new open source project

.gitignore

+
+#ignore thumbnails created by windows
+Thumbs.db
+#Ignore files build by Visual Studio
+*.obj
+*.exe
+*.pdb
+*.user
+*.aps
+*.pch
+*.vspscc
+*_i.c
+*_p.c
+*.ncb
+*.suo
+*.tlb
+*.tlh
+*.bak
+*.cache
+*.ilk
+*.log
+[Bb]in
+[Dd]ebug*/
+*.lib
+*.sbr
+obj/
+[Rr]elease*/
+_ReSharper*/
+[Tt]est[Rr]esult*
+*.asv

GapSpectral.m

+% /******************************************************************************
+% 
+% This program, "NCDM", the associated MATLAB scripts and all 
+% provided data, are copyright (C) 2014 Andrew R. Cohen, All rights reserved.
+% 
+% This program uses bzip2 compressor as a static library.
+% A built version for windows 64 is included. for other platforms, see 
+% the files in the bzlib project on https://git-bioimage.coe.drexel.edu
+% 
+% This software may be referenced as:
+% 
+% A.R. Cohen, C. Bjornsson, S. Temple, G. Banker,  and B. Roysam, 
+% "Automatic Summarization of Changes in Biological Image  Sequences 
+% using Algorithmic Information Theory".  IEEE Transactions on Pattern 
+% Analysis  and Machine Intelligence, 2009. 31(8): p.  1386-1403. 
+% 
+% Redistribution and use in source and binary forms, with or without
+% modification, are permitted provided that the following conditions
+% are met:
+% 
+% 1. Redistributions of source code must retain the above copyright
+%    notice, this list of conditions and the following disclaimer.
+% 
+% 2. The origin of this software must not be misrepresented; you must 
+%    not claim that you wrote the original software.  If you use this 
+%    software in a product, an acknowledgment in the product 
+%    documentation would be appreciated but is not required.
+% 
+% 3. Altered source versions must be plainly marked as such, and must
+%    not be misrepresented as being the original software.
+% 
+% 4. The name of the author may not be used to endorse or promote 
+%    products derived from this software without specific prior written 
+%    permission.
+% 
+% THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
+% OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+% WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+% ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
+% DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+% DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+% GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+% WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+% NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+% SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+% 
+% Andrew R. Cohen acohen@coe.drexel.edu
+% GapSpectral version 1.0 (release) November 2014
+% 
+% ******************************************************************************/
+
+function [kGap Gap S idx] = GapSpectral(DistanceMatrix,nMaxClusters,bAlgorithmicInformationDistance)
+
+if nargin<3
+    bAlgorithmicInformationDistance=1;
+end
+B = 50; % size of Monte Carlo distribution
+if nMaxClusters>size(DistanceMatrix,1)
+    nMaxClusters = size(DistanceMatrix,1)-1;
+end
+
+D =   Regularize(DistanceMatrix);
+bound=D;
+for i=1: size(bound,1)
+    bound(i,i)=NaN;
+end
+a =  min(min(bound));%;
+b = max(max(bound));
+UV =  a + (b-a)*rand(size (D,1),size (D,2),B); % uniform distribution
+for k=1:nMaxClusters
+    if (1==k) %
+        % one happy cluster
+        idx = ones(size (D,1),1);
+    else
+        idx = SpectralCluster(D,k);
+    end
+    W(k)=WkSpectral(k,idx,D);
+    for ib =1:B
+        uni =  UV(:,:,ib);
+        uni = Regularize(uni); % make uni a valid distance matrix
+        if (1==k) %
+            % one happy cluster
+            idx = ones(size (D,1),1);
+        else
+            idx = SpectralCluster(uni,k);
+        end
+        Wb(ib,k)=WkSpectral(k,idx,uni);;
+    end
+    Wkb = Wb(:,k);
+    lkb = log(Wkb);
+    if bAlgorithmicInformationDistance
+        Gap(k) = 1/B*sum(Wkb) - W(k);
+        sdk = std(Wkb,1);
+    else
+        Gap(k) = 1/B*sum(lkb) - log(W(k));
+        sdk = std(lkb,1);
+    end
+    S(k)=sdk * sqrt(1+1/B);
+    %     Gap
+    %     S
+end
+
+figure
+errorbar( [1:nMaxClusters],Gap,S)
+set(gca,'XTick',[1:nMaxClusters])
+
+k=1;
+while ((k<nMaxClusters) && (Gap(k) < Gap(k+1)-S(k+1)))
+    k=k+1;
+end
+kGap=k;
+if (kGap>1)
+    idx = SpectralCluster(D,kGap);
+else
+    idx = ones(size (D,1),1);
+end
+
+function w=WkSpectral(k,idx,DistanceMatrix)
+% called by GapSpectral
+
+for r =1:k
+    % find points in cluster r
+    pr = find(idx==r);
+    D(r) = 0;
+    for i=1:size(pr,1)
+        for j=i:size(pr,1)
+            D(r) = D(r)+DistanceMatrix(pr(i),pr(j));
+        end
+    end
+    D(r) = D(r)/(2*size(pr,1)); %(2) in paper
+end
+
+w =  sum(D);
+    

