def process_sample(self, test, fold=None):
## get prior
prior, mask = load_or_compute_prior_and_mask(
test, force_recompute=self.force_recompute_prior, pca=True, fold=fold
)
seeds = (-1) * mask
mask = mask.astype(bool)
## load image
file_name = config.dir_reg + test + "gray.hdr"
logger.info("segmenting data: {}".format(file_name))
im = io_analyze.load(file_name)
file_gt = config.dir_reg + test + "seg.hdr"
seg = io_analyze.load(file_gt)
seg.flat[~np.in1d(seg, self.labelset)] = self.labelset[0]
## normalize image
nim = im / np.std(im)
## init anchor_api
anchor_api = MetaAnchor(
prior=prior, prior_models=self.prior_models, prior_weights=self.prior_weights, image=nim
)
## start segmenting
# import ipdb; ipdb.set_trace()
sol, impca = rwsegment_pca.segment(nim, anchor_api, seeds=seeds, labelset=self.labelset, **self.params)
## compute Dice coefficient per label
dice = compute_dice_coef(sol, seg, labelset=self.labelset)
logger.info("Dice: {}".format(dice))
dice_pca = compute_dice_coef(impca, seg, labelset=self.labelset)
logger.info("Dice pca only: {}".format(dice_pca))
if not config.debug:
if fold is not None:
test_name = "f{}_{}".format(fold[0][:2], test)
else:
test_name = test
outdir = config.dir_seg + "/{}/{}".format(self.model_name, test_name)
logger.info("saving data in: {}".format(outdir))
if not os.path.isdir(outdir):
os.makedirs(outdir)
io_analyze.save(outdir + "sol.hdr", sol.astype(np.int32))
io_analyze.save(outdir + "solpca.hdr", impca.astype(np.int32))
np.savetxt(outdir + "dice.txt", np.c_[dice.keys(), dice.values()], fmt="%d %.8f")
np.savetxt(outdir + "dice_pca.txt", np.c_[dice.keys(), dice_pca.values()], fmt="%d %.8f")
def run_svm_inference(self, test, w):
logger.info('running inference on: {}'.format(test))
outdir = self.dir_inf + test
if not os.path.isdir(outdir):
os.makedirs(outdir)
## segment test image with trained w
def wwf(im, _w):
''' meta weight function'''
data = 0
for iwf, wf in enumerate(self.weight_functions.values()):
ij, _data = wf(im)
data += _w[iwf] * _data
return ij, data
## load images and ground truth
file_seg = self.dir_reg + test + 'seg.hdr'
file_im = self.dir_reg + test + 'gray.hdr'
im = io_analyze.load(file_im)
seg = io_analyze.load(file_seg)
seg.flat[~np.in1d(seg.ravel(), self.labelset)] = self.labelset[0]
## save image
im = im / np.std(im) # normalize image by variance
## prior
anchor_api = BaseAnchorAPI(
self.prior,
anchor_weight=w[-1],
)
sol, y = rwsegment.segment(im,
anchor_api,
seeds=self.seeds,
weight_function=lambda im: wwf(im, w),
**self.rwparams_inf)
np.save(outdir + 'y.test.npy', y)
io_analyze.save(outdir + 'sol.test.hdr', sol.astype(np.int32))
## compute Dice coefficient
dice = compute_dice_coef(sol, seg, labelset=self.labelset)
np.savetxt(outdir + 'dice.test.txt',
np.c_[dice.keys(), dice.values()],
fmt='%d %.8f')
## inference compare with gold standard
dice_gold = np.loadtxt(outdir + 'dice.gold.txt')
y_gold = np.load(outdir + 'y.gold.npy')
sol_gold = io_analyze.load(outdir + 'sol.gold.hdr')
np.testing.assert_allclose(dice.values(),
dict(dice_gold).values(),
err_msg='FAIL: dice coef mismatch',
atol=1e-8)
np.testing.assert_allclose(y, y_gold, err_msg='FAIL: y mismatch')
np.testing.assert_equal(sol, sol_gold, err_msg='FAIL: sol mismatch')
print 'PASS: inference tests'
def run_svm_inference(self,test,w, test_dir):
logger.info('running inference on: {}'.format(test))
## normalize w
# w = w / np.sqrt(np.dot(w,w))
strw = ' '.join('{:.3}'.format(val) for val in np.asarray(w)*self.psi_scale)
logger.debug('scaled w=[{}]'.format(strw))
weights_laplacians = np.asarray(w)[self.indices_laplacians]
weights_laplacians_h = np.asarray(self.hand_tuned_w)[self.indices_laplacians]
weights_priors = np.asarray(w)[self.indices_priors]
weights_priors_h = np.asarray(self.hand_tuned_w)[self.indices_priors]
## segment test image with trained w
'''
def meta_weight_functions(im,i,j,_w):
data = 0
for iwf,wf in enumerate(self.laplacian_functions):
_data = wf(im,i,j)
data += _w[iwf]*_data
return data
weight_function = lambda im: meta_weight_functions(im,i,j,weights_laplacians)
weight_function_h = lambda im: meta_weight_functions(im,i,j,weights_laplacians_h)
'''
weight_function = MetaLaplacianFunction(
weights_laplacians,
self.laplacian_functions)
weight_function_h = MetaLaplacianFunction(
weights_laplacians_h,
self.laplacian_functions)
## load images and ground truth
file_seg = self.dir_reg + test + 'seg.hdr'
file_im = self.dir_reg + test + 'gray.hdr'
im = io_analyze.load(file_im)
seg = io_analyze.load(file_seg)
seg.flat[~np.in1d(seg.ravel(),self.labelset)] = self.labelset[0]
