def create_model():
from elektronn2 import neuromancer
in_sh = (None, 1, 111+16*5, 111+16*5, 13+4*5)
inp = neuromancer.Input(in_sh, 'b,f,x,y,z', name='raw')
out = neuromancer.Conv(inp, 12, (6, 6, 1), (2, 2, 1))
out = neuromancer.Conv(out, 24, (4, 4, 1), (2, 2, 1))
out = neuromancer.Conv(out, 36, (4, 4, 4), (2, 2, 2))
out = neuromancer.Conv(out, 48, (4, 4, 2), (2, 2, 2))
out = neuromancer.Conv(out, 48, (4, 4, 2), (1, 1, 1))
out = neuromancer.Conv(out, 4, (1, 1, 1), (1, 1, 1),
activation_func='lin', name='sy')
probs = neuromancer.Softmax(out)
target = neuromancer.Input_like(probs, override_f=1, name='target')
loss_pix = neuromancer.MultinoulliNLL(probs, target, target_is_sparse=True)
loss = neuromancer.AggregateLoss(loss_pix, name='loss')
errors = neuromancer.Errors(probs, target, target_is_sparse=True)
model = neuromancer.model_manager.getmodel()
model.designate_nodes(
input_node=inp,
target_node=target,
loss_node=loss,
prediction_node=probs,
prediction_ext=[loss, errors, probs]
)
return model
def create_model():
from elektronn2 import neuromancer as nm
in_sh = (None, 1, 11, 155, 155)
inp = nm.Input(in_sh, 'b,f,z,x,y', name='raw')
out = nm.Conv(inp, 20, (1, 4, 4), (1, 2, 2))
out = nm.Conv(out, 40, (3, 3, 3), (1, 2, 2))
out = nm.Conv(out, 150, (2, 4, 4), (2, 1, 1))
out = nm.Conv(out, 200, (1, 3, 3))
out = nm.Conv(out, 200, (1, 3, 3))
out = nm.Conv(out, 200, (1, 1, 1))
out = nm.Conv(out, 2, (1, 1, 1), activation_func='lin')
probs = nm.Softmax(out)
target = nm.Input_like(probs, override_f=1, name='target')
loss_pix = nm.MultinoulliNLL(probs, target, target_is_sparse=True)
loss = nm.AggregateLoss(loss_pix, name='loss')
errors = nm.Errors(probs, target, target_is_sparse=True)
model = nm.model_manager.getmodel()
model.designate_nodes(input_node=inp,
target_node=target,
loss_node=loss,
prediction_node=probs,
prediction_ext=[loss, errors, probs])
return model
def create_model():
from elektronn2 import neuromancer as nm
in_sh = (None, 1, 26, 26)
inp = nm.Input(in_sh, 'b,f,y,x', name='raw')
out = nm.Conv(inp, 12, (3, 3), (2, 2), batch_normalisation='train')
out = nm.Conv(out, 36, (3, 3), (2, 2), batch_normalisation='train')
out = nm.Conv(out, 64, (3, 3), (1, 1), batch_normalisation='train')
out = nm.Perceptron(out, 200, flatten=True)
out = nm.Perceptron(out, 10, activation_func='lin')
out = nm.Softmax(out)
target = nm.Input_like(out, override_f=1, name='target')
loss = nm.MultinoulliNLL(out, target, name='nll_', target_is_sparse=True)
# Objective
loss = nm.AggregateLoss(loss)
# Monitoring / Debug outputs
errors = nm.Errors(out, target, target_is_sparse=True)
model = nm.model_manager.getmodel()
model.designate_nodes(input_node=inp,
target_node=target,
loss_node=loss,
prediction_node=out,
prediction_ext=[loss, errors, out])
return model
def create_model():
from elektronn2 import neuromancer
in_sh = (20, 20 * 58)
inp = neuromancer.Input(in_sh, 'b,f', name='raw')
