def __init__(self, cparams, logfiles, pparams, cport, pport):
"""Initialize the controller.
Args:
cparams: configuration parameters.
logfiles: names of files to log to.
pparams: pump parameters.
cport: controller serial port.
pport: pump serial port.
"""
pumpdriver_package = 'plugins.%s' % pparams['pumpdriver']
control_function_package = 'plugins.%s' % cparams['controlfun']
# Import pumpdriver
pumpdriver = __import__(pumpdriver_package, globals(), locals(),
['Pump'], -1)
# Fetch the control computation, make it a method of self.
_temp = __import__(control_function_package, globals(), locals(),
['computeControl'], -1)
self.computeControl = types.MethodType(_temp.computeControl, self)
#self.ser_lock = cport.lock
self.stdout_lock = threading.RLock()
# Make the pump driver as appropriate.
self.pump = pumpdriver.Pump(cparams, logfiles, pparams, cport, pport)
# Data from config.ini
self.logfiles = logfiles
self.pparams = pparams
self.cparams = cparams # all controller parameters live here
self.blank_filename = self.logfiles['blanklog']
# Serial ports
self.serpt = cport
self.pport = pport
# This lock is for the following tx/rx raw values.
# TODO: should the controller know the number of chambers
# in advance of measuring?
self.OD_datalock = threading.RLock()
self.tx_blank = []
self.rx_blank = []
self.rx_val = []
self.tx_val = []
self.z = []
# Make sure to close all the pinch valves at startup.
with self.serpt.lock:
print 'Closing all valves;'
self.serpt.write("clo;")
# Construct the timer threads that perform repeated actions.
# TODO: make serial check period configurable.
self.start_time = None # Set on call to start()
control_period = int(cparams['period'])
self.cont_timer = mytimer(control_period, self.controlLoop)
self.ser_timer = mytimer(2, self.serialCheck)
def __init__(self, cparams, logfiles, pparams, cport, pport):
"""Initialize the controller.
Args:
cparams: configuration parameters.
logfiles: names of files to log to.
pparams: pump parameters.
cport: controller serial port.
pport: pump serial port.
"""
pumpdriver_package = 'plugins.%s' % pparams['pumpdriver']
control_function_package = 'plugins.%s' % cparams['controlfun']
# Import pumpdriver
pumpdriver = __import__(pumpdriver_package, globals(), locals(),
['Pump'], -1)
# Fetch the control computation, make it a method of self.
_temp = __import__(control_function_package, globals(), locals(),
['computeControl'], -1)
self.computeControl = types.MethodType(_temp.computeControl, self)
#self.ser_lock = cport.lock
self.stdout_lock = threading.RLock()
# Make the pump driver as appropriate.
self.pump = pumpdriver.Pump(cparams, logfiles, pparams, cport, pport)
# Data from config.ini
self.logfiles = logfiles
self.pparams = pparams
self.cparams = cparams # all controller parameters live here
self.blank_filename = self.logfiles['blanklog']
# Serial ports
self.serpt = cport
self.pport = pport
# This lock is for the following tx/rx raw values.
# TODO: should the controller know the number of chambers
# in advance of measuring?
self.OD_datalock = threading.RLock()
self.tx_blank = []
self.rx_blank = []
self.rx_val = []
self.tx_val = []
self.z = []
# Make sure to close all the pinch valves at startup.
with self.serpt.lock:
print 'Closing all valves;'
self.serpt.write("clo;")
# Construct the timer threads that perform repeated actions.
# TODO: make serial check period configurable.
self.start_time = None # Set on call to start()
control_period = int(cparams['period'])
self.cont_timer = mytimer(control_period, self.controlLoop)
self.ser_timer = mytimer(2, self.serialCheck)
def __init__(self,cparams,logfiles,pparams,cport,pport):
pumpdriver = __import__('plugins.'+pparams['pumpdriver'],globals(),
locals(),['Pump'],-1)
_temp = __import__('plugins.'+cparams['controlfun'],globals(),locals(),
['computeControl'],-1)
self.computeControl = types.MethodType(_temp.computeControl,self)
# self.ser_lock = cport.lock
self.stdout_lock = threading.RLock()
self.pump = pumpdriver.Pump(cparams,logfiles,pparams,cport,pport)
self.odcal = 1
#data from config.ini
self.logfiles = logfiles
self.pparams = pparams
self.cparams = cparams #all controller parameters live here
#serial ports
self.serpt = cport
self.pport = pport
#This lock is for the following tx/rx raw values.
