def plot_trajectory(savefig=False):
## Phase space
plt.figure(figsize=(12, 6))
plt.title('Phase Space')
plt.xlabel('q')
plt.ylabel('p')
plt.plot(env.trajectory[:, 0],
env.trajectory[:, 1],
'--k',
label='Ground truth')
plt.plot(env.X[:, 0], env.X[:, 1], 'xk', label='Training data', alpha=0.3)
plt.plot(cdl_data[:, 0],
cdl_data[:, 1],
'-',
label='CD-Lagrange, RMSE: {:.3f}'.format(RMSE(env, cdl_data)))
plt.plot(resnet_data[:, 0],
resnet_data[:, 1],
'-',
label='ResNet, RMSE: {:.3f}'.format(RMSE(env, resnet_data)))
if _train_vin:
plt.plot(vin_data[:, 0],
vin_data[:, 1],
'-',
label='VIN VV, RMSE: {:.3f}'.format(RMSE(env, vin_data)))
plt.legend()
if savefig:
plt.savefig(env.get_filename('trajectory'))
plt.show()
def plot_trajectory(savefig=False):
# bottom_right=(0.3, -2.1)
top_right = (0.25, 1.95)
plt.figure(figsize=(14, 10))
plt.subplot(2, 2, 1)
plt.title('Ground Truth')
plt.plot(env.trajectory[:, 0], env.trajectory[:, 2], 'o--', label='1')
plt.plot(env.trajectory[:, 1], env.trajectory[:, 3], 'o--', label='2')
plt.legend()
plt.subplot(2, 2, 2)
plt.title('CD-Lagrange')
rmse_cdl = RMSE(env, cdl_data)
plt.text(top_right[0], top_right[1], 'RMSE={:.3f}'.format(rmse_cdl))
plt.plot(cdl_data[:, 0], cdl_data[:, 2], 'o--', label='1')
plt.plot(cdl_data[:, 1], cdl_data[:, 3], 'o--', label='2')
plt.legend()
plt.subplot(2, 2, 3)
plt.title('ResNet')
rmse_resnet = RMSE(env, resnet_data)
plt.text(top_right[0], top_right[1], 'RMSE={:.3f}'.format(rmse_resnet))
plt.plot(resnet_data[:, 0], resnet_data[:, 2], 'o--', label='1')
plt.plot(resnet_data[:, 1], resnet_data[:, 3], 'o--', label='2')
plt.legend()
if savefig:
plt.savefig(env.get_filename('trajectory'))
plt.show()
def test(test_data_loader, model):
srocc = SROCC()
plcc = PLCC()
rmse = RMSE()
len_test = len(test_data_loader)
pb = ProgressBar(len_test, show_step=True)
print("Testing")
model.eval()
with torch.no_grad():
for i, ((img, ref), score) in enumerate(test_data_loader):
img, ref = img.cuda(), ref.cuda()
output = model(img, ref).cpu().data.numpy()
score = score.data.numpy()
srocc.update(score, output)
plcc.update(score, output)
rmse.update(score, output)
pb.show(
i, "Test: [{0:5d}/{1:5d}]\t"
"Score: {2:.4f}\t"
"Label: {3:.4f}".format(i + 1, len_test, float(output),
float(score)))
print("\n\nSROCC: {0:.4f}\n"
"PLCC: {1:.4f}\n"
"RMSE: {2:.4f}".format(srocc.compute(), plcc.compute(),
rmse.compute()))
def solve(self,
A: torch.Tensor,
b: torch.Tensor,
sizeA: tuple,
initialX: torch.Tensor = None):
x = initialX if initialX is not None else torch.randn(
sizeA[0], dtype=torch.float32, device=global_device)
assert sizeA[0] == sizeA[1]
diff: float = 0.0
iter = 0
r = b - sparseMatmul(A, x, sizeA)
p = r.clone()
lastRR = torch.mul(r, r).sum()
for iter in range(self.maxiter):
Ap = sparseMatmul(A, p, sizeA)
a = lastRR / torch.mul(p, Ap).sum()
newX = x + a * p
newR = r - a * Ap
newRR = torch.mul(newR, newR).sum()
b = newRR / lastRR
p = newR + b * p
r = newR
lastRR = newRR
diff = RMSE(x, newX)
x = newX
if diff <= self.tolerance:
break
print(iter + 1, diff)
return x
def solve(self,
A: torch.Tensor,
b: torch.Tensor,
sizeA: tuple,
initialX: torch.Tensor = None):
x = initialX if initialX is not None else torch.randn(
sizeA[0], dtype=torch.float32, device=global_device)
assert sizeA[0] == sizeA[1]
dia = torch.zeros(sizeA[0], dtype=torch.float32, device=global_device)
boolDiagonalInA = A[:, 0] == A[:, 1]
dia[A[boolDiagonalInA, 0].to(torch.int64)] = A[boolDiagonalInA,
2] # 对角元
A = A[~boolDiagonalInA] # A现在仅含有非对角元元素的稀疏表示
diff: float = 0.0
iter = 0
for iter in range(self.maxiter):
AxNoDiag = sparseMatmul(A, x, sizeA)
newX = (b - AxNoDiag) / dia
diff = RMSE(x, newX)
x = newX
if diff <= self.tolerance:
break
print(iter + 1, diff)
return x
def main(input_img, Threshold):
#compute binary image using threshold
out_img = (255 * (input_img > Threshold).astype(np.int)).astype(np.uint8)
#compute rmse
rmse = RMSE(input_img, out_img)
fidelity = Fidelity(input_img, out_img)
return out_img, rmse, fidelity
def evalvqa(evalset, predictions, isVQAeval=True):
predans = []
MCans = []
VQA_acc = 0
assert_eq(len(evalset), len(predictions))
for i, ent in enumerate(evalset):
#all qids are integers
qid = int(ent['question_id'])
#all predictions/answers are string
pred = str(predictions[qid])
if isVQAeval:
ansfreq = Counter([ans['answer'] for ans in ent['answers']])
MC = ent['multiple_choice_answer']
#prediction is a string
agreeing = ansfreq[pred]
