def anaPsf(xaxis,yaxis,data):
# centroids
xCentroid = (xaxis*data).sum()/data.sum()
yCentroid = (yaxis*data).sum()/data.sum()
# radial sum -- around Centroid
raxis = numpy.sqrt((xaxis-xCentroid)*(xaxis-xCentroid)+(yaxis-yCentroid)*(yaxis-yCentroid))
# histogram
nsumbin = 1000
npix,bin_edges = scipy.histogram(raxis,nsumbin,(0.,100.))
rsumpix,bin_edges = scipy.histogram(raxis,nsumbin,(0.,100.),weights=data)
# calculate ee80
rsumpixNorm = rsumpix/rsumpix.sum()
rcumsum = numpy.cumsum(rsumpixNorm)
# at this point rcumsum[0] is = rsumpixNorm[0], rsumsum[1] to the sum of rsumpixnorm[0] and [1] etc.
# so rcumsum[0] is the integral for r<bin_edges[1] and in general rcumsum[i] is the integral of r<bin_edges[i+1]
# thus icumsum gives the appropriate limits for each rcumsum bin
#
icumsum = bin_edges[1:nsumbin+1]
ee80 = numpy.interp(0.8,rcumsum,icumsum)
# calculate polarization (w/o seeing, CCD diffusion)
norm = data.sum()
qxx = ( (xaxis-xCentroid)*(xaxis-xCentroid)*data ).sum() / norm
qyy = ( (yaxis-yCentroid)*(yaxis-yCentroid)*data ).sum() / norm
qyx = ( (yaxis-yCentroid)*(xaxis-xCentroid)*data ).sum() / norm
e1 = (qxx-qyy)/(qxx+qyy)
e2 = 2.0*qyx/(qxx+qyy)
return ee80,qxx,qyy,qyx,e1,e2
def generate_scipy_comparison(csvPathname):
# this is some hack code for reading the csv and doing some percentile stuff in scipy
from numpy import loadtxt, genfromtxt, savetxt
dataset = loadtxt(
open(csvPathname, 'r'),
delimiter=',',
dtype='float64');
print "csv read for training, done"
# we're going to strip just the last column for percentile work
# used below
NUMCLASSES = 10
print "csv read for training, done"
# data is last column
# drop the output
print dataset.shape
from scipy import histogram
import numpy
if 1==1:
print "histogram of dataset"
print histogram(dataset,bins=NUMCLASSES)
print numpy.mean(dataset, axis=0, dtype=numpy.float64)
print numpy.std(dataset, axis=0, dtype=numpy.float64, ddof=0)
print numpy.std(dataset, axis=0, dtype=numpy.float64, ddof=1)
from scipy import stats
def genMCHistogramsOpenCL(distribution, rng, iterations=100, numBins=1000):
# get OpenCL CPU devices
openCLDevices = [device for device in clsim.I3CLSimOpenCLDevice.GetAllDevices() if device.cpu]
if len(openCLDevices)==0:
raise RuntimeError("No CPU OpenCL devices available!")
openCLDevice = openCLDevices[0]
openCLDevice.useNativeMath=False
workgroupSize = 1
workItemsPerIteration = 10240
print(" using platform:", openCLDevice.platform)
print(" using device:", openCLDevice.device)
print(" workgroupSize:", workgroupSize)
print(" workItemsPerIteration:", workItemsPerIteration)
tester = clsim.I3CLSimRandomDistributionTester(device=openCLDevice,
workgroupSize=workgroupSize,
workItemsPerIteration=workItemsPerIteration,
randomService=rng,
randomDistribution=distribution)
print("maxWorkgroupSizeForKernel:", tester.maxWorkgroupSize)
angles = tester.GenerateRandomNumbers(iterations)
samples = len(angles)
print("generated")
angles = numpy.array(angles) # convert to numpy array
print("converted")
numAng_orig, binsAng = scipy.histogram(numpy.arccos(angles)*(180./math.pi), range=(0.,180.), bins=numBins)
print("hist1 complete")
numCos_orig, binsCos = scipy.histogram(angles, range=(-1.,1.), bins=numBins)
print("hist2 complete")
del angles # not needed anymore
print("deleted")
numAng=[]
for i, number in enumerate(numAng_orig):
binWidth = math.cos(binsAng[i]*math.pi/180.) - math.cos(binsAng[i+1]*math.pi/180.)
numAng.append(float(number)/float(samples)/binWidth)
numAng=numpy.array(numAng)
numCos=[]
for i, number in enumerate(numCos_orig):
numCos.append(float(number)/float(samples)/float(2./float(numBins)))
numCos=numpy.array(numCos)
binsAng = numpy.array(binsAng[:-1])+(binsAng[1]-binsAng[0])/2.
binsCos = numpy.array(binsCos[:-1])+(binsCos[1]-binsCos[0])/2.
return dict(cos=dict(num=numCos, bins=binsCos), ang=dict(num=numAng, bins=binsAng))
def determine_dominant_color_in_image(self, image):
NUM_CLUSTERS = 5
ar = scipy.misc.fromimage(image)
shape = ar.shape
if len(shape) > 2:
ar = ar.reshape(scipy.product(shape[:2]), shape[2])
codes, _ = scipy.cluster.vq.kmeans(ar, NUM_CLUSTERS)
# print "Before: %s" % codes
original_codes = codes
for low, hi in [(60, 200), (35, 230), (10, 250)]:
codes = scipy.array([code for code in codes
if not ((code[0] < low and code[1] < low and code[2] < low) or
(code[0] > hi and code[1] > hi and code[2] > hi))])
if not len(codes): codes = original_codes
else: break
# print "After: %s" % codes
vecs, _ = scipy.cluster.vq.vq(ar, codes) # assign codes
counts, bins = scipy.histogram(vecs, len(codes)) # count occurrences
# colors = [''.join(chr(c) for c in code).encode('hex') for code in codes]
# total = scipy.sum(counts)
# print dict(zip(colors, [count/float(total) for count in counts]))
index_max = scipy.argmax(counts) # find most frequent
peak = codes[index_max]
color = ''.join(chr(c) for c in peak).encode('hex')
# print 'most frequent is %s (#%s)' % (peak, color)
return color[:6]
def include_image_level_features(orig_imga,fvector_l,featsel):
# include grayscale values ?
f_input_gray = featsel['input_gray']
if f_input_gray is not None:
shape = f_input_gray
#print orig_imga.shape
fvector_l += [sp.misc.imresize(colorconv.gray_convert(orig_imga), shape).ravel()]
# include color histograms ?
f_input_colorhists = featsel['input_colorhists']
if f_input_colorhists is not None:
nbins = f_input_colorhists
colorhists = sp.empty((3,nbins), 'f')
if orig_imga.ndim == 3:
for d in xrange(3):
h = sp.histogram(orig_imga[:,:,d].ravel(),
bins=nbins,
range=[0,255])
binvals = h[0].astype('f')
colorhists[d] = binvals
else:
raise ValueError, "orig_imga.ndim == 3"
#h = sp.histogram(orig_imga[:,:].ravel(),
# bins=nbins,
# range=[0,255])
#binvals = h[0].astype('f')
#colorhists[:] = binvals
#feat_l += [colorhists.ravel()]
fvector_l += [colorhists.ravel()]
return fvector_l
def blobs(shape, porosity, blobiness=8):
"""
Generates an image containing amorphous blobs
Parameters
----------
shape : list
The size of the image to generate in [Nx, Ny, Nz] where N is the
number of voxels
blobiness : scalar
Controls the morphology of the image. A higher number results in
a larger number of smaller blobs.
porosity : scalar
The porosity of the final image. This number is approximated by
the method so the returned result may not have exactly the
specified value.
"""
if sp.size(shape) == 1:
shape = sp.full((3, ), int(shape))
[Nx, Ny, Nz] = shape
sigma = sp.mean(shape)/(4*blobiness)
mask = sp.rand(Nx, Ny, Nz)
mask = spim.gaussian_filter(mask, sigma=sigma)
hist = sp.histogram(mask, bins=1000)
cdf = sp.cumsum(hist[0])/sp.size(mask)
xN = sp.where(cdf >= porosity)[0][0]
im = mask <= hist[1][xN]
return im
def _computeEntropy(self):
''' Compute the entropy of the histogram of distances from the pivot element. Low entropy
scores means the distribution is concentrated, and thus may be a good candidate for splitting.