out = neuromancer.Perceptron(inp, 700, 'lin')
out = neuromancer.Perceptron(inp, 500, 'lin')
out = neuromancer.Perceptron(inp, 300, 'lin')
out = neuromancer.Perceptron(out, 2*58, 'lin')
out = neuromancer.Softmax(out, n_indep=58)
target = neuromancer.Input_like(out, override_f=1, name='target')
weights = neuromancer.ValueNode((116, ), 'f', value=[0.2, 1.8]*58)
loss = neuromancer.MultinoulliNLL(
out, target, target_is_sparse=True, class_weights=weights, name='nll'
)
# Objective
loss = neuromancer.AggregateLoss(loss)
# Monitoring / Debug outputs
errors = neuromancer.Errors(out, target, target_is_sparse=True)
model = neuromancer.model_manager.getmodel()
model.designate_nodes(
input_node=inp,
target_node=target,
loss_node=loss,
prediction_node=out,
prediction_ext=[loss, errors, out]
)
return model
def create_model():
import numpy as np
from elektronn2 import neuromancer
from elektronn2.neuromancer import graph_manager
from elektronn2.model import Model
graph_manager.reset()
inp = neuromancer.Input((1, 1, 1, 59, 59), 'b,f,x,y,z', name='raw')
out = neuromancer.Conv(inp, 2, (1, 6, 6), (1, 2, 2), dropout_rate=0.8)
out = neuromancer.Conv(out, 3, (1, 6, 6), (1, 2, 2), dropout_rate=0.5)
out = neuromancer.Conv(out, 4, (1, 4, 4), (1, 1, 1))
out = neuromancer.Conv(out, 5, (1, 1, 1), (1, 1, 1))
out = neuromancer.Conv(out, 2, (1, 1, 1), (1, 1, 1), activation_func='lin')
out = neuromancer.Softmax(out, n_indep=1, name='probs')
l_sh = out.shape.copy()
l_sh.updateshape('f', 1)
l = neuromancer.Input_like(l_sh, dtype='int16', name='labels')
loss_pix = neuromancer.MultinoulliNLL(out, l, target_is_sparse=True)
loss = neuromancer.AggregateLoss(loss_pix, name='nll')
graph_manager.designate_nodes(input=inp,
target=l,
loss=loss,
prediction=out,
prediction_ext=[loss, loss, out])
m = Model(graph_manager)
return m
def create_model():
from elektronn2 import neuromancer
act = 'relu'
in_sh = (batch_size, 1 if data_init_kwargs["raw_only"] else 4, nb_views,
int(x), int(y))
inp = neuromancer.Input(in_sh, 'b,f,z,y,x', name='raw')
out0 = neuromancer.Conv(inp,
13, (1, 5, 5), (1, 2, 2),
activation_func=act,
dropout_rate=dr)
out0 = neuromancer.Conv(out0,
19, (1, 5, 5), (1, 2, 2),
activation_func=act,
dropout_rate=dr)
out0 = neuromancer.Conv(out0,
25, (1, 4, 4), (1, 2, 2),
activation_func=act,
dropout_rate=dr)
out0 = neuromancer.Conv(out0,
25, (1, 4, 4), (1, 2, 2),
activation_func=act,
dropout_rate=dr)
out0 = neuromancer.Conv(out0,
30, (1, 2, 2), (1, 2, 2),
activation_func=act,
dropout_rate=dr)
out0 = neuromancer.Conv(out0,
30, (1, 1, 1), (1, 2, 2),
activation_func=act,
dropout_rate=dr)
out = neuromancer.Conv(out0,
31, (1, 1, 1), (1, 1, 1),
activation_func=act,
dropout_rate=dr)
out = neuromancer.Perceptron(out, 50, flatten=True, dropout_rate=dr)
out = neuromancer.Perceptron(out, 30, flatten=True, dropout_rate=dr)
out = neuromancer.Perceptron(out, 4, activation_func='lin')
