def RandomGraph(nodes=list(np.arange(10)),
probability=0.1,
width=400,
height=300,
curvature=lambda: np.random.uniform(1.1, 1.5)):
"""Construct a random graph, with the specified nodes, and random links.
The nodes are laid out randomly on a (width x height) rectangle.
Then each node is connected to the min_links nearest neighbors.
Because inverse links are added, some nodes will have more connections.
The distance between nodes is the hypotenuse times curvature(),
where curvature() defaults to a random number between 1.1 and 1.5."""
min_links = int(probability * len(nodes))
g = UndirectedGraph()
g.locations = {}
# Build the nodes
for node in nodes:
g.locations[node] = (np.random.randint(width),
np.random.randint(height))
# Build edges from each node to at least min_links nearest neighbors.
for _ in range(min_links):
for node in nodes:
if len(g.get(node)) < min_links:
here = g.locations[node]
def distance_to_node(n):
if n is node or g.get(node, n):
return infinity
return distance(g.locations[n], here)
neighbor = argmin(nodes, key=distance_to_node)
d = distance(g.locations[neighbor], here) * curvature()
g.connect(node, neighbor, int(d))
return g
def pmus_ingmar(fs, rr, pp, tp, tf):
"""
Sinusoidal profile
:param fs: sample frequency
:param rr: respiratory rate
:param pp: peak pressure
:param tp: peak time
:param tf: end of effort
:return: pmus profile
"""
ntp = np.floor(tp * fs)
ntf = np.floor(tf * fs)
ntN = np.floor(60.0 * fs / rr)
pmus1 = np.sin(np.pi * np.arange(0, ntp + 1, 1) / fs / 2.0 / tp)
pmus2 = np.sin(np.pi / 2.0 / (tf - tp) *
(np.arange(ntp + 1, ntf + 1, 1) / fs + tf - 2.0 * tp))
pmus3 = 0 * np.arange(ntf + 1, ntN + 1, 1) / fs
pmus = pp * np.concatenate((pmus1, pmus2, pmus3))
return pmus
def ConnectedGraph(nodes=list(np.arange(10)),
min_links=2,
width=400,
height=300,
curvature=lambda: np.random.uniform(1.1, 1.5)):
"""Construct a random connected graph."""
g = RandomGraph(nodes, min_links, width, height, curvature)
c_cs = connected_components(g)
for i in range(len(c_cs) - 1):
# Pick two random node from different components
# and then connect them
g.connect(np.random.choice(c_cs[i]), np.random.choice(c_cs[i + 1]))
return g
def pmus_parexp(fs, rr, pp, tp, tf):
"""
Parabolic-exponential profile
:param fs: sample frequency
:param rr: respiratory rate
:param pp: peak pressure
:param tp: peak time
:param tf: end of effort
:return: pmus profile
"""
ntp = np.floor(tp * fs)
ntN = np.floor(60.0 / rr * fs)
taur = abs(tf - tp) / 4.0
pmus1 = pp * (60.0 * rr - np.arange(0, ntp + 1, 1) / fs) * (
np.arange(0, ntp + 1, 1) / fs) / (tp * (60.0 * rr - tp))
pmus2 = pp * (np.exp(-(np.arange(ntp + 1, ntN + 1, 1) / fs - tp) / taur) -
np.exp(-(60.0 * rr - tp) / taur)) / (
1.0 - np.exp(-(60.0 * rr - tp) / taur))
pmus = np.concatenate((pmus1, pmus2))
return pmus
def read_channels(channels,
latitudes,
longitudes,
dfb_beginning,
dfb_ending,
slot_step=1):
dir, pattern = read_channels_dir_and_pattern()
satellite = read_satellite_name()
satellite_step = read_satellite_step()
nb_slots = get_nb_slots_per_day(satellite_step, slot_step)
patterns = [
pattern.replace("{SATELLITE}", satellite).replace('{CHANNEL}', chan)
for chan in channels
]
nb_days = dfb_ending - dfb_beginning + 1
content = np.empty(
(nb_slots * nb_days, len(latitudes), len(longitudes), len(patterns)))
start = read_start_slot()
for k in range(len(patterns)):
pattern = patterns[k]
chan = channels[k]
dataset = DataSet.read(
dirs=dir,
extent={
'latitude': latitudes,
'longitude': longitudes,
'dfb': {
'start': dfb_beginning,
'end': dfb_ending,
"end_inclusive": True,
