1_Flow_Experiment.py

from Machines import PHDSyringePump as PHDPump
import time
import seabreeze.spectrometers as sb
import datetime
import logging
import os
import sys
import numpy as np
import serial

import pyqtgraph as pg
from pyqtgraph.Qt import QtGui
from PySide import QtCore


experiment_name = input("Enter Experiment Name: ")
experiment_time = float(input("How long should the experiment run? (Minutes) "))
experiment_time = float(experiment_time * 60)
pump_flow1 =  float(input("Pump1 Flow Rate (ml/min): "))
pump_flow2 =  float(input("Pump2 Flow Rate (ml/min): "))
spectral_int_time =  float(input("Spectral Integration Time (Seconds): "))
start_time = float(time.time())
today = datetime.date.today()  
todaystr = today.isoformat() 
experiment_name = "./data/" + todaystr + "/" + experiment_name
spectral_int_time = float(spectral_int_time * 1000000)


#create directory

#if not os.path.exists(experiment_name):
 #   os.makedirs(experiment_name)

if os.path.exists(experiment_name):
	print("Experiment already exists . . . . exiting")
	time.sleep (5)
	sys.exit()
else:
	os.makedirs(experiment_name)


#############	
##Set up logging##
#############

log_formatter = logging.Formatter('%(asctime)s %(name)-12s %(levelname)-8s %(message)s', datefmt='%d/%m/%Y %H:%M:%S')

#File to log to
logFile = os.path.join(experiment_name) + "/logfile.txt"

#Setup File handler
file_handler = logging.FileHandler(logFile)
file_handler.setFormatter(log_formatter)
file_handler.setLevel(logging.INFO)

#Setup Stream Handler (console)
#stream_handler = logging.StreamHandler()
#stream_handler.setFormatter(log_formatter)
#stream_handler.setLevel(logging.INFO)

#Get logger
logger = logging.getLogger('root')
logger.setLevel(logging.INFO)

#Add both Handlers
logger.addHandler(file_handler)
#logger.addHandler(stream_handler)

	
#################
##Connect to machines##
#################

#Pump

Pump1 = PHDPump.sPump("COM6")
Pump2 = PHDPump.sPump("COM8")
#Dilution_pump = connect_here
logger.info("Connected to Pumps")

#Spectrometer
specdevs = sb.list_devices()
spec = sb.Spectrometer(specdevs[0])
logger.info("Connected to: " + str(specdevs[0]))


def start_dark_reference():
	global dark_ref
	spec.integration_time_micros(spectral_int_time)
	dark_ref = spec.intensities()


def start_reference():
	global reference
	#Dilution_pump.start()
	#time.sleep(10)
	spec.integration_time_micros(spectral_int_time)
	reference = spec.intensities()
	#time.sleep(1)
	#Dilution_pump.stop()


	

def start_experiment():
	global wl
	global raw_spectral_data
	global refd_spectral_data
	global start_time
	global spec_time
	global lambda_max

	wl = spec.wavelengths()
	raw_spectral_data = spec.wavelengths()
	Abs_spectral_data = spec.wavelengths()
	spec_time = np.array(0) 
	start_time = time.time()
	lambda_max = np.array(0)
	logger.info ("Experiment started at: " + time.strftime("%H:%M:%S | %d-%m-%Y"))
	
	#set-up and start pump
	Pump1.set_flow_rate(pump_flow1)
	Pump2.set_flow_rate(pump_flow2)
	Pump1.start()
	Pump2.start()
	
