def iadist(f, Bc=iasecross(), METRIC=None):
from ia870 import iagray, iaintersec, iaisequal, iaero, iasebox
if METRIC is not None: METRIC = METRIC.upper()
f = iagray(f, 'uint16')
y = iaintersec(f, 0)
if (METRIC == 'EUCLIDEAN') or (METRIC == 'EUC2'):
f = np.int32(f)
b = np.int32(np.zeros((3, 3)))
i = 1
while np.any(f != y):
a4, a2 = -4 * i + 2, -2 * i + 1
b = np.int32([[a4, a2, a4], [a2, 0, a2], [a4, a2, a4]])
y = f
i = i + 1
f = iaero(f, b)
if METRIC == 'EUCLIDEAN':
y = np.uint16(np.sqrt(f) + 0.5)
else:
if iaisequal(Bc, iasecross()):
b = np.int32([[-2147483647, -1, -2147483647], [-1, 0, -1],
[-2147483647, -1, -2147483647]])
elif iaisequal(Bc, iasebox()):
b = np.int32([[-1, -1, -1], [-1, 0, -1], [-1, -1, -1]])
else:
b = Bc
while np.any(f != y):
y = f
f = iaero(f, b)
return y
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 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 get_spline(seg, s):
nz = np.nonzero(seg)
x1, x2, y1, y2 = np.amin(nz[0]), np.amax(nz[0]), np.amin(nz[1]), np.amax(
nz[1])
M0 = seg[x1 - 5:x2 + 5, y1 - 5:y2 + 5]
nescala = [4 * M0.shape[-2], 4 * M0.shape[-1]]
M0 = FW.resizedti(M0, nescala).astype('bool')
con_M0 = np.logical_xor(MM.iaero(M0), M0)
seq = FW.get_seq_graph(con_M0)
tck, _ = spline.splprep(seq, k=5, s=s)
return tck
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 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)
