def connectIntermediateLayers(self, layersToConnect,
inputSampleInFullyCN_Train,
inputSampleInFullyCN_Test,
featMapsInFullyCN):
centralVoxelsTrain = self.centralVoxelsTrain
centralVoxelsTest = self.centralVoxelsTest
for l_i in layersToConnect:
currentLayer = self.networkLayers[l_i]
output_train = currentLayer.outputTrain
output_trainShape = currentLayer.outputShapeTrain
output_test = currentLayer.outputTest
output_testShape = currentLayer.outputShapeTest
# Get the middle part of feature maps at intermediate levels to make them of the same shape at the beginning of the
# first fully connected layer
featMapsCenter_Train = extractCenterFeatMaps(
output_train, output_trainShape, centralVoxelsTrain)
featMapsCenter_Test = extractCenterFeatMaps(
output_test, output_testShape, centralVoxelsTest)
featMapsInFullyCN = featMapsInFullyCN + currentLayer._numberOfFeatureMaps
inputSampleInFullyCN_Train = T.concatenate(
[inputSampleInFullyCN_Train, featMapsCenter_Train], axis=1)
inputSampleInFullyCN_Test = T.concatenate(
[inputSampleInFullyCN_Test, featMapsCenter_Test], axis=1)
return [
featMapsInFullyCN, inputSampleInFullyCN_Train,
inputSampleInFullyCN_Test
]
def connectIntermediateLayers(self,
layersToConnect,
inputSampleInFullyCN_Train,
inputSampleInFullyCN_Test,
featMapsInFullyCN):
centralVoxelsTrain = self.centralVoxelsTrain
centralVoxelsTest = self.centralVoxelsTest
for l_i in layersToConnect :
currentLayer = self.networkLayers[l_i]
output_train = currentLayer.outputTrain
output_trainShape = currentLayer.outputShapeTrain
output_test = currentLayer.outputTest
output_testShape = currentLayer.outputShapeTest
# Get the middle part of feature maps at intermediate levels to make them of the same shape at the beginning of the
# first fully connected layer
featMapsCenter_Train = extractCenterFeatMaps(output_train, output_trainShape, centralVoxelsTrain)
featMapsCenter_Test = extractCenterFeatMaps(output_test, output_testShape, centralVoxelsTest)
featMapsInFullyCN = featMapsInFullyCN + currentLayer._numberOfFeatureMaps
inputSampleInFullyCN_Train = T.concatenate([inputSampleInFullyCN_Train, featMapsCenter_Train], axis=1)
inputSampleInFullyCN_Test = T.concatenate([inputSampleInFullyCN_Test, featMapsCenter_Test], axis=1)
return [featMapsInFullyCN, inputSampleInFullyCN_Train, inputSampleInFullyCN_Test]
def generateNetworkLayers(self,
cnnLayers,
kernel_Shapes,
maxPooling_Layer,
sampleShape_Train,
sampleShape_Test,
inputSample_Train,
inputSample_Train_Bottom,
inputSample_Test,
inputSample_Test_Bottom,
layersToConnect):
rng = np.random.RandomState(24575)
# Define inputs for first layers (which will be re-used for next layers)
inputSampleToNextLayer_Train = inputSample_Train
inputSampleToNextLayer_Test = inputSample_Test
inputSampleToNextLayer_Train_Bottom = inputSample_Train_Bottom
inputSampleToNextLayer_Test_Bottom = inputSample_Test_Bottom
inputSampleToNextLayerShape_Train = sampleShape_Train
inputSampleToNextLayerShape_Test = sampleShape_Test
# Get the convolutional layers
numLayers = len(kernel_Shapes)
numberCNNLayers = []
numberFCLayers = []
for l_i in range(1,len(kernel_Shapes)):
if len(kernel_Shapes[l_i]) == 3:
numberCNNLayers = l_i + 1
numberFCLayers = numLayers - numberCNNLayers
######### -------------- Generate the convolutional layers -------------- #########
# Some checks
if self.weight_Initialization_CNN == 2:
if len(self.weightsTrainedIdx) <> numberCNNLayers:
print(" ... WARNING!!!! Number of indexes specified for trained layers does not correspond with number of conv layers in the created architecture...")
