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rng for tip shaping
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Autotip shaping now uses an rng to determine tip lift between 1 nm and -ztip.

Turn off message reactions if we're not using zulip
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@ceds92
ceds92 committed Apr 27, 2023
1 parent 17bee6d commit f1a3e1d
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Showing 2 changed files with 75 additions and 16 deletions.
47 changes: 35 additions & 12 deletions scanbot/scanbot.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1315,7 +1315,7 @@ def moveTipToTarget(self,lightOnOff, cameraPort, xStep, zStep, xV, zV, xF, zF, a
self.survey2(user_args=[],_help=False,surveyParams=self.survey2Params)
return

def autoTipShape(self,n,wh,symTarget,sizeTarget,zQA,ztip,sleepTime,tipShape_hk,message="",iamauto=False):
def autoTipShape(self,n,wh,symTarget,sizeTarget,zQA,ztip,rng,sleepTime,tipShape_hk,message="",iamauto=False):
NTCP,connection_error = self.connect() # Connect to nanonis via TCP
if(connection_error):
global_.running.clear() # Free up the running flag
Expand All @@ -1339,9 +1339,12 @@ def autoTipShape(self,n,wh,symTarget,sizeTarget,zQA,ztip,sleepTime,tipShape_hk,m
self.interface.sendReply("Tip lifts -zQA and -ztip must be < 0")
return

if(rng == 1): rng = np.random.default_rng()
else: rng = 0

tipShapeProps[10] = 1 # Make sure feedback on after tip shape
tipShapeProps[3] = ztip # Amount to dip the tip into the surface
tipShapeProps[7] = -3*ztip # Amount to withdraw the tip from the surface
tipShapeProps[7] = -3*ztip # Amount to withdraw the tip from the surface

tipCheckerProps = tipShaper.PropsGet() # These will be the tip shaper properties used to perform a light tip-shaping action which is scanned over to assess tip quality
tipCheckerProps[1] = 1 # Turn on the change bias checkbox
Expand All @@ -1363,9 +1366,26 @@ def autoTipShape(self,n,wh,symTarget,sizeTarget,zQA,ztip,sleepTime,tipShape_hk,m

attempt = 0 # Keep track of number of attempts to tip shape
tipQA = False # Temp flag
xy = np.array([0,0])
while(attempt < n or n==-1):
scanModule.FrameSet(*xy, w=wh, h=wh)

piezo = Piezo(NTCP)
range_x,range_y,_ = piezo.RangeGet()
dx = 3*wh
x = np.linspace(-1, 1,n) * (n-1)*dx/2
y = x

snakedGrid = []
for j in y:
for i in x:
snakedGrid.append(np.array([i, j, wh, wh]))
if(i>range_x/2 or j>range_y/2):
self.interface.sendReply("Error: Grid size exceeds scan area. Reduce -n",message=message)
self.disconnect(NTCP) # Close the TCP connection
global_.running.clear() # Free up the running flag
return
x = np.array(list(reversed(x))) # Snake the grid - better for drift

for frame in snakedGrid:
scanModule.FrameSet(*frame)

scanModule.Action(scan_action="start",scan_direction="up") # Start an upward scan
for numSeconds in range(sleepTime): # Sleep at one second intervals so we can still stop the routine without lag if we need to
Expand All @@ -1385,18 +1405,16 @@ def autoTipShape(self,n,wh,symTarget,sizeTarget,zQA,ztip,sleepTime,tipShape_hk,m
cleanImage = np.flipud(cleanImage) # Flip because the scan direction is up
if(not isClean):
scanModule.Action(scan_action='stop')
xy = xy + np.array([2*wh,0]) # Move the scan frame
self.interface.sendReply("Bad area, moving scan frame")
continue # Don't count the attempt if the area sucks

if(not filePath): break # If the scan was stopped before finishing, stop program

tipCheckPos = utilities.getCleanCoordinate(cleanImage, lxy=wh) # Do some processing to find a clean location to assess tip quality
if(not len(tipCheckPos)): # If no coordinate is returned because the area is bad...
xy = xy + np.array([2*wh,0]) # Move the scan frame
continue # Don't count the attempt if the area sucks

tipCheckPos += xy # Convert frame-relative coordinate to absolute coordinate
tipCheckPos += frame[0:2] # Convert frame-relative coordinate to absolute coordinate
folme.XYPosSet(*tipCheckPos,Wait_end_of_move=True) # Move the tip to a clean place

self.tipShapeProps(*tipCheckerProps) # Set the tip shaping properties up for the very light action
Expand All @@ -1415,19 +1433,25 @@ def autoTipShape(self,n,wh,symTarget,sizeTarget,zQA,ztip,sleepTime,tipShape_hk,m
# Probably do something here to periodically check scan area (as
# above) in case the tip blew up and left the area a mess.

tipCheckPos -= xy # Convert absolute coodinate to frame-relative coordinate
tipCheckPos -= frame[0:2] # Convert absolute coodinate to frame-relative coordinate
symmetry,size = utilities.assessTip(tipImprint,wh,tipCheckPos) # Assess the quality of the tip based on the imprint it leaves on the surface

self.interface.sendReply("Imprint size: " + str(size) + "\nImprint symm: " + str(symmetry))
# if(size < 0): contour not found, do something about that.