		#QtGui.QApplication.setGraphicsSystem('raster')
	app = QtGui.QApplication([])
	mw = QtGui.QMainWindow()
	mw.setWindowTitle("Flow Experimental System")
	#mw.resize(600,400)
	mw.setGeometry(6,150, 650,450 )
	cw = QtGui.QWidget()
	mw.setCentralWidget(cw)
	l = QtGui.QVBoxLayout()
	cw.setLayout(l)

	
	pw = pg.PlotWidget(name="UV Spectrum") 
	l.addWidget(pw)
	pw2 = pg.PlotWidget(name="Lambda Max Vs Time")
	l.addWidget(pw2)

	mw.show()
	## Create an empty plot curve to be filled later, set its pen
	p1 = pw.plot(pen=2, title="UV Spectrum" )
	pw.enableAutoRange(enable=True)
	pw.setYRange(-2,2,padding=0)
	pw.setLabel('left', 'Absorbance', units='Arbitr. Units')
	pw.setLabel('bottom', 'Wavelength', units='nm')
	p2 = pw2.plot(pen=2, symbol = 'o', symbolPen = 2, title="Lambda Max Vs Time")
	pw2.enableAutoRange(enable=True)
	pw2.setLabel('left', 'Max Intensity', units='Arbitr. Units')
	pw2.setLabel('bottom', 'Time', units='s')
	
	
	
	
	while (float(time.time()) < start_time+float(experiment_time)):
		spectrum = spec.intensities()
		sp_time = time.time() 
		raw_spectral_data = np.vstack((raw_spectral_data, spectrum))
		Abs_spectral_data = np.vstack((Abs_spectral_data, np.log10((reference - dark_ref)/(spectrum - dark_ref))))
		spec_time =  np.append(spec_time, [sp_time-start_time])
		curr_lambda_max = np.amax(spectrum - reference)
		lambda_max = np.append(lambda_max, [curr_lambda_max])
		
		#Update Plot
		
		p1.setData(wl,np.log10((reference - dark_ref)/(spectrum - dark_ref)))
		p2.setData(spec_time, lambda_max)
		pg.QtGui.QApplication.processEvents()
		
		time.sleep((spectral_int_time/1000000)+0.05)
		
def shutdown_and_save():
	global wl
	global raw_spectral_data
	global refd_spectral_data
	global start_time
	global spec_time
	global lambda_max
	global Abs_spectral_data
	
	
	
	logger.info("Experiment complete at: " + time.strftime("%H:%M:%S | %d-%m-%Y"))
	Pump1.stop()
	Pump2.stop()
	final_data = raw_spectral_data
	final_Abs = Abs_spectral_data
	Where_Nan = np.isnan(Abs_spectral_data)
	Where_Inf = np.isinf(Abs_spectral_data)
	final_Abs[Where_Nan] = 0
	final_Abs[Where_Inf] = 0
	np.savetxt(os.path.join(experiment_name) + "/spectral_results.csv", final_data , fmt="%s", delimiter=",")
	np.savetxt(os.path.join(experiment_name) + "/Abs_spectral_results.csv", final_Abs, fmt="%s", delimiter=",")
	np.savetxt(os.path.join(experiment_name) + "/reference.csv", reference, fmt="%s", delimiter=",")
	np.savetxt(os.path.join(experiment_name) + "/dark_reference.csv", dark_ref, fmt="%s", delimiter=",")
	np.savetxt(os.path.join(experiment_name) + "/wl.csv", wl, fmt="%s", delimiter=",")
	np.savetxt(os.path.join(experiment_name) + "/times.csv", spec_time, fmt="%s", delimiter=",")
	logger.info("Spectral data saved as: " + os.path.join(experiment_name) + "/spectral_results.csv")
	
###############
## RUNNING CODE ##
###############
input("Close light shutter and push enter . . . ")
time.sleep(1)
start_dark_reference()
input("Open light shutter and push enter . . . ")
input("Start dilution pump and push enter when ready to take reference . . .")
start_reference()
logger.info ("Reference Acquired at: " + time.strftime("%H:%M:%S | %d-%m-%Y"))
input("Push Enter to Start Experiment. . . ")

try:

	start_experiment()
	shutdown_and_save()
	Pump1.disconnect()
	Pump2.disconnect()
	exit()
	
except KeyboardInterrupt:
	logger.info("Experiment Interrupted at: " + time.strftime("%H:%M:%S | %d-%m-%Y"))
	shutdown_and_save()
	Pump1.disconnect()
	Pump2.disconnect()
	exit()

	
if __name__ == '__main__':
    import sys
    if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
        QtGui.QApplication.instance().exec_()