if self.weight_Initialization_CNN == 2:
weightsNames = getWeightsSet(self.weightsFolderName, self.weightsTrainedIdx)
for l_i in xrange(0, numberCNNLayers) :
# Get properties of this layer
# The second element is the number of feature maps of previous layer
currentLayerKernelShape = [cnnLayers[l_i], inputSampleToNextLayerShape_Train[1]] + kernel_Shapes[l_i]
# If weights are going to be initialized from other pre-trained network they should be loaded in this stage
# Otherwise
weights = []
if self.weight_Initialization_CNN == 2:
weights = np.load(weightsNames[l_i])
maxPoolingParameters = []
dropoutRate = 0.0
### TOP ##
myLiviaNet3DConvLayerTop = LiviaNet3DConvLayer.LiviaNet3DConvLayer(rng,
l_i,
inputSampleToNextLayer_Train,
inputSampleToNextLayer_Test,
inputSampleToNextLayerShape_Train,
inputSampleToNextLayerShape_Test,
currentLayerKernelShape,
self.applyBatchNorm,
self.numberEpochToApplyBatchNorm,
maxPoolingParameters,
self.weight_Initialization_CNN,
weights,
self.activationType,
dropoutRate
)
self.networkLayers.append(myLiviaNet3DConvLayerTop)
## BOTTOM ##
myLiviaNet3DConvLayerBottom = LiviaNet3DConvLayer.LiviaNet3DConvLayer(rng,
l_i,
inputSampleToNextLayer_Train_Bottom,
inputSampleToNextLayer_Test_Bottom,
inputSampleToNextLayerShape_Train,
inputSampleToNextLayerShape_Test,
currentLayerKernelShape,
self.applyBatchNorm,
self.numberEpochToApplyBatchNorm,
maxPoolingParameters,
self.weight_Initialization_CNN,
weights,
self.activationType,
dropoutRate
)
self.networkLayers.append(myLiviaNet3DConvLayerBottom)
# Just for printing
inputSampleToNextLayer_Train_Old = inputSampleToNextLayerShape_Train
inputSampleToNextLayer_Test_Old = inputSampleToNextLayerShape_Test
# Update inputs for next layer
inputSampleToNextLayer_Train = myLiviaNet3DConvLayerTop.outputTrain
inputSampleToNextLayer_Test = myLiviaNet3DConvLayerTop.outputTest
inputSampleToNextLayer_Train_Bottom = myLiviaNet3DConvLayerBottom.outputTrain
inputSampleToNextLayer_Test_Bottom = myLiviaNet3DConvLayerBottom.outputTest
inputSampleToNextLayerShape_Train = myLiviaNet3DConvLayerTop.outputShapeTrain
inputSampleToNextLayerShape_Test = myLiviaNet3DConvLayerTop.outputShapeTest
print(" ----- (Training) Input shape: {} ---> Output shape: {} || kernel shape {}".format(inputSampleToNextLayer_Train_Old,inputSampleToNextLayerShape_Train, currentLayerKernelShape))
print(" ----- (Testing) Input shape: {} ---> Output shape: {}".format(inputSampleToNextLayer_Test_Old,inputSampleToNextLayerShape_Test))
### Create the semi-dense connectivity
centralVoxelsTrain = self.centralVoxelsTrain
centralVoxelsTest = self.centralVoxelsTest
numLayersPerPath = len(self.networkLayers)/2
featMapsInFullyCN = 0
# ------- TOP -------- #
print(" ----------- TOP PATH ----------------")
for l_i in xrange(0,numLayersPerPath-1) :
print(' --- concatennating layer {} ...'.format(str(l_i)))
currentLayer = self.networkLayers[2*l_i] # to access the layers from the top path
