Merge branch 'develop' into feature/write_windowed

contrib/aff/README

 this is <README>
 ============================================================================
 AFF --- A container for numbers
--------------------------------
-$Id$
 ============================================================================
 
-For compilation instructions see README.1st in the root directory of the tar-ball or
-http://gpitrsvn.gpi.uni-karlsruhe.de:8000/TFSoftware/wiki/docs/installation 
+This software is part of the project Seitosh. See README.1st in the root
+directory of the collection or https://git.scc.kit.edu/Seitosh/Seitosh for
+general installation instructions.
 
 The AFF (Array of Friederich and Forbriger) is a lightweight class library. It
 offers a simple and easy to use container for numbers as is necessary in

contrib/fourier/COPYING

 this is <COPYING>
 ============================================================================
 libfourier
-----------
-$Id$
 ============================================================================
 
 Copyright (c) 2002, 2013 by Thomas Forbriger

contrib/fourier/Makefile

 # this is <Makefile>
 # ----------------------------------------------------------------------------
-# $Id$
 # 
 # Copyright (c) 2002 by Thomas Forbriger (IMG Frankfurt) 
 # 
@@ -76,6 +75,8 @@ $(LOCLIBDIR)/%: install-include %
 
 #----------------------------------------------------------------------
 
+DOXYTXT=$(wildcard doxygen*txt)
+
 flist: Makefile $(wildcard *.f *.inc *.h *.cc *.c README *.cfg) COPYING \
 	$(DOXYTXT)
 	echo $^ | tr ' ' '\n' | sort > $@

contrib/fourier/README

 this is <README>
 ============================================================================
 FOURIER --- Fourier coefficients library
--------------------------------
-$Id$
 ============================================================================
 
-For compilation instructions see README.1st in the root directory of the tar-ball or
-http://gpitrsvn.gpi.uni-karlsruhe.de:8000/TFSoftware/wiki/docs/installation 
+This software is part of the project Seitosh. See README.1st in the root
+directory of the collection or https://git.scc.kit.edu/Seitosh/Seitosh for
+general installation instructions.
 
 The library provides modules to perform Fourier transformations and to 
 operate on Fourier transforms.An interface to FFTW is available.Signal 

contrib/fourier/cfftwtest.c

@@ -3,8 +3,6 @@
  * 
  * ----------------------------------------------------------------------------
  * 
- * $Id$
- *
  * ----
  * libfourier is free software; you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
@@ -41,8 +39,6 @@
  */
 #define TF_CFFTWTEST_C_VERSION \
   "TF_CFFTWTEST_C   V1.0   "
-#define TF_CFFTWTEST_C_CVSID \
-  "$Id$"
 
 #include<drfftw.h>
 #include<stdio.h>
@@ -105,7 +101,6 @@ void process(int n, int m)
 int main()
 {
   printf("%s\n", TF_CFFTWTEST_C_VERSION);
-  printf("%s\n", TF_CFFTWTEST_C_CVSID);
 
 /*
  * the code provided in the tutorial for rfftw_one produces segmentation

contrib/fourier/cxxfftwartest.cc

@@ -3,7 +3,6 @@
  * 
  * ----------------------------------------------------------------------------
  * 
- * $Id$
  * \author Thomas Forbriger
  * \date 16/05/2011
  * 
@@ -37,8 +36,6 @@
  */
 #define CXXFFTWARTEST_VERSION \
   "CXXFFTWARTEST   V1.2   test fftw3 array engine"
-#define CXXFFTWARTEST_CVSID \
-  "$Id$"
 
 // use the input/output facilities from the standard library
 #include <iostream>
@@ -140,7 +137,6 @@ int main(int iargc, char* argv[])
   // define full help text
   char help_text[]=
   {
-    CXXFFTWARTEST_CVSID
     "\n"
     "input        input file name\n"
     "output       output file name\n"
@@ -218,7 +214,7 @@ int main(int iargc, char* argv[])
 
   // report program version if in verbose mode
   if (opt.verbose)
-  { cout << CXXFFTWARTEST_VERSION << endl << CXXFFTWARTEST_CVSID << endl; }
+  { cout << CXXFFTWARTEST_VERSION << endl; }
 
