Romulus Urakagi Ts'ai Romulus Urakagi Ts'ai - 5 months ago 136
Python Question

How to feed caffe multi label data in HDF5 format?

I want to use caffe with a vector label, not integer. I have checked some answers, and it seems HDF5 is a better way. But then I'm stucked with error like:


accuracy_layer.cpp:34] Check failed:
outer_num_ * inner_num_ == bottom[1]->count()
(50 vs. 200) Number of labels must match number of predictions; e.g., if label axis == 1 and prediction shape is (N, C, H, W), label count (number of labels) must be
N*H*W
, with integer values in {0, 1, ..., C-1}.


with HDF5 created as:

f = h5py.File('train.h5', 'w')
f.create_dataset('data', (1200, 128), dtype='f8')
f.create_dataset('label', (1200, 4), dtype='f4')


My network is generated by:

def net(hdf5, batch_size):
n = caffe.NetSpec()
n.data, n.label = L.HDF5Data(batch_size=batch_size, source=hdf5, ntop=2)
n.ip1 = L.InnerProduct(n.data, num_output=50, weight_filler=dict(type='xavier'))
n.relu1 = L.ReLU(n.ip1, in_place=True)
n.ip2 = L.InnerProduct(n.relu1, num_output=50, weight_filler=dict(type='xavier'))
n.relu2 = L.ReLU(n.ip2, in_place=True)
n.ip3 = L.InnerProduct(n.relu1, num_output=4, weight_filler=dict(type='xavier'))
n.accuracy = L.Accuracy(n.ip3, n.label)
n.loss = L.SoftmaxWithLoss(n.ip3, n.label)
return n.to_proto()

with open(PROJECT_HOME + 'auto_train.prototxt', 'w') as f:
f.write(str(net('/home/romulus/code/project/train.h5list', 50)))

with open(PROJECT_HOME + 'auto_test.prototxt', 'w') as f:
f.write(str(net('/home/romulus/code/project/test.h5list', 20)))


It seems I should increase label number and put things in integer rather than array, but if I do this, caffe complains number of data and label is not equal, then exists.

So, what is the correct format to feed multi label data?

Also, I'm so wondering why no one just simply write the data format how HDF5 maps to caffe blobs?

Answer

Answer to this question's title:

The HDF5 file should have two dataset in root, named "data" and "label", respectively. The shape is (data amount, dimension). I'm using only one-dimension data, so I'm not sure what's the order of channel, width, and height. Maybe it does not matter. dtype should be float or double.

A sample code creating train set with h5py is:

import h5py, os
import numpy as np

f = h5py.File('train.h5', 'w')
# 1200 data, each is a 128-dim vector
f.create_dataset('data', (1200, 128), dtype='f8')
# Data's labels, each is a 4-dim vector
f.create_dataset('label', (1200, 4), dtype='f4')

# Fill in something with fixed pattern
# Regularize values to between 0 and 1, or SigmoidCrossEntropyLoss will not work
for i in range(1200):
    a = np.empty(128)
    if i % 4 == 0:
        for j in range(128):
            a[j] = j / 128.0;
        l = [1,0,0,0]
    elif i % 4 == 1:
        for j in range(128):
            a[j] = (128 - j) / 128.0;
        l = [1,0,1,0]
    elif i % 4 == 2:
        for j in range(128):
            a[j] = (j % 6) / 128.0;
        l = [0,1,1,0]
    elif i % 4 == 3:
        for j in range(128):
            a[j] = (j % 4) * 4 / 128.0;
        l = [1,0,1,1]
    f['data'][i] = a
    f['label'][i] = l

f.close()

Also, the accuracy layer is not needed, simply removing it is fine. Next problem is the loss layer. Since SoftmaxWithLoss has only one output (index of the dimension with max value), it can't be used for multi-label problem. Thank to Adian and Shai, I find SigmoidCrossEntropyLoss is good in this case.

