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make_3D_DenseSeg.py
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from __future__ import print_function
caffe_root = '/home/toanhoi/caffe/'
import sys
sys.path.insert(0, caffe_root + 'python')
import caffe
import math
from caffe import layers as L
from caffe.proto import caffe_pb2
def bn_relu_conv_bn_relu(bottom, nout, dropout,split):
if split == 'train':
use_global_stats = False
else:
use_global_stats=True
batch_norm1 = L.BatchNorm(bottom, batch_norm_param=dict(use_global_stats=use_global_stats), in_place=False,
param=[dict(lr_mult=0, decay_mult=0), dict(lr_mult=0, decay_mult=0),
dict(lr_mult=0, decay_mult=0)])
scale1 = L.Scale(batch_norm1, bias_term=True, in_place=True,filler=dict(value=1), bias_filler=dict(value=0))
relu1 = L.ReLU(scale1, in_place=True)
conv1 = L.Convolution(relu1, kernel_size=[1, 1, 1], pad=[0, 0, 0], stride=[1,1,1],
param=[dict(lr_mult=1, decay_mult=1)], bias_term=False,
num_output=nout * 4, axis=1, weight_filler=dict(type='msra'),
bias_filler=dict(type='constant'))
batch_norm2 = L.BatchNorm(conv1, batch_norm_param=dict(use_global_stats=use_global_stats), in_place=False,
param=[dict(lr_mult=0, decay_mult=0), dict(lr_mult=0, decay_mult=0),
dict(lr_mult=0, decay_mult=0)])
scale2 = L.Scale(batch_norm2, bias_term=True, in_place=True,filler=dict(value=1), bias_filler=dict(value=0))
relu2 = L.ReLU(scale2, in_place=True)
conv2 = L.Convolution(relu2, param=[dict(lr_mult=1, decay_mult=1)], bias_term=False,
axis=1, num_output=nout, pad=[1, 1, 1], kernel_size=[3, 3, 3], stride=[1,1,1],
weight_filler=dict(type='msra'), bias_filler=dict(type='constant'))
if dropout > 0:
conv2 = L.Dropout(conv2, dropout_ratio=dropout)
return conv2
def add_layer(bottom, num_filter, dropout,split):
conv = bn_relu_conv_bn_relu(bottom, nout=num_filter, dropout=dropout,split=split)
concate = L.Concat(bottom, conv, axis=1)
return concate
def transition(bottom, num_filter, split):
if split == 'train':
use_global_stats = False
else:
use_global_stats=True
batch_norm1 = L.BatchNorm(bottom, batch_norm_param=dict(use_global_stats=use_global_stats), in_place=False,
param=[dict(lr_mult=0, decay_mult=0), dict(lr_mult=0, decay_mult=0),
dict(lr_mult=0, decay_mult=0)])
scale1 = L.Scale(batch_norm1, bias_term=True, in_place=True,filler=dict(value=1), bias_filler=dict(value=0))
relu1 = L.ReLU(scale1, in_place=True)
conv1 = L.Convolution(relu1, param=[dict(lr_mult=1, decay_mult=1)], bias_term=False,
axis=1, num_output=num_filter, pad=[0, 0, 0], kernel_size=[1, 1, 1],stride=[1,1,1],
weight_filler=dict(type='msra'), bias_filler=dict(type='constant'))
batch_norm2 = L.BatchNorm(conv1, batch_norm_param=dict(use_global_stats=use_global_stats), in_place=False,
param=[dict(lr_mult=0, decay_mult=0), dict(lr_mult=0, decay_mult=0),
dict(lr_mult=0, decay_mult=0)])
scale2 = L.Scale(batch_norm2, bias_term=True, in_place=True, filler=dict(value=1), bias_filler=dict(value=0))
relu2 = L.ReLU(scale2, in_place=True)
conv_down = L.Convolution(relu2, param=[dict(lr_mult=1, decay_mult=1)], bias_term=False,
axis=1, num_output=num_filter, pad=[0, 0, 0], kernel_size=[2, 2, 2], stride=2,
weight_filler=dict(type='msra'), bias_filler=dict(type='constant'))
