile in the kidney mask
t = mahotas.otsu(img.astype(np.uint8))
if t > np.percentile(ch, 75) * 1.5:
cells = img > t
cells[np.where(kmask == 0)] = 0
cells = mahotas.open(
cells, mahotas.disk(int(float(params.minrad) / 2. / xsize)))
else:
cells = np.zeros_like(img)
else:
cells = np.zeros_like(img)
#save indices of the glomeruli mask
ind = np.where(cells > 0)
ind = np.array(ind)
np.save(
params.inputfolder + '../segmented/masks/glomeruli/' + params.folder +
filename[:-4] + '.npy', ind)
skimage.io.imsave(
params.inputfolder + '../segmented/masks/glomeruli/' + params.folder +
filename[:-4] + '.tif', (cells > 0).astype(np.uint8) * 255)
def get_psf_secondpeak(fn,
show_image=False,
min_radial_extent=1.5 * u.arcsec,
max_radial_extent=5 * u.arcsec):
""" REDUNDANT with get_psf_secondpeak, but this one is better
Process:
1. Find the first minimum of the PSF by taking the radial profile within 50 pixels
2. Take the integral of the PSF within that range
3. Calculate the residual of the PSF minus the CASA-fitted Gaussian beam
4. Integrate that to get the fraction of flux outside the synthesized
beam in the main lobe of the dirty beam
5. Find the peak and the location of the peak residual
"""
with warnings.catch_warnings():
warnings.simplefilter("ignore")
cube = SpectralCube.read(
fn, format='casa_image' if not fn.endswith('.fits') else 'fits')
psfim = cube[0]
pixscale = wcs.utils.proj_plane_pixel_scales(cube.wcs.celestial)[0] * u.deg
center = np.unravel_index(np.argmax(psfim), psfim.shape)
cy, cx = center
cutout = psfim[cy - 100:cy + 101, cx - 100:cx + 101]
psfim = cutout
fullbeam = cube.beam.as_kernel(
pixscale,
x_size=201,
y_size=201,
)
shape = cutout.shape
sy, sx = shape
Y, X = np.mgrid[0:sy, 0:sx]
beam = cube.beam
center = np.unravel_index(np.argmax(cutout), cutout.shape)
cy, cx = center
# elliptical version...
dy = (Y - cy)
dx = (X - cx)
costh = np.cos(beam.pa)
sinth = np.sin(beam.pa)
rmajmin = beam.minor / beam.major
rr = ((dx * costh + dy * sinth)**2 / rmajmin**2 +
(dx * sinth - dy * costh)**2 / 1**2)**0.5
rbin = (rr).astype(np.int)
# assume the PSF first minimum is within 100 pixels of center
radial_mean = ndimage.mean(cutout**2, labels=rbin, index=np.arange(100))
# find the first negative peak (approximately); we include anything
# within this radius as part of the main beam
first_min_ind = scipy.signal.find_peaks(-radial_mean)[0][0]
view = (slice(cy - first_min_ind.astype('int'),
cy + first_min_ind.astype('int') + 1),
slice(cx - first_min_ind.astype('int'),
cx + first_min_ind.astype('int') + 1))
data = cutout[view].value
bm = fullbeam.array[view]
# the data and beam must be concentric
# and there must be only one peak location
# (these checks are to avoid the even-kernel issue in which the center
# of the beam can have its flux spread over four pixels)
assert np.argmax(data) == np.argmax(bm)
assert (bm.max() == bm).sum() == 1
bmfit_residual = data - bm / bm.max()
radial_mask = rr[view] < first_min_ind
psf_integral_firstpeak = (data * radial_mask).sum()
psf_residual_integral = (bmfit_residual * radial_mask).sum()
residual_peak = bmfit_residual.max()
residual_peak_loc = rr[view].flat[bmfit_residual.argmax()]
peakloc_as = (residual_peak_loc * pixscale).to(u.arcsec)
# pl.figure(3).clf()
# bmradmean = ndimage.mean((fullbeam.array/fullbeam.array.max())**2, labels=rbin, index=np.arange(100))
# pl.plot(radial_mean)
# pl.plot(bmradmean)
# pl.figure(1)
if show_image:
import pylab as pl
#pl.clf()
# this finds the second peak
# (useful for display)
outside_first_peak_mask = (rr > first_min_ind) & (fullbeam.array <
1e-5)
#first_sidelobe_ind = scipy.signal.find_peaks(radial_mean * (np.arange(len(radial_mean)) > first_min_ind))[0][0]
max_sidelobe = cutout[outside_first_peak_mask].max()
max_sidelobe_loc = cutout[outside_first_peak_mask].argmax()
r_max_sidelobe = rr[outside_first_peak_mask][max_sidelobe_loc]
#r_max_sidelobe = first_sidelobe_ind
if r_max_sidelobe * pixscale < min_radial_extent:
radial_extent = (min_radial_extent / pixscale).decompose().value
else:
radial_extent = r_max_sidelobe
if radial_extent * pixscale > max_radial_extent:
radial_extent = (max_radial_extent / pixscale).decompose().value
bm2 = cube.beam.as_kernel(
pixscale,
x_size=radial_extent.astype('int') * 2 + 1,
y_size=radial_extent.astype('int') * 2 + 1,
)
view = (slice(cy - radial_extent.astype('int'),
cy + radial_extent.astype('int') + 1),
slice(cx - radial_extent.astype('int'),
cx + radial_extent.astype('int') + 1))
bmfit_residual2 = cutout[view].value - bm2.array / bm2.array.max()
#extent = np.array([-first_min_ind, first_min_ind, -first_min_ind, first_min_ind])*pixscale.to(u.arcsec).value
extent = np.array([
-radial_extent, radial_extent, -radial_extent, radial_extent
]) * pixscale.to(u.arcsec).value
pl.imshow(bmfit_residual2,
origin='lower',
interpolation='nearest',
extent=extent,
cmap='gray_r')
cb = pl.colorbar()
pl.matplotlib.colorbar.ColorbarBase.add_lines(self=cb,
levels=[max_sidelobe],
colors=[(0.1, 0.7, 0.1,
0.9)],
linewidths=1)
pl.contour(bm2.array / bm2.array.max(),
levels=[0.1, 0.5, 0.9],
colors=['r'] * 3,
extent=extent)
pl.contour(rr[view],
levels=[first_min_ind, r_max_sidelobe],
linestyles=['--', ':'],
colors=[(0.2, 0.2, 1, 0.5), (0.1, 0.7, 0.1, 0.5)],
extent=extent)
pl.xlabel("RA Offset [arcsec]")
pl.ylabel("Dec Offset [arcsec]")
return (residual_peak, peakloc_as.value,
psf_residual_integral / psf_integral_firstpeak)
def run(self, workspace):
parents = workspace.object_set.get_objects(self.parent_name.value)
children = workspace.object_set.get_objects(self.sub_object_name.value)
child_count, parents_of = parents.relate_children(children)
m = workspace.measurements
assert isinstance(m, cpmeas.Measurements)
if self.wants_per_parent_means.value:
parent_indexes = np.arange(np.max(parents.segmented)) + 1
for feature_name in m.get_feature_names(
self.sub_object_name.value):
if not self.should_aggregate_feature(feature_name):
continue
data = m.get_current_measurement(self.sub_object_name.value,
feature_name)
if data is not None:
if len(parents_of) > 0:
means = fix(
scind.mean(data.astype(float), parents_of,
parent_indexes))
else:
means = np.zeros((0, ))
mean_feature_name = FF_MEAN % (self.sub_object_name.value,
feature_name)
m.add_measurement(self.parent_name.value,
mean_feature_name, means)
m.add_measurement(self.sub_object_name.value,
FF_PARENT % (self.parent_name.value), parents_of)
m.add_measurement(self.parent_name.value,
FF_CHILDREN_COUNT % (self.sub_object_name.value),
child_count)
group_index = m.get_current_image_measurement(cpmeas.GROUP_INDEX)
group_indexes = np.ones(np.sum(parents_of != 0), int) * group_index
good_parents = parents_of[parents_of != 0]
good_children = np.argwhere(parents_of != 0).flatten() + 1
if np.any(good_parents):
m.add_relate_measurement(self.module_num, R_PARENT,
self.parent_name.value,
self.sub_object_name.value, group_indexes,
good_parents, group_indexes,
good_children)
m.add_relate_measurement(self.module_num, R_CHILD,
self.sub_object_name.value,
self.parent_name.value, group_indexes,
good_children, group_indexes,
good_parents)
parent_names = self.get_parent_names()
for parent_name in parent_names:
if self.find_parent_child_distances in (D_BOTH, D_CENTROID):
self.calculate_centroid_distances(workspace, parent_name)
if self.find_parent_child_distances in (D_BOTH, D_MINIMUM):
self.calculate_minimum_distances(workspace, parent_name)
if workspace.frame is not None:
figure = workspace.create_or_find_figure(
title="RelateObjects, image cycle #%d" %
(workspace.measurements.image_set_number),
subplots=(2, 2))
figure.subplot_imshow_labels(0,
0,
parents.segmented,
title=self.parent_name.value)
figure.subplot_imshow_labels(1,
0,
children.segmented,
title=self.sub_object_name.value,
sharex=figure.subplot(0, 0),
sharey=figure.subplot(0, 0))
parent_labeled_children = np.zeros(children.segmented.shape, int)
parent_labeled_children[children.segmented > 0] = \
parents_of[children.segmented[children.segmented > 0]-1]
figure.subplot_imshow_labels(
0,
1,
parent_labeled_children,
"%s labeled by %s" %
(self.sub_object_name.value, self.parent_name.value),
sharex=figure.subplot(0, 0),
sharey=figure.subplot(0, 0))
def test_mean03():
labels = np.array([1, 2])
for type in types:
input = np.array([[1, 2], [3, 4]], type)
output = ndimage.mean(input, labels=labels, index=2)
assert_almost_equal(output, 3.0)
# From Bi Rico on StackOverflow
def radial_profile(data, center):
y, x = np.indices((data.shape))
# running as stand-alone program
if __name__ == "__main__":