nim = im/np.std(im) # normalize image by std
## test training data ?
inference_train = True
if inference_train:
train_ims, train_segs, train_metas = self.training_set
for tim, tz, tmeta in zip(train_ims, train_segs, train_metas):
## retrieve metadata
islices = tmeta.pop('islices',None)
imask = tmeta.pop('imask', None)
iimask = tmeta.pop('iimask',None)
if islices is not None:
tseeds = self.seeds[islices]
tprior = {
'data': np.asarray(self.prior['data'])[:,iimask],
'imask': imask,
'variance': np.asarray(self.prior['variance'])[:,iimask],
'labelset': self.labelset,
}
if 'intensity' in self.prior:
tprior['intensity'] = self.prior['intensity']
else:
tseeds = self.seeds
tprior = self.prior
## prior
tseg = self.labelset[np.argmax(tz, axis=0)].reshape(tim.shape)
tanchor_api = MetaAnchor(
tprior,
self.prior_functions,
weights_priors,
image=tim,
)
tsol,ty = rwsegment.segment(
tim,
tanchor_api,
seeds=tseeds,
weight_function=weight_function,
**self.rwparams_inf
)
## compute Dice coefficient
tdice = compute_dice_coef(tsol, tseg, labelset=self.labelset)
logger.info('Dice coefficients for train: \n{}'.format(tdice))
nlabel = len(self.labelset)
tflatmask = np.zeros(ty.shape, dtype=bool)
tflatmask[:,imask] = True
loss0 = loss_functions.ideal_loss(tz,ty,mask=tflatmask)
logger.info('Tloss = {}'.format(loss0))
## loss2: squared difference with ztilde
loss1 = loss_functions.anchor_loss(tz,ty,mask=tflatmask)
logger.info('SDloss = {}'.format(loss1))
## loss3: laplacian loss
loss2 = loss_functions.laplacian_loss(tz,ty,mask=tflatmask)
logger.info('LAPloss = {}'.format(loss2))
tanchor_api_h = MetaAnchor(
tprior,
self.prior_functions,
weights_priors_h,
image=tim,
)
tsol,ty = rwsegment.segment(
tim,
tanchor_api_h,
seeds=tseeds,
weight_function=weight_function_h,
**self.rwparams_inf
)
## compute Dice coefficient
tdice = compute_dice_coef(tsol, tseg, labelset=self.labelset)
logger.info('Dice coefficients for train (hand-tuned): \n{}'.format(tdice))
loss0 = loss_functions.ideal_loss(tz,ty,mask=tflatmask)
logger.info('Tloss (hand-tuned) = {}'.format(loss0))
## loss2: squared difference with ztilde
loss1 = loss_functions.anchor_loss(tz,ty,mask=tflatmask)
logger.info('SDloss (hand-tuned) = {}'.format(loss1))
## loss3: laplacian loss
loss2 = loss_functions.laplacian_loss(tz,ty,mask=tflatmask)
logger.info('LAPloss (hand-tuned) = {}'.format(loss2))
break
## prior
anchor_api = MetaAnchor(
self.prior,
self.prior_functions,
weights_priors,
image=nim,
)
sol,y = rwsegment.segment(
nim,
anchor_api,
seeds=self.seeds,
weight_function=weight_function,
**self.rwparams_inf
)
## compute Dice coefficient
dice = compute_dice_coef(sol, seg,labelset=self.labelset)
logger.info('Dice coefficients: \n{}'.format(dice))
## objective
en_rw = rwsegment.energy_rw(
nim, y, seeds=self.seeds,weight_function=weight_function, **self.rwparams_inf)
en_anchor = rwsegment.energy_anchor(
nim, y, anchor_api, seeds=self.seeds, **self.rwparams_inf)
obj = en_rw + en_anchor
logger.info('Objective = {:.3}'.format(obj))
## compute losses
z = seg.ravel()==np.c_[self.labelset]
mask = self.seeds < 0
flatmask = mask.ravel()*np.ones((len(self.labelset),1))
## loss 0 : 1 - Dice(y,z)
loss0 = loss_functions.ideal_loss(z,y,mask=flatmask)
logger.info('Tloss = {}'.format(loss0))
## loss2: squared difference with ztilde
loss1 = loss_functions.anchor_loss(z,y,mask=flatmask)
logger.info('SDloss = {}'.format(loss1))
## loss3: laplacian loss
loss2 = loss_functions.laplacian_loss(z,y,mask=flatmask)
logger.info('LAPloss = {}'.format(loss2))
## loss4: linear loss
loss3 = loss_functions.linear_loss(z,y,mask=flatmask)
logger.info('LINloss = {}'.format(loss3))
## saving
if self.debug:
pass
elif self.isroot:
outdir = self.dir_inf + test_dir
logger.info('saving data in: {}'.format(outdir))
if not os.path.isdir(outdir):
os.makedirs(outdir)