output_train = currentLayer.outputTrain
output_trainShape = currentLayer.outputShapeTrain
output_test = currentLayer.outputTest
output_testShape = currentLayer.outputShapeTest
# Get the middle part of feature maps at intermediate levels to make them of the same shape at the beginning of the
# first fully connected layer
featMapsCenter_Train = extractCenterFeatMaps(output_train, output_trainShape, centralVoxelsTrain)
featMapsCenter_Test = extractCenterFeatMaps(output_test, output_testShape, centralVoxelsTest)
featMapsInFullyCN = featMapsInFullyCN + currentLayer._numberOfFeatureMaps
inputSampleToNextLayer_Train = T.concatenate([inputSampleToNextLayer_Train, featMapsCenter_Train], axis=1)
inputSampleToNextLayer_Test = T.concatenate([inputSampleToNextLayer_Test, featMapsCenter_Test], axis=1)
# ------- Bottom -------- #
print(" ---------- BOTTOM PATH ---------------")
for l_i in xrange(0,numLayersPerPath-1) :
print(' --- concatennating layer {} ...'.format(str(l_i)))
currentLayer = self.networkLayers[2*l_i+1] # to access the layers from the bottom path
output_train = currentLayer.outputTrain
output_trainShape = currentLayer.outputShapeTrain
output_test = currentLayer.outputTest
output_testShape = currentLayer.outputShapeTest
# Get the middle part of feature maps at intermediate levels to make them of the same shape at the beginning of the
# first fully connected layer
featMapsCenter_Train = extractCenterFeatMaps(output_train, output_trainShape, centralVoxelsTrain)
featMapsCenter_Test = extractCenterFeatMaps(output_test, output_testShape, centralVoxelsTest)
featMapsInFullyCN = featMapsInFullyCN + currentLayer._numberOfFeatureMaps
inputSampleToNextLayer_Train_Bottom = T.concatenate([inputSampleToNextLayer_Train_Bottom, featMapsCenter_Train], axis=1)
inputSampleToNextLayer_Test_Bottom = T.concatenate([inputSampleToNextLayer_Test_Bottom, featMapsCenter_Test], axis=1)
######### -------------- Generate the Fully Connected Layers ----------------- ##################
inputToFullyCN_Train = inputSampleToNextLayer_Train
inputToFullyCN_Train = T.concatenate([inputToFullyCN_Train, inputSampleToNextLayer_Train_Bottom], axis=1)
inputToFullyCN_Test = inputSampleToNextLayer_Test
inputToFullyCN_Test = T.concatenate([inputToFullyCN_Test, inputSampleToNextLayer_Test_Bottom], axis=1)
featMapsInFullyCN = featMapsInFullyCN + inputSampleToNextLayerShape_Train[1] * 2 # Because we have two symmetric paths
# Define inputs
inputFullyCNShape_Train = [self.batch_Size, featMapsInFullyCN] + inputSampleToNextLayerShape_Train[2:5]
inputFullyCNShape_Test = [self.batch_Size, featMapsInFullyCN] + inputSampleToNextLayerShape_Test[2:5]
# Kamnitsas applied padding and mirroring to the images when kernels in FC layers were larger than 1x1x1.
# For this current work, we employed kernels of this size (i.e. 1x1x1), so there is no need to apply padding or mirroring.
# TODO. Check
print(" --- Starting to create the fully connected layers....")