out = neuromancer.Softmax(out)
target = neuromancer.Input_like(out, override_f=1, name='target')
weights = neuromancer.ValueNode((4, ), 'f', value=(1, 1, 2, 2))
loss = neuromancer.MultinoulliNLL(out,
target,
name='nll_',
target_is_sparse=True,
class_weights=weights)
# Objective
loss = neuromancer.AggregateLoss(loss)
# Monitoring / Debug outputs
errors = neuromancer.Errors(out, target, target_is_sparse=True)
model = neuromancer.model_manager.getmodel()
model.designate_nodes(input_node=inp,
target_node=target,
loss_node=loss,
prediction_node=out,
prediction_ext=[loss, errors, out])
return model
def demo_new_split():
act = 'tanh'
data = neuromancer.Input((30, 10, 20), 'r,b,f', name='data')
a, b = neuromancer.split(data, axis='r', index=1, name=['a', 'b'])
c, d = neuromancer.split(data,
axis='r',
index=1,
strip_singleton_dims=True)
x = np.random.rand(30, 10, 20).astype(np.float32)
aa, bb = a(x), b(x)
cc, dd = c(x), d(x)
print(aa.shape, bb.shape, cc.shape, dd.shape)
model = neuromancer.model_manager.current
model.designate_nodes(input_node=data)
# , target_node=target, loss_node=loss,
# prediction_node=pred,
# prediction_ext=[loss, nll_barr, pred],
# debug_outputs =[nll_barr, nll_obj, nll_branch, mse_skel])
model.save("/tmp/test.mdl")
model2 = neuromancer.model.modelload("/tmp/test.mdl")
def create_model():
from elektronn2 import neuromancer as nm
in_sh = (None, 1, 22, 140, 140)
inp = nm.Input(in_sh, 'b,f,z,x,y', name='raw') # high res
# Convolution, downsampling of intermediate features
conv0 = nm.Conv(inp, 20, (1, 3, 3))
conv1 = nm.Conv(conv0, 20, (1, 3, 3))
down0 = nm.Pool(conv1, (1, 2, 2), mode='max') # mid res
conv2 = nm.Conv(down0, 30, (1, 3, 3))
conv3 = nm.Conv(conv2, 30, (1, 3, 3))
down1 = nm.Pool(conv3, (1, 2, 2), mode='max') # low res
conv4 = nm.Conv(down1, 35, (1, 3, 3))
conv5 = nm.Conv(conv4, 35, (1, 3, 3))
down2 = nm.Pool(conv5, (1, 2, 2), mode='max') # very low res
conv6 = nm.Conv(down2, 42, (3, 3, 3))
down2b = nm.Pool(conv6, (1, 2, 2), mode='max') # very low res, even lower
conv7 = nm.Conv(down2b, 42, (3, 3, 3))
# Merging very low-res features with low-res features
mrg0 = nm.UpConvMerge(conv5, conv7, 45)
mconv0 = nm.Conv(mrg0, 42, (1, 3, 3))
mconv1 = nm.Conv(mconv0, 42, (1, 3, 3))
# Merging low-res with mid-res features
mrg1 = nm.UpConvMerge(conv3, mconv1, 42)
mconv2 = nm.Conv(mrg1, 35, (3, 3, 3))
mconv3 = nm.Conv(mconv2, 35, (3, 3, 3))
# Merging mid-res with high-res features
mrg2 = nm.UpConvMerge(conv1, mconv3, 30)
mconv4 = nm.Conv(mrg2, 20, (3, 3, 3))
mconv5 = nm.Conv(mconv4, 20, (3, 3, 3))
barr = nm.Conv(mconv5, 2, (1, 1, 1), activation_func='lin', name='barr')
probs = nm.Softmax(barr)
target = nm.Input_like(mconv5, override_f=1, name='target')
loss_pix = nm.MultinoulliNLL(probs,
target,
target_is_sparse=True,
name='nll_barr')
loss = nm.AggregateLoss(loss_pix, name='loss')
