def __init__(self, pretrained_model, n_layers):
super(ResNetLayers, self).__init__()
if pretrained_model:
# As a sampling process is time-consuming,
# we employ a zero initializer for faster computation.
kwargs = {'initialW': constant.Zero()}
else:
# employ default initializers used in the original paper
kwargs = {'initialW': normal.HeNormal(scale=1.0)}
if n_layers == 50:
block = [3, 4, 6, 3]
elif n_layers == 101:
block = [3, 4, 23, 3]
elif n_layers == 152:
block = [3, 8, 36, 3]
else:
raise ValueError('The n_layers argument should be either 50, 101,'
' or 152, but {} was given.'.format(n_layers))
with self.init_scope():
self.conv1 = Convolution2D(3, 64, 7, 2, 3, **kwargs)
self.bn1 = BatchNormalization(64)
self.res2 = BuildingBlock(block[0], 64, 64, 256, 1, **kwargs)
self.res3 = BuildingBlock(block[1], 256, 128, 512, 2, **kwargs)
self.res4 = BuildingBlock(block[2], 512, 256, 1024, 2, **kwargs)
self.res5 = BuildingBlock(block[3], 1024, 512, 2048, 2, **kwargs)
self.fc6 = Linear(2048, 1000)
if pretrained_model and pretrained_model.endswith('.caffemodel'):
_retrieve(n_layers, 'ResNet-{}-model.npz'.format(n_layers),
pretrained_model, self)
elif pretrained_model:
npz.load_npz(pretrained_model, self)
def __init__(self, pretrained_model='auto'):
if pretrained_model:
# As a sampling process is time-consuming,
# we employ a zero initializer for faster computation.
kwargs = {'initialW': constant.Zero()}
else:
# employ default initializers used in the original paper
kwargs = {'initialW': normal.HeNormal(scale=1.0)}
super(ResNet50Layers, self).__init__(
conv1=Convolution2D(3, 64, 7, 2, 3, **kwargs),
bn1=BatchNormalization(64),
res2=BuildingBlock(3, 64, 64, 256, 1, **kwargs),
res3=BuildingBlock(4, 256, 128, 512, 2, **kwargs),
res4=BuildingBlock(6, 512, 256, 1024, 2, **kwargs),
res5=BuildingBlock(3, 1024, 512, 2048, 2, **kwargs),
fc6=Linear(2048, 1000),
)
if pretrained_model == 'auto':
_retrieve(
'ResNet-50-model.npz', 'ResNet-50-model.caffemodel', self)
elif pretrained_model:
npz.load_npz(pretrained_model, self)
self.functions = OrderedDict([
('conv1', [self.conv1, self.bn1, relu]),
('pool1', [lambda x: max_pooling_2d(x, ksize=3, stride=2)]),
('res2', [self.res2]),
('res3', [self.res3]),
('res4', [self.res4]),
('res5', [self.res5]),
('pool5', [_global_average_pooling_2d]),
('fc6', [self.fc6]),
('prob', [softmax]),
])
def test_load(self):
obj = mock.MagicMock()
npz.load_npz(self.temp_file_path, obj)
self.assertEqual(obj.serialize.call_count, 1)
(serializer,), _ = obj.serialize.call_args
self.assertIsInstance(serializer, npz.NpzDeserializer)
def test_load_with_path(self):
target = link.Chain()
with target.init_scope():
target.child_linear = links.Linear(2, 3)
npz.load_npz(self.file, target, 'child/')
numpy.testing.assert_array_equal(
self.source_child.child_linear.W.data, target.child_linear.W.data)
def test_load_without_path(self):
target = link.Chain()
with target.init_scope():
target.parent_linear = links.Linear(3, 2)
npz.load_npz(self.file, target, path='')
numpy.testing.assert_array_equal(
self.source_parent.parent_linear.W.data,
target.parent_linear.W.data)
def _make_npz(path_npz, url, model):
path_caffemodel = download.cached_download(url)
sys.stderr.write(
'Now loading caffemodel (usually it may take few minutes)\n')
sys.stderr.flush()
GoogLeNet.convert_caffemodel_to_npz(path_caffemodel, path_npz)
npz.load_npz(path_npz, model)
return model
def test_load_without_strict(self):
obj = mock.MagicMock()
npz.load_npz(self.file, obj, strict=False)
self.assertEqual(obj.serialize.call_count, 1)
(serializer,), _ = obj.serialize.call_args
self.assertFalse(serializer.strict)
self.assertIsInstance(serializer, npz.NpzDeserializer)
def __init__(self, pretrained_model='auto', n_layers=16):
super(VGGLayers, self).__init__()
if pretrained_model:
# As a sampling process is time-consuming,
# we employ a zero initializer for faster computation.
init = constant.Zero()
kwargs = {'initialW': init, 'initial_bias': init}
else:
# employ default initializers used in the original paper
kwargs = {
'initialW': normal.Normal(0.01),
'initial_bias': constant.Zero(),
}
if n_layers not in [16, 19]:
raise ValueError(
'The n_layers argument should be either 16 or 19,'
'but {} was given.'.format(n_layers)
)
with self.init_scope():
self.conv1_1 = Convolution2D(3, 64, 3, 1, 1, **kwargs)
self.conv1_2 = Convolution2D(64, 64, 3, 1, 1, **kwargs)
self.conv2_1 = Convolution2D(64, 128, 3, 1, 1, **kwargs)
self.conv2_2 = Convolution2D(128, 128, 3, 1, 1, **kwargs)
self.conv3_1 = Convolution2D(128, 256, 3, 1, 1, **kwargs)
self.conv3_2 = Convolution2D(256, 256, 3, 1, 1, **kwargs)
self.conv3_3 = Convolution2D(256, 256, 3, 1, 1, **kwargs)
self.conv4_1 = Convolution2D(256, 512, 3, 1, 1, **kwargs)
self.conv4_2 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
self.conv4_3 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
self.conv5_1 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
self.conv5_2 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
self.conv5_3 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
self.fc6 = Linear(512 * 7 * 7, 4096, **kwargs)
self.fc7 = Linear(4096, 4096, **kwargs)
self.fc8 = Linear(4096, 1000, **kwargs)
if n_layers == 19:
self.conv3_4 = Convolution2D(256, 256, 3, 1, 1, **kwargs)
self.conv4_4 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
self.conv5_4 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
if pretrained_model == 'auto':
if n_layers == 16:
_retrieve(
'VGG_ILSVRC_16_layers.npz',
'https://www.robots.ox.ac.uk/%7Evgg/software/very_deep/'
'caffe/VGG_ILSVRC_16_layers.caffemodel',
self)
else:
_retrieve(
'VGG_ILSVRC_19_layers.npz',
'http://www.robots.ox.ac.uk/%7Evgg/software/very_deep/'
'caffe/VGG_ILSVRC_19_layers.caffemodel',
self)
elif pretrained_model:
npz.load_npz(pretrained_model, self)
def test_load_npz_ignore_names(self):
chain = link.Chain()
with chain.init_scope():
chain.x = chainer.variable.Parameter(shape=())
chain.yy = chainer.variable.Parameter(shape=(2, 3))
npz.load_npz(
self.temp_file_path, chain, ignore_names=self.ignore_names)
self.assertEqual(chain.x.data, self.x)
self.assertFalse(numpy.all(chain.yy.data == self.yy))
def test_load_optimizer(self):
for param in self.parent.params():
param.data.fill(1)
npz.save_npz(self.temp_file_path, self.parent, self.compress)
for param in self.parent.params():
param.data.fill(0)
npz.load_npz(self.temp_file_path, self.parent)
for param in self.parent.params():
self.assertTrue((param.data == 1).all())
def test_load_optimizer_with_strict(self):
for param in self.parent.params():
param.data.fill(1)
self._save_npz(self.file, self.parent, self.compress)
for param in self.parent.params():
param.data.fill(0)
npz.load_npz(self.file, self.parent)
for param in self.parent.params():
self.assertTrue((param.data == 1).all())
def _make_npz(path_npz, path_caffemodel, model):
print('Now loading caffemodel (usually it may take few minutes)')
if not os.path.exists(path_caffemodel):
raise IOError(
'The pre-trained caffemodel does not exist. Please download it '
'from \'https://github.com/KaimingHe/deep-residual-networks\', '
'and place it on {}'.format(path_caffemodel))
ResNet50Layers.convert_caffemodel_to_npz(path_caffemodel, path_npz)
npz.load_npz(path_npz, model)
return model
def test_load_optimizer_without_strict(self):
for param in self.parent.params():
param.data.fill(1)
self._save_npz(self.file, self.parent, self.compress)
# Remove a param
del self.parent.child.linear.b
for param in self.parent.params():
param.data.fill(0)
npz.load_npz(self.file, self.parent, strict=False)
for param in self.parent.params():
self.assertTrue((param.data == 1).all())
self.assertFalse(hasattr(self.parent.child.linear, 'b'))
def test_serialization(self):
lin1 = links.SimplifiedDropconnect(None, self.out_size)
x = chainer.Variable(self.x)