   // extract commandline arguments
   // here the rest of the command line is parsed; i.e. the names of input

contrib/fourier/cxxfftwtest.cc

@@ -3,7 +3,6 @@
  * 
  * ----------------------------------------------------------------------------
  * 
- * $Id$
  * \author Thomas Forbriger
  * \date 12/09/2007
  * 
@@ -35,8 +34,6 @@
  */
 #define CXXFFTWTEST_VERSION \
   "CXXFFTWTEST   V1.1   a small test program for fftw when called from C++"
-#define CXXFFTWTEST_CVSID \
-  "$Id$"
 
 #include <iostream>
 #include <tfxx/commandline.h>
@@ -123,7 +120,6 @@ int main(int iargc, char* argv[])
   // define full help text
   char help_text[]=
   {
-    CXXFFTWTEST_CVSID
     "\n"
     "-n n   set number of samples to n\n"
     "-m f   set frequency to f\n"

contrib/fourier/doxygen.txt

@@ -2,8 +2,6 @@
  * \brief C++ library to operate on Fourier transforms (libfourierxx)
  *
  * ----------------------------------------------------------------------------
- *
- * $Id$
  * 
  * Copyright (c) 2002 by Thomas Forbriger (IMG Frankfurt) 
  * 
@@ -34,8 +32,6 @@
 /*! \mainpage
 \author Thomas Forbriger
 \since 2002
-\date $Date$
-\version $Id$
 
 The library provides modules to perform Fourier transformations and to operate
 on Fourier transforms.
@@ -128,6 +124,14 @@ Further stuff will be collected in this library in the future.
  * integral transform, where
  * \f$\Delta\omega=2\pi/T\f$ and \f$T=N\Delta t\f$.
  *
+ * The library provides functions which return the appropriate scaling factors
+ * such that application of a inverse transformation in sequence with a
+ * forward transformation is an identity-operation.
+ *
+ * \sa fourier::fft::DRFFTWAFFArrayEngine::scale_series,
+ *     fourier::fft::DRFFTWAFFArrayEngine::scale_spectrum,
+ *     fourier::fft::DRFFTWAFF::scale_series,
+ *     fourier::fft::DRFFTWAFF::scale_spectrum
  */
 
 // ----- END OF doxygen.txt ----- 

contrib/fourier/error.cc

@@ -3,7 +3,6 @@
  * 
  * ----------------------------------------------------------------------------
  * 
- * $Id$
  * \author Thomas Forbriger
  * \date 11/09/2007
  * 
@@ -35,8 +34,6 @@
  */
 #define FOURIER_ERROR_CC_VERSION \
   "FOURIER_ERROR_CC   V1.1"
-#define FOURIER_ERROR_CC_CVSID \
-  "$Id$"
 
 #include <iostream>
 #include <fourier/error.h>

contrib/fourier/error.h

@@ -3,7 +3,6 @@
  * 
  * ----------------------------------------------------------------------------
  * 
- * $Id$
  * \author Thomas Forbriger
  * \date 11/09/2007
  * 
@@ -39,8 +38,6 @@
 
 #define FOURIER_ERROR_H_VERSION \
   "FOURIER_ERROR_H   V1.0"
-#define FOURIER_ERROR_H_CVSID \
-  "$Id$"
 
 namespace fourier {
 

contrib/fourier/fcommand.cc

@@ -3,7 +3,6 @@
  * 
  * ----------------------------------------------------------------------------
  * 
- * $Id$
  * \author Thomas Forbriger
  * \date 05/01/2003
  * 
@@ -35,8 +34,6 @@
  */
 #define TF_FCOMMAND_CC_VERSION \
   "TF_FCOMMAND_CC   V1.0   "
-#define TF_FCOMMAND_CC_CVSID \
-  "$Id$"
 