errors = nm.Errors(probs, target, target_is_sparse=True)
model = nm.model_manager.getmodel()
model.designate_nodes(input_node=inp,
target_node=target,
loss_node=loss,
prediction_node=probs,
prediction_ext=[loss, errors, probs])
return model
def demo_restore():
# records = ut.pickleload('/tmp/model.pkl')
# graph_manager.restore(records)
# print "="*50
# print "="*50
# out = graph_manager.sinks
# print out
# x_val = np.linspace(0,1, num=64*784).astype(np.float32).reshape((64, 784))
# loss = graph_manager.nodes['loss']
# enc_mu = graph_manager.nodes['enc mu']
# print loss(x_val)
# print enc_mu(x_val)
# pack = False
# if pack:
# inp = gr.Input((2,6,20,20), 'b,f,x,y')
# out1, out2 = gr.split(inp, 'f', 2, name='test_split')
# x_val = np.random.rand(2,6,20,20).astype(np.float32)
# print out1(x_val).shape, out2(x_val).shape
# ut.picklesave(graph_manager.get_records(), '/tmp/model2.pkl')
# print graph_manager.nodes.keys()
#
# if not pack:
# graph_manager.reset()
# records = ut.pickleload('/tmp/model2.pkl')
# graph_manager.restore(records)
# print "="*50
# print "="*50
# out = graph_manager.sinks
# print out
# out1 = graph_manager.nodes['test_split1']
# out2 = graph_manager.nodes['test_split2']
# x_val = np.random.rand(2,6,20,20).astype(np.float32)
# print out1(x_val).shape, out2(x_val).shape
# print graph_manager.nodes.keys()
in_sh = (1, 1, 183, 183, 31)
x = gr.Input(in_sh, 'b,f,z,x,y')
in_val = np.random.rand(*in_sh).astype(np.float32)
y1 = Conv(x, 12, (1, 6, 6)[::-1], (1, 2, 2)[::-1], mfp=False)
y2 = Conv(y1, 24, (4, 4, 4)[::-1], (2, 2, 2)[::-1], mfp=False)
y3 = Conv(y2, 64, (4, 4, 4)[::-1], (1, 2, 2)[::-1], mfp=False)
y4 = Conv(y3, 64, (4, 4, 4)[::-1], (1, 1, 1)[::-1], mfp=False)
# z4 = Perceptron(y4, 12)
s4 = UpConv(y4, 64, (4, 4, 4), (2, 2, 2))
d4 = y4.make_dual(y4, activation_func='lin')
p4 = gr.Softmax(d4)
lab = gr.Input_like(p4, name='lab')
loss = gr.loss.MultinoulliNLL(p4, lab)
def demo_pooling_2d():
img = plt.imread(os.path.expanduser('~/devel/Lichtenstein.png')).transpose(
(2, 0, 1))[None, ]
sig_shape = img.shape
# x_val = np.random.rand(*sig_shape).astype(np.float32)
inp = neuromancer.Input(sig_shape, 'b,f,x,y')
conv = neuromancer.Conv(inp, 3, (3, 3), (3, 3), activation_func='tanh')
w = np.zeros((3, 3, 3, 3), dtype=np.float32)
w[[0, 1, 2], [0, 1, 2]] = 1
upconv = neuromancer.UpConv(conv, 3, (3, 3), activation_func='tanh')
upconv.w.set_value(upconv.w.get_value() * 0.07 + w)
y0 = conv(img)
y2 = upconv(img)
plt.imshow(y0[0].transpose((1, 2, 0)), interpolation='none')
plt.show()
plt.figure()
plt.imshow(y2[0].transpose((1, 2, 0)), interpolation='none')
plt.show()
def create_model():
from elektronn2 import neuromancer
in_sh = (40, 40, 58)
inp = neuromancer.Input(in_sh, 'r,b,f', name='raw')
inp0, _ = neuromancer.split(inp, 'r', index=1, strip_singleton_dims=True)
inp_mem = neuromancer.InitialState_like(inp0,
override_f=750,
init_kwargs={
'mode': 'fix-uni',
