def iagradm(f, Bdil=None, Bero=None):
from ia870 import iasubm,iadil,iaero,iasecross
if Bdil is None: Bdil = iasecross()
if Bero is None: Bero = iasecross()
y = iasubm( iadil(f,Bdil),iaero(f,Bero))
return y
def iasedisk(r=3, DIM="2D", METRIC="EUCLIDEAN", FLAT="FLAT", h=0):
from ia870 import iabinary, iasecross, iasedil, iasesum
from ia870 import iasebox, iaseintersec, iagray
METRIC = METRIC.upper()
FLAT = FLAT.upper()
assert DIM == '2D', 'Supports only 2D structuring elements'
if FLAT == 'FLAT': y = iabinary([1])
else: y = int32([h])
if r == 0: return y
if METRIC == 'CITY-BLOCK':
if FLAT == 'FLAT':
b = iasecross(1)
else:
b = int32([[-2147483647, 0, -2147483647], [0, 1, 0],
[-2147483647, 0, -2147483647]])
return iasedil(y, iasesum(b, r))
elif METRIC == 'CHESSBOARD':
if FLAT == 'FLAT':
b = iasebox(1)
else:
b = int32([[1, 1, 1], [1, 1, 1], [1, 1, 1]])
return iasedil(y, iasesum(b, r))
elif METRIC == 'OCTAGON':
if FLAT == 'FLAT':
b1, b2 = iasebox(1), iasecross(1)
else:
b1 = int32([[1, 1, 1], [1, 1, 1], [1, 1, 1]])
b2 = int32([[-2147483647, 0, -2147483647], [0, 1, 0],
[-2147483647, 0, -2147483647]])
if r == 1: return b1
else:
return iasedil(iasedil(y, iasesum(b1, r // 2)),
iasesum(b2, (r + 1) // 2))
elif METRIC == 'EUCLIDEAN':
v = arange(-r, r + 1)
x = resize(v, (len(v), len(v)))
y = transpose(x)
Be = iabinary(sqrt(x * x + y * y) <= (r + 0.5))
if FLAT == 'FLAT':
return Be
be = h + int32(
sqrt(maximum((r + 0.5) * (r + 0.5) - (x * x) - (y * y), 0)))
be = iaintersec(iagray(Be, 'int32'), be)
return be
else:
assert 0, 'Non valid metric'
return B
def iadil(f, b=None):
from ia870 import iamat2set, ialimits, iaisbinary
from ia870 import iaintersec, iagray, iaadd4dil, iasecross
if b is None: b = iasecross()
if len(f.shape) == 1: f = f[newaxis, :]
h, w = f.shape
x, v = iamat2set(b)
if len(x) == 0:
y = (ones((h, w)) * ialimits(f)[0]).astype(f.dtype)
else:
if iaisbinary(v):
v = iaintersec(iagray(v, 'int32'), 0)
mh, mw = max(abs(x)[:, 0]), max(abs(x)[:, 1])
y = (ones((h + 2 * mh, w + 2 * mw)) * ialimits(f)[0]).astype(f.dtype)
for i in range(x.shape[0]):
if v[i] > -2147483647:
y[mh + x[i, 0]:mh + x[i, 0] + h,
mw + x[i, 1]:mw + x[i, 1] + w] = maximum(
y[mh + x[i, 0]:mh + x[i, 0] + h,
mw + x[i, 1]:mw + x[i, 1] + w], iaadd4dil(f, v[i]))
y = y[mh:mh + h, mw:mw + w]
return y
def iabshow(f1, f2=None, f3=None, factor=17):
from ia870 import iabinary, iaframe, iadil, iaunion
from ia870 import iasedisk, iaserot, iasecross, iasesum
assert f1.dtype == bool, 'f1 must be boolean image'
factor = max(factor, 9)
hfactor = factor // 2
