def __init__(self, prior_weights=[1.,0,0], name='constant1'):
self.labelset = np.asarray(config.labelset)
self.model_name = name
self.force_recompute_prior = False
self.params = {
'beta' : 50, # contrast parameter
'return_arguments' :['image','y'],
# optimization parameter
'per_label': True,
'optim_solver':'unconstrained',
'rtol' : 1e-6,
'maxiter' : 2e3,
}
laplacian_type = 'std_b50'
logger.info('laplacian type is: {}'.format(laplacian_type))
self.weight_functions = {
'std_b10' : lambda im: wflib.weight_std(im, beta=10),
'std_b50' : lambda im: wflib.weight_std(im, beta=50),
'std_b100' : lambda im: wflib.weight_std(im, beta=100),
'inv_b100o1' : lambda im: wflib.weight_inv(im, beta=100, offset=1),
'pdiff_r1b10': lambda im: wflib.weight_patch_diff(im, r0=1, beta=10),
'pdiff_r2b10': lambda im: wflib.weight_patch_diff(im, r0=2, beta=10),
'pdiff_r1b50' : lambda im: wflib.weight_patch_diff(im, r0=1, beta=50),
}
self.weight_function = self.weight_functions[laplacian_type]
self.prior_models = [
prior_models.Constant,
prior_models.Entropy_no_D,
prior_models.Intensity,
prior_models.Variance_no_D,
prior_models.Variance_no_D_Cmap,
]
self.prior_weights = prior_weights
logger.info('Model name = {}, using prior weights={}'\
.format(self.model_name, self.prior_weights))
def __init__(self,
use_parallel=True,
**kwargs
):
## paths
self.dir_reg = config.dir_reg
self.dir_inf = config.dir_inf
self.dir_svm = config.dir_svm
self.training_vols = config.vols
## params
self.force_recompute_prior = False
self.use_parallel = use_parallel
self.labelset = np.asarray(config.labelset)
C = kwargs.pop('C',1.0)
Cprime = kwargs.pop('Cprime',0.0)
self.scale_only = kwargs.pop('scale_only', False)
self.loss_type = kwargs.pop('loss_type', 'squareddiff')
self.loss_factor = kwargs.pop('loss_factor', 1.)
self.use_latent = kwargs.pop('use_latent', False)
self.approx_aci = kwargs.pop('approx_aci', False)
self.debug = kwargs.pop('debug', False)
self.retrain = kwargs.pop('retrain', True)
self.minimal_svm = kwargs.pop('minimal', False)
self.one_iteration = kwargs.pop('one_iteration', False)
self.start_script = kwargs.pop('start_script', '')
self.use_mosek = kwargs.pop('use_mosek',True)
#switch_loss = kwargs.pop('switch_loss', False)
crop = kwargs.pop('crop','none')
if crop=='none':
self.crop = False
else:
self.crop = True
ncrop = int(crop)
self.slice_size = ncrop
self.slice_step = ncrop
ntrain = kwargs.pop('ntrain', 'all')
if ntrain.isdigit():
n = int(ntrain)
self.select_vol = slice(n,n+1)
else:
self.select_vol = slice(None)
## parameters for rw learning
self.rwparams_svm = {
'labelset':self.labelset,
# optimization
'rtol': 1e-6,
'maxiter': 1e3,
'per_label':True,
'optim_solver':'unconstrained',
# contrained optim
'use_mosek': self.use_mosek,
'logbarrier_mu': 10,
'logbarrier_initial_t': 10,
'logbarrier_modified': False,
'logbarrier_maxiter': 10,
'newton_maxiter': 50,
}
## parameters for svm api
self.svm_api_params = {
'loss_type': self.loss_type, #'laplacian','squareddif', 'ideal', 'none'
'loss_factor': self.loss_factor,
'approx_aci': self.approx_aci,
}
## parameters for rw inference
self.rwparams_inf = {
'labelset':self.labelset,
'return_arguments':['image','y'],
# optimization
'rtol': 1e-6,
'maxiter': 1e3,
'per_label':True,
'optim_solver':'unconstrained',
}
## svm params
self.svmparams = {
'C': C,
'Cprime': Cprime,
'nitermax': 100,
'epsilon': 1e-5,
#'do_switch_loss': switch_loss,
# latent
'latent_niter_max': 100,
'latent_epsilon': 1e-3,
'latent_use_parallel': self.use_parallel,
}
self.trainparams = {
'scale_only': self.scale_only,
}
## weight functions
if self.minimal_svm:
self.hand_tuned_w = [1, 1e-2]
self.weight_functions = {'std_b50': lambda im: wflib.weight_std(im, beta=50)}
self.prior_models = {'constant': models.Constant}
else:
self.hand_tuned_w = [1.0, 0.0, 0.0, 0.0, 1e-2, 0.0, 0.0]
self.weight_functions = {
'std_b10' : lambda im,i,j: wflib.weight_std(im,i,j, beta=10),
'std_b50' : lambda im,i,j: wflib.weight_std(im,i,j, beta=50),
'std_b100' : lambda im,i,j: wflib.weight_std(im,i,j, beta=100),
'inv_b100o1' : lambda im,i,j: wflib.weight_inv(im,i,j, beta=100, offset=1),
}
self.prior_models = {
'constant': models.Constant,
'entropy': models.Entropy_no_D,
'intensity': models.Intensity,
}
## indices of w
nlaplacian = len(self.weight_functions)
nprior = len(self.prior_models)
self.indices_laplacians = np.arange(nlaplacian)
self.indices_priors = np.arange(nlaplacian,nlaplacian + nprior)
## compute the scale of psi
#self.psi_scale = [1e4] * nlaplacian + [1e5] * nprior
self.psi_scale = [1.0] * nlaplacian + [1.0] * nprior
self.svmparams['psi_scale'] = self.psi_scale
## make arrays of function
self.laplacian_functions = self.weight_functions.values()
self.laplacian_names = self.weight_functions.keys()
self.prior_functions = self.prior_models.values()
self.prior_names = self.prior_models.keys()
## parallel ?
if self.use_parallel:
self.comm = mpi.COMM
self.MPI_rank = mpi.RANK
self.MPI_size = mpi.SIZE
self.isroot = self.MPI_rank==0
if self.MPI_size==1:
logger.warning('Found only one process. Not using parallel')
self.use_parallel = False
self.svmparams['use_parallel'] = self.use_parallel
self.svmparams['latent_use_parallel'] = self.use_parallel
else:
self.isroot = True
if self.isroot:
logger.info('passed these command line arguments: {}'.format(str(sys.argv)))
logger.info('using parallel?: {}'.format(use_parallel))
logger.info('using latent?: {}'.format(self.use_latent))
logger.info('train data: {}'.format(ntrain))
strkeys = ', '.join(self.laplacian_names)
logger.info('laplacian functions (in order): {}'.format(strkeys))
strkeys = ', '.join(self.prior_names)
logger.info('prior models (in order): {}'.format(strkeys))
logger.info('using loss type: {}'.format(self.loss_type))
logger.info('SVM parameters: {}'.format(self.svmparams))
logger.info('Computing one iteration at a time ?: {}'.format(self.one_iteration))
if self.debug:
logger.info('debug mode, no saving')
else:
logger.info('writing svm output to: {}'.format(self.dir_svm))
def compute_features(test, train, y):
im = io_analyze.load(config.dir_reg + test + train + 'reggray.hdr')
nim = im/np.std(im)
prior,mask = load_or_compute_prior_and_mask(
test, force_recompute=False)
seeds = (-1)*mask.astype(int)
from rwsegment import rwsegment_prior_models as models
from rwsegment import weight_functions as wflib
rwparams = {
'labelset': np.asarray(config.labelset),
}
weight_functions = {
'std_b10' : lambda im: wflib.weight_std(im, beta=10),
'std_b50' : lambda im: wflib.weight_std(im, beta=50),
'std_b100' : lambda im: wflib.weight_std(im, beta=100),
'inv_b100o1' : lambda im: wflib.weight_inv(im, beta=100, offset=1),
# 'pdiff_r1b10': lambda im: wflib.weight_patch_diff(im, r0=1, beta=10),
# 'pdiff_r2b10': lambda im: wflib.weight_patch_diff(im, r0=2, beta=10),
# 'pdiff_r1b50' : lambda im: wflib.weight_patch_diff(im, r0=1, beta=50),
}
prior_models = {
'constant': models.Constant,
'entropy': models.Entropy_no_D,
'intensity': models.Intensity,
}
## indices of w
nlaplacian = len(weight_functions)
nprior = len(prior_models)
indices_laplacians = np.arange(nlaplacian)
indices_priors = np.arange(nlaplacian,nlaplacian + nprior)
laplacian_functions = weight_functions.values()
