hdf5格式的matlab读写操作

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最近要用caffe处理一个multi-label的回归问题，就是输出是一个向量，不是一个具体的数值，这个时候之前的leveldb格式就不凑效了，因为caffe源代码里面默认label是一个数值，网上搜了下，都说hdf5格式可以解决这个问题

在caffe里面，有一个hdf5的datalayer作为数据输入，从源代码来看，对于label的维数没做限制，剩下的问题就是如何生成hdf5的数据，目前只是找到了github上的一个人共享的用matlab写的hdf5数据的读写操作，在这我把代码粘贴出来

testHDF5.m

%% WRITING TO HDF5
filename='trial.h5';

num_total_samples=10000;
% to simulate data being read from disk / generated etc.
data_disk=rand(5,5,1,num_total_samples); 
label_disk=rand(10,num_total_samples); 

chunksz=100;
created_flag=false;
totalct=0;
for batchno=1:num_total_samples/chunksz
  fprintf('batch no. %d\n', batchno);
  last_read=(batchno-1)*chunksz;

  % to simulate maximum data to be held in memory before dumping to hdf5 file 
  batchdata=data_disk(:,:,1,last_read+1:last_read+chunksz); 
  batchlabs=label_disk(:,last_read+1:last_read+chunksz);

  % store to hdf5
  startloc=struct('dat',[1,1,1,totalct+1], 'lab', [1,totalct+1]);
  curr_dat_sz=store2hdf5(filename, batchdata, batchlabs, ~created_flag, startloc, chunksz); 
  created_flag=true;% flag set so that file is created only once
  totalct=curr_dat_sz(end);% updated dataset size (#samples)
end

% display structure of the stored HDF5 file
h5disp(filename);

%% READING FROM HDF5

% Read data and labels for samples #1000 to 1999
data_rd=h5read(filename, '/data', [1 1 1 1000], [5, 5, 1, 1000]);
label_rd=h5read(filename, '/label', [1 1000], [10, 1000]);
fprintf('Testing ...\n');
try 
  assert(isequal(data_rd, single(data_disk(:,:,:,1000:1999))), 'Data do not match');
  assert(isequal(label_rd, single(label_disk(:,1000:1999))), 'Labels do not match');

  fprintf('Success!\n');
catch err
  fprintf('Test failed ...\n');
  getReport(err)
end

%delete(filename);

% CREATE list.txt containing filename, to be used as source for HDF5_DATA_LAYER
FILE=fopen('list.txt', 'w');
fprintf(FILE, '%s', filename);
fclose(FILE);
fprintf('HDF5 filename listed in %s \n', 'list.txt');

% NOTE: In net definition prototxt, use list.txt as input to HDF5_DATA as: 
% layers {
%   name: "data"
%   type: HDF5_DATA
%   top: "data"
%   top: "labelvec"
%   hdf5_data_param {
%     source: "/path/to/list.txt"
%     batch_size: 64
%   }
% }

store2hdf5.m

<span style="font-family:Microsoft YaHei;font-size:18px;">function [curr_dat_sz, curr_lab_sz] = store2hdf5(filename, data, labels, create, startloc, chunksz)  
  % *data* is W*H*C*N matrix of images should be normalized (e.g. to lie between 0 and 1) beforehand
  % *label* is D*N matrix of labels (D labels per sample) 
  % *create* [0/1] specifies whether to create file newly or to append to previously created file, useful to store information in batches when a dataset is too big to be held in memory  (default: 1)
  % *startloc* (point at which to start writing data). By default, 
  % if create=1 (create mode), startloc.data=[1 1 1 1], and startloc.lab=[1 1]; 
  % if create=0 (append mode), startloc.data=[1 1 1 K+1], and startloc.lab = [1 K+1]; where K is the current number of samples stored in the HDF
  % chunksz (used only in create mode), specifies number of samples to be stored per chunk (see HDF5 documentation on chunking) for creating HDF5 files with unbounded maximum size - TLDR; higher chunk sizes allow faster read-write operations 

  % verify that format is right
  dat_dims=size(data);
  lab_dims=size(labels);
  num_samples=dat_dims(end);

  assert(lab_dims(end)==num_samples, 'Number of samples should be matched between data and labels');

  if ~exist('create','var')
    create=true;
  end

  
  if create
    %fprintf('Creating dataset with %d samples\n', num_samples);
    if ~exist('chunksz', 'var')
      chunksz=1000;
    end
    if exist(filename, 'file')
      fprintf('Warning: replacing existing file %s \n', filename);
      delete(filename);
    end      
    h5create(filename, '/data', [dat_dims(1:end-1) Inf], 'Datatype', 'single', 'ChunkSize', [dat_dims(1:end-1) chunksz]); % width, height, channels, number 
    h5create(filename, '/label', [lab_dims(1:end-1) Inf], 'Datatype', 'single', 'ChunkSize', [lab_dims(1:end-1) chunksz]); % width, height, channels, number 
    if ~exist('startloc','var') 
      startloc.dat=[ones(1,length(dat_dims)-1), 1];
      startloc.lab=[ones(1,length(lab_dims)-1), 1];
    end 
  else  % append mode
    if ~exist('startloc','var')
      info=h5info(filename);
      prev_dat_sz=info.Datasets(1).Dataspace.Size;
      prev_lab_sz=info.Datasets(2).Dataspace.Size;
      assert(prev_dat_sz(1:end-1)==dat_dims(1:end-1), 'Data dimensions must match existing dimensions in dataset');
      assert(prev_lab_sz(1:end-1)==lab_dims(1:end-1), 'Label dimensions must match existing dimensions in dataset');
      startloc.dat=[ones(1,length(dat_dims)-1), prev_dat_sz(end)+1];
      startloc.lab=[ones(1,length(lab_dims)-1), prev_lab_sz(end)+1];
    end
  end

  if ~isempty(data)
    h5write(filename, '/data', single(data), startloc.dat, size(data));
    h5write(filename, '/label', single(labels), startloc.lab, size(labels));  
  end

  if nargout
    info=h5info(filename);
    curr_dat_sz=info.Datasets(1).Dataspace.Size;
    curr_lab_sz=info.Datasets(2).Dataspace.Size;
  end
end</span>

hdf5格式的matlab读写操作

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原文地址：http://blog.csdn.net/kuaitoukid/article/details/43448517