if size(f1.shape) == 1:
f1 = f1[newaxis, :]
if f2 != None: f2 = f2[newaxis, :]
if f3 != None: f3 = f3[newaxis, :]
bz = zeros(factor * array(f1.shape)).astype(bool)
b0 = asarray(bz)
b0[hfactor::factor, hfactor::factor] = f1
fr1 = iaframe(zeros((factor, factor), bool))
fr1 = iadil(b0, fr1)
if f2 is not None:
assert f1.shape == f2.shape, 'f1 and f2 must have same shape'
b1 = asarray(bz)
b1[hfactor::factor, hfactor::factor] = f2
fr2 = iadil(b1, iasedisk(hfactor - 4))
fr1 = iaunion(fr1, fr2)
if f3 is not None:
assert f1.shape == f3.shape, 'f1 and f3 must have same shape'
bz[hfactor::factor, hfactor::factor] = f3
fr3 = iadil(bz, iasesum(iaserot(iasecross(1), 45), hfactor - 1))
fr1 = iaunion(fr1, fr3)
return fr1
def iaareaclose(f, a, Bc=None):
from ia870 import ianeg,iaareaopen,iasecross
if Bc is None:
Bc = iasecross()
y = ianeg( iaareaopen( ianeg(f),a,Bc))
return y
def iawatershed(f, Bc=iasecross(), option='LINES'):
from ipdp import se2offset
offset = se2offset(Bc)
w = connectedComponents(f, offset)
if option == 'LINES':
w = iasubm(w, iaero(w))
w = iabinary(w)
return w
def iaclose(f, b=None):
from ia870 import iaero, iadil, iasecross
if b is None:
b = iasecross()
y = iaero(iadil(f, b), b)
return y
def iawatershed(f, Bc=iasecross(), option='LINES'):
from ipdp import se2offset
offset = se2offset(Bc)
w = connectedComponents(f, offset)
if option == 'LINES':
w = iasubm(w, iaero(w))
w = iabinary(w)
return w
def iacwatershed(f, g, Bc=iasecross(), option='LINES'):
from ia870.ipdp import se2offset
if iaisbinary(g):
g = ialabel(g, Bc)
offset = se2offset(Bc)
w = ift_m(f, offset, g)
if option == 'LINES':
w = iasubm(w, iaero(w))
w = iabinary(w)
return w
def iacwatershed(f, g, Bc=iasecross(), option='LINES'):
from ipdp import se2offset
if iaisbinary(g):
g = ialabel(g, Bc)
offset = se2offset(Bc)
w = ift_m(f, offset, g)
if option == 'LINES':
w = iasubm(w, iaero(w))
w = iabinary(w)
return w
def iaero(f, b=None):
from ia870 import ianeg, iadil, iasereflect, iasecross
if b is None: b = iasecross()
y = ianeg(iadil(ianeg(f), iasereflect(b)))
return y
def iablob(fr, measurement, option="image"):
measurement = upper(measurement)
option = upper(option)
if len(fr.shape) == 1: fr = fr[newaxis,:]
n = fr.max()
if option == 'DATA': y = []
elif measurement == 'CENTROID': y = np.zeros(fr.shape,bool)
elif measurement == 'BOUNDINGBOX': y = np.zeros(fr.shape,bool)
elif measurement == 'PERIMETER': y = np.zeros(fr.shape,np.int32)
elif measurement == 'AREA': y = np.zeros(fr.shape,np.int32)
else: y = np.zeros(fr.shape)