self.OD_datalock = threading.RLock()
self.tx_blank = []
self.rx_blank = []
self.rx_val = []
self.tx_val = []
self.z = []
with self.serpt.lock:
self.serpt.write("clo;")
# self.serpt.flush()
#start the control-loop timer.
self.start_time = time();
self.cont_timer = mytimer(int(cparams['period']),self.controlLoop)
self.cont_timer.start()
#start the serial polling timer
self.ser_timer = mytimer(2, self.serialCheck)
self.ser_timer.start()
"""
--------------------------------
@Author: Dyson
@Contact: [email protected]
@file: mytimer.py
@time: 2017/7/20 11:18
--------------------------------
"""
import sys
import os
sys.path.append(sys.prefix + "\\Lib\\MyWheels")
reload(sys)
sys.setdefaultencoding('utf8')
import mytimer
mytimer = mytimer.mytimer()
class timer0(object):
def __init__(self):
pass
def main(self):
mytimer.cmd_timer('python %s' % (os.getcwd() + r'\controller.py'),
'17:00', 60 * 60 * 24)
if __name__ == '__main__':
timer0 = timer0()
timer0.main()
def exeSim(self):
x = 2 + 6
if not self.load1:
self.openSubKinDef()
if self.load1 and not self.load2:
self.openSubSigList()
#if self.file1.get() == "" or self.file2.get() == "":
if not (self.load1 and self.load2):
# dialog = Tk()
# dialog.grid()
# label1 = Label(dialog, text="You must PICK and LOAD source files first").grid(row=0)
# ok = Button(dialog, text=' OK ', command=dialog.quit).grid(row=1)
print "Simulations not started due to input file error"
self.textBox.insert(
Tkinter.END,
"Simulations not started due to input file error\n")
self.lineCount += 1
else:
#print "numSimulations = "+self.numSimulations.get()
numSubstrates = len(self.sigSubstrates)
mt = mytimer()
mt.start()
kinaseSimulationsCounts = dict()
#empty array with one member for each simulation
s = self.numSimulations.get().replace(',', '')
emptyCounts = [0 for x in range(0, int(s))]
simulations = dict()
for kinase in self.allKinases.keys():
simulations[kinase] = copy.deepcopy(emptyCounts)
#now simulations[kin][s] points to kinase by name kin, sth simulation
for s in range(0, int(self.numSimulations.get().replace(',', ''))):
(substratesChosen,
kinaseCounts) = rsr.randoPermutationSimulation(
self.substrate2kinases, numSubstrates)
for substrate in substratesChosen:
kinases = self.substrate2kinases[substrate]
for kinase in kinases:
#k = allKinases.keys().index(kinase)
simulations[kinase][s] += 1
if (s % 100 == 99):
print "Simulation " + str(
s + 1) + " complete\t" + mt.elapsed()
self.textBox.insert(
Tkinter.END, "Simulation " + str(s + 1) +
" complete\t" + mt.elapsed() + "\n")
self.textBox.see(Tkinter.END)
self.lineCount += 1
if self.lineCount % 10 == 0: self.parent.update()
self.currSim.set(str(s))
meanSimulations = [0 for x in self.allKinases.keys()]
stdSimulations = [0 for x in self.allKinases.keys()]
self.zscoreKinases = [0 for x in self.allKinases.keys()]
self.pvalueKinases = [0 for x in self.allKinases.keys()]
self.results = []
for k in range(0, len(self.allKinases.keys())):
#meanSimulations[k] = math.mean(simulations[k])
meanSimulations[k] = numpy.mean(
simulations[self.allKinases.keys()[k]])
#stdSimulations[k] = math.stdev(simulations[k])
stdSimulations[k] = numpy.std(
simulations[self.allKinases.keys()[k]])