#pooling = L.Pooling(conv1, type="Pooling", pool=P.Pooling.MAX, kernel_size=2, stride=2, engine=1)
return conv_down
# first_output -- #channels before entering the first dense block, set it to be comparable to growth_rate
# growth_rate -- growth rate
# dropout -- set to 0 to disable dropout, non-zero number to set dropout rate
def densenet(split, batch_size=4, first_output=32, growth_rate=16, dropout=0.2):
source_train_path = './train_list.txt'
source_test_path = './test_list.txt'
patch_size = [64, 64, 64]
n = caffe.NetSpec()
num_classes = 4
reduction= 0.5
N=[4,4,4,4]
if split == 'train':
n.data, n.label = L.HDF5Data(name="data", batch_size=batch_size, source=source_train_path, ntop=2, shuffle=True,
transform_param=dict(crop_size_l=patch_size[0], crop_size_h=patch_size[1],
crop_size_w=patch_size[2]), include={'phase': caffe.TRAIN})
elif split == 'val':
n.data, n.label = L.HDF5Data(name="data", batch_size=batch_size, source=source_test_path, ntop=2, shuffle=True,
transform_param=dict(crop_size_l=patch_size[0], crop_size_h=patch_size[1],
crop_size_w=patch_size[2]),
include={'phase': caffe.TEST})
else:
n.data = L.Input(name="data", ntop=1, input_param={'shape': {'dim': [1, 2, patch_size[0], patch_size[1], patch_size[2]]}})
nchannels = first_output
# Fist layers
n.conv1a = L.Convolution(n.data, param=[dict(lr_mult=1, decay_mult=1), dict(lr_mult=2, decay_mult=0)],
axis=1, num_output=nchannels, pad=[1,1,1], kernel_size=[3, 3, 3], stride=[1,1,1],
weight_filler=dict(type='msra'), bias_filler=dict(type='constant',value=-0.1))
if split == 'train':
use_global_stats = False
else:
use_global_stats=True
n.bnorm1a = L.BatchNorm(n.conv1a, batch_norm_param=dict(use_global_stats=use_global_stats), param=[dict(lr_mult=0, decay_mult=0), dict(lr_mult=0, decay_mult=0),
dict(lr_mult=0, decay_mult=0)], in_place=False)
n.scale1a = L.Scale(n.bnorm1a, in_place=True, bias_term=True,filler=dict(value=1), bias_filler=dict(value=0))
n.relu1a = L.ReLU(n.bnorm1a, in_place=True)
# conv 1b, after BN set bias_term=false
n.conv1b = L.Convolution(n.relu1a, param=[dict(lr_mult=1, decay_mult=1)], bias_term=False,
axis=1, num_output=nchannels, pad=[1, 1, 1], kernel_size=[3, 3, 3], stride=[1,1,1],
weight_filler=dict(type='msra'), bias_filler=dict(type='constant'))
n.bnorm1b = L.BatchNorm(n.conv1b, batch_norm_param=dict(use_global_stats=use_global_stats), param=[dict(lr_mult=0, decay_mult=0), dict(lr_mult=0, decay_mult=0),
dict(lr_mult=0, decay_mult=0)], in_place=False)
n.scale1b = L.Scale(n.bnorm1b, in_place=True, bias_term=True, filler=dict(value=1), bias_filler=dict(value=0))
n.relu1b = L.ReLU(n.bnorm1b, in_place=True)
n.conv1c = L.Convolution(n.relu1b, param=[dict(lr_mult=1, decay_mult=1)], bias_term=False,
axis=1, num_output=nchannels, pad=[1, 1, 1], kernel_size=[3, 3, 3],stride=[1,1,1],
weight_filler=dict(type='msra'), bias_filler=dict(type='constant'))
print (nchannels)
# model = L.Pooling(n.conv1c, type="Pooling", pool=P.Pooling.MAX, kernel_size=2, stride=2, engine=1)
n.bnorm1c = L.BatchNorm(n.conv1c, batch_norm_param=dict(use_global_stats=use_global_stats), param=[dict(lr_mult=0, decay_mult=0), dict(lr_mult=0, decay_mult=0),
dict(lr_mult=0, decay_mult=0)], in_place=False)
n.scale1c = L.Scale(n.bnorm1c, in_place=True, bias_term=True, filler=dict(value=1), bias_filler=dict(value=0))
