def hough_circles(d2image, d2_iscanny=False, radius_samples=200, xy_samples=[200,200], N_return=5,
return_all=False, **kwargs ):
if not d2_iscanny:
data = itktest.canny_edge_detector(d2image, returnNP=True, **kwargs)
else:
data = d2image
data=np.asanyarray(data, dtype="bool8")
coords = processing.get_coords(data)
#We're going to assume that Radius is less than the hypotenuse of the image
#This is convenient, because it only allows for circles completely contained in the image
r_max= np.sqrt(np.float32(np.square(data.shape[0]) + np.square(data.shape[1])))
x0=np.linspace(0.0, d2image.shape[1], num=xy_samples[0], endpoint=False, retstep=False)
y0=np.linspace(0.0, d2image.shape[0], num=xy_samples[1], endpoint=False, retstep=False)
r2_space=np.square(np.linspace(0.0,r_max, num=radius_samples, endpoint=False))
r_space=np.linspace(0.0,r_max, num=radius_samples, endpoint=True)
#Create a list of index arrays
x0_ind=np.arange(0, len(x0), dtype="uint16")
y0_ind=np.arange(0, len(y0), dtype="uint16")
r2_ind=np.arange(0, len(r2_space),dtype="uint16")
accum=np.zeros((len(r2_space)+1,len(y0),len(x0)),dtype="uint32")
#Create a 1-D view
accum_x=np.ravel(accum)
xy=processing.right_join((x0,y0),sublists=False)
xy_ind=processing.right_join((x0_ind, y0_ind),sublists=False)
#Choosing to split them for the equation
x0_eq,y0_eq=xy[:,0], xy[:,1]
x_ind,y_ind=xy_ind[:,0], xy_ind[:,1]
#Now going to
for x, y in coords:
#Perform the transform to this space
r2=np.square(x-x0_eq)+np.square(y-y0_eq)
r2_sort=np.searchsorted(r2_space,r2)
#Get the equivalent coordinates for the output
#Make the 2-D results into 1-D results for easy indexing of the accumulator
index=np.ravel_multi_index((r2_sort, y0_ind, x0_ind),accum.shape, mode="raise")
accum_x[index]+=1
indices=np.argwhere(
accum >= processing.findNthGreatestValue(accum, count=N_return)
)
r2_y_x=np.column_stack((np.sqrt(r2_space[indices[:,0]]),y0[indices[:,1],x0[indices[:,2]]]))
if return_all:
return r2_y_x,(accum, x0,y0,r2_space)
else:
return r2_y_x
def hough_lines(d2image, d2_iscanny=False, angle_samples=181, ro_samples=200, N_return=5,
return_all=False, **kwargs):
if not d2_iscanny:
data = itktest.canny_edge_detector(d2image, returnNP=True, **kwargs)
else:
data = np.asanyarray(d2image,dtype="bool8")
coords=np.asanyarray(np.argwhere(data),dtype="int16")
#Number of divisions in 180 degrees to use for angle sampling.
#Largest value is the hypotenuse of the image dimensions
romax = np.sqrt(float(data.shape[0] ** 2 + data.shape[1] ** 2))
#The evenly spaced bins of RO and theta
rospace=np.linspace(0.0, romax, num=ro_samples, endpoint=False, retstep=False)
theta = np.linspace(0.0, np.pi/2., num=angle_samples, endpoint=True, retstep=False)
theta_ind=np.arange(0,len(theta),dtype="uint16")
#Generate the accumulator space. X axis
accum = np.zeros(( len(theta),len(rospace)+1), dtype="uint32")
accum_x=np.ravel(accum)
#Something to store extra results
for (x, y) in coords:
#Perform the transform to this space
#For each coordinate, apply theta equation to calculate ro
ri=x * np.cos(theta) + y * np.sin(theta)
ri_sort=np.searchsorted(rospace, ri)
if ri_sort.max()>(ro_samples-1):
print("Wat")
# print(x,y, " ",ri_sort.max(), ri_sort.min())
#Get the equivalent coordinates for the output
#Make the 2-D results into 1-D results for easy indexing of the accumulator
index=np.ravel_multi_index((theta_ind,ri_sort),accum.shape, mode="raise")
accum_x[index]+=1
#Index locations where the greatest values are. Returned as numpy arrays of point coordinates
plt.figure(1,figsize=(15,15))
plt.imshow(accum)
peakVal=processing.findNthGreatestValue(accum, count=N_return)
indices=np.argwhere(
accum >= peakVal
)
ro_the=np.column_stack((rospace[indices[:,1]],theta[indices[:,0]]))
if return_all:
return ro_the, (accum,rospace,theta)
else:
return ro_the
def test():
# print("Test not yet written, ending program")
import main, itktest
# import processing
testfish = "/scratch/images/J29-33/rec_J29-33_33D_PTAwt_16p2_30mm_w4Dd__x218_y232_z1013_orig_10um.nhdr"
hparts, npdata = main.unpacker(testfish, hdrstring=False)
npdata = npdata.reshape(hparts["dsize"][::-1])
#Canny Testing
npcanny = itktest.canny_edge_detector(npdata[85], returnNP=True)
#Hough Lines testing
#output = hough_lines(npcanny, d2_iscanny=True)
#print(output)
#Coordinate testing
boolean_data=npdata>18783.5193537
print(get_coordinates(boolean_data))