LICENSE.txt

+
+/******************************************************************************
+
+This program, "NCDM", the associated MATLAB scripts and all 
+provided data, are copyright (C) 2014 Andrew R. Cohen, All rights reserved.
+
+This program uses bzip2 compressor as a static library.
+A built version for windows 64 is included. for other platforms, see 
+the files in the bzlib project on https://git-bioimage.coe.drexel.edu
+
+This software may be referenced as:
+
+A.R. Cohen, C. Bjornsson, S. Temple, G. Banker,  and B. Roysam, 
+"Automatic Summarization of Changes in Biological Image  Sequences 
+using Algorithmic Information Theory".  IEEE Transactions on Pattern 
+Analysis  and Machine Intelligence, 2009. 31(8): p.  1386-1403. 
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions
+are met:
+
+1. Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+
+2. The origin of this software must not be misrepresented; you must 
+   not claim that you wrote the original software.  If you use this 
+   software in a product, an acknowledgment in the product 
+   documentation would be appreciated but is not required.
+
+3. Altered source versions must be plainly marked as such, and must
+   not be misrepresented as being the original software.
+
+4. The name of the author may not be used to endorse or promote 
+   products derived from this software without specific prior written 
+   permission.
+
+THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
+OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
+DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Andrew R. Cohen acohen@coe.drexel.edu
+GapSpectral version 1.0 (release) November 2014
+
+******************************************************************************/
\ No newline at end of file

NCD.m

+% /******************************************************************************
+% 
+% This program, "NCDM", the associated MATLAB scripts and all 
+% provided data, are copyright (C) 2014 Andrew R. Cohen, All rights reserved.
+% 
+% This program uses bzip2 compressor as a static library.
+% A built version for windows 64 is included. for other platforms, see 
+% the files in the bzlib project on https://git-bioimage.coe.drexel.edu
+% 
+% This software may be referenced as:
+% 
+% A.R. Cohen, C. Bjornsson, S. Temple, G. Banker,  and B. Roysam, 
+% "Automatic Summarization of Changes in Biological Image  Sequences 
+% using Algorithmic Information Theory".  IEEE Transactions on Pattern 
+% Analysis  and Machine Intelligence, 2009. 31(8): p.  1386-1403. 
+% 
+% Redistribution and use in source and binary forms, with or without
+% modification, are permitted provided that the following conditions
+% are met:
+% 
+% 1. Redistributions of source code must retain the above copyright
+%    notice, this list of conditions and the following disclaimer.
+% 
+% 2. The origin of this software must not be misrepresented; you must 
+%    not claim that you wrote the original software.  If you use this 
+%    software in a product, an acknowledgment in the product 
+%    documentation would be appreciated but is not required.
+% 
+% 3. Altered source versions must be plainly marked as such, and must
+%    not be misrepresented as being the original software.
+% 
+% 4. The name of the author may not be used to endorse or promote 
+%    products derived from this software without specific prior written 
+%    permission.
+% 
+% THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
+% OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+% WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+% ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
+% DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+% DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+% GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+% WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+% NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+% SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+% 
+% Andrew R. Cohen acohen@coe.drexel.edu
+% GapSpectral version 1.0 (release) November 2014
+% 
+% ******************************************************************************/
+
+% NCD
+% Returns the normalized compression distance between V1,V2
+% this is the pairwise NCD
+
+function ncd = NCD(V1,V2)
+
+n1 = Press(V1,[]);
+n2 = Press(V2,[]);
+nBoth = Press(V1, V2);
+
+ncd= (nBoth-min(n1,n2))/max(n1,n2);
+
+end
+
+

