diff options
Diffstat (limited to 'sci-mathematics/tisean/files')
-rw-r--r-- | sci-mathematics/tisean/files/tisean-3.0.1-backport.patch | 752 | ||||
-rw-r--r-- | sci-mathematics/tisean/files/tisean-3.0.1-gentoo.patch | 57 |
2 files changed, 809 insertions, 0 deletions
diff --git a/sci-mathematics/tisean/files/tisean-3.0.1-backport.patch b/sci-mathematics/tisean/files/tisean-3.0.1-backport.patch new file mode 100644 index 000000000..dc86d1f16 --- /dev/null +++ b/sci-mathematics/tisean/files/tisean-3.0.1-backport.patch @@ -0,0 +1,752 @@ +From 377911cf0ba30428e8e6095162ac9d63689838b8 Mon Sep 17 00:00:00 2001 +From: Rainer Hegger <hegger@theochem.uni-frankfurt.de> +Date: Thu, 16 Apr 2015 15:49:31 +0200 +Subject: [PATCH] Collected changes over the last years + +--- + configure | 22 +++++----- + docs/docs_c/corr.html | 5 +++ + docs/docs_c/lfo-ar.html | 2 +- + docs/docs_c/lyap_spec.html | 4 +- + docs/tutorial/ex1.html | 2 +- + docs/tutorial/ex2.html | 10 ++--- + docs/tutorial/ex3.html | 2 +- + source_c/corr.c | 28 +++++++++--- + source_c/false_nearest.c | 10 ++++- + source_c/histogram.c | 55 +++++++++++++++--------- + source_c/lzo-run.c | 2 +- + source_c/mem_spec.c | 5 ++- + source_c/mutual.c | 105 +++++++++++++++++++++++++++++---------------- + source_c/polynom.c | 7 ++- + source_c/polynomp.c | 2 +- + source_c/xcor.c | 2 +- + source_f/cluster.f | 3 +- + 17 files changed, 172 insertions(+), 94 deletions(-) + +diff --git a/configure b/configure +index c27cf28..095e16d 100755 +--- a/configure ++++ b/configure +@@ -35,17 +35,17 @@ verbose= + x_includes=NONE + x_libraries=NONE + bindir='bin' +-sbindir='${exec_prefix}/sbin' +-libexecdir='${exec_prefix}/libexec' +-datadir='${prefix}/share' +-sysconfdir='${prefix}/etc' +-sharedstatedir='${prefix}/com' +-localstatedir='${prefix}/var' +-libdir='${exec_prefix}/lib' +-includedir='${prefix}/include' ++sbindir='sbin' ++libexecdir='libexec' ++datadir='share' ++sysconfdir='etc' ++sharedstatedir='com' ++localstatedir='var' ++libdir='lib' ++includedir='include' + oldincludedir='/usr/include' +-infodir='${prefix}/info' +-mandir='${prefix}/man' ++infodir='info' ++mandir='man' + + # Initialize some other variables. + subdirs= +@@ -1020,7 +1020,7 @@ fi + + + +-for fff in "$FC" f77 g77 "f77 +U77" "f77 -q -f -B108 -lU77"; do ++for fff in "$FC" f77 g77 gfortran "f77 +U77" "f77 -q -f -B108 -lU77"; do + if test -z "$fff"; then + continue + fi +diff --git a/docs/docs_c/corr.html b/docs/docs_c/corr.html +index 8b2eb8c..f2aa4f2 100644 +--- a/docs/docs_c/corr.html ++++ b/docs/docs_c/corr.html +@@ -57,6 +57,11 @@ <h2 align=center>Usage:</h2> + <td>100 + </tr> + <tr> ++<th>-s# ++<td>calculate the correlation only every #-th step ++<td>1 ++</tr> ++<tr> + <th>-n + <td>don't use normalization to standard deviation + <td>not set +diff --git a/docs/docs_c/lfo-ar.html b/docs/docs_c/lfo-ar.html +index 59263b6..11a9b4e 100644 +--- a/docs/docs_c/lfo-ar.html ++++ b/docs/docs_c/lfo-ar.html +@@ -117,7 +117,7 @@ <h2 align=center>Description of the Output:</h2> + The output consists of 5 columns for each neighborhood size:</b> + <ul> + <li> neighborhood size (units of the data) +-<li> relative forecast error ((forecast error)/(variance