High entropy (at limit, a uniform distribution), may indicate that there is no good separation
of the elements in this node.
'''
assert(self.Pivot != None)
assert(self.Ds != None)
assert(len(self.Ds) >= self.Tau)
assert(len(self.Ds) == len(self.items))
#create a list of distances not including the sample which was selected as the pivot
#...which will have a distance of zero, within numerical errors.
Dx = [D for D in self.Ds if D>0.01]
#compute histogram using 10 bins of the Dx list
HistInfo = scipy.histogram(Dx, bins=10)
pk = scipy.array( HistInfo[0] )
epsilon = 0.000001
H = entropy(pk+epsilon) #avoids log0 warnings
#print "Histogram: ", HistInfo[0]
#print "Entropy: %f"%H
#print "Range: Min(>0)=%f, Max=%f, Mean=%f, Median=%f"%(min(Dx),max(self.Ds),scipy.mean(self.Ds),scipy.median(self.Ds))
return H
def tag_images_with_color_value(NUM_CLUSTERS = 4, INPUT_FOLDER = './data/covers/'):
isbn = list()
cover_color = list()
files = os.listdir(INPUT_FOLDER)
for eachFile in files:
print eachFile
im = Image.open(INPUT_FOLDER + eachFile)
im = im.resize((50, 50)) # optional, to reduce time
ar = scipy.misc.fromimage(im)
shape = ar.shape
print len(shape)
if len(shape) == 2:
ar = ar.reshape(scipy.product(shape[:1]), shape[1])
else:
ar = ar.reshape(scipy.product(shape[:2]), shape[2])
# finding clusters
codes, dist = scipy.cluster.vq.kmeans(ar, NUM_CLUSTERS)
# cluster centres:\n', codes
vecs, dist = scipy.cluster.vq.vq(ar, codes) # assign codes
counts, bins = scipy.histogram(vecs, len(codes)) # count occurrences
index_max = scipy.argmax(counts) # find most frequent
peak = codes[index_max]
colour = ''.join(chr(c) for c in peak).encode('hex')
isbn.append(eachFile[:-4])
cover_color.append(colour)
result = zip(isbn, cover_color)
return result
def getPredominantColor(filename):
im = Image.open(filename).convert('RGB')
# Convert to numpy array
ar = scipy.misc.fromimage(im)
# Get dimensions
shape = ar.shape
# Convert to bidimensional array of width x height rows and 3 columns (RGB)
ar = ar.reshape(scipy.product(shape[:2]), shape[2])
# Find cluster centers and their distortions
# codes contains the RGB value of the centers
codes, dist = scipy.cluster.vq.kmeans(ar.astype(float), NUM_CLUSTERS)
# Maps all the pixels in the image to their respective centers
vecs, dist = scipy.cluster.vq.vq(ar, codes)
# Counts the occurances of each color (NUM_CLUSTER different colors after the mapping)
counts, bins = scipy.histogram(vecs, len(codes))
# Find most frequent color
index_max = scipy.argmax(counts)
peak = codes[index_max]
return peak.astype(int)
def makehistmult(testpathlist,npulseslist):
sns.set_style("whitegrid")
sns.set_context("notebook")
params = ['Ne','Te','Ti','Vi']
paramsLT = ['N_e','T_e','T_i','V_i']
errdictlist =[ makehistdata(params,itest)[0] for itest in testpathlist]
(figmplf, axmat) = plt.subplots(2, 2,figsize=(12,8), facecolor='w')
axvec = axmat.flatten()
histlims = [[4e10,2e11],[1200.,3000.],[300.,1900.],[-250.,250.]]
histvecs = [sp.linspace(ipm[0],ipm[1],100) for ipm in histlims]
linehand = []
lablist= ['J = {:d}'.format(i) for i in npulseslist]
for iax,iparam in enumerate(params):
for idict,inpulse in zip(errdictlist,npulseslist):
curvals = idict[iparam]
curhist,binout = sp.histogram(curvals,bins=histvecs[iax])
dx=binout[1]-binout[0]
curhist_norm = curhist.astype(float)/(curvals.size*dx)
plthand = axvec[iax].plot(binout[:-1],curhist_norm,label='J = {:d}'.format(inpulse))[0]
linehand.append(plthand)
axvec[iax].set_xlabel(r'$'+paramsLT[iax]+'$')
axvec[iax].set_title(r'Histogram for $'+paramsLT[iax]+'$')
leg = figmplf.legend(linehand[:len(npulseslist)],lablist)
plt.tight_layout()
plt.subplots_adjust(top=0.9)
spti = figmplf.suptitle('Parameter Distributions',fontsize=18)
return (figmplf,axvec,linehand)
def find_a_dominant_color(image):
# K-mean clustering to find the k most dominant color, from:
# http://stackoverflow.com/questions/3241929/python-find-dominant-most-common-color-in-an-image
n_clusters = 5
# Get image into a workable form
im = image.copy()
im = im.resize((150, 150)) # optional, to reduce time
ar = scipy.misc.fromimage(im)
im_shape = ar.shape
ar = ar.reshape(scipy.product(im_shape[:2]), im_shape[2])
ar = np.float_(ar)
# Compute clusters
codes, dist = scipy.cluster.vq.kmeans(ar, n_clusters)
vecs, dist = scipy.cluster.vq.vq(ar, codes) # assign codes
counts, bins = scipy.histogram(vecs, len(codes)) # count occurrences
# Get the indexes of the most frequent, 2nd most frequent, 3rd, ...
sorted_idxs = np.argsort(counts)
# Get the color
peak = codes[sorted_idxs[1]] # get second most frequent color
return [int(i) for i in peak.tolist()] # list comprehension to quickly cast everything to int
def reduce_colors(image, k):
'''Apply kmeans algorithm.
Input: image, number of clusters to use
Returns: colors,
counts per color,
new image
'''
if k > 32:
print "Setting colors to maximum allowed of 32"
k = 32
rows, cols, rgb = image.shape
# reshape the image in a single row array of RGB pixels
image_row = np.reshape(image,(rows * cols, 3))
#HERE ADD CODE TO GET A GOOD GUESS OF COLORS AND PASS THAT AS
#SECOND ARGUMENT TO kmeans
#image_array_sample = shuffle(image_row, random_state=0)[:1000]
#kguess = kmeans(image_array_sample, k)
#colors,_ = kmeans(image_row, kguess)
# perform the clustering
colors,_ = kmeans(image_row, k)
# vector quantization, assign to each pixel the index of the nearest centroid (i=1..k)
qnt,_ = vq(image_row,colors)
# reshape the qnt vector to the original image shape
image_centers_id = np.reshape(qnt,(rows, cols))
# assign the color value to each pixel
newimage = colors[image_centers_id]
#count number of pixels of each cluster color
counts,bins = sp.histogram(qnt, len(colors))
return colors, counts, newimage
def degree_distrib(net, deg_type="total", node_list=None, use_weights=True,
log=False, num_bins=30):
'''
Computing the degree distribution of a network.
Parameters
----------
net : :class:`~nngt.Graph` or subclass
the network to analyze.
deg_type : string, optional (default: "total")
type of degree to consider ("in", "out", or "total").
node_list : list or numpy.array of ints, optional (default: None)
Restrict the distribution to a set of nodes (default: all nodes).
use_weights : bool, optional (default: True)
use weighted degrees (do not take the sign into account: all weights
are positive).
log : bool, optional (default: False)
use log-spaced bins.