if measurement == 'AREA':
area = np.bincount(fr.ravel())
if option == 'DATA':
y = area[1::]
else:
for i in xrange(1,n+1):
y[fr==i] = area[i]
elif measurement == 'CENTROID':
for i in xrange(1,n+1):
aux = (fr==i)
xind,yind = np.nonzero(aux)
area = len(xind)
centroid = [xind.sum()/area,yind.sum()/area]
if option == 'DATA': y.append([centroid[1],centroid[0]])
else : y[centroid[0],centroid[1]] = 1
elif measurement == 'BOUNDINGBOX':
for i in xrange(1,n+1):
aux = (fr==i)
col, = np.nonzero(aux.any(0))
row, = np.nonzero(aux.any(1))
if option == 'DATA': y.append([col[0],row[0],col[-1],row[-1]])
else:
y[row[0]:row[-1],col[0] ] = 1
y[row[0]:row[-1],col[-1]] = 1
y[row[0], col[0]:col[-1]] = 1
y[row[-1],col[0]:col[-1]] = 1
elif measurement == 'PERIMETER':
Bc = ia870.iasecross()
for i in xrange(1,n+1):
aux = fr == i
grad = aux - ia870.iaero(aux,Bc)
if option == 'DATA': y.append(grad.sum())
else:
y[aux] = grad.sum()
elif measurement == 'CIRCULARITY':
Bc = ia870.iasecross()
area = np.bincount(fr.ravel())
perim = []
for i in xrange(1,n+1):
aux = fr == i
grad = aux - ia870.iaero(aux,Bc)
perim.append(grad.sum())
if option != 'DATA':
y[aux] = 4*np.pi*area[i]/(perim[i-1]**2)
if option == 'DATA':
perim = np.array(perim)
y = 4*np.pi*area[1::]/(perim**2)
elif measurement == 'ASPECTRATIO':
for i in xrange(1,n+1):
aux = (fr==i)
col, = np.nonzero(aux.any(0))
row, = np.nonzero(aux.any(1))
if option == 'DATA': y.append(1.*(min(col[-1]-col[0],row[-1]-row[0])+1)/(max(col[-1]-col[0],row[-1]-row[0])+1))
else:
y[aux] = 1.*(min(col[-1]-col[0],row[-1]-row[0])+1)/(max(col[-1]-col[0],row[-1]-row[0])+1)
elif measurement == 'COMPACTNESS':
for i in xrange(1,n+1):
aux = (fr==i)
xind,yind = np.nonzero(aux)
area = len(xind)
centroid = [xind.sum()/area,yind.sum()/area]
m20 = ((1.*xind-centroid[0])**2).sum()/area
m02 = ((1.*yind-centroid[1])**2).sum()/area
compactness = area/(2*np.pi*(m20+m02))
if option == 'DATA': y.append(compactness)
else : y[aux] = compactness
elif measurement == 'ECCENTRICITY':
for i in xrange(1,n+1):
aux = (fr==i)
xind,yind = np.nonzero(aux)
area = len(xind)
centroid = [xind.sum()/area,yind.sum()/area]
m11 = ((1.*xind-centroid[0])*(yind-centroid[1])).sum()/area
m20 = ((1.*xind-centroid[0])**2).sum()/area
m02 = ((1.*yind-centroid[1])**2).sum()/area
eccentricity = sqrt((m20-m02)**2+4*m11**2)/(m20+m02)
if option == 'DATA': y.append(eccentricity)
else : y[aux] = eccentricity
else:
print "Measurement option should be 'AREA','CENTROID', 'BOUNDINGBOX', 'PERIMETER', "
print "'ASPECTRATIO', 'CIRCULARITY', 'COMPACTNESS' or 'ECCENTRICITY'."