'start_inclusive': True,
},
'slot': np.arange(start, start + nb_slots, step=slot_step)
},
file_pattern=pattern,
variable_name=chan,
fill_value=np.nan,
interpolation='N',
max_processes=0,
)
data = dataset['data'].data
day_slot_b = 0
day_slot_e = nb_slots
for day in range(nb_days):
content[day_slot_b:day_slot_e, :, :, k] = data[day]
day_slot_b += nb_slots
day_slot_e += nb_slots
return content
def read_classes(latitudes,
longitudes,
dfb_beginning,
dfb_ending,
slot_step=1):
dir, pattern = read_indexes_dir_and_pattern('classes')
satellite_step = read_satellite_step()
nb_slots = get_nb_slots_per_day(satellite_step, slot_step)
nb_days = dfb_ending - dfb_beginning + 1
content = np.empty((nb_slots * nb_days, len(latitudes), len(longitudes)))
dataset = DataSet.read(
dirs=dir,
extent={
'latitude': latitudes,
'longitude': longitudes,
'dfb': {
'start': dfb_beginning,
'end': dfb_ending,
"end_inclusive": True,
'start_inclusive': True,
},
'slot': {
"enumeration": np.arange(0, nb_slots, step=slot_step),
"override_type": "slot"
},
},
file_pattern=pattern,
variable_name='Classes',
fill_value=np.nan,
interpolation='N',
max_processes=0,
)
data = dataset['data'].data
day_slot_b = 0
day_slot_e = nb_slots
for day in range(nb_days):
content[day_slot_b:day_slot_e, :, :] = data[day]
day_slot_b += nb_slots
day_slot_e += nb_slots
return content
def pmus_linear(fs, rr, pp, tp, tf):
"""
Linear profile
:param fs: sample frequency
:param rr: respiratory rate
:param pp: peak pressure
:param tp: peak time
:param tf: end of effort
:return: pmus profile
"""
nsamples = np.floor(60.0 / rr * fs)
time = np.arange(0, nsamples + 1, 1) / fs
pmus = 0 * time
for i in range(len(time)):
if time[i] <= tp:
pmus[i] = time[i] / tp
elif time[i] <= tf:
pmus[i] = (tf - time[i]) / (tf - tp)
else:
pmus[i] = 0.0
pmus[i] = pp * pmus[i]
return pmus
def solve_model(header_params,params,header_features,features,debugmsg):
#Extracts each parameter
fs = params[header_params.index('Fs')]
rvent = params[header_params.index('Rvent')]
c = params[header_params.index('C')]
rins = params[header_params.index('Rins')]
rexp = rins # params[4]
peep = params[header_params.index('PEEP')]
sp = params[header_params.index('SP')]
trigger_type = features[header_features.index('Triggertype')]
trigger_arg = params[header_params.index('Triggerarg')]
rise_type = features[header_features.index('Risetype')]
rise_time = params[header_params.index('Risetime')]
cycle_off = params[header_params.index('Cycleoff')]
rr = params[header_params.index('RR')]
pmus_type = features[header_features.index('Pmustype')]
pp = params[header_params.index('Pp')]
tp = params[header_params.index('Tp')]
tf = params[header_params.index('Tf')]
noise = params[header_params.index('Noise')]
e2 = params[header_params.index('E2')]
model = features[header_features.index('Model')]
expected_len = int(np.floor(180.0 / np.min(RR) * np.max(Fs)) + 1)
#Assings pmus profile
pmus = pmus_profile(fs, rr, pmus_type, pp, tp, tf)
pmus = pmus + peep #adjusts PEEP
pmus = np.concatenate((np.array([0]), pmus)) #sets the first value to zero
#Unit conversion from cmH2O.s/L to cmH2O.s/mL
rins = rins / 1000.0
rexp = rexp / 1000.0
rvent = rvent / 1000.0
#Generates time, flow, volume, insex and paw waveforms
time = np.arange(0, np.floor(60.0 / rr * fs) + 1, 1) / fs
time = np.concatenate((np.array([0]), time))
flow = np.zeros(len(time))
volume = np.zeros(len(time))
insex = np.zeros(len(time))
paw = np.zeros(len(time)) + peep #adjusts PEEP
len_time = len(time)
#Peak flow detection
peak_flow = flow[0]
detect_peak_flow = False
#Support detection