Returns
-------
counts : :class:`numpy.array`
number of nodes in each bin
deg : :class:`numpy.array`
bins
'''
ia_node_deg = net.get_degrees(node_list, deg_type, use_weights)
ra_bins = sp.linspace(ia_node_deg.min(), ia_node_deg.max(), num_bins)
if log:
ra_bins = sp.logspace(sp.log10(sp.maximum(ia_node_deg.min(),1)),
sp.log10(ia_node_deg.max()), num_bins)
counts,deg = sp.histogram(ia_node_deg, ra_bins)
ia_indices = sp.argwhere(counts)
return counts[ia_indices], deg[ia_indices]
def getImageDescriptor(model, im, conf):
im = standardizeImage(im)
height, width = im.shape[:2]
numWords = model.vocab.shape[1]
frames, descrs = getPhowFeatures(im, conf.phowOpts)
# quantize appearance
if model.quantizer == 'vq':
binsa, _ = vq(descrs.T, model.vocab.T)
elif model.quantizer == 'kdtree':
raise ValueError('quantizer kdtree not implemented')
else:
raise ValueError('quantizer {0} not known or understood'.format(model.quantizer))
hist = []
for n_spatial_bins_x, n_spatial_bins_y in zip(model.numSpatialX, model.numSpatialX):
binsx, distsx = vq(frames[0, :], linspace(0, width, n_spatial_bins_x))
binsy, distsy = vq(frames[1, :], linspace(0, height, n_spatial_bins_y))
# binsx and binsy list to what spatial bin each feature point belongs to
if (numpy.any(distsx < 0)) | (numpy.any(distsx > (width/n_spatial_bins_x+0.5))):
print ("something went wrong")
import pdb; pdb.set_trace()
if (numpy.any(distsy < 0)) | (numpy.any(distsy > (height/n_spatial_bins_y+0.5))):
print ("something went wrong")
import pdb; pdb.set_trace()
# combined quantization
number_of_bins = n_spatial_bins_x * n_spatial_bins_y * numWords
temp = arange(number_of_bins)
# update using this: http://stackoverflow.com/questions/15230179/how-to-get-the-linear-index-for-a-numpy-array-sub2ind
temp = temp.reshape([n_spatial_bins_x, n_spatial_bins_y, numWords])
bin_comb = temp[binsx, binsy, binsa]
hist_temp, _ = histogram(bin_comb, bins=range(number_of_bins+1), density=True)
hist.append(hist_temp)
hist = hstack(hist)
hist = array(hist, 'float32') / sum(hist)
return hist
def getDominantColor(img_url):
if r.exists(img_url):
cache_result = r.hmget(img_url, ['r', 'g', 'b'])
return cache_result
NUM_CLUSTERS = 5
im = Image.open(StringIO.StringIO(urllib2.urlopen(img_url).read()))
img_arr = scipy.misc.fromimage(im)
img_shape = img_arr.shape
if len(img_shape) > 2:
img_arr = img_arr.reshape(scipy.product(img_shape[:2]), img_shape[2])
codes, _ = scipy.cluster.vq.kmeans(img_arr, NUM_CLUSTERS)
original_codes = codes
for low, hi in [(60, 200), (35, 230), (10, 250)]:
codes = scipy.array([code for code in codes if not (all([c < low for c in code]) or all([c > hi for c in code]))])
if not len(codes):
codes = original_codes
else:
break
vecs, _ = scipy.cluster.vq.vq(img_arr, codes)
counts, bins = scipy.histogram(vecs, len(codes))
index_max = scipy.argmax(counts)
peak = codes[index_max]
color = [int(c) for c in peak[:3]]
r.hmset(img_url, {'r':color[0], 'g':color[1], 'b':color[2]})
#r.expire(img_url, 86400)
return color
def cluster_colors(image_url, num_clusters=5):
"""
Return the most clustered colors of an image.
Use scipy's k-means clustering algorithm.
"""
print 'Reading image...'
response = requests.get(image_url)
im = Image.open(StringIO(response.content))
im = im.resize((150, 150)) # optional, to reduce time
ar = scipy.misc.fromimage(im)
shape = ar.shape
ar = ar.reshape(scipy.product(shape[:2]), shape[2])
ar = ar.astype(float)
print 'Finding clusters...'
# k-means clustering
codes, dist = scipy.cluster.vq.kmeans(ar, num_clusters)
vecs, dist = scipy.cluster.vq.vq(ar, codes) # assign codes
counts, bins = scipy.histogram(vecs, len(codes)) # count occurrences
sorted_index = sorted(range(len(counts)), key=lambda index: counts[index], reverse=True)
most_common_colors = []
for index in sorted_index:
peak = codes[index]
peak = peak.astype(int)
colour = ''.join(format(c, '02x') for c in peak)
most_common_colors.append('#' + colour)
return most_common_colors
def genMCHistogramsHost(distribution, hist_range, iterations=10000000, numBins=1000):
print("generating (host)")
values = []
for i in range(iterations):
values.append(distribution.SampleFromDistribution(rng, []))
samples = len(values)
print("generated (host)")
values = numpy.array(values)/I3Units.nanometer # convert to numpy array and convert units
print("converted (host)")
range_width=hist_range[1]-hist_range[0]
num_orig, bins = scipy.histogram(values, range=hist_range, bins=numBins)
print("hist1 complete (host)")
del values # not needed anymore
print("deleted (host)")
num=[]
for number in num_orig:
num.append(float(number)/float(samples)/float(range_width/float(numBins)))
num=numpy.array(num)
bins = numpy.array(bins[:-1])+(bins[1]-bins[0])/2.
return dict(num=num, bins=bins)
def genMCHistogramsOpenCL(distribution, range, iterations=1000, numBins=1000):
tester = clsim.I3CLSimRandomDistributionTester(device=openCLDevice,
workgroupSize=workgroupSize,
workItemsPerIteration=workItemsPerIteration,
randomService=rng,
randomDistribution=distribution)
values = tester.GenerateRandomNumbers(iterations)
samples = len(values)
print("generated")
values = numpy.array(values)/I3Units.nanometer # convert to numpy array and convert units
print("converted")
range_width=range[1]-range[0]
num_orig, bins = scipy.histogram(values, range=range, bins=numBins)
print("hist1 complete")
del values # not needed anymore
print("deleted")
num=[]
for number in num_orig:
num.append(float(number)/float(samples)/float(range_width/float(numBins)))
num=numpy.array(num)
bins = numpy.array(bins[:-1])+(bins[1]-bins[0])/2.
return dict(num=num, bins=bins)
def get_dominant_color(image_path):
'''
Parse image and return dominant color in image.
@param image_path: Image path to parse.
@return: Return dominant color, format as hexadecimal number.
'''
# print 'reading image'
im = Image.open(image_path)
im = im.resize((150, 150)) # optional, to reduce time
ar = scipy.misc.fromimage(im)
shape = ar.shape
ar = ar.reshape(scipy.product(shape[:2]), shape[2])
# print 'finding clusters'
NUM_CLUSTERS = 5
codes, dist = scipy.cluster.vq.kmeans(ar, NUM_CLUSTERS)
# print 'cluster centres:\n', codes
vecs, dist = scipy.cluster.vq.vq(ar, codes) # assign codes
counts, bins = scipy.histogram(vecs, len(codes)) # count occurrences
index_max = scipy.argmax(counts) # find most frequent
peak = codes[index_max]
colour = ''.join(chr(c) for c in peak).encode('hex')
# print 'most frequent is %s (#%s)' % (peak, colour)
return "#%s" % (colour[0:6])
def hist(fcms, index, savefile=None, display=True, **kwargs):
"""Plot overlay histogram.
fcms is a list of FCMData objects/arrays
index is channel to plot
"""
figure = pylab.figure()
for fcm in fcms:
if isinstance(index, str):
index = fcm.name_to_index(index)
y = fcm[:, index]
h, b = histogram(y, bins=200, **kwargs)
b = (b[:-1] + b[1:]) / 2.0
unused_x = pylab.linspace(min(y), max(y), 100)
pylab.plot(b, h, label=fcm.name)
pylab.legend()
pylab.xlabel(fcms[0].channels[index])
if display:
pylab.show()
if savefile:
pylab.savefig(savefile)
return figure
def test_Intensity_1(self):
"""Test a case of distributed intensity values."""