#io_analyze.save(outdir + 'im.hdr',im.astype(np.int32))
#np.save(outdir + 'y.npy',y)
#io_analyze.save(outdir + 'sol.hdr',sol.astype(np.int32))
np.savetxt(outdir + 'objective.txt', [obj])
np.savetxt(
outdir + 'dice.txt',
np.c_[dice.keys(),dice.values()],fmt='%d %f')
f = open(outdir + 'losses.txt', 'w')
f.write('ideal_loss\t{}\n'.format(loss0))
f.write('anchor_loss\t{}\n'.format(loss1))
f.write('laplacian_loss\t{}\n'.format(loss2))
f.close()
def process_sample(self, train, test):
outdir = config.dir_work + 'autoseeds/' + config.basis + '/' + train + '/' + test
logger.info('saving data in: {}'.format(outdir))
if not os.path.isdir(outdir):
os.makedirs(outdir)
## get prior
from scipy import ndimage
segtrain = io_analyze.load(config.dir_reg + test + train +
'/regseg.hdr')
segtrain.flat[~np.in1d(segtrain, self.labelset)] = self.labelset[0]
struct = np.ones((10, ) * segtrain.ndim)
mask = ndimage.binary_dilation(
segtrain > 0,
structure=struct,
).astype(bool)
#prior, mask = load_or_compute_prior_and_mask(
# test,force_recompute=self.force_recompute_prior)
#mask = mask.astype(bool)
## load image
file_name = config.dir_reg + test + 'gray.hdr'
logger.info('segmenting data: {}'.format(file_name))
im = io_analyze.load(file_name).astype(float)
file_gt = config.dir_reg + test + 'seg.hdr'
seg = io_analyze.load(file_gt)
seg.flat[~np.in1d(seg, self.labelset)] = self.labelset[0]
## normalize image
nim = im / np.std(im)
#orient_scores = self.load_or_compute_orientations(train,test, mask=mask)
if 1: #not os.path.isfile(outdir + 'points.npy'):
from rwsegment import boundary_utils
reload(boundary_utils)
## sample points
points = boundary_utils.sample_points(im, self.step, mask=mask)
points = points[mask[tuple(points.T)]]
impoints = np.zeros(im.shape, dtype=int)
impoints[tuple(points.T)] = np.arange(len(points)) + 1
ipoints = np.where(impoints.ravel())[0]
points = np.argwhere(impoints)
np.save(outdir + 'points.npy', points)
impoints[tuple(points.T)] = np.arange(len(points)) + 1
## set unary potentials from prior: array of unary costs
nlabel = len(self.labelset)
dist = self.distance_to_train(segtrain, points)
T = 10.0
prob_pts = np.exp(-(dist / T)**2) / np.c_[np.sum(
np.exp(-(dist / T)**2), axis=1)]
#prob = np.c_[np.ones(im.size), np.zeros((im.size, nlabel-1))]
#prob[mask.ravel(),:] = prior['data'].T
#prob_pts = prob[ipoints,:]
np.save(outdir + 'prob_points.npy', prob_pts)
## binary potentials
## compute edges
edges, edgev, labels = boundary_utils.get_edges(im,
points,
mask=mask)
edges = np.sort(edges, axis=1)
np.save(outdir + 'edges.npy', edges)
## get orientation hist
orient_scores, hist = self.load_or_compute_orientations(train,
test,
mask=mask)
##classify edges
vecs = points[edges[:, 1]] - points[edges[:, 0]]
vecs = vecs / np.c_[np.sqrt(np.sum(vecs**2, axis=1))]
scores = self.get_orient_scores(vecs)
prob_orient = np.dot(scores, orient_scores)
#prob_orient = prob_orient/np.c_[np.sum(prob_orient, axis=1)]
np.save(outdir + 'prob_orient.npy', prob_orient)
'''
## load classifier
classifier = self.load_or_compute_classifier(train,test, mask=mask)
## extract profiles
profiles,emap,dists = boundary_utils.get_profiles(nim, points, edges, rad=0)
## make features
x = boundary_utils.make_features(
profiles,
size=self.sizex,
additional=[dists,edgev,edgev/dists],
)
## classify
cl, scores = classifier.classify(x)
## ground truth
z = boundary_utils.is_boundary(points, edges, seg)
logger.info('non boundary classification: {}%'\
.format(np.sum((np.r_[z]==0)*(np.r_[cl]==0))/float(np.sum(np.r_[z]==0))*100))
logger.info('boundary classification: {}%'\
.format(np.sum((np.r_[z]==1)*(np.r_[cl]==1))/float(np.sum(np.r_[z]==1))*100))
np.save(outdir + 'classified.npy', cl)
## probabilities
prob_edges = 1. - scores/np.c_[np.sum(scores, axis=1)]
##save probs
np.save(outdir + 'prob_edges.npy',prob_edges)
'''
else:
points = np.load(outdir + 'points.npy')
edges = np.load(outdir + 'edges.npy')
cl = np.load(outdir + 'classified.npy')
prob_pts = np.load(outdir + 'prob_points.npy')
#prob_edges = np.load(outdir + 'prob_edges.npy')
prob_orient = np.load(outdir + 'prob_orient.npy')
## make potentials
unary = -np.log(prob_pts + 1e-10)
#binary = - np.log(prob_edges + 1e-10)
#thresh = (prob_orient.shape[1] - 1.0)/prob_orient.shape[1]
thresh = (len(self.orients) - 1.0) / len(self.orients)
orient_cost = -np.log(np.clip(prob_orient + thresh, 0, 1) +
1e-10) * 100
orient_cost = np.clip(orient_cost, 0, 1e10)
#import ipdb; ipdb.set_trace()
## solve MRF:
import ipdb
ipdb.set_trace()
'''
from rwsegment.mrf import fastPD
class CostFunction(object):
def __init__(self,**kwargs):
self.binary = kwargs.pop('binary',0)
self.orient_indices = kwargs.pop('orient_indices')
self.orient_cost = kwargs.pop('orient_cost')
def __call__(self,e,l1,l2):
idpair = self.orient_indices[l1,l2]
pair_cost = self.orient_cost[e,idpair]
cost = (l1!=l2)*pair_cost
#return (l1!=l2)*(1-cl[e])*0.1
#return (l1!=l2)*self.binary[e,1]*0.1
#y = l1!=l2
#return self.binary[e, y]*pair_cost
print e, l1, l2, cost
return cost
#sol, en = fastPD.fastPD_callback(unary, edges, cost_function(binary), debug=True)
cost_function = CostFunction(
#binary=binary,
orient_indices=self.orient_indices,
orient_cost=orient_cost,
)
sol, en = fastPD.fastPD_callback(unary, edges, cost_function, debug=True)
'''
wpairs = orient_cost
from rwsegment.mrf import trw
sol, en = trw.TRW_general(unary,
edges,
wpairs,
niters=1000,
verbose=True)
labels = self.labelset[sol]
imsol = np.ones(im.shape, dtype=np.int32) * 20
imsol[tuple(points.T)] = labels
io_analyze.save(outdir + 'imseeds.hdr', imsol)
## classify sol
gtlabels = seg[tuple(points.T)]
priorlabels = self.labelset[np.argmin(unary, axis=1)]
err_prior = 1 - np.sum(gtlabels == priorlabels) / float(len(points))
err = 1 - np.sum(gtlabels == labels) / float(len(points))
logger.info('error in prior sol: {}%'.format(err_prior * 100))
logger.info('error in sol: {}%'.format(err * 100))
import ipdb
ipdb.set_trace()
## start segmenting
sol, y = rwsegment.segment(nim,
seeds=seeds,
labelset=self.labelset,
weight_function=self.weight_function,
**self.params)
## compute Dice coefficient per label
dice = compute_dice_coef(sol, seg, labelset=self.labelset)
logger.info('Dice: {}'.format(dice))
if not config.debug:
io_analyze.save(outdir + 'sol.hdr', sol.astype(np.int32))
np.savetxt(outdir + 'dice.txt',
np.c_[dice.keys(), dice.values()],
fmt='%d %.8f')
def run_svm_inference(self, test, w, test_dir):
logger.info('running inference on: {}'.format(test))
## normalize w
# w = w / np.sqrt(np.dot(w,w))
strw = ' '.join('{:.3}'.format(val)
for val in np.asarray(w) * self.psi_scale)
logger.debug('scaled w=[{}]'.format(strw))
weights_laplacians = np.asarray(w)[self.indices_laplacians]
weights_laplacians_h = np.asarray(
self.hand_tuned_w)[self.indices_laplacians]
weights_priors = np.asarray(w)[self.indices_priors]
weights_priors_h = np.asarray(self.hand_tuned_w)[self.indices_priors]
## segment test image with trained w
'''
def meta_weight_functions(im,i,j,_w):
data = 0
for iwf,wf in enumerate(self.laplacian_functions):
_data = wf(im,i,j)
data += _w[iwf]*_data
return data
weight_function = lambda im: meta_weight_functions(im,i,j,weights_laplacians)
weight_function_h = lambda im: meta_weight_functions(im,i,j,weights_laplacians_h)
'''
weight_function = MetaLaplacianFunction(weights_laplacians,
self.laplacian_functions)
weight_function_h = MetaLaplacianFunction(weights_laplacians_h,
self.laplacian_functions)
## load images and ground truth
file_seg = self.dir_reg + test + 'seg.hdr'
file_im = self.dir_reg + test + 'gray.hdr'
im = io_analyze.load(file_im)
seg = io_analyze.load(file_seg)
seg.flat[~np.in1d(seg.ravel(), self.labelset)] = self.labelset[0]