Press.m

+% /******************************************************************************
+% 
+% This program, "NCDM", the associated MATLAB scripts and all 
+% provided data, are copyright (C) 2014 Andrew R. Cohen, All rights reserved.
+% 
+% This program uses bzip2 compressor as a static library.
+% A built version for windows 64 is included. for other platforms, see 
+% the files in the bzlib project on https://git-bioimage.coe.drexel.edu
+% 
+% This software may be referenced as:
+% 
+% A.R. Cohen, C. Bjornsson, S. Temple, G. Banker,  and B. Roysam, 
+% "Automatic Summarization of Changes in Biological Image  Sequences 
+% using Algorithmic Information Theory".  IEEE Transactions on Pattern 
+% Analysis  and Machine Intelligence, 2009. 31(8): p.  1386-1403. 
+% 
+% Redistribution and use in source and binary forms, with or without
+% modification, are permitted provided that the following conditions
+% are met:
+% 
+% 1. Redistributions of source code must retain the above copyright
+%    notice, this list of conditions and the following disclaimer.
+% 
+% 2. The origin of this software must not be misrepresented; you must 
+%    not claim that you wrote the original software.  If you use this 
+%    software in a product, an acknowledgment in the product 
+%    documentation would be appreciated but is not required.
+% 
+% 3. Altered source versions must be plainly marked as such, and must
+%    not be misrepresented as being the original software.
+% 
+% 4. The name of the author may not be used to endorse or promote 
+%    products derived from this software without specific prior written 
+%    permission.
+% 
+% THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
+% OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+% WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+% ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
+% DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+% DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+% GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+% WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+% NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+% SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+% 
+% Andrew R. Cohen acohen@coe.drexel.edu
+% GapSpectral version 1.0 (release) November 2014
+% 
+% ******************************************************************************/
+
+
+% Helper function called by NCD 
+% uses libbz2.dll to bzip Compress V1,V2
+% Returns the size in bytes of the compressed data
+% 
+function nBytes = Press(V1,V2)
+
+persistent  lib
+if ~libisloaded('lib')
+    loadlibrary bz2dll.dll bzlib.h  alias lib
+end
+
+if iscell(V1)
+    V1=cell2mat(V1);
+end
+
+if iscell(V2)
+    V2=cell2mat(V2);
+end
+vv= mat2str([V1;V2]);
+
+sz=length(vv(:));
+dsz=sz+1024;
+dest= mat2str(zeros(dsz,1));
+pstr=libpointer('cstring', vv);
+pdest=libpointer('cstring', dest);
+pdsz = libpointer('uint32Ptr',dsz);
+
+rval=calllib('lib', 'BZ2_bzBuffToBuffCompress', pdest,pdsz,vv,sz,9,0,30);
+if rval
+    disp 'ACK! bad return from bzip'
+    rval
+end
+nBytes=double(get(pdsz, 'Value'));
+
+end
+
+