# Create label image with only one region
label_image = scipy.zeros(2*2*2, dtype=scipy.int8).reshape(2,2,2)
# Create original image with two equally distibuted intensity value
original_image = scipy.zeros(2*2*2, dtype=scipy.int8)
original_image[:4] = -1
original_image[4:] = 1
original_image = original_image.reshape(2,2,2)
# Initialize object
statistics = LabelImageStatistics(label_image, original_image)
# Computed expected result
i = scipy.array([-1,-1,-1,-1,1,1,1,1])
h = scipy.histogram(i, statistics._intensity_distribution_local_histogram_width)
hr = scipy.array(h[0]) / float(h[0].sum())
g = stats.norm(*stats.norm.fit(i))
r = abs(hr - g.pdf(h[1][:-1]))
r *= h[1][-2] - h[1][0]
r = r.sum()
# Check created intensity distribution
intensity_distributions = statistics.get_intensity_distributions()
self.assertEqual(len(intensity_distributions), 1)
self.assertEqual(intensity_distributions[0], i.std())
intensity_distribution_histogram = statistics.get_intensity_distribution_histogram()
self.assertEqual(intensity_distribution_histogram[0][statistics.get_intensity_distribution_histogram_width()/2], 1)
self.assertEqual(intensity_distribution_histogram[0].max(), 1)
self.assertEqual(intensity_distribution_histogram[0].min(), 0)
self.assertEqual(intensity_distribution_histogram[1].mean(), i.std())
def getDomIMAGEColor( imName ):
# Reference:
# http://stackoverflow.com/questions/3241929/
# python-find-dominant-most-common-color-in-an-image
# number of k-means clusters
NUM_CLUSTERS = 4
# Open target image
im = imName
im = im.resize((150, 150)) # optional, to reduce time
ar = scipy.misc.fromimage(im)
shape = ar.shape
ar = ar.reshape(scipy.product(shape[:2]), shape[2])
ar = ar.astype(float)
# Find clusters
codes, dist = scipy.cluster.vq.kmeans(ar, NUM_CLUSTERS)
vecs, dist = scipy.cluster.vq.vq(ar, codes) # assign codes
counts, bins = scipy.histogram(vecs, len(codes)) # count occurrences
# Find most frequent
index_max = scipy.argmax(counts)
peak = codes[index_max]
color = ''.join(chr(int(c)) for c in peak).encode('hex')
return (peak, color)
def create_histogram(parameter_name, nbins=100, writeFile=True, skipfirst=0, truncate=False, smooth=False):
"""
Returns a histogram and some statistics about this parameter.
@param writeFile: if true, write the histogram to paramname.histogram
"""
f = "%s-chain-0.prob.dump" % parameter_name
values = numpy.recfromtxt(f)[skipfirst::nevery]
statistics = {
'min': float(values.min()),
'max': float(values.max()),
'stdev': float(values.std()),
'mean': float(values.mean()),
'median':float(numpy.median(values)),
'q1': float(scipy.stats.scoreatpercentile(values, 25)),
'q3': float(scipy.stats.scoreatpercentile(values, 75)),
'p5': float(scipy.stats.scoreatpercentile(values, 5)),
'p95': float(scipy.stats.scoreatpercentile(values, 95)),
}
hist = scipy.histogram(values, bins = nbins if not smooth else nbins*10, normed=True)
histwithborders = numpy.dstack([hist[1][0:nbins], hist[1][1:nbins+1], hist[0]])
if writeFile:
scipy.savetxt('%s.histogram' % parameter_name, histwithborders[0], delimiter="\t")
return histwithborders[0], statistics
def generate_scipy_comparison(csvPathname):
# this is some hack code for reading the csv and doing some percentile stuff in scipy
# from numpy import loadtxt, genfromtxt, savetxt
import numpy as np
import scipy as sp
dataset = np.genfromtxt(
open(csvPathname, 'r'),
delimiter=',',
skip_header=1,
dtype=None); # guess!
print "csv read for training, done"
# we're going to strip just the last column for percentile work
# used below
NUMCLASSES = 10
print "csv read for training, done"
# data is last column
# drop the output
print dataset.shape
target = [x[1] for x in dataset]
# we may have read it in as a string. coerce to number
targetFP = np.array(target, np.float)
if 1==0:
n_features = len(dataset[0]) - 1;
print "n_features:", n_features
# get the end
# target = [x[-1] for x in dataset]
# get the 2nd col
print "histogram of target"
print target
print sp.histogram(target, bins=NUMCLASSES)
print target[0]
print target[1]
# per = [100 * t for t in thresholds]
per = [1 * t for t in thresholds]
print "sp per:", per
from scipy import stats
# a = stats.scoreatpercentile(target, per=per)
a = stats.mstats.mquantiles(targetFP, prob=per)
print "sp percentiles:", a
def abs_n_ent_diff(v1,v2,nbins=10):
"""
Absolute normalized entropy difference, between v1 and v2
(not symmetric!)
Quantized the values in 100 bins, measure entropy
of each of those bins, look at the difference of
entropy between the two distributions for each of
those bins.
nbins - quantization level between 0 and 1
"""
assert v1.size == v2.size,'v1 and v2 different sizes'
edges = np.array(range(0,nbins+1),'float') / nbins
h1 = histogram(v1.flatten(),edges)[0] + 2
h2 = histogram(v2.flatten(),edges)[0] + 2
ents1 = -np.log2(h1*1./h1.sum())
ents2 = -np.log2(h2*1./h2.sum())
return np.abs(((ents1 - ents2)/ents1)).mean()
def histeq(im,nbr_bins=256):
""" Histogram equalization of a grayscale image. """
# get image histogram
imhist,bins = sp.histogram(im.flatten(),nbr_bins,normed=True)
cdf = imhist.cumsum() # cumulative distribution function
cdf = 255 * cdf / cdf[-1] # normalize
# use linear interpolation of cdf to find new pixel values
im2 = interp(im.flatten(),bins[:-1],cdf)
return im2.reshape(im.shape), cdf
def calculateThreshold(image, coveragePercent):
import scipy
data = image.data
histogram = scipy.histogram(data, len(scipy.unique(data)))
cumsum = scipy.cumsum(histogram[0])
targetValue = cumsum[-1] * coveragePercent
index = scipy.argmin(scipy.absolute(cumsum - targetValue))
threshold = histogram[1][index]
return threshold * image.unit
def get_size_histogram(self):
"""
Gives the region size distribution.
@return: A histogram created from the normalized region sizes with
scipy.histogram.
@note: The width and therefore the number of distinct values of the histogram can
be set with @see: LabelImageStatistics.set_size_histogram_width.
"""
return scipy.histogram(self._sizes.values(), self._size_histogram_width)
def nonna_select_data(data, outlier_threshold, level='high'): """ This function returns a list of indexed after identifying the main outliers. It applies a cut on the data to remove exactly a fraction (1-outlier_threshold) of all data points. By default the cut is applied only at the higher end of the data values, but the parameter level can be used to change this Input arguments: data = vector containing all data points outlier_threshold = remove outliers until we are left with exactly this fraction of the original data level = 'high|low|both' determines if the outliers are removed only from the high values end, the low values end of both ends. Output: idx = index of selected (good) data """ # histogram all the data values n,x = scipy.histogram(data, len(data)/10) # compute the cumulative distribution and normalize nn = scipy.cumsum(n) nn = nn / float(max(nn)) if level=='high': # select the value such that a fraction outlier_threshold of the data lies below it if outlier_threshold < 1: val = x[pylab.find(nn/float(max(nn)) >= outlier_threshold)[0]] else: val = max(data) # use that fraction of data only idx = data <= val elif level=='low': # select the value such that a fraction outlier_threshold of the data lies above it if outlier_threshold < 1: val = x[pylab.find(nn/float(max(nn)) <= (1-outlier_threshold))[-1]] else: val = min(data) # use that fraction of data only idx = data >= val elif level=='both': # select the value such that a fraction outlier_threshold/2 of the data lies below it if outlier_threshold < 1: Hval = x[pylab.find(nn/float(max(nn)) >= 1-(1-outlier_threshold)/2)[0]] else: Hval = max(data) # select the value such that a fraction outlier_threshold/2 of the data lies above it if outlier_threshold < 1: Lval = x[pylab.find(nn/float(max(nn)) <= (1-outlier_threshold)/2)[-1]] else: Lval = min(data) # use that fraction of data only idx = scipy.logical_and(data >= Lval, data <= Hval) return idx
def _bin_single_spike_train(train, bins):
""" Return a binned representation of SpikeTrain object.