# Stand-alone programs must create a GX context before calling Geosoft methods.
with gxpy.gx.GXpy() as gxc:
with gxpy.grid.Grid.open(grid_path) as grid:
f = grid.np()
sx, sy = f.shape
X, Y = np.ogrid[0:sx, 0:sy]
r = np.hypot(X - sx/2, Y) # r is the same shape as grid, contains radius to every point
print(pd.DataFrame((bins * (r/r.max())).astype(np.int)))
# you need to correlate the bin numbers with their radii (frequency in CYC/km)
rbin = (bins* r/r.max()).astype(np.int) # array where each position has its bin number
index=np.arange(1, rbin.max() +1) # array from 1 to rbin.max()
radial_mean = ndimage.mean(f, labels=rbin, index=index)
plt.figure()
plt.title("with rbins")
plt.scatter(index, radial_mean)
plt.show()
def test_mean01():
labels = np.array([1, 0], bool)
for type in types:
input = np.array([[1, 2], [3, 4]], type)
output = ndimage.mean(input, labels=labels)
assert_almost_equal(output, 2.0)
def run(self, workspace):
if self.show_window:
workspace.display_data.col_labels = ("Image", "Object", "Feature",
"Mean", "Median", "STD")
workspace.display_data.statistics = statistics = []
for image_name in [img.name for img in self.images]:
image = workspace.image_set.get_image(image_name.value,
must_be_grayscale=True)
for object_name in [obj.name for obj in self.objects]:
# Need to refresh image after each iteration...
img = image.pixel_data
if image.has_mask:
masked_image = img.copy()
masked_image[~image.mask] = 0
else:
masked_image = img
objects = workspace.object_set.get_objects(object_name.value)
nobjects = objects.count
integrated_intensity = np.zeros((nobjects, ))
integrated_intensity_edge = np.zeros((nobjects, ))
mean_intensity = np.zeros((nobjects, ))
mean_intensity_edge = np.zeros((nobjects, ))
std_intensity = np.zeros((nobjects, ))
std_intensity_edge = np.zeros((nobjects, ))
min_intensity = np.zeros((nobjects, ))
min_intensity_edge = np.zeros((nobjects, ))
max_intensity = np.zeros((nobjects, ))
max_intensity_edge = np.zeros((nobjects, ))
mass_displacement = np.zeros((nobjects, ))
lower_quartile_intensity = np.zeros((nobjects, ))
median_intensity = np.zeros((nobjects, ))
mad_intensity = np.zeros((nobjects, ))
upper_quartile_intensity = np.zeros((nobjects, ))
cmi_x = np.zeros((nobjects, ))
cmi_y = np.zeros((nobjects, ))
max_x = np.zeros((nobjects, ))
max_y = np.zeros((nobjects, ))
for labels, lindexes in objects.get_labels():
lindexes = lindexes[lindexes != 0]
labels, img = cpo.crop_labels_and_image(labels, img)
_, masked_image = cpo.crop_labels_and_image(
labels, masked_image)
outlines = cpmo.outline(labels)
if image.has_mask:
_, mask = cpo.crop_labels_and_image(labels, image.mask)
masked_labels = labels.copy()
masked_labels[~mask] = 0
masked_outlines = outlines.copy()
masked_outlines[~mask] = 0
else:
masked_labels = labels
masked_outlines = outlines
lmask = masked_labels > 0 & np.isfinite(
img) # Ignore NaNs, Infs
has_objects = np.any(lmask)
if has_objects:
limg = img[lmask]
llabels = labels[lmask]
mesh_y, mesh_x = np.mgrid[0:masked_image.shape[0],
0:masked_image.shape[1]]
mesh_x = mesh_x[lmask]
mesh_y = mesh_y[lmask]
lcount = fix(
nd.sum(np.ones(len(limg)), llabels, lindexes))
integrated_intensity[lindexes-1] = \
fix(nd.sum(limg, llabels, lindexes))
mean_intensity[lindexes-1] = \
integrated_intensity[lindexes-1] / lcount
std_intensity[lindexes - 1] = np.sqrt(
fix(
nd.mean(
(limg - mean_intensity[llabels - 1])**2,
llabels, lindexes)))
min_intensity[lindexes - 1] = fix(
nd.minimum(limg, llabels, lindexes))
max_intensity[lindexes - 1] = fix(
nd.maximum(limg, llabels, lindexes))
# Compute the position of the intensity maximum
max_position = np.array(fix(
nd.maximum_position(limg, llabels, lindexes)),
dtype=int)
max_position = np.reshape(max_position,
(max_position.shape[0], ))
max_x[lindexes - 1] = mesh_x[max_position]
max_y[lindexes - 1] = mesh_y[max_position]
# The mass displacement is the distance between the center
# of mass of the binary image and of the intensity image. The
# center of mass is the average X or Y for the binary image
# and the sum of X or Y * intensity / integrated intensity
cm_x = fix(nd.mean(mesh_x, llabels, lindexes))
cm_y = fix(nd.mean(mesh_y, llabels, lindexes))
i_x = fix(nd.sum(mesh_x * limg, llabels, lindexes))
i_y = fix(nd.sum(mesh_y * limg, llabels, lindexes))
cmi_x[lindexes -
1] = i_x / integrated_intensity[lindexes - 1]
cmi_y[lindexes -
1] = i_y / integrated_intensity[lindexes - 1]
diff_x = cm_x - cmi_x[lindexes - 1]
diff_y = cm_y - cmi_y[lindexes - 1]
mass_displacement[lindexes-1] = \
np.sqrt(diff_x * diff_x+diff_y*diff_y)
#
# Sort the intensities by label, then intensity.
# For each label, find the index above and below
# the 25%, 50% and 75% mark and take the weighted
# average.
#
order = np.lexsort((limg, llabels))
areas = lcount.astype(int)
indices = np.cumsum(areas) - areas
for dest, fraction in ((lower_quartile_intensity,
1.0 / 4.0), (median_intensity,
1.0 / 2.0),
(upper_quartile_intensity,
3.0 / 4.0)):
qindex = indices.astype(float) + areas * fraction
qfraction = qindex - np.floor(qindex)
qindex = qindex.astype(int)
qmask = qindex < indices + areas - 1
qi = qindex[qmask]
qf = qfraction[qmask]
dest[lindexes[qmask] -
1] = (limg[order[qi]] * (1 - qf) +
limg[order[qi + 1]] * qf)