nim = im / np.std(im) # normalize image by std
## test training data ?
inference_train = True
if inference_train:
train_ims, train_segs, train_metas = self.training_set
for tim, tz, tmeta in zip(train_ims, train_segs, train_metas):
## retrieve metadata
islices = tmeta.pop('islices', None)
imask = tmeta.pop('imask', None)
iimask = tmeta.pop('iimask', None)
if islices is not None:
tseeds = self.seeds[islices]
tprior = {
'data': np.asarray(self.prior['data'])[:, iimask],
'imask': imask,
'variance': np.asarray(self.prior['variance'])[:,
iimask],
'labelset': self.labelset,
}
if 'intensity' in self.prior:
tprior['intensity'] = self.prior['intensity']
else:
tseeds = self.seeds
tprior = self.prior
## prior
tseg = self.labelset[np.argmax(tz, axis=0)].reshape(tim.shape)
tanchor_api = MetaAnchor(
tprior,
self.prior_functions,
weights_priors,
image=tim,
)
tsol, ty = rwsegment.segment(tim,
tanchor_api,
seeds=tseeds,
weight_function=weight_function,
**self.rwparams_inf)
## compute Dice coefficient
tdice = compute_dice_coef(tsol, tseg, labelset=self.labelset)
logger.info('Dice coefficients for train: \n{}'.format(tdice))
nlabel = len(self.labelset)
tflatmask = np.zeros(ty.shape, dtype=bool)
tflatmask[:, imask] = True
loss0 = loss_functions.ideal_loss(tz, ty, mask=tflatmask)
logger.info('Tloss = {}'.format(loss0))
## loss2: squared difference with ztilde
loss1 = loss_functions.anchor_loss(tz, ty, mask=tflatmask)
logger.info('SDloss = {}'.format(loss1))
## loss3: laplacian loss
loss2 = loss_functions.laplacian_loss(tz, ty, mask=tflatmask)
logger.info('LAPloss = {}'.format(loss2))
tanchor_api_h = MetaAnchor(
tprior,
self.prior_functions,
weights_priors_h,
image=tim,
)
tsol, ty = rwsegment.segment(tim,
tanchor_api_h,
seeds=tseeds,
weight_function=weight_function_h,
**self.rwparams_inf)
## compute Dice coefficient
tdice = compute_dice_coef(tsol, tseg, labelset=self.labelset)
logger.info(
'Dice coefficients for train (hand-tuned): \n{}'.format(
tdice))
loss0 = loss_functions.ideal_loss(tz, ty, mask=tflatmask)
logger.info('Tloss (hand-tuned) = {}'.format(loss0))
## loss2: squared difference with ztilde
loss1 = loss_functions.anchor_loss(tz, ty, mask=tflatmask)
logger.info('SDloss (hand-tuned) = {}'.format(loss1))
## loss3: laplacian loss
loss2 = loss_functions.laplacian_loss(tz, ty, mask=tflatmask)
logger.info('LAPloss (hand-tuned) = {}'.format(loss2))
break
## prior
anchor_api = MetaAnchor(
self.prior,
self.prior_functions,
weights_priors,
image=nim,
)
sol, y = rwsegment.segment(nim,
anchor_api,
seeds=self.seeds,
weight_function=weight_function,
**self.rwparams_inf)
## compute Dice coefficient
dice = compute_dice_coef(sol, seg, labelset=self.labelset)
logger.info('Dice coefficients: \n{}'.format(dice))
## objective
en_rw = rwsegment.energy_rw(nim,
y,
seeds=self.seeds,
weight_function=weight_function,
**self.rwparams_inf)
en_anchor = rwsegment.energy_anchor(nim,
y,
anchor_api,
seeds=self.seeds,
**self.rwparams_inf)
obj = en_rw + en_anchor
logger.info('Objective = {:.3}'.format(obj))
## compute losses
z = seg.ravel() == np.c_[self.labelset]
mask = self.seeds < 0
flatmask = mask.ravel() * np.ones((len(self.labelset), 1))
## loss 0 : 1 - Dice(y,z)
loss0 = loss_functions.ideal_loss(z, y, mask=flatmask)
logger.info('Tloss = {}'.format(loss0))
## loss2: squared difference with ztilde
loss1 = loss_functions.anchor_loss(z, y, mask=flatmask)
logger.info('SDloss = {}'.format(loss1))
## loss3: laplacian loss
loss2 = loss_functions.laplacian_loss(z, y, mask=flatmask)
logger.info('LAPloss = {}'.format(loss2))
## loss4: linear loss
loss3 = loss_functions.linear_loss(z, y, mask=flatmask)
logger.info('LINloss = {}'.format(loss3))
## saving
if self.debug:
pass
elif self.isroot:
outdir = self.dir_inf + test_dir
logger.info('saving data in: {}'.format(outdir))
if not os.path.isdir(outdir):
os.makedirs(outdir)
#io_analyze.save(outdir + 'im.hdr',im.astype(np.int32))
#np.save(outdir + 'y.npy',y)