:param train: A spike train to bin.
:type train: :class:`neo.core.SpikeTrain`
:param bins: The bin edges, including the rightmost edge, with time units.
:type bins: Quantity 1D
:returns: The binned spike train.
:rtype: 1-D array
"""
return sp.histogram(train.rescale(bins.units), bins)[0]
def chord_length_distribution(im, bins=25, log=False):
r"""
Determines the distribution of chord lengths in a image containing chords.
Parameters
----------
im : ND-image
An image with chords drawn in the pore space, as produced by
``apply_chords`` or ``apply_chords_3d``.
bins : scalar or array_like
If a scalar is given it is interpreted as the number of bins to use,
and if an array is given they are used as the bins directly.
log : Boolean
If true, the logarithm of the chord lengths will be used, which can
make the data more clear.
Returns
-------
A tuple containing the ``chord_length_bins``, and four separate pieces of
information: ``cumulative_chord_count`` and ``cumulative_chord_length``,
as well as the ``differenial_chord_count`` and
``differential_chord_length``.
"""
h = chord_length_counts(im)
if log:
h = sp.log10(h)
y_num, x = sp.histogram(h, bins=bins, density=True)
y_len, x = sp.histogram(h, bins=bins, weights=h, density=True)
y_num_cum = sp.cumsum((y_num*(x[1:]-x[:-1]))[::-1])[::-1]
y_len_cum = sp.cumsum((y_len*(x[1:]-x[:-1]))[::-1])[::-1]
data = namedtuple('chord_distribution', ('chord_length_bins',
'cumulative_chord_count',
'cumulative_chord_length',
'differential_chord_count',
'differential_chord_length'))
return data(x[:-1], y_num_cum, y_len_cum, y_num, y_len)
def Mclast():
fig = plt.figure(1, figsize=(6,9))
gs = gridspec.GridSpec(2,1,height_ratios=[4,1])
ax = plt.subplot(gs[0])
mvir, mclast, mratio = ioformat.rcol(fwind, [1,5,14], linestart=1)
print("Mvir Range: ", min(mvir), max(mvir))
x, y = [], []
for i in range(len(mclast)):
if(mclast[i] > mclast_cut and mratio[i] < 20.0):
x.append(mvir[i])
y.append(mclast[i])
xbins = linspace(11.0, 13.5, 30)
ybins = linspace(0.05, 1.0, 40)
xgrid, ygrid = meshgrid(xbins, ybins)
z, edx, edy = histogram2d(x, y, bins=[xbins,ybins])
z = z.T + 0.01
zf = ndimage.gaussian_filter(z, sigma=1.0, order=0)
cont = ax.contour(xbins[1:], ybins[1:], zf, colors="red")
#plt.pcolor(xgrid, ygrid, z, cmap="Purples", norm=LogNorm(vmin=z.min(), vmax=z.max()))
ax.pcolor(xgrid, ygrid, z, cmap="Purples")
setp(ax.get_xticklabels(), visible=False)
ax.set_ylabel("Mc (Rejoin)")
plt.title(modelname+", Z~1.0")
ax = plt.subplot(gs[1])
plt.subplots_adjust(hspace=0.0, top=0.9, bottom=0.15)
hist1, bins = histogram(mvir, bins=linspace(11.0,13.5,30))
hist2, bins = histogram(x, bins=linspace(11.0,13.5,30))
hist = []
for i in range(len(hist1)):
if(hist1[i] > 0): hist.append(float(hist2[i])/float(hist1[i]))
else: hist.append(0.0)
#width=0.8*(bins[1]-bins[0])
center = (bins[:-1] + bins[1:]) / 2.0
ax.plot(center, hist, "b.-")
ax.set_ylim(0.0, 1.0)
ax.set_xlabel("Mvir")
ax.set_ylabel("f_rej")
plt.show()
def anaPsf(xaxis, yaxis, data):
# centroids
xCentroid = (xaxis * data).sum() / data.sum()
yCentroid = (yaxis * data).sum() / data.sum()
# radial sum -- around Centroid
raxis = numpy.sqrt((xaxis - xCentroid) * (xaxis - xCentroid) +
(yaxis - yCentroid) * (yaxis - yCentroid))
# histogram
nsumbin = 1000
npix, bin_edges = scipy.histogram(raxis, nsumbin, (0., 100.))
rsumpix, bin_edges = scipy.histogram(raxis,
nsumbin, (0., 100.),
weights=data)
# calculate ee80
rsumpixNorm = rsumpix / rsumpix.sum()
rcumsum = numpy.cumsum(rsumpixNorm)
# at this point rcumsum[0] is = rsumpixNorm[0], rsumsum[1] to the sum of rsumpixnorm[0] and [1] etc.
# so rcumsum[0] is the integral for r<bin_edges[1] and in general rcumsum[i] is the integral of r<bin_edges[i+1]
# thus icumsum gives the appropriate limits for each rcumsum bin
#
icumsum = bin_edges[1:nsumbin + 1]
ee80 = numpy.interp(0.8, rcumsum, icumsum)
# calculate polarization (w/o seeing, CCD diffusion)
norm = data.sum()
qxx = ((xaxis - xCentroid) * (xaxis - xCentroid) * data).sum() / norm
qyy = ((yaxis - yCentroid) * (yaxis - yCentroid) * data).sum() / norm
qyx = ((yaxis - yCentroid) * (xaxis - xCentroid) * data).sum() / norm
e1 = (qxx - qyy) / (qxx + qyy)
e2 = 2.0 * qyx / (qxx + qyy)
return ee80, qxx, qyy, qyx, e1, e2
def ejercicio_4():
my_list = []
with open('numeros.txt') as f:
for line in f:
for i in line:
if i.isdigit() == True:
my_list.append(int(i))
my_list.sort()
hist, bin_edges = scipy.histogram([my_list],
bins=range(int(my_list[-1]) + 2))
plt.bar(bin_edges[:-1], hist, width=1)
plt.xlim(min(bin_edges), max(bin_edges))
plt.show()
def plotCurrentErrors(currentErrors, labelSize=22, barScale=1.0):
# make histogram of current errors
fig = pyplot.figure()
numBins = max(20, round(scipy.sqrt(len(currentErrors))))
hist, bins = scipy.histogram(currentErrors, bins=numBins)
barWidth = barScale * (bins[1] - bins[0])
binCenters = 0.5 * (bins[:-1] + bins[1:])
pyplot.bar(binCenters, hist, align='center', width=barWidth)
pyplot.ylabel('Number of parameter sets', fontsize=labelSize)
pyplot.xlabel('Parameter set error')
pyplot.title('Distribution of errors', fontsize=labelSize)
def determine_dominant_color_in_image(self, image):
NUM_CLUSTERS = 5
# Convert image into array of values for each point.
if image.mode == '1':
image.convert('L')
ar = numpy.array(image)
# ar = scipy.misc.fromimage(image)
shape = ar.shape
# Reshape array of values to merge color bands. [[R], [G], [B], [A]] => [R, G, B, A]
if len(shape) > 2:
ar = ar.reshape(scipy.product(shape[:2]), shape[2])
# Get NUM_CLUSTERS worth of centroids.
ar = ar.astype(numpy.float)
codes, _ = scipy.cluster.vq.kmeans(ar, NUM_CLUSTERS)
# Pare centroids, removing blacks and whites and shades of really dark and really light.
original_codes = codes
for low, hi in [(60, 200), (35, 230), (10, 250)]:
codes = scipy.array([
code for code in codes
if not ((code[0] < low and code[1] < low and code[2] < low) or
(code[0] > hi and code[1] > hi and code[2] > hi))
])
if not len(codes):
codes = original_codes
else:
break
# Assign codes (vector quantization). Each vector is compared to the centroids
# and assigned the nearest one.
vecs, _ = scipy.cluster.vq.vq(ar, codes)
# Count occurences of each clustered vector.
counts, bins = scipy.histogram(vecs, len(codes))
