WIP: Maddie's ringfinding python modules development branch

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)
+
+

xpdtools/calib3.py

@@ -0,0 +1,171 @@
+
+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)