sf-mx/PBSwissMX
0
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

good working findxtal.py

Browse Source
This commit is contained in:
zamofing_t
2018-04-19 11:20:16 +02:00
parent 2465fc86c6
commit fda9750710
1 changed files with 131 additions and 48 deletions
Download Patch File Download Diff File Expand all files Collapse all files

179
python/findxtal.py
View File

@@ -81,7 +81,7 @@ def ffttest2(phi=45.,frq=4.2,amp=1.,n=256.):
pass
def findGrid(image,numPeak=2):
def findGrid(image,numPeak=2,limFrq=None,debug=255):
d2r=np.pi/180.
#image = ndimage.imread('/home/zamofing_t/Documents/prj/SwissFEL/epics_ioc_modules/ESB_MX/python/images/grid_20180409_115332.png', flatten=True) # flatten=True gives a greyscale image
s=image.shape
@@ -97,21 +97,28 @@ def findGrid(image,numPeak=2):
fft2 = np.fft.fft2(image)
fft2=np.fft.fftshift(fft2)
fa =abs(fft2)
plt.figure(num='log of fft: hamming wnd*image')
hi=plt.imshow(fa, interpolation="nearest",norm=mpl.colors.LogNorm(vmin=.1, vmax=fa.max()))
#plt.xlim(s[1]/2-50, s[1]/2+50);plt.ylim(s[0]/2-50, s[0]/2+50)
if debug&1:
plt.figure(num='log of fft: hamming wnd*image')
hi=plt.imshow(fa, interpolation="nearest",norm=mpl.colors.LogNorm(vmin=.1, vmax=fa.max()))
#plt.xlim(s[1]/2-50, s[1]/2+50);plt.ylim(s[0]/2-50, s[0]/2+50)
ctr=np.array(image.shape,dtype=np.int16)/2
fa[ctr[0] - 1:ctr[0] + 2, ctr[1] - 1:ctr[1] + 2]=0 # set dc to 0
hi.set_data(fa)
gen = np.zeros(fft2.shape)
# limit to maximal frequency
if limFrq is not None:
fa[:ctr[0]-limFrq,:]=0;fa[ctr[0]+limFrq:,:]=0
fa[:,:ctr[1]-limFrq]=0;fa[:,ctr[1]+limFrq:]=0
x=np.arange(s[1])/float(s[1])*2.*np.pi
y=np.arange(s[0])/float(s[0])*2.*np.pi
#x=np.linspace(0,2*np.pi,s[1],endpoint=False)
#y=np.linspace(0,2*np.pi,s[0],endpoint=False)
if debug&1:
hi.set_data(fa)
gen = np.zeros(fft2.shape)
#x=np.linspace(0,2*np.pi,s[1],endpoint=False)
#y=np.linspace(0,2*np.pi,s[0],endpoint=False)
xx, yy = np.meshgrid(x, y)
my=int(s[0]/2)
mx=int(s[1]/2)
xx, yy = np.meshgrid(x, y)
res=[] #list of tuples (freq_x,freq_y, phase)
for i in range(numPeak):
@@ -119,8 +126,9 @@ def findGrid(image,numPeak=2):
maxAmpPos=np.array(divmod(maxAmpIdx,fa.shape[1]),dtype=np.int16)
peakPos=maxAmpPos-ctr
peak=fft2[maxAmpPos[0] - 1:maxAmpPos[0] + 2, maxAmpPos[1] - 1:maxAmpPos[1] + 2]
print(peakPos)
print(abs(peak))
if debug&2:
print(peakPos)
print(abs(peak))
(vn, v0, vp)=np.log(fa[maxAmpPos[0], maxAmpPos[1] - 1:maxAmpPos[1] + 2]) #using log for interpolation is more precise
freq_x=peakPos[1]+(vn-vp)/(2.*(vp+vn-2*v0))
(vn, v0, vp)=np.log(fa[maxAmpPos[0]-1:maxAmpPos[0]+2,maxAmpPos[1]])
@@ -137,9 +145,10 @@ def findGrid(image,numPeak=2):
fy=peakPos[0]+iy
amp=np.abs(v)/n; ang=np.angle(v)
sumAmp+=amp
sumCos+=amp*np.cos(fx*x[mx] + fy*y[my] + ang)
sumSin+=amp*np.sin(fx*x[mx] + fy*y[my] + ang)
gen+=amp*np.cos(fx*xx + fy*yy + ang)
sumCos+=amp*np.cos(fx*x[mx+ix] + fy*y[my+iy] + ang)
sumSin+=amp*np.sin(fx*x[mx+ix] + fy*y[my+iy] + ang)
if debug&1:
gen+=amp*np.cos(fx*xx + fy*yy + ang)
sumAmp*=2. #double because of conjugate part
sumCos*=2.
sumSin*=2.
