caffe pixel-wise classification / regression - deep-learning

What I want to do is to do a simple pixel-wise classification or regression task. Therefore I have an input image and a ground_truth. What I want to do is to do an easy segmentation task where I have a circle and a rectangle. And I want to train, where the circle or where the rectangle is. That means I have an ground_truth images which has value "1" at all the locations where the circle is and value "2" at all the locations where the rectangle is. Then I have my images and ground_truth images as input in form of .png images.
Then I think I can either to a regression or classification task depending on my loss layer: I have been using the fully convolutional AlexNet from fcn alexnet
classification:
layer {
name: "upscore"
type: "Deconvolution"
bottom: "score_fr"
top: "upscore"
param {
lr_mult: 0
}
convolution_param {
num_output: 3 ## <<---- 0 = backgrund 1 = circle 2 = rectangle
bias_term: false
kernel_size: 63
stride: 32
}
}
layer {
name: "score"
type: "Crop"
bottom: "upscore"
bottom: "data"
top: "score"
crop_param {
axis: 2
offset: 18
}
}
layer {
name: "loss"
type: "SoftmaxWithLoss" ## <<----
bottom: "score"
bottom: "ground_truth"
top: "loss"
loss_param {
ignore_label: 0
}
}
regression:
layer {
name: "upscore"
type: "Deconvolution"
bottom: "score_fr"
top: "upscore"
param {
lr_mult: 0
}
convolution_param {
num_output: 1 ## <<---- 1 x height x width
bias_term: false
kernel_size: 63
stride: 32
}
}
layer {
name: "score"
type: "Crop"
bottom: "upscore"
bottom: "data"
top: "score"
crop_param {
axis: 2
offset: 18
}
}
layer {
name: "loss"
type: "EuclideanLoss" ## <<----
bottom: "score"
bottom: "ground_truth"
top: "loss"
}
However, this produces not even the results I want to have. I think there is something wrong with my understanding of pixel-wise classification / regression. Could you tell me where my mistake is?
EDIT 1
For regression the retrieval of the output would look like this:
output_blob = pred['result'].data
predicated_image_array = np.array(output_blob)
predicated_image_array = predicated_image_array.squeeze()
print predicated_image_array.shape
#print predicated_image_array.shape
#print mean_array
range_value = np.ptp(predicated_image_array)
min_value = predicated_image_array.min()
max_value = predicated_image_array.max()
# make positive
predicated_image_array[:] -= min_value
if not range_value == 0:
predicated_image_array /= range_value
predicated_image_array *= 255
predicated_image_array = predicated_image_array.astype(np.int64)
print predicated_image_array.shape
cv2.imwrite('predicted_output.jpg', predicated_image_array)
This is easy since the output is 1 x height x width and the values are the actual output values. But how would one retrieve the output for classification / SotMaxLayer since the output is 3 (num labels) x height x width. But I do not know the meaning of the content of this shape.

first of all, your problem is not regression, but classification!
if you want to teach the net recognise circles and rectangles you have to make a different data set - an images and labels, for example: circle - 0 and rectangle - 1. you do it by making text file that containsthe images path and the images labels, for example: /path/circle1.png 0 /path/circle2.png 0 /path/rectangle1.png 1 /path/rectangle1.png 1. here is a nice tutorial for a problem like yours. good luck.

Related

Deconvolution in Caffe - blob size exceeds INT_MAX

I have, admittedly, a rather large network. It's based on a network from a paper that claims to use Caffe for the implementation. Here's the topology:
To the best of my ability, I've tried to recreate the model. The authors use the term "upconv" which is a combination of 2x2 unpooling followed by 5x5 convolution. I've taken this to mean a deconvolutional layer with stride 2 and kernel size 5 (please do correct me if you believe otherwise). Here's a short snippet from the full model and solver:
...
# upconv2
layer {
name: "upconv2"
type: "Deconvolution"
bottom: "upconv1rec"
top: "upconv2"
convolution_param {
num_output: 65536 # 256x16x16
kernel_size: 5
stride: 2
}
}
layer {
name: "upconv2-rec"
type: "ReLU"
bottom: "upconv2"
top: "upconv2rec"
relu_param {
negative_slope: 0.01
}
}
# upconv3
layer {
name: "upconv3"
type: "Deconvolution"
bottom: "upconv2rec"
top: "upconv3"
convolution_param {
num_output: 94208 # 92x32x32
kernel_size: 5
stride: 2
}
}
...
But it seems this is too large for Caffe to handle:
I0502 10:42:08.859184 13048 net.cpp:86] Creating Layer upconv3
I0502 10:42:08.859184 13048 net.cpp:408] upconv3 <- upconv2rec
I0502 10:42:08.859184 13048 net.cpp:382] upconv3 -> upconv3
F0502 10:42:08.859184 13048 blob.cpp:34] Check failed: shape[i] <= 2147483647 / count_ (94208 vs. 32767) blob size exceeds INT_MAX
How can I get around this limitation?