#
# In some situations (e.g. only 3 points), there may
# not be an upper bound.
#
qmask = (~qmask) & (areas > 0)
dest[lindexes[qmask] -
1] = limg[order[qindex[qmask]]]
#
# Once again, for the MAD
#
madimg = np.abs(limg - median_intensity[llabels - 1])
order = np.lexsort((madimg, llabels))
qindex = indices.astype(float) + areas / 2.0
qfraction = qindex - np.floor(qindex)
qindex = qindex.astype(int)
qmask = qindex < indices + areas - 1
qi = qindex[qmask]
qf = qfraction[qmask]
mad_intensity[lindexes[qmask] -
1] = (madimg[order[qi]] * (1 - qf) +
madimg[order[qi + 1]] * qf)
qmask = (~qmask) & (areas > 0)
mad_intensity[lindexes[qmask] -
1] = madimg[order[qindex[qmask]]]
emask = masked_outlines > 0
eimg = img[emask]
elabels = labels[emask]
has_edge = len(eimg) > 0
if has_edge:
ecount = fix(
nd.sum(np.ones(len(eimg)), elabels, lindexes))
integrated_intensity_edge[lindexes-1] = \
fix(nd.sum(eimg, elabels, lindexes))
mean_intensity_edge[lindexes-1] = \
integrated_intensity_edge[lindexes-1] / ecount
std_intensity_edge[lindexes-1] = \
np.sqrt(fix(nd.mean(
(eimg - mean_intensity_edge[elabels-1])**2,
elabels, lindexes)))
min_intensity_edge[lindexes - 1] = fix(
nd.minimum(eimg, elabels, lindexes))
max_intensity_edge[lindexes - 1] = fix(
nd.maximum(eimg, elabels, lindexes))
m = workspace.measurements
for category, feature_name, measurement in \
((INTENSITY, INTEGRATED_INTENSITY, integrated_intensity),
(INTENSITY, MEAN_INTENSITY, mean_intensity),
(INTENSITY, STD_INTENSITY, std_intensity),
(INTENSITY, MIN_INTENSITY, min_intensity),
(INTENSITY, MAX_INTENSITY, max_intensity),
(INTENSITY, INTEGRATED_INTENSITY_EDGE, integrated_intensity_edge),
(INTENSITY, MEAN_INTENSITY_EDGE, mean_intensity_edge),
(INTENSITY, STD_INTENSITY_EDGE, std_intensity_edge),
(INTENSITY, MIN_INTENSITY_EDGE, min_intensity_edge),
(INTENSITY, MAX_INTENSITY_EDGE, max_intensity_edge),
(INTENSITY, MASS_DISPLACEMENT, mass_displacement),
(INTENSITY, LOWER_QUARTILE_INTENSITY, lower_quartile_intensity),
(INTENSITY, MEDIAN_INTENSITY, median_intensity),
(INTENSITY, MAD_INTENSITY, mad_intensity),
(INTENSITY, UPPER_QUARTILE_INTENSITY, upper_quartile_intensity),
(C_LOCATION, LOC_CMI_X, cmi_x),
(C_LOCATION, LOC_CMI_Y, cmi_y),
(C_LOCATION, LOC_MAX_X, max_x),
(C_LOCATION, LOC_MAX_Y, max_y)):
measurement_name = "%s_%s_%s" % (category, feature_name,
image_name.value)
m.add_measurement(object_name.value, measurement_name,
measurement)
if self.show_window and len(measurement) > 0:
statistics.append(
(image_name.value, object_name.value, feature_name,
np.round(np.mean(measurement),
3), np.round(np.median(measurement), 3),
np.round(np.std(measurement), 3)))
def prep_gcm_wrevap(workspace):
"""Prepare GCM WREVAP monthly data files
Calculate and save daily Thornton-Running solar
Calculate and save daily Tdew
Calculate Monthly Tmean, Tdew, and Rs
Save monthly data to WREVAP data files
Build WREVAP input files
"""
logging.info('\nPreparing GCM WREVAP data')
# Folder with the csv data files
input_ws = r'Z:\USBR_Ag_Demands_Project\reservoir_evap\GCM_data\BC\CSV'
input_daily_temp = 'F'
input_daily_prcp = 'IN'
output_daily_temp = 'C'
# Output folder
output_ws = r'Z:\USBR_Ag_Demands_Project\reservoir_evap\WREVAP_GCM'
wrevap_temp = 'C'
res_list = []
# res_list = ['Lake_Mead']
res_list = ['Lake_Tahoe', 'Lake_Mead', 'Lake_Powell']
# res_list = [
# 'American_Falls', 'Boysen', 'Canyon_Ferry', 'Elephant_Butte',
# 'Grand_Coulee', 'Lahontan', 'Millerton_Lake', 'Shasta_Lake',
# 'Upper_Klamath']
# Adjust precipitation
# PPT will be multiplied by these ratios
# (i.e. decrease the estimated values that are read in)
ppt_month_factor_dict = dict()
# New factors from Justin (2014-09-23)
ppt_month_factor_dict['Lake_Tahoe'] = [
0.683793809, 0.696432660, 0.691828784, 0.712677417, 0.743181881,
0.668170098, 0.543929977, 0.604882144, 0.607345296, 0.675140118,
0.678983427, 0.779749794
]
# Old factors
# ppt_month_factor_dict['Lake_Tahoe'] = [
# 0.702914491, 0.720976639, 0.720924194, 0.774378465,
# 0.850691236, 0.828274127, 0.872059365, 0.866350328,
# 0.758308161, 0.738646093, 0.708893856, 0.804691107]
# Adjust incoming solar
# From: Lake_Tahoe_Solar_Calibration_Check.xlxs
# Ratios are estimated divided by measured
# (i.e. decrease the estimated values that are read in)
rs_month_factor_dict = dict()
rs_month_factor_dict['Lake_Tahoe'] = [
1.233, 1.144, 1.084, 1.025, 1.015, 1.041, 1.065, 1.031, 1.029, 1.013,
1.132, 1.396
]
rs_month_factor_dict['Lahontan'] = [
1.108210828, 1.086, 1.066844029, 1.05, 1.030296257, 1.011742403,
1.013442609, 1.013532861, 1.01, 1.017420093, 1.072664479, 1.133997425
]
rs_month_factor_dict['Lake_Mead'] = [
1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0
]
rs_month_factor_dict['Lake_Powell'] = [
1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0
]
# Output solar is in W/m^2 for dailies, and MJ/m^2/d for WREVAP inputs
# Ancillary files
res_param_name = 'reservoir_parameters.csv'
res_param_temp = 'C'
default_ini_name = 'default.ini'
# header_name = 'HEADER.txt'
# bad_data_name = 'bad_data.csv'
# Reservoir parameter fields
# gcm_name_field = 'GCM_NAME'
input_name_field = 'GCM_NAME'
output_name_field = 'OUTPUT_NAME'
depth_field = 'DEPTH'
salin_field = 'SALINITY'
elev_field = 'ELEVATION'
lat_field = 'LATITUDE'
# lon_field = 'LONGITUDE'
tr_b0_field = 'TR_B0'
tr_b1_field = 'TR_B1'
tr_b2_field = 'TR_B2'
ko_field = 'KO_'
# Overwrite existing files
overwrite_flag = True
# DeltaT year range
delta_t_year_range = (1950, 1999)
# Check inputs
if not os.path.isdir(input_ws):
logging.error(
'\nERROR: The input workspace {} does not exist'.format(input_ws))
raise SystemExit
if not os.path.isdir(output_ws):
os.mkdir(output_ws)
res_param_path = os.path.join(workspace, res_param_name)
if not os.path.isfile(res_param_path):
logging.error(('\nERROR: The reservoir parameter file (\'{}\')' +
' does not exist').format(res_param_path))
raise SystemExit()
default_ini_path = os.path.join(workspace, default_ini_name)
if not os.path.isfile(default_ini_path):
logging.error(('\nERROR: The default config file (\'{}\')' +
' does not exist').format(default_ini_path))
raise SystemExit()
# bad_data_path = os.path.join(workspace, bad_data_name)
# if os.path.isfile(bad_data_path): os.remove(bad_data_path)
input_daily_temp = input_daily_temp.upper()
input_daily_prcp = input_daily_prcp.upper()
output_daily_temp = output_daily_temp.upper()
wrevap_temp = wrevap_temp.upper()
res_param_temp = res_param_temp.upper()
if input_daily_temp not in ['F', 'C']:
logging.error('\nERROR: The input daily temperature must be F or C\n')
raise SystemExit()
if input_daily_prcp not in ['MM', 'IN']:
logging.error(
'\nERROR: The input daily prcipitation must be MM or IN\n')
raise SystemExit()
if output_daily_temp not in ['F', 'C']:
logging.error('\nERROR: The output daily temperature must be F or C\n')
raise SystemExit()
if wrevap_temp not in ['F', 'C']:
logging.error('\nERROR: The WREVAP temperature must be F or C\n')
raise SystemExit()
if res_param_temp not in ['F', 'C']:
logging.error('\nERROR: The reservoir parameter temperature ' +
'must be F or C\n')
raise SystemExit()
# Input file regular expressions
csv_re = re.compile('\w+_\w+.csv$')
tmax_csv_re = re.compile('\w+_TMAX.csv$')
tmin_csv_re = re.compile('\w+_TMIN.csv$')
# dtrg_csv_re = re.compile('\w+_DTRG.csv$')
prcp_csv_re = re.compile('\w+_PRCP.csv$')
# tdew_csv_re = re.compile('\w+_TDEW.csv$')
# rso_csv_re = re.compile('\w+_RSO.csv$')
# rs_csv_re = re.compile('\w+_RS.csv$')
# Build list of reservoirs with TMAX and TMIN data
csv_list = [item for item in os.listdir(input_ws) if csv_re.match(item)]