ans_p = min(agreeing * 0.3, 1)
else: # not VQA style
MC = ent['answer']
ans_p = (MC == pred)
VQA_acc += ans_p
predans.append(int(pred))
MCans.append(int(MC))
VQA_acc = 100.0 * VQA_acc / len(evalset)
rmse = RMSE(MCans, predans)
return VQA_acc, rmse
def generateFinalResult(
self, vddRes: torch.Tensor, gndRes: torch.Tensor
) -> Tuple[Dict[str, float], Union[float, None]]:
"""
把Tensor格式的结果数组转化为结点的字典。
:param vddRes: <Tensor n_vdd> n_vdd是vdd平面待定结点个数
:param gndRes: <Tensor n_gnd> n_gnd是gnd平面待定结点个数
:return: (计算结果-node名称到算出的电压值对应的字典， 均方误差开根号（RMSE）)
"""
result = {}
for nodename in self.nodenameDict:
idx = self.nodenameDict[nodename]
if self.connectToVSource[idx]:
result[nodename] = self.nodeVoltages[idx]
else:
if self.nodeLabel[idx] == L_VDD:
result[nodename] = vddRes[self.vddMapping[idx]].item()
elif self.nodeLabel[idx] == L_GND:
result[nodename] = gndRes[self.gndMapping[idx]].item()
rmse = None
if len(self.groundTruth) > 0:
# 计算RMSE
gtArr = []
resArr = []
for nodename in result:
resArr.append(result[nodename])
gtArr.append(self.groundTruth[nodename])
rmse = RMSE(torch.tensor(gtArr, device=global_device),
torch.tensor(resArr, device=global_device))
return result, rmse
def solve(self,
A: torch.Tensor,
b: torch.Tensor,
sizeA: tuple,
initialX: torch.Tensor = None):
assert sizeA[0] == sizeA[1]
diff: float = 0.0
iter = 0
with torch.enable_grad():
x = initialX if initialX is not None else torch.randn(
sizeA[0], dtype=torch.float32, device=global_device)
for iter in range(self.maxiter):
x.requires_grad = True
Ax = sparseMatmul(A, x, sizeA)
loss = torch.norm(Ax - b)
loss.backward()
newX = (x - self.lr * x.grad).detach()
diff = RMSE(x, newX)
x = newX
if diff <= self.tolerance:
break
print(iter + 1, diff)
return x
def compile(self):
self.is_compiled = True
self.other_args = other_args
self.batch_size = batch_size
self.loss = nn.MSELoss()
self.optimizer = optimizer_dict[opt_type](self.parameters(), **other_args)
self.metrics = [MAE(), RMSE(), RMSLE(), NDEI(), R2_SCORE(), MAAPE()]
def plot_trajectory(savefig=False):
bottom_right = (0.3, -2.1)
top_right = (0.25, 1.95)
rmse_pos = bottom_right
plt.figure(figsize=(8, 6.6))
plt.subplot(2, 2, 1)
plt.title('Ground Truth')
plt.plot(env.trajectory[:, 0], env.trajectory[:, 2], '--', label='1')
plt.plot(env.trajectory[:, 1], env.trajectory[:, 3], '--', label='2')
plt.plot(env.X[:, 0], env.X[:, 2], 'C0x', label='Data 1', alpha=0.3)
plt.plot(env.X[:, 1], env.X[:, 3], 'C1x', label='Data 2', alpha=0.3)
# plt.legend()
plt.subplot(2, 2, 2)
plt.title('CD-Lagrange')
rmse_cdl = RMSE(env, cdl_data)
print('CDL RMSE={:.3f}'.format(rmse_cdl))
plt.plot(cdl_data[:, 0], cdl_data[:, 2], 'x--', label='1')
plt.plot(cdl_data[:, 1], cdl_data[:, 3], 'x--', label='2')
# plt.legend()
plt.subplot(2, 2, 3)
plt.title('ResNet')
rmse_resnet = RMSE(env, resnet_data)
print('Resnet RMSE={:.3f}'.format(rmse_resnet))
plt.plot(resnet_data[:, 0], resnet_data[:, 2], 'x--', label='1')
plt.plot(resnet_data[:, 1], resnet_data[:, 3], 'x--', label='2')
# plt.legend()
plt.subplot(2, 2, 4)
plt.title('ResNet Contact')
rmse_resnet_c = RMSE(env, resnet_c_data)
print('ResnetContact RMSE={:.3f}'.format(rmse_resnet_c))
plt.plot(resnet_c_data[:, 0], resnet_c_data[:, 2], 'x--', label='1')
plt.plot(resnet_c_data[:, 1], resnet_c_data[:, 3], 'x--', label='2')
# plt.legend()
plt.tight_layout()
if savefig:
plt.savefig(env.get_filename('trajectory'), bbox_inches="tight")
plt.show()
def compile(self):
#, training_dataset, validation_dataset): #compile(loss=criterion, optimizer=optimizer, metrics=metrics,
# loss_weights=loss_weights)
# self.optimizer = optimizer
self.is_compiled = True
self.other_args = other_args
self.batch_size = batch_size
# self.train_dataset = training_dataset
# self.val_dataset = validation_dataset
self.loss = nn.MSELoss()
self.optimizer = optimizer_dict[opt_type](self.parameters(), **other_args)
self.metrics = [MAE(), RMSE(), RMSLE(), NDEI(), R2_SCORE(), MAAPE()]
def test(test_data_loader, model):
scores = []
srocc = SROCC()
plcc = PLCC()
rmse = RMSE()
len_test = len(test_data_loader)
pb = ProgressBar(len_test-1, show_step=True)
print("Testing")
model.eval()
with torch.no_grad():
for i, ((img, ref), score) in enumerate(test_data_loader):
img, ref = img.cuda(), ref.cuda()
output = model(img, ref).cpu().data.numpy()
score = score.data.numpy()
srocc.update(score, output)
plcc.update(score, output)
rmse.update(score, output)
pb.show(i, 'Test: [{0:5d}/{1:5d}]\t'
'Score: {2:.4f}\t'
