def simulate1(T, trial, mu0, mu1, std0, std1):
rct_res = []
adpt0_res = []
adpt1_res = []
opt0_res = []
opt1_res = []
for t in range(trial):
rct = RCT()
adpt0 = Adapt(pretraining=10)
adpt1 = Adapt(pretraining=50)
opt0 = OPT()
opt1 = OPT()
rct_temp = []
adpt0_temp = []
adpt1_temp = []
opt0_temp = []
opt1_temp = []
for period_t in range(T):
X, Y0, Y1, EY0_2, EY1_2, Var0, Var1 = sampler(mu0, mu1, std0, std1)
rct(period_t, X, Y0, Y1)
adpt0(period_t, X, Y0, Y1)
adpt1(period_t, X, Y0, Y1)
opt0(period_t, X, Y0, Y1, EY0_2, EY1_2)
opt1(period_t, X, Y0, Y1, Var0, Var1)
if period_t > 2:
rct_temp.append(rct.effect())
adpt0_temp.append(adpt0.effect())
adpt1_temp.append(adpt1.effect())
opt0_temp.append(opt0.effect())
opt1_temp.append(opt1.effect(estimate=True))
rct_res.append(rct_temp)
adpt0_res.append(adpt0_temp)
adpt1_res.append(adpt1_temp)
opt0_res.append(opt0_temp)
opt1_res.append(opt1_temp)
return rct_res, adpt0_res, adpt1_res, opt0_res, opt1_res
T.Normalize(mean = base_model.rgb_mean, std = base_model.rgb_std),
T.Lambda(lambda x: x[[2, 1, 0], ...])
])
dataset_train = opts.dataset(opts.data, train = True, transform = transforms.Compose([
T.RandomSizedCrop(base_model.input_side),
T.RandomHorizontalFlip(),
normalize
]), download = True)
dataset_eval = opts.dataset(opts.data, train = False, transform = transforms.Compose([
T.Scale(256),
T.CenterCrop(base_model.input_side),
normalize
]), download = True)
adapt_sampler = lambda batch, dataset, sampler, **kwargs: type('', (torch.utils.data.Sampler, ), dict(__len__ = dataset.__len__, __iter__ = lambda _: itertools.chain.from_iterable(sampler(batch, dataset, **kwargs))))()
loader_train = torch.utils.data.DataLoader(dataset_train, sampler = adapt_sampler(opts.batch, dataset_train, opts.sampler), num_workers = opts.threads, batch_size = opts.batch, drop_last = True, pin_memory = True)
loader_eval = torch.utils.data.DataLoader(dataset_eval, shuffle = False, num_workers = opts.threads, batch_size = opts.batch, pin_memory = True)
model = opts.model(base_model, dataset_train.num_training_classes).cuda()
model_weights, model_biases, base_model_weights, base_model_biases = [[p for k, p in model.named_parameters() if p.requires_grad and ('bias' in k) == is_bias and ('base' in k) == is_base] for is_base in [False, True] for is_bias in [False, True]]
base_model_lr_mult = model.optimizer_params.pop('base_model_lr_mult', 1.0)
optimizer = model.optimizer([dict(params = base_model_weights, lr = base_model_lr_mult * model.optimizer_params['lr']), dict(params = base_model_biases, lr = base_model_lr_mult * model.optimizer_params['lr'], weight_decay = 0.0), dict(params = model_biases, weight_decay = 0.0)], **model.optimizer_params)
scheduler = torch.optim.lr_scheduler.StepLR(optimizer, **model.lr_scheduler_params)
log = open(opts.log, 'w', 0)
for epoch in range(opts.epochs):
scheduler.step()
model.train()
loss_all, norm_all = [], []
def getdist(question):
""" function getdist(question): calls function sampler with various parameters, then outputs plots and prints acceptance rates and other values of interest. Accepts inputs 'b' 'c' or 'd' """
if question == 'b':
# PART B
# Define inputs
ff = '(1.0/2.0)*np.exp(-abs(x))' # Laplace(0,1)
gg = stats.cauchy
n = 1000
# Call sampler
m, samples, ratio = sampler(ff,gg,n)
# Create distributions and perform K-S test
grid = np.linspace(-10,10,num=1000)
actual = []
cc = []
for x in grid:
actual.append(eval(ff))
cc.append(stats.cauchy.pdf(x))
ks = stats.kstest(samples,'laplace')
# Print and plot relevant information
print 'calculated M value: ',m
print 'acceptance rate: ',int(ratio*100),'%'
print 'K-S test finds a ',int(ks[1]*100),'% chance that these points were sampled from a Laplace(0,1) distribution'
plt.hist(samples,50,normed=True,label='samples')
plt.plot(grid,actual,linewidth=3,color='red',linestyle='--',label='f(x)')
plt.plot(grid,[m*cci for cci in cc],color='green',label='Mg(x)')
plt.title('Histogram of Samples, with Laplace(0,1) Distribution')
plt.legend()
plt.show()
if question == 'c':
# PART C
# Define inputs
ff = '(1.0/2.0)*np.exp(-abs(x))'
gg = stats.t(2)
n = 1000