How to get the probabilities for each class for multi-label classification in Caffe

I'm training a network on a multi-label dataset.
My training file looks like this:
img1 1 0 1 0 0 0 0 1 .... 1
...
...
imgN 0 1 0 1 0 1 0 0 .... 0
From reading the tutorials I understand that I have to use the SigmoidCrossEntropyLoss layer.
My question is, after training, what layer do I need to use to extract with the extract_feat.bin script the probabilities for each label?
Bellow I wrote the last layer of my network.
Thank you!
layer {
name: "fc8-1"
type: "InnerProduct"
bottom: "fc7"
top: "fc8-1"
inner_product_param {
num_output: 12400
weight_filler {
type: "xavier"
}
bias_filler {
type: "constant"
value: 0.1
}
}
}
layer {
name: "loss"
type: "SigmoidCrossEntropyLoss"
bottom: "fc8-1"
bottom: "label"
top: "loss"
}
When training with "SigmoidCrossEntropy" loss layer, you need to replace the loss layer with a simple "Sigmoid" layer for test time:
layer {
type: "Sigmoid"
bottom: "fc8-1"
top: "class_prob"
name: "class_prob"
}
Your test-time output should be 12,400 dimensional vector (per input) all entries in range [0..1] representing class probabilities.

Convert Caffe configuration to DeepLearning4J configuration

I need to implement an existing Caffe model with DeepLearning4j. However i am new to DL4J so dont know how to implement. Searching through docs and examples had little help, the terminolgy of those two are very different.
How would you write the below caffe prototxt in dl4j ?
Layer1:
layers {
name: "myLayer1"
type: CONVOLUTION
bottom: "data"
top: "myLayer1"
blobs_lr: 1
blobs_lr: 2
convolution_param {
num_output: 20
kernel_w: 2
kernel_h: 2
stride_w: 1
stride_h: 1
weight_filler {
type: "msra"
variance_norm: AVERAGE
}
bias_filler {
type: "constant"
}
}
}
Layer 2
layers {
name: "myLayer1Relu"
type: RELU
relu_param {
negative_slope: 0.3
}
bottom: "myLayer1"
top: "myLayer1"
}
Layer 3
layers {
name: "myLayer1_dropout"
type: DROPOUT
bottom: "myLayer1"
top: "myLayer1"
dropout_param {
dropout_ratio: 0.2
}
}
Layer 4
layers {
name: "final_class"
type: INNER_PRODUCT
bottom: "myLayer4"
top: "final_class"
blobs_lr: 1
blobs_lr: 2
weight_decay: 1
weight_decay: 0
inner_product_param {
num_output: 10
weight_filler {
type: "xavier"
variance_norm: AVERAGE
}
bias_filler {
type: "constant"
value: 0
}
}
}
This Github repo contains comparisons on the same model between DL4J, Caffe, Tensorflow, Torch.
1st layer is DL4J ConvolutionLayer and you can pass in attributes regarding nOut, kernel, stride and weightInit. From quick search it appears msra is equivalent to WeightInit.RELU and variance_norm is not a feature the model supports yet.
2nd layer is party of the ConvolutionLayer which is the activation
attribute; thus, set the attribute for the layer to "relu". Negative slope is not a feature that the model supports yet.
3rd layer is also an attribute on ConvolutionLayer which is dropOut
and you would pass in 0.2. There is work in progress to create a
specific DropOutLayer but its not merged yet.
4th layer would be a DenseLayer if there was another layer after it
but since its the last layer it is an OutputLayer
blobs_lr applies multiplier to weight lr and bias lr respectively. You can
change the learning rate on the layer by setting attributes on that
layer for learningRate and biasLearningRate
weight_decay is setting the l1 or l2 on the layer which you can set
for each layer with the attributes l1 or l2. DL4J defaults to not
applying l1 or l2 to bias thus the second weight_decay set to 0 in
Caffe.
bias filler is already default to constant and defaults to 0.
Below is a quick example of how your code would translate. More information can be found in DL4J examples:
int learningRate = 0.1;
int l2 = 0.005;
int intputHeight = 28;
int inputWidth = 28;
int channels = 1;