# Must call the link to initialize weights.
lin1(x)
w1 = lin1.W.data
fd, temp_file_path = tempfile.mkstemp()
os.close(fd)
npz.save_npz(temp_file_path, lin1)
lin2 = links.SimplifiedDropconnect(None, self.out_size)
npz.load_npz(temp_file_path, lin2)
w2 = lin2.W.data
self.assertEqual((w1 == w2).all(), True)
def _retrieve(name_npz, name_caffemodel, model):
root = download.get_dataset_directory('pfnet/chainer/models/')
path = os.path.join(root, name_npz)
path_caffemodel = os.path.join(root, name_caffemodel)
return download.cache_or_load_file(
path, lambda path: _make_npz(path, path_caffemodel, model),
lambda path: npz.load_npz(path, model))
def __init__(self, pretrained_model, n_layers):
if pretrained_model:
# As a sampling process is time-consuming,
# we employ a zero initializer for faster computation.
kwargs = {'initialW': constant.Zero()}
else:
# employ default initializers used in the original paper
kwargs = {'initialW': normal.HeNormal(scale=1.0)}
if n_layers == 50:
block = [3, 4, 6, 3]
elif n_layers == 101:
block = [3, 4, 23, 3]
elif n_layers == 152:
block = [3, 8, 36, 3]
else:
raise ValueError('The n_layers argument should be either 50, 101,'
' or 152, but {} was given.'.format(n_layers))
super(ResNetLayers, self).__init__(
conv1=Convolution2D(3, 64, 7, 2, 3, **kwargs),
bn1=BatchNormalization(64),
res2=BuildingBlock(block[0], 64, 64, 256, 1, **kwargs),
res3=BuildingBlock(block[1], 256, 128, 512, 2, **kwargs),
res4=BuildingBlock(block[2], 512, 256, 1024, 2, **kwargs),
res5=BuildingBlock(block[3], 1024, 512, 2048, 2, **kwargs),
fc6=Linear(2048, 1000),
)
if pretrained_model and pretrained_model.endswith('.caffemodel'):
_retrieve(n_layers, 'ResNet-{}-model.npz'.format(n_layers),
pretrained_model, self)
elif pretrained_model:
npz.load_npz(pretrained_model, self)
self.functions = collections.OrderedDict([
('conv1', [self.conv1, self.bn1, relu]),
('pool1', [lambda x: max_pooling_2d(x, ksize=3, stride=2)]),
('res2', [self.res2]),
('res3', [self.res3]),
('res4', [self.res4]),
('res5', [self.res5]),
('pool5', [_global_average_pooling_2d]),
('fc6', [self.fc6]),
('prob', [softmax]),
])
def __init__(self, pretrained_model='auto'):
super(GoogLeNet, self).__init__()
if pretrained_model:
# As a sampling process is time-consuming,
# we employ a zero initializer for faster computation.
kwargs = {'initialW': constant.Zero()}
else:
# employ default initializers used in BVLC. For more detail, see
# https://github.com/chainer/chainer/pull/2424#discussion_r109642209
kwargs = {'initialW': uniform.LeCunUniform(scale=1.0)}
with self.init_scope():
self.conv1 = Convolution2D(3, 64, 7, stride=2, pad=3, **kwargs)
self.conv2_reduce = Convolution2D(64, 64, 1, **kwargs)
self.conv2 = Convolution2D(64, 192, 3, stride=1, pad=1, **kwargs)
self.inc3a = Inception(192, 64, 96, 128, 16, 32, 32)
self.inc3b = Inception(256, 128, 128, 192, 32, 96, 64)
self.inc4a = Inception(480, 192, 96, 208, 16, 48, 64)
self.inc4b = Inception(512, 160, 112, 224, 24, 64, 64)
self.inc4c = Inception(512, 128, 128, 256, 24, 64, 64)
self.inc4d = Inception(512, 112, 144, 288, 32, 64, 64)
self.inc4e = Inception(528, 256, 160, 320, 32, 128, 128)
self.inc5a = Inception(832, 256, 160, 320, 32, 128, 128)
self.inc5b = Inception(832, 384, 192, 384, 48, 128, 128)
self.loss3_fc = Linear(1024, 1000, **kwargs)
self.loss1_conv = Convolution2D(512, 128, 1, **kwargs)
self.loss1_fc1 = Linear(2048, 1024, **kwargs)
self.loss1_fc2 = Linear(1024, 1000, **kwargs)
self.loss2_conv = Convolution2D(528, 128, 1, **kwargs)
self.loss2_fc1 = Linear(2048, 1024, **kwargs)
self.loss2_fc2 = Linear(1024, 1000, **kwargs)
if pretrained_model == 'auto':
_retrieve(
'bvlc_googlenet.npz',
'http://dl.caffe.berkeleyvision.org/bvlc_googlenet.caffemodel',
self)
elif pretrained_model:
npz.load_npz(pretrained_model, self)
def __init__(self, pretrained_model='auto'):
if pretrained_model:
