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WIP: initial commit of Maddie's ringfinding python modules #82

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209 changes: 209 additions & 0 deletions xpdtools/calib2.py
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import numpy as np

import tifffile as tf
import matplotlib as mpl

mpl.use('TkAgg')
import matplotlib.pyplot as plt


filename = 'Ni_pin_20181101-075909_973de2_0001.tiff'

imarray=tf.imread(filename)
print(imarray)

class Slyce():
def __init__(self,direction,index,imarray):
self.direction=direction
self.index=index
self.pixels=[]
if direction=='v':
self.data=list(imarray[:,index])
if direction=='h':
self.data=list(imarray[index,:])

def findringcenter(image,thres=.20,d=20):

def findcenter(image):
s=image.shape
# number of rows divided by 2
r=s[0]/2
# number of columns divided by 2
c=s[1]/2
return r,c

r,c=findcenter(image)

slyce1=Slyce('v',c-d,image)
slyce2=Slyce('v',c+d,image)
slyce3=Slyce('v',c,image)
slyce4=Slyce('v',c-d/2,image)
slyce5=Slyce('v',c+d/2,image)

slyce6=Slyce('h',r-d,image)
slyce7=Slyce('h',r+d,image)
slyce8=Slyce('h',r,image)
slyce9=Slyce('h',r+d/2,image)
slyce10=Slyce('h',r-d/2,image)
slyces=[slyce1, slyce2, slyce3, slyce4, slyce5, slyce6, slyce7, slyce8, slyce9, slyce10]

def findthreshold(image,thres):
return thres*np.max(image)

thresh=findthreshold(image,thres)

def clickpoints(slyce,thresh):
p1=np.argmax(slyce.data)
p2=np.argmax(slyce.data[:p1]+slyce.data[p1+1:])

if slyce.data[p2]>=thresh:
slyce.pixels.append(p1)
slyce.pixels.append(p2)

elif slyce.data[p1]>=thresh:

slyce.pixels.append(p1)

points2click=[]
for slyce in slyces:
clickpoints(slyce,thresh)
if slyce.direction=='v':
for pixel in slyce.pixels:
points2click.append([pixel,slyce.index])
if slyce.direction=='h':
for pixel in slyce.pixels:
points2click.append([slyce.index,pixel])

highlight=np.mean(image)*.9
image_new=image

def finddistance(a,b):
dif1=a[1]-b[1]
dif2=a[0]-b[0]
d_sq=np.abs(dif1**2+dif2**2)
return np.sqrt(d_sq)


#f, ax = plt.subplots(1)
#ax.imshow(image)
ring_mask=np.ones_like(image,dtype=bool)


for point in points2click:
#ax.scatter(point[0],point[1])
ring_mask[point[0],point[1]]=False
image_new[point[0],point[1]]=0

coords=[]
spread=[]
for row in range (int(r-3*d),int(r+3*d)):
for col in range (int(c-3*d),int(c+3*d)):
pointdist=[]
for point in points2click:
pointdist.append(finddistance([row,col],point))
spread.append(max(pointdist)-min(pointdist))
coords.append([row,col])

center=coords[spread.index(min(spread))]
return center
print(center)



#take a horizontal cut out from the center of the ring to the end of the image
#row is constant and column index goes from col index of center to end

def findrings(image):
center=findringcenter(image)
cs1=Slyce('h',center[0]-2,image)
cs2=Slyce('h',center[0]-1,image)
cs3=Slyce('h',center[0],image)
cs4=Slyce('h',center[0]+1,image)
cs5=Slyce('h',center[0]+2,image)

cs=[cs1,cs2,cs3,cs4,cs5]

value1=cs1.data
value2=cs2.data
value3=cs3.data
value4=cs4.data
value5=cs5.data
value_cs=np.zeros(np.shape(value1)[0])
for i, blank in enumerate(value_cs):
value_cs[i]=np.median([value1[i],value2[i],value3[i],value4[i],value5[i]])


halfcs=list(value_cs[(center[1]):])

#find derivative of values on the slyce
dx=1
deriv=list(np.gradient(halfcs,dx))

#creates a function that finds the indices of a list where the derivative changes sign
def zerocross(lines):
z=[]
for i in range(1,len(lines)-1):
if (np.sign(lines[i]) == -1) and (np.sign(lines[i-1]) in [0,1]):
if np.abs(lines[i]-lines[i-1])>np.max(lines)/80.0:
z.append(i)
return z


center=findringcenter(image)
rings=zerocross(deriv)
clickpts=[]
firstpoint=[center[0],rings[0]+center[1]]

if (halfcs[rings[0]]>0.7*np.max(halfcs)) or (halfcs[rings[0]-1]>0.7*np.max(halfcs)) or (halfcs[rings[0]+1]>0.7*np.max(halfcs)):
clickpts.append(rings[0])
clickpts.append(rings[1])
clickpts.append(rings[2])
clickpts.append(rings[5])
else:
clickpts.append(rings[1])
clickpts.append(rings[2])
clickpts.append(rings[3])
clickpts.append(rings[6])



points_image=[]
for clickpt in clickpts:
points_image.append([center[0],clickpt+center[1]])

print(points_image)

plt.plot(range(0,len(halfcs)), halfcs)
plt.scatter(range(0,len(deriv)),deriv)
plt.plot(deriv)
plt.plot(np.zeros(len(deriv)))
for clickpt in clickpts:
plt.scatter(clickpt,0,color='r')
plt.show()


new_img = np.empty((image.shape[0],image.shape[1],4))
max_img = np.amax(image)
min_img = np.amin(image)
for i, row in enumerate(new_img):
for j, elem in enumerate(row):
old_val = image[i][j]
scaled = (old_val-min_img)/(max_img-min_img)
new_img[i][j] = np.array([1.0-scaled, 1.0-scaled, 1.0-scaled, 1.0])

for point_image in points_image:
for i in range(-2,2):
for j in range(-2,2):
new_img[point_image[0]+i][point_image[1]+j]=np.array([1.0, 0.0, 0.0, 1.0])



plt.imshow(new_img)
plt.show()
return points_image


findrings(imarray)