MultiLayerConfiguration conf = new NeuralNetConfiguration.Builder()
.seed(seed)
.iterations(iterations)
.regularization(false).l2(l2)
.learningRate(learningRate)
.list()
.layer(0, new ConvolutionLayer.Builder(new int[]{2,2}, new int[] {1,1})
.name("myLayer1")
.activation("relu").dropOut(0.2).nOut(20)
.biasLearningRate(2*learningRate).weightInit(WeightInit.RELU)
.build())
.layer(1, new OutputLayer.Builder()
.name("myLayer4").nOut(10)
.activation("softmax").l2(1 * l2).biasLearningRate(2*learningRate)
.weightInit(WeightInit.XAVIER).build())
.setInputType(InputType.convolutionalFlat(inputHeight,inputWidth,channels))
.build();
there's no automated way to do this but mapping the builder DSL for only a few laayers shouldn't be hard. A bare minimum example is here:
https://github.com/deeplearning4j/dl4j-examples/blob/master/dl4j-examples/src/main/java/org/deeplearning4j/examples/convolution/LenetMnistExample.java
You can see the same primitives, eg: stride,padding, xavier, biasInit all in there.
Our upcoming keras import might be a way for you to bridge caffe -> keras -> dl4j though.
Edit: I'm not going to build it for you. (I'm not sure if that's what you're looking for here)
Dl4j has the right primitives already though. It doesn't have an input layer for variance_norm: you use zero mean and unit variance normalization on the input before passing it in.
We have bias Init as part of the config if you just read the javadoc:
http://deeplearning4j.org/doc

How can I define a constant vector layer in Caffe?

I have a data with 10-d label vector, and I want to use a caffe model to make regression against these data with 10-d output. But now, I only want to check loss of some outputs (for example, 1, 3, 4, 5, 6-d of 10-d vector), so I define a layer with 5-d output at the bottom of the last output layer, But I'v no idea how to get corresponding 5-d label vector groundtruth, I think may be I can define a constant layer to indicate which entries I want get. Please help me if you have any ideas.
update: example
This is my original InnerProduct and Loss layer
layer {
name: "score"
type: "InnerProduct"
bottom: "fc7"
top: "score"
inner_product_param {
num_output: 10
weight_filler {
type: "gaussian"
std: 0.005
}
bias_filler {
type: "constant"
value: 1
}
}
}
layer {
name: "loss"
type: "EuclideanLoss"
bottom: "score"
bottom: "label"
top: "loss"
include {
phase: TRAIN
}
}
I care more about $n_1$ (like 1,3,4,5,6) entries of the 10-dimension output and their loss, so I want to fetch the loss of these entries, like
layer {
name: "score1"
type: "InnerProduct"
bottom: "fc7"
top: "score1"
inner_product_param {
num_output: 5 # n_1
weight_filler {
type: "gaussian"
std: 0.005
}
bias_filler {
type: "constant"
value: 1
}
}
}
layer {
name: "loss1"
type: "EuclideanLoss"
bottom: "score1"
bottom: "label"
top: "loss1"
include {
phase: TRAIN
}
}
How can I get score1 from score directly?
From what I interpret from your question, I think you would like to calculate the loss of the output layer w.r.t the labels for a regression model. But you would like to not bring some of the labels to the equation.
If my interpretation is true, being a regression model, I am expecting your new layer to be something similar to that of EuclidieanLayer. If it is so, the caffe_sub function in the layer could be replaced by the following code segment.
int arrayPos[5] = {1,3,4,5,6};
int count = 5;
Dtype *newBottom0=(Dtype*)malloc(sizeof(Dtype)*count);
Dtype *newBottom1=(Dtype*)malloc(sizeof(Dtype)*count);
for(int varI=0; varI<count; varI++)
{
newBottom0[varI] = (Dtype) bottom[0]->cpu_data()[arrayPos[varI]];
newBottom1[varI] = (Dtype) bottom[1]->cpu_data()[arrayPos[varI]];
}
caffe_sub( count, newBottom0, newBottom1, diff_.mutable_cpu_data());
free(newBottom0);
free(newBottom1);

How to use 1-dim vector as input for caffe?