laplacian_names = weight_functions.keys()
prior_functions = prior_models.values()
prior_names = prior_models.keys()
#from svm_rw_api import MetaAnchor
#anchor_api = MetaAnchor(
# prior,
# prior_functions,
# weights_priors,
# image=im,
# )
from rwsegment import rwsegment
for fname in weight_functions:
wf = weight_functions[fname]
en_rw = rwsegment.energy_rw(
nim,
y,
seeds=seeds,
weight_function=wf,
**rwparams
)
print fname, en_rw
for mname in prior_models:
pm = prior_models[mname](prior,1., image=nim)
en_anchor = rwsegment.energy_anchor(
nim,
y,
pm,
seeds=seeds,
**rwparams
)
print mname, en_anchor
def compute_objective(test, y, w):
im = io_analyze.load(config.dir_reg + test + 'gray.hdr')
nim = im/np.std(im)
prior,mask = load_or_compute_prior_and_mask(
test, force_recompute=False)
seeds = (-1)*mask.astype(int)
from rwsegment import rwsegment_prior_models as models
from rwsegment import weight_functions as wflib
rwparams = {
'labelset': np.asarray(config.labelset),
# optimization
'rtol': 1e-6,
'maxiter': 1e3,
'per_label':True,
'optim_solver':'unconstrained',
}
weight_functions = {
'std_b10' : lambda im: wflib.weight_std(im, beta=10),
'std_b50' : lambda im: wflib.weight_std(im, beta=50),
'std_b100' : lambda im: wflib.weight_std(im, beta=100),
'inv_b100o1' : lambda im: wflib.weight_inv(im, beta=100, offset=1),
# 'pdiff_r1b10': lambda im: wflib.weight_patch_diff(im, r0=1, beta=10),
# 'pdiff_r2b10': lambda im: wflib.weight_patch_diff(im, r0=2, beta=10),
# 'pdiff_r1b50' : lambda im: wflib.weight_patch_diff(im, r0=1, beta=50),
}
prior_models = {
'constant': models.Constant,
'entropy': models.Entropy_no_D,
'intensity': models.Intensity,
}
## indices of w
nlaplacian = len(weight_functions)
nprior = len(prior_models)
indices_laplacians = np.arange(nlaplacian)
indices_priors = np.arange(nlaplacian,nlaplacian + nprior)
laplacian_functions = weight_functions.values()
laplacian_names = weight_functions.keys()
prior_functions = prior_models.values()
prior_names = prior_models.keys()
weights_laplacians = np.asarray(w)[indices_laplacians]
weights_priors = np.asarray(w)[indices_priors]
def meta_weight_functions(im,_w):
''' meta weight function'''
data = 0
for iwf,wf in enumerate(laplacian_functions):
ij,_data = wf(im)
data += _w[iwf]*_data
return ij, data
weight_function = lambda im: meta_weight_functions(im, weights_laplacians)
from svm_rw_api import MetaAnchor
anchor_api = MetaAnchor(
prior,
prior_functions,
weights_priors,
image=nim,
)
from rwsegment import rwsegment
en_rw = rwsegment.energy_rw(
nim,
y,
seeds=seeds,
weight_function=weight_function,
**rwparams
)
en_anchor = rwsegment.energy_anchor(
nim,
y,
anchor_api,
seeds=seeds,
**rwparams
)
obj = en_rw + en_anchor
return obj
def compute_features(test, train, y):
im = io_analyze.load(config.dir_reg + test + train + 'reggray.hdr')
nim = im / np.std(im)
prior, mask = load_or_compute_prior_and_mask(test, force_recompute=False)
seeds = (-1) * mask.astype(int)
from rwsegment import rwsegment_prior_models as models
from rwsegment import weight_functions as wflib
rwparams = {
'labelset': np.asarray(config.labelset),
}
weight_functions = {
'std_b10': lambda im: wflib.weight_std(im, beta=10),
'std_b50': lambda im: wflib.weight_std(im, beta=50),
'std_b100': lambda im: wflib.weight_std(im, beta=100),
'inv_b100o1': lambda im: wflib.weight_inv(im, beta=100, offset=1),
# 'pdiff_r1b10': lambda im: wflib.weight_patch_diff(im, r0=1, beta=10),
# 'pdiff_r2b10': lambda im: wflib.weight_patch_diff(im, r0=2, beta=10),
# 'pdiff_r1b50' : lambda im: wflib.weight_patch_diff(im, r0=1, beta=50),
}