'Label: {3:.4f}'
.format(i, len_test, float(output), float(score)))
scores.append(output)
# Write scores to file
with open('../test/scores.txt', 'w') as f:
stat = list(map(lambda s: f.write(str(s)+'\n'), scores))
print('\n\nSROCC: {0:.4f}\n'
'PLCC: {1:.4f}\n'
'RMSE: {2:.4f}'
.format(srocc.compute(), plcc.compute(), rmse.compute())
)
def Cal_eval_index(epoch, out, val_target, arr, validation_losses,
validation_MAE, validation_RMSE, validation_MAPE, means,
stds):
# def Cal_eval_index(epoch, out, val_target, arr, validation_losses, validation_MAE, validation_RMSE, validation_MAPE, max_X, min_X):
for item in arr:
# out_index = out[:, :, item, :]
# val_target_index = val_target[:, :, item, :]
out_index = out #[:, :, item, :]
#val_target_index = val_target[:, :, item, :]
val_target_index = val_target
out_unnormalized = (out_index * stds + means) # [85,24,24]
target_unnormalized = (out_unnormalized * stds + means)
val_loss = loss_criterion(out_index,
target_unnormalized).to(device="cpu")
validation_losses.append(np.asscalar(val_loss.detach().numpy()))
# out_unnormalized = out_index.detach().cpu().numpy() * stds + means
# target_unnormalized = val_target_index.detach().cpu().numpy() * stds + means
# pd.DataFrame(i_start_pred).to_csv("./results_oneto_test120/{}_to_others_pred".format(i) + str(epoch) +".csv",index=None,header=None)
# pd.DataFrame(i_start_true).to_csv("./results_oneto_test120/{}_to_others_true".format(i) + str(epoch) +".csv",index=None,header=None)
# 按类分
out_unnormalized = (out_index.detach().cpu().numpy() * stds + means
) # [85,24,24]
target_unnormalized = (val_target_index.detach().cpu().numpy() * stds +
means)
if (epoch % 500 == 0) & (epoch != 0):
spatial_pre4 = []
spatial_true4 = []
pd.DataFrame(spatial_pre4).to_csv("" + str(epoch) + ".csv",
index=None,
header=None)
pd.DataFrame(spatial_true4).to_csv("" + str(epoch) + ".csv",
index=None,
header=None)
print()
mae = MAE(target_unnormalized, out_unnormalized)
validation_MAE.append(mae)
rmse = RMSE(target_unnormalized, out_unnormalized)
validation_RMSE.append(rmse)
mape = MAPE(target_unnormalized, out_unnormalized)
validation_MAPE.append(mape)
return validation_losses, validation_MAE, validation_RMSE, validation_MAPE
def train(self, train_data=None, vali_data=None):
train_loss_list = []
vali_rmse_list = []
last_vali_rmse = None
# monemtum
momuntum_u = np.zeros(self.U.shape)
momuntum_v = np.zeros(self.V.shape)
for it in range(self.iterations):
# derivate of Vi
grads_u = np.dot(self.I * (self.R - np.dot(self.U, self.V.T)),
-self.V) + self.lambda_alpha * self.U
# derivate of Tj
grads_v = np.dot((self.I * (self.R - np.dot(self.U, self.V.T))).T,
-self.U) + self.lambda_beta * self.V
# update the parameters
momuntum_u = (self.momuntum * momuntum_u) + self.lr * grads_u
momuntum_v = (self.momuntum * momuntum_v) + self.lr * grads_v
self.U = self.U - momuntum_u
self.V = self.V - momuntum_v
# training evaluation
train_loss = self.loss()
train_loss_list.append(train_loss)
vali_preds = self.predict(vali_data)
vali_rmse = RMSE(vali_data[:, 2], vali_preds)
vali_rmse_list.append(vali_rmse)
print('iteration:{: d} ,loss:{: f}, valid_rmse:{: f}'.format(
it, train_loss, vali_rmse))
if last_vali_rmse and (last_vali_rmse - vali_rmse) <= 0:
print('convergence at iterations:{: d}'.format(it))
break
else:
last_vali_rmse = vali_rmse
return self.U, self.V, train_loss_list, vali_rmse_list
def superlinear(Set, Label, ShowSet, ShowLabel):
from sklearn.linear_model import LinearRegression
pre = []
## model training
splitnum = len(Set) // 10
for i in range(10):
# make data sets
srange = np.arange(splitnum * i, splitnum * i + splitnum)
#testset=Set[srange, :]
#testlabel=Label[srange, :]
trainset = np.delete(Set, srange, axis=0)
trainlabel = np.delete(Label, srange, axis=0)
## build the model
lmodel = LinearRegression()
lmodel.fit(trainset, trainlabel)
pre.append(lmodel.predict(ShowSet))
pre = np.mean(np.array(pre), axis=0)
rmse = RMSE(ShowLabel, pre)
pe = PE(ShowLabel, pre)
lc = corrcal(ShowLabel, pre)
return rmse, pe, lc
print()
Numeric_model.numerical_solution(x=x_data,
y=y_data,
epochs=_epoch,
batch_size=_batch_size,
lr=_lr,
optim=optimizer)
print('Trained weight: \n', Numeric_model.W.reshape(-1))
print()
# model evaluation
inference = Numeric_model.eval(x_data)
# Error calculation
error = RMSE(inference, y_data)
print('RMSE on Train Data : %.4f \n' % error)
'''
You should get results as:
Initial weight:
[0. 0. 0. 0.]