I'd like to train a neural network (NN) on my own 1-dim data, which I stored in a hdf5 database for caffe. According to the documetation this should work. It also works for me as far as I only use "Fully Connected Layers", "Relu" and "Dropout". However I get an error when I try to use "Convolution" and "Max Pooling" layers in the NN architecture. The error complains about the input dimension of the data.
I0622 16:44:20.456007 9513 net.cpp:84] Creating Layer conv1
I0622 16:44:20.456015 9513 net.cpp:380] conv1 <- data
I0622 16:44:20.456048 9513 net.cpp:338] conv1 -> conv1
I0622 16:44:20.456061 9513 net.cpp:113] Setting up conv1
F0622 16:44:20.456487 9513 blob.cpp:28] Check failed: shape[i] >= 0 (-9 vs. 0)
This is the error when I only want to use a "Pooling" layer behind an "InnerProduct" layer:
I0622 16:52:44.328660 9585 net.cpp:338] pool1 -> pool1
I0622 16:52:44.328666 9585 net.cpp:113] Setting up pool1
F0622 16:52:44.328680 9585 pooling_layer.cpp:84] Check failed: 4 == bottom[0]->num_axes() (4 vs. 2) Input must have 4 axes, corresponding to (num, channels, height, width)
However I don't know how to change the input dimensions such that it works.
This is the beginning of my prototxt file specifying the network architecture:
name: "LeNet"
layer {
name: "myNet"
type: "HDF5Data"
top: "data"
top: "label"
include {
phase: TRAIN
}
hdf5_data_param {
source: "/path/to/my/data/train.txt"
batch_size: 200
}
}
layer {
name: "myNet"
type: "HDF5Data"
top: "data"
top: "label"
include {
phase: TEST
}
hdf5_data_param {
source: "/path/to/my/data/test.txt"
batch_size: 200
}
}
layer {
name: "conv1"
type: "Convolution"
bottom: "data"
top: "conv1"
param {
lr_mult: 1
decay_mult: 1
}
param {
lr_mult: 2
decay_mult: 0
}
convolution_param {
num_output: 1
kernel_h: 11
kernel_w: 1
stride: 1
weight_filler {
type: "gaussian"
std: 0.01
}
bias_filler {
type: "constant"
value: 0
}
}
}
layer {
name: "relu1"
type: "ReLU"
bottom: "conv1"
top: "conv1"
}
layer {
name: "pool1"
type: "Pooling"
bottom: "conv1"
top: "pool1"
pooling_param {
pool: MAX
kernel_h: 3
kernel_w: 1
stride: 2
}
}
And this is how I output my 4D-database (with two singleton dimensions) using Matlabs h5write function:
h5create('train.h5','/data',[dimFeats 1 1 numSamplesTrain]);
h5write('train.h5','/data', traindata);
You seem to be outputting your data using the wrong shape. Caffe blobs have the dimensions (n_samples, n_channels, height, width) .
Other than that your prototxt seems to be fine for doing predictions based on a 1D input.
As I have no experience in using the h5create and h5write in Matlab, I am not sure on whether the training dataset is generated with the dimensions that you expect it to generate.
The error msg for the convolution layer says that shape[i] = -9. This means that either the width, height, channels or number of images in a batch is being set to -9.
The error msg when using pooling layer alone says that the network could detect only an input of 2D while the network is expecting an input of 4D.
The error messages in both the layers are related to reshaping the blobs and this is a clear indication that the dimensions of the input are not as expected.
Try debugging the Reshape functions present in blob.cpp & layers/pooling_layer.cpp to get an insight on which value is actually going rogue.