theta-2theta-Slits-Step.py

#!/opt/SW/venv/bin/python

import argparse
import sys
import os
import time
import decimal
import json
import shutil
import signal
import threading 
from tqdm import tqdm
import numpy

import log 
from SEDSS.SEDSupplements import CLIMessage, CLIInputReq
from SEDSS.SEDSupport import readFile, dataTransfer, timeModule, instantDataTransfer
from slitsOperations import slitsOperations

from datetime import datetime
import datetime

from matplotlib import pyplot as plt
from matplotlib.ticker import MaxNLocator

import matplotlib.animation as animation
from matplotlib import style

from multiprocessing import Process

try:
	import epics
except ImportError as error:
	CLIMessage("Please ensure that the following packages are installed properly", "W")
	CLIMessage("pyepics")
	sys.exit()

class XRD:
	def __init__(self):
		self.clear()
		
		# Set ^C interrupt to abort the scan
		signal.signal(signal.SIGINT, self.signal_handler)
		self.expCFG = {} # exp. configurations dic 
		self.metadata = {} # exp. metadata dic 
		self.creationTime = str(time.strftime("%Y%m%dT%H%M%S"))
		self.metadata["creationTime"] = self.creationTime

		log.setup_custom_logger("./SED_MS_Scantool.log")
		log.info("Start scanning tool")
		self.ScanToolCFGFile = "configurations/theta-2theta-Slits-Step.json" # 2ϴ Slits config file 
		self.metadata["ScanToolCFGFile"] = self.ScanToolCFGFile
		self.expname = "xrd_{}".format(self.creationTime)

		self.parser = argparse.ArgumentParser(description="2theta-step is a DAQ script for MS beamline used to do step scanning for 2theta with pialtus 300k detector")
		self.parser.add_argument('-start', 		type=float, default=10.0,        	help='2theta start angle (degree)')
		self.parser.add_argument('-end',   		type=float, default=11.0,			help='2theta end angle (degree)')
		self.parser.add_argument('-size',  		type=float, default=1.0,        	help='2theta angle step size (degree)')
		self.parser.add_argument('-exp',		type=float, default=1.0,        	help='exposure time (seconds)')
		self.parser.add_argument('-expTitle',  	type=str,   default="XXXX",			help='Experiment  name')
		#self.parser.add_argument('-name',  		type=str,  	help='Experiment  name')
		self.parser.add_argument('-exptype',  	type=str,   default="local",		help='Experiment  type (local,users)')
		self.parser.add_argument('-proposal',	type=int,	default=99999999,		help='Experiment  proposal number')      
		self.parser.add_argument('-devMode',	type=str,	default="No",			help='development mode, yes means you can run with no Beam')      
		self.parser.add_argument('-plotting',	type=str,	default="Yes",			help='Live data visualization')

		self.args = self.parser.parse_args()

		self.start		= 	self.args.start
		self.end		= 	self.args.end
		self.stepsize	= 	self.args.size
		self.exptime	= 	self.args.exp
		self.expname	= 	self.args.expTitle
		self.exptype	= 	self.args.exptype
		self.proposal	= 	self.args.proposal
		self.devMode 	=	self.args.devMode
		self.plotting 	= 	self.args.plotting

		log.info("Experiment name: {}".format(self.expname))

		#self.startTime = str(time.strftime("%Y%m%dT%H%M%S"))

		##########################
		"""
		The order here is important 
		"""
		self.loadconfig()
		self.pvs["SCAN:pause"].put(0)
		self.preCheck()
		self.runPauseMonitor() # a method runs a thread to keep monitoring the scanning
		self.initDir()
		self.createDir() # creates exp directory and update the self.expdir with errror handiling
		self.detectorInit()
		self.writeExpCFGFile() # this method writes the exp. configuration file 
		self.collectExtraMetadata() # a method to collects metadata 
		self.scan()
		##########################
	def initPlotting(self):
		"""
		This method deletes the temp plottingData file at 
		the begining of each scan in order to let 
		MSDataWriter creates anew one 
		"""
		try:
			os.remove("plottingData.csv")
		except:
			pass

		if self.plotting == "Yes": 
			liveDataThread = threading.Thread(target=self.liveDataThread, args=(), daemon=True)
			liveDataThread.start()
	
	def liveDataThread(self):
		os.system("runMSDataViewer")

	def scan(self):
		#self.clear()
		log.info("Showing scan parameters to be confirmed before scan starts")
		startTime = time.time()
		self.metadata["startTime"] = startTime

		print("\n")
		