Below is the full code, from data creation, training network, and getting test result:

main.py (modified from caffe lanet example)

import os, sys

PROJECT_HOME = '.../project/'
CAFFE_HOME = '.../caffe/'
os.chdir(PROJECT_HOME)

sys.path.insert(0, CAFFE_HOME + 'caffe/python')
import caffe, h5py

from pylab import *
from caffe import layers as L

def net(hdf5, batch_size):
    n = caffe.NetSpec()
    n.data, n.label = L.HDF5Data(batch_size=batch_size, source=hdf5, ntop=2)
    n.ip1 = L.InnerProduct(n.data, num_output=50, weight_filler=dict(type='xavier'))
    n.relu1 = L.ReLU(n.ip1, in_place=True)
    n.ip2 = L.InnerProduct(n.relu1, num_output=50, weight_filler=dict(type='xavier'))
    n.relu2 = L.ReLU(n.ip2, in_place=True)
    n.ip3 = L.InnerProduct(n.relu2, num_output=4, weight_filler=dict(type='xavier'))
    n.loss = L.SigmoidCrossEntropyLoss(n.ip3, n.label)
    return n.to_proto()

with open(PROJECT_HOME + 'auto_train.prototxt', 'w') as f:
    f.write(str(net(PROJECT_HOME + 'train.h5list', 50)))
with open(PROJECT_HOME + 'auto_test.prototxt', 'w') as f:
    f.write(str(net(PROJECT_HOME + 'test.h5list', 20)))

caffe.set_device(0)
caffe.set_mode_gpu()
solver = caffe.SGDSolver(PROJECT_HOME + 'auto_solver.prototxt')

solver.net.forward()
solver.test_nets[0].forward()
solver.step(1)

niter = 200
test_interval = 10
train_loss = zeros(niter)
test_acc = zeros(int(np.ceil(niter * 1.0 / test_interval)))
print len(test_acc)
output = zeros((niter, 8, 4))

# The main solver loop
for it in range(niter):
    solver.step(1)  # SGD by Caffe
    train_loss[it] = solver.net.blobs['loss'].data
    solver.test_nets[0].forward(start='data')
    output[it] = solver.test_nets[0].blobs['ip3'].data[:8]

    if it % test_interval == 0:
        print 'Iteration', it, 'testing...'
        correct = 0
        data = solver.test_nets[0].blobs['ip3'].data
        label = solver.test_nets[0].blobs['label'].data
        for test_it in range(100):
            solver.test_nets[0].forward()
            # Positive values map to label 1, while negative values map to label 0
            for i in range(len(data)):
                for j in range(len(data[i])):
                    if data[i][j] > 0 and label[i][j] == 1:
                        correct += 1
                    elif data[i][j] %lt;= 0 and label[i][j] == 0:
                        correct += 1
        test_acc[int(it / test_interval)] = correct * 1.0 / (len(data) * len(data[0]) * 100)

# Train and test done, outputing convege graph
_, ax1 = subplots()
ax2 = ax1.twinx()
ax1.plot(arange(niter), train_loss)
ax2.plot(test_interval * arange(len(test_acc)), test_acc, 'r')
ax1.set_xlabel('iteration')
ax1.set_ylabel('train loss')
ax2.set_ylabel('test accuracy')
_.savefig('converge.png')

# Check the result of last batch
print solver.test_nets[0].blobs['ip3'].data
print solver.test_nets[0].blobs['label'].data

h5list files simply contain paths of h5 files in each line:

train.h5list

/home/foo/bar/project/train.h5

test.h5list

/home/foo/bar/project/test.h5

and the solver:

auto_solver.prototxt

train_net: "auto_train.prototxt"
test_net: "auto_test.prototxt"
test_iter: 10
test_interval: 20
base_lr: 0.01
momentum: 0.9
weight_decay: 0.0005
lr_policy: "inv"
gamma: 0.0001
power: 0.75
display: 100
max_iter: 10000
snapshot: 5000
snapshot_prefix: "sed"
solver_mode: GPU

Converge graph: Converge graph

Last batch result:

[[ 35.91593933 -37.46276474 -6.2579031 -6.30313492]
[ 42.69248581 -43.00864792 13.19664764 -3.35134125]
[ -1.36403108 1.38531208 2.77786589 -0.34310576]
[ 2.91686511 -2.88944006 4.34043217 0.32656598]
...
[ 35.91593933 -37.46276474 -6.2579031 -6.30313492]
[ 42.69248581 -43.00864792 13.19664764 -3.35134125]
[ -1.36403108 1.38531208 2.77786589 -0.34310576]
[ 2.91686511 -2.88944006 4.34043217 0.32656598]]

[[ 1. 0. 0. 0.]
[ 1. 0. 1. 0.]
[ 0. 1. 1. 0.]
[ 1. 0. 1. 1.]
...
[ 1. 0. 0. 0.]
[ 1. 0. 1. 0.]
[ 0. 1. 1. 0.]
[ 1. 0. 1. 1.]]

I think this code still has many things to improve. Any suggestion is appreciated.