added documentation and licensing information

darcs-hash:20071106223150-4ed31-5081cfd33b91210716a4e89f4731d06ea3cd361f.gz
ronw · Nov 6, 2007 · 07be09e · 07be09e
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diff --git a/COPYING b/COPYING
diff --git a/celltools/@lazymap/lazymap.m b/celltools/@lazymap/lazymap.m
@@ -28,6 +28,21 @@
 % 
 % 2007-11-01 ronw@ee.columbia.edu
 
+% Copyright (C) 2007 Ron J. Weiss
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 if ~isa(fun, 'function_handle')
   error('1st argument must be a function handle')
 end

diff --git a/celltools/README b/celltools/README
@@ -0,0 +1,5 @@
+This package contains a set of standard functional programming tools
+that can be used on cell arrays.  Contains implementations of map,
+reduce, filter (called cfilter so as not to conflict with the filter()
+function in the Signal Processing Toolbox), and lazymap which has the
+same semantics as map but uses lazy evaluation.
diff --git a/celltools/cfilter.m b/celltools/cfilter.m
@@ -5,6 +5,21 @@
 %
 % 2007-11-06 ronw@ee.columbia.edu
 
+% Copyright (C) 2007 Ron J. Weiss
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 if ~isa(fun, 'function_handle')
   error('1st argument must be a function handle')
 end

diff --git a/celltools/map.m b/celltools/map.m
@@ -7,6 +7,21 @@
 %
 % 2007-11-06 ronw@ee.columbia.edu
 
+% Copyright (C) 2007 Ron J. Weiss
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 if ~isa(fun, 'function_handle')
   error('1st argument must be a function handle')
 end

diff --git a/celltools/reduce.m b/celltools/reduce.m
@@ -12,6 +12,21 @@
 %
 % 2007-11-06 ronw@ee.columbia.edu
 
+% Copyright (C) 2007 Ron J. Weiss
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 if ~isa(fun, 'function_handle')
   error('1st argument must be a function handle')
 end

diff --git a/hmm/README b/hmm/README
@@ -0,0 +1,59 @@
+This package contains a set of functions for evaluating HMMs and GMMs.
+
+* Functions
+
+ - The important ones:
+   - eval_gmm             - compute the posterior probability of a GMM given data
+   - eval_hmm             - compute the posterior probabilities of all possible HMM
+                            state sequences given data
+   - decode_hmm           - find the most likely state sequence through the HMM
+                            given data
+
+ - Utility functions:
+   - logsum           - takes the sum of a matrix of log likelihoods
+   - lmvnpdf          - compute the log probability of data under a
+                        multivariate Gaussian distribution
+
+* Data Structures
+
+The functions in this toolbox pass around the following structures:
+Note: all probabilities are stored as log probabilities
+
+** GMM
+  - gmm.nmix   - number of components in the mixture
+  - gmm.priors - array of prior log probabilities over each state
+  - gmm.means  - matrix of means (column x is mean of component x)
+  - gmm.covars - matrix of covariance (column x is the diagonal of the
+                 covariance matrix of component x)
+
+** HMM with GMM observations
+  - hmm.name          - 
+  - hmm.nstates       - number of states in the HMM
+  - hmm.emission_type - 'GMM'
+  - hmm.start_prob    - array of log probs P(first observation is state x)
+  - hmm.end_prob      - array of log probs P(last observation is state x)
+  - hmm.transmat      - matrix of transition log probs (transmat(x,y) 
+                        = log(P(transition from state x to state y)))
+  - hmm.labels        - optional cell array of labels for each state in the HMM
+                        (for use in composing HMMs)
+  - hmm.gmms          - array of GMM structures 
+
+** HMM with Gaussian observations
+  - hmm.nstates       - number of states in the HMM
+  - hmm.emission_type - 'gaussian'
+  - hmm.start_prob    - array of log probs P(first observation is state x)
+  - hmm.end_prob      - array of log probs P(last observation is state x)
+  - hmm.transmat      - matrix of transition log probs (transmat(x,y) 
+                        = log(P(transition from state x to state y)))
+  - hmm.labels        - optional cell array of labels for each state in the HMM
+                        (for use in composing HMMs)
+  - hmm.means         - matrix of means (column x is mean of state x)
+  - hmm.covars        - matrix of means (column x is the diagonal of the
+                        covariance matrix of component x)
+
+Note that each row of exp(hmm.transmat) does not necessarily sum to 1
+because for each state x there is some probability
+(exp(hmm.exit_prob(x))) that the next transition will be to a
+non-emitting exit state (i.e. the current observation is the last
+observation in the sequence).  The correct invariant is:
+sum(exp(hmm.transmat, 2)) + exp(hmm.exit_prob) == ones(hmm.nstates, 1)
diff --git a/hmm/convert_hmm_to_gaussian_emissions.m b/hmm/convert_hmm_to_gaussian_emissions.m
@@ -6,6 +6,21 @@
 %
 % 2007-01-18 ronw@ee.columbia.edu
 
