Matlab demo for Caffe-compatible HDF5 read/write

3 files changed, 125 insertions, 0 deletions

diff --git a/matlab/caffe/hdf5creation/.gitignore b/matlab/caffe/hdf5creation/.gitignore
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+++ b/matlab/caffe/hdf5creation/.gitignore
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+*.h5
+list.txt
diff --git a/matlab/caffe/hdf5creation/demo.m b/matlab/caffe/hdf5creation/demo.m
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+++ b/matlab/caffe/hdf5creation/demo.m
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+%% 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
+%   }
+% }
diff --git a/matlab/caffe/hdf5creation/store2hdf5.m b/matlab/caffe/hdf5creation/store2hdf5.m
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+++ b/matlab/caffe/hdf5creation/store2hdf5.m
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+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