Regularize.m

+% /******************************************************************************
+% 
+% This program, "NCDM", the associated MATLAB scripts and all 
+% provided data, are copyright (C) 2014 Andrew R. Cohen, All rights reserved.
+% 
+% This program uses bzip2 compressor as a static library.
+% A built version for windows 64 is included. for other platforms, see 
+% the files in the bzlib project on https://git-bioimage.coe.drexel.edu
+% 
+% This software may be referenced as:
+% 
+% A.R. Cohen, C. Bjornsson, S. Temple, G. Banker,  and B. Roysam, 
+% "Automatic Summarization of Changes in Biological Image  Sequences 
+% using Algorithmic Information Theory".  IEEE Transactions on Pattern 
+% Analysis  and Machine Intelligence, 2009. 31(8): p.  1386-1403. 
+% 
+% Redistribution and use in source and binary forms, with or without
+% modification, are permitted provided that the following conditions
+% are met:
+% 
+% 1. Redistributions of source code must retain the above copyright
+%    notice, this list of conditions and the following disclaimer.
+% 
+% 2. The origin of this software must not be misrepresented; you must 
+%    not claim that you wrote the original software.  If you use this 
+%    software in a product, an acknowledgment in the product 
+%    documentation would be appreciated but is not required.
+% 
+% 3. Altered source versions must be plainly marked as such, and must
+%    not be misrepresented as being the original software.
+% 
+% 4. The name of the author may not be used to endorse or promote 
+%    products derived from this software without specific prior written 
+%    permission.
+% 
+% THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
+% OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+% WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+% ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
+% DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+% DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+% GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+% WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+% NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+% SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+% 
+% Andrew R. Cohen acohen@coe.drexel.edu
+% GapSpectral version 1.0 (release) November 2014
+% 
+% ******************************************************************************/
+
+% make the distance matrix symetric (positive semi-definite), so
+% eigen* are all real. needed due to slight asymetry in compression for NCD
+% called by GapSpectral and SpectralCluster
+%
+% degenerate is two elements having zero distance - violates the identity
+% axiom
+function [D,degenerate] = Regularize(DistanceMatrix)
+
+% turn output from NCD into well behaved  distance matrix
+
+D=DistanceMatrix;
+% b = max(max(D));
+% D=D/b; 
+for i=1:size (D,1)
+     for j= 1:size(D,2)
+         D(i,j)= max(D(i,j),D(j,i));
+     end
+     D(i,i)=0;
+end
+
+bound=D;
+for i=1: size(bound,1)
+    bound(i,i)=NaN;
+end
+a =  min(min(bound));
+if 0==a
+    degenerate=1;
+else
+    degenerate=0;
+end
+     
+        

SpectralCluster.m

+% /******************************************************************************
+% 
+% This program, "NCDM", the associated MATLAB scripts and all 
+% provided data, are copyright (C) 2014 Andrew R. Cohen, All rights reserved.
+% 
+% This program uses bzip2 compressor as a static library.
+% A built version for windows 64 is included. for other platforms, see 
+% the files in the bzlib project on https://git-bioimage.coe.drexel.edu
+% 
+% This software may be referenced as:
+% 
+% A.R. Cohen, C. Bjornsson, S. Temple, G. Banker,  and B. Roysam, 
+% "Automatic Summarization of Changes in Biological Image  Sequences 
+% using Algorithmic Information Theory".  IEEE Transactions on Pattern 
+% Analysis  and Machine Intelligence, 2009. 31(8): p.  1386-1403. 
+% 
+% Redistribution and use in source and binary forms, with or without
+% modification, are permitted provided that the following conditions
+% are met:
+% 
+% 1. Redistributions of source code must retain the above copyright
+%    notice, this list of conditions and the following disclaimer.
+% 
+% 2. The origin of this software must not be misrepresented; you must 
+%    not claim that you wrote the original software.  If you use this 
+%    software in a product, an acknowledgment in the product 
+%    documentation would be appreciated but is not required.
+% 
+% 3. Altered source versions must be plainly marked as such, and must
+%    not be misrepresented as being the original software.
+% 
+% 4. The name of the author may not be used to endorse or promote 
+%    products derived from this software without specific prior written 
+%    permission.
+% 
+% THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
+% OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+% WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+% ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
+% DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+% DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+% GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+% WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+% NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+% SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+% 
+% Andrew R. Cohen acohen@coe.drexel.edu
+% GapSpectral version 1.0 (release) November 2014
+% 
+% ******************************************************************************/
+
+% distance matrix A into k clusters
+function idx= SpectralCluster(A,k)
+
+NREP=5;
+if (1==k)
+    idx=ones(size(A,2),1);
+    return;
+end
+for i=1:size(A,1)
+    D(i,i)=sum(A(i,:));
+end
+
+L=D^(-.5)*A*D^(-.5);
+L=Regularize(L); % remove the miniscule asymmetry from L
+
+[eVec eVal]=eig(L);
+
+X=[eVec(:,end) eVec(:,1:k-1)];
+for i=1:size(X,1)
+    Y(i,:)=X(i,:)./norm(X(i,:));
+end
+
+idx=kmeans(Y,k,'emptyaction','singleton','replicates',NREP);
+
+end
+