prior_models = {
'constant': models.Constant,
'entropy': models.Entropy_no_D,
'intensity': models.Intensity,
}
## indices of w
nlaplacian = len(weight_functions)
nprior = len(prior_models)
indices_laplacians = np.arange(nlaplacian)
indices_priors = np.arange(nlaplacian, nlaplacian + nprior)
laplacian_functions = weight_functions.values()
laplacian_names = weight_functions.keys()
prior_functions = prior_models.values()
prior_names = prior_models.keys()
#from svm_rw_api import MetaAnchor
#anchor_api = MetaAnchor(
# prior,
# prior_functions,
# weights_priors,
# image=im,
# )
from rwsegment import rwsegment
for fname in weight_functions:
wf = weight_functions[fname]
en_rw = rwsegment.energy_rw(nim,
y,
seeds=seeds,
weight_function=wf,
**rwparams)
print fname, en_rw
for mname in prior_models:
pm = prior_models[mname](prior, 1., image=nim)
en_anchor = rwsegment.energy_anchor(nim,
y,
pm,
seeds=seeds,
**rwparams)
print mname, en_anchor
def compute_objective(test, y, w):
im = io_analyze.load(config.dir_reg + test + 'gray.hdr')
nim = im / np.std(im)
prior, mask = load_or_compute_prior_and_mask(test, force_recompute=False)
seeds = (-1) * mask.astype(int)
from rwsegment import rwsegment_prior_models as models
from rwsegment import weight_functions as wflib
rwparams = {
'labelset': np.asarray(config.labelset),
# optimization
'rtol': 1e-6,
'maxiter': 1e3,
'per_label': True,
'optim_solver': 'unconstrained',
}
weight_functions = {
'std_b10': lambda im: wflib.weight_std(im, beta=10),
'std_b50': lambda im: wflib.weight_std(im, beta=50),
'std_b100': lambda im: wflib.weight_std(im, beta=100),
'inv_b100o1': lambda im: wflib.weight_inv(im, beta=100, offset=1),
# 'pdiff_r1b10': lambda im: wflib.weight_patch_diff(im, r0=1, beta=10),
# 'pdiff_r2b10': lambda im: wflib.weight_patch_diff(im, r0=2, beta=10),
# 'pdiff_r1b50' : lambda im: wflib.weight_patch_diff(im, r0=1, beta=50),
}
prior_models = {
'constant': models.Constant,
'entropy': models.Entropy_no_D,
'intensity': models.Intensity,
}
## indices of w
nlaplacian = len(weight_functions)
nprior = len(prior_models)
indices_laplacians = np.arange(nlaplacian)
indices_priors = np.arange(nlaplacian, nlaplacian + nprior)
laplacian_functions = weight_functions.values()
laplacian_names = weight_functions.keys()
prior_functions = prior_models.values()
prior_names = prior_models.keys()
weights_laplacians = np.asarray(w)[indices_laplacians]
weights_priors = np.asarray(w)[indices_priors]
def meta_weight_functions(im, _w):
''' meta weight function'''
data = 0
for iwf, wf in enumerate(laplacian_functions):
ij, _data = wf(im)
data += _w[iwf] * _data
return ij, data
weight_function = lambda im: meta_weight_functions(im, weights_laplacians)
from svm_rw_api import MetaAnchor
anchor_api = MetaAnchor(
prior,
prior_functions,
weights_priors,
image=nim,
)
from rwsegment import rwsegment
en_rw = rwsegment.energy_rw(nim,
y,
seeds=seeds,
weight_function=weight_function,
**rwparams)
en_anchor = rwsegment.energy_anchor(nim,
y,
anchor_api,
seeds=seeds,
**rwparams)
obj = en_rw + en_anchor
return obj
def __init__(self, use_parallel=True, **kwargs):
## paths
self.dir_reg = config.dir_reg
self.dir_inf = config.dir_inf
self.dir_svm = config.dir_svm
self.training_vols = config.vols
## params
self.force_recompute_prior = False
self.use_parallel = use_parallel
self.labelset = np.asarray(config.labelset)
C = kwargs.pop('C', 1.0)
Cprime = kwargs.pop('Cprime', 0.0)
self.scale_only = kwargs.pop('scale_only', False)
self.loss_type = kwargs.pop('loss_type', 'squareddiff')
self.loss_factor = kwargs.pop('loss_factor', 1.)