Trained weight:
[ 22.15868831 -11.56430191 31.24868975 34.05022129]
RMSE on Train Data : 22.1719
'''
#======================================================================================================
print('prediction shape:', pre.shape)
# true value
pre += 8
# plot the results
fig = plt.figure(figsize=(20, 6.8))
# plt.subplots_adjust(left=None, bottom=None, right=None, top=None, wspace=0, hspace=0)
#fig.subplots_adjust(left=0, right=1, wspace=0, hspace=0)
plt.subplots_adjust(wspace=0, hspace=0.4)
res = []
oneyear = 344
for i in range(7):
fluxtrue = Label[i * oneyear:(i + 1) * oneyear].reshape(-1, 1)
prediction = pre[i, :].reshape(-1, 1)
PE1 = PE(fluxtrue, prediction)
RMSE1 = RMSE(fluxtrue, prediction)
linreg = LinearRegression()
line1 = linreg.fit(fluxtrue, prediction)
Cor1 = np.corrcoef(fluxtrue.reshape(-1), prediction.reshape(-1))[0, 1]
res.append([RMSE1, PE1, Cor1])
#### figure plot
fsize = 15
xx = np.arange(5.5, 10, 0.1)
# plot the flux
fig.add_subplot(2, 8, i + 1)
plt.plot(fluxtrue, 'b', linewidth=0.8)
#plt.plot(prediction, 'r', linewidth=0.8)
plt.xlim([0, 344])
plt.ylim([6, 10.5])
plt.xticks([])
def supermodel2(Set, Label, ShowSet, ShowLabel, config):
import time
T0 = time.time()
trloss, teloss, shloss, trainPE, testPE, showPE, trainCC, testCC, showCC, pre1, pre2, pre3 = \
[], [], [], [], [], [], [], [], [], [], [], []
seed = 1
## parameters of the network
num_in = 85
node1 = 25
node2 = 25
## parameters of training
batch_size = 200
epochs = 1500
learnrate = 0.01
reg2 = 0.001
Loss = 'L2'
f1 = 'selu'
f2 = 'sigmoid'
if hasattr(config, 'seed'):
seed = config.seed
if hasattr(config, 'num_in'):
num_in = config.num_in
if hasattr(config, 'node1'):
node1 = config.node1
if hasattr(config, 'node2'):
node2 = config.node2
if hasattr(config, 'batch_size'):
batch_size = config.batch_size
if hasattr(config, 'epochs'):
epochs = config.epochs
if hasattr(config, 'learnrate'):
learnrate = config.learnrate
if hasattr(config, 'reg2'):
reg2 = config.reg2
if hasattr(config, 'Loss'):
Loss = config.Loss
if hasattr(config, 'fun1'):
f1 = config.fun1
if hasattr(config, 'fun2'):
f2 = config.fun2
## model training (10 cross validation)
splitnum = len(Set) // 10
NN = Set.shape[1]
for i in range(10):
# make data sets
srange = np.arange(splitnum * i, splitnum * i + splitnum)
testset = Set[srange, :]
testlabel = Label[srange, :]
trainset = np.delete(Set, srange, axis=0)
trainlabel = np.delete(Label, srange, axis=0)
# training set shuffle
data2 = np.hstack((trainset, trainlabel))
np.random.seed(2020) # This year is 2020
np.random.shuffle(data2)
trainset = data2[:, 0:-1]
trainlabel = data2[:, -1].reshape(-1, 1)
## build model
x = tf.placeholder(tf.float32, [None, num_in])
y0 = tf.placeholder(tf.float32, [None, 1])
y1, totalloss, loss = create_model2( \
x, y0, num_in, reg2=reg2, node1=node1, node2=node2, \
seed=seed, Loss=Loss, f1=f1, f2=f2)
# Adam optimizer
learningrate_base = learnrate
learningrate_decay = 0.999
global_step = tf.Variable(0, trainable=False)
learning_rate = tf.train.exponential_decay(learningrate_base,
global_step,
epochs // batch_size,
learningrate_decay,
staircase=False)
trainstep = tf.train.AdamOptimizer(learning_rate).minimize(
totalloss, global_step=global_step)
# training
with tf.Session() as sess:
init_op = tf.global_variables_initializer()
sess.run(init_op)
X = trainset
Y = trainlabel
for ii in range(epochs):
start = (ii * batch_size) % len(trainlabel)
end = start + batch_size
sess.run(trainstep,
feed_dict={
x: X[start:end],
y0: Y[start:end]
})
# if ii%200==0:
# print('Loss:', sess.run(loss, feed_dict={x: X[start:end], y0: Y[start:end]}))
# print('Total Loss:', sess.run(totalloss, feed_dict={x: X[start:end], y0: Y[start:end]}))
trainloss = sess.run(loss, feed_dict={x: X, y0: Y})