		CLIMessage(" --> Experiment Parameters <-- ")
		CLIMessage("2theta | start angle: {}".format(self.start),"M")
		CLIMessage("2theta | stop angle: {}".format(self.end),"M")
		CLIMessage("2theta | angle step: {}".format(self.stepsize),"M")
		CLIMessage("Exposure time: {}".format(self.exptime),"M")
		CLIMessage("Experiment name: {}".format(self.expname),"M")
		CLIMessage("Experiment type: {}".format(self.exptype),"M")
		CLIMessage("experiment proposal number: {}".format(self.proposal),"M")
		CLIMessage("experimnet data path: {}".format(self.expdir), "M")
		print("\n")

		if CLIInputReq("Do you want to continue?(Y/N)").YNQuestion():
			log.info("Confirm starting the scan") 
			#return
		else:
			log.warning("Decline starting the scan")
			sys.exit()

		self.initPlotting() # a method to removes tmp plotting data of the old scan

		try:
			self.scanpoints = self.drange(self.start,self.end,self.stepsize)
			for index,point in enumerate(self.scanpoints,start=1):
				self.checkPause()

				# create parallel threads 
				log.info("Mvoing ϴ and 2ϴ ....")
				moveTThetaMotor = threading.Thread(target=self.move2theta, args=(index, point), daemon=True)
				moveThetaMotor = threading.Thread(target=self.movetheta, args=(index, point), daemon=True)
				# Start the threads 
				moveTThetaMotor.start()
				moveThetaMotor.start()
				# Join the motor moving threads before moving further
				moveTThetaMotor.join()
				moveThetaMotor.join()

				self.motors["2theta"].move(point, wait=True) # move 2 theta (detector arm)
				CLIMessage("2ϴ encoder readout: {}".format(self.motors["2theta"].readback), "I")
				CLIMessage("ϴ encoder readout: {}".format(self.motors["theta"].readback), "I")
				
				
				#for t in range(4): # Number of trials to get exactly to target position
				#	self.motors["2theta"].move(point, wait=True) # move 2 theta (detector arm)
				#	while not self.motors["2theta"].done_moving:
				#		CLIMessage("2theta moving {}".format(self.motors["2theta"].readback), "IG")
				#time.sleep(0.2)
				current2theta = self.motors["2theta"].readback
				currentImgName = "{}_{}_{:.4f}.tiff".format(self.expname,index,current2theta)

				self.metadata["IC01RBV"] = self.pvs["IC01"].get()
				self.metadata["current"] = self.pvs["current"].get()

				self.pvs["ImgName"].put(str(currentImgName)) # set Image Name
				self.pvs["isacq"].put(1) # disable temp measurment
				self.pvs["acq"].put(1) 
				self.pvs["isacq"].put(0) # re-enable temp measurment
				log.info("Collecting image \"{}\" from detector (camserver)".format(currentImgName))

				for i in tqdm(range(int(self.exptime*10)), desc = "Collecting image {}: ".format(currentImgName),
					ascii=False, ncols=100):
					time.sleep(0.1)

				self.tranfser() # transfer images from detector server(10.3.3.8) to the local data path
				#imgPath = self.paths["localTmpData"] + "/" + currentImgName
				imgPath = self.expdir + "/" + currentImgName
				
				slitsOperations(imgFullPath = imgPath,tTheta = current2theta, metadata=self.metadata, theta = self.motors["theta"].readback)
				instantDataTransfer(self.expdir, self.paths["remoteDataServer"]).scp()


			self.scanTime = timeModule.timer(startTime)
			shutil.move("SED_MS_Scantool.log", self.expdir+"/"+"SED_MS_Scantool.log")
			dataTransfer(self.expdir, self.paths["remoteDataServer"]).scp()
			print ("###########################################################")
			CLIMessage("Scan is finished !!", "I")
			CLIMessage("Actual scan time is: {} hours".format(self.scanTime), "I")
			print ("###########################################################")
			#plt.show()
			try:
				os.remove("plottingData.csv")
			except:
				pass
			input("Press [enter] to continue.")