# if stdSimulations[k] == 0:
# print "nan detected"
# if numpy.isnan(stdSimulations[k]):
# print "nan detected"
kinase = self.allKinases.keys()[k]
if stdSimulations[k] == 0:
self.zscoreKinases[k] = 0.0
self.pvalueKinases[k] = 0.0
else:
if kinase in self.sigKinaseCount:
self.zscoreKinases[k] = (
self.sigKinaseCount[kinase] -
meanSimulations[k]) / stdSimulations[k]
else:
self.zscoreKinases[k] = (
0 - meanSimulations[k]) / stdSimulations[k]
self.pvalueKinases[k] = scipy.stats.norm.sf(
abs(self.zscoreKinases[k])) * 2
self.results.append(
(self.pvalueKinases[k], self.allKinases.keys()[k],
self.zscoreKinases[k]))
print "sorting results\t" + mt.elapsed()
#self.textBox.insert(Tkinter.END, "sorting results\t"+mt.elapsed())
self.results.sort()
print "sorting complete\t" + mt.elapsed()
self.textBox.insert(Tkinter.END,
"sorting complete\t" + mt.elapsed() + "\n")
self.textBox.see(Tkinter.END)
self.lineCount += 1
outFile = None
if self.outFilename != self.OPTIONAL:
outFile = open(self.outFilename.get(), 'w')
print "(kinase)\t(z-score)\t(p-value 2 tail)"
self.textBox.insert(Tkinter.END,
"(kinase)\t(z-score)\t(p-value 2 tail)" + "\n")
if outFile:
outFile.write("(kinase)\t(z-score)\t(p-value 2 tail)" + "\n")
self.textBox.see(Tkinter.END)
self.lineCount += 1
for result in self.results:
(p, kinase, z) = result
print kinase + "\t%.03f\t%.03f" % (z, p)
self.textBox.insert(Tkinter.END,
kinase + "\t%.03f\t%.03f\n" % (z, p))
self.textBox.see(Tkinter.END)
self.lineCount += 1
if self.lineCount % 10 == 0: self.parent.update()
if outFile:
outFile.write(kinase + "\t%.03f\t%.03f\n" % (z, p))
import subprocess
from effect import *
import pygame
import os
import time
from mytimer import mytimer
from utils import fix_model
import json
from time import sleep
myTimer = None
cv2_WND_PROP_FULLSCREEN = cv2.WND_PROP_FULLSCREEN
cv2_WINDOW_FULLSCREEN = cv2.WINDOW_FULLSCREEN
cv2.namedWindow("frame", cv2_WND_PROP_FULLSCREEN)
cv2.setWindowProperty("frame", cv2_WND_PROP_FULLSCREEN, cv2_WINDOW_FULLSCREEN)
mTimer = mytimer()
currrDir = (os.path.dirname(os.path.realpath(__file__)))
print(currrDir + "/screensaver/1.jpg")
global screensaverImg
screensaverImg = cv2.imread(currrDir + "/screensaver/1.jpg")
def getRez():
cmd = ['xrandr']
cmd2 = ['grep', '*']
p = subprocess.Popen(cmd, stdout=subprocess.PIPE)
p2 = subprocess.Popen(cmd2, stdin=p.stdout, stdout=subprocess.PIPE)
p.stdout.close()
resolution_string, junk = p2.communicate()
resolution = resolution_string.split()[0].decode("utf-8")
first = True
#allows user to choose clades investigated
# start at 0 (FirstTaxon) thru Phylum (Kingdom and Superkingdom unreliable)
clades_to_proces = range(0, 7)
#Want general to specific
clades_to_proces.reverse()
cladeBaseCounts = [0 for x in range(len(clades_to_proces))]
#cladeIndex = ["firstTAXON"]+[tl.LINNAEUS_TAXONOMY_REVERSE[x] for x in clades_to_proces]
#cladeIndex.reverse()
mt = mytimer.mytimer()
mt.start()
print >> sys.stderr, "OPENING FILE " + sys.argv[1] + "\t" + (
mt.elapsedAsTimeStamp())
k = 0
period = 100 * 1000
for line in open(sys.argv[1]):
splits = line.split('\t')
if first:
colnames = splits
clades = colnames[1:-1]
first = False
else:
curr_dict = taxonomyTree