'scale': 0.1
})
out = neuromancer.GRU(inp0, inp_mem, 750)
out = neuromancer.Scan(out,
inp_mem,
in_iterate=inp,
in_iterate_0=inp0,
n_steps=40,
last_only=True)
out = neuromancer.Perceptron(out, 2 * 58, 'lin')
out = neuromancer.Softmax(out, n_indep=58)
target = neuromancer.Input_like(out, override_f=1, name='target')
weights = neuromancer.ValueNode((116, ), 'f', value=(0.2, 1.8))
loss = neuromancer.MultinoulliNLL(out,
target,
name='nll',
target_is_sparse=True,
class_weights=weights)
# Objective
loss = neuromancer.AggregateLoss(loss)
# Monitoring / Debug outputs
errors = neuromancer.Errors(out, target, target_is_sparse=True)
model = neuromancer.model_manager.getmodel()
model.designate_nodes(input_node=inp,
target_node=target,
loss_node=loss,
prediction_node=out,
prediction_ext=[loss, errors, out])
return model
def create_model():
from elektronn2 import neuromancer
import theano.tensor as T
import numpy as np
in_sh = (None,1,572-32*9,572-32*9)
img = neuromancer.Input(in_sh, 'b,f,x,y', name='raw')
out0 = neuromancer.Conv(img, 64, (3,3), (1,1))
out1 = neuromancer.Conv(out0, 64, (3,3), (1,1))
out2 = neuromancer.Pool(out1, (2,2))
out3 = neuromancer.Conv(out2, 128, (3,3), (1,1))
out4 = neuromancer.Conv(out3, 128, (3,3), (1,1))
out5 = neuromancer.Pool(out4, (2,2))
out6 = neuromancer.Conv(out5, 256, (3,3), (1,1))
out7 = neuromancer.Conv(out6, 256, (3,3), (1,1))
out8 = neuromancer.Pool(out7, (2,2))
out9 = neuromancer.Conv(out8, 512, (3,3), (1,1))
out10 = neuromancer.Conv(out9, 512, (3,3), (1,1))
out11 = neuromancer.Pool(out10, (2,2))
out12 = neuromancer.Conv(out11, 1024, (3,3), (1,1))
out13 = neuromancer.Conv(out12, 1024, (3,3), (1,1))
out14 = neuromancer.Pool(out13, (2,2))
####
up0 = neuromancer.UpConvMerge(out10, out14, 1024)
up1 = neuromancer.Conv(up0, 512, (3,3), (1,1))
up2 = neuromancer.Conv(up1, 512, (3,3), (1,1))
up3 = neuromancer.UpConvMerge(out7, up2, 512)
up4 = neuromancer.Conv(up3, 256, (3,3), (1,1))
up5 = neuromancer.Conv(up4, 256, (3,3), (1,1))
up6 = neuromancer.UpConvMerge(out4, up5, 256)
up7 = neuromancer.Conv(up6, 128, (3,3), (1,1))
up8 = neuromancer.Conv(up7, 128, (3,3), (1,1))
up9 = neuromancer.UpConvMerge(out1, up8, 128)
up10 = neuromancer.Conv(up9, 64, (3,3), (1,1))
top_feat = neuromancer.Conv(up10, 64, (3,3), (1,1))
# Target outputs
barr_out = neuromancer.Conv(top_feat, 3, (1,1), (1,1), activation_func='lin', name='barr')
obj_out = neuromancer.Conv(top_feat, 4, (1,1), (1,1), activation_func='lin', name='obj')
my_out = neuromancer.Conv(top_feat, 3, (1,1), (1,1), activation_func='lin', name='my')
barr_out = neuromancer.Softmax(barr_out)
obj_out = neuromancer.Softmax(obj_out)
my_out = neuromancer.Softmax(my_out)
target = neuromancer.Input_like(top_feat, dtype='int16', override_f=3, name='target')
barr, obj, my = neuromancer.split(target, 'f', n_out=3, name=['barr_t', 'obj_t', 'my_t'])