detect_support = False
time_support = -1
#Expiration detection
detect_exp = False
time_exp = -1
if trigger_type == 'flow':
# units conversion from L/min to mL/s
trigger_arg = trigger_arg / 60.0 * 1000.0
for i in range(1, len(time)):
# period until the respiratory effort beginning
if (((trigger_type == 'flow' and flow[i] < trigger_arg) or
(trigger_type == 'pressure' and paw[i] > trigger_arg + peep) or
(trigger_type == 'delay' and time[i] < trigger_arg)) and
(not detect_support) and (not detect_exp)):
paw[i] = peep
y0 = volume[i - 1]
tspan = [time[i - 1], time[i]]
args = (paw[i], pmus[i], model, c, e2, rins)
sol = odeint(flow_model, y0, tspan, args=args)
volume[i] = sol[-1]
flow[i] = flow_model(volume[i], time[i], paw[i], pmus[i], model, c, e2, rins)
if debugmsg:
print('volume[i]= {:.2f}, flow[i]= {:.2f}, paw[i]= {:.2f}, waiting'.format(volume[i], flow[i], paw[i]))
if (((trigger_type == 'flow' and flow[i] >= trigger_arg) or
(trigger_type == 'pressure' and paw[i] <= trigger_arg + peep) or
(trigger_type == 'delay' and time[i] >= trigger_arg))):
detect_support = True
time_support = time[i+1]
continue
# detection of inspiratory effort
# ventilator starts to support the patient
elif (detect_support and (not detect_exp)):
if rise_type == 'step':
paw[i] = sp + peep
elif rise_type == 'exp':
rise_type = rise_type if np.random.random() > 0.01 else 'linear'
if paw[i] < sp + peep:
paw[i] = (1.0 - np.exp(-(time[i] - time_support) / rise_time )) * sp + peep
if paw[i] >= sp + peep:
paw[i] = sp + peep
elif rise_type == 'linear':
rise_type = rise_type if np.random.random() > 0.01 else 'exp'
if paw[i] < sp + peep:
paw[i] = (time[i] - time_support) / rise_time * sp + peep
if paw[i] >= sp + peep:
paw[i] = sp + peep
y0 = volume[i - 1]
tspan = [time[i - 1], time[i]]
args = (paw[i], pmus[i], model, c, e2, rins)
sol = odeint(flow_model, y0, tspan, args=args)
volume[i] = sol[-1]
flow[i] = flow_model(volume[i], time[i], paw[i], pmus[i], model, c, e2, rins)
if debugmsg:
print('volume[i]= {:.2f}, flow[i]= {:.2f}, paw[i]= {:.2f}, supporting'.format(volume[i], flow[i], paw[i]))
if flow[i] >= flow[i - 1]:
peak_flow = flow[i]
detect_peak_flow = False
elif flow[i] < flow[i - 1]:
detect_peak_flow = True
if (flow[i] <= cycle_off * peak_flow) and detect_peak_flow and i<len_time:
detect_exp = True
time_exp = i+1
try:
paw[i + 1] = paw[i]
except IndexError:
pass
elif detect_exp:
if rise_type == 'step':
paw[i] = peep
elif rise_type == 'exp':
if paw[i - 1] > peep:
paw[i] = sp * (np.exp(-(time[i] - time[time_exp-1]) / rise_time )) + peep
if paw[i - 1] <= peep:
paw[i] = peep
elif rise_type == 'linear':
rise_type = rise_type if np.random.random() > 0.01 else 'exp'
if paw[i - 1] > peep:
paw[i] = sp * (1 - (time[i] - time[time_exp-1]) / rise_time) + peep
if paw[i - 1] <= peep:
paw[i] = peep
y0 = volume[i - 1]
tspan = [time[i - 1], time[i]]
args = (paw[i], pmus[i], model, c, e2, rexp + rvent)
sol = odeint(flow_model, y0, tspan, args=args)
volume[i] = sol[-1]
flow[i] = flow_model(volume[i], time[i], paw[i], pmus[i], model, c, e2, rexp + rvent)
if debugmsg:
print('volume[i]= {:.2f}, flow[i]= {:.2f}, paw[i]= {:.2f}, exhaling'.format(volume[i], flow[i], paw[i]))
#Generates InsEx trace
if time_exp > -1:
insex = np.concatenate((np.ones(time_exp), np.zeros(len(time) - time_exp)))
#Drops the first element
flow = flow[1:] / 1000.0 * 60.0 # converts back to L/min
volume = volume[1:]
paw = paw[1:]
pmus = pmus[1:] - peep #reajust peep again
insex = insex[1:]
flow,volume,pmus,insex,paw = generate_cycle(expected_len,flow,volume,pmus,insex,paw,peep=peep)