bzlib.h

+
+/*-------------------------------------------------------------*/
+/*--- Public header file for the library.                   ---*/
+/*---                                               bzlib.h ---*/
+/*-------------------------------------------------------------*/
+
+/* ------------------------------------------------------------------
+   This file is part of bzip2/libbzip2, a program and library for
+   lossless, block-sorting data compression.
+
+   bzip2/libbzip2 version 1.0.4 of 20 December 2006
+   Copyright (C) 1996-2006 Julian Seward <jseward@bzip.org>
+
+   Please read the WARNING, DISCLAIMER and PATENTS sections in the 
+   README file.
+
+   This program is released under the terms of the license contained
+   in the file LICENSE.
+   ------------------------------------------------------------------ */
+
+
+#ifndef _BZLIB_H
+#define _BZLIB_H
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#define BZ_RUN               0
+#define BZ_FLUSH             1
+#define BZ_FINISH            2
+
+#define BZ_OK                0
+#define BZ_RUN_OK            1
+#define BZ_FLUSH_OK          2
+#define BZ_FINISH_OK         3
+#define BZ_STREAM_END        4
+#define BZ_SEQUENCE_ERROR    (-1)
+#define BZ_PARAM_ERROR       (-2)
+#define BZ_MEM_ERROR         (-3)
+#define BZ_DATA_ERROR        (-4)
+#define BZ_DATA_ERROR_MAGIC  (-5)
+#define BZ_IO_ERROR          (-6)
+#define BZ_UNEXPECTED_EOF    (-7)
+#define BZ_OUTBUFF_FULL      (-8)
+#define BZ_CONFIG_ERROR      (-9)
+
+typedef 
+   struct {
+      char *next_in;
+      unsigned int avail_in;
+      unsigned int total_in_lo32;
+      unsigned int total_in_hi32;
+
+      char *next_out;
+      unsigned int avail_out;
+      unsigned int total_out_lo32;
+      unsigned int total_out_hi32;
+
+      void *state;
+
+      void *(*bzalloc)(void *,int,int);
+      void (*bzfree)(void *,void *);
+      void *opaque;
+   } 
+   bz_stream;
+
+
+#ifndef BZ_IMPORT
+#define BZ_EXPORT
+#endif
+
+#ifndef BZ_NO_STDIO
+/* Need a definitition for FILE */
+#include <stdio.h>
+#endif
+
+#ifdef _WIN32
+#   include <windows.h>
+#   ifdef small
+      /* windows.h define small to char */
+#      undef small
+#   endif
+#   ifdef BZ_EXPORT
+#   define BZ_API(func) WINAPI func
+#   define BZ_EXTERN extern
+#   else
+   /* import windows dll dynamically */
+#   define BZ_API(func) (WINAPI * func)
+#   define BZ_EXTERN
+#   endif
+#else
+#   define BZ_API(func) func
+#   define BZ_EXTERN extern
+#endif
+
+
+/*-- Core (low-level) library functions --*/
+
+BZ_EXTERN int BZ_API(BZ2_bzCompressInit) ( 
+      bz_stream* strm, 
+      int        blockSize100k, 
+      int        verbosity, 
+      int        workFactor 
+   );
+
+BZ_EXTERN int BZ_API(BZ2_bzCompress) ( 
+      bz_stream* strm, 
+      int action 
+   );
+
+BZ_EXTERN int BZ_API(BZ2_bzCompressEnd) ( 
+      bz_stream* strm 
+   );
+
+BZ_EXTERN int BZ_API(BZ2_bzDecompressInit) ( 
+      bz_stream *strm, 
+      int       verbosity, 
+      int       small
+   );
+
+BZ_EXTERN int BZ_API(BZ2_bzDecompress) ( 
+      bz_stream* strm 
+   );
+
+BZ_EXTERN int BZ_API(BZ2_bzDecompressEnd) ( 
+      bz_stream *strm 
+   );
+
+
+
+/*-- High(er) level library functions --*/
+
+#ifndef BZ_NO_STDIO
+#define BZ_MAX_UNUSED 5000
+