# As a sampling process is time-consuming,
# we employ a zero initializer for faster computation.
init = constant.Zero()
kwargs = {'initialW': init, 'initial_bias': init}
else:
# employ default initializers used in the original paper
kwargs = {
'initialW': normal.Normal(0.01),
'initial_bias': constant.Zero(),
}
super(VGG16Layers, self).__init__()
with self.init_scope():
self.conv1_1 = Convolution2D(3, 64, 3, 1, 1, **kwargs)
self.conv1_2 = Convolution2D(64, 64, 3, 1, 1, **kwargs)
self.conv2_1 = Convolution2D(64, 128, 3, 1, 1, **kwargs)
self.conv2_2 = Convolution2D(128, 128, 3, 1, 1, **kwargs)
self.conv3_1 = Convolution2D(128, 256, 3, 1, 1, **kwargs)
self.conv3_2 = Convolution2D(256, 256, 3, 1, 1, **kwargs)
self.conv3_3 = Convolution2D(256, 256, 3, 1, 1, **kwargs)
self.conv4_1 = Convolution2D(256, 512, 3, 1, 1, **kwargs)
self.conv4_2 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
self.conv4_3 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
self.conv5_1 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
self.conv5_2 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
self.conv5_3 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
self.fc6 = Linear(512 * 7 * 7, 4096, **kwargs)
self.fc7 = Linear(4096, 4096, **kwargs)
self.fc8 = Linear(4096, 1000, **kwargs)
if pretrained_model == 'auto':
_retrieve(
'VGG_ILSVRC_16_layers.npz',
'http://www.robots.ox.ac.uk/%7Evgg/software/very_deep/'
'caffe/VGG_ILSVRC_16_layers.caffemodel',
self)
elif pretrained_model:
npz.load_npz(pretrained_model, self)
def __init__(self, pretrained_model, n_layers, downsample_fb=False):
super(ResNetLayers, self).__init__()
if pretrained_model:
# As a sampling process is time-consuming,
# we employ a zero initializer for faster computation.
conv_kwargs = {'initialW': constant.Zero()}
else:
# employ default initializers used in the original paper
conv_kwargs = {'initialW': normal.HeNormal(scale=1.0)}
kwargs = conv_kwargs.copy()
kwargs['downsample_fb'] = downsample_fb
if n_layers == 50:
block = [3, 4, 6, 3]
elif n_layers == 101:
block = [3, 4, 23, 3]
elif n_layers == 152:
block = [3, 8, 36, 3]
else:
raise ValueError('The n_layers argument should be either 50, 101,'
' or 152, but {} was given.'.format(n_layers))
with self.init_scope():
self.conv1 = Convolution2D(3, 64, 7, 2, 3, **conv_kwargs)
self.bn1 = BatchNormalization(64)
self.res2 = BuildingBlock(block[0], 64, 64, 256, 1, **kwargs)
self.res3 = BuildingBlock(block[1], 256, 128, 512, 2, **kwargs)
self.res4 = BuildingBlock(block[2], 512, 256, 1024, 2, **kwargs)
self.res5 = BuildingBlock(block[3], 1024, 512, 2048, 2, **kwargs)
self.fc6 = Linear(2048, 1000)
if pretrained_model and pretrained_model.endswith('.caffemodel'):
_retrieve(n_layers, 'ResNet-{}-model.npz'.format(n_layers),
pretrained_model, self)
elif pretrained_model:
npz.load_npz(pretrained_model, self)
def __init__(self, pretrained_model="auto"):
if pretrained_model:
kwargs = {'initialW': constant.Zero()}
else:
kwargs = {'initialW': normal.HeNormal(scale=1.0)}
super(ResNet, self).__init__(
conv1=L.Convolution2D(3, 64, 7, 2, 3, **kwargs),
bn1=L.BatchNormalization(64),
res2=Block(3, 64, 64, 256, 1, **kwargs),
res3=Block(4, 256, 128, 512, 2, **kwargs),
res4=Block(6, 512, 256, 1024, 2, **kwargs),
res5=Block(3, 1024, 512, 2048, 2, **kwargs),
fc6=L.Linear(None, 1000),
)
if pretrained_model == 'auto':
print("[ PREPROCESS ] Use caffe model of ResNet.")
_retrieve('ResNet-50-model.npz', 'ResNet-50-model.caffemodel',
self)
self.fc6 = L.Linear(None, 25)
elif pretrained_model:
npz.load_npz(pretrained_model, self)
self.train = True
def main(id):
with chainer.using_config("train", False):
with chainer.using_config("enable_backprop", False):
model_path = "/efs/fMRI_AE/SimpleFCAE_E32D32/model/model_iter_108858"
gpu = 0
get_device_from_id(gpu).use()
"""NibDataset
def __init__(self, directory: str, crop: list):
"""
crop = [[9, 81], [11, 99], [0, 80]]
test_dataset = NibDataset("/data/test", crop=crop)
"""
def __init__(self, dataset, batch_size, repeat=True, shuffle=True):
"""
mask = load_mask_nib("/data/mask/average_optthr.nii", crop)
model = Model(mask, 2, "mask", "mask")
load_npz(model_path, model)
model.to_gpu()
for i in range(len(test_dataset)):
if i % 8 != id:
continue
inp = to_gpu(test_dataset.get_example(i))
inp = xp.expand_dims(inp, 0)
subject = test_dataset.get_subject(i)
frame = test_dataset.get_frame(i)
sys.stdout.write("\rsubject{:03d} frame{:03d}".format(
subject, frame))
sys.stdout.flush()
out = model.reconstruct(inp).array
out = xp.squeeze(out)
xp.save(
"/efs/fMRI_AE/SimpleFCAE_E32D32/reconstruct/reconstruction_subject{:03d}_frame{:03d}.npy"
.format(subject, frame), out)
def _make_npz(path_npz, url, model):
path_caffemodel = download.cached_download(url)
print('Now loading caffemodel (usually it may take few minutes)')
VGG16Layers.convert_caffemodel_to_npz(path_caffemodel, path_npz)
npz.load_npz(path_npz, model)
return model
def __init__(self, pretrained_model='auto'):
if pretrained_model:
# As a sampling process is time-consuming,
# we employ a zero initializer for faster computation.
kwargs = {'initialW': constant.Zero()}
else:
# employ default initializers used in the original paper
kwargs = {'initialW': uniform.GlorotUniform(scale=1.0)}
super(GoogLeNet,
self).__init__(conv1=Convolution2D(3,
64,
7,
stride=2,
pad=3,
**kwargs),
conv2_reduce=Convolution2D(64, 64, 1, **kwargs),
conv2=Convolution2D(64,
192,
3,
stride=1,
pad=1,
**kwargs),
inc3a=Inception(192, 64, 96, 128, 16, 32, 32),
inc3b=Inception(256, 128, 128, 192, 32, 96, 64),
inc4a=Inception(480, 192, 96, 208, 16, 48, 64),
inc4b=Inception(512, 160, 112, 224, 24, 64, 64),
inc4c=Inception(512, 128, 128, 256, 24, 64, 64),
inc4d=Inception(512, 112, 144, 288, 32, 64, 64),
inc4e=Inception(528, 256, 160, 320, 32, 128, 128),
inc5a=Inception(832, 256, 160, 320, 32, 128, 128),
inc5b=Inception(832, 384, 192, 384, 48, 128, 128),
loss3_fc=Linear(1024, 1000, **kwargs),
loss1_conv=Convolution2D(512, 128, 1, **kwargs),
loss1_fc1=Linear(2048, 1024, **kwargs),
loss1_fc2=Linear(1024, 1000, **kwargs),
loss2_conv=Convolution2D(528, 128, 1, **kwargs),
loss2_fc1=Linear(2048, 1024, **kwargs),
loss2_fc2=Linear(1024, 1000, **kwargs))
if pretrained_model == 'auto':
_retrieve(
'bvlc_googlenet.npz',
'http://dl.caffe.berkeleyvision.org/bvlc_googlenet.caffemodel',
self)
elif pretrained_model:
npz.load_npz(pretrained_model, self)
self.functions = OrderedDict([
('conv1', [self.conv1, relu]),
('pool1', [_max_pooling_2d, _local_response_normalization]),
('conv2_reduce', [self.conv2_reduce, relu]),
('conv2', [self.conv2, relu, _local_response_normalization]),
('pool2', [_max_pooling_2d]),
('inception_3a', [self.inc3a]),
('inception_3b', [self.inc3b]),
('pool3', [_max_pooling_2d]),
('inception_4a', [self.inc4a]),
('inception_4b', [self.inc4b]),
('inception_4c', [self.inc4c]),
('inception_4d', [self.inc4d]),
('inception_4e', [self.inc4e]),
('pool4', [_max_pooling_2d]),
('inception_5a', [self.inc5a]),
('inception_5b', [self.inc5b]),
('pool5', [_average_pooling_2d_k7]),
('loss3_fc', [_dropout, self.loss3_fc]),
('prob', [softmax]),
# Since usually the following outputs are not used, they are put
# after 'prob' to be skipped for efficiency.
('loss1_fc2', [
_average_pooling_2d_k5, self.loss1_conv, relu, self.loss1_fc1,
relu, self.loss1_fc2
]),
('loss2_fc2', [
_average_pooling_2d_k5, self.loss2_conv, relu, self.loss2_fc1,
relu, self.loss2_fc2
])
])
def test_load_without_path(self):
target = link.Chain(parent_linear=links.Linear(3, 2))
npz.load_npz(self.temp_file_path, target, path='')
numpy.testing.assert_array_equal(
self.source_parent.parent_linear.W.data,
target.parent_linear.W.data)
def _make_npz(
caffe_path="./all_data/train_gaze_det/model/model/binary_w.caffemodel",
npz_path="./all_data/train_gaze_det/model/model/GazeFollow.npz"):
GazeFollow.convert_caffemodel_to_npz(caffe_path, npz_path)
npz.load_npz(npz_path, self)
return self
def __init__(self, pretrained_model='auto'):
if pretrained_model:
# As a sampling process is time-consuming,
# we employ a zero initializer for faster computation.
init = constant.Zero()
kwargs = {'initialW': init, 'initial_bias': init}
else:
# employ default initializers used in the original paper
kwargs = {
'initialW': normal.Normal(0.01),
'initial_bias': constant.Zero(),
}
super(VGG16Layers, self).__init__(
conv1_1=Convolution2D(3, 64, 3, 1, 1, **kwargs),
conv1_2=Convolution2D(64, 64, 3, 1, 1, **kwargs),
conv2_1=Convolution2D(64, 128, 3, 1, 1, **kwargs),
conv2_2=Convolution2D(128, 128, 3, 1, 1, **kwargs),
conv3_1=Convolution2D(128, 256, 3, 1, 1, **kwargs),
conv3_2=Convolution2D(256, 256, 3, 1, 1, **kwargs),
conv3_3=Convolution2D(256, 256, 3, 1, 1, **kwargs),
conv4_1=Convolution2D(256, 512, 3, 1, 1, **kwargs),
conv4_2=Convolution2D(512, 512, 3, 1, 1, **kwargs),
conv4_3=Convolution2D(512, 512, 3, 1, 1, **kwargs),
conv5_1=Convolution2D(512, 512, 3, 1, 1, **kwargs),
conv5_2=Convolution2D(512, 512, 3, 1, 1, **kwargs),
conv5_3=Convolution2D(512, 512, 3, 1, 1, **kwargs),
fc6=Linear(512 * 7 * 7, 4096, **kwargs),
fc7=Linear(4096, 4096, **kwargs),
fc8=Linear(4096, 1000, **kwargs),
)
if pretrained_model == 'auto':
_retrieve(
'VGG_ILSVRC_16_layers.npz',
'http://www.robots.ox.ac.uk/%7Evgg/software/very_deep/'
'caffe/VGG_ILSVRC_16_layers.caffemodel',
self)
elif pretrained_model:
npz.load_npz(pretrained_model, self)
self.functions = collections.OrderedDict([
('conv1_1', [self.conv1_1, relu]),
('conv1_2', [self.conv1_2, relu]),
('pool1', [_max_pooling_2d]),
('conv2_1', [self.conv2_1, relu]),
('conv2_2', [self.conv2_2, relu]),
('pool2', [_max_pooling_2d]),
('conv3_1', [self.conv3_1, relu]),
('conv3_2', [self.conv3_2, relu]),
('conv3_3', [self.conv3_3, relu]),
('pool3', [_max_pooling_2d]),
('conv4_1', [self.conv4_1, relu]),
('conv4_2', [self.conv4_2, relu]),
('conv4_3', [self.conv4_3, relu]),
('pool4', [_max_pooling_2d]),
('conv5_1', [self.conv5_1, relu]),
('conv5_2', [self.conv5_2, relu]),
('conv5_3', [self.conv5_3, relu]),
('pool5', [_max_pooling_2d]),
('fc6', [self.fc6, relu, dropout]),
('fc7', [self.fc7, relu, dropout]),
('fc8', [self.fc8]),
('prob', [softmax]),
])
def _make_npz(path_npz, url, model):
path_caffemodel = download.cached_download(url)
print('Now loading caffemodel (usually it may take few minutes)')
GoogLeNet.convert_caffemodel_to_npz(path_caffemodel, path_npz)
npz.load_npz(path_npz, model)
return model
def main():
parser = argparse.ArgumentParser(description='Train Encoder')
parser.add_argument('--batchsize', '-b', type=int, default=64,
help='Number of images in each mini-batch')
parser.add_argument('--epoch', '-e', type=int, default=100,
help='Number of sweeps over the dataset to train')
parser.add_argument('--gpu', '-g', type=int, default=-1,
help='GPU ID (negative value indicates CPU)')
parser.add_argument('--dataset', '-i', default='data/celebA/',
help='Directory of image files.')