#io_analyze.save(outdir + 'sol.hdr',sol.astype(np.int32))
np.savetxt(outdir + 'objective.txt', [obj])
np.savetxt(outdir + 'dice.txt',
np.c_[dice.keys(), dice.values()],
fmt='%d %f')
f = open(outdir + 'losses.txt', 'w')
f.write('ideal_loss\t{}\n'.format(loss0))
f.write('anchor_loss\t{}\n'.format(loss1))
f.write('laplacian_loss\t{}\n'.format(loss2))
f.close()
def run_svm_inference(self,test,w):
logger.info('running inference on: {}'.format(test))
outdir = self.dir_inf + test
if not os.path.isdir(outdir):
os.makedirs(outdir)
## segment test image with trained w
def wwf(im,_w):
''' meta weight function'''
data = 0
for iwf,wf in enumerate(self.weight_functions.values()):
ij,_data = wf(im)
data += _w[iwf]*_data
return ij, data
## load images and ground truth
file_seg = self.dir_reg + test + 'seg.hdr'
file_im = self.dir_reg + test + 'gray.hdr'
im = io_analyze.load(file_im)
seg = io_analyze.load(file_seg)
seg.flat[~np.in1d(seg.ravel(),self.labelset)] = self.labelset[0]
## save image
im = im/np.std(im) # normalize image by variance
## prior
anchor_api = BaseAnchorAPI(
self.prior,
anchor_weight=w[-1],
)
sol,y = rwsegment.segment(
im,
anchor_api,
seeds=self.seeds,
weight_function=lambda im: wwf(im, w),
**self.rwparams_inf
)
np.save(outdir + 'y.test.npy',y)
io_analyze.save(outdir + 'sol.test.hdr',sol.astype(np.int32))
## compute Dice coefficient
dice = compute_dice_coef(sol, seg,labelset=self.labelset)
np.savetxt(
outdir + 'dice.test.txt', np.c_[dice.keys(),dice.values()],fmt='%d %.8f')
## inference compare with gold standard
dice_gold = np.loadtxt(outdir + 'dice.gold.txt')
y_gold = np.load(outdir + 'y.gold.npy')
sol_gold = io_analyze.load(outdir + 'sol.gold.hdr')
np.testing.assert_allclose(
dice.values(),
dict(dice_gold).values(),
err_msg='FAIL: dice coef mismatch',
atol=1e-8)
np.testing.assert_allclose(y, y_gold, err_msg='FAIL: y mismatch')
np.testing.assert_equal(sol, sol_gold, err_msg='FAIL: sol mismatch')
print 'PASS: inference tests'
def process_sample(self,test,fold=None):
## get prior
prior, mask = load_or_compute_prior_and_mask(
test,
fold=fold,
force_recompute=self.force_recompute_prior)
seeds = (-1)*mask
## load image
file_name = config.dir_reg + test + 'gray.hdr'
logger.info('segmenting data: {}'.format(file_name))
im = io_analyze.load(file_name)
file_gt = config.dir_reg + test + 'seg.hdr'
seg = io_analyze.load(file_gt)
seg.flat[~np.in1d(seg, self.labelset)] = self.labelset[0]
## normalize image
nim = im/np.std(im)
## init anchor_api
anchor_api = MetaAnchor(
prior=prior,
prior_models=self.prior_models,
prior_weights=self.prior_weights,
image=nim,
)
## start segmenting
#import ipdb; ipdb.set_trace()
sol,y = rwsegment.segment(
nim,
anchor_api,
seeds=seeds,
labelset=self.labelset,
weight_function=self.weight_function,
**self.params
)
## compute losses
z = seg.ravel()==np.c_[self.labelset]
flatmask = mask.ravel()*np.ones((len(self.labelset),1))
## loss 0 : 1 - Dice(y,z)
loss0 = loss_functions.ideal_loss(z,y,mask=flatmask)
logger.info('Tloss = {}'.format(loss0))
## loss2: squared difference with ztilde
loss1 = loss_functions.anchor_loss(z,y,mask=flatmask)
logger.info('SDloss = {}'.format(loss1))
## loss3: laplacian loss
loss2 = loss_functions.laplacian_loss(z,y,mask=flatmask)
logger.info('LAPloss = {}'.format(loss2))
## loss4: linear loss
loss3 = loss_functions.linear_loss(z,y,mask=flatmask)
logger.info('LINloss = {}'.format(loss3))
## compute Dice coefficient per label
dice = compute_dice_coef(sol, seg,labelset=self.labelset)
logger.info('Dice: {}'.format(dice))
if not config.debug:
if fold is not None:
test_name = 'f{}_{}'.format(fold[0][:2], test)
else:
test_name = test
outdir = config.dir_seg + \
'/{}/{}'.format(self.model_name,test_name)
logger.info('saving data in: {}'.format(outdir))
if not os.path.isdir(outdir):
os.makedirs(outdir)
f = open(outdir + 'losses.txt', 'w')
f.write('ideal_loss\t{}\n'.format(loss0))
f.write('anchor_loss\t{}\n'.format(loss1))