+typedef void BZFILE;
+
+BZ_EXTERN BZFILE* BZ_API(BZ2_bzReadOpen) ( 
+      int*  bzerror,   
+      FILE* f, 
+      int   verbosity, 
+      int   small,
+      void* unused,    
+      int   nUnused 
+   );
+
+BZ_EXTERN void BZ_API(BZ2_bzReadClose) ( 
+      int*    bzerror, 
+      BZFILE* b 
+   );
+
+BZ_EXTERN void BZ_API(BZ2_bzReadGetUnused) ( 
+      int*    bzerror, 
+      BZFILE* b, 
+      void**  unused,  
+      int*    nUnused 
+   );
+
+BZ_EXTERN int BZ_API(BZ2_bzRead) ( 
+      int*    bzerror, 
+      BZFILE* b, 
+      void*   buf, 
+      int     len 
+   );
+
+BZ_EXTERN BZFILE* BZ_API(BZ2_bzWriteOpen) ( 
+      int*  bzerror,      
+      FILE* f, 
+      int   blockSize100k, 
+      int   verbosity, 
+      int   workFactor 
+   );
+
+BZ_EXTERN void BZ_API(BZ2_bzWrite) ( 
+      int*    bzerror, 
+      BZFILE* b, 
+      void*   buf, 
+      int     len 
+   );
+
+BZ_EXTERN void BZ_API(BZ2_bzWriteClose) ( 
+      int*          bzerror, 
+      BZFILE*       b, 
+      int           abandon, 
+      unsigned int* nbytes_in, 
+      unsigned int* nbytes_out 
+   );
+
+BZ_EXTERN void BZ_API(BZ2_bzWriteClose64) ( 
+      int*          bzerror, 
+      BZFILE*       b, 
+      int           abandon, 
+      unsigned int* nbytes_in_lo32, 
+      unsigned int* nbytes_in_hi32, 
+      unsigned int* nbytes_out_lo32, 
+      unsigned int* nbytes_out_hi32
+   );
+#endif
+
+
+/*-- Utility functions --*/
+
+BZ_EXTERN int BZ_API(BZ2_bzBuffToBuffCompress) ( 
+      char*         dest, 
+      unsigned int* destLen,
+      char*         source, 
+      unsigned int  sourceLen,
+      int           blockSize100k, 
+      int           verbosity, 
+      int           workFactor 
+   );
+
+BZ_EXTERN int BZ_API(BZ2_bzBuffToBuffDecompress) ( 
+      char*         dest, 
+      unsigned int* destLen,
+      char*         source, 
+      unsigned int  sourceLen,
+      int           small, 
+      int           verbosity 
+   );
+
+
+/*--
+   Code contributed by Yoshioka Tsuneo (tsuneo@rr.iij4u.or.jp)
+   to support better zlib compatibility.
+   This code is not _officially_ part of libbzip2 (yet);
+   I haven't tested it, documented it, or considered the
+   threading-safeness of it.
+   If this code breaks, please contact both Yoshioka and me.
+--*/
+
+BZ_EXTERN const char * BZ_API(BZ2_bzlibVersion) (
+      void
+   );
+
+#ifndef BZ_NO_STDIO
+BZ_EXTERN BZFILE * BZ_API(BZ2_bzopen) (
+      const char *path,
+      const char *mode
+   );
+
+BZ_EXTERN BZFILE * BZ_API(BZ2_bzdopen) (
+      int        fd,
+      const char *mode
+   );
+         
+BZ_EXTERN int BZ_API(BZ2_bzread) (
+      BZFILE* b, 
+      void* buf, 
+      int len 
+   );
+
+BZ_EXTERN int BZ_API(BZ2_bzwrite) (
+      BZFILE* b, 
+      void*   buf, 
+      int     len 
+   );
+
+BZ_EXTERN int BZ_API(BZ2_bzflush) (
+      BZFILE* b
+   );
+
+BZ_EXTERN void BZ_API(BZ2_bzclose) (
+      BZFILE* b
+   );
+
+BZ_EXTERN const char * BZ_API(BZ2_bzerror) (
+      BZFILE *b, 
+      int    *errnum
+   );
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
+
+/*-------------------------------------------------------------*/
+/*--- end                                           bzlib.h ---*/
+/*-------------------------------------------------------------*/