		except KeyboardInterrupt as kint:
			CLIMessage("Scan has been interubted by user input", "E")
			sys.exit()
		
	def move2theta(self,index, TThetaTarPosition):
		CLIMessage("Mvoing 2ϴ to step index number {} for step value {}".format(index, TThetaTarPosition), "I")
		self.motors["2theta"].move(TThetaTarPosition, wait=True) # move 2 theta (detector arm)

	def movetheta(self, index, TThetaTarPosition): 
		
		# ALL THE TIME, 2 theta should be double theta. 
		# this means, theta = 2ϴ/2 = (half 2ϴ)
		#print ("--------->",self.slitsConfiguration["Y"][0])
		# calculating 2theta on slit
		twoThetaOnSlit = TThetaTarPosition + (3.170 - (self.slitsConfiguration["Y"][0] * 0.0133))
		# calculate theta position 
		thetaPosition = twoThetaOnSlit / 2
		CLIMessage("Mvoing ϴ to step index number {} for step value {}".format(index, thetaPosition), "I")
		#CLIMessage("Theta position = {}".format(thetaPosition), "E")
		self.motors["theta"].move(thetaPosition, wait=True) # move theta
		#self.motors["theta"].move(TThetaTarPosition, wait=True) # move theta

	def drange(self,start,stop,step,prec=10):
		decimal.getcontext().prec = prec
		points = []
		r= decimal.Decimal(start)
		step = decimal.Decimal(step)
		while r <=stop:
			points.append(float(r))
			r += step
		return points
	
	def loadconfig(self):

		self.scanLimites = readFile("configurations/limites.json").readJSON()# reading limites.json file

		filefd = open(self.ScanToolCFGFile,"r")
		log.info("Load configurations from theta-2theta-Slits-Step.json file")
		cfgfile = json.load(filefd)
		pvlist = cfgfile["pv"]
		motorlist = cfgfile["motor"]
		paths = cfgfile["paths"]
		pcs = cfgfile["pc"]

		self.pvs = {}
		self.motors = {}
		self.paths = {}
		self.pcs = {}
		self.slitsConfiguration = cfgfile["slitsConfiguration"]
		
		for entry,name in pvlist.items():
			PvObj = epics.PV(name)
			status = str(PvObj.get())
			if not status == 'None':
				CLIMessage ("The PV {} is connected".format(name), "I")
				self.pvs[entry] = PvObj
			else:
				CLIMessage ("The PV {} is not connected".format(name), "E")
				sys.exit()
		
		for entry,name in motorlist.items():
			PvObj = epics.Motor(name)
			if PvObj:
				CLIMessage ("The PV {} is connected".format(name), "I")
				self.motors[entry] = PvObj
			else:
				CLIMessage ("The PV {} is not connected".format(name), "E")
				sys.exit()
		
		for entry,path in paths.items():
			self.paths[entry] = path
		
		for entry,pc in pcs.items():
			self.pcs[entry] = pc
				
		filefd.close()

	def preCheck(self):
		log.info("Pre start and input parameters checking ...")
		self.check((self.end >= self.start),"end angle must be greater than start angle")
		self.check((self.stepsize > 0 and self.stepsize <= self.end),"invalid angle step size")
		self.check((self.exptime >0),"invalid exposure time")
		self.check((self.exptype in ["local", "users"]),"invalid experiment type (local, users)")
		self.check((len(str(self.proposal))== 8),"invalid proposal number")
		self.check((self.start >= 5 and self.end <=90),"angle out of range")
		self.check((self.pvs["current"].get() > 1 and self.pvs["energy"].get() > 2.49),"No Beam avaiable")
		self.check((self.pvs["shutter"].get() == 3),"Photon shutter is closed")
		#self.check((self.motors["spinner"].done_moving == 0),"spinner motor is not rotating")