 #include <fourier/fcommand.h>
 #include <fstream>
@@ -79,11 +76,8 @@ namespace fourier {
     {
       os << endl;
       os << TF_FCOMMAND_H_VERSION << endl;
-      os << TF_FCOMMAND_H_CVSID << endl;
       os << TF_FILTERS_H_VERSION << endl;
-      os << TF_FILTERS_H_CVSID << endl;
       os << TF_POLESNZEROES_H_VERSION << endl;
-      os << TF_POLESNZEROES_H_CVSID << endl;
     }
   }
 

contrib/fourier/fcommand.h

@@ -3,7 +3,6 @@
  * 
  * ----------------------------------------------------------------------------
  * 
- * $Id$
  * \author Thomas Forbriger
  * \date 05/01/2003
  * 
@@ -39,8 +38,6 @@
 
 #define TF_FCOMMAND_H_VERSION \
   "TF_FCOMMAND_H   V1.0   "
-#define TF_FCOMMAND_H_CVSID \
-  "$Id$"
 
 #include<iostream>
 #include<fourier/filters.h>

contrib/fourier/fftwaff.cc

@@ -3,7 +3,6 @@
  * 
  * ----------------------------------------------------------------------------
  * 
- * $Id$
  * \author Thomas Forbriger
  * \date 11/07/2006
  * 
@@ -42,8 +41,6 @@
  */
 #define TF_FFTWAFF_CC_VERSION \
   "TF_FFTWAFF_CC   V1.4"
-#define TF_FFTWAFF_CC_CVSID \
-  "$Id$"
 
 #include <iostream>
 #include <fourier/fftwaff.h>
@@ -308,7 +305,15 @@ namespace fourier {
 
     /*----------------------------------------------------------------------*/
     
-    //! Return appropriate scaling factor for sampling interval dt.
+    /*! \brief Return appropriate scaling factor for sampling interval dt.
+     *
+     * Factor to be applied when transforming to time domain.
+     *
+     * \param[in] dt sampling interval
+     * \return scalar factor to be applied to all samples
+     *
+     * \sa \ref sec_fftw3_integral_transform
+     */
     DRFFTWAFF::Tsample DRFFTWAFF::scale_series(const Tsample& dt) const
     {
       return(1./(Msize*dt));
@@ -316,7 +321,15 @@ namespace fourier {
 
     /*----------------------------------------------------------------------*/
     
-    //! Return appropriate scaling factor for sampling interval dt.
+    /*! \brief Return appropriate scaling factor for sampling interval dt.
+     *
+     * Factor to be applied when transforming to Fourier domain.
+     *
+     * \param[in] dt sampling interval
+     * \return scalar factor to be applied to all samples
+     *
+     * \sa \ref sec_fftw3_integral_transform
+     */
     DRFFTWAFF::Tsample DRFFTWAFF::scale_spectrum(const Tsample& dt) const
     {
       return(dt);

contrib/fourier/fftwaff.h

@@ -3,7 +3,6 @@
  * 
  * ----------------------------------------------------------------------------
  * 
- * $Id$
  * \author Thomas Forbriger
  * \date 11/07/2006
  * 
@@ -75,8 +74,6 @@
 
 #define TF_FFTWAFF_H_VERSION \
   "TF_FFTWAFF_H   V1.3"
-#define TF_FFTWAFF_H_CVSID \
-  "$Id$"
 
 #include<complex>
 #ifdef FFTWFALLBACK

contrib/fourier/fftwaffar.cc

@@ -3,7 +3,6 @@
  * 
  * ----------------------------------------------------------------------------
  * 
- * $Id$
  * \author Thomas Forbriger
  * \date 13/05/2011
  * 
@@ -37,8 +36,6 @@
  */
 #define TF_FFTWAFFAR_CC_VERSION \
   "TF_FFTWAFFAR_CC   V1.1"
-#define TF_FFTWAFFAR_CC_CVSID \
-  "$Id$"
 
 #include <iostream>
 #include <fourier/fftwaffar.h>
@@ -253,7 +250,15 @@ namespace fourier {
     