return np.array(y)
def iatz(f, Bc=iasecross()):
from ipdp import se2offset
offset = se2offset(Bc)
return tieZone(f, offset)
def iablob(fr, measurement, option="image"):
measurement = upper(measurement)
option = upper(option)
if len(fr.shape) == 1: fr = fr[newaxis, :]
n = fr.max()
if option == 'DATA': y = []
elif measurement == 'CENTROID': y = np.zeros(fr.shape, bool)
elif measurement == 'BOUNDINGBOX': y = np.zeros(fr.shape, bool)
elif measurement == 'PERIMETER': y = np.zeros(fr.shape, np.int32)
elif measurement == 'AREA': y = np.zeros(fr.shape, np.int32)
else: y = np.zeros(fr.shape)
if measurement == 'AREA':
area = np.bincount(fr.ravel())
if option == 'DATA':
y = area[1::]
else:
for i in xrange(1, n + 1):
y[fr == i] = area[i]
elif measurement == 'CENTROID':
for i in xrange(1, n + 1):
aux = (fr == i)
xind, yind = np.nonzero(aux)
area = len(xind)
centroid = [xind.sum() / area, yind.sum() / area]
if option == 'DATA': y.append([centroid[1], centroid[0]])
else: y[centroid[0], centroid[1]] = 1
elif measurement == 'BOUNDINGBOX':
for i in xrange(1, n + 1):
aux = (fr == i)
col, = np.nonzero(aux.any(0))
row, = np.nonzero(aux.any(1))
if option == 'DATA': y.append([col[0], row[0], col[-1], row[-1]])
else:
y[row[0]:row[-1], col[0]] = 1
y[row[0]:row[-1], col[-1]] = 1
y[row[0], col[0]:col[-1]] = 1
y[row[-1], col[0]:col[-1]] = 1
elif measurement == 'PERIMETER':
Bc = ia870.iasecross()
for i in xrange(1, n + 1):
aux = fr == i
grad = aux - ia870.iaero(aux, Bc)
if option == 'DATA': y.append(grad.sum())
else:
y[aux] = grad.sum()
elif measurement == 'CIRCULARITY':
Bc = ia870.iasecross()
area = np.bincount(fr.ravel())
perim = []
for i in xrange(1, n + 1):
aux = fr == i
grad = aux - ia870.iaero(aux, Bc)
perim.append(grad.sum())
if option != 'DATA':
y[aux] = 4 * np.pi * area[i] / (perim[i - 1]**2)
if option == 'DATA':
perim = np.array(perim)
y = 4 * np.pi * area[1::] / (perim**2)
elif measurement == 'ASPECTRATIO':
for i in xrange(1, n + 1):
aux = (fr == i)
col, = np.nonzero(aux.any(0))
row, = np.nonzero(aux.any(1))
if option == 'DATA':
y.append(1. * (min(col[-1] - col[0], row[-1] - row[0]) + 1) /
(max(col[-1] - col[0], row[-1] - row[0]) + 1))
else:
y[aux] = 1. * (min(col[-1] - col[0], row[-1] - row[0]) + 1) / (
max(col[-1] - col[0], row[-1] - row[0]) + 1)
elif measurement == 'COMPACTNESS':
for i in xrange(1, n + 1):
aux = (fr == i)
xind, yind = np.nonzero(aux)
area = len(xind)
centroid = [xind.sum() / area, yind.sum() / area]
m20 = ((1. * xind - centroid[0])**2).sum() / area
m02 = ((1. * yind - centroid[1])**2).sum() / area
compactness = area / (2 * np.pi * (m20 + m02))
if option == 'DATA': y.append(compactness)
else: y[aux] = compactness
elif measurement == 'ECCENTRICITY':
for i in xrange(1, n + 1):
aux = (fr == i)
xind, yind = np.nonzero(aux)
area = len(xind)
centroid = [xind.sum() / area, yind.sum() / area]
m11 = ((1. * xind - centroid[0]) *
(yind - centroid[1])).sum() / area
m20 = ((1. * xind - centroid[0])**2).sum() / area
m02 = ((1. * yind - centroid[1])**2).sum() / area
eccentricity = sqrt((m20 - m02)**2 + 4 * m11**2) / (m20 + m02)
if option == 'DATA': y.append(eccentricity)
else: y[aux] = eccentricity
else:
print "Measurement option should be 'AREA','CENTROID', 'BOUNDINGBOX', 'PERIMETER', "
print "'ASPECTRATIO', 'CIRCULARITY', 'COMPACTNESS' or 'ECCENTRICITY'."
return np.array(y)
def iatz(f, Bc=iasecross()):
from ipdp import se2offset
offset = se2offset(Bc)
return tieZone(f, offset)