parser.add_argument('--out', '-o', default='result',
help='Directory to output the result')
parser.add_argument('--resume', '-r', default='',
help='Resume the training from snapshot')
parser.add_argument('--snapshot_interval', type=int, default=10000,
help='Interval of snapshot')
parser.add_argument('--display_interval', type=int, default=1000,
help='Interval of displaying log to console')
parser.add_argument('--gen', default='gen.npz')
parser.add_argument('--enc', default=None)
args = parser.parse_args()
print('GPU: {}'.format(args.gpu))
print('# batchsize: {}'.format(args.batchsize))
print('# epoch: {}'.format(args.epoch))
print('')
# Set up a neural network to train
gen = Generator()
npz.load_npz(args.gen, gen)
enc = Encoder()
if args.enc is not None:
npz.load_npz(args.enc, enc)
if args.gpu >= 0:
chainer.cuda.get_device_from_id(args.gpu).use()
gen.to_gpu()
enc.to_gpu()
# Setup an optimizer
def make_optimizer(model, alpha=0.0005, beta1=0.9):
optimizer = chainer.optimizers.Adam(alpha=alpha, beta1=beta1)
optimizer.setup(model)
optimizer.add_hook(chainer.optimizer.WeightDecay(0.0001), 'hook_dec')
return optimizer
opt_gen = make_optimizer(gen)
gen.disable_update()
opt_enc = make_optimizer(enc)
# Setup a dataset
all_files = os.listdir(args.dataset)
image_files = [f for f in all_files if ('png' in f or 'jpg' in f)]
print('{} contains {} image files'.format(args.dataset, len(image_files)))
train = CelebADataset(paths=image_files, root=args.dataset)
train_iter = chainer.iterators.SerialIterator(train, args.batchsize)
# Set up a trainer
updater = EncUpdater(
models=(gen, enc),
iterator=train_iter,
optimizer={'gen': opt_gen, 'enc': opt_enc},
device=args.gpu)
trainer = training.Trainer(updater, (args.epoch, 'epoch'), out=args.out)
snapshot_interval = (args.snapshot_interval, 'iteration')
display_interval = (args.display_interval, 'iteration')
trainer.extend(
extensions.snapshot(filename='snapshot_enc_iter_{.updater.iteration}.npz'),
trigger=snapshot_interval)
trainer.extend(extensions.ExponentialShift(
'alpha', 0.5, optimizer=opt_enc), trigger=(10, 'epoch'))
trainer.extend(extensions.snapshot_object(
enc, 'enc_iter_{.updater.iteration}.npz'), trigger=snapshot_interval)
trainer.extend(extensions.LogReport(trigger=display_interval, log_name='train_enc.log'))
trainer.extend(extensions.PrintReport([
'epoch', 'iteration', 'enc/loss',
]), trigger=display_interval)
trainer.extend(extensions.PlotReport(
['enc/loss'], trigger=display_interval, file_name='enc-loss.png'))
trainer.extend(extensions.ProgressBar(update_interval=10))
if args.resume:
chainer.serializers.load_npz(args.resume, trainer)
# Run the training
trainer.run()
def main():
config = get_config()
# print("configured as follows:")
# print(yaml_dump(config))
while True:
s = input("ok? (y/n):")
if s == 'y' or s == 'Y':
log_config(config, "training start")
break
elif s == 'n' or s == 'N':
destroy_config(config)
exit(1)
try:
try:
print("mask loading...")
load_mask_module = import_module(
config["additional information"]["mask"]["loader"]["module"],
config["additional information"]["mask"]["loader"]["package"])
load_mask = getattr(
load_mask_module,
config["additional information"]["mask"]["loader"]["function"])
mask = load_mask(
**config["additional information"]["mask"]["loader"]["params"])
print("done.")
print("mask.shape: {}".format(mask.shape))
except FileNotFoundError as e:
raise e
model_module = import_module(config["model"]["module"],
config["model"]["package"])
Model = getattr(model_module, config["model"]["class"])
model = Model(mask=mask, **config["model"]["params"])
finetune_config = config["additional information"][
"finetune"] if "finetune" in config[
"additional information"] else None
if finetune_config is not None:
load_npz(path.join(finetune_config["directory"],
finetune_config["file"]),
model,
strict=False)
try:
chainer.cuda.get_device_from_id(0).use()
gpu = 0
print("transferring model to GPU...")
model.to_gpu(gpu)
print("GPU enabled")
except RuntimeError:
gpu = -1
print("GPU disabled")
dataset_module = import_module(config["dataset"]["module"],
config["dataset"]["package"])
Dataset = getattr(dataset_module, config["dataset"]["class"])
train_dataset = Dataset(**config["dataset"]["train"]["params"])
valid_dataset = Dataset(**config["dataset"]["valid"]["params"])
train_iterator = Iterator(train_dataset, config["batch"]["train"],
True, True)
valid_iterator = Iterator(valid_dataset, config["batch"]["valid"],
False, False)
Optimizer = getattr(chainer.optimizers, config["optimizer"]["class"])
optimizer = Optimizer(**config["optimizer"]["params"])
optimizer.setup(model)
for hook_config in config["optimizer"]["hook"]:
hook_module = import_module(hook_config["module"],
hook_config["package"])
Hook = getattr(hook_module, hook_config["class"])
hook = Hook(**hook_config["params"])
optimizer.add_hook(hook)
updater = Updater(train_iterator, optimizer, device=gpu)
trainer = Trainer(updater, **config["trainer"]["params"])
trainer.extend(snapshot(),
trigger=config["trainer"]["snapshot_interval"])
trainer.extend(snapshot_object(model,
"model_iter_{.updater.iteration}"),
trigger=config["trainer"]["model_interval"])
trainer.extend(observe_lr(), trigger=config["trainer"]["log_interval"])
trainer.extend(
LogReport(
["epoch", "iteration", "main/loss", "validation/main/loss"],
trigger=config["trainer"]["log_interval"]))
trainer.extend(Evaluator(valid_iterator, model, device=gpu),
trigger=config["trainer"]["eval_interval"])
trainer.extend(PrintReport(
["epoch", "iteration", "main/loss", "validation/main/loss"]),
trigger=config["trainer"]["log_interval"])
trainer.extend(ProgressBar(update_interval=1))
if "schedule" in config["additional information"].keys():
for i, interval_funcs in enumerate(
config["additional information"]["schedule"].items()):
interval, funcs = interval_funcs
f = lambda trainer, funcs=funcs: [
trainer.updater.get_optimizer('main').target.
__getattribute__(func["function"])(*func["params"])
for func in funcs
]
trainer.extend(f,
name="schedule_{}".format(i),
trigger=ManualScheduleTrigger(*interval))
trainer.run()
log_config(config, "succeeded")
except Exception as e:
log_config(config, "unintentional termination")
raise e
def __init__(self, pretrained_model='auto'):
if pretrained_model:
# As a sampling process is time-consuming,
# we employ a zero initializer for faster computation.
kwargs = {'initialW': constant.Zero()}
else:
# employ default initializers used in BVLC. For more detail, see
# https://github.com/pfnet/chainer/pull/2424#discussion_r109642209
kwargs = {'initialW': uniform.LeCunUniform(scale=1.0)}
super(GoogLeNet, self).__init__(
conv1=Convolution2D(3, 64, 7, stride=2, pad=3, **kwargs),
conv2_reduce=Convolution2D(64, 64, 1, **kwargs),
conv2=Convolution2D(64, 192, 3, stride=1, pad=1, **kwargs),
inc3a=Inception(192, 64, 96, 128, 16, 32, 32),
inc3b=Inception(256, 128, 128, 192, 32, 96, 64),
inc4a=Inception(480, 192, 96, 208, 16, 48, 64),
inc4b=Inception(512, 160, 112, 224, 24, 64, 64),
inc4c=Inception(512, 128, 128, 256, 24, 64, 64),
inc4d=Inception(512, 112, 144, 288, 32, 64, 64),
inc4e=Inception(528, 256, 160, 320, 32, 128, 128),
inc5a=Inception(832, 256, 160, 320, 32, 128, 128),
inc5b=Inception(832, 384, 192, 384, 48, 128, 128),
loss3_fc=Linear(1024, 1000, **kwargs),
loss1_conv=Convolution2D(512, 128, 1, **kwargs),
loss1_fc1=Linear(2048, 1024, **kwargs),
loss1_fc2=Linear(1024, 1000, **kwargs),
loss2_conv=Convolution2D(528, 128, 1, **kwargs),
loss2_fc1=Linear(2048, 1024, **kwargs),
loss2_fc2=Linear(1024, 1000, **kwargs)
)
if pretrained_model == 'auto':
_retrieve(
'bvlc_googlenet.npz',
'http://dl.caffe.berkeleyvision.org/bvlc_googlenet.caffemodel',
self)
elif pretrained_model:
npz.load_npz(pretrained_model, self)
self.functions = collections.OrderedDict([
('conv1', [self.conv1, relu]),
('pool1', [_max_pooling_2d, _local_response_normalization]),
('conv2_reduce', [self.conv2_reduce, relu]),
('conv2', [self.conv2, relu, _local_response_normalization]),
('pool2', [_max_pooling_2d]),
('inception_3a', [self.inc3a]),
('inception_3b', [self.inc3b]),
('pool3', [_max_pooling_2d]),
('inception_4a', [self.inc4a]),
('inception_4b', [self.inc4b]),
('inception_4c', [self.inc4c]),
('inception_4d', [self.inc4d]),
('inception_4e', [self.inc4e]),
('pool4', [_max_pooling_2d]),
('inception_5a', [self.inc5a]),
('inception_5b', [self.inc5b]),
('pool5', [_average_pooling_2d_k7]),
('loss3_fc', [_dropout, self.loss3_fc]),
('prob', [softmax]),
# Since usually the following outputs are not used, they are put
# after 'prob' to be skipped for efficiency.
('loss1_fc2', [_average_pooling_2d_k5, self.loss1_conv, relu,
self.loss1_fc1, relu, self.loss1_fc2]),
('loss2_fc2', [_average_pooling_2d_k5, self.loss2_conv, relu,
self.loss2_fc1, relu, self.loss2_fc2])
])
self.conv3 = L.Convolution2D(None, 384, 3, pad=1)
self.conv4 = L.Convolution2D(None, 384, 3, pad=1)
self.conv5 = L.Convolution2D(None, 256, 3, pad=1)
self.fc6 = L.Linear(None, 4096)
self.fc7 = L.Linear(None, 4096)
self.fc8 = L.Linear(None, nb_class)
def __call__(self, x, t):
h = F.max_pooling_2d(F.local_response_normalization(
F.relu(self.conv1(x))),
3,
stride=2)
h = F.max_pooling_2d(F.local_response_normalization(
F.relu(self.conv2(h))),
3,
stride=2)
h = F.relu(self.conv3(h))
h = F.relu(self.conv4(h))
h = F.max_pooling_2d(F.relu(self.conv5(h)), 3, stride=2)
h = F.dropout(F.relu(self.fc6(h)))
h = F.dropout(F.relu(self.fc7(h)))
h = self.fc8(h)
return h
if __name__ == "__main__":
caffemodel = CaffeFunction("bvlc_alexnet.caffemodel")
npz.save_npz("alexnet.npz", caffemodel, compression=False)
alexnet = Alex()
npz.load_npz("alexnet.npz", alexnet)
def main():
attr_columns = [
'5_o_Clock_Shadow', 'Arched_Eyebrows', 'Attractive', 'Bags_Under_Eyes',
'Bald', 'Bangs', 'Big_Lips', 'Big_Nose', 'Black_Hair', 'Blond_Hair',
'Blurry', 'Brown_Hair', 'Bushy_Eyebrows', 'Chubby', 'Double_Chin',
'Eyeglasses', 'Goatee', 'Gray_Hair', 'Heavy_Makeup', 'High_Cheekbones',
'Male', 'Mouth_Slightly_Open', 'Mustache', 'Narrow_Eyes', 'No_Beard',
'Oval_Face', 'Pale_Skin', 'Pointy_Nose', 'Receding_Hairline',
'Rosy_Cheeks', 'Sideburns', 'Smiling', 'Straight_Hair', 'Wavy_Hair',
'Wearing_Earrings', 'Wearing_Hat', 'Wearing_Lipstick',
'Wearing_Necklace', 'Wearing_Necktie', 'Young'
]
parser = argparse.ArgumentParser(description='Get Attribute Vector')
parser.add_argument('--batchsize',
'-b',
type=int,
default=512,
help='Number of images in each mini-batch')
parser.add_argument('--gpu',
'-g',
type=int,
default=-1,
help='GPU ID (negative value indicates CPU)')
parser.add_argument('--dataset',
'-i',
default='data/celebA/',
help='Directory of image files.')