of the data)) ++<li> relative forecast error ((forecast error)/(standard deviation of data)) + <li> fraction of points for which neighbors were found for this neighborhood + size + <li> average number of neighbors found per point +diff --git a/docs/docs_c/lyap_spec.html b/docs/docs_c/lyap_spec.html +index ab67d84..189482a 100644 +--- a/docs/docs_c/lyap_spec.html ++++ b/docs/docs_c/lyap_spec.html +@@ -58,7 +58,9 @@ <h2 align=center>Usage:</h2> + --> + <tr> + <th>-r# +-<td>minimal neighborhood size ++<td>minimal neighborhood size. This option dominates -k. This means ++ that if -r is set and more than -k neighbors are found, the number ++ of neighbors will not be reduced to the value given with -k. + <td>not set + </tr> + <tr> +diff --git a/docs/tutorial/ex1.html b/docs/tutorial/ex1.html +index e77be7b..660811b 100644 +--- a/docs/tutorial/ex1.html ++++ b/docs/tutorial/ex1.html +@@ -146,7 +146,7 @@ + variable <font color=blue>x </font> of the logistic equation for + various parameter values (e.g.: <font color=green> + gnuplot> plot '< henon -B0 -A2 -l10000 | histogram -b100' with +-hist</font>). When a sufficiently long transient has been ++histeps</font>). When a sufficiently long transient has been + discarded, such a histogram is the approximation to the invaraint + measure on the bins of the histogram. Verify numerically:<br> + <ul> +diff --git a/docs/tutorial/ex2.html b/docs/tutorial/ex2.html +index 5324a15..a0fbb11 100644 +--- a/docs/tutorial/ex2.html ++++ b/docs/tutorial/ex2.html +@@ -82,7 +82,7 @@ + the two histograms, you thus should shift the one with respect to the + other by the mean value of the data:<br> + <font color=green> +-set data style histep<br> ++set style data histep<br> + plot '< histogram amplitude.dat' u ($1-.146):2,'< histogram + ar.dat' </font> + <br>Result: The data sets are differnt: the distribution of <font +@@ -95,7 +95,7 @@ + <a href="../docs_f/spectrum.html">spectrum</a>) of both of them:<br> + <font color=red> corr amplitude.dat -D500 -o<br> + corr ar.dat -D500 -o</font><br> +-<font color=green>set data style lines</font><br> ++<font color=green>set style data lines</font><br> + <font color=green> plot 'ar.dat.cor','amplitude.dat.cor'</font><br> + <font color=red>spectrum amplitude.dat -o<br> + spectrum ar.dat -o</font><br> +@@ -150,7 +150,7 @@ + <ul> + <li> compute the false nearest neighbour statistics + (<a href="../docs_c/false_nearest.html">false_nearest</a>):<br> +-<font color=red> false_nearest amplitude.dat -M8 -d8 -o ++<font color=red> false_nearest amplitude.dat -M1,8 -d8 -o + -t200 -f5 </font><br> + Study the output, <font color=blue>amplitude.dat.fnn</font>, and + observe the invariance of the result (namely that the embedding dimension +@@ -158,9 +158,9 @@ + <br><br> + + <li> Use the zeorth-order predictor +-(<a href="../docs_c/zeroth.html">zeroth</a>) ++(<a href="../docs_c/lzo-test.html">zeroth</a>) + on amplitude.dat and on ar.dat.