for l_i in xrange(numberCNNLayers, numLayers) :
numberOfKernels = cnnLayers[l_i]
kernel_shape = [kernel_Shapes[l_i][0],kernel_Shapes[l_i][0],kernel_Shapes[l_i][0]]
currentLayerKernelShape = [cnnLayers[l_i], inputFullyCNShape_Train[1]] + kernel_shape
# If weights are going to be initialized from other pre-trained network they should be loaded in this stage
# Otherwise
weights = []
applyBatchNorm = True
epochsToApplyBatchNorm = 60
maxPoolingParameters = []
dropoutRate = self.dropout_Rates[l_i-numberCNNLayers]
myLiviaNet3DFullyConnectedLayer = LiviaNet3DConvLayer.LiviaNet3DConvLayer(rng,
l_i,
inputToFullyCN_Train,
inputToFullyCN_Test,
inputFullyCNShape_Train,
inputFullyCNShape_Test,
currentLayerKernelShape,
self.applyBatchNorm,
self.numberEpochToApplyBatchNorm,
maxPoolingParameters,
self.weight_Initialization_FCN,
weights,
self.activationType,
dropoutRate
)
self.networkLayers.append(myLiviaNet3DFullyConnectedLayer)
# Just for printing
inputFullyCNShape_Train_Old = inputFullyCNShape_Train
inputFullyCNShape_Test_Old = inputFullyCNShape_Test
# Update inputs for next layer
inputToFullyCN_Train = myLiviaNet3DFullyConnectedLayer.outputTrain
inputToFullyCN_Test = myLiviaNet3DFullyConnectedLayer.outputTest
inputFullyCNShape_Train = myLiviaNet3DFullyConnectedLayer.outputShapeTrain
inputFullyCNShape_Test = myLiviaNet3DFullyConnectedLayer.outputShapeTest
# Print
print(" ----- (Training) Input shape: {} ---> Output shape: {} || kernel shape {}".format(inputFullyCNShape_Train_Old,inputFullyCNShape_Train, currentLayerKernelShape))
print(" ----- (Testing) Input shape: {} ---> Output shape: {}".format(inputFullyCNShape_Test_Old,inputFullyCNShape_Test))
######### -------------- Do Classification layer ----------------- ##################
# Define kernel shape for classification layer
featMaps_LastLayer = self.cnnLayers[-1]
filterShape_ClassificationLayer = [self.n_classes, featMaps_LastLayer, 1, 1, 1]
# Define inputs and shapes for the classification layer
inputImageClassificationLayer_Train = inputToFullyCN_Train
inputImageClassificationLayer_Test = inputToFullyCN_Test
inputImageClassificationLayerShape_Train = inputFullyCNShape_Train
inputImageClassificationLayerShape_Test = inputFullyCNShape_Test
print(" ----- (Classification layer) kernel shape {}".format(filterShape_ClassificationLayer))
classification_layer_Index = l_i
weights = []
applyBatchNorm = True
epochsToApplyBatchNorm = 60
maxPoolingParameters = []
dropoutRate = self.dropout_Rates[len(self.dropout_Rates)-1]
softmaxTemperature = 1.0
myLiviaNet_ClassificationLayer = LiviaSoftmax.LiviaSoftmax(rng,
classification_layer_Index,
inputImageClassificationLayer_Train,
inputImageClassificationLayer_Test,
inputImageClassificationLayerShape_Train,
inputImageClassificationLayerShape_Test,
filterShape_ClassificationLayer,
self.applyBatchNorm,
self.numberEpochToApplyBatchNorm,
maxPoolingParameters,
self.weight_Initialization_FCN,
weights,
0, #self.activationType,
dropoutRate,
softmaxTemperature
)
self.networkLayers.append(myLiviaNet_ClassificationLayer)
self.lastLayer = myLiviaNet_ClassificationLayer
print(" ----- (Training) Input shape: {} ---> Output shape: {} || kernel shape {}".format(inputImageClassificationLayerShape_Train,myLiviaNet_ClassificationLayer.outputShapeTrain, filterShape_ClassificationLayer))
print(" ----- (Testing) Input shape: {} ---> Output shape: {}".format(inputImageClassificationLayerShape_Test,myLiviaNet_ClassificationLayer.outputShapeTest))
def generateNetworkLayers(self, cnnLayers, kernel_Shapes, maxPooling_Layer,
sampleShape_Train, sampleShape_Test,
inputSample_Train, inputSample_Train_Bottom,
inputSample_Test, inputSample_Test_Bottom,
layersToConnect):
rng = np.random.RandomState(24575)
# Define inputs for first layers (which will be re-used for next layers)
inputSampleToNextLayer_Train = inputSample_Train
inputSampleToNextLayer_Test = inputSample_Test
inputSampleToNextLayer_Train_Bottom = inputSample_Train_Bottom
inputSampleToNextLayer_Test_Bottom = inputSample_Test_Bottom
inputSampleToNextLayerShape_Train = sampleShape_Train
inputSampleToNextLayerShape_Test = sampleShape_Test
# Get the convolutional layers
numLayers = len(kernel_Shapes)
numberCNNLayers = []
numberFCLayers = []
for l_i in range(1, len(kernel_Shapes)):
if len(kernel_Shapes[l_i]) == 3:
numberCNNLayers = l_i + 1
numberFCLayers = numLayers - numberCNNLayers
######### -------------- Generate the convolutional layers -------------- #########
# Some checks
if self.weight_Initialization_CNN == 2:
if len(self.weightsTrainedIdx) <> numberCNNLayers:
print(
" ... WARNING!!!! Number of indexes specified for trained layers does not correspond with number of conv layers in the created architecture..."