print('##-------------------#', i)
print('total_loss1:', trainloss)
### evaluation of the results
prediction1 = sess.run(y1, feed_dict={x: trainset})
prediction2 = sess.run(y1, feed_dict={x: testset})
prediction3 = sess.run(y1, feed_dict={x: ShowSet})
pre2.append(prediction2.reshape(-1))
pre3.append(prediction3.reshape(-1))
# true value of trainlabel and prediction1
trainlabel += 8
prediction1 += 8
trloss.append(RMSE(trainlabel, prediction1))
trainPE.append(PE(trainlabel, prediction1))
trainCC.append(corrcal(trainlabel, prediction1))
prediction2 = np.array(pre2).reshape(-1)
prediction3 = np.mean(np.array(pre3), axis=0)
# true value of prediction2 and prediction3, Label and ShowLabel
prediction2 += 8
prediction3 += 8
Label += 8
ShowLabel += 8
trloss = np.mean(np.array(trloss))
trainPE = np.mean(np.array(trainPE))
trainCC = np.mean(np.array(trainCC))
# calculate teloss, shloss, testPE, showPE
## attention, due to "//10", the datasize may not be consistent
prediction2_num = len(prediction2)
teloss = RMSE(Label.reshape(-1)[0:prediction2_num], prediction2)
testPE = PE(Label.reshape(-1)[0:prediction2_num], prediction2)
testCC = corrcal(Label.reshape(-1)[0:prediction2_num], prediction2)
shloss = RMSE(ShowLabel.reshape(-1), prediction3)
showPE = PE(ShowLabel.reshape(-1), prediction3)
showCC = corrcal(ShowLabel.reshape(-1), prediction3)
TT = time.time()
print('Time', TT - T0)
print(
'>>>>>>>>>>\n>>>>>>>>>>>>>>>>>>>>>>>>\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>'
)
return trloss, teloss, shloss, trainPE, testPE, showPE, trainCC, testCC, showCC, TT - T0
lr=space,
optim=optim)
else:
model.numerical_solution(x=x_train_data,
y=y_train_data,
epochs=_epoch,
batch_size=space,
lr=_lr,
optim=optim)
################### Evaluate on train data
# Inference
inference = model.eval(x_train_data)
# Assess model
error = RMSE(inference, y_train_data)
print('[Search %d] RMSE on Train Data : %.4f' % (i + 1, error))
train_results.append(error)
################### Evaluate on test data
# Inference
inference = model.eval(x_test_data)
# Assess model
error = RMSE(inference, y_test_data)
print('[Search %d] RMSE on test data : %.4f' % (i + 1, error))
test_results.append(error)
# ========================= EDIT HERE ========================
def plot_trajectory(savefig=False):
plt.figure(figsize=(12,8))
plt.title('Phase Space'); plt.xlabel('q'); plt.ylabel('p')
plt.plot(cdl_data[:, 0], cdl_data[:, 1], 'x--', label='CD-Lagrange, RMSE: {:.3f}'.format(RMSE(env, cdl_data)))
plt.plot(resnet_data[:, 0], resnet_data[:, 1], 'x--', label='ResNet, RMSE: {:.3f}'.format(RMSE(env, resnet_data)))
plt.plot(env.trajectory[:, 0], env.trajectory[:, 1], 'xk', label='Ground truth')
plt.legend()
if savefig:
plt.savefig(env.get_filename('trajectory'))
plt.show()
imp_mean = IterativeImputer(random_state=0, max_iter=50)
data_nas = copy.deepcopy(ground_truth)
data_nas[data["mask"][-1] == 1] = np.nan
imp_mean.fit(data_nas)
sk_imp = torch.tensor(imp_mean.transform(data_nas))
mean_imp = (1 - mask) * X_true + mask * mean_impute(X_true, mask)
mean_sk, cov_sk = moments(sk_imp[M])
mean_mean, cov_mean = moments(mean_imp[M])
data["imp"]["scikit"].append(sk_imp.cpu().numpy())
data["imp"]["mean"].append(mean_imp.cpu().numpy())
scikit_scores['MAE'].append(MAE(sk_imp, X_true, mask).cpu().numpy())
scikit_scores['RMSE'].append(RMSE(sk_imp, X_true, mask).cpu().numpy())
scikit_scores['bures'].append([
((mean_sk - mean_truth)**2).sum().item(),
ns_bures(cov_sk, cov_truth).item()
])
if nimp < OTLIM:
scikit_scores['OT'].append(ot.emd2(np.ones(nimp) / nimp, np.ones(nimp) / nimp, \
((sk_imp[M][:, None] - X_true[M])**2).sum(2).cpu().numpy()) / 2.)