171 changes: 171 additions & 0 deletions xpdtools/calib3.py
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import numpy as np

import tifffile as tf
import matplotlib as mpl

mpl.use('TkAgg')
import matplotlib.pyplot as plt


filename = 'Ni_pin_20181101-075909_973de2_0001.tiff'




#take a horizontal cut out from the center of the ring to the end of the image
#row is constant and column index goes from col index of center to end

def findrings(file_name):

image=tf.imread(file_name)
class Slyce():
def __init__(self,direction,index,image):
self.direction=direction
self.index=index
self.pixels=[]
if direction=='v':
self.data=list(image[:,index])
if direction=='h':
self.data=list(image[index,:])

def findringcenter(image,thres=0.2,d=20):

def findcenter(image):
s=image.shape
# number of rows divided by 2
r=s[0]/2
# number of columns divided by 2
c=s[1]/2
return r,c

r,c=findcenter(image)

slyce1=Slyce('v',c-d,image)
slyce2=Slyce('v',c+d,image)
slyce3=Slyce('v',c,image)
slyce4=Slyce('v',c-d/2,image)
slyce5=Slyce('v',c+d/2,image)

slyce6=Slyce('h',r-d,image)
slyce7=Slyce('h',r+d,image)
slyce8=Slyce('h',r,image)
slyce9=Slyce('h',r+d/2,image)
slyce10=Slyce('h',r-d/2,image)
slyces=[slyce1, slyce2, slyce3, slyce4, slyce5, slyce6, slyce7, slyce8, slyce9, slyce10]

def findthreshold(image,thres):
return thres*np.max(image)

thresh=findthreshold(image,thres)

def clickpoints(slyce,thresh):
p1=np.argmax(slyce.data)
p2=np.argmax(slyce.data[:p1]+slyce.data[p1+1:])

if slyce.data[p2]>=thresh:
slyce.pixels.append(p1)
slyce.pixels.append(p2)

elif slyce.data[p1]>=thresh:

slyce.pixels.append(p1)

points2click=[]
for slyce in slyces:
clickpoints(slyce,thresh)
if slyce.direction=='v':
for pixel in slyce.pixels:
points2click.append([pixel,slyce.index])
if slyce.direction=='h':
for pixel in slyce.pixels:
points2click.append([slyce.index,pixel])


def finddistance(a,b):
dif1=a[1]-b[1]
dif2=a[0]-b[0]
d_sq=np.abs(dif1**2+dif2**2)
return np.sqrt(d_sq)


coords=[]
spread=[]
for row in range (int(r-3*d),int(r+3*d)):
for col in range (int(c-3*d),int(c+3*d)):
pointdist=[]
for point in points2click:
pointdist.append(finddistance([row,col],point))
spread.append(max(pointdist)-min(pointdist))
coords.append([row,col])

center=coords[spread.index(min(spread))]
return center


center_pt=findringcenter(image)
cs1=Slyce('h',center_pt[0]-2,image)
cs2=Slyce('h',center_pt[0]-1,image)
cs3=Slyce('h',center_pt[0],image)
cs4=Slyce('h',center_pt[0]+1,image)
cs5=Slyce('h',center_pt[0]+2,image)

cs=[cs1,cs2,cs3,cs4,cs5]

value1=cs1.data
value2=cs2.data
value3=cs3.data
value4=cs4.data
value5=cs5.data
value_cs=np.zeros(np.shape(value1)[0])
for i, blank in enumerate(value_cs):
value_cs[i]=np.median([value1[i],value2[i],value3[i],value4[i],value5[i]])


halfcs=list(value_cs[(center_pt[1]):])

#find derivative of values on the slyce
dx=1
deriv=list(np.gradient(halfcs,dx))

#creates a function that finds the indices of a list where the derivative changes sign
def zerocross(lines):
z=[]
for i in range(1,len(lines)-1):
if (np.sign(lines[i]) == -1) and (np.sign(lines[i-1]) in [0,1]):
if np.abs(lines[i]-lines[i-1])>np.max(lines)/80.0:
z.append(i)
return z



rings=zerocross(deriv)
clickpts=[]
firstpoint=[center_pt[0],rings[0]+center_pt[1]]

if (halfcs[rings[0]]>0.7*np.max(halfcs)) or (halfcs[rings[0]-1]>0.7*np.max(halfcs)) or (halfcs[rings[0]+1]>0.7*np.max(halfcs)):
clickpts.append(rings[0])
clickpts.append(rings[1])
clickpts.append(rings[2])
clickpts.append(rings[5])
else:
clickpts.append(rings[1])
clickpts.append(rings[2])
clickpts.append(rings[3])
clickpts.append(rings[6])



points_image=[]
for clickpt in clickpts:
points_image.append([center_pt[0],clickpt+center_pt[1]])

print(points_image)
print(center_pt)



return points_image


findrings(filename)