# Call sampler
m, samples, ratio = sampler(ff,gg,n)
mb, samplesb, ratiob = sampler(ff,stats.cauchy,n)
# Create distributions
grid = np.linspace(-10,10,num=1000)
actual=[]
st=[]
for x in grid:
actual.append(eval(ff))
st.append(stats.t.pdf(x,2))
# Print and plot relevant information
print 'calculated M value: ',m
print 'acceptance rate: ',int(ratio*100),'%'
print 'compare to acceptance rate of ',int(ratiob*100),'% from part b'
plt.hist(samples,50,normed=True,label='samples')
plt.plot(grid,actual,linewidth=3,color='red',linestyle='--',label='f(x)')
plt.plot(grid,[m*sti for sti in st],color='green',label='Mg(x)')
plt.title('Histogram of Samples, with Laplace(0,1) Distribution')
plt.legend()
plt.show()
if question == 'd':
# PART D
# Define inputs
ff = 'np.sqrt(2/np.pi)*x**2*np.exp(-x**2/2)'
gg = stats.truncnorm(-math.pi/2,10,loc=math.pi/2)
n = 5000
# Call sampler
m, samples, ratio = sampler(ff,gg,n)
# Create distributions
grid = np.linspace(0,10,num=1000)
actual=[]
nm=[]
for x in np.linspace(0,10,num=1000):
actual.append(eval(ff))
nm.append(stats.truncnorm.pdf(x,-math.pi/2,10,loc=math.pi/2))
ks = stats.kstest(samples,'maxwell')
# Print and plot relevant information
print 'calculated M value: ',m
print 'acceptance rate: ',int(ratio*100),'%'
print 'K-S test finds a ',int(ks[1]*100),'% chance that these points were sampled from a Maxwell distribution'
plt.hist(samples,50,normed=True,label='samples')
plt.plot(grid,[m*nmi for nmi in nm],color='blue',label='Mg(x)')
plt.plot(grid,actual,linewidth=3,color='red',linestyle='--',label='f(x)')
plt.title('Histogram of Samples, with Maxwell Distribution')
plt.legend()
plt.show()
def register(self,
image,
template,
tform,
sampler=sampler.bilinear,
method=metric.forwardsAdditive,
p=None,
alpha=None,
verbose=False
):
"""
Computes the registration between the image and template.
Parameters
----------
image: nd-array
The floating image.
template: nd-array
The target image.
tform: deformation (class)
The deformation model (shift, affine, projective)
method: collection, optional.
The registration method (defaults to FrowardsAdditive)
p: list (or nd-array), optional.
First guess at fitting parameters.
alpha: float
The dampening factor.
verbose: boolean
A debug flag for text status updates.
Returns
-------
step: optimization step.
The best optimization step (after convergence).
search: list (of optimization steps)
The set of optimization steps (good and bad)
"""
p = tform.identity if p is None else p
deltaP = np.zeros_like(p)
# Dampening factor.
alpha = alpha if alpha is not None else 1e-4
# Variables used to implement a back-tracking algorithm.
search = []
badSteps = 0
bestStep = None
for itteration in range(0, self.MAX_ITER):
# Compute the transformed coordinates.
coords = tform(p, template.coords)
# Sample to the template frame using the transformed coordinates.
warpedImage = sampler(image.data, coords.tensor)
# Evaluate the error metric.
e = method.error(warpedImage, template.data)
# Cache the optimization step.
searchStep = optStep(
error=np.abs(e).sum() / np.prod(image.data.shape),
p=p.copy(),
deltaP=deltaP.copy(),
decreasing=True
)
# Update the current best step.
bestStep = searchStep if bestStep is None else bestStep
if verbose:
log.warn(
REGISTRATION_STEP.format(
itteration,
' '.join('{0:3.2f}'.format(param) for param in searchStep.p),
searchStep.error
)
)
# Append the search step to the search.
search.append(searchStep)
if len(search) > 1:
searchStep.decreasing = (searchStep.error < bestStep.error)
alpha = self.__dampening(alpha, searchStep.decreasing)
if searchStep.decreasing:
bestStep = searchStep
else:
badSteps += 1
if badSteps > self.MAX_BAD:
if verbose:
log.warn(REGISTRATION_STOP)
break
# Restore the parameters from the previous best iteration.
p = bestStep.p.copy()
# Computes the derivative of the error with respect to model
# parameters.
J = method.jacobian(warpedImage, template, tform, p)
# Compute the parameter update vector.
deltaP = self.__deltaP(J, e, alpha, p)
# Evaluate stopping condition:
if np.dot(deltaP.T, deltaP) < 1e-4:
break
# Update the estimated parameters.
p = method.update(p, deltaP, tform)
return bestStep, search