logging.info(
f'scikit imputation : MAE = {scikit_scores["MAE"][-1]}, OT = {scikit_scores["OT"][-1]}'
)
else:
logging.info(
f'scikit imputation : MAE = {scikit_scores["MAE"][-1]}')
mean_scores['MAE'].append(MAE(mean_imp, X_true, mask).cpu().numpy())
out_img[i,j] = 255
else:
out_img[i,j] = 0
return out_img.astype(np.uint8)
if __name__=="__main__":
input_img_name = sys.argv[1]
dither_size = np.int(sys.argv[2])
output_img_name = get_base(input_img_name)+ '_dither'+str(dither_size)
gamma=2.2
print(output_img_name)
im = Image.open(input_img_name)
input_img = np.array(im)
out_img= main(input_img, dither_size, gamma)
#compute rmse
rmse = RMSE(input_img, out_img)
fidelity = Fidelity(input_img, out_img)
#print info
print("RMSE:%0.3f \t Fidelity:%0.3f"%(rmse, fidelity))
#save plots and images
gray = cm.get_cmap('gray',256)
plt.figure(frameon=False)
plt.imshow(out_img, cmap=gray, interpolation='none')
plt.axis('off')
plt.savefig(output_img_name+'.pdf', bbox_inches='tight', pad_inches=0)
out_im = Image.fromarray(out_img)
out_im.save(output_img_name+'.tif')
def run(data_path,
out_path,
training_dataset,
n_targets,
testing_datasets,
regressor,
out_log,
sst_method='predictions',
sst_n_part=None,
seed=2018):
print('Regressor: {}'.format(regressor))
training_name = os.path.join(data_path, '{}.csv'.format(training_dataset))
training_data = pd.read_csv(training_name)
training_data = training_data.values
X_train, Y_train = training_data[:, :-n_targets], \
training_data[:, -n_targets:]
scaler = preprocessing.StandardScaler().fit(X_train)
X_train = scaler.transform(X_train)
regr, params = get_regressor(regressor, seed=seed)
sst = StackedSingleTarget(regressor=regr,
regressor_params=params,
method=sst_method,
n_part=sst_n_part)
sst.fit(X_train, Y_train)
print('SST-{} done'.format(sst_method))
for pos, d in enumerate(testing_datasets):
regr, params = get_regressor(regressor, seed=seed)
st = regr(**params)
st.fit(X_train, Y_train[:, pos])
print('ST done')
testing_name = os.path.join(data_path, '{}.csv'.format(d))
testing_data = pd.read_csv(testing_name)
testing_data = testing_data.values
X_test, y_test = testing_data[:, :-1], testing_data[:, -1:]
X_test = scaler.transform(X_test)
y_test = y_test[:, 0]
st_predictions = st.predict(X_test)
sst_predictions = sst.predict(X_test)
out_log.loc[pos, 'st_rmse'] = \
RMSE(y_test, st_predictions)
out_log.loc[pos, 'st_rrmse'] = \
RRMSE(y_test, st_predictions)
out_log.loc[pos, 'sst_rmse'] = \
RMSE(y_test, sst_predictions[:, pos])
out_log.loc[pos, 'sst_rrmse'] = \
RRMSE(y_test, sst_predictions[:, pos])
if sst_method == 'predictions':
log_name = 'results_sst_train_test_TgTliq_{}_predictions.csv'.\
format(regressor)
elif sst_method == 'internal_cv':
log_name = 'results_sst_train_test_TgTliq_{}_internal_cv_{}.csv'.\
format(regressor, sst_n_part)
elif sst_method == 'targets_values':
log_name = 'results_sst_train_test_TgTliq_{}_targets_values.csv'.\
format(regressor)
out_log.to_csv(os.path.join(out_path, log_name), index=False)
def get_acc_rmse(gt, pred):
acc = accuracy(gt, pred)
rmse = RMSE(gt, pred)
return acc, rmse
def fit_transform(self, X, verbose=True, report_interval=500, X_true=None):
"""
Imputes missing values using a batched OT loss
Parameters
----------
X : torch.DoubleTensor or torch.cuda.DoubleTensor
Contains non-missing and missing data at the indices given by the
"mask" argument. Missing values can be arbitrarily assigned
(e.g. with NaNs).
mask : torch.DoubleTensor or torch.cuda.DoubleTensor
mask[i,j] == 1 if X[i,j] is missing, else mask[i,j] == 0.
verbose: bool, default=True
If True, output loss to log during iterations.
X_true: torch.DoubleTensor or None, default=None
Ground truth for the missing values. If provided, will output a
validation score during training, and return score arrays.
For validation/debugging only.
Returns
-------
X_filled: torch.DoubleTensor or torch.cuda.DoubleTensor
Imputed missing data (plus unchanged non-missing data).
"""
X = X.clone()
n, d = X.shape
if self.batchsize > n // 2:
e = int(np.log2(n // 2))
self.batchsize = 2**e
if verbose:
logging.info(
f"Batchsize larger that half size = {len(X) // 2}. Setting batchsize to {self.batchsize}."
)
mask = torch.isnan(X).double()
imps = (self.noise * torch.randn(mask.shape).double() +
nanmean(X, 0))[mask.bool()]
imps.requires_grad = True
optimizer = self.opt([imps], lr=self.lr)
if verbose:
logging.info(
f"batchsize = {self.batchsize}, epsilon = {self.eps:.4f}")
if X_true is not None:
maes = np.zeros(self.niter)
rmses = np.zeros(self.niter)
for i in range(self.niter):
X_filled = X.detach().clone()
X_filled[mask.bool()] = imps
loss = 0
for _ in range(self.n_pairs):
idx1 = np.random.choice(n, self.batchsize, replace=False)
idx2 = np.random.choice(n, self.batchsize, replace=False)
X1 = X_filled[idx1]
X2 = X_filled[idx2]
loss = loss + self.sk(X1, X2)
if torch.isnan(loss).any() or torch.isinf(loss).any():
### Catch numerical errors/overflows (should not happen)
logging.info("Nan or inf loss")
break
optimizer.zero_grad()
loss.backward()
optimizer.step()
if X_true is not None:
maes[i] = MAE(X_filled, X_true, mask).item()
rmses[i] = RMSE(X_filled, X_true, mask).item()
if verbose and (i % report_interval == 0):
if X_true is not None:
logging.info(
f'Iteration {i}:\t Loss: {loss.item() / self.n_pairs:.4f}\t '
f'Validation MAE: {maes[i]:.4f}\t'
f'RMSE: {rmses[i]:.4f}')
else:
logging.info(
f'Iteration {i}:\t Loss: {loss.item() / self.n_pairs:.4f}'
)
X_filled = X.detach().clone()
X_filled[mask.bool()] = imps
if X_true is not None:
return X_filled, maes, rmses
else:
return X_filled
def run(dconf, tconf):
np.random.seed(seed)
torch.manual_seed(seed)
torch.backends.cudnn.deterministic = True
torch.backends.cudnn.benchmark = False
ds_factory = DatasetFactory(dconf)
train_ds = ds_factory.get_train_dataset()
test_ds = ds_factory.get_test_dataset()
train_loader = DataLoader(
dataset=train_ds,
batch_size=tconf.batch_size,
shuffle=True,
num_workers=1
)
test_loader = DataLoader(
dataset=test_ds,
batch_size=tconf.batch_size,
shuffle=False,
num_workers=1
)
model = Model(dconf)
if tconf.pretrained is not None:
print('load pretrained model...')