parser.add_argument('--attr_list',
'-a',
default='data/list_attr_celeba.txt')
parser.add_argument('--get_attr',
default='all',
nargs='+',
choices=attr_columns + ['all'])
parser.add_argument('--outfile', '-o', default='attr_vec.json')
parser.add_argument('--enc', default='pre-trained/enc_iter_310000.npz')
args = parser.parse_args()
enc = Encoder()
npz.load_npz(args.enc, enc)
if args.gpu >= 0:
chainer.cuda.get_device_from_id(args.gpu).use()
enc.to_gpu()
all_files = os.listdir(args.dataset)
image_files = [f for f in all_files if ('png' in f or 'jpg' in f)]
vectors = {}
attr_df = pd.read_csv(args.attr_list, delim_whitespace=True, header=1)
if args.get_attr == 'all':
args.get_attr = attr_columns
for attr_name in tqdm(list(set(args.get_attr) & set(attr_df.columns))):
with_attr_files = attr_df[attr_df[attr_name] == 1].index.tolist()
with_attr_files = list(set(with_attr_files) & set(image_files))
with_attr_vec = get_vector(enc, with_attr_files, args)
without_attr_files = attr_df[attr_df[attr_name] != 1].index.tolist()
without_attr_files = list(set(without_attr_files) & set(image_files))
without_attr_vec = get_vector(enc, without_attr_files, args)
vectors[attr_name] = (with_attr_vec - without_attr_vec).tolist()
with open(args.outfile, 'w') as f:
f.write(
json.dumps(vectors,
indent=4,
sort_keys=True,
separators=(',', ': ')))
def main(id):
model_path = "/efs/fMRI_AE/SimpleFCAE_E32D32/model/model_iter_108858"
gpu = 0
get_device_from_id(gpu).use()
"""NibDataset
def __init__(self, directory: str, crop: list):
"""
crop = [[9, 81], [11, 99], [0, 80]]
test_dataset = NibDataset("/data/test", crop=crop)
mask = load_mask_nib("/data/mask/average_optthr.nii", crop)
"""SimpleFCAE_E32D32
def __init__(self, mask, r: int, in_mask: str, out_mask: str):
"""
model = Model(mask, 2, "mask", "mask")
load_npz(model_path, model)
model.to_gpu()
# feature_idx = 0
# feature_idx = (0, 4, 5, 5) # == [0, 9/2, 11/2, 10/2]
# feature_idx = (0, 1, 1, 1)
feature_idx = (0, 2, 7, 4)
resample_size = 100
batch_size = 10
noise_level = 0.2
for i in range(len(test_dataset)):
if i % 8 != id:
continue
print("{:4}/{:4}".format(i, len(test_dataset)))
subject = test_dataset.get_subject(i)
frame = test_dataset.get_frame(i)
test_img = xp.asarray(test_dataset[i])
resample_remain = resample_size
resample_processed = 0
ret = xp.zeros(test_img.shape)
while resample_remain > 0:
batch_size_this_loop = min(batch_size, resample_remain)
resample_remain -= batch_size_this_loop
batch = xp.broadcast_to(
test_img, chain((batch_size_this_loop, ), test_img.shape))
sigma = noise_level / (xp.max(test_img) - xp.min(test_img))
batch += sigma * xp.random.randn(*batch.shape)
x = Variable(batch)
feature = model.extract(x)
assert feature.shape == (batch_size, 1, 9, 11, 10)
feature = F.sum(feature, axis=0)
assert feature.shape == (1, 9, 11, 10)
feature = F.get_item(feature, feature_idx)
feature.backward()
grad = xp.mean(x.grad, axis=0)
ret = (ret * resample_processed + grad * batch_size_this_loop) / (
resample_processed + batch_size_this_loop)
model.cleargrads()
xp.save(
"/efs/fMRI_AE/SimpleFCAE_E32D32/grad/sensitivity_map_feature_{}_{}_{}_subject{:03d}_frame{:03d}"
.format(feature_idx[1], feature_idx[2], feature_idx[3], subject,
frame), ret)
def __init__(self, pretrained_model='auto'):
if pretrained_model:
# As a sampling process is time-consuming,
# we employ a zero initializer for faster computation.
init = constant.Zero()
kwargs = {'initialW': init, 'initial_bias': init}
else:
# employ default initializers used in the original paper
kwargs = {
'initialW': normal.Normal(0.01),
'initial_bias': constant.Zero(),
}
super(VGG16Layers, self).__init__()
with self.init_scope():
self.conv1_1 = Convolution2D(3, 64, 3, 1, 1, **kwargs)
self.conv1_2 = Convolution2D(64, 64, 3, 1, 1, **kwargs)
self.conv2_1 = Convolution2D(64, 128, 3, 1, 1, **kwargs)
self.conv2_2 = Convolution2D(128, 128, 3, 1, 1, **kwargs)
self.conv3_1 = Convolution2D(128, 256, 3, 1, 1, **kwargs)
self.conv3_2 = Convolution2D(256, 256, 3, 1, 1, **kwargs)
self.conv3_3 = Convolution2D(256, 256, 3, 1, 1, **kwargs)
self.conv4_1 = Convolution2D(256, 512, 3, 1, 1, **kwargs)
self.conv4_2 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
self.conv4_3 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
self.conv5_1 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
self.conv5_2 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
self.conv5_3 = Convolution2D(512, 512, 3, 1, 1, **kwargs)
self.fc6 = Linear(512 * 7 * 7, 4096, **kwargs)
self.fc7 = Linear(4096, 4096, **kwargs)
self.fc8 = Linear(4096, 1000, **kwargs)
if pretrained_model == 'auto':
_retrieve(
'VGG_ILSVRC_16_layers.npz',
'http://www.robots.ox.ac.uk/%7Evgg/software/very_deep/'
'caffe/VGG_ILSVRC_16_layers.caffemodel', self)
elif pretrained_model:
npz.load_npz(pretrained_model, self)
self.functions = collections.OrderedDict([
('conv1_1', [self.conv1_1, relu]),
('conv1_2', [self.conv1_2, relu]),
('pool1', [_max_pooling_2d]),
('conv2_1', [self.conv2_1, relu]),
('conv2_2', [self.conv2_2, relu]),
('pool2', [_max_pooling_2d]),
('conv3_1', [self.conv3_1, relu]),
('conv3_2', [self.conv3_2, relu]),
('conv3_3', [self.conv3_3, relu]),
('pool3', [_max_pooling_2d]),
('conv4_1', [self.conv4_1, relu]),
('conv4_2', [self.conv4_2, relu]),
('conv4_3', [self.conv4_3, relu]),
('pool4', [_max_pooling_2d]),
('conv5_1', [self.conv5_1, relu]),
('conv5_2', [self.conv5_2, relu]),
('conv5_3', [self.conv5_3, relu]),
('pool5', [_max_pooling_2d]),
('fc6', [self.fc6, relu, dropout]),
('fc7', [self.fc7, relu, dropout]),
('fc8', [self.fc8]),
('prob', [softmax]),
])
def test_load_with_path(self):
target = link.Chain(child_linear=links.Linear(2, 3))
npz.load_npz(self.temp_file_path, target, 'child/')
numpy.testing.assert_array_equal(
self.source_child.child_linear.W.data, target.child_linear.W.data)
def __init__(self,
pretrained_model='auto',
n_channels=3,
n_outputs=101,
mean_path='datasets/models/mean2.npz'):
super(C3DVersion1UCF101, self).__init__()
if pretrained_model:
# As a sampling process is time-consuming,
# we employ a zero initializer for faster computation.
init = constant.Zero()
conv_kwargs = {'initialW': init, 'initial_bias': init}
fc_kwargs = conv_kwargs
else:
# employ default initializers used in the original paper
conv_kwargs = {
'initialW': normal.Normal(0.01),
'initial_bias': constant.Zero(),
}
fc_kwargs = {
'initialW': normal.Normal(0.005),
'initial_bias': constant.One(),
}
with self.init_scope():
self.conv1a = ConvolutionND(3, n_channels, 64, 3, 1, 1,
**conv_kwargs)
self.conv2a = ConvolutionND(3, 64, 128, 3, 1, 1, **conv_kwargs)
self.conv3a = ConvolutionND(3, 128, 256, 3, 1, 1, **conv_kwargs)
self.conv3b = ConvolutionND(3, 256, 256, 3, 1, 1, **conv_kwargs)
self.conv4a = ConvolutionND(3, 256, 512, 3, 1, 1, **conv_kwargs)
self.conv4b = ConvolutionND(3, 512, 512, 3, 1, 1, **conv_kwargs)
self.conv5a = ConvolutionND(3, 512, 512, 3, 1, 1, **conv_kwargs)
self.conv5b = ConvolutionND(3, 512, 512, 3, 1, 1, **conv_kwargs)
self.fc6 = Linear(512 * 4 * 4, 4096, **fc_kwargs)
self.fc7 = Linear(4096, 4096, **fc_kwargs)
self.fc8 = Linear(4096, n_outputs, **fc_kwargs)
if pretrained_model == 'auto':
_retrieve(
'conv3d_deepnetA_ucf.npz', 'http://vlg.cs.dartmouth.edu/c3d/'
'c3d_ucf101_finetune_whole_iter_20000', self)
elif pretrained_model:
npz.load_npz(pretrained_model, self)
self.pre = ConvolutionND(3,
n_channels,
n_channels,
1,
1,
0,
nobias=True,
**conv_kwargs)
self.pre.W.data[:] = 0
self.pre.W.data[[0, 1, 2], [2, 1, 0]] = 128
# self.pre.b.data[:] = 128 - numpy.array([90.25164795, 97.65701294, 101.4083252])
self.mean = Bias(shape=(3, 16, 112, 112))
mean = numpy.load(mean_path)['mean']
self.mean.b.data[:] = 128 - mean[:, :, 8:8 + 112, 8:8 + 112]
self.functions = collections.OrderedDict([
('pre', [self.pre, _resize, self.mean]),
('conv1a', [self.conv1a, relu]),
('pool1', [_max_pooling_2d]),
('conv2a', [self.conv2a, relu]),
('pool2', [_max_pooling_3d]),
('conv3a', [self.conv3a, relu]),
('conv3b', [self.conv3b, relu]),
('pool3', [_max_pooling_3d]),
('conv4a', [self.conv4a, relu]),
('conv4b', [self.conv4b, relu]),
('pool4', [_max_pooling_3d]),
('conv5a', [self.conv5a, relu]),
('conv5b', [self.conv5b, relu]),
('pool5', [_max_pooling_3d, dropout]),
('fc6', [self.fc6, relu, dropout]),
('fc7', [self.fc7, relu, dropout]),
('fc8', [self.fc8]),
('prob', [softmax]),
])
def _retrieve(name, url, model):
root = download.get_dataset_directory('pfnet/chainer/models/')
path = os.path.join(root, name)
return download.cache_or_load_file(
path, lambda path: _make_npz(path, url, model),
lambda path: npz.load_npz(path, model))
def main():
experiment_name = "Stacked_16_16_16_16"
snapshot_name = "snapshot_iter_27215"
config_path = "/efs/fMRI_AE/{}/log/config.yml".format(experiment_name)
config = load_config(config_path)
config["additional information"]["mask"]["loader"]["params"][
"mask_path"] = path.join(
config["additional information"]["mask"]["directory"],
config["additional information"]["mask"]["file"])
config["additional information"]["mask"]["loader"]["params"][
"crop"] = config["additional information"]["crop"]
snapshot_path = "/efs/fMRI_AE/{}/model/{}".format(experiment_name,
snapshot_name)
# print("configured as follows:")
# print(yaml_dump(config))
while True:
s = input("ok? (y/n):")
if s == 'y' or s == 'Y':
log_config(config, "training start")
break
elif s == 'n' or s == 'N':
destroy_config(config)
exit(1)
try:
try:
print("mask loading...")
load_mask_module = import_module(
config["additional information"]["mask"]["loader"]["module"],
config["additional information"]["mask"]["loader"]["package"])
load_mask = getattr(
load_mask_module,
config["additional information"]["mask"]["loader"]["function"])
mask = load_mask(
**config["additional information"]["mask"]["loader"]["params"])
print("done.")
print("mask.shape: {}".format(mask.shape))
except FileNotFoundError as e:
raise e
model_module = import_module(config["model"]["module"],
config["model"]["package"])
Model = getattr(model_module, config["model"]["class"])
model = Model(mask=mask, **config["model"]["params"])
finetune_config = config["additional information"]["finetune"]
if finetune_config is not None:
load_npz(path.join(finetune_config["directory"],
finetune_config["file"]),
model,
strict=False)
try:
chainer.cuda.get_device_from_id(0).use()
gpu = 0
print("transferring model to GPU...")
model.to_gpu(gpu)
print("GPU enabled")
except RuntimeError:
gpu = -1
print("GPU disabled")
dataset_module = import_module(config["dataset"]["module"],
config["dataset"]["package"])
Dataset = getattr(dataset_module, config["dataset"]["class"])
train_dataset = Dataset(**config["dataset"]["train"]["params"])
valid_dataset = Dataset(**config["dataset"]["valid"]["params"])
train_iterator = Iterator(train_dataset, config["batch"]["train"],
True, True)
valid_iterator = Iterator(valid_dataset, config["batch"]["valid"],
False, False)
Optimizer = getattr(chainer.optimizers, config["optimizer"]["class"])
optimizer = Optimizer(**config["optimizer"]["params"])
optimizer.setup(model)
for hook_config in config["optimizer"]["hook"]:
hook_module = import_module(hook_config["module"],
hook_config["package"])
Hook = getattr(hook_module, hook_config["class"])
hook = Hook(**hook_config["params"])
optimizer.add_hook(hook)
updater = Updater(train_iterator, optimizer, device=gpu)
trainer = Trainer(updater, **config["trainer"]["params"])
trainer.extend(snapshot(),
trigger=config["trainer"]["snapshot_interval"])
trainer.extend(snapshot_object(model,
"model_iter_{.updater.iteration}"),
trigger=config["trainer"]["model_interval"])
trainer.extend(observe_lr(), trigger=config["trainer"]["log_interval"])
trainer.extend(
LogReport([
"epoch", "iteration", "main/loss", "main/pca_loss",
"main/reconstruction_loss", "validation/main/loss"
],
trigger=config["trainer"]["log_interval"]))
trainer.extend(Evaluator(valid_iterator, model, device=gpu),
trigger=config["trainer"]["eval_interval"])
trainer.extend(PrintReport([
"epoch", "iteration", "main/loss", "main/pca_loss",
"main/reconstruction_loss", "validation/main/loss"
]),
trigger=config["trainer"]["log_interval"])
trainer.extend(ProgressBar(update_interval=1))
if "schedule" in config["additional information"].keys():
for i, interval_funcs in enumerate(
config["additional information"]["schedule"].items()):
interval, funcs = interval_funcs
f = lambda trainer, funcs=funcs: [
trainer.updater.get_optimizer('main').target.
__getattribute__(func["function"])(*func["params"])
for func in funcs
]
trainer.extend(f,
name="schedule_{}".format(i),
trigger=ManualScheduleTrigger(*interval))
load_npz(snapshot_path, trainer)
target = trainer.updater.get_optimizer("main").target
target.reset_pca()
target.attach_pca()
ipca_param = np.load(
"/efs/fMRI_AE/Stacked_8_8_8_8_feature/ipca_mean_7920_components_990_7920.npz"
)
target.pca.W = chainer.Parameter(ipca_param["components"])
target.pca.bias = chainer.Parameter(ipca_param["mean"])
target.pca.disable_update()
target.pca.to_gpu(gpu)
target.detach_pca_loss()
target.attach_reconstruction_loss()
target.release_decoder()
target.freeze_encoder()
trainer.run()
log_config(config, "succeeded")
except Exception as e:
log_config(config, "unintentional termination")
raise e