<br> +-<font color=red> zeroth amplitude.dat -m1,4 -d8 -o ++<font color=red> lzo-test amplitude.dat -m1,4 -d8 -o + -s250<br> + zeroth ar.dat -m1,4 -d8 -o + -s250</font><br> +diff --git a/docs/tutorial/ex3.html b/docs/tutorial/ex3.html +index 91735dd..2894689 100644 +--- a/docs/tutorial/ex3.html ++++ b/docs/tutorial/ex3.html +@@ -196,7 +196,7 @@ + <font color=red> ll-ar optimal.dat -d10 -m3 -i2000 -s1 -o</font>,<br> + and compare the results:<br> + <font color=green> +-set data style linespoints<br> ++set style data linespoints<br> + plot 'whatisit.dat.ll', 'whatisit.dat.ll' u 1:3,'optimal.dat.ll', + 'optimal.dat.ll' u 1:3</font><br> + <br> +diff --git a/source_c/corr.c b/source_c/corr.c +index 06da07a..4c79b9a 100644 +--- a/source_c/corr.c ++++ b/source_c/corr.c +@@ -30,7 +30,7 @@ + char *format,*outfile=NULL,stout=1,normalize=1; + unsigned int column=1; + unsigned int verbosity=0xff; +-unsigned long tau=100,length=ULONG_MAX,exclude=0; ++unsigned long tau=100,step=1,length=ULONG_MAX,exclude=0; + double *array; + double av,var; + char *infile=NULL; +@@ -48,6 +48,8 @@ void show_options(char *progname) + fprintf(stderr,"\t-x # of lines to be ignored [default 0]\n"); + fprintf(stderr,"\t-c column to read [default is 1]\n"); + fprintf(stderr,"\t-D corrlength [default is 100]\n"); ++ fprintf(stderr,"\t-s # calculate the correlation only every #-th step " ++ "[default is 1]\n"); + fprintf(stderr,"\t-n don\'t normalize to the variance" + " of the data [not set]\n"); + fprintf(stderr,"\t-o output_file [default is 'datafile'.cor; no -o" +@@ -72,6 +74,8 @@ void scan_options(int argc,char **argv) + sscanf(out,"%u",&column); + if ((out=check_option(argv,argc,'D','u')) != NULL) + sscanf(out,"%lu",&tau); ++ if ((out=check_option(argv,argc,'s','u')) != NULL) ++ sscanf(out,"%lu",&step); + if ((out=check_option(argv,argc,'n','n')) != NULL) + normalize=0; + if ((out=check_option(argv,argc,'V','u')) != NULL) +@@ -88,16 +92,17 @@ double corr(long i) + long j; + double c=0.0; + +- for (j=0;j<(length-i);j++) ++ for (j=0;j<(length-i);j++) { + c += array[j]*array[j+i]; ++ } + +- return c/(length-i); ++ return c/(double)(length-i); + } + + int main(int argc,char** argv) + { +- char stdi=0; +- long i; ++ char stdi=0,done=0; ++ unsigned long i; + FILE *fout=NULL; + + if (scan_help(argc,argv)) +@@ -157,14 +162,25 @@ int main(int argc,char** argv) + else + var=1.0; + +- for (i=0;i<=tau;i++) ++ for (i=0;i<=tau;i += step) + if (!stout) { + fprintf(fout,"%ld %e\n",i,corr(i)/var); + fflush(fout); ++ if (i == tau) done=1; + } + else { + fprintf(stdout,"%ld %e\n",i,corr(i)/var); + fflush(stdout); ++ if (i == tau) done=1; ++ } ++ if (!done) ++ if (!stout) { ++ fprintf(fout,"%ld %e\n",tau,corr(tau)/var); ++ fflush(fout); ++ } ++ else { ++ fprintf(stdout,"%ld %e\n",tau,corr(tau)/var); ++ fflush(stdout); + } + if (!stout) + fclose(fout); +diff --git a/source_c/false_nearest.c b/source_c/false_nearest.c +index f8a16e9..f5eed04 100644 +--- a/source_c/false_nearest.c ++++ b/source_c/false_nearest.c +@@ -21,6 +21,7 @@ + /*Changes: + 12/10/05: It's multivariate now + 12/16/05: Scaled <eps> and sigma(eps) ++ 03/08/09: delay was missing in delay embedding of univariate case + */ + + #include <stdio.h> +@@ -37,7 +38,7 @@ char *infile=NULL; + char stdo=1,dimset=0; + char *column=NULL; + unsigned long length=ULONG_MAX,exclude=0,theiler=0; +-unsigned int delay=1,maxdim=5,minemb=1; ++unsigned int delay=1,maxdim=6,minemb=1; + unsigned int comp=1,maxemb=5; + unsigned int verbosity=0xff; + double rt=2.0; +@@ -226,6 +227,11 @@ int main(int argc,char **argv) + series=(double**)get_multi_series(infile,&length,exclude,&comp,column, + dimset,verbosity); + ++ if ((maxemb*delay+1) >= length) { ++ fprintf(stderr,"Not enough points!