# paw = generate_cycle(expected_len,paw,peep=peep)[0]
flow,volume,paw,pmus,insex = generate_noise(noise,flow,volume,paw,pmus,insex)
# plt.plot(flow)
# plt.plot(volume)
# plt.plot(paw)
# plt.plot(pmus)
# plt.show()
return flow, volume, paw, pmus, insex, rins,rexp, c
num_samples = flow.shape[1]
(min_flow, max_flow, flow) = normalize_data(flow)
(min_volume, max_volume, volume) = normalize_data(volume)
(min_paw, max_paw, paw) = normalize_data(paw)
(min_resistance, max_resistance, resistances) = normalize_data(resistances)
(min_capacitance, max_capacitance, capacitances) = normalize_data(capacitances)
print("normalized data")
input_data = np.zeros((num_examples, num_samples, 3))
input_data[:, :, 0] = flow
input_data[:, :, 1] = volume
input_data[:, :, 2] = paw
output_data = np.concatenate((resistances, capacitances), axis=1)
indices = np.arange(num_examples)
print("input created")
input_train, input_test, output_train, output_test, indices_train, indices_test = \
train_test_split(input_data, output_data, indices, test_size=0.3, shuffle=False)
input_validation, input_test, output_validation, output_test, indices_validation, indices_test = \
train_test_split(input_test, output_test, indices_test, test_size=0.5, shuffle=False)
np.save('./data/input_test.npy', input_test)
np.save('./data/output_test.npy', output_test)
print("before CNN")
model = CNN_Model(num_samples, input_volume=3).get_model()
err_pmus = []
# R_hat = np.average([denormalize_data(output_pred_test[i, 0], minimum=min_resistances, maximum=max_resistances) for i in range(num_examples)])
# C_hat = np.average([denormalize_data(output_pred_test[i, 1], minimum= min_capacitances, maximum= max_capacitances) for i in range(num_examples)])
R_hat = denormalize_data(output_pred_test[0, 0],
minimum=min_resistances,
maximum=max_resistances)
C_hat = denormalize_data(output_pred_test[0, 1],
minimum=min_capacitances,
maximum=max_capacitances)
alpha = 0.2
rr = min(RR)
fs = max(Fs)
time = np.arange(0, np.floor(180.0 / rr * fs) + 1, 1) / fs
err_pmus_hat = []
err_nmsre = []
for i in range(num_examples - 1):
# R_hat = alpha*denormalize_data(output_pred_test[i, 0], minimum=min_resistances, maximum=max_resistances) + (1-alpha)*R_hat
# C_hat = alpha*denormalize_data(output_pred_test[i, 1], minimum= min_capacitances, maximum= max_capacitances) + (1-alpha)*C_hat
R_hat = denormalize_data(output_pred_test[i, 0],
minimum=min_resistances,
maximum=max_resistances)
C_hat = denormalize_data(output_pred_test[i, 1],
minimum=min_capacitances,
maximum=max_capacitances)
# R = denormalize_data(output_data[i, 0], min_resistances, max_resistances)
def train(rank, args, shared_model, optimizer, env_conf):
ptitle('Training Agent: {}'.format(rank))
gpu_id = args.gpu_ids[rank % len(args.gpu_ids)]
torch.manual_seed(args.seed + rank)
if gpu_id >= 0:
torch.cuda.manual_seed(args.seed + rank)
env = atari_env(args.env, env_conf, args)
if optimizer is None:
if args.optimizer == 'RMSprop':
optimizer = optim.RMSprop(shared_model.parameters(), lr=args.lr)
if args.optimizer == 'Adam':
optimizer = optim.Adam(shared_model.parameters(),
lr=args.lr,
amsgrad=args.amsgrad)
env.seed(args.seed + rank)
tp_weight = args.tp
player = Agent(None, env, args, None)
player.gpu_id = gpu_id
player.model = A3Clstm(player.env.observation_space.shape[0],
player.env.action_space, args.terminal_prediction,
args.reward_prediction)
player.state = player.env.reset()
player.state = torch.from_numpy(player.state).float()
if gpu_id >= 0:
with torch.cuda.device(gpu_id):
player.state = player.state.cuda()
player.model = player.model.cuda()
player.model.train()
