def test():
print 'here we go'
# while s.read(100000):
# print 'flush serial'
uc = uControl()
# junk = s.read(1000)
print 'here'
try:
print 'uc.cuff_pressure', uc.cuff_pressure
print 'maintain()'
uc.maintain(200, 230, 3)
uc.record(True)
print 'len(uc.hirate)', len(uc.hirate)
while uc.pump_state:
print 'uc.cuff_pressure', uc.cuff_pressure
serial_interact()
print 'deflate'
uc.deflate(40)
uc.record(False)
print 'len(uc.hirate)', len(uc.hirate)
hirate = array(uc.hirate)
if len(uc.hirate) > 0:
dt = 0.004
n_tap = 100
lp_taps = util.get_lowpass_taps(5, dt, n_tap)
llp_taps = util.get_lowpass_taps(.25, dt, n_tap)
lpd = util.filter(hirate[:, 1] - hirate[0, 1],
lp_taps)[::10] + hirate[0, 1]
llpd = util.filter(hirate[:, 1] - hirate[0, 1],
llp_taps)[::10] + hirate[0, 1]
print len(lpd)
times = hirate[::10, 0]
ax = pylab.subplot(211)
pylab.plot(times, lpd)
pylab.plot(times, llpd)
pylab.subplot(212, sharex=ax)
pylab.plot(times, lpd - llpd)
pfn = 'hirate.pkl'
pickle.dump(hirate, open(pfn, 'w'))
print 'write', pfn
# pylab.figure(2); pylab.plot(uc.lpf.out)
# pylab.figure(3); pylab.plot(hirate[:,1])
print 'done'
finally:
uc.deflate(50)
send_cmd(pump_rate=False, valve=getValveByte(valve0=True))
time.sleep(2)
send_cmd(pump_rate=False, valve=getValveByte(valve0=False), interval=0)
pylab.show()
def test():
print 'here we go'
# while s.read(100000):
# print 'flush serial'
uc = uControl()
# junk = s.read(1000)
print 'here'
try:
print 'uc.cuff_pressure', uc.cuff_pressure
print 'maintain()'
uc.maintain(200, 230, 3)
uc.record(True)
print 'len(uc.hirate)', len(uc.hirate)
while uc.pump_state:
print 'uc.cuff_pressure', uc.cuff_pressure
serial_interact()
print 'deflate'
uc.deflate(40)
uc.record(False)
print 'len(uc.hirate)', len(uc.hirate)
hirate = array(uc.hirate)
if len(uc.hirate) > 0:
dt = 0.004
n_tap = 100
lp_taps = util.get_lowpass_taps(5, dt, n_tap)
llp_taps = util.get_lowpass_taps(.25, dt, n_tap)
lpd = util.filter(hirate[:,1] - hirate[0, 1], lp_taps)[::10] + hirate[0, 1]
llpd = util.filter(hirate[:,1] - hirate[0, 1], llp_taps)[::10] + hirate[0, 1]
print len(lpd)
times = hirate[::10,0]
ax = pylab.subplot(211)
pylab.plot(times, lpd)
pylab.plot(times, llpd)
pylab.subplot(212, sharex=ax)
pylab.plot(times, lpd - llpd)
pfn = 'hirate.pkl'
pickle.dump(hirate, open(pfn, 'w'))
print 'write', pfn
# pylab.figure(2); pylab.plot(uc.lpf.out)
# pylab.figure(3); pylab.plot(hirate[:,1])
print 'done'
finally:
uc.deflate(50)
send_cmd(pump_rate=False, valve=getValveByte(valve0=True))
time.sleep(2)
send_cmd(pump_rate=False, valve=getValveByte(valve0=False), interval=0)
pylab.show()
def plot_hirate(hirate):
times = hirate[:,0]
gage = hirate[:,1]
flow = hirate[:,2]
figure(1)
ax = pylab.subplot(211)
ylabel('Gage mmHG')
pylab.plot(times, gage)
pylab.subplot(212)
xlabel('Time sec.')