f.write('laplacian_loss\t{}\n'.format(loss2))
f.close()
io_analyze.save(outdir + 'sol.hdr', sol.astype(np.int32))
np.savetxt(
outdir + 'dice.txt', np.c_[dice.keys(),dice.values()],fmt='%d %.8f')
def compute_mean_segmentation(self, list):
for test in list:
file_gt = config.dir_reg + test + 'seg.hdr'
seg = io_analyze.load(file_gt)
seg.flat[~np.in1d(seg, self.labelset)] = self.labelset[0]
## get prior
prior, mask = load_or_compute_prior_and_mask(
test,force_recompute=self.force_recompute_prior)
mask = mask.astype(bool)
y = np.zeros((len(self.labelset),seg.size))
y[:,0] = 1
y.flat[prior['imask']] = prior['data']
sol = np.zeros(seg.shape,dtype=np.int32)
sol[mask] = self.labelset[np.argmax(prior['data'],axis=0)]
## compute losses
z = seg.ravel()==np.c_[self.labelset]
flatmask = mask.ravel()*np.ones((len(self.labelset),1))
## loss 0 : 1 - Dice(y,z)
loss0 = loss_functions.ideal_loss(z,y,mask=flatmask)
logger.info('Tloss = {}'.format(loss0))
## loss2: squared difference with ztilde
#loss1 = loss_functions.anchor_loss(z,y,mask=flatmask)
#logger.info('SDloss = {}'.format(loss1))
## loss3: laplacian loss
#loss2 = loss_functions.laplacian_loss(z,y,mask=flatmask)
#logger.info('LAPloss = {}'.format(loss2))
## loss4: linear loss
#loss3 = loss_functions.linear_loss(z,y,mask=flatmask)
#logger.info('LINloss = {}'.format(loss3))
## compute Dice coefficient per label
dice = compute_dice_coef(sol, seg,labelset=self.labelset)
logger.info('Dice: {}'.format(dice))
if not config.debug:
outdir = config.dir_seg + \
'/{}/{}'.format('mean',test)
logger.info('saving data in: {}'.format(outdir))
if not os.path.isdir(outdir):
os.makedirs(outdir)
#f = open(outdir + 'losses.txt', 'w')
#f.write('ideal_loss\t{}\n'.format(loss0))
#f.write('anchor_loss\t{}\n'.format(loss1))
#f.write('laplacian_loss\t{}\n'.format(loss2))
#f.close()
io_analyze.save(outdir + 'sol.hdr', sol.astype(np.int32))
np.savetxt(
outdir + 'dice.txt', np.c_[dice.keys(),dice.values()],fmt='%d %.8f')
def process_sample(self,train, test):
outdir = config.dir_work + 'autoseeds/' + config.basis + '/' + train + '/' + test
logger.info('saving data in: {}'.format(outdir))
if not os.path.isdir(outdir):
os.makedirs(outdir)
## get prior
from scipy import ndimage
segtrain = io_analyze.load(config.dir_reg + test + train + '/regseg.hdr')
segtrain.flat[~np.in1d(segtrain, self.labelset)] = self.labelset[0]
struct = np.ones((10,)*segtrain.ndim)
mask = ndimage.binary_dilation(
segtrain>0,
structure=struct,
).astype(bool)
#prior, mask = load_or_compute_prior_and_mask(
# test,force_recompute=self.force_recompute_prior)
#mask = mask.astype(bool)
## load image
file_name = config.dir_reg + test + 'gray.hdr'
logger.info('segmenting data: {}'.format(file_name))
im = io_analyze.load(file_name).astype(float)
file_gt = config.dir_reg + test + 'seg.hdr'
seg = io_analyze.load(file_gt)
seg.flat[~np.in1d(seg, self.labelset)] = self.labelset[0]
## normalize image
nim = im/np.std(im)
#orient_scores = self.load_or_compute_orientations(train,test, mask=mask)
if 1:#not os.path.isfile(outdir + 'points.npy'):
from rwsegment import boundary_utils
reload(boundary_utils)
## sample points
points = boundary_utils.sample_points(im, self.step, mask=mask)
points = points[mask[tuple(points.T)]]
impoints = np.zeros(im.shape,dtype=int)
impoints[tuple(points.T)] = np.arange(len(points)) + 1
ipoints = np.where(impoints.ravel())[0]
points = np.argwhere(impoints)
np.save(outdir + 'points.npy', points)
impoints[tuple(points.T)] = np.arange(len(points)) + 1
## set unary potentials from prior: array of unary costs
nlabel = len(self.labelset)
dist = self.distance_to_train(segtrain, points)
T = 10.0
prob_pts = np.exp(-(dist/T)**2) / np.c_[np.sum(np.exp(-(dist/T)**2),axis=1)]
#prob = np.c_[np.ones(im.size), np.zeros((im.size, nlabel-1))]
#prob[mask.ravel(),:] = prior['data'].T
#prob_pts = prob[ipoints,:]
np.save(outdir + 'prob_points.npy', prob_pts)