if(symmetry > symTarget):
if(size < sizeTarget and size > 0):
tipQA = True # Tip quality is good if it meets the target scores
break # Stop the routine if a good tip has been achieved

edgeOfFrame = xy - np.array([wh,0])/2
edgeOfFrame = frame[0:2] - np.array([wh,0])/2
folme.XYPosSet(*edgeOfFrame,Wait_end_of_move=True) # Move the tip to the left edge of the scan frame

if(rng):
r = rng.integers(low=1000, high=-ztip*1000e9, size=1)[0]
r /= -1000e9
tipShapeProps[3] = r # Amount to dip the tip into the surface
tipShapeProps[7] = -3*r # Amount to withdraw the tip from the surface

if(tipShape_hk):
try:
import hk_tipShape
Expand All @@ -1447,7 +1471,6 @@ def autoTipShape(self,n,wh,symTarget,sizeTarget,zQA,ztip,sleepTime,tipShape_hk,m
time.sleep(1)
if(self.checkEventFlags()): break # Check event flags

xy = xy + np.array([2*wh,0]) # Move the scan frame
attempt += 1

scanModule.PropsSet(series_name=basename) # Put back the original basename
Expand Down
44 changes: 40 additions & 4 deletions scanbot/scanbot_interface.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -508,6 +508,7 @@ def autoTipShape(self,user_args,_help=False):
'-size' : ['1.2', lambda x: float(x), "(float) Max size of the desired tip imprint in units of nm2"],
'-zQA' : ['-0.9e-9', lambda x: float(x), "(float) z-lift when performing a light tip shape to asses quality of tip (m)"],
'-ztip' : ['-1.5e-9', lambda x: float(x), "(float) z-lift when performing a tip shape to alter the tip (m)"],
'-rng' : ['1', lambda x: int(x), "(int) Flag to randomise -ztip from 1 nm to -ztip value. 1=Yes, 0=No"],
'-st' : ['10', lambda x: int(x), "(int) Drift compensation time (s)"],
'-hk_tipShape' : ['0', lambda x: int(x), "(int) Flag to call the hook hk_tipShape. Use this hook to adjust the tip shaping parameters based on size/symmetry scores, or based on the image of the tip imprint itself. 0=Don't call, 1=Call"],}

Expand Down Expand Up @@ -739,7 +740,7 @@ def reactToMessage(self,reaction,message=""):
"""
if(not self.bot_handler): # If we're not using zulip
print("Scanbot reaction: " + reaction) # Send reaction to console
# print("Scanbot reaction: " + reaction) # Send reaction to console
return

reactTo = message # If we're reacting to a specific zulip message
Expand Down Expand Up @@ -787,7 +788,7 @@ def sendPNG(self,pngFilename,notify=True,message=""):
###############################################################################
# Misc
###############################################################################
def stop(self,user_args,_help=False):
def stop(self,user_args=[],_help=False):
arg_dict = {'-s' : ['1', lambda x: int(x), "(int) Stop scan in progress. 1=Yes"]}

if(_help): return arg_dict
Expand All @@ -808,7 +809,7 @@ def stop(self,user_args,_help=False):
if(args[0] == 1): self.scanbot.stop()

def threadTask(self,func,override=False):
if(override): self.stop(args=[])
if(override): self.stop()
if global_.running.is_set(): return "Error: something already running"
global_.running.set()
t = threading.Thread(target=func)
Expand Down Expand Up @@ -895,6 +896,7 @@ def _quit(self,arg_dict):
###############################################################################
handler_class = scanbot_interface

finish = False
if('-z' in sys.argv):
rcfile = ''
try:
Expand All @@ -915,8 +917,9 @@ def _quit(self,arg_dict):
sys.exit()

os.system("zulip-run-bot scanbot_interface.py --config=" + rcfile)
finish = True

if('-c' in sys.argv):
if('-c' in sys.argv and not finish):
print("Console mode: type 'exit' to end scanbot")
go = True
handler_class = scanbot_interface(run_mode='c')
Expand All @@ -928,6 +931,39 @@ def _quit(self,arg_dict):

finish = True

# if('-g' in sys.argv and not finish):
# import customtkinter as ctk
# from MainPanel import MainPanel as mp
# import ctypes

# class App(ctk.CTk):
# WIDTH = 512
# HEIGHT = 512
# def __init__(self):
# super().__init__()
# self.title("EPWE")
# self.protocol("WM_DELETE_WINDOW", self.on_closing)

# dpi = self.winfo_fpixels('1i')
# try:
# scaleFactor = ctypes.windll.shcore.GetScaleFactorForDevice(0)/100 # Account for windows scale factor in display settings
# except:
# scaleFactor = 1 # Might not work on mac - haven't tested

# handler_class = scanbot_interface(run_mode='g')
# self.mainPanel = mp(self, handler_class, width=self.WIDTH, height=self.HEIGHT, dpi=dpi, scaleFactor=scaleFactor)
# self.geometry("%dx%d" % (self.WIDTH, 850))

# def on_closing(self, event=0):
# self.mainPanel.quit()

# if('-g' in sys.argv and not finish):
# ctk.set_appearance_mode("Dark") # Modes: system (default), light, dark
# ctk.set_default_color_theme("blue") # Themes: blue (default), dark-blue, green

# app = App()
# app.mainloop()

# if('-g' in sys.argv and not finish):
# print("Booting in GUI mode...")
# import tkinter as tk
Expand Down

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