# Show colors for each code in its hex value.
# colors = [''.join(chr(c) for c in code).encode('hex') for code in codes]
# total = scipy.sum(counts)
# print dict(zip(colors, [count/float(total) for count in counts]))
# Find the most frequent color, based on the counts.
index_max = scipy.argmax(counts)
peak = codes.astype(int)[index_max]
color = "{:02x}{:02x}{:02x}".format(peak[0], peak[1], peak[2])
color = self.feed.adjust_color(color[:6], 21)
return color
def prominent_colors(image, num_colors):
thumbnail = create_thumbnail(image)
vertices = vertices_from_image(thumbnail)
# Because the vertices are colors they should all form finite
# numbers, so we can disable check_finite
num_clusters = num_colors
(centroid_codebook, _) = kmeans(vertices, num_clusters, check_finite = False)
(codes, _) = vq(vertices, centroid_codebook, check_finite = False)
(counts, bins) = histogram(codes, len(centroid_codebook))
most_frequent = argsort(counts)[::-1]
centroid_codebook = centroid_codebook.astype(int)
return [tuple(centroid_codebook[most_frequent[i]]) for i in range(num_colors)]
def get_dominant_color(img, RESIZE=15):
NUM_CLUSTERS = 3
orig_img = cv2.resize(img, (CODE_IMG_SIZE, CODE_IMG_SIZE))
img = cv2.resize(img, (RESIZE, RESIZE))
shape = img.shape
ar = img.reshape(scipy.product(shape[:2]), shape[2]).astype(float)
codes, _ = scipy.cluster.vq.kmeans(ar, NUM_CLUSTERS)
vecs, _ = scipy.cluster.vq.vq(ar, codes) # assign codes
counts, _ = scipy.histogram(vecs, len(codes)) # count occurrences
index_max = scipy.argmax(counts) # find most frequent
dominant_color = codes[index_max]
return dominant_color, orig_img
def _test():
seed = 274
numpy.random.seed(274)
N = 10
M = 1000
u = numpy.random.rand()
w = numpy.random.rand(N)
sample = fast_sample(w, M, u)
num, bins = scipy.histogram(sample, numpy.arange(N))
u = 0.2
print 'u = ', u
print 'w = ', w / sum(w)
print 'frequency = ', num / float(M)
print 'w - sample frequency = ', w / sum(w) - num / float(M)
u = 0.98
sample = fast_sample(w, M, u)
num, bins = scipy.histogram(sample, numpy.arange(N))
print 'u = ', u
print 'w = ', w / sum(w)
print 'frequency = ', num / float(M)
print 'w - sample frequency = ', w / sum(w) - num / float(M)
def _histogram(x, bins):
h = sp.histogram(x, bins=bins, density=True)
delta_x = h[1]
P = h[0]
temp = P * (delta_x[1:] - delta_x[:-1])
C = sp.cumsum(temp[-1::-1])[-1::-1]
S = P * (delta_x[1:] - delta_x[:-1])
bin_edges = delta_x
bin_widths = delta_x[1:] - delta_x[:-1]
bin_centers = (delta_x[1:] + delta_x[:-1]) / 2
psd = namedtuple(
'histogram',
('pdf', 'cdf', 'relfreq', 'bin_centers', 'bin_edges', 'bin_widths'))
return psd(P, C, S, bin_centers, bin_edges, bin_widths)
def findDominantMostCommonColorInAnImageFile(image):
NUM_CLUSTERS = 5
ar = np.asarray(image)
shape = ar.shape
ar = ar.reshape(scipy.product(shape[:2]), shape[2]).astype(float)
# print('finding clusters')
codes, dist = scipy.cluster.vq.kmeans(ar, NUM_CLUSTERS)
# print('cluster centres:\n', codes)
vecs, dist = scipy.cluster.vq.vq(ar, codes) # assign codes
counts, bins = scipy.histogram(vecs, len(codes)) # count occurrences
index_max = scipy.argmax(counts) # find most frequent
peak = codes[index_max]
colour = binascii.hexlify(bytearray(int(c) for c in peak)).decode('ascii')
return colour
def main(img):
image = Image.open(img)
# image = ImageGrab.grab()
image = image.resize((200, 200))
NUM_CLUSTERS = 5
# Convert image into array of values for each point.
ar = scipy.misc.fromimage(image)
# Reshape array of values to merge color bands.
ar = ar.reshape(scipy.product(ar.shape[:2]), ar.shape[2])
# Get NUM_CLUSTERS worth of centroids.
codes, _ = scipy.cluster.vq.kmeans(ar.astype(float), NUM_CLUSTERS)
# Pare centroids, removing blacks and whites and shades of really dark and really light.
original_codes = codes
for low, hi in [(60, 200), (35, 230), (10, 250)]:
codes = scipy.array([
code for code in codes
if not ((code[0] < low and code[1] < low and code[2] < low) or
(code[0] > hi and code[1] > hi and code[2] > hi))
])
if not len(codes):
codes = original_codes
else:
break
# Assign codes (vector quantization). Each vector is compared to the centroids
# and assigned the nearest one.
vecs, _ = scipy.cluster.vq.vq(ar, codes)
# Count occurences of each clustered vector.
counts, bins = scipy.histogram(vecs, len(codes))
normalized_codes = codes / codes.max()
# Show colors for each code in its hex value.
colors = [rgb2hex(c) for c in normalized_codes]
total = float(scipy.sum(counts))
# top N colors as a proportion of the image
color_dist = dict(zip(colors, (count / total for count in counts)))
pprint(color_dist)
# Find the most frequent color, based on the counts.
# TODO: no need to use scipy for this.
index_max = scipy.argmax(counts)
peak = normalized_codes[index_max]
color = rgb2hex(peak)
print(color)
def dominant_color(img):
if(img != None):
NUM_CLUSTERS = 1
img = img.resize((150,150))
arr = np.asarray(img)
shape = arr.shape
arr = arr.reshape(scipy.product(shape[:2]), shape[2]).astype(float)
codes, dist = scipy.cluster.vq.kmeans(arr, NUM_CLUSTERS)
vecs, dist = scipy.cluster.vq.vq(arr, codes)
counts, bins = scipy.histogram(vecs, len(codes)) # count occurrences
index_max = scipy.argmax(counts) # find most frequent
peak = codes[index_max]
return list(peak)
else:
return None
def draw_from_inputted_distribution(data, dt, n_samples):
#function for using empirical release data to
#draw from the time-varying departure rate they exhibit
#Input: the empirical release data (a list of times)
#dt determines the bin size
#n_samples is the number of samples to return
t_max = max(data)
t_min = min(data)
bins = scipy.linspace(t_min, t_max, (t_max - t_min) / dt)
hist, bin_edges = scipy.histogram(data, bins=bins, density=True)
cum_values = np.zeros(bin_edges.shape)
cum_values[1:] = np.cumsum(hist * np.diff(bin_edges))
inv_cdf = interpolate.interp1d(cum_values, bin_edges)
r = np.random.rand(n_samples)
return inv_cdf(r)
def FindRegionColour(self, region, resizeRatio=1, numClusters=5):
reWidth, reHieght = region.size
region = region.resize(
(int(reWidth * resizeRatio), int(reHieght * resizeRatio)))
ar = np.asarray(region)
shape = ar.shape
ar = ar.reshape(scipy.product(shape[:2]), shape[2]).astype(float)
codes, dist = cluster.vq.kmeans(ar, numClusters)
vecs, dist = cluster.vq.vq(ar, codes)
counts, bins = scipy.histogram(vecs, len(codes))
index_max = scipy.argmax(counts)
peak = codes[index_max]
return peak
def est4(data, _):
h = histogram(data, data.max(), range=(0, data.max()), normed=1)[0]
ns = N.arange(0, data.max())
#k, theta, x0 = est2(data)