## binary potentials
## compute edges
edges,edgev,labels = boundary_utils.get_edges(im, points, mask=mask)
edges = np.sort(edges,axis=1)
np.save(outdir + 'edges.npy', edges)
## get orientation hist
orient_scores,hist = self.load_or_compute_orientations(train,test, mask=mask)
##classify edges
vecs = points[edges[:,1]] - points[edges[:,0]]
vecs = vecs / np.c_[np.sqrt(np.sum(vecs**2,axis=1))]
scores = self.get_orient_scores(vecs)
prob_orient = np.dot(scores, orient_scores)
#prob_orient = prob_orient/np.c_[np.sum(prob_orient, axis=1)]
np.save(outdir + 'prob_orient.npy', prob_orient)
'''
## load classifier
classifier = self.load_or_compute_classifier(train,test, mask=mask)
## extract profiles
profiles,emap,dists = boundary_utils.get_profiles(nim, points, edges, rad=0)
## make features
x = boundary_utils.make_features(
profiles,
size=self.sizex,
additional=[dists,edgev,edgev/dists],
)
## classify
cl, scores = classifier.classify(x)
## ground truth
z = boundary_utils.is_boundary(points, edges, seg)
logger.info('non boundary classification: {}%'\
.format(np.sum((np.r_[z]==0)*(np.r_[cl]==0))/float(np.sum(np.r_[z]==0))*100))
logger.info('boundary classification: {}%'\
.format(np.sum((np.r_[z]==1)*(np.r_[cl]==1))/float(np.sum(np.r_[z]==1))*100))
np.save(outdir + 'classified.npy', cl)
## probabilities
prob_edges = 1. - scores/np.c_[np.sum(scores, axis=1)]
##save probs
np.save(outdir + 'prob_edges.npy',prob_edges)
'''
else:
points = np.load(outdir + 'points.npy')
edges = np.load(outdir + 'edges.npy')
cl = np.load(outdir + 'classified.npy')
prob_pts = np.load(outdir + 'prob_points.npy')
#prob_edges = np.load(outdir + 'prob_edges.npy')
prob_orient = np.load(outdir + 'prob_orient.npy')
## make potentials
unary = - np.log(prob_pts + 1e-10)
#binary = - np.log(prob_edges + 1e-10)
#thresh = (prob_orient.shape[1] - 1.0)/prob_orient.shape[1]
thresh = (len(self.orients) - 1.0) / len(self.orients)
orient_cost = - np.log(np.clip(prob_orient + thresh,0,1) + 1e-10)*100
orient_cost = np.clip(orient_cost, 0, 1e10)
#import ipdb; ipdb.set_trace()
## solve MRF:
import ipdb; ipdb.set_trace()
'''
from rwsegment.mrf import fastPD
class CostFunction(object):
def __init__(self,**kwargs):
self.binary = kwargs.pop('binary',0)
self.orient_indices = kwargs.pop('orient_indices')
self.orient_cost = kwargs.pop('orient_cost')
def __call__(self,e,l1,l2):
idpair = self.orient_indices[l1,l2]
pair_cost = self.orient_cost[e,idpair]
cost = (l1!=l2)*pair_cost
#return (l1!=l2)*(1-cl[e])*0.1
#return (l1!=l2)*self.binary[e,1]*0.1
#y = l1!=l2
#return self.binary[e, y]*pair_cost
print e, l1, l2, cost
return cost
#sol, en = fastPD.fastPD_callback(unary, edges, cost_function(binary), debug=True)
cost_function = CostFunction(
#binary=binary,
orient_indices=self.orient_indices,
orient_cost=orient_cost,
)
sol, en = fastPD.fastPD_callback(unary, edges, cost_function, debug=True)
'''
wpairs = orient_cost
from rwsegment.mrf import trw
sol, en = trw.TRW_general(
unary, edges, wpairs, niters=1000, verbose=True)
labels = self.labelset[sol]
imsol = np.ones(im.shape, dtype=np.int32)*20
imsol[tuple(points.T)] = labels
io_analyze.save(outdir + 'imseeds.hdr', imsol)
## classify sol
gtlabels = seg[tuple(points.T)]
priorlabels = self.labelset[np.argmin(unary,axis=1)]
err_prior = 1 - np.sum(gtlabels==priorlabels)/float(len(points))
err = 1 - np.sum(gtlabels==labels)/float(len(points))
logger.info('error in prior sol: {}%'.format(err_prior*100))
logger.info('error in sol: {}%'.format(err*100))
import ipdb; ipdb.set_trace()
## start segmenting
sol,y = rwsegment.segment(
nim,
seeds=seeds,
labelset=self.labelset,
weight_function=self.weight_function,
**self.params
)
## compute Dice coefficient per label
dice = compute_dice_coef(sol, seg,labelset=self.labelset)
logger.info('Dice: {}'.format(dice))
if not config.debug:
io_analyze.save(outdir + 'sol.hdr', sol.astype(np.int32))
np.savetxt(
outdir + 'dice.txt', np.c_[dice.keys(),dice.values()],fmt='%d %.8f')