esym2d.m

+% 
+% 
+% /******************************************************************************
+% 
+% This program, "NCDM", the associated MATLAB scripts and all 
+% provided data, are copyright (C) 2014 Andrew R. Cohen, All rights reserved.
+% 
+% This program uses bzip2 compressor as a static library.
+% A built version for windows 64 is included. for other platforms, see 
+% the files in the bzlib project on https://git-bioimage.coe.drexel.edu
+% 
+% This software may be referenced as:
+% 
+% A.R. Cohen, C. Bjornsson, S. Temple, G. Banker,  and B. Roysam, 
+% "Automatic Summarization of Changes in Biological Image  Sequences 
+% using Algorithmic Information Theory".  IEEE Transactions on Pattern 
+% Analysis  and Machine Intelligence, 2009. 31(8): p.  1386-1403. 
+% 
+% Redistribution and use in source and binary forms, with or without
+% modification, are permitted provided that the following conditions
+% are met:
+% 
+% 1. Redistributions of source code must retain the above copyright
+%    notice, this list of conditions and the following disclaimer.
+% 
+% 2. The origin of this software must not be misrepresented; you must 
+%    not claim that you wrote the original software.  If you use this 
+%    software in a product, an acknowledgment in the product 
+%    documentation would be appreciated but is not required.
+% 
+% 3. Altered source versions must be plainly marked as such, and must
+%    not be misrepresented as being the original software.
+% 
+% 4. The name of the author may not be used to endorse or promote 
+%    products derived from this software without specific prior written 
+%    permission.
+% 
+% THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
+% OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+% WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+% ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
+% DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+% DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+% GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+% WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+% NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+% SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+% 
+% Andrew R. Cohen acohen@coe.drexel.edu
+% GapSpectral version 1.0 (release) November 2014
+% 
+% ******************************************************************************/
+
+% this function is used for quantizing time sequence data
+function sData=esym2d(N,c2,mu,s1,Data)
+
+sData=[];
+
+for i=1:size(Data,1)
+    rcv=Data(i,:);
+    if isinf(rcv)
+        sData{i,1}=char(10);
+    else
+        z=(rcv-mu)*s1*(rcv-mu)';
+        zs=sum(z>c2,2);
+        sData{i,1}=[char('a'+zs)];
+    end
+end
+
+

goTestGapSpectral.m

+% /******************************************************************************
+% 
+% This program, "NCDM", the associated MATLAB scripts and all 
+% provided data, are copyright (C) 2014 Andrew R. Cohen, All rights reserved.
+% 
+% This program uses bzip2 compressor as a static library.
+% A built version for windows 64 is included. for other platforms, see 
+% the files in the bzlib project on https://git-bioimage.coe.drexel.edu
+% 
+% This software may be referenced as:
+% 
+% A.R. Cohen, C. Bjornsson, S. Temple, G. Banker,  and B. Roysam, 
+% "Automatic Summarization of Changes in Biological Image  Sequences 
+% using Algorithmic Information Theory".  IEEE Transactions on Pattern 
+% Analysis  and Machine Intelligence, 2009. 31(8): p.  1386-1403. 
+% 
+% Redistribution and use in source and binary forms, with or without
+% modification, are permitted provided that the following conditions
+% are met:
+% 
+% 1. Redistributions of source code must retain the above copyright
+%    notice, this list of conditions and the following disclaimer.
+% 
+% 2. The origin of this software must not be misrepresented; you must 
+%    not claim that you wrote the original software.  If you use this 
+%    software in a product, an acknowledgment in the product 
+%    documentation would be appreciated but is not required.
+% 
+% 3. Altered source versions must be plainly marked as such, and must
+%    not be misrepresented as being the original software.
+% 
+% 4. The name of the author may not be used to endorse or promote 
+%    products derived from this software without specific prior written 
+%    permission.
+% 
+% THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
+% OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+% WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+% ARE DISCLAIMED.  IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
+% DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+% DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
+% GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+% WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+% NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+% SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+% 
+% Andrew R. Cohen acohen@coe.drexel.edu
+% GapSpectral version 1.0 (release) November 2014
+% 
+% ******************************************************************************/
+
+% goTestGapSpectral - toy application to try it all out
+tsData=[];
+means=[1 1 1 2 2 2 3 3 3];
+for i=1:length(means)
+    nlen = 100 + round(100*rand());
+    tsData{i}=normrnd(means(i),0.25,nlen,1);
+end
+d=[];
+for i=1:length(tsData)
+    for j=1:length(tsData)
+        d(i,j)=NCD(tsData(i),tsData(j));
+    end
+end
+
+[kGap Gap S idx] = GapSpectral(d,6,1)
\ No newline at end of file