#k, theta, x0 = _k, _theta, _x0
print "shape =", len(data), type(data), data.shape
x0 = data.min()
x0 = 10
sd = data.std()
print "SD", sd, sd**2, data.mean()
x0 = data.mean() - 4 * sd
x0 = fmin(hist_dist_P, (x0, ), args=(data.mean(), h, ns), xtol=1.0)
return 0, 0, x0
def getDominantColorFromImage(im):
NUM_CLUSTERS = 5
im = im.resize((50, 50)) # optional, to reduce time
ar = np.asarray(im)
shape = ar.shape
ar = ar.reshape(scipy.product(shape[:2]), shape[2]).astype(float)
codes, dist = scipy.cluster.vq.kmeans(ar, NUM_CLUSTERS)
vecs, dist = scipy.cluster.vq.vq(ar, codes) # assign codes
counts, bins = scipy.histogram(vecs, len(codes)) # count occurrences
index_max = scipy.argmax(counts) # find most frequent
peak = codes[index_max]
return '#%02x%02x%02x' % tuple(int(i) for i in peak)
def get_color(screenshot):
NUM_CLUSTERS = 5
im = screenshot
ar = np.asarray(im)
shape = ar.shape
ar = ar.reshape(scipy.product(shape[:2]), shape[2]).astype(float)
codes, dist = scipy.cluster.vq.kmeans(ar, NUM_CLUSTERS)
vecs, dist = scipy.cluster.vq.vq(ar, codes) # assign codes
counts, bins = scipy.histogram(vecs, len(codes)) # count occurrences
index_max = scipy.argmax(counts) # find most frequent
peak = codes[index_max]
colour = binascii.hexlify(bytearray(int(c) for c in peak)).decode('ascii')
return colour
def plotcounts(self, binsize, pngfile):
""" bin the data based on a bin size of binsize days """
#vector_datetime2epoch = scipy.vectorize(converttime.datetime2epoch)
#etime = vector_d2e(self['etime'])
etime = self['etime']
etimemin = scipy.floor(min(etime) / 86400) * 86400
etimemax = scipy.ceil(max(etime) / 86400) * 86400
r = [etimemin, etimemax]
nbins = (etimemax - etimemin) / (binsize * 86400)
h = scipy.histogram(etime, nbins, r)
ecount = h.__getitem__(0)
ebin = h.__getitem__(1)
#vector_e2d = scipy.vectorize(converttime.epoch2datetime)
edt = vector_epoch2datetime(ebin)
pylab.plot_date(edt, ecount, linestyle='steps-mid')
pylab.savefig(pngfile)
def makeHist(cosAnglesAndWeights, numBins=2000):
numCos_orig, binsCos = scipy.histogram(cosAnglesAndWeights[0],
range=(-1., 1.),
weights=cosAnglesAndWeights[1],
bins=numBins)
sumWeights = sum(cosAnglesAndWeights[1])
numCos = []
for i, number in enumerate(numCos_orig):
numCos.append(
float(number) / float(sumWeights) / float(2. / float(numBins)))
numCos = numpy.array(numCos)
binsCos = numpy.array(binsCos[:-1]) + (binsCos[1] - binsCos[0]) / 2.
return numpy.array([binsCos, numCos])
def getImageDescriptor(model, im, idx, imageName): #gets histograms
extension = -(len(imageName.rpartition('.')[2])+1) #find how long the extension is, ie .jpg
imageName = imageName.rpartition('/')[2][:extension] #get just the image name minus the extension and path
sift = str('-'.join(map(str, conf.phowOpts.Sizes)))
if not isdir(conf.imageCropPath+"histos/"):
mkdir(conf.imageCropPath+"histos/")
if isfile(conf.imageCropPath+"histos/"+imageName+'_'+sift+'.histo'):
with open(conf.imageCropPath+"histos/"+imageName+'_'+sift+'.histo', 'rb') as fp:
histo = load(fp)
return [idx, histo]
im = standardizeImage(im) #scale image to 640x480
height, width = im.shape[:2]
numWords = model.vocab.shape[1]
frames, descrs = getPhowFeatures(im, conf.phowOpts) #extract features
# quantize appearance
if model.quantizer == 'vq':
binsa, _ = vq(descrs.T, model.vocab.T) #slowest function - assigns words from vocab to features in descrs
elif model.quantizer == 'kdtree':
raise ValueError('quantizer kdtree not implemented')
else:
raise ValueError('quantizer {0} not known or understood'.format(model.quantizer))
hist = []
#generate the histogram bins
for n_spatial_bins_x, n_spatial_bins_y in zip(model.numSpatialX, model.numSpatialX):
binsx, distsx = vq(frames[0, :], linspace(0, width, n_spatial_bins_x))
binsy, distsy = vq(frames[1, :], linspace(0, height, n_spatial_bins_y))
# binsx and binsy list to what spatial bin each feature point belongs to
if (numpy.any(distsx < 0)) | (numpy.any(distsx > (width/n_spatial_bins_x+0.5))) | (numpy.any(distsy > (height/n_spatial_bins_y+0.5))):
print ("something went wrong")
import pdb; pdb.set_trace()
# combined quantization
number_of_bins = n_spatial_bins_x * n_spatial_bins_y * numWords
temp = arange(number_of_bins)
# update using this: http://stackoverflow.com/questions/15230179/how-to-get-the-linear-index-for-a-numpy-array-sub2ind
temp = temp.reshape([n_spatial_bins_x, n_spatial_bins_y, numWords])
bin_comb = temp[binsx, binsy, binsa]
hist_temp, _ = histogram(bin_comb, bins=range(number_of_bins+1), density=True) #generate histogram
hist.append(hist_temp)
hist = hstack(hist)
hist = array(hist, 'float32') / sum(hist)
numTot = float(conf.numClasses*(conf.numTrain+conf.numTest)*(len(conf.rotation)+1))
sys.stdout.write ("\r"+str(datetime.now())+" Histograms Calculated: "+str(((idx+1)/numTot)*100.0)[:5]+"%") #make progress percentage
sys.stdout.flush()
with open(conf.imageCropPath+"histos/"+imageName+'_'+sift+'.histo', 'wb') as fp:
dump(hist, fp)
return [idx, hist]
def compute_MI_origemcee(seq_matQ,seq_matR,batches,ematQ,ematR,gamma,R_0):
# preliminaries
n_seqs = len(batches)
n_batches = int(batches.max()) + 1 # assumes zero indexed batches
n_bins = 1000
#energies = sp.zeros(n_seqs)
f = sp.zeros((n_batches,n_seqs))
# compute energies
# for i in range(n_seqs):
# energies[i] = sp.sum(seqs[:,:,i]*emat)
# alternate way
energies = np.zeros(n_seqs)
for i in range(n_seqs):
RNAP = (seq_matQ[:,:,i]*ematQ).sum()
TF = (seq_matR[:,:,i]*ematR).sum() + R_0
energies[i] = -RNAP + mp.log(1 + mp.exp(-TF - gamma)) - mp.log(1 + mp.exp(-TF))
# sort energies
inds = sp.argsort(energies)
for i,ind in enumerate(inds):
f[batches[ind],i] = 1.0/n_seqs # batches aren't zero indexed
# bin and convolve with Gaussian
f_binned = sp.zeros((n_batches,n_bins))
for i in range(n_batches):
f_binned[i,:] = sp.histogram(f[i,:].nonzero()[0],bins=n_bins,range=(0,n_seqs))[0]
#f_binned = f_binned/f_binned.sum()
f_reg = sp.ndimage.gaussian_filter1d(f_binned,0.04*n_bins,axis=1)
f_reg = f_reg/f_reg.sum()
# compute marginal probabilities
p_b = sp.sum(f_reg,axis=1)
p_s = sp.sum(f_reg,axis=0)
# finally sum to compute the MI
MI = 0
for i in range(n_batches):
for j in range(n_bins):
if f_reg[i,j] != 0:
MI = MI + f_reg[i,j]*sp.log2(f_reg[i,j]/(p_b[i]*p_s[j]))
print MI
return MI,f_reg
def append_data_peaks(self, data, force=False):
"""append bin(s) calculated from a strip of data
with this method the data is first queried for peaks. this should
reduce the noise/smoothness of the histogram as observed from the
amplitude distribution of the pure signal.