@@ -148,32 +157,82 @@ def findGrid(image,numPeak=2):
if sumSin<0: w=-w
phi_= freq_x*x[mx]+freq_y*y[my]-w
phi_%=(np.pi*2)
#have main frequency positive and phase positive (for convinient)
if (freq_x<0 and abs(freq_x)> abs(freq_y)) or \
(freq_y<0 and abs(freq_y)> abs(freq_x)):
freq_x = -freq_x; freq_y = -freq_y; phi_=-phi_
if phi_<0: phi_+=2*np.pi
res.append((freq_x,freq_y,phi_))
fa[maxAmpPos[0]-1:maxAmpPos[0]+2,maxAmpPos[1]-1:maxAmpPos[1]+2]=0 # clear peak
maxAmpPos_=2*ctr-maxAmpPos
fa[maxAmpPos_[0]-1:maxAmpPos_[0]+2,maxAmpPos_[1]-1:maxAmpPos_[1]+2]=0 # clear conjugated peak
hi.set_data(fa)
if debug&1:
hi.set_data(fa)
gen*=2. # double because of conjugate part
for fx,fy,phase in res:
print('fx: %g fy: %g phase: %g deg'%(fx,fy,phase/d2r))
if debug&1:
gen*=2. # double because of conjugate part
if debug&2:
for fx,fy,phase in res:
print('fx: %g fy: %g phase: %g deg'%(fx,fy,phase/d2r))
if debug&1:
plt.xlim(s[1]/2-50, s[1]/2+50)
plt.ylim(s[0]/2-50, s[0]/2+50)
plt.figure('image*wnd')
plt.imshow(image,interpolation="nearest")
plt.figure('reconstruct')
plt.imshow(gen,interpolation="nearest")
plt.figure()
x=range(s[1])
y=int(s[0]/2)-1
plt.plot(x,image[y,:],'r')
plt.plot(x,gen[y,:],'g')
return res
def plotGrid(grid,shape):
#x=np.linspace(0,2*np.pi,shape[1],endpoint=False)
#y=np.linspace(0,2*np.pi,shape[0],endpoint=False)
#for (freq_x, freq_y, phase) in grid:
#find points were: np.cos(freq_x*xx + freq_y*yy - phase) is max
#freq_x*xx + freq_y*yy - phase = 0 2pi, 4pi
# grid should have 2 entries
# -> 2 equations to solve
# points for:
# entry1 entry2 = (0 0), (0, 2*pi), (2*pi 0)
(fx0,fy0,p0)=grid[0]
(fx1,fy1,p1)=grid[1]
A=np.array([[fx0,fy0],[fx1,fy1]])
A*=np.array([2*np.pi/shape[1],2*np.pi/shape[0]])
Ai=np.asmatrix(A).I
plt.xlim(s[1]/2-50, s[1]/2+50)
plt.ylim(s[0]/2-50, s[0]/2+50)
plt.figure('image*wnd')
plt.imshow(image,interpolation="nearest")
plt.figure('reconstruct')
plt.imshow(gen,interpolation="nearest")
na=int(max(abs(fx0),abs(fy0)))+1
nb=int(max(abs(fx1),abs(fy1)))+1
p=np.ndarray((na*nb,2))
#p=np.ndarray((3,2))
#i=0
#for x,y in ((0,0),(1,0),(0,1)):
# v = np.array([p0+x*2.*np.pi, p1+y*2.*np.pi]).reshape(-1, 1)
# p[i,:]=(Ai*v).reshape(-1)
# i+=1
plt.figure()
x=range(s[1])
y=int(s[0]/2)-1
plt.plot(x,image[y,:],'r')
plt.plot(x,gen[y,:],'g')
i=0
for b in range(nb):
for a in range(na):
v = np.array([p0+a*2.*np.pi, p1+b*2.*np.pi]).reshape(-1, 1)
p[i,:]=(Ai*v).reshape(-1)
i+=1
#plt.plot([400,500],[400,500],'r+',markeredgewidth=2, markersize=10)
plt.plot(p[:,0],p[:,1],'r+',markeredgewidth=2, markersize=10)
plt.axis('image')
pass
def findObj(image,objSize=150,tol=0,viz=0):
def findObj(image,objSize=150,tol=0,debug=0):
#objSiz is the rough diameter of the searched features in pixels
#tol = tolerance in object size (not yet implemented)
@@ -188,7 +247,7 @@ def findObj(image,objSize=150,tol=0,viz=0):
#img2=ndi.filters.convolve1d(img2,box.reshape(-1),1)
img2=ndi.filters.uniform_filter(np.float32(image),objSize*2)
if viz&32:
if debug&32:
plt.imshow(image, interpolation="nearest", cmap='gray')
plt.figure()
plt.imshow(img2, interpolation="nearest", cmap='gray')
@@ -196,14 +255,14 @@ def findObj(image,objSize=150,tol=0,viz=0):
w=np.where(img2>image)
img2[w]=image[w]
img3=image-img2
if viz&16:
if debug&16:
plt.figure()
plt.imshow(img3, interpolation="nearest", cmap='gray')
#plt.show()
l=int(objSize/30)
if l>0:
img4=ndi.binary_fill_holes(img3, structure=np.ones((l,l)))
if viz&8:
if debug&8:
plt.figure()
plt.imshow(img4, interpolation="nearest", cmap='gray')
#plt.show()
@@ -215,7 +274,7 @@ def findObj(image,objSize=150,tol=0,viz=0):
#img5=ndi.binary_opening(img4, structure=np.ones((l,l)))
#img5=ndi.binary_erosion(img4, structure=np.ones((l,l)))
img5=ndi.binary_erosion(img4, iterations=l)
if viz&4:
if debug&4:
plt.figure()
plt.imshow(img5, interpolation="nearest", cmap='gray')
#plt.show()
@@ -237,7 +296,7 @@ def findObj(image,objSize=150,tol=0,viz=0):
m=cv2.moments(contours[0])
lbl = ndi.label(img5)
if viz&2:
if debug&2:
plt.figure()
plt.imshow(lbl[0], interpolation="nearest")
#plt.show()
@@ -259,7 +318,7 @@ def findObj(image,objSize=150,tol=0,viz=0):
pass
#ctr2[i, :]=c[0,0]
if viz&1:
if debug&1:
plt.figure()
plt.imshow(image, interpolation="nearest", cmap='gray')
plt.plot(ctr[:,1],ctr[:,0],'or',markeredgewidth=2, markersize=10)
@@ -281,32 +340,56 @@ def genImg(shape,*args):
image = dc+np.cos(freq_x*xx + freq_y*yy - phase)
else:
image += np.cos(freq_x * xx + freq_y * yy - phase)
plt.imshow(image, interpolation="nearest")
return image
if __name__ == '__main__':
#plt.ion()
#ffttest()
image = ndimage.imread('/home/zamofing_t/Documents/prj/SwissFEL/epics_ioc_modules/ESB_MX/python/images/grid_20180409_115332.png')
#image = ndimage.imread('/home/zamofing_t/Documents/prj/SwissFEL/epics_ioc_modules/ESB_MX/python/images/grid_20180409_115332_45deg.png')
image = ndimage.imread('/home/zamofing_t/Documents/prj/SwissFEL/epics_ioc_modules/ESB_MX/python/images/honeycomb.png')
image=-image
#image = ndimage.imread('/home/zamofing_t/Documents/prj/SwissFEL/epics_ioc_modules/ESB_MX/python/images/honeycomb.png')
grid=findGrid(image,numPeak=2,limFrq=25,debug=2)
plt.imshow(image, interpolation="nearest", cmap='gray')
plotGrid(grid,image.shape)
plt.show()
image = ndimage.imread('/home/zamofing_t/Documents/prj/SwissFEL/epics_ioc_modules/ESB_MX/python/images/grid_20180409_115332.png')
image=-image
grid=findGrid(image,numPeak=2,debug=2)
plt.imshow(image, interpolation="nearest", cmap='gray')
plotGrid(grid,image.shape)
plt.show()
image = ndimage.imread('/home/zamofing_t/Documents/prj/SwissFEL/epics_ioc_modules/ESB_MX/python/images/grid_20180409_115332_45deg.png')
image=-image
grid=findGrid(image,numPeak=2,debug=2)
plt.imshow(image, interpolation="nearest", cmap='gray')
plotGrid(grid,image.shape)
plt.show()
objPos=findObj(image,debug=1)
plt.show()
d2r=np.pi/180.
#for phi in np.arange(0.,180.,10.):
# image = genImg((600, 800), (4.5, .2, phi*d2r))
# plt.show()
#image=genImg((600,800),(4.,1.0,10.*d2r))
#image=genImg((600,800),(4.5,.2,20.*d2r))
#image=genImg((600,800),(4.5,-3.2,70.*d2r))
#image=genImg((600,800),(-4.5,3.2,290.*d2r)) #same image
#findGrid(image,numPeak=1)
#findGrid(image,numPeak=1,debug=2)
#image=genImg((600,800),(9.5,.2,20.*d2r),(.4,5.2,60.*d2r))
#image=genImg((600,800),(3.5,0.,0.*d2r),(0,5.,0.*d2r))
findGrid(image,numPeak=2)
#for v in np.arange(0,2,.3):
# image=genImg((600,800),(8,.2+v,40.*d2r),(.4,5.2,30.*d2r))
# grid=findGrid(image,numPeak=2,debug=2)
# plt.figure(1);plt.cla()
# plt.imshow(image, interpolation="nearest", cmap='gray')
# plotGrid(grid,image.shape)
# plt.show()
#image=genImg((600,800),(9.5,.2,0),(.4,5.2,0),(4,8,0))
#findObj(image,viz=1)
#findObj(image,viz=255)
#print(findObj(image))
plt.show()