tmax_csv_dict = dict([(item.split('_')[0], item) for item in csv_list
if tmax_csv_re.match(item)])
tmin_csv_dict = dict([(item.split('_')[0], item) for item in csv_list
if tmin_csv_re.match(item)])
prcp_csv_dict = dict([(item.split('_')[0], item) for item in csv_list
if prcp_csv_re.match(item)])
# tdew_csv_dict = dict([
# (item.split('_')[0], item) for item in csv_list
# if tdew_csv_re.match(item)])
# output_res_list = sorted(list(
# set(tmax_csv_dict.keys() + tmin_csv_dict.keys())))
# Read in reservoir parameters as structured array
res_param_array = np.atleast_2d(
np.genfromtxt(res_param_path, delimiter=',', names=True, dtype=None))
# res_param_fields = res_param_array.dtype.names
# DEADBEEF
# res_param_names = res_param_array[gcm_name_field]
input_res_array = res_param_array[input_name_field]
output_res_array = res_param_array[output_name_field]
# Use reservoir parameters file to set input and output name lists
input_res_list = input_res_array[0]
output_res_list = output_res_array[0]
# Write bad data to a txt file
# bad_data_f = open(bad_data_path, 'w')
# Check keys on factors
for output_res in ppt_month_factor_dict.keys():
if output_res not in output_res_list:
logging.error(
'The reservoir name {} is invalid'.format(output_res))
raise SystemExit()
for output_res in rs_month_factor_dict.keys():
if output_res not in output_res_list:
logging.error(
'The reservoir name {} is invalid'.format(output_res))
raise SystemExit()
# Process each reservoir
for input_res, output_res in sorted(zip(input_res_list, output_res_list)):
logging.info('{}'.format(output_res))
# Process target reservoirs
if res_list and output_res not in res_list:
continue
# A TMAX and TMIN csv must be present to run
try:
tmax_csv_path = os.path.join(input_ws, tmax_csv_dict[input_res])
tmin_csv_path = os.path.join(input_ws, tmin_csv_dict[input_res])
prcp_csv_path = os.path.join(input_ws, prcp_csv_dict[input_res])
except KeyError:
continue
logging.info(' GCM Name: {}'.format(input_res))
# Daily output file names
tdew_csv_name = '{}_TDEW.csv'.format(input_res)
rso_csv_name = '{}_RSO.csv'.format(input_res)
rs_csv_name = '{}_RS.csv'.format(input_res)
# Daily output file paths
tdew_csv_path = os.path.join(input_ws, tdew_csv_name)
rso_csv_path = os.path.join(input_ws, rso_csv_name)
rs_csv_path = os.path.join(input_ws, rs_csv_name)
# Remove existing daily files if necessary
if overwrite_flag and os.path.isfile(tdew_csv_path):
os.remove(tdew_csv_path)
if overwrite_flag and os.path.isfile(rso_csv_path):
os.remove(rso_csv_path)
if overwrite_flag and os.path.isfile(rs_csv_path):
os.remove(rs_csv_path)
# Get reservoir parameter data from file using output_res as key
if output_res not in output_res_array:
logging.info(
' Reservoir does not have data in {}'.format(output_res))
continue
res_param = res_param_array[output_res_array == output_res]
# output_name = res_param[output_name_field][0]
depth_flt = float(res_param[depth_field][0])
salin_flt = float(res_param[salin_field][0])
elev_flt = float(res_param[elev_field][0])
lat_flt = float(res_param[lat_field][0])
# lon_flt = float(res_param[lon_field][0])
tr_b0_flt = float(res_param[tr_b0_field][0])
tr_b1_flt = float(res_param[tr_b1_field][0])
tr_b2_flt = float(res_param[tr_b2_field][0])
ko_month_array = np.array([
float(res_param[ko_field + month_abbr.upper()][0])
for month_i, month_abbr in enumerate(calendar.month_abbr)
if month_abbr
])
del res_param
# Convert ko temperature to celsius
if res_param_temp == 'F':
ko_month_array = fahrenheit_to_celsius(ko_month_array)
elif res_param_temp == 'C':
pass
else:
continue
# Monthly output workspace
res_output_ws = os.path.join(output_ws, output_res)
if not os.path.isdir(res_output_ws):
os.mkdir(res_output_ws)
res_data_ws = os.path.join(res_output_ws, 'input_data')
if not os.path.isdir(res_data_ws):
os.mkdir(res_data_ws)
# Read header row for each file to get GCM list
# First field is date field, skip
with open(tmax_csv_path, 'r') as f:
header_str = f.readline().strip()
# Header str has a comma at the end
if header_str[-1] == ',':
header_str = header_str[:-1]
f.closed
gcm_name_list = [i.strip() for i in header_str.split(',') if i][1:]
header_fmt_str = '%d,' + ','.join(['%7.4f'] * len(gcm_name_list))
# Read in daily Tmin and Tmax data, skip header row
tmax_csv_array = np.loadtxt(tmax_csv_path, delimiter=',', skiprows=1)
tmin_csv_array = np.loadtxt(tmin_csv_path, delimiter=',', skiprows=1)
prcp_csv_array = np.loadtxt(prcp_csv_path, delimiter=',', skiprows=1)
del tmax_csv_path, tmin_csv_path, prcp_csv_path
# Get data subsets from full csv array
date_array = tmax_csv_array[:, 0].astype(np.int)
tmax_array = tmax_csv_array[:, 1:]
tmin_array = tmin_csv_array[:, 1:]
prcp_array = prcp_csv_array[:, 1:]
del tmax_csv_array, tmin_csv_array, prcp_csv_array
# Convert input temperature to celsius (for Thornton-Running)
if input_daily_temp == 'F':
tmax_array = fahrenheit_to_celsius(tmax_array)
tmin_array = fahrenheit_to_celsius(tmin_array)
elif input_daily_temp == 'C':
pass
else:
continue
# Convert input precipitation to mm (from inches)
if input_daily_prcp == 'IN':
prcp_array *= 25.4
elif input_daily_prcp == 'MM':
pass
else:
continue
# Calculate Tmax-Tmin
tmax_tmin_array = tmax_array - tmin_array
# Where Tmax > Tmin, set to nan and save
tmax_tmin_mask = (tmax_tmin_array >= 0)
if not np.all(tmax_tmin_mask):
logging.warning(' WARNING: TMIN > TMAX for {} cells'.format(
np.sum(~tmax_tmin_mask)))
tmax_tmin_mask_i = np.nonzero(~tmax_tmin_mask)
for gcm, date in zip(
np.array(gcm_name_list)[tmax_tmin_mask_i[1]],
date_array[tmax_tmin_mask_i[0]]):
# bad_data_f.write(
# ','.join([output_res, gcm, str(date)]) + '\n')
logging.debug(' {} {}'.format(gcm, date))
del date, gcm
del tmax_tmin_mask_i
tmax_tmin_array[~tmax_tmin_mask] = np.nan
tmax_array[~tmax_tmin_mask] = np.nan
tmin_array[~tmax_tmin_mask] = np.nan
# Calculate mean temperature
tmean_array = 0.5 * (tmax_array + tmin_array)
del tmax_array
# Get Year/Month for each DOY
ym_daily_array = np.array([
dt.datetime.strptime(str(d), '%Y%m%d').strftime('%Y_%m')
for d in date_array
])
year_array = np.array([
dt.datetime.strptime(str(d), '%Y%m%d').strftime('%Y')
for d in date_array
]).astype(np.int)
month_array = np.array([
dt.datetime.strptime(str(d), '%Y%m%d').strftime('%m')
for d in date_array
]).astype(np.int)
# Get DOY from date
doy_array = np.array([
dt.datetime.strptime(str(d), '%Y%m%d').strftime('%j')
for d in date_array
]).astype(np.int)
# Get Year/Month for each month
ym_month_array = np.unique(ym_daily_array)
# Calculate mean monthly temperature difference for each day
delta_t_array = np.zeros(tmean_array.shape)
# Only use "historical" temperatures
year_mask = ((year_array >= delta_t_year_range[0]) &
(year_array <= delta_t_year_range[1]))
for gcm_i, gcm_name in enumerate(gcm_name_list):
# Only calculate mean for days with Tmax > Tmin
gcm_mask = (year_mask & tmax_tmin_mask[:, gcm_i])
mean_array = ndimage.mean(tmax_tmin_array[:, gcm_i][gcm_mask],
labels=month_array[gcm_mask],
index=range(1, 13))
for month_i, month in enumerate(range(1, 13)):
month_mask = (month_array == month)
delta_t_array[:, gcm_i][month_mask] = mean_array[month_i]
del month_mask
del mean_array, gcm_mask
# Map KO from mean monthlies to individual dailies
ko_array = np.zeros(tmin_array.shape)
for month_i, month in enumerate(range(1, 13)):
ko_array[month_array == month] = ko_month_array[month_i]
# Calculate Tdew
tdew_array = (tmin_array - ko_array)
del ko_array, tmin_array
# Calculate vapor pressure
ea_array = calc_vapor_pressure(tdew_array)