\n"); ++ exit(FALSE_NEAREST_NOT_ENOUGH_POINTS); ++ } ++ + for (i=0;i<comp;i++) { + rescale_data(series[i],length,&min,&ind_inter); + variance(series[i],length,&av,&ind_var); +@@ -259,7 +265,7 @@ int main(int argc,char **argv) + for (i=0;i<maxdim;i++) { + if (comp == 1) { + vcomp[i]=0; +- vemb[i]=i; ++ vemb[i]=i*delay; + } + else { + vcomp[i]=i%comp; +diff --git a/source_c/histogram.c b/source_c/histogram.c +index 6ab9f02..a45576d 100644 +--- a/source_c/histogram.c ++++ b/source_c/histogram.c +@@ -17,10 +17,8 @@ + * along with TISEAN; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + */ +-/*Author: Rainer Hegger. Last modified Dec 6, 2005*/ +-/*Changes: +- 12/06/05: shift output x value to center of interval +-*/ ++/*Author: Rainer Hegger. Last modified May 16, 2014*/ ++ + #include <math.h> + #include <limits.h> + #include <stdio.h> +@@ -28,7 +26,7 @@ + #include <string.h> + #include "routines/tsa.h" + +-#define WID_STR "Makes a histogram of the data" ++#define WID_STR "Creates a histogram of a onedimensional dataset" + + unsigned long length=ULONG_MAX; + unsigned long base=50; +@@ -36,15 +34,10 @@ unsigned long exclude=0; + unsigned int column=1; + unsigned int verbosity=0xff; + double size; +-char my_stdout=1,gotsize=0; ++char my_stdout=1,gotsize=0,density=0; + char *outfile=NULL; + char *infile=NULL; + +-double *series; +-double average,var; +-double min,max; +-long *box; +- + void show_options(char *progname) + { + what_i_do(progname,WID_STR); +@@ -57,6 +50,8 @@ void show_options(char *progname) + fprintf(stderr,"\t-x # of lines to ignore [default %ld]\n",exclude); + fprintf(stderr,"\t-c column to read [default %d]\n",column); + fprintf(stderr,"\t-b # of intervals [default %ld]\n",base); ++ fprintf(stderr,"\t-D output densities not relative frequencies" ++ " [default not set]\n"); + fprintf(stderr,"\t-o output file [default 'datafile'.dat ;" + " If no -o is given: stdout]\n"); + fprintf(stderr,"\t-V verbosity level [default 1]\n\t\t" +@@ -80,6 +75,8 @@ void scan_options(int n,char **str) + sscanf(out,"%lu",&base); + if ((out=check_option(str,n,'V','u')) != NULL) + sscanf(out,"%u",&verbosity); ++ if ((out=check_option(str,n,'D','n')) != NULL) ++ density=1; + if ((out=check_option(str,n,'o','o')) != NULL) { + my_stdout=0; + if (strlen(out) > 0) +@@ -92,6 +89,10 @@ int main(int argc,char **argv) + char stdi=0; + unsigned long i,j; + double x,norm,size=1.0,size2=1.0; ++ double min,max; ++ double *series; ++ double average,var; ++ long *box; + FILE *fout; + + if (scan_help(argc,argv)) +@@ -123,24 +124,36 @@ int main(int argc,char **argv) + + series=(double*)get_series(infile,&length,exclude,column,verbosity); + variance(series,length,&average,&var); +- rescale_data(series,length,&min,&max); +- +- ++ ++ min=max=series[0]; ++ for (i=1;i<length;i++) { ++ if (series[i] < min) min=series[i]; ++ else if (series[i] > max) max=series[i]; ++ } ++ max -= min; ++ ++ for (i=0;i<length;i++) ++ series[i]=(series[i]-min); ++ + if (base > 0) { + check_alloc(box=(long*)malloc(sizeof(long)*base)); + for (i=0;i<base;i++) + box[i]=0; + size=1./base; +- size2=size/2.0; ++ size2=(1.0-size/2.0)*max; + for (i=0;i<length;i++) { +- if (series[i] > (1.0-size2)) +- series[i]=1.0-size2; +- j=(long)(series[i]*base); ++ if (series[i] > size2) ++ series[i]=size2; ++ j=(long)(series[i]*base/max); + box[j]++; + } + } + +- norm=1.0/(double)length; ++ if (!density) ++ norm=1.0/(double)length; ++ else ++ norm=1.0/(double)length*(double)base/max; ++ + if (!my_stdout) { + fout=fopen(outfile,"w"); + if (verbosity&VER_INPUT) +@@ -150,7 +163,7 @@ int main(int argc,char **argv) + fprintf(fout,"#standard deviation= %e\n",var); + for (i=0;i<base;i++) { + x=(double)(i*size); +- fprintf(fout,"%e %e\n",(x+size2)*max+min,(double)box[i]*norm); ++ fprintf(fout,"%e %e\n",(x+size/2.0)*max+min,(double)box[i]*norm); + } + fclose(fout); + } +@@ -162,7 +175,7 @@ int main(int argc,char **argv) + fprintf(stdout,"#standard deviation= %e\n",var); + for (i=0;i<base;i++) { + x=(double)(i*size); +- fprintf(stdout,"%e %e\n",(x+size2)*max+min,(double)box[i]*norm); ++ fprintf(stdout,"%e %e\n",(x+size/2.0)*max+min,(double)box[i]*norm); + fflush(stdout); + } + } +diff --git a/source_c/lzo-run.c b/source_c/lzo-run.c +index 5393e9f..bc54fb5 100644 +--- a/source_c/lzo-run.c ++++ b/source_c/lzo-run.c +@@ -49,7 +49,7 @@ unsigned int MINN=50; + unsigned int **indexes; + unsigned long LENGTH=ULONG_MAX,FLENGTH=1000,exclude=0; + unsigned long seed=0x9074325L; +-double EPS0=1.e-3,EPSF=1.2,Q=10.0; ++double EPS0=1.e-3,EPSF=1.2,Q=0.0; + + double **mat,*vec,*hsum,*newav; + +diff --git a/source_c/mem_spec.c b/source_c/mem_spec.c +index a38fcfd..9821488 100644 +--- a/source_c/mem_spec.c ++++ b/source_c/mem_spec.c +@@ -22,6 +22,7 @@ + Feb 19, 2007: changed meaning of -f flag and added -P flag to be + consistent with spectrum + Dec 5, 2006: Seg fault when poles > length; ++ Mar 15, 2007: normalization now the same as in spectrum + */ + #include <stdio.h> + #include <string.h> +@@ -216,7 +217,7 @@ int main(int argc,char **argv) + fdt=i/(2.0*out); + pow_spec=powcoef(fdt,cof); + fprintf(fout,"%e %e\n",fdt*samplingrate, +- pm/pow_spec/sqrt((double)length)); ++ pm/pow_spec/(double)length); + fflush(fout); + } + fclose(fout); +@@ -233,7 +234,7 @@ int main(int argc,char **argv) + fdt=i/(2.0*out); + pow_spec=powcoef(fdt,cof); + fprintf(stdout,"%e %e\n",fdt*samplingrate, +- pm/pow_spec/*/sqrt((double)length)*/); ++ pm/pow_spec/(double)length); + } + } + +diff --git a/source_c/mutual.c b/source_c/mutual.c +index fbea470..0496e92 100644 +--- a/source_c/mutual.c ++++ b/source_c/mutual.c +@@ -17,7 +17,7 @@ + * along with TISEAN; if not, write to the Free Software + * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA + */ +-/*Author: Rainer Hegger. Last modified, Sep 20, 2000 */ ++/*Author: Rainer Hegger. Last modified, Jul 13, 2010 */ + #include <stdio.h> + #include <stdlib.h> + #include <math.h> +@@ -26,16 +26,17 @@ + #include "routines/tsa.h" + + #define WID_STR "Estimates the time delayed mutual information\n\t\ +-of the data set" ++of one or two