# Target loss
barr_loss_pix = neuromancer.MultinoulliNLL(barr_out, barr, target_is_sparse=True,name='nll_barr')
obj_loss_pix = neuromancer.MultinoulliNLL(obj_out, obj, target_is_sparse=True, name='nll_obj')
my_loss_pix = neuromancer.MultinoulliNLL(my_out, my, target_is_sparse=True, name='nll_my')
pred = neuromancer.Concat([barr_out, obj_out, my_out], axis='f')
pred.feature_names = ['barrier_bg', 'barr_mem', 'barr_ecs', 'obj_bg',
'obj_mito', 'obj_ves', 'obj_syn', 'my_bg', 'my_out', 'my_in']
# Objective
weights = np.array([2.154, 0.42, 0.42])
weights *= len(weights) / weights.sum()
loss = neuromancer.AggregateLoss([barr_loss_pix,
obj_loss_pix,
my_loss_pix],
mixing_weights=weights)
# Monitoring / Debug outputs
nll_barr = neuromancer.ApplyFunc(barr_loss_pix, T.mean, name='mnll_barr')
nll_obj = neuromancer.ApplyFunc(obj_loss_pix, T.mean, name='mnll_obj')
nll_my = neuromancer.ApplyFunc(my_loss_pix, T.mean, name='mnll_my')
errors = neuromancer.Errors(barr_out, barr, target_is_sparse=True)
model = neuromancer.model_manager.getmodel()
model.designate_nodes(input_node=img, target_node=target, loss_node=loss,
prediction_node=pred,
prediction_ext=[loss, errors, pred],
debug_outputs =[nll_barr, errors, nll_obj, nll_my])
return model
def create_model():
from elektronn2 import neuromancer
act = 'relu'
in_sh = (batch_size, 4, 3, 128, 256)
inp = neuromancer.Input(in_sh, 'b,f,z,y,x', name='raw')
out0 = neuromancer.Conv(inp,
13, (1, 5, 5), (1, 2, 2),
activation_func=act,
dropout_rate=dr)
out0 = neuromancer.Conv(out0,
19, (1, 5, 5), (1, 2, 2),
activation_func=act,
dropout_rate=dr)
out0 = neuromancer.Conv(out0,
25, (1, 4, 4), (1, 2, 2),
activation_func=act,
dropout_rate=dr)
out0 = neuromancer.Conv(out0,
25, (1, 4, 4), (1, 2, 2),
activation_func=act,
dropout_rate=dr)
out0 = neuromancer.Conv(out0,
30, (1, 2, 2), (1, 2, 2),
activation_func=act,
dropout_rate=dr)
out0 = neuromancer.Conv(out0,
30, (1, 1, 1), (1, 2, 2),
activation_func=act,
dropout_rate=dr)
out = neuromancer.Conv(out0,
31, (1, 1, 1), (1, 1, 1),
activation_func=act,
dropout_rate=dr)
out0, out1, out2 = neuromancer.split(out, axis="z", n_out=3)
out0 = neuromancer.Reshape(out0,
shape=(inp.shape[0], out0.shape.stripbatch_prod,
1),
tags="b,f,z")
out1 = neuromancer.Reshape(out1,
shape=(inp.shape[0], out1.shape.stripbatch_prod,
1),
tags="b,f,z")
out2 = neuromancer.Reshape(out2,
shape=(inp.shape[0], out2.shape.stripbatch_prod,
1),
tags="b,f,z")
out = neuromancer.Concat([out0, out1, out2], axis="z")
out = neuromancer.Perceptron(out, 40, flatten=False, dropout_rate=dr)
out = neuromancer.Perceptron(out, 10, flatten=False, dropout_rate=dr)
out0, out1, out2 = neuromancer.split(out, axis="z", n_out=3)
d_small = neuromancer.EuclideanDistance(out0, out1)
d_big = neuromancer.EuclideanDistance(out0, out2)
loss = neuromancer.RampLoss(d_small, d_big, margin=0.2)
loss = neuromancer.AggregateLoss(loss)
model = neuromancer.model_manager.getmodel()