# Calculate pressure
pres_flt = float(calc_pressure(elev_flt))
# Calculate Thornton-Running Solar
rso_array, rs_array = calc_tr_rso(lat_flt, pres_flt, ea_array,
doy_array[:, np.newaxis],
delta_t_array, tmax_tmin_array,
tr_b0_flt, tr_b1_flt, tr_b2_flt)
del ea_array, pres_flt, delta_t_array, tmax_tmin_array
del doy_array
# Scale Rso values by monthly factor
if output_res in rs_month_factor_dict.keys():
for month_i, month in enumerate(range(1, 13)):
logging.info(' Scaling Monthly Rs: {} {}'.format(
month, rs_month_factor_dict[output_res][month_i]))
rs_array[month_array ==
month] /= rs_month_factor_dict[output_res][month_i]
# Make copies of output arrays for unit conversions
tdew_daily_array = np.copy(tdew_array)
rso_daily_array = np.copy(rso_array)
rs_daily_array = np.copy(rs_array)
# Convert output daily dew point temperature from celsius
if output_daily_temp == 'F':
tdew_daily_array = celsius_to_fahrenheit(tdew_daily_array)
elif output_daily_temp == 'C':
pass
else:
continue
# Convert daily solar from MJ/m2/d to w/m2
rso_daily_array *= 11.574
rs_daily_array *= 11.574
# Save daily values
# Append date_array at beginning
if not os.path.isfile(tdew_csv_path):
np.savetxt(tdew_csv_path,
np.hstack((date_array[:,
np.newaxis], tdew_daily_array)),
delimiter=',',
header=header_str,
fmt=header_fmt_str,
comments='')
if not os.path.isfile(rso_csv_path):
np.savetxt(rso_csv_path,
np.hstack((date_array[:, np.newaxis], rso_daily_array)),
delimiter=',',
header=header_str,
fmt=header_fmt_str,
comments='')
if not os.path.isfile(rs_csv_path):
np.savetxt(rs_csv_path,
np.hstack((date_array[:, np.newaxis], rs_daily_array)),
delimiter=',',
header=header_str,
fmt=header_fmt_str,
comments='')
del tdew_daily_array, rso_daily_array, rs_daily_array,
del date_array, header_fmt_str
# Calculat fixed monthly values
year_array = np.array([int(ym.split('_')[0])
for ym in ym_month_array]).astype(np.int)
month_array = np.array(
[int(ym.split('_')[1]) for ym in ym_month_array]).astype(np.int)
start_array = np.ones(ym_month_array.size).astype(np.int)
length_array = np.array([
calendar.monthrange(*map(int, ym.split('_')))[1]
# calendar.monthrange(int(ym.split('_')[0]), int(ym.split('_')[1]))[1]
for ym in ym_month_array
]).astype(np.int)
# Calculate variable monthly values (Rso, Rs, Tdew, Tmean)
tmean_month_array = np.zeros(
(ym_month_array.size, tmean_array.shape[1]))
tdew_month_array = np.zeros(
(ym_month_array.size, tmean_array.shape[1]))
rso_month_array = np.zeros((ym_month_array.size, tmean_array.shape[1]))
rs_month_array = np.zeros((ym_month_array.size, tmean_array.shape[1]))
prcp_month_array = np.zeros((ym_month_array.size, prcp_array.shape[1]))
for gcm_i, gcm_name in enumerate(gcm_name_list):
tmean_month_array[:, gcm_i] = ndimage.mean(
tmean_array[:, gcm_i][tmax_tmin_mask[:, gcm_i]],
labels=ym_daily_array[tmax_tmin_mask[:, gcm_i]],
index=ym_month_array)
tdew_month_array[:, gcm_i] = ndimage.mean(
tdew_array[:, gcm_i][tmax_tmin_mask[:, gcm_i]],
labels=ym_daily_array[tmax_tmin_mask[:, gcm_i]],
index=ym_month_array)
rso_month_array[:, gcm_i] = ndimage.mean(
rso_array[:, gcm_i][tmax_tmin_mask[:, gcm_i]],
labels=ym_daily_array[tmax_tmin_mask[:, gcm_i]],
index=ym_month_array)
rs_month_array[:, gcm_i] = ndimage.mean(
rs_array[:, gcm_i][tmax_tmin_mask[:, gcm_i]],
labels=ym_daily_array[tmax_tmin_mask[:, gcm_i]],
index=ym_month_array)
prcp_month_array[:, gcm_i] = ndimage.sum(
prcp_array[:, gcm_i][tmax_tmin_mask[:, gcm_i]],
labels=ym_daily_array[tmax_tmin_mask[:, gcm_i]],
index=ym_month_array)
del tmean_array, tdew_array, rso_array, rs_array, prcp_array
del ym_month_array, ym_daily_array
# Convert output daily dew point temperature from celsius
if wrevap_temp == 'F':
tdew_month_array = celsius_to_fahrenheit(tdew_month_array)
tmean_month_array = celsius_to_fahrenheit(tmean_month_array)
elif wrevap_temp == 'C':
pass
else:
continue
# Scale PPT values by monthly factor
if output_res in ppt_month_factor_dict.keys():
for month_i, month in enumerate(range(1, 13)):
logging.info(' Scaling Monthly PPT: {} {}'.format(
month, ppt_month_factor_dict[output_res][month_i]))
prcp_month_array[
month_array ==
month] *= ppt_month_factor_dict[output_res][month_i]
# Save monthly data for each GCM to a separate data file
wrevap_header_str = 'YEAR,MONTH,STARTDAY,LENGTH,TD,T,S,PPT'
wrevap_fmt_str = '%d,%d,%d,%d,%f,%f,%f,%f'
for gcm_i, gcm_name in enumerate(gcm_name_list):
output_csv_name = '{}_{}.csv'.format(output_res,
gcm_name.replace('.', '_'))
output_csv_path = os.path.join(res_data_ws, output_csv_name)
if overwrite_flag and os.path.isfile(output_csv_path):
os.remove(output_csv_path)
if not os.path.isfile(output_csv_path):
np.savetxt(output_csv_path,
np.vstack((year_array, month_array, start_array,
length_array, tdew_month_array[:, gcm_i],
tmean_month_array[:, gcm_i],
rs_month_array[:, gcm_i],
prcp_month_array[:, gcm_i])).T,
delimiter=',',
header=wrevap_header_str,
comments='',
fmt=wrevap_fmt_str)
del year_array, month_array, start_array, length_array
del tdew_month_array, tmean_month_array
del rs_month_array, rso_month_array, prcp_month_array
# Build a Python WREVAP_gcm input file
output_ini_name = '{}.ini'.format(output_res.lower())
output_ini_path = os.path.join(res_output_ws, output_ini_name)
if os.path.isfile(output_ini_path):
os.remove(output_ini_path)
default_ini_f = open(default_ini_path, 'r')
output_ini_f = open(output_ini_path, 'w')
for default_line in default_ini_f:
if default_line.strip().startswith('SITE = '):
default_line = 'SITE = {}\n'.format(output_res.upper().replace(
' ', '_'))
elif default_line.strip().startswith('PHID = '):
default_line = 'PHID = {}\n'.format(lat_flt)
elif default_line.strip().startswith('P = '):
default_line = 'P = {}\n'.format(elev_flt)
elif default_line.strip().startswith('DA = '):
default_line = 'DA = {}\n'.format(depth_flt)
elif default_line.strip().startswith('SALT = '):
default_line = 'SALT = {}\n'.format(salin_flt)
elif default_line.strip().startswith('LK = '):
default_line = 'LK = 2\n'
elif default_line.strip().startswith('IT = '):
if wrevap_temp == 'C':
default_line = 'IT = 0\n'
elif wrevap_temp == 'F':
default_line = 'IT = 1\n'
elif default_line.strip().startswith('IS = '):
default_line = 'IS = 3\n'
elif default_line.strip().startswith('IV = '):
default_line = 'IV = 0\n'
elif default_line.strip().startswith('IP = '):
default_line = 'IP = 1\n'
output_ini_f.write(default_line)
default_ini_f.close()
output_ini_f.close()
# Cleanup
del header_str, gcm_name_list
del depth_flt, salin_flt, elev_flt, lat_flt
del input_res_list, output_res_list
qbinsc = np.copy(qbins)
qbinsc[1:] += qstep / 2.
#create an array labeling each voxel according to which qbin it belongs
qbin_labels = np.searchsorted(qbins, qr, "right")
qbin_labels -= 1
#assume rho is given as electron density, not electron count
#convert from density to electron count for FFT calculation
rho *= dV
#create list of qbin indices just in region of data for later F scaling
qbin_args = np.copy(qbinsc)
F = np.fft.fftn(rho)
I3D = np.abs(F)**2
Imean = ndimage.mean(I3D,
labels=qbin_labels,
index=np.arange(0,
qbin_labels.max() + 1))
if args.plot:
plt.plot(qbinsc, Imean, label='Default dq = %.4f' % (2 * np.pi / side))
print('Default dq = %.4f' % (2 * np.pi / side))
if args.dq is not None or args.n is not None:
#padded to get desired dq value (or near it)
if args.n is not None:
n = args.n
else:
current_dq = 2 * np.pi / side
desired_dq = args.dq
if desired_dq > current_dq:
def _calculateArrayId(self):
"""
Calculates statistics (see methods calculate) when ids are array, even
if ids have one element only.