ylabel('Flow')
pylab.plot(times, flow)
figure(2) ## plot high pass data
lp_taps = util.get_lowpass_taps(.5, dt=.004, n=100)
hpd = util.filter(gage - gage[0], lp_taps) + gage[0]
plot(gage, gage - hpd)
def __init__(self, listener=None, dummy=False, port=None):
self.__abort = False
self.recording = False # flag to indicate times when data is to be captured
self.hirate = [] # store hirate data when recording
self.lorate = [] # not used
self.mpid_count = 0
self.lpid_count = 0 # not used
## uControl readings
self.cuff_pressure = None
self.flow_rate = None
self.pulse_rate = None
self.amb_pressure = None
self.amb_temp = None
self.pump_state = None
self.valve_state = None
self.short_msg = None
self.last_update = None
## used to control inflation and deflation
self.max_pressure = 1e6
self.min_pressure = -1
self.listener = listener
self.dt = 0.004 ## DO NOT Change without also changing uControl firmware
self.n_tap = 20
self.lp_taps = util.get_lowpass_taps(10, self.dt, self.n_tap) ## 0 - 5 Hz filter for data
self.lpf = util.StreamingFir(self.lp_taps, 2500, 10)
## get notifed of new messages from uControl firmware
subscribe(MPID.PID, self.mpid_cb)
subscribe(ShortPID.PID, self.short_cb)
subscribe(StatusPID.PID, self.status_cb)
### connect to uControl hardware
connect(port)
send_cmd(cuff_pressure=True, interval=1) ## interval=1 ==> .004 sec dt
tries = 0
if not dummy:
while self.cuff_pressure is None:
serial_interact()
tries += 1
if tries % 10 == 9:
print 'tries', tries
def __init__(self, listener=None, dummy=False):
self.__abort = False
self.recording = False # flag to indicate times when data is to be captured
self.hirate = [] # store hirate data when recording
self.lorate = [] # not used
self.mpid_count = 0
self.lpid_count = 0 # not used
## uControl readings
self.cuff_pressure = None
self.flow_rate = None
self.pulse_rate = None
self.amb_pressure = None
self.amb_temp = None
self.pump_state = None
self.valve_state = None
self.short_msg = None
self.last_update = None
## used to control inflation and deflation
self.max_pressure = 1e6
self.min_pressure = -1
self.listener = listener
self.dt = 0.004 ## DO NOT Change without also changing uControl firmware
self.n_tap = 20
self.lp_taps = util.get_lowpass_taps(10, self.dt, self.n_tap) ## 0 - 5 Hz filter for data
self.lpf = util.StreamingFir(self.lp_taps, 2500, 10)
## get notifed of new messages from uControl firmware
subscribe(MPID.PID, self.mpid_cb)
subscribe(ShortPID.PID, self.short_cb)
subscribe(StatusPID.PID, self.status_cb)
### connect to uControl hardware
send_cmd(cuff_pressure=True, interval=1) ## interval=1 ==> .004 sec dt
tries = 0
if not dummy:
while self.cuff_pressure is None:
serial_interact()
tries += 1
if tries % 10 == 9:
print 'tries', tries
def plot_hirate(hirate, color):
dt = 0.004
n_tap = 100
fmax = 10 ## Hz
lp_taps = util.get_lowpass_taps(fmax, dt, n_tap)
delay_taps = zeros(defaults['n_tap'])
delay_taps[defaults['n_tap'] // 2] = 1
lpd = util.filter(hirate[:,1] - hirate[0, 1], lp_taps) + hirate[0, 1]
ax = pylab.subplot(211)
times = hirate[:,0]
pylab.plot(times, lpd)
peaks, troughs = util.find_peaks_and_troughs(lpd, eps=.1, edit=False)
if peaks[0] < troughs[0]:
peaks = peaks[1:]
if peaks[-1] < troughs[-1]:
troughs = troughs[:-1]
pylab.plot(times[peaks], lpd[peaks], 'ro')
pylab.plot(times[troughs], lpd[troughs], 'bo')
deltas = lpd[peaks] - lpd[troughs]
print std(deltas)
pylab.subplot(212)
pylab.plot(lpd[troughs], deltas)
import glob
import csv
import os.path
import sys
import pickle
import time
from pylab import *
from numpy import *
from constants import *
import util
import scipy.interpolate.interpolate as interp
import scipy.integrate
## Filter taps
LP_TAPS = util.get_lowpass_taps(defaults["high_cuttoff_hz"], defaults["dt"], defaults["n_tap"])
LLP_TAPS = util.get_lowpass_taps(defaults["low_cuttoff_hz"], defaults["dt"], defaults["n_tap"])
DELAY_TAPS = zeros(defaults["n_tap"])
DELAY_TAPS[defaults["n_tap"] // 2] = 1
def get_flow(gage, cba):
c, b, a = cba
return (-b + sqrt(b ** 2 - 4 * a * (c - gage))) / (2 * a)
def flow_of_gage(flow, gage, cba=None):
"""
return the quadratic smoothed flow values
flow -- flow measurements corrected for temp and pressure
r_artery = .2
delta_r_artery = .04 * r_artery
l_artery = 10
deltaVa_n = 2 * pi * r_artery * delta_r_artery * l_artery
# Cn = deltaVa_n / PP
# print Cn
Pamb = 760 ## mmHg
OVERSAMPLE = 1
DT = defaults['dt'] / OVERSAMPLE
Tmax = 140
LP_TAPS = util.get_lowpass_taps(defaults['high_cuttoff_hz'],
defaults['dt'],
defaults['n_tap'])
LLP_TAPS = util.get_lowpass_taps(defaults['low_cuttoff_hz'],
defaults['dt'],
defaults['n_tap'])
T_OFFSET = .123123
def smooth_dP_dt(t, r0, p0):
'''
return average pressure change rate as a function of t
'''
return -r0 * exp(-(r0 / p0) * t)
def smooth_P(t, r0, p0):
return P0 * exp(-(r0 / p0) * t)