)
if self.weight_Initialization_CNN == 2:
weightsNames = getWeightsSet(self.weightsFolderName,
self.weightsTrainedIdx)
numberOfOutputKernels = [0]
for l_i in xrange(0, numberCNNLayers):
# Get properties of this layer
# The second element is the number of feature maps of previous layer
currentLayerKernelShape = [
cnnLayers[l_i], inputSampleToNextLayerShape_Train[1]
] + kernel_Shapes[l_i]
# If weights are going to be initialized from other pre-trained network they should be loaded in this stage
# Otherwise
weights = []
if self.weight_Initialization_CNN == 2:
weights = np.load(weightsNames[l_i])
maxPoolingParameters = []
dropoutRate = 0.0
### TOP ##
print('--' * 50)
print(' **** TOP ****')
myLiviaNet3DConvLayerTop = HyperDenseNetConvLayer.HyperDenseNetConvLayer(
rng, l_i, inputSampleToNextLayer_Train,
inputSampleToNextLayer_Test, inputSampleToNextLayerShape_Train,
inputSampleToNextLayerShape_Test, currentLayerKernelShape,
self.applyBatchNorm, self.numberEpochToApplyBatchNorm,
maxPoolingParameters, self.weight_Initialization_CNN, weights,
self.activationType, dropoutRate)
self.networkLayers.append(myLiviaNet3DConvLayerTop)
numberOfOutputKernels.append(
myLiviaNet3DConvLayerTop.outputShapeTrain[1])
## BOTTOM ##
print(' **** BOTTOM ****')
myLiviaNet3DConvLayerBottom = HyperDenseNetConvLayer.HyperDenseNetConvLayer(
rng, l_i, inputSampleToNextLayer_Train_Bottom,
inputSampleToNextLayer_Test_Bottom,
inputSampleToNextLayerShape_Train,
inputSampleToNextLayerShape_Test, currentLayerKernelShape,
self.applyBatchNorm, self.numberEpochToApplyBatchNorm,
maxPoolingParameters, self.weight_Initialization_CNN, weights,
self.activationType, dropoutRate)
self.networkLayers.append(myLiviaNet3DConvLayerBottom)
# Update inputs for next layer
#inputSampleToNextLayer_Train = myLiviaNet3DConvLayerTop.outputTrain
#inputSampleToNextLayer_Test = myLiviaNet3DConvLayerTop.outputTest
#inputSampleToNextLayer_Train_Bottom = myLiviaNet3DConvLayerBottom.outputTrain
#inputSampleToNextLayer_Test_Bottom = myLiviaNet3DConvLayerBottom.outputTest
#inputSampleToNextLayerShape_Train = myLiviaNet3DConvLayerTop.outputShapeTrain
#inputSampleToNextLayerShape_Test = myLiviaNet3DConvLayerTop.outputShapeTest
# ~~~~~~~ Make here the dense connections ~~~~~~~~~~~
print(" -Output Layer shape: {}".format(
myLiviaNet3DConvLayerTop.outputShapeTrain))
shapeTrain = []
shapeTrain.append(myLiviaNet3DConvLayerTop.outputShapeTrain[0])
shapeTrain.append(myLiviaNet3DConvLayerTop.outputShapeTrain[1])
shapeTrain.append(myLiviaNet3DConvLayerTop.outputShapeTrain[2])
shapeTrain.append(myLiviaNet3DConvLayerTop.outputShapeTrain[3])
shapeTrain.append(myLiviaNet3DConvLayerTop.outputShapeTrain[4])
shapeTest = []
shapeTest.append(myLiviaNet3DConvLayerTop.outputShapeTest[0])
shapeTest.append(myLiviaNet3DConvLayerTop.outputShapeTest[1])
shapeTest.append(myLiviaNet3DConvLayerTop.outputShapeTest[2])
shapeTest.append(myLiviaNet3DConvLayerTop.outputShapeTest[3])
shapeTest.append(myLiviaNet3DConvLayerTop.outputShapeTest[4])
# Define the sizes of the convolutional layers (denselly connected)
denseInputNextLayerShape = shapeTrain
denseInputNextLayerShapeTesting = shapeTest
print(" -Adding Dense connections....")