"""
# make sure the result data structures are ok
self._prepareArrays(arrays=('mean', 'std', 'min', 'max', 'minPos',
'maxPos'),
widths=(1, 1, 1, 1, self.ndim, self.ndim),
dtypes=(float, float, float, float, int, int))
# do calculations for each segment separately
self.mean[self._ids] = ndimage.mean(input=self.data,
labels=self.labels,
index=self._ids)
self.std[self._ids] = ndimage.standard_deviation(input=self.data,
labels=self.labels,
index=self._ids)
extr = ndimage.extrema(input=self.data,
labels=self.labels,
index=self._ids)
# figure out if 0 is the only id
zero_id = False
if isinstance(self._ids, (numpy.ndarray, list)):
zero_id = (self._ids[0] == 0)
else:
zero_id = (self._ids == 0)
# do calculations for all segments together
if not zero_id:
from .segment import Segment
seg = Segment()
locLabels = seg.keep(ids=self._ids, data=self.labels.copy())
self.mean[0] = ndimage.mean(input=self.data,
labels=locLabels,
index=None)
self.std[0] = ndimage.standard_deviation(input=self.data,
labels=locLabels,
index=None)
extr0 = ndimage.extrema(input=self.data,
labels=locLabels,
index=None)
# put extrema for individual labels in data arrays
(self.min[self._ids], self.max[self._ids]) = (extr[0], extr[1])
#self.max[self._ids] = -numpy.array(extr_bug[0])
if (self._ids.size == 1) and not isinstance(extr[2], list):
self.minPos[self._ids] = [extr[2]]
self.maxPos[self._ids] = [extr[3]]
#self.maxPos[self._ids] = [extr_bug[2]]
else:
self.minPos[self._ids] = extr[2]
self.maxPos[self._ids] = extr[3]
#self.maxPos[self._ids] = extr_bug[3]
# put total extrema in data arrays at index 0
if not zero_id:
(self.min[0], self.max[0]) = (extr0[0], extr0[1])
#self.max[0] = -extr0_bug[0]
if self.ndim == 1:
self.minPos[0] = extr0[2][0]
self.maxPos[0] = extr0[3][0]
#self.maxPos[0] = extr0_bug[2][0]
else:
self.minPos[0] = extr0[2]
self.maxPos[0] = extr0[3]
def freqListStat(freqlist):
freqnumpy = numpy.asarray(freqlist, dtype=numpy.int32)
print "min=", ndimage.minimum(freqnumpy)
print "max=", ndimage.maximum(freqnumpy)
print "mean=", ndimage.mean(freqnumpy)
print "stdev=", ndimage.standard_deviation(freqnumpy)
def groupsstats_1d(y, x, labelsunique):
'''use ndimage to get fast mean and variance'''
labelmeans = np.array(ndimage.mean(x, labels=y, index=labelsunique))
labelvars = np.array(ndimage.var(x, labels=y, index=labelsunique))
return labelmeans, labelvars
center = np.unravel_index(np.argmax(cutout), cutout.shape)
cy, cx = center
dy = (Y - cy)
dx = (X - cx)
costh = np.cos(beams_table[plot_channel][2] * (np.pi / 180))
sinth = np.sin(beams_table[plot_channel][2] * (np.pi / 180))
rmajmin = beams_table[plot_channel][1] / beams_table[plot_channel][0]
rr = ((dx * costh + dy * sinth)**2 / rmajmin**2 +
(dx * sinth - dy * costh)**2 / 1**2)**0.5
rbin = (rr).astype(int)
#radial_mean = ndimage.mean(cutout**2, labels=rbin, index=np.arange(max_npix_peak))
radial_mean = ndimage.mean(np.abs(cutout),
labels=rbin,
index=np.arange(max_npix_peak))
first_min_ind = signal.find_peaks(-radial_mean)[0][0]
#cutout_posit = np.where(cutout > 0, cutout, 0.)
#radial_sum = ndimage.sum(cutout_posit, labels=rbin, index=np.arange(first_min_ind))
radial_sum = ndimage.sum(cutout, labels=rbin, index=np.arange(first_min_ind))
psf_sum = np.sum(radial_sum)
#Z = np.full(shape, 0)
bmaj_npix = beams_table[plot_channel][0] / (header['CDELT2'] * 3600.)
bmin_npix = beams_table[plot_channel][1] / (header['CDELT2'] * 3600.)
clean_beam_sum = (np.pi / (4 * np.log(2))) * bmaj_npix * bmin_npix
scale_factor = clean_beam_sum / psf_sum
lv_mask = np.where(labels == lv_val, 1, 0)
# Find bounding box of left ventricle
bboxes = ndi.find_objects(lv_mask)
print('Number of objects:', len(bboxes))
print('Indices for first box:', bboxes[0])
## MEASURING INTENSITY
# after segmentation of objects their properties can be identified using scipy tools
# mean, mean standard deviation and labeled_comprehension
vol = imageio.volread("SCD-3d.npz")
label = imageio.volread("labels.npz")
# all pixel
ndi.mean(vol)
# by doing it with label, you'll restrict the analysis to non zero pixels
ndi.mean(vol, label)
# if provided the index value with label, you can get mean intensity for a single
# label or multiple labels
ndi.mean(vol, label, index=1)
ndi.mean(vol, label, index=[1, 2])
# Object Histograms can also use labels to be specific about an object in an image
hist = ndi.histogram(vol, min=0, max=255, bins=256) # for whole image
obj_hist = ndi.histogram(vol, 0, 255, 256, labels, index=[1, 2])
## these histograms are very informative at object segmentations
# if it has alot of peaks and variations, it means the object has vrious tissue types
else:
# get the parcel-level affiliations if we have parcellated data
data = data.assign(networks=getattr(networks, 'parcels'))
# when working with parcellated data, our spins were NOT generated with
# the medial wall / corpuscallosum included, so we should drop these
# parcels (which should [ideally] have values of ~=0)
todrop = np.array(putils.DROP)[np.isin(putils.DROP, data.index)]
if len(todrop) > 0:
data = data.drop(todrop, axis=0)
return data
if __name__ == "__main__":
data = load_data('yeo', PARC, SCALE)
netmeans = ndimage.mean(data['myelin'], data['networks'],
np.unique(data['networks']))
fig, axes = plt.subplots(len(NETWORKS),
len(METHODS),
sharex=True,
sharey=True,
figsize=(25, 10))
for row, network in enumerate(NETWORKS):
for col, spatnull in enumerate(METHODS):
idx = YEO_CODES[network] - 1
ax = axes[row, col]
fn = (HCPDIR / PARC / 'nulls' / 'yeo' / spatnull / THRESH /
f'{SCALE}_nulls.csv')
null = np.loadtxt(fn, delimiter=',')[:, idx]
sns.kdeplot(null, fill=True, alpha=0.4, color=SPATHUES[col], ax=ax)
sns.despine(ax=ax)
def pixelPeak(self, newimage=None, guess=None, limit=None):
"""
guess = where to center your search for the peak (row,col)
limit = shape of the search box (with guess at the center)
Setting guess and limit can serve two purposes:
1) You can imit your peak search if you are pretty sure
where it will be
2) Given that the image may wrap around into negative
space, you can specify that you want to search for the peak
in these out of bounds areas. For instance, a (512,512)
image may have a peak at (500,500). You may specify a guess
of (-10,-10) and a relatively small limit box.
The (500,500) peak will be found, but it will be returned
as (-12,-12).
"""
if newimage is not None:
self.setImage(newimage)
if self.results['pixel peak'] is None:
if None not in (guess, limit):
cropcenter = limit[0] / 2.0 - 0.5, limit[1] / 2.0 - 0.5
im = imagefun.crop_at(self.image, guess, limit)
else:
cropcenter = None
im = self.image
peak = numpy.argmax(im.ravel())
peakvalue = im.flat[peak]
rows, cols = im.shape
peakrow = peak / cols
peakcol = peak % cols
if cropcenter is not None:
peakrow = int(round(guess[0] + peakrow - cropcenter[0]))
peakcol = int(round(guess[1] + peakcol - cropcenter[1]))
pixelpeak = (peakrow, peakcol)
self.results['pixel peak'] = pixelpeak
self.results['pixel peak value'] = peakvalue
if peakrow < 0:
unsignedr = peakrow + self.image.shape[0]
else:
unsignedr = peakrow
if peakcol < 0:
unsignedc = peakcol + self.image.shape[0]
else:
unsignedc = peakcol
self.results['unsigned pixel peak'] = unsignedr, unsignedc
#NEIL's SNR calculation
self.results['noise'] = nd_image.standard_deviation(im)
self.results['mean'] = nd_image.mean(im)
self.results['signal'] = self.results[
'pixel peak value'] - self.results['mean']
if self.results['noise'] == self.results[
