def compute_value(self):
value = 0
for i in xrange(self.n_batches):
pred = self.compute_batch_classes(i)
id1 = i * self.batch_size
id2 = (i + 1) * self.batch_size
value += error_rate(pred, np.argmax(self.ds.outputs[id1:id2], axis=1)) * self.batch_size
if self.last_batch_size > 0:
pred = self.compute_last_batch_classes()
tg = np.argmax(self.ds.outputs[self.ds.n_data-self.last_batch_size:], axis=1)
value += error_rate(pred, tg) * self.last_batch_size
return value / self.ds.n_data
def compute_value(self):
value = 0
for i in xrange(self.n_batches):
pred = self.compute_batch_classes(i)
id1 = i * self.batch_size
id2 = (i + 1) * self.batch_size
value += error_rate(pred,
np.argmax(self.ds.outputs[id1:id2],
axis=1)) * self.batch_size
if self.last_batch_size > 0:
pred = self.compute_last_batch_classes()
tg = np.argmax(self.ds.outputs[self.ds.n_data -
self.last_batch_size:],
axis=1)
value += error_rate(pred, tg) * self.last_batch_size
return value / self.ds.n_data
def predict_from_generator(self, batches_generator, scaler, pred_functions=None, raw=False):
"""
Returns the predictions of the batches of voxels, features and targets yielded by the batches_generator
"""
if pred_functions is None:
pred_functions = {}
ls_vx = []
ls_pred = []
id_batch = 0
for vx_batch, patch_batch, tg_batch in batches_generator:
id_batch += 1
batch_size_current = len(vx_batch)
if batch_size_current not in pred_functions:
pred_functions[batch_size_current] = self.generate_testing_function(batch_size_current)
if scaler is not None:
scaler.scale(patch_batch)
pred_raw = pred_functions[batch_size_current](patch_batch)
pred = np.argmax(pred_raw, axis=1)
err = error_rate(pred, np.argmax(tg_batch, axis=1))
print(" {"+str(err)+"}")
ls_vx.append(vx_batch)
if raw:
ls_pred.append(pred_raw)
else:
ls_pred.append(pred)
# Count the number of voxels
n_vx = 0
for vx in ls_vx:
n_vx += vx.shape[0]
# Aggregate the data
vx_all = np.zeros((n_vx, 3), dtype=int)
if raw:
pred_all = np.zeros((n_vx, 135), dtype=float)
else:
pred_all = np.zeros((n_vx,), dtype=int)
idx = 0
for vx, pred in zip(ls_vx, ls_pred):
next_idx = idx+vx.shape[0]
vx_all[idx:next_idx] = vx
pred_all[idx:next_idx] = pred
idx = next_idx
return vx_all, pred_all
def predict_from_generator(self, batches_generator, scaler, pred_functions=None):
"""
Returns the predictions of the batches of voxels, features and targets yielded by the batches_generator
"""
if pred_functions is None:
pred_functions = {}
ls_vx = []
ls_pred = []
id_batch = 0
for vx_batch, patch_batch, tg_batch in batches_generator:
id_batch += 1
batch_size_current = len(vx_batch)
if batch_size_current not in pred_functions:
pred_functions[batch_size_current] = self.generate_testing_function(batch_size_current)
if scaler is not None:
scaler.scale(patch_batch)
pred_raw = pred_functions[batch_size_current](patch_batch)
pred = np.argmax(pred_raw, axis=1)
err = error_rate(pred, np.argmax(tg_batch, axis=1))
print " {}".format(err)
ls_vx.append(vx_batch)
ls_pred.append(pred)
# Count the number of voxels
n_vx = 0
for vx in ls_vx:
n_vx += vx.shape[0]
# Aggregate the data
vx_all = np.zeros((n_vx, 3), dtype=int)
pred_all = np.zeros((n_vx,), dtype=int)
idx = 0
for vx, pred in zip(ls_vx, ls_pred):
next_idx = idx+vx.shape[0]
vx_all[idx:next_idx] = vx
pred_all[idx:next_idx] = pred
idx = next_idx
return vx_all, pred_all
def stat_of_all_models(self, img_true, n_out):
'''
return two lists of dice coefficient and error of all models in the ensemble
'''
dices = []
errs = []
count = 1
for pred_raw in self.pred_raws:
# Compute img_pred
pred_all = np.argmax(pred_raw, axis=1)
img_pred = create_img_from_pred(self.vx_all, pred_all,
img_true.shape)
# Compute the dice coefficient and the error
non_zo = img_pred.nonzero() or img_true.nonzero()
pred = img_pred[non_zo]
true = img_true[non_zo]
dice_regions = compute_dice(pred, true, n_out)
dices.append(dice_regions.mean())
err_global = error_rate(pred, true)
errs.append(err_global)
count = count + 1
return dices, errs
region_centroids,
batch_size, True)
vx_all, pred_all = net.predict_from_generator(brain_batches, scaler,
pred_functions)
# Construct the predicted image
img_true = data_gen.atlases[atlas_id][1]
img_pred = create_img_from_pred(vx_all, pred_all, img_true.shape)
# Compute the dice coefficient and the error
non_zo = img_pred.nonzero() or img_true.nonzero()
pred = img_pred[non_zo]
true = img_true[non_zo]
dice_regions = compute_dice(pred, true, n_out)
err_global = error_rate(pred, true)
end_time = time.clock()
print "It took {} seconds to evaluate the whole brain.".format(
end_time - start_time)
print "The mean dice is {}".format(dice_regions.mean())
print "The error rateis {}".format(err_global)
# Save the results
errors[atlas_id] = err_global
dices[atlas_id, :] = dice_regions
# Diff Image
img_diff = (img_pred == img_true).astype(np.uint8)
img_diff += 1
img_diff[img_pred == 0] = 0
ls_vx = []
ls_pred = []
brain_batches = data_gen.generate_single_atlas(atlas_id, None, region_centroids, batch_size, True)
vx_all, pred_all = net.predict_from_generator(brain_batches, scaler, pred_functions)
# Construct the predicted image
img_true = data_gen.atlases[atlas_id][1]
img_pred = create_img_from_pred(vx_all, pred_all, img_true.shape)
# Compute the dice coefficient and the error
non_zo = img_pred.nonzero() or img_true.nonzero()
pred = img_pred[non_zo]
true = img_true[non_zo]
dice_regions = compute_dice(pred, true, n_out)
err_global = error_rate(pred, true)
end_time = time.clock()
print "It took {} seconds to evaluate the whole brain.".format(end_time - start_time)
print "The mean dice is {}".format(dice_regions.mean())
print "The error rateis {}".format(err_global)
# Save the results
errors[atlas_id] = err_global
dices[atlas_id, :] = dice_regions
# Diff Image
img_diff = (img_pred == img_true).astype(np.uint8)
img_diff += 1
img_diff[img_pred == 0] = 0