self.use_latent = kwargs.pop('use_latent', False)
self.approx_aci = kwargs.pop('approx_aci', False)
self.debug = kwargs.pop('debug', False)
self.retrain = kwargs.pop('retrain', True)
self.minimal_svm = kwargs.pop('minimal', False)
self.one_iteration = kwargs.pop('one_iteration', False)
self.start_script = kwargs.pop('start_script', '')
self.use_mosek = kwargs.pop('use_mosek', True)
#switch_loss = kwargs.pop('switch_loss', False)
crop = kwargs.pop('crop', 'none')
if crop == 'none':
self.crop = False
else:
self.crop = True
ncrop = int(crop)
self.slice_size = ncrop
self.slice_step = ncrop
ntrain = kwargs.pop('ntrain', 'all')
if ntrain.isdigit():
n = int(ntrain)
self.select_vol = slice(n, n + 1)
else:
self.select_vol = slice(None)
## parameters for rw learning
self.rwparams_svm = {
'labelset': self.labelset,
# optimization
'rtol': 1e-6,
'maxiter': 1e3,
'per_label': True,
'optim_solver': 'unconstrained',
# contrained optim
'use_mosek': self.use_mosek,
'logbarrier_mu': 10,
'logbarrier_initial_t': 10,
'logbarrier_modified': False,
'logbarrier_maxiter': 10,
'newton_maxiter': 50,
}
## parameters for svm api
self.svm_api_params = {
'loss_type':
self.loss_type, #'laplacian','squareddif', 'ideal', 'none'
'loss_factor': self.loss_factor,
'approx_aci': self.approx_aci,
}
## parameters for rw inference
self.rwparams_inf = {
'labelset': self.labelset,
'return_arguments': ['image', 'y'],
# optimization
'rtol': 1e-6,
'maxiter': 1e3,
'per_label': True,
'optim_solver': 'unconstrained',
}
## svm params
self.svmparams = {
'C': C,
'Cprime': Cprime,
'nitermax': 100,
'epsilon': 1e-5,
#'do_switch_loss': switch_loss,
# latent
'latent_niter_max': 100,
'latent_epsilon': 1e-3,
'latent_use_parallel': self.use_parallel,
}
self.trainparams = {
'scale_only': self.scale_only,
}
## weight functions
if self.minimal_svm:
self.hand_tuned_w = [1, 1e-2]
self.weight_functions = {
'std_b50': lambda im: wflib.weight_std(im, beta=50)
}
self.prior_models = {'constant': models.Constant}
else:
self.hand_tuned_w = [1.0, 0.0, 0.0, 0.0, 1e-2, 0.0, 0.0]
self.weight_functions = {
'std_b10':
lambda im, i, j: wflib.weight_std(im, i, j, beta=10),
'std_b50':
lambda im, i, j: wflib.weight_std(im, i, j, beta=50),
'std_b100':
lambda im, i, j: wflib.weight_std(im, i, j, beta=100),
'inv_b100o1':
lambda im, i, j: wflib.weight_inv(im, i, j, beta=100, offset=1
),
}
self.prior_models = {
'constant': models.Constant,
'entropy': models.Entropy_no_D,
'intensity': models.Intensity,
}
## indices of w
nlaplacian = len(self.weight_functions)
nprior = len(self.prior_models)
self.indices_laplacians = np.arange(nlaplacian)
self.indices_priors = np.arange(nlaplacian, nlaplacian + nprior)
## compute the scale of psi
#self.psi_scale = [1e4] * nlaplacian + [1e5] * nprior
self.psi_scale = [1.0] * nlaplacian + [1.0] * nprior
self.svmparams['psi_scale'] = self.psi_scale
## make arrays of function
self.laplacian_functions = self.weight_functions.values()
self.laplacian_names = self.weight_functions.keys()
self.prior_functions = self.prior_models.values()
self.prior_names = self.prior_models.keys()
## parallel ?
if self.use_parallel:
self.comm = mpi.COMM
self.MPI_rank = mpi.RANK
self.MPI_size = mpi.SIZE
self.isroot = self.MPI_rank == 0
if self.MPI_size == 1:
logger.warning('Found only one process. Not using parallel')
self.use_parallel = False
self.svmparams['use_parallel'] = self.use_parallel
self.svmparams['latent_use_parallel'] = self.use_parallel
else:
self.isroot = True
if self.isroot:
logger.info('passed these command line arguments: {}'.format(
str(sys.argv)))
logger.info('using parallel?: {}'.format(use_parallel))
logger.info('using latent?: {}'.format(self.use_latent))
logger.info('train data: {}'.format(ntrain))
strkeys = ', '.join(self.laplacian_names)
logger.info('laplacian functions (in order): {}'.format(strkeys))
strkeys = ', '.join(self.prior_names)
logger.info('prior models (in order): {}'.format(strkeys))
logger.info('using loss type: {}'.format(self.loss_type))
logger.info('SVM parameters: {}'.format(self.svmparams))
logger.info('Computing one iteration at a time ?: {}'.format(
self.one_iteration))
if self.debug:
logger.info('debug mode, no saving')
else:
logger.info('writing svm output to: {}'.format(self.dir_svm))