		# write the scan parameters to experimient confige file. 
		self.metadata["expStartAngle"]	= 	self.expCFG["start"] 			= self.start
		self.metadata["expEndAngle"]	= 	self.expCFG["end"] 				= self.end
		self.metadata["angleStepSize"] 	= 	self.expCFG["stepSize"] 		= self.stepsize
		self.metadata["exposureTime"] 	= 	self.expCFG["exposureTime"] 	= self.exptime
		self.metadata["experimentType"]	=	self.expCFG["experimentType"] 	= self.exptype
		self.metadata["proposalNumber"] =	self.expCFG["proposal"] 		= self.proposal
		self.metadata["experimentName"] =	self.expCFG["expName"] 			= self.expname

	def detectorInit(self):
		log.info("Detector initialization")
		self.pvs["detdatapath"].put(self.paths["detdatapath"]) #ImgPath /home/det/images
		self.pvs["NImages"].put(1) #NImages 1
		self.pvs["detexptime"].put(self.exptime)

	def print(self,*args):
		os.system("clear")
		print(*args)
		sys.stdout.write("\033[F")
	
	def tranfser(self):
		log.info("Transfering detector data to local DAQ workstation")
		try: 
			os.system("rsync --remove-source-files -aqc {}@{}:{}/* {} ".format(
				self.pcs["pilatusserver.user"],self.pcs["pilatusserver"],
				self.paths["detdatapath"],self.expdir))
			
		except: 
			time.sleep(1)
			os.system("rsync --remove-source-files -aqc {}@{}:{}/* {} ".format(
				self.pcs["pilatusserver.user"],self.pcs["pilatusserver"],
				self.paths["detdatapath"],self.expdir))


	def initDir(self):
		if self.exptype == "local":
			self.expdir = "{}".format(self.paths["localTmpData"])
		elif self.exptype == "users":
			self.expdir = "{}".format(self.paths["localTmpData"])

	def createDir(self):
		"""
		This method:
		- cteats the experimint directory
		- updates the expiriment directory
		"""
		expDir = self.expdir + "/" + self.expname + "_" +self.creationTime
		try: 
			os.mkdir(expDir)
			self.expdir = expDir
			self.metadata["expDir"] = self.expdir
		except OSError as error: 
			CLIMessage("{}".format(error), "E")
			sys.exit()

	def writeExpCFGFile(self):
		self.exCFGFile = self.expdir + "/" + self.expname + "_config_" + self.creationTime + ".cfg"

		with open(self.exCFGFile,'w') as cfgfile:
			json.dump(self.expCFG,cfgfile)
			cfgfile.close()

	def collectExtraMetadata(self): 
		self.metadata["current"] = self.pvs["current"].get()
		self.metadata["energy"] = self.pvs["energy"].get()
		self.metadata["IDGap"] = self.pvs["IDGap"].get()
		#self.metadata["expBaseName"] = self.expname

	def signal_handler(self, sig, frame):
		"""Calls abort_scan when ^C is typed"""
		if sig == signal.SIGINT:
			log.warning("Ctrl + C (^C) has been pressed, runinig scan is terminated !!")
			#os.rename("SED_Scantool.log", "SEDScanTool_{}.log".format(self.creationTime))
			shutil.move("SED_MS_Scantool.log", self.expdir+"/"+"SED_MS_Scantool.log")
			dataTransfer(self.expdir, self.paths["remoteDataServer"]).scp()
			try:
				os.remove("plottingData.csv")
			except:
				pass
			sys.exit()

	def clear(self):
		os.system("clear")
	
	def check(self,exp,msg,eval=False):
		if exp == eval:
			CLIMessage("{}".format(msg), "E")
			while True:
				#reply = input("Do you want to continue?(Y/N)\n")
				reply = CLIInputReq("Do you want to continue?(Y/N)").YNQuestion()
				#if reply in ["y","n","Y","N"]:
				if reply:
					return
				else: 
					sys.exit()