# Below is where the cores are running episodes continously ...
average_ep_length = 0
while True:
if gpu_id >= 0:
with torch.cuda.device(gpu_id):
player.model.load_state_dict(shared_model.state_dict())
else:
player.model.load_state_dict(shared_model.state_dict())
if player.done:
if gpu_id >= 0:
with torch.cuda.device(gpu_id):
player.cx = Variable(torch.zeros(1, 128).cuda())
player.hx = Variable(torch.zeros(1, 128).cuda())
else:
player.cx = Variable(torch.zeros(1, 128))
player.hx = Variable(torch.zeros(1, 128))
else:
player.cx = Variable(player.cx.data)
player.hx = Variable(player.hx.data)
for step in range(args.num_steps):
player.eps_len += 1
player.action_train()
if player.done:
break
if player.done:
state = player.env.reset()
player.state = torch.from_numpy(state).float()
if gpu_id >= 0:
with torch.cuda.device(gpu_id):
player.state = player.state.cuda()
R = torch.zeros(1, 1)
if not player.done:
value, _, _, _, _ = player.model(
(Variable(player.state.unsqueeze(0)), (player.hx, player.cx)))
R = value.data
if gpu_id >= 0:
with torch.cuda.device(gpu_id):
R = R.cuda()
player.values.append(Variable(R))
policy_loss = 0
value_loss = 0
reward_pred_loss = 0
terminal_loss = 0
gae = torch.zeros(1, 1)
if gpu_id >= 0:
with torch.cuda.device(gpu_id):
gae = gae.cuda()
R = Variable(R) # TODO why this is here?
for i in reversed(range(len(player.rewards))):
R = args.gamma * R + player.rewards[i]
advantage = R - player.values[i]
value_loss = value_loss + 0.5 * advantage.pow(2)
# Generalized Advantage Estimataion
delta_t = player.rewards[i] + args.gamma * player.values[
i + 1].data - player.values[i].data
gae = gae * args.gamma * args.tau + delta_t
policy_loss = policy_loss - player.log_probs[i] * Variable(
gae) - 0.01 * player.entropies[i]
if args.reward_prediction:
reward_pred_loss = reward_pred_loss + (
player.reward_predictions[i] - player.rewards[i]).pow(2)
if args.terminal_prediction: # new way of using emprical episode length as a proxy for current length.
if player.average_episode_length is None:
end_predict_labels = np.arange(
player.eps_len - len(player.terminal_predictions),
player.eps_len) / player.eps_len # heuristic
else:
end_predict_labels = np.arange(
player.eps_len - len(player.terminal_predictions),
player.eps_len) / player.average_episode_length
for i in range(len(player.terminal_predictions)):
terminal_loss = terminal_loss + (
player.terminal_predictions[i] -
end_predict_labels[i]).pow(2)
terminal_loss = terminal_loss / len(player.terminal_predictions)
player.model.zero_grad()
#print(f"policy loss {policy_loss} and value loss {value_loss} and terminal loss {terminal_loss} and reward pred loss {reward_pred_loss}")
total_loss = policy_loss + 0.5 * value_loss + tp_weight * terminal_loss + 0.5 * reward_pred_loss
total_loss.backward() # will free memory ...
# Visualize Computation Graph
#graph = make_dot(total_loss)
#from graphviz import Source
#Source.view(graph)
ensure_shared_grads(player.model, shared_model, gpu=gpu_id >= 0)
optimizer.step()
player.clear_actions()
if player.done:
if player.average_episode_length is None: # initial one
player.average_episode_length = player.eps_len
else:
player.average_episode_length = int(
0.99 * player.average_episode_length +
0.01 * player.eps_len)
#print(player.average_episode_length, 'current one is ', player.eps_len)
player.eps_len = 0 # reset here