data columns" + + +-char *file_out=NULL,stout=1; ++char *file_out=NULL,stout=1,dimset=0; + char *infile=NULL; + unsigned long length=ULONG_MAX,exclude=0; +-unsigned int column=1; ++unsigned int dim=1; + unsigned int verbosity=0xff; + long partitions=16,corrlength=20; +-long *array,*h1,*h11,**h2; ++long **array,*h1,*h11,**h2; ++char *column=NULL; + + void show_options(char *progname) + { +@@ -48,7 +49,7 @@ void show_options(char *progname) + " means stdin\n"); + fprintf(stderr,"\t-l # of points to be used [Default is all]\n"); + fprintf(stderr,"\t-x # of lines to be ignored [Default is 0]\n"); +- fprintf(stderr,"\t-c column to read [Default is 1]\n"); ++ fprintf(stderr,"\t-c columns to read [Default is 1]\n"); + fprintf(stderr,"\t-b # of boxes [Default is 16]\n"); + fprintf(stderr,"\t-D max. time delay [Default is 20]\n"); + fprintf(stderr,"\t-o output file [-o without name means 'datafile'.mut;" +@@ -69,8 +70,8 @@ void scan_options(int n,char** in) + sscanf(out,"%lu",&length); + if ((out=check_option(in,n,'x','u')) != NULL) + sscanf(out,"%lu",&exclude); +- if ((out=check_option(in,n,'c','u')) != NULL) +- sscanf(out,"%u",&column); ++ if ((out=check_option(in,n,'c','s')) != NULL) ++ column=out; + if ((out=check_option(in,n,'b','u')) != NULL) + sscanf(out,"%lu",&partitions); + if ((out=check_option(in,n,'D','u')) != NULL) +@@ -86,7 +87,7 @@ void scan_options(int n,char** in) + + double make_cond_entropy(long t) + { +- long i,j,hi,hii,count=0; ++ long i,j,hi,hii,count=0,start,stop; + double hpi,hpj,pij,cond_ent=0.0,norm; + + for (i=0;i<partitions;i++) { +@@ -94,15 +95,23 @@ double make_cond_entropy(long t) + for (j=0;j<partitions;j++) + h2[i][j]=0; + } +- for (i=0;i<length;i++) +- if (i >= t) { +- hii=array[i]; +- hi=array[i-t]; +- h1[hi]++; +- h11[hii]++; +- h2[hi][hii]++; +- count++; +- } ++ if (t < 0) { ++ start=0; ++ stop=length+t; ++ } ++ else { ++ start=t; ++ stop=length; ++ } ++ ++ for (i=start;i<stop;i++) { ++ hii=array[0][i]; ++ hi=array[1][i+t]; ++ h1[hi]++; ++ h11[hii]++; ++ h2[hi][hii]++; ++ count++; ++ } + + norm=1.0/(double)count; + cond_ent=0.0; +@@ -127,8 +136,8 @@ double make_cond_entropy(long t) + int main(int argc,char** argv) + { + char stdi=0; +- long tau,i; +- double *series,min,interval,shannon; ++ long tau,i,j; ++ double **series,min1,min2,interval1,interval2,shannon,condent; + FILE *file; + + if (scan_help(argc,argv)) +@@ -140,7 +149,7 @@ int main(int argc,char** argv) + what_i_do(argv[0],WID_STR); + #endif + +- infile=search_datafile(argc,argv,&column,verbosity); ++ infile=search_datafile(argc,argv,NULL,verbosity); + if (infile == NULL) + stdi=1; + +@@ -158,20 +167,44 @@ int main(int argc,char** argv) + if (!stout) + test_outfile(file_out); + +- series=(double*)get_series(infile,&length,exclude,column,verbosity); +- rescale_data(series,length,&min,&interval); ++ if (column == NULL) { ++ series=(double**)get_multi_series(infile,&length,exclude,&dim,"", ++ dimset,verbosity); ++ } ++ else { ++ series=(double**)get_multi_series(infile,&length,exclude,&dim,column, ++ dimset,verbosity); ++ } + + check_alloc(h1=(long *)malloc(sizeof(long)*partitions)); + check_alloc(h11=(long *)malloc(sizeof(long)*partitions)); + check_alloc(h2=(long **)malloc(sizeof(long *)*partitions)); + for (i=0;i<partitions;i++) + check_alloc(h2[i]=(long *)malloc(sizeof(long)*partitions)); +- check_alloc(array=(long *)malloc(sizeof(long)*length)); +- for (i=0;i<length;i++) +- if (series[i] < 1.0) +- array[i]=(long)(series[i]*(double)partitions); +- else +- array[i]=partitions-1; ++ check_alloc(array=(long **)malloc(sizeof(long*)*2)); ++ check_alloc(array[0]=(long *)malloc(sizeof(long)*length)); ++ check_alloc(array[1]=(long *)malloc(sizeof(long)*length)); ++ if (dim == 1) { ++ rescale_data(series[0],length,&min1,&interval1); ++ for (i=0;i<length;i++) ++ if (series[0][i] < 1.0) ++ array[0][i]=array[1][i]=(long)(series[0][i]*(double)partitions); ++ else ++ array[0][i]=array[1][i]=partitions-1; ++ free(series[0]); ++ } ++ else { ++ rescale_data(series[0],length,&min1,&interval1); ++ rescale_data(series[1],length,&min2,&interval2); ++ for (j=0;j<2;j++) { ++ for (i=0;i<length;i++) ++ if (series[j][i] < 1.0) ++ array[j][i]=(long)(series[j][i]*(double)partitions); ++ else ++ array[j][i]=partitions-1; ++ free(series[j]); ++ } ++ } + free(series); + + shannon=make_cond_entropy(0); +@@ -182,10 +215,9 @@ int main(int argc,char** argv) + file=fopen(file_out,"w"); + if (verbosity&VER_INPUT) + fprintf(stderr,"Opened %s for writing\n",file_out); +- fprintf(file,"#shannon= %e\n",shannon); +- fprintf(file,"%d %e\n",0,shannon); +- for (tau=1;tau<=corrlength;tau++) { +- fprintf(file,"%ld %e\n",tau,make_cond_entropy(tau)); ++ for (tau=-corrlength;tau<=corrlength;tau++) { ++ condent=make_cond_entropy(tau); ++ fprintf(file,"%ld %e %e\n",tau,condent,condent/log((double)partitions)); + fflush(file); + } + fclose(file); +@@ -193,10 +225,9 @@ int main(int argc,char** argv) + else { + if (verbosity&VER_INPUT) + fprintf(stderr,"Writing to stdout\n"); +- fprintf(stdout,"#shannon= %e\n",shannon); +- fprintf(stdout,"%d %e\n",0,shannon); +- for (tau=1;tau<=corrlength;tau++) { +- fprintf(stdout,"%ld %e\n",tau,make_cond_entropy(tau)); ++ for (tau=-corrlength;tau<=corrlength;tau++) { ++ condent=make_cond_entropy(tau); ++ fprintf(stdout,"%ld %e %e\n",tau,condent,condent/log((double)partitions)); + fflush(stdout); + } + } +diff --git a/source_c/polynom.c b/source_c/polynom.c +index bc57ba8..6448f49 100644 +--- a/source_c/polynom.c ++++ b/source_c/polynom.c +@@ -20,6 +20,8 @@ + /*Author: Rainer Hegger*/ + /* Changes: + 6/30/2006: Norm of the errors was wrong ++ 6/5/2008: Norm was still wrong. Now its given as an absolute value in ++ units of the data + */ + #include <stdio.h> + #include <stdlib.h> +@@ -265,6 +267,7 @@ int main(int argc,char **argv) + + series=(double*)get_series(infile,&LENGTH,exclude,COLUMN,verbosity); + variance(series,LENGTH,&av,&std_dev); ++ + for (i=0;i<LENGTH;i++) + series[i] /= std_dev; + +@@ -307,11 +310,11 @@ int main(int argc,char **argv) + + in_error=make_error((unsigned long)0,INSAMPLE); + +- fprintf(file,"#average insample error= %e\n",sqrt(in_error)); ++ fprintf(file,"#average insample error= %e\n",sqrt(in_error)*std_dev); + + if (INSAMPLE < LENGTH) { + out_error=make_error(INSAMPLE,LENGTH); +- fprintf(file,"#average out of sample error= %e\n",sqrt(out_error)); ++ fprintf(file,"#average out of sample error= %e\n",sqrt(out_error)*std_dev); + } + + if (CAST) +diff --git a/source_c/polynomp.c b/source_c/polynomp.c +index 6021e19..5b32e58 100644 +--- a/source_c/polynomp.c ++++ b/source_c/polynomp.c +@@ -239,7 +239,7 @@ int main(int argc,char **argv) + fclose(file); + + dummy=(double**)get_multi_series(parin,&plength,0LU, +- &dim,"",(char)"1",verbosity); ++ &dim,"",1,verbosity); + + check_alloc(order=(unsigned int**)malloc(sizeof(int*)*plength)); + for (i=0;i<plength;i++) { +diff --git a/source_c/xcor.c b/source_c/xcor.c +index ec1ed7f..8f50609 100644 +--- a/source_c/xcor.c ++++ b/source_c/xcor.c +@@ -30,7 +30,7 @@ given as two columns of one file." + + char *columns=NULL,*outfile=NULL,stout=1; + unsigned long length=ULONG_MAX,exclude=0; +-long tau=100; ++unsigned long tau=100; + unsigned int verbosity=0xff; + double *array1,*array2; + char *infile=NULL; +diff --git a/source_f/cluster.f b/source_f/cluster.f +index 61357ff..d564fc7 100644 +--- a/source_f/cluster.f ++++ b/source_f/cluster.f +@@ -47,7 +47,8 @@ + d(i,j)=dij + np=max(i,j,np) + goto 1 +- 999 if(iv_io(iverb).eq.1) write(0,'(a,i)') "matrix size ", np ++c 999 if(iv_io(iverb).eq.1) write(0,'(a,i)') "matrix size ", np ++ 999 if(iv_io(iverb).eq.1) write(0,*) "matrix size ", np + dmean=0 + nd=0 + do 20 i=1,np diff --git a/sci-mathematics/tisean/files/tisean-3.0.1-gentoo.patch b/sci-mathematics/tisean/files/tisean-3.0.1-gentoo.patch new file mode 100644 index 000000000..7f80f6276 --- /dev/null +++ b/sci-mathematics/tisean/files/tisean-3.0.1-gentoo.patch @@ -0,0 +1,57 @@ +diff --git a/Makefile.in b/Makefile.in +index c1f3e0c..60f9720 100644 +--- a/Makefile.in ++++ b/Makefile.in +@@ -9,8 +9,8 @@ HAVE_NR = @HAVE_NR@ + + all: + @head -20 README +- -if test -n "${FC}"; then (cd source_f && $(MAKE) $@); fi +- -if test -n "${CC}"; then (cd source_c && $(MAKE) $@); fi ++ $(MAKE) -C source_f $@ ++ $(MAKE) -C source_c $@ + + install: do_install missing + @echo "******************************************************************" +diff --git a/source_c/Makefile.in b/source_c/Makefile.in +index 1ab10e4..2efb803 100644 +--- a/source_c/Makefile.in ++++ b/source_c/Makefile.in +@@ -23,10 +23,10 @@ LOADLIBS = routines/libddtsa.a -lm + all: $(ALL) + + routines/libddtsa.a: +- (cd routines && $(MAKE)) ++ $(MAKE) -C routines + + $(ALL): routines/libddtsa.a *.c +- -$(CC) $(CFLAGS) $(COPTS) -o $@ $@.c $(LOADLIBS) ++ -$(CC) $(LDFLAGS) $(CFLAGS) $(COPTS) -o $@ $@.c $(LOADLIBS) + + install: all + -for bin in $(ALL); do $(INSTALL) $$bin $(BINDIR); done +diff --git a/source_f/Makefile.in b/source_f/Makefile.in +index 6525b72..e45eea7 100644 +--- a/source_f/Makefile.in ++++ b/source_f/Makefile.in +@@ -37,17 +37,17 @@ istdio.o: istdio_temp.f + $(FC) $(FFLAGS) -c istdio.f -o istdio.o + + $(BINS): libtsa.a libsla.a *.f +- -$(FC) $(FFLAGS) -o $@ $@.f $(LOADLIBES) $(LDFLAGS) ++ -$(FC) $(LDFLAGS) $(FFLAGS) -o $@ $@.f $(LOADLIBES) + + libtsa.a: $(INC) + $(AR) $(ARFLAGS) libtsa.a $? + $(RANLIB) libtsa.a + + libsla.a: slatec/*.f +- (cd slatec && $(MAKE)) ++ $(MAKE) -C slatec + + Randomize: libtsa.a libsla.a +- -(cd randomize && $(MAKE)) ++ $(MAKE) -C randomize + + clean: + @rm -f istdio.f |