try:
model.load_state_dict(torch.load(tconf.pretrained))
except Exception as e:
model = torch.load(tconf.pretrained)
else:
model.apply(weights_init)
model = model.cuda()
criterion = nn.MSELoss().cuda()
optimizer = optim.Adam(model.parameters(), lr=tconf.learning_rate)
log_dir = log_name+str(dconf.len_close)+str(dconf.len_period)+str(dconf.len_trend)+'/'
writer = SummaryWriter(log_dir)
confs = {
'Data Config': dconf,
'Train Config': tconf,
'Model Config': model.mconf
}
save_confs(log_dir+'confs', confs)
step = 0
for epoch in range(tconf.max_epoch):
if epoch in tconf.milestones:
print('Set lr=',tconf.milestones[epoch])
for param_group in optimizer.param_groups:
param_group["lr"] = tconf.milestones[epoch]
model.train()
for i, (X, X_ext, Y, Y_ext) in enumerate(train_loader, 0):
X = X.cuda()
X_ext = X_ext.cuda()
Y = Y.cuda()
Y_ext = Y_ext.cuda()
optimizer.zero_grad()
h = model(X, X_ext, Y_ext)
loss = criterion(h, Y)
loss.backward()
nn.utils.clip_grad_norm_(model.parameters(), tconf.grad_threshold)
optimizer.step()
if step % 10 == 0:
rmse = RMSE(h, Y, ds_factory.ds.mmn, ds_factory.dataset.m_factor)
print("[epoch %d][%d/%d] mse: %.4f rmse: %.4f" % (epoch, i+1, len(train_loader), loss.item(), rmse.item()))
writer.add_scalar('mse', loss.item(), step)
writer.add_scalar('rmse', rmse.item(), step)
step += 1
model.eval()
mse = 0.0
mae = 0.0
with torch.no_grad():
for i, (X, X_ext, Y, Y_ext) in enumerate(test_loader, 0):
X = X.cuda()
X_ext = X_ext.cuda()
Y = Y.cuda()
Y_ext = Y_ext.cuda()
h = model(X, X_ext, Y_ext)
loss = criterion(h, Y)
mse += X.size()[0] * loss.item()
mae += X.size()[0] * torch.mean(torch.abs(Y - h)).item()
mse /= ds_factory.ds.X_test.shape[0]
rmse = math.sqrt(mse) * (ds_factory.ds.mmn.max - ds_factory.ds.mmn.min) / 2. * ds_factory.dataset.m_factor
print("[epoch %d] test_rmse: %.4f\n" % (epoch, rmse))
writer.add_scalar('test_rmse', rmse, epoch)
torch.save(model.state_dict(), log_dir+'{}.model'.format(epoch))
train_data = data[:int(ratio * data.shape[0])]
vali_data = data[int(ratio * data.shape[0]):int((ratio + (1 - ratio) / 2) *
data.shape[0])]
test_data = data[int((ratio + (1 - ratio) / 2) * data.shape[0]):]
# complete rating matrix
rows = max(dict_userid_to_index.values()) + 1
columns = max(dict_itemid_to_index.values()) + 1
R = np.zeros((rows, columns))
for tuple in train_data:
R[int(tuple[0]), int(tuple[1])] = float(tuple[2])
# model
model = PMF(R=R,
lambda_alpha=lambda_alpha,
lambda_beta=lambda_beta,
latent_size=latent_size,
momuntum=0.9,
lr=lr,
iters=iters,
seed=1)
U, V, train_loss_list, vali_rmse_list = model.train(train_data=train_data,
vali_data=vali_data)
preds = model.predict(data=test_data)
test_rmse = RMSE(preds, test_data[:, 2])
print('test rmse:{}'.format(test_rmse))
def run(data_path, out_path, datasets, regressor, n_parts=10,
sst_method='predictions', sst_n_part=None, seed=2018):
idx_column = ['fold_{:02d}'.format(k + 1) for k in range(n_parts)]
idx_column.append('mean')
for d, nt in datasets.items():
print(d)
dataset_file = os.path.join(data_path, '{}.csv'.format(d))
data = pd.read_csv(dataset_file)
target_names = list(data)[-nt:]
# Transform data in numpy.ndarray
data = data.values
log_columns = ['armse', 'arrmse']
log_columns.extend(['rmse_{}'.format(tn) for tn in target_names])
log_columns.extend(['rrmse_{}'.format(tn) for tn in target_names])
out_log = pd.DataFrame(
np.zeros((n_parts + 1, 2 * nt + 2)),
columns=log_columns
)
kf = KFold(n_splits=n_parts, shuffle=True, random_state=seed)
for k, (train_index, test_index) in enumerate(kf.split(data)):
print('Fold {:02d}'.format(k + 1))
X_train, X_test = data[train_index, :-nt], data[test_index, :-nt]
Y_train, Y_test = data[train_index, -nt:], data[test_index, -nt:]
scaler = preprocessing.StandardScaler().fit(X_train)
X_train = scaler.transform(X_train)
X_test = scaler.transform(X_test)
regr, params = get_regressor(regressor, seed=seed)
sst = StackedSingleTarget(
regressor=regr,
regressor_params=params,
method=sst_method,
n_part=sst_n_part
)
sst.fit(X_train, Y_train)
predictions = sst.predict(X_test)
for t in range(nt):
out_log.loc[k, 'rrmse_{}'.format(target_names[t])] = \
RRMSE(Y_test[:, t], predictions[:, t])
out_log.loc[k, 'rmse_{}'.format(target_names[t])] = \
RMSE(Y_test[:, t], predictions[:, t])
out_log.loc[k, 'arrmse'] = aRRMSE(Y_test, predictions)
out_log.loc[k, 'armse'] = aRMSE(Y_test, predictions)
for c in range(2*nt + 2):
out_log.iloc[-1:, c] = np.mean(out_log.iloc[:-1, c])
out_log.insert(0, 'partition', idx_column)
if sst_method == 'predictions':
log_name = 'results_sst_{}_{}_predictions.csv'.format(d, regressor)
elif sst_method == 'internal_cv':
log_name = 'results_sst_{}_{}_internal_cv_{}.csv'.\
format(d, regressor, sst_n_part)
elif sst_method == 'targets_values':
log_name = 'results_sst_{}_{}_targets_values.csv'.\
format(d, regressor)
out_log.to_csv(os.path.join(out_path, log_name), index=False)
def fit_transform(self, X, verbose=True, report_interval=1, X_true=None):
"""
Fits the imputer on a dataset with missing data, and returns the
imputations.