# model = neuromancer.model.modelload("/wholebrain/scratch/pschuber/CNN_Training/nupa_cnn/t_net/ssv6_tripletnet_v9/ssv6_tripletnet_v9-FINAL.mdl")
model.designate_nodes(input_node=inp,
target_node=None,
loss_node=loss,
prediction_node=out,
prediction_ext=[loss, loss, out])
# params = neuromancer.model.params_from_model_file("/wholebrain/scratch/pschuber/CNN_Training/nupa_cnn/t_net/ssv6_tripletnet_v9/ssv6_tripletnet_v9-FINAL.mdl")
# params = dict(filter(lambda x: x[0].startswith('conv'), params.items()))
# model.set_param_values(params)
return model
# if __name__ == "__main__":
# model = create_model()
# "Test" if model is saveable
# model.save("/tmp/"+save_name)
])
f_grad = theano.function([x, skel_var], grad_var + [loss_var, pred_var])
test_vals = np.array([1, 2, 3], dtype=np.float32)
skel = DummySkel()
print(f(test_vals, skel))
print(f_grad(test_vals, skel))
theano.printing.pydotprint(f_grad, '/tmp/step_result.svg')
###########################################################################
from elektronn2 import neuromancer
import theano
act = 'tanh'
data = neuromancer.Input((1, 20), 'b,f', name='data')
mem_0 = neuromancer.Input((1, 120), 'b,f', name='mem')
mlp1 = neuromancer.Dot(data, 120, activation_func=act)
join = neuromancer.Concat([mlp1, mem_0])
out = neuromancer.Dot(join, 120, activation_func=act)
out2 = neuromancer.Dot(out, 13, activation_func='lin')
# recurrent = neuromancer.Scan(out, in_memory=mem_0, n_steps=10)
recurrent, out2r = neuromancer.Scan([out, out2],
out_memory=out,
in_memory=mem_0,
n_steps=7)
loss = neuromancer.AggregateLoss(recurrent)
loss = neuromancer.AggregateLoss(out2r)
grad = theano.grad(loss.output,
loss.all_trainable_params.values(),
"/Users/liammcgoldrick/Code/ELEKTRONN2/examples/affinities.npy") raw_data = np.asarray(raw_data) print(np.shape(affinities)) #data is in format: # raw data=(1,16,128,128) as NP array # affinities=(3,16,128,128) as NP array ################### # BUILD GRAPH # ################### in_sh = (None, 1, 16, 128, 128) inp = nm.Input(in_sh, 'b,f,z,x,y', name='raw') # high res # Convolution, downsampling of intermediate features conv0 = nm.Conv(inp, 8, (15, 15, 15), (1, 1, 1), "same", name="c0") down0 = nm.Pool(conv0, (1, 4, 4), mode="max", name="d0") #full conv1 = nm.Conv(down0, 32, (15, 15, 15), (1, 1, 1), "same", name="c1") down1 = nm.Pool(conv1, (1, 2, 2), mode="max", name="d1") #high conv2 = nm.Conv(down1, 64, (15, 15, 15), (1, 1, 1), "same", name="c2") #mid down2 = nm.Pool(conv2, (1, 2, 2), mode="max", name="d2") #high conv3 = nm.Conv(down2, 64, (15, 15, 15), (1, 1, 1), "same", name="c3") #low #merge C2 and C3 and convolve
def demo_new_gm():
mfp = False
in_sh = (1, 1, 15, 198, 198) if mfp else (1, 1, 25, 171, 171)
inp = neuromancer.Input(in_sh, 'b,f,z,x,y', name='raw')
out = neuromancer.Conv(inp,
20, (1, 6, 6), (1, 1, 1),
mfp=mfp,
batch_normalisation='train')