'noise'] and self.results['noise'] != 0.0:
self.results[
'snr'] = self.results['signal'] / self.results['noise']
else:
self.results['snr'] = self.results['pixel peak value']
#print self.results['noise'],self.results['mean'],self.results['signal'],self.results['snr']
return self.results['pixel peak']
def run_on_objects(self, object_name, workspace):
"""Run, computing the area measurements for a single map of objects"""
objects = workspace.get_objects(object_name)
if len(objects.shape) == 2:
#
# Do the ellipse-related measurements
#
i, j, l = objects.ijv.transpose()
centers, eccentricity, major_axis_length, minor_axis_length, \
theta, compactness = \
ellipse_from_second_moments_ijv(i, j, 1, l, objects.indices, True)
del i
del j
del l
self.record_measurement(workspace, object_name, F_ECCENTRICITY,
eccentricity)
self.record_measurement(workspace, object_name,
F_MAJOR_AXIS_LENGTH, major_axis_length)
self.record_measurement(workspace, object_name,
F_MINOR_AXIS_LENGTH, minor_axis_length)
self.record_measurement(workspace, object_name, F_ORIENTATION,
theta * 180 / np.pi)
self.record_measurement(workspace, object_name, F_COMPACTNESS,
compactness)
is_first = False
if len(objects.indices) == 0:
nobjects = 0
else:
nobjects = np.max(objects.indices)
mcenter_x = np.zeros(nobjects)
mcenter_y = np.zeros(nobjects)
mextent = np.zeros(nobjects)
mperimeters = np.zeros(nobjects)
msolidity = np.zeros(nobjects)
euler = np.zeros(nobjects)
max_radius = np.zeros(nobjects)
median_radius = np.zeros(nobjects)
mean_radius = np.zeros(nobjects)
min_feret_diameter = np.zeros(nobjects)
max_feret_diameter = np.zeros(nobjects)
zernike_numbers = self.get_zernike_numbers()
zf = {}
for n, m in zernike_numbers:
zf[(n, m)] = np.zeros(nobjects)
if nobjects > 0:
chulls, chull_counts = convex_hull_ijv(objects.ijv,
objects.indices)
for labels, indices in objects.get_labels():
to_indices = indices - 1
distances = distance_to_edge(labels)
mcenter_y[to_indices], mcenter_x[to_indices] = \
maximum_position_of_labels(distances, labels, indices)
max_radius[to_indices] = fix(
scind.maximum(distances, labels, indices))
mean_radius[to_indices] = fix(
scind.mean(distances, labels, indices))
median_radius[to_indices] = median_of_labels(
distances, labels, indices)
#
# The extent (area / bounding box area)
#
mextent[to_indices] = calculate_extents(labels, indices)
#
# The perimeter distance
#
mperimeters[to_indices] = calculate_perimeters(
labels, indices)
#
# Solidity
#
msolidity[to_indices] = calculate_solidity(labels, indices)
#
# Euler number
#
euler[to_indices] = euler_number(labels, indices)
#
# Zernike features
#
if self.calculate_zernikes.value:
zf_l = cpmz.zernike(zernike_numbers, labels, indices)
for (n, m), z in zip(zernike_numbers,
zf_l.transpose()):
zf[(n, m)][to_indices] = z
#
# Form factor
#
ff = 4.0 * np.pi * objects.areas / mperimeters**2
#
# Feret diameter
#
min_feret_diameter, max_feret_diameter = \
feret_diameter(chulls, chull_counts, objects.indices)
else:
ff = np.zeros(0)
for f, m in ([(F_AREA, objects.areas), (F_CENTER_X, mcenter_x),
(F_CENTER_Y, mcenter_y),
(F_CENTER_Z, np.ones_like(mcenter_x)),
(F_EXTENT, mextent), (F_PERIMETER, mperimeters),
(F_SOLIDITY, msolidity), (F_FORM_FACTOR, ff),
(F_EULER_NUMBER, euler),
(F_MAXIMUM_RADIUS, max_radius),
(F_MEAN_RADIUS, mean_radius),
(F_MEDIAN_RADIUS, median_radius),
(F_MIN_FERET_DIAMETER, min_feret_diameter),
(F_MAX_FERET_DIAMETER, max_feret_diameter)] +
[(self.get_zernike_name((n, m)), zf[(n, m)])
for n, m in zernike_numbers]):
self.record_measurement(workspace, object_name, f, m)
else:
labels = objects.segmented
props = skimage.measure.regionprops(labels)
# Area
areas = [prop.area for prop in props]
self.record_measurement(workspace, object_name, F_AREA, areas)
# Extent
extents = [prop.extent for prop in props]
self.record_measurement(workspace, object_name, F_EXTENT, extents)
# Centers of mass
centers = objects.center_of_mass()
center_z, center_x, center_y = centers.transpose()
self.record_measurement(workspace, object_name, F_CENTER_X,
center_x)
self.record_measurement(workspace, object_name, F_CENTER_Y,
center_y)
self.record_measurement(workspace, object_name, F_CENTER_Z,
center_z)
# Perimeters
perimeters = []
for label in np.unique(labels):
if label == 0:
continue
volume = np.zeros_like(labels, dtype='bool')
volume[labels == label] = True
verts, faces, _, _ = skimage.measure.marching_cubes(
volume,
spacing=objects.parent_image.spacing
if objects.has_parent_image else (1.0, ) * labels.ndim,
level=0)
perimeters += [skimage.measure.mesh_surface_area(verts, faces)]
if len(perimeters) == 0:
self.record_measurement(workspace, object_name, F_PERIMETER,
[0])
else:
self.record_measurement(workspace, object_name, F_PERIMETER,
perimeters)
for feature in self.get_feature_names():
if feature in [
F_AREA, F_EXTENT, F_CENTER_X, F_CENTER_Y, F_CENTER_Z,
F_PERIMETER
]:
continue
self.record_measurement(workspace, object_name, feature,
[np.nan])
def calcNormConvMap(image, imagefft, tmplmask, oversized, pixrad):
t1 = time.time()
print " ... computing FindEM's norm_conv_map"
#print " IMAGE"
#imageinfo(image)
#numeric_to_jpg(image,"image.jpg")
#print " TMPLMASK"
#imageinfo(tmplmask)
#numeric_to_jpg(tmplmask,"tmplmask.jpg")
if(nd_image.minimum(image) < 0.0 or nd_image.minimum(tmplmask) < 0.0):
print " !!! WARNING image or mask is less than zero"
tmplsize = (tmplmask.shape)[1]
nmask = tmplmask.sum()
tmplshape = tmplmask.shape
imshape = image.shape
shift = int(-1*tmplsize/2.0)
#tmplmask2 = nd_image.shift(tmplmask, shift, mode='wrap', order=0)
#tmplmask2 = tmplmask
err = 0.000001
#print " IMAGESQ"
#imageinfo(image*image)
#print " CNV2 = convolution(image**2, mask)"
tmplmaskfft = fft.real_fft2d(tmplmask, s=oversized)
imagesqfft = fft.real_fft2d(image*image, s=oversized)
cnv2 = convolution_fft(imagesqfft, tmplmaskfft, oversized)
cnv2 = cnv2 + err
del imagesqfft
#SHIFTING CAN BE SLOW
#cnv2 = nd_image.shift(cnv2, shift, mode='wrap', order=0)
#imageinfo(cnv2)
#print cnv2[499,499],cnv2[500,500],cnv2[501,501]
#numeric_to_jpg(cnv2,"cnv2.jpg")
#print " CNV1 = convolution(image, mask)"
cnv1 = convolution_fft(imagefft, tmplmaskfft, oversized)
cnv1 = cnv1 + err
del tmplmaskfft
#SHIFTING CAN BE SLOW
cnv1 = nd_image.shift(cnv1, shift, mode='wrap', order=0)
#imageinfo(cnv1)
#print cnv1[499,499],cnv1[500,500],cnv1[501,501]
#numeric_to_jpg(cnv1*cnv1,"cnv1.jpg")
#print " V2 = ((nm*cnv2)-(cnv1*cnv1))/(nm*nm)"
a1 = nmask*cnv2
a1 = a1[ tmplshape[0]/2-1:imshape[0]+tmplshape[0]/2-1, tmplshape[1]/2-1:imshape[1]+tmplshape[1]/2-1 ]
#imageinfo(a1)
#print a1[499,499],a1[500,500],a1[501,501]
b1 = cnv1*cnv1
b1 = b1[ tmplshape[0]/2-1:imshape[0]+tmplshape[0]/2-1, tmplshape[1]/2-1:imshape[1]+tmplshape[1]/2-1 ]
del cnv2
del cnv1
#imageinfo(b1)
#print b1[499,499],b1[500,500],b1[501,501]
#print (a1[500,500]-b1[500,500])
#print nmask**2
#cross = cross_correlate(a1,b1)
#print numarray.argmax(numarray.ravel(cross))
#cross = normRange(cross)
#cross = numarray.where(cross > 0.8,cross,0.7)
#cross = nd_image.shift(cross, (cross.shape)[0]/2, mode='wrap', order=0)
#numeric_to_jpg(cross,"cross.jpg")
#phase = phase_correlate(a1[128:896,128:896],b1[128:896,128:896])
#print numarray.argmax(numarray.ravel(phase))
#phase = normRange(phase)
#phase = numarray.where(phase > 0.7,phase,0.6)
#phase = nd_image.shift(phase, (phase.shape)[0]/2, mode='wrap', order=0)
#numeric_to_jpg(phase,"phase.jpg")
v2= (a1 - b1)
v2 = v2/(nmask**2)