numLayersPerPath = len(self.networkLayers) / 2
for d_l in xrange(numLayersPerPath):
denseInputNextLayerShape[1] = denseInputNextLayerShape[
1] + numberOfOutputKernels[d_l]
denseInputNextLayerShapeTesting[
1] = denseInputNextLayerShapeTesting[
1] + numberOfOutputKernels[d_l]
denseInputNextLayerShape[1] = 2 * denseInputNextLayerShape[1]
denseInputNextLayerShapeTesting[
1] = 2 * denseInputNextLayerShapeTesting[1]
print(" -denseInput Next Layer shape: {}".format(
denseInputNextLayerShape))
inputSampleToNextLayerShape_Train = denseInputNextLayerShape
inputSampleToNextLayerShape_Test = denseInputNextLayerShapeTesting
numberOfCentralVoxelsToGetTraining = inputSampleToNextLayerShape_Train[
2:5]
numberOfCentralVoxelsToGetTesting = inputSampleToNextLayerShape_Test[
2:5]
# Get first outputs
#~~~~ TOP ~~~~~~
inputSampleToNextLayer_Train = myLiviaNet3DConvLayerTop.outputTrain # inputImageToNextLayer_Top
inputSampleToNextLayer_Test = myLiviaNet3DConvLayerTop.outputTest # inputImageToNextLayerTesting_Top
#~~~~ BOTTOM ~~~~~~
inputSampleToNextLayer_Train_Bottom = myLiviaNet3DConvLayerBottom.outputTrain # inputImageToNextLayer_Bottom
inputSampleToNextLayer_Test_Bottom = myLiviaNet3DConvLayerBottom.outputTest # inputImageToNextLayerTesting_Bottom
print(" ----- Concatennating feature maps.... ----- ")
# Concatennate feat maps in first layer
#~~~~ TOP ~~~~~~
inputImageToNextLayer_Top_Temp = inputSampleToNextLayer_Train
inputImageToNextLayerTesting_Top_Temp = inputSampleToNextLayer_Test
inputSampleToNextLayer_Train = T.concatenate(
[
inputSampleToNextLayer_Train,
inputSampleToNextLayer_Train_Bottom
],
axis=1) # inputImageToNextLayer_Top
inputSampleToNextLayer_Test = T.concatenate(
[
inputSampleToNextLayer_Test,
inputSampleToNextLayer_Test_Bottom
],
axis=1) # inputImageToNextLayerTesting_Top
#~~~~ BOTTOM ~~~~~~
inputSampleToNextLayer_Train_Bottom = T.concatenate([
inputSampleToNextLayer_Train_Bottom,
inputImageToNextLayer_Top_Temp
],
axis=1)
inputSampleToNextLayer_Test_Bottom = T.concatenate([
inputSampleToNextLayer_Test_Bottom,
inputImageToNextLayerTesting_Top_Temp
],
axis=1)
# Concatennate feature maps in remaining layers
for d_l in xrange(0, numLayersPerPath - 1):
print(" ----> Layer {} ".format(d_l))
print(" ----> outputShapeTrain {} ".format(
self.networkLayers[2 * d_l].outputShapeTrain))
# ~~~~~ TOP ~~~~ #
# Training samples
featMapsCenter_Train_Top = extractCenterFeatMaps(
self.networkLayers[2 * d_l].outputTrain,
self.networkLayers[2 * d_l].outputShapeTrain,
numberOfCentralVoxelsToGetTraining)
# Testing samples
featMapsCenter_Test_Top = extractCenterFeatMaps(
self.networkLayers[2 * d_l].outputTest,
self.networkLayers[2 * d_l].outputShapeTest,
numberOfCentralVoxelsToGetTesting)