Parameters
----------
X : torch.DoubleTensor or torch.cuda.DoubleTensor, shape (n, d)
Contains non-missing and missing data at the indices given by the
"mask" argument. Missing values can be arbitrarily assigned
(e.g. with NaNs).
mask : torch.DoubleTensor or torch.cuda.DoubleTensor, shape (n, d)
mask[i,j] == 1 if X[i,j] is missing, else mask[i,j] == 0.
verbose : bool, default=True
If True, output loss to log during iterations.
report_interval : int, default=1
Interval between loss reports (if verbose).
X_true: torch.DoubleTensor or None, default=None
Ground truth for the missing values. If provided, will output a
validation score during training. For debugging only.
Returns
-------
X_filled: torch.DoubleTensor or torch.cuda.DoubleTensor
Imputed missing data (plus unchanged non-missing data).
"""
X = X.clone()
n, d = X.shape
mask = torch.isnan(X).double()
normalized_tol = self.tol * torch.max(torch.abs(X[~mask.bool()]))
if self.batchsize > n // 2:
e = int(np.log2(n // 2))
self.batchsize = 2**e
if verbose:
logging.info(
f"Batchsize larger that half size = {len(X) // 2}."
f" Setting batchsize to {self.batchsize}.")
order_ = torch.argsort(mask.sum(0))
optimizers = [
self.opt(self.models[i].parameters(),
lr=self.lr,
weight_decay=self.weight_decay) for i in range(d)
]
imps = (self.noise * torch.randn(mask.shape).double() +
nanmean(X, 0))[mask.bool()]
X[mask.bool()] = imps
X_filled = X.clone()
if X_true is not None:
maes = np.zeros(self.max_iter)
rmses = np.zeros(self.max_iter)
for i in range(self.max_iter):
if self.order == 'random':
order_ = np.random.choice(d, d, replace=False)
X_old = X_filled.clone().detach()
loss = 0
for l in range(d):
j = order_[l].item()
n_not_miss = (~mask[:, j].bool()).sum().item()
if n - n_not_miss == 0:
continue # no missing value on that coordinate
for k in range(self.niter):
loss = 0
X_filled = X_filled.detach()
X_filled[mask[:, j].bool(), j] = self.models[j](
X_filled[mask[:,
j].bool(), :][:,
np.r_[0:j,
j + 1:d]]).squeeze()
for _ in range(self.n_pairs):
idx1 = np.random.choice(n,
self.batchsize,
replace=False)
X1 = X_filled[idx1]
if self.unsymmetrize:
n_miss = (~mask[:, j].bool()).sum().item()
idx2 = np.random.choice(
n_miss,
self.batchsize,
replace=self.batchsize > n_miss)
X2 = X_filled[~mask[:, j].bool(), :][idx2]
else:
idx2 = np.random.choice(n,
self.batchsize,
replace=False)
X2 = X_filled[idx2]
loss = loss + self.sk(X1, X2)
optimizers[j].zero_grad()
loss.backward()
optimizers[j].step()
# Impute with last parameters
with torch.no_grad():
X_filled[mask[:, j].bool(), j] = self.models[j](
X_filled[mask[:,
j].bool(), :][:,
np.r_[0:j,
j + 1:d]]).squeeze()
if X_true is not None:
maes[i] = MAE(X_filled, X_true, mask).item()
rmses[i] = RMSE(X_filled, X_true, mask).item()
if verbose and (i % report_interval == 0):
if X_true is not None:
logging.info(
f'Iteration {i}:\t Loss: {loss.item() / self.n_pairs:.4f}\t'
f'Validation MAE: {maes[i]:.4f}\t'
f'RMSE: {rmses[i]: .4f}')
else:
logging.info(
f'Iteration {i}:\t Loss: {loss.item() / self.n_pairs:.4f}'
)
if torch.norm(X_filled - X_old, p=np.inf) < normalized_tol:
break
if i == (self.max_iter - 1) and verbose:
logging.info('Early stopping criterion not reached')
self.is_fitted = True
if X_true is not None:
return X_filled, maes, rmses
else:
return X_filled