+% Copyright (C) 2007 Ron J. Weiss
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 for n = 1:length(hmms)
   if strcmp(hmms(n).emission_type, 'gaussian')
     new_hmms(n) = hmms(n);

diff --git a/hmm/decode_hmm.m b/hmm/decode_hmm.m
@@ -6,6 +6,21 @@
 %
 % 2007-02-26 ronw@ee.columbia.edu
 
+% Copyright (C) 2007 Ron J. Weiss
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 zeroLogProb = -1e200;
 
 % no rank pruning by default

diff --git a/hmm/eval_gmm.m b/hmm/eval_gmm.m
@@ -9,6 +9,21 @@
 %
 % 2005-11-20 ronw@ee.columbia.edu
 
+% Copyright (C) 2005-2007 Ron J. Weiss
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 [ndim, ndat] = size(data);
 
 p = zeros(gmm.nmix, ndat);

diff --git a/hmm/eval_hmm.m b/hmm/eval_hmm.m
@@ -6,6 +6,21 @@
 %
 % 2007-02-26 ronw@ee.columbia.edu
 
+% Copyright (C) 2007 Ron J. Weiss
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 zeroLogProb = -1e200;
 
 % no rank pruning by default

diff --git a/hmm/lmvnpdf.m b/hmm/lmvnpdf.m
@@ -12,6 +12,21 @@
 %
 % 2006-06-19 ronw@ee.columbia.edu
 
+% Copyright (C) 2006-2007 Ron J. Weiss
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 if nargin < 3
   cv = 1;
 end

diff --git a/matlab_htk/apply_mllr_transform.m b/matlab_htk/apply_mllr_transform.m
@@ -6,6 +6,21 @@
 %
 % 2007-02-20 ronw@ee.columbia.edu
 
+% Copyright (C) 2007 Ron J. Weiss
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 if isfield(hmms, 'hmms')
   % we got a recognizer structure, not a list of hmms
   hmms.hmms = apply_mllr_transform(hmms.hmms, W, b);

diff --git a/matlab_htk/compose_hmms.m b/matlab_htk/compose_hmms.m
@@ -13,6 +13,21 @@
 %
 % 2006-12-01 ronw@ee.columbia.edu
 
+% Copyright (C) 2006-2007 Ron J. Weiss
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 % shutup with the logOfZero warnings when in this function
 w = warning('query', 'MATLAB:log:logOfZero');
 if strcmp(w.state, 'on')

diff --git a/matlab_htk/eval_htk_recognizer.m b/matlab_htk/eval_htk_recognizer.m
@@ -10,6 +10,21 @@
 %
 % 2007-01-17  ronw@ee.columbia.edu
 
+% Copyright (C) 2007 Ron J. Weiss
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 if isstr(data)
   % data contains the name of an SCP file
   data = read_text_file(data);

diff --git a/matlab_htk/kmeans.m b/matlab_htk/kmeans.m
@@ -5,6 +5,21 @@
 %
 % 2006-12-07 ronw@ee.columbia.edu
 
+% Copyright (C) 2006 Ron J. Weiss
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 if nargin < 2
   nclust = 10;
 end

diff --git a/matlab_htk/learn_mllr_transform.m b/matlab_htk/learn_mllr_transform.m
@@ -6,6 +6,21 @@
 %
 % 2007-02-13 ronw@ee.columbia.edu
 
+% Copyright (C) 2007 Ron J. Weiss
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 % is adaptation data a list of filenames?
 adapt_dat_contains_data = 0;
 if iscell(adapt_dat)

diff --git a/matlab_htk/read_htk_hmm.m b/matlab_htk/read_htk_hmm.m
@@ -7,6 +7,21 @@
 %
 % 2006-06-09 ronw@ee.columbia.edu
 
+% Copyright (C) 2006-2007 Ron J. Weiss
+%
+% This program is free software: you can redistribute it and/or modify
+% it under the terms of the GNU General Public License as published by
+% the Free Software Foundation, either version 3 of the License, or
+% (at your option) any later version.
+%
+% This program is distributed in the hope that it will be useful,
+% but WITHOUT ANY WARRANTY; without even the implied warranty of
+% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+% GNU General Public License for more details.
+%
+% You should have received a copy of the GNU General Public License
+% along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
 % Read the M-file into a cell array of strings: 
 [fid, message] = fopen(filename, 'rt');
 warning(message)