# ~~~~~ BOTTOM ~~~~ #
# Training samples
featMapsCenter_Train_Bottom = extractCenterFeatMaps(
self.networkLayers[2 * d_l + 1].outputTrain,
self.networkLayers[2 * d_l + 1].outputShapeTrain,
numberOfCentralVoxelsToGetTraining)
# Testing samples
featMapsCenter_Test_Bottom = extractCenterFeatMaps(
self.networkLayers[2 * d_l + 1].outputTest,
self.networkLayers[2 * d_l + 1].outputShapeTest,
numberOfCentralVoxelsToGetTesting)
# ~~~~ TOP ~~~~ #
# (Dense) Connections with same path
inputSampleToNextLayer_Train = T.concatenate(
[inputSampleToNextLayer_Train, featMapsCenter_Train_Top],
axis=1)
inputSampleToNextLayer_Test = T.concatenate(
[inputSampleToNextLayer_Test, featMapsCenter_Test_Top],
axis=1)
# (Dense) Connections with the other path
inputSampleToNextLayer_Train = T.concatenate([
inputSampleToNextLayer_Train, featMapsCenter_Train_Bottom
],
axis=1)
inputSampleToNextLayer_Test = T.concatenate(
[inputSampleToNextLayer_Test, featMapsCenter_Test_Bottom],
axis=1)
# ~~~~ BOTTOM ~~~~ #
# Connections with same path
inputSampleToNextLayer_Train_Bottom = T.concatenate([
inputSampleToNextLayer_Train_Bottom,
featMapsCenter_Train_Bottom
],
axis=1)
inputSampleToNextLayer_Test_Bottom = T.concatenate([
inputSampleToNextLayer_Test_Bottom,
featMapsCenter_Test_Bottom
],
axis=1)
# Connections with the other path
inputSampleToNextLayer_Train_Bottom = T.concatenate([
inputSampleToNextLayer_Train_Bottom,
featMapsCenter_Train_Top
],
axis=1)
inputSampleToNextLayer_Test_Bottom = T.concatenate([
inputSampleToNextLayer_Test_Bottom, featMapsCenter_Test_Top
],
axis=1)
######### -------------- Generate the Fully Connected Layers ----------------- ##################
inputToFullyCN_Train = inputSampleToNextLayer_Train
inputToFullyCN_Train = T.concatenate(
[inputToFullyCN_Train, inputSampleToNextLayer_Train_Bottom],
axis=1)
inputToFullyCN_Test = inputSampleToNextLayer_Test
inputToFullyCN_Test = T.concatenate(
[inputToFullyCN_Test, inputSampleToNextLayer_Test_Bottom], axis=1)
featMapsInFullyCN = inputSampleToNextLayerShape_Train[1] * 2
#featMapsInFullyCN = featMapsInFullyCN + inputSampleToNextLayerShape_Train[1]
# Define inputs
inputFullyCNShape_Train = [
self.batch_Size, featMapsInFullyCN,
inputSampleToNextLayerShape_Train[2],
inputSampleToNextLayerShape_Train[3],
inputSampleToNextLayerShape_Train[4]
]
inputFullyCNShape_Test = [
self.batch_Size, featMapsInFullyCN,
inputSampleToNextLayerShape_Test[2],
inputSampleToNextLayerShape_Test[3],
inputSampleToNextLayerShape_Test[4]
]
# Kamnitsas applied padding and mirroring to the images when kernels in FC layers were larger than 1x1x1.Jose Dolz. April, 2018.
# For this current work, we employed kernels of this size (i.e. 1x1x1), so there is no need to apply padding or mirroring.