	def runPauseMonitor(self):
		"""
		This method: 
		- checks if devMode is choosen or not. If yes, you can scan without beam (helpful for depuging and testing)
		- runs a thread to keep monitoring scan parameters and conditions. If problems happen in proplem happen in scan 
		  parameters and conditions, then the scan is paused. 
		"""
		if self.devMode == "No":
			#log.info("Testing mode: No")
			log.info("start pause trigger monitor") 
			PauseMonitorThread = threading.Thread(target=self.pauseTrigger, args=(), daemon=True)
			PauseMonitorThread.start()
			#print ("fdfghfgh")
			time.sleep(4)
		else:
			log.info("Testing mode: Yes")


	def pauseTrigger(self): 
		currentOk = True
		shutter1Ok = True
		shutter2Ok = True
		stopperOk = True

		# imported from limites.json 
		ringLowerCurrent = self.scanLimites["SRLowerCurrent"] 
		ringUpperCurrent = self.scanLimites["SRUpperCurrent"]

		"""
		setup writing flages to avoid continues writing logs in the log file
		"""
		currentLogFlag = 0
		shutter1LogFlag = 0
		shutter2LogFlag = 0
		stopperLogFlag = 0
		
		while True:

			shutter1Status = self.pvs["SHUTTER1:Status"].get()
			shutter2Status = self.pvs["SHUTTER2:Status"].get()
			StopperStatus = self.pvs["STOPPER:Status"].get()
			currentCurrent = self.pvs["current"].get()

			################### Check current parameters ###############
			if ringLowerCurrent <= currentCurrent <= ringUpperCurrent:
				currentOk = True
				if currentLogFlag == 1: 
					log.warning("SR current is returned to allowed limites, now it is: {} mA."
						.format(currentCurrent))
					currentLogFlag = 0
			else:
				currentOk = False
				if currentLogFlag == 0:
					log.warning("Scan is paused | SR current is: {} mA.".format(currentCurrent))
					currentLogFlag = 1

			################### Check Shutter1 parameters ###############
			#print (self.PVs["SHUTTER1:Status"].get())
			if shutter1Status == 3: # shutter is open 3, closed 1
				shutter1Ok = True
				if shutter1LogFlag == 1: 
					log.warning("Shutter1 status is returned to allowed limites, now it is: open")
					shutter1LogFlag = 0
			else:
				shutter1Ok = False
				if shutter1LogFlag == 0:
					log.warning("Scan is paused | Shutter1 status is: closed")
					shutter1LogFlag = 1

			################### Check Shutter2 parameters ###############
			if shutter2Status == 3: # shutter is open 3, closed 1
				shutter2Ok = True
				if shutter2LogFlag == 1: 
					log.warning("Shutter2 status is returned to allowed limites, now it is: open")
					shutter2LogFlag =0
			else:
				shutter2Ok = False
				if shutter2LogFlag == 0:
					log.warning("Scan is paused | Shutter2 status is: closed")
					shutter2LogFlag = 1
			################### Check stopper parameters ###############
			if StopperStatus == 3: # stopper is open 3, closed 1
				stopperOk = True
				if stopperLogFlag == 1: 
					log.warning("stopper status is returned to allowed limites, now it is: open")
					stopperLogFlag = 0 
			else:
				stopperOk = False
				if stopperLogFlag == 0:
					log.warning("Scan is paused | stopper status is: closed")
					stopperLogFlag = 1

			# if any of below is false, pause the scan 
			if False in (currentOk, shutter1Ok, shutter2Ok, stopperOk): 
				self.pvs["SCAN:pause"].put(1) # 1 pause, 0 release 
			else:
				self.pvs["SCAN:pause"].put(0)
				


			time.sleep(self.scanLimites["checkLimitesEvery"]) # time in seconds 
		

	def checkPause(self):
		diffTime = 0 
		pauseFlag = 0 
		startTime = time.time()

		while self.pvs["SCAN:pause"].get():
			pauseFlag = 1
			diffTime = time.time() - startTime
			CLIMessage("Scan is paused | pausing time(sec): {}".format(diffTime), "IO")
			time.sleep(0.1)
		
		if pauseFlag == 1:
			log.warning("Scan was paused | pausing time(sec): %f ", diffTime)



if __name__ == '__main__':
	XRD()