:type data: ndarray
:param data: the data to generate the bin(s) to append from
:type force: bool
:param force: if True, immediately start a new bin before calculation
"""
# check data
data_ = sp.asanyarray(data)
if data.ndim < 2:
data_ = sp.atleast_2d(data_)
if data_.shape[0] < data_.shape[1]:
data_ = data_.T
nsmpl, nchan = data_.shape
if nchan != self._nchan:
raise ValueError('data has channel count %s, expected %s' %
(nchan, self._nchan))
# generate bin set
bin_set = [0]
if self._cur_bin_smpl != 0:
bin_set.append(self._bin_size - self._cur_bin_smpl)
while bin_set[-1] < nsmpl:
bin_set.append(bin_set[-1] + self._bin_size)
if bin_set[-1] > nsmpl:
bin_set[-1] = nsmpl
# process bins
idx = 1
while idx < len(bin_set):
data_bin = data_[bin_set[idx - 1]:bin_set[idx], :]
for c in xrange(self._nchan):
self._cur_bin[c] += sp.histogram(data_bin[:, c],
bins=self._ampl_range)[0]
self._cur_bin_smpl += data_bin.shape[0]
if self._cur_bin_smpl == self._bin_size:
self.append_bin(self._cur_bin)
self._cur_bin[:] = 0
self._cur_bin_smpl = 0
idx += 1
def ejercicio_3():
print("Ingrese numeros, termine con quit: ")
my_list = []
while True:
inp = input()
if inp == "quit":
break
my_list.append(inp)
print(my_list)
my_list.sort()
hist, bin_edges = scipy.histogram([my_list], bins = range(int(my_list[-1])+2))
plt.bar(bin_edges[:-1], hist, width = 1)
plt.xlim(min(bin_edges), max(bin_edges))
plt.show()
def getImageDescriptor(model, im):
im = standardizeImage(im)
height, width = im.shape[:2]
numWords = model.vocab.shape[1]
frames, descrs = getPhowFeatures(im, conf.phowOpts)
# quantize appearance
if model.quantizer == 'vq':
binsa, _ = vq(descrs.T, model.vocab.T)
elif model.quantizer == 'kdtree':
raise ValueError('quantizer kdtree not implemented')
else:
raise ValueError('quantizer {0} not known or understood'.format(
model.quantizer))
hist = []
for n_spatial_bins_x, n_spatial_bins_y in zip(model.numSpatialX,
model.numSpatialX):
binsx, distsx = vq(frames[0, :], linspace(0, width, n_spatial_bins_x))
binsy, distsy = vq(frames[1, :], linspace(0, height, n_spatial_bins_y))
# binsx and binsy list to what spatial bin each feature point belongs to
if (numpy.any(distsx < 0)) | (numpy.any(
distsx > (width / n_spatial_bins_x + 0.5))):
print 'something went wrong'
import pdb
pdb.set_trace()
if (numpy.any(distsy < 0)) | (numpy.any(
distsy > (height / n_spatial_bins_y + 0.5))):
print 'something went wrong'
import pdb
pdb.set_trace()
# combined quantization
number_of_bins = n_spatial_bins_x * n_spatial_bins_y * numWords
temp = arange(number_of_bins)
# update using this: http://stackoverflow.com/questions/15230179/how-to-get-the-linear-index-for-a-numpy-array-sub2ind
temp = temp.reshape([n_spatial_bins_x, n_spatial_bins_y, numWords])
bin_comb = temp[binsx, binsy, binsa]
hist_temp, _ = histogram(bin_comb,
bins=range(number_of_bins + 1),
density=True)
hist.append(hist_temp)
hist = hstack(hist)
hist = array(hist, 'float32') / sum(hist)
return hist
def createPattern(image):
colorArray = []
ar = np.asarray(image)
shape = ar.shape
ar = ar.reshape(scipy.product(shape[:2]), shape[2]).astype(float)
codes, dist = scipy.cluster.vq.kmeans(ar, 5) #Baskın 5 rengin kümelenmesi.
vecs, dist = scipy.cluster.vq.vq(ar, codes)
counts, bins = scipy.histogram(vecs, len(codes))
index_max = scipy.argmax(
counts) #En sık kullanılan 1 rengin indexini bulur
peak = codes[index_max]
for i in range(0, 5):
colorArray.append(codes[i].astype("uint8").tolist())
colorArray.append(peak.astype("uint8").tolist()) #En baskın renk
return colorArray
def kde(data, N=None, MIN=None, MAX=None):
# Parameters to set up the mesh on which to calculate
N = 2**12 if N is None else int(2**scipy.ceil(scipy.log2(N)))
if MIN is None or MAX is None:
minimum = min(data)
maximum = max(data)
Range = maximum - minimum
MIN = minimum - Range / 10 if MIN is None else MIN
MAX = maximum + Range / 10 if MAX is None else MAX
# Range of the data
R = MAX - MIN
# Histogram the data to get a crude first approximation of the density
M = len(data)
DataHist, bins = scipy.histogram(data, bins=N, range=(MIN, MAX))
DataHist = DataHist / M
DCTData = scipy.fftpack.dct(DataHist, norm=None)
I = [iN * iN for iN in range(1, N)]
SqDCTData = (DCTData[1:] / 2)**2
# The fixed point calculation finds the bandwidth = t_star
guess = 0.1
try:
t_star = scipy.optimize.brentq(fixed_point,
0,
guess,
args=(M, I, SqDCTData))
except ValueError:
print('Oops!')
return None
# Smooth the DCTransformed data using t_star
SmDCTData = DCTData * scipy.exp(
-scipy.arange(N)**2 * scipy.pi**2 * t_star / 2)
# Inverse DCT to get density
density = scipy.fftpack.idct(SmDCTData, norm=None) * N / R
mesh = [(bins[i] + bins[i + 1]) / 2 for i in range(N)]
bandwidth = scipy.sqrt(t_star) * R
density = density / scipy.trapz(density, mesh)
cdf = np.cumsum(density) * (mesh[1] - mesh[0])
return bandwidth, mesh, density, cdf
def compute_scc_histogram(self):
'''
Computes a histogram of abs correlation coefficients from the pickled R(a,b) matrix.
'''
if not os.path.exists(self.rabDirectory):
raise RAICARRabException
if not os.path.exists(os.path.join(self.rabDirectory, 'rabmatrix.db')):
raise RAICARRabException
with open(os.path.join(self.rabDirectory, 'rabmatrix.db'), 'rb') as rabPtr:
RabDict = pickle.load(rabPtr)
rPDF = dict.fromkeys(['bin edges', 'counts', 'bar width'])
rPDF['bin edges'] = np.linspace(0, 1.0, 101)
rPDF['counts'], _ = histogram(a=np.hstack(list(RabDict.values())[
i].flatten() for i in range(0, len(RabDict))), bins=rPDF['bin edges'])
rPDF['bin edges'] = rPDF['bin edges'][0:-1]
rPDF['bar width'] = 0.01
return rPDF
def dominant_color(img, nb_clusters=5, need_resize=False):
if need_resize:
img = img.resize((150, 150))
img_arr = np.asarray(img)
shape = img_arr.shape
img_arr = img_arr.reshape(scipy.product(shape[:2]), shape[2]).astype(float)
codes, dist = scipy.cluster.vq.kmeans(img_arr, nb_clusters)
vecs, dist = scipy.cluster.vq.vq(img_arr, codes)
counts, bins = scipy.histogram(vecs, len(codes))
index_max = scipy.argmax(counts)
peak = codes[index_max]
colour = binascii.hexlify(bytearray(int(c) for c in peak)).decode('ascii')
return colour
def GetnewColors():
NUM_CLUSTERS = 7
im = Image.open('static/images/image.jpg')
im = im.resize((150, 150))
ar = scipy.misc.fromimage(im)
shape = ar.shape
ar = ar.reshape(scipy.product(shape[:2]), shape[2])
codes, dist = scipy.cluster.vq.kmeans(ar.astype(float), NUM_CLUSTERS)
vecs, dist = scipy.cluster.vq.vq(ar, codes) # assign codes
counts, bins = scipy.histogram(vecs, len(codes)) # count occurrences
s = set()
s = counts
x = set()
x = getcol(codes, NUM_CLUSTERS)
return x