     /*----------------------------------------------------------------------*/
 
-    //! Return appropriate scaling factor for sampling interval dt.
+    /*! \brief Return appropriate scaling factor for sampling interval dt.
+     *
+     * Factor to be applied when transforming to time domain.
+     *
+     * \param[in] dt sampling interval
+     * \return scalar factor to be applied to all samples
+     *
+     * \sa \ref sec_fftw3_integral_transform
+     */
     DRFFTWAFFArrayEngine::Tsample
       DRFFTWAFFArrayEngine::scale_series(const Tsample& dt) const
     {
@@ -262,7 +267,15 @@ namespace fourier {
 
     /*----------------------------------------------------------------------*/
     
-    //! Return appropriate scaling factor for sampling interval dt.
+    /*! \brief Return appropriate scaling factor for sampling interval dt.
+     *
+     * Factor to be applied when transforming to Fourier domain.
+     *
+     * \param[in] dt sampling interval
+     * \return scalar factor to be applied to all samples
+     *
+     * \sa \ref sec_fftw3_integral_transform
+     */
     DRFFTWAFFArrayEngine::Tsample
       DRFFTWAFFArrayEngine::scale_spectrum(const Tsample& dt) const
     {

contrib/fourier/fftwaffar.h

@@ -3,7 +3,6 @@
  * 
  * ----------------------------------------------------------------------------
  * 
- * $Id$
  * \author Thomas Forbriger
  * \date 13/05/2011
  * 
@@ -44,8 +43,6 @@
 
 #define TF_FFTWAFFAR_H_VERSION \
   "TF_FFTWAFFAR_H   V1.2"
-#define TF_FFTWAFFAR_H_CVSID \
-  "$Id$"
 
 #include<complex>
 #include<fftw3.h>

contrib/fourier/filters.cc

@@ -3,7 +3,6 @@
  * 
  * ----------------------------------------------------------------------------
  * 
- * $Id$
  * \author Thomas Forbriger
  * \date 05/01/2003
  * 
@@ -34,16 +33,15 @@
  * ============================================================================
  */
 #define TF_FILTER_CC_VERSION \
-  "TF_FILTER_CC   V1.0   "
-#define TF_FILTER_CC_CVSID \
-  "$Id$"
+  "TF_FILTER_CC   V1.0"
 
 #include <fourier/filters.h>
 #include <fourier/error.h>
+#include <cmath>
 
 namespace fourier {
 
-  const double Filter::pi;
+  const double Filter::pi=M_PI;
   const Filter::Tcvalue Filter::ime=Tcvalue(0.,1.);
 
   /*----------------------------------------------------------------------*/

contrib/fourier/filters.h

@@ -3,7 +3,6 @@
  * 
  * ----------------------------------------------------------------------------
  * 
- * $Id$
  * \author Thomas Forbriger
  * \date 05/01/2003
  * 
@@ -40,9 +39,7 @@
 #ifndef TF_FILTERS_H_VERSION
 
 #define TF_FILTERS_H_VERSION \
-  "TF_FILTERS_H   V1.0   "
-#define TF_FILTERS_H_CVSID \
-  "$Id$"
+  "TF_FILTERS_H   V1.0"
 
 #include<fourier/polesnzeroes.h>
   
@@ -53,7 +50,7 @@ namespace fourier {
       typedef PolesNZeroes Tbase;
       typedef Tbase::Tcvalue Tcvalue;
 
-      static const double pi=3.141592653589793;
+      static const double pi;
       static const Tcvalue ime;
 
       Filter(): Tbase(), Mfrequency(false) { }

contrib/fourier/filters.inc

 c this is <filters.inc>
 c ----------------------------------------------------------------------------
-c   ($Id$)
 c
 c Copyright (c) 2002 by Thomas Forbriger (IMG Frankfurt) 
 c

contrib/fourier/polesnzeroes.cc

@@ -3,7 +3,6 @@
  * 
  * ----------------------------------------------------------------------------
  * 
- * $Id$
  * \author Thomas Forbriger
  * \date 05/01/2003
  * 
@@ -34,8 +33,6 @@
  */
 #define TF_POLESNZEROES_CC_VERSION \
   "TF_POLESNZEROES_CC   V1