out = neuromancer.Conv(out, 40, (1, 5, 5), (1, 2, 2), mfp=mfp)
out = neuromancer.Conv(out, 50, (1, 4, 4), (1, 2, 2), mfp=mfp)
out = neuromancer.Conv(out, 80, (1, 4, 4), (1, 1, 1), mfp=mfp)
out = neuromancer.Conv(out, 80, (4, 1, 1), (2, 1, 1),
mfp=mfp) # first z kernel, 2 pool
out = neuromancer.Conv(out, 80, (3, 4, 4), (1, 1, 1), mfp=mfp)
out = neuromancer.Conv(out, 80, (3, 4, 4), (1, 1, 1), mfp=mfp)
out = neuromancer.Conv(out, 100, (2, 4, 4), (1, 1, 1), mfp=mfp)
out = neuromancer.Conv(out, 120, (2, 4, 4), (1, 1, 1), mfp=mfp)
out = neuromancer.Conv(out, 120, (1, 2, 2), (1, 1, 1), mfp=mfp)
out = neuromancer.Conv(out, 120, (1, 1, 1), (1, 1, 1), mfp=mfp)
out1, out2 = neuromancer.split(out, 1, n_out=2)
probs = neuromancer.Conv(out1,
2, (1, 1, 1), (1, 1, 1),
mfp=mfp,
activation_func='lin')
probs = neuromancer.Softmax(probs, name='probs')
discard, mode = neuromancer.split(probs, 1, n_out=2)
concentration = neuromancer.Conv(out2,
1, (1, 1, 1), (1, 1, 1),
mfp=mfp,
activation_func='lin',
name='concentration')
t_sh = probs.shape.copy()
t_sh.updateshape('f', 1)
target = neuromancer.Input_like(t_sh, dtype='float32', name='target')
loss_pix = neuromancer.BetaNLL(mode, concentration, target)
loss = neuromancer.AggregateLoss(loss_pix)
errors = neuromancer.Errors(probs, target, target_is_sparse=True)
prediction = neuromancer.Concat([mode, concentration],
axis=1,
name='prediction')
loss_std = neuromancer.ApplyFunc(loss_pix, T.std)
model = neuromancer.model_manager.getmodel()
model.designate_nodes(input_node=inp,
target_node=target,
loss_node=loss,
prediction_node=prediction,
prediction_ext=[loss, errors, prediction])
### --- ###
model2 = neuromancer.model_manager.newmodel("second")
inp2 = neuromancer.Input(in_sh, 'b,f,z,x,y', name='raw')
out2 = neuromancer.Conv(inp2, 20, (1, 6, 6), (1, 1, 1), mfp=mfp)
out2 = neuromancer.Conv(out2, 40, (1, 5, 5), (1, 2, 2), mfp=mfp)
out2 = neuromancer.Conv(out2, 50, (1, 4, 4), (1, 2, 2), mfp=mfp)
out2 = neuromancer.Conv(out2, 120, (2, 4, 4), (1, 1, 1), mfp=mfp)
out2 = neuromancer.Conv(out2, 120, (1, 2, 2), (1, 1, 1), mfp=mfp)
out2 = neuromancer.Conv(out2, 120, (1, 1, 1), (1, 1, 1), mfp=mfp)
probs2 = neuromancer.Conv(out2,
2, (1, 1, 1), (1, 1, 1),
mfp=mfp,
activation_func='lin')
probs2 = neuromancer.Softmax(probs2, name='probs')
t_sh = probs2.shape.copy()
t_sh.updateshape('f', 1)
target2 = neuromancer.Input_like(t_sh, dtype='float32', name='target')
loss_pix2 = neuromancer.MultinoulliNLL(probs2, target2)
loss2 = neuromancer.AggregateLoss(loss_pix2)
errors2 = neuromancer.Errors(probs2, target2, target_is_sparse=True)
model2.designate_nodes(input_node=inp2,
target_node=target2,
loss_node=loss2,
prediction_node=probs2,
prediction_ext=[loss2, errors2, probs2])
model.save('/tmp/test.pkl')
model2.save('/tmp/test2.pkl')
model2_reloaded = modelload('/tmp/test2.pkl')
model2_reloaded.save('/tmp/test2_reloaded.pkl')
print(neuromancer.model_manager)