# TODO. Check
print("**" * 50)
print(" --- Starting to create the fully connected layers....")
print("**" * 50)
for l_i in xrange(numberCNNLayers, numLayers):
numberOfKernels = cnnLayers[l_i]
kernel_shape = [
kernel_Shapes[l_i][0], kernel_Shapes[l_i][0],
kernel_Shapes[l_i][0]
]
currentLayerKernelShape = [
cnnLayers[l_i], inputFullyCNShape_Train[1]
] + kernel_shape
# If weights are going to be initialized from other pre-trained network they should be loaded in this stage
# Otherwise
weights = []
applyBatchNorm = True
epochsToApplyBatchNorm = 60
maxPoolingParameters = []
dropoutRate = self.dropout_Rates[l_i - numberCNNLayers]
myLiviaNet3DFullyConnectedLayer = HyperDenseNetConvLayer.HyperDenseNetConvLayer(
rng, l_i, inputToFullyCN_Train, inputToFullyCN_Test,
inputFullyCNShape_Train, inputFullyCNShape_Test,
currentLayerKernelShape, self.applyBatchNorm,
self.numberEpochToApplyBatchNorm, maxPoolingParameters,
self.weight_Initialization_FCN, weights, self.activationType,
dropoutRate)
self.networkLayers.append(myLiviaNet3DFullyConnectedLayer)
# Just for printing
inputFullyCNShape_Train_Old = inputFullyCNShape_Train
inputFullyCNShape_Test_Old = inputFullyCNShape_Test
# Update inputs for next layer
inputToFullyCN_Train = myLiviaNet3DFullyConnectedLayer.outputTrain
inputToFullyCN_Test = myLiviaNet3DFullyConnectedLayer.outputTest
inputFullyCNShape_Train = myLiviaNet3DFullyConnectedLayer.outputShapeTrain
inputFullyCNShape_Test = myLiviaNet3DFullyConnectedLayer.outputShapeTest
# Print
print(
" ----- (Training) Input shape: {} ---> Output shape: {} || kernel shape {}"
.format(inputFullyCNShape_Train_Old, inputFullyCNShape_Train,
currentLayerKernelShape))
print(" ----- (Testing) Input shape: {} ---> Output shape: {}".
format(inputFullyCNShape_Test_Old, inputFullyCNShape_Test))
print("--" * 35)
######### -------------- Do Classification layer ----------------- ##################
# Define kernel shape for classification layer
featMaps_LastLayer = self.cnnLayers[-1]
filterShape_ClassificationLayer = [
self.n_classes, featMaps_LastLayer, 1, 1, 1
]
# Define inputs and shapes for the classification layer
inputImageClassificationLayer_Train = inputToFullyCN_Train
inputImageClassificationLayer_Test = inputToFullyCN_Test
inputImageClassificationLayerShape_Train = inputFullyCNShape_Train
inputImageClassificationLayerShape_Test = inputFullyCNShape_Test
print("--" * 35)
print(" ----- (Classification layer) kernel shape {}".format(
filterShape_ClassificationLayer))
classification_layer_Index = l_i
weights = []
applyBatchNorm = True
epochsToApplyBatchNorm = 60
maxPoolingParameters = []
dropoutRate = self.dropout_Rates[len(self.dropout_Rates) - 1]
softmaxTemperature = 1.0
myLiviaNet_ClassificationLayer = LiviaSoftmax.LiviaSoftmax(
rng,
classification_layer_Index,
inputImageClassificationLayer_Train,
inputImageClassificationLayer_Test,
inputImageClassificationLayerShape_Train,
inputImageClassificationLayerShape_Test,
filterShape_ClassificationLayer,
self.applyBatchNorm,
self.numberEpochToApplyBatchNorm,
maxPoolingParameters,
self.weight_Initialization_FCN,
weights,
0, #self.activationType,
dropoutRate,
softmaxTemperature)
self.networkLayers.append(myLiviaNet_ClassificationLayer)
self.lastLayer = myLiviaNet_ClassificationLayer
print(
" ----- (Training) Input shape: {} ---> Output shape: {} || kernel shape {}"
.format(inputImageClassificationLayerShape_Train,
myLiviaNet_ClassificationLayer.outputShapeTrain,
filterShape_ClassificationLayer))
print(
" ----- (Testing) Input shape: {} ---> Output shape: {}".format(
inputImageClassificationLayerShape_Test,
myLiviaNet_ClassificationLayer.outputShapeTest))