#REMOVE OUTSIDE AREA
cshape = v2.shape
white1 = 0.01
v2[ 0:pixrad*2, 0:cshape[1] ] = white1
v2[ 0:cshape[0], 0:pixrad*2 ] = white1
v2[ cshape[0]-pixrad*2:cshape[0], 0:cshape[1] ] = white1
v2[ 0:cshape[0], cshape[1]-pixrad*2:cshape[1] ] = white1
xn = (v2.shape)[0]/2
#IMPORTANT TO CHECK FOR ERROR
if(v2[xn-1,xn-1] > 1.0 or v2[xn,xn] > 1.0 or v2[xn+1,xn+1] > 1.0 \
or nd_image.mean(v2[xn/2:3*xn/2,xn/2:3*xn/2]) > 1.0):
print " !!! MAJOR ERROR IN NORMALIZATION CALCUATION (values > 1)"
imageinfo(v2)
print " ... VALUES: ",v2[xn-1,xn-1],v2[xn,xn],v2[xn+1,xn+1],nd_image.mean(v2)
numeric_to_jpg(a1,"a1.jpg")
numeric_to_jpg(b1,"b1.jpg")
numeric_to_jpg(b1,"v2.jpg")
sys.exit(1)
if(v2[xn-1,xn-1] < 0.0 or v2[xn,xn] < 0.0 or v2[xn+1,xn+1] < 0.0 \
or nd_image.mean(v2[xn/2:3*xn/2,xn/2:3*xn/2]) < 0.0):
print " !!! MAJOR ERROR IN NORMALIZATION CALCUATION (values < 0)"
imageinfo(v2)
print " ... VALUES: ",v2[xn-1,xn-1],v2[xn,xn],v2[xn+1,xn+1],nd_image.mean(v2)
numeric_to_jpg(a1,"a1.jpg")
numeric_to_jpg(b1,"b1.jpg")
numeric_to_jpg(b1,"v2.jpg")
sys.exit(1)
del a1
del b1
#numeric_to_jpg(v2,"v2.jpg")
#print " Normconvmap = sqrt(v2)"
v2 = numarray.where(v2 < err, err, v2)
normconvmap = numarray.sqrt(v2)
#numeric_to_jpg(normconvmap,"normconvmap-zero.jpg")
#normconvmap = numarray.where(v2 > err, numarray.sqrt(v2), 0.0)
del v2
#imageinfo(normconvmap)
#print normconvmap[499,499],normconvmap[500,500],normconvmap[501,501]
#numeric_to_jpg(normconvmap,"normconvmap-big.jpg")
print " ... ... time %.2f sec" % float(time.time()-t1)
#RETURN CENTER
return normconvmap
print "Computing Gaussian sub-band1.5 image from Original image"
Fsubband = fouriergausssubband15(ksp.shape, 0.707)
image_filtered = simpleifft(procpar, dims, hdr, (ksp * Fsubband), args)
# print "Saving Gaussian image"
save_nifti(normalise(np.abs(image_filtered)), 'gauss_subband')
# inhomogeneous correction
image_corr = inhomogeneouscorrection(ksp, ksp.shape, 3.0 / 60.0)
# print "Saving Correction image"
save_nifti(np.abs(image_filtered / image_corr), 'image_inhCorr3')
# print "Computing Laplacian enhanced image"
laplacian = simpleifft(
procpar, dims, hdr, (kspgauss * fourierlaplace(ksp.shape)), args)
alpha = ndimage.mean(np.abs(image_filtered)) / \
ndimage.mean(np.abs(laplacian))
kspgauss = kspacegaussian_filter2(ksp, 1.707)
image_filtered = simpleifft(procpar, dims, hdr, kspgauss, args)
image_filtered = (np.abs(image_filtered))
image_filtered = normalise(image_filtered)
image_lfiltered = image_filtered - 0.5 * alpha * laplacian
print '''Saving enhanced image g(x, y, z) = f(x, y, z) -
Laplacian[f(x, y, z)]'''
save_nifti(np.abs(image_lfiltered), 'laplacian_enhanced')
# print "Computing Laplace of Gaussian smoothed image"
Flaplace = fourierlaplace(ksp.shape)
# Flaplace = (Flaplace - ndimage.minimum(Flaplace)) /
# (ndimage.maximum(Flaplace)
# - ndimage.minimum(Flaplace))
def video_roi_extractor_faster(video_file=None):
#DISCOVER VIDEO INFORMATION
if video_file is None:
video_find = re.compile('^video.*nd2$')
video_file = list(filter(video_find.match, os.listdir()))[0]
roi_file = glob.glob('roi.1024*')
#DISCOVER ROI INFORMATION
rois = imread(roi_file)
rois_unique = np.setdiff1d(np.unique(rois), [0])
nregions = len(rois_unique)
print("You have ", nregions, "rois to process")
#INITIALIZE EMPTY FRAMES
ImageNumber = []
ObjectNumber = []
f2_340 = []
f2_380 = []
#LOAD AND PROCESS VIDEO
images = ND2Reader(video_file)
nframes = images.sizes['t']
print("You have ", nframes, " frames to process")
start_time = time.time()
#EXTRACT ROI INFORMATION FROM EACH VIDEO FRAMES
for frame_index in range(nframes):
if frame_index % 100 == 0:
print(frame_index, "/", nframes, "in",
round(time.time() - start_time, 0), " s")
#KEEP TRACK OF IMAGE NUMBER
ImageNumber_value = np.repeat(frame_index + 1, nregions)
ImageNumber.append(ImageNumber_value)
#KEEP TRACK OF OBJECT NUMBER
ObjectNumber_value = np.arange(0, nregions) + 1
ObjectNumber.append(ObjectNumber_value)
#EXTRACT 340 INFO
frame_340 = images.get_frame_2D(t=frame_index, c=0)
f2_340_val = ndimage.mean(frame_340, rois, rois_unique)
f2_340.append(f2_340_val)
#EXTRACT 380 INFO
frame_380 = images.get_frame_2D(t=frame_index, c=1)
f2_380_val = ndimage.mean(frame_380, rois, rois_unique)
f2_380.append(f2_380_val)
images.close()
print("Reading: %s seconds ---" % (time.time() - start_time))
#CONCATENATE THE LISTS MADE DURING THE LOOP TOGETHER
start_time = time.time()
ImageNumber = np.concatenate(ImageNumber)
ObjectNumber = np.concatenate(ObjectNumber)
f2_340 = np.concatenate(f2_340)
f2_380 = np.concatenate(f2_380)
print("concatentation: %s seconds ---" % (time.time() - start_time))
#CREATE DATAFRAME TO EXPORT
total_data = np.column_stack([ImageNumber, ObjectNumber, f2_340, f2_380])
df_data = pd.DataFrame(total_data)
df_data.columns = [
'ImageNumber', 'ObjectNumber', 'Intensity_MeanIntensity_f2_340',
'Intensity_MeanIntensity_f2_380'
]
df_data.to_csv('video_data.txt', header=True, index=False, sep='\t')
print("Write complete")
def test_mean02():
labels = np.array([1, 0], bool)
input = np.array([[1, 2], [3, 4]], bool)
output = ndimage.mean(input, labels=labels)
assert_almost_equal(output, 1.0)
def run(self, ips, imgs, para=None):
inten = self.app.get_img(para['inten'])
if not para['slice']:
imgs = [inten.img]
msks = [ips.img]
else:
msks = ips.imgs
imgs = inten.imgs
if len(msks) == 1:
msks *= len(imgs)
buf = imgs[0].astype(np.uint32)
strc = ndimage.generate_binary_structure(
2, 1 if para['con'] == '4-connect' else 2)
idct = ['Max', 'Min', 'Mean', 'Variance', 'Standard', 'Sum']
key = {
'Max': 'max',
'Min': 'min',
'Mean': 'mean',
'Variance': 'var',
'Standard': 'std',
'Sum': 'sum'
}
idct = [i for i in idct if para[key[i]]]
titles = ['Slice', 'ID'][0 if para['slice'] else 1:]
if para['center']: titles.extend(['Center-X', 'Center-Y'])
if para['extent']: titles.extend(['Min-Y', 'Min-X', 'Max-Y', 'Max-X'])
titles.extend(idct)
k = ips.unit[0]
data, mark = [], {'type': 'layers', 'body': {}}
# data,mark=[],[]
for i in range(len(imgs)):
if para['labeled']:
n, buf[:] = msks[i].max(), msks[i]
else:
n = ndimage.label(msks[i], strc, output=buf)
index = range(1, n + 1)
dt = []
if para['slice']: dt.append([i] * n)
dt.append(range(n))
xy = ndimage.center_of_mass(buf, buf, index)
xy = np.array(xy).round(2).T
if para['center']: dt.extend([xy[1] * k, xy[0] * k])
boxs = [None] * n
if para['extent']:
boxs = ndimage.find_objects(buf)
boxs = [(i[1].start, i[0].start, i[1].stop - i[1].start,
i[0].stop - i[0].start) for i in boxs]
for j in (0, 1, 2, 3):
dt.append([i[j] * k for i in boxs])
if para['max']:
dt.append(ndimage.maximum(imgs[i], buf, index).round(2))
if para['min']:
dt.append(ndimage.minimum(imgs[i], buf, index).round(2))
if para['mean']:
dt.append(ndimage.mean(imgs[i], buf, index).round(2))
if para['var']:
dt.append(ndimage.variance(imgs[i], buf, index).round(2))
if para['std']:
dt.append(
ndimage.standard_deviation(imgs[i], buf, index).round(2))
if para['sum']:
dt.append(ndimage.sum(imgs[i], buf, index).round(2))
layer = {'type': 'layer', 'body': []}
xy = np.int0(xy).T
texts = [(i[1], i[0]) + ('id=%d' % n, )
for i, n in zip(xy, range(len(xy)))]
layer['body'].append({'type': 'texts', 'body': texts})
if para['extent']:
layer['body'].append({'type': 'rectangles', 'body': boxs})
mark['body'][i] = layer
data.extend(list(zip(*dt)))
self.app.show_table(pd.DataFrame(data, columns=titles),
inten.title + '-pixels')
inten.mark = mark2shp(mark)
inten.update()