n.relu1c = L.ReLU(n.bnorm1c, in_place=True)
model = L.Convolution(n.relu1c, param=[dict(lr_mult=1, decay_mult=1)], bias_term=False,
axis=1, num_output=nchannels, pad=[0, 0, 0], kernel_size=[2, 2, 2], stride=2,
weight_filler=dict(type='msra'), bias_filler=dict(type='constant'))
n.__setattr__("Conv_down_1", model)
# ===============Dense block 2=====================
for i in range(N[0]):
if (i == 0):
concat = add_layer(model, growth_rate, dropout,split)
n.__setattr__("Concat_%d" % (i + 1), concat)
nchannels += growth_rate
continue
concat = add_layer(concat, growth_rate, dropout,split)
n.__setattr__("Concat_%d" % (i + 1), concat)
nchannels += growth_rate
# ===============End dense block 2=================
print (nchannels)
# ===============Deconvolution layer 2==============
model_deconv_x2 = L.Deconvolution(concat, param=[dict(lr_mult=0.1, decay_mult=1)],
convolution_param=dict(kernel_size=[4,4,4], stride=[2,2,2], num_output=num_classes,
pad=[1, 1, 1], group=num_classes,
weight_filler=dict(type='bilinear_3D'),
bias_term=False))
n.__setattr__("Deconvolution_%d" % (N[0] + 1), model_deconv_x2)
# ===============End Deconvolution layer 2==============
# ===============Transition layer 2=================
model = transition(concat, int(math.floor(nchannels * reduction)), split)
n.__setattr__("Conv_down_%d" % (N[0] + 1), model)
nchannels = int(math.floor(nchannels * reduction))
# ===============End Transition layer2==============
# ===============Dense block 3=====================
for i in range(N[1]):
if (i == 0):
concat = add_layer(model, growth_rate, dropout, split)
n.__setattr__("Concat_%d" % (N[1] + i + 2), concat)
nchannels += growth_rate
continue
concat = add_layer(concat, growth_rate, dropout, split)
n.__setattr__("Concat_%d" % (N[1] + i + 2), concat)
nchannels += growth_rate
# ===============End dense block 3=================
print (nchannels)
# ===============Deconvolution layer 3==============
model_deconv_x4 = L.Deconvolution(concat, param=[dict(lr_mult=0.1, decay_mult=1)],
convolution_param=dict(kernel_size=[6,6,6], stride=[4,4,4], num_output=num_classes,
pad=[1, 1, 1], group=num_classes,
weight_filler=dict(type='bilinear_3D'),
bias_term=False))
n.__setattr__("Deconvolution_%d" % (N[0] + N[1] + 2), model_deconv_x4)
# ==============Transition layer 3=================
model = transition(concat, int(math.floor(nchannels * reduction)), split)
n.__setattr__("Conv_down_%d" % (N[0] + N[1] + 2), model)
# ===============End Transition layer3==============
nchannels = int(math.floor(nchannels * reduction))
# ===============Dense block 4=====================
for i in range(N[2]):
if (i == 0):
concat = add_layer(model, growth_rate, dropout, split)
n.__setattr__("Concat_%d" % (N[0] + N[1] + i + 3), concat)
nchannels += growth_rate
continue
concat = add_layer(concat, growth_rate, dropout, split)
n.__setattr__("Concat_%d" % (N[0] + N[1] + i + 3), concat)
nchannels += growth_rate
# ===============End dense block 4=================
# ===============Transition layer 4=================
print(nchannels)
# ===============Deconvolution layer 4==============
model_deconv_x8 = L.Deconvolution(concat, param=[dict(lr_mult=0.1, decay_mult=1)],
convolution_param=dict(kernel_size=[10,10,10], stride=[8,8,8], num_output=num_classes,
pad=[1, 1, 1], group=num_classes,
weight_filler=dict(type='bilinear_3D'),
bias_term=False))
n.__setattr__("Deconvolution_%d" % (N[0] + N[1] + N[2] + 3), model_deconv_x8)
# ===============End Deconvolution layer 4==============
# ===============Transition layer 4=================
model = transition(concat, int(math.floor(nchannels * reduction)), split)
n.__setattr__("Conv_down_%d" % (N[0] + N[1] + N[2] + 3), model)
nchannels = int(math.floor(nchannels * reduction))
# ===============End Transition layer3==============
# ===============Dense block 5=====================
for i in range(N[3]):
if (i == 0):
concat = add_layer(model, growth_rate, dropout, split)
n.__setattr__("Concat_%d" % (N[0] + N[1] + N[2] + N[3] + i + 3), concat)
nchannels += growth_rate
continue
concat = add_layer(concat, growth_rate, dropout, split)
n.__setattr__("Concat_%d" % (N[0] + N[1] + N[2] + N[3] + i + 3), concat)
nchannels += growth_rate
# ===============End dense block 5=================
print(nchannels)
# ===============Deconvolution layer 5==============
model_deconv_x16 = L.Deconvolution(concat, param=[dict(lr_mult=0.1, decay_mult=1)],
convolution_param=dict(kernel_size=[18, 18, 18], stride=[16,16,16],
num_output=num_classes,
pad=[1, 1, 1], group=num_classes,
weight_filler=dict(type='bilinear_3D'),
bias_term=False))
n.__setattr__("Deconvolution_%d" % (N[0] + N[1] + N[2] + N[3] + 4), model_deconv_x16)
model = L.Concat(n.conv1c,model_deconv_x2, model_deconv_x4, model_deconv_x8, model_deconv_x16,
axis=1)
n.bnorm_concat= L.BatchNorm(model, batch_norm_param=dict(use_global_stats=use_global_stats), param=[dict(lr_mult=0, decay_mult=0), dict(lr_mult=0, decay_mult=0),
dict(lr_mult=0, decay_mult=0)], in_place=False)
n.scale_concat = L.Scale(n.bnorm_concat, in_place=True, bias_term=True, filler=dict(value=1), bias_filler=dict(value=0))
n.relu_concat = L.ReLU(n.scale_concat, in_place=True)
model_conv_concate = L.Convolution(n.relu_concat,
param=[dict(lr_mult=1, decay_mult=1), dict(lr_mult=2, decay_mult=0)],
axis=1, num_output=num_classes, pad=[0, 0, 0], kernel_size=[1, 1, 1],
weight_filler=dict(type='msra'))
if (split == 'train'):
n.loss = L.SoftmaxWithLoss(model_conv_concate, n.label)
elif (split == 'val'):
n.loss = L.SoftmaxWithLoss(model_conv_concate, n.label)
else:
n.softmax = L.Softmax(model_conv_concate, ntop=1, in_place=False)
return n.to_proto()
def make_net():
with open('train_3d_denseseg.prototxt', 'w') as f:
print(str(densenet('train', batch_size=4)), file=f)
with open('test_3d_denseseg.prototxt', 'w') as f:
print(str(densenet('val', batch_size=4)), file=f)
with open('deploy_3d_denseseg.prototxt', 'w') as f:
print(str(densenet('deploy', batch_size=0)), file=f)
def make_solver():
s = caffe_pb2.SolverParameter()
s.random_seed = 0xCAFFE
s.train_net = 'train_3d_denseseg.prototxt'
s.max_iter = 200000
s.type = 'Adam'
s.display = 20
s.base_lr = 0.0002
#s.power=0.9
s.momentum = 0.97
s.weight_decay = 0.0005
s.average_loss=20
s.iter_size = 1
s.lr_policy='step'
s.stepsize=50000
s.gamma = 0.1
s.snapshot_prefix ='./snapshot/3d_denseseg_iseg'
s.snapshot = 2000
s.solver_mode = caffe_pb2.SolverParameter.GPU
solver_path = 'solver.prototxt'
with open(solver_path, 'w') as f:
f.write(str(s))
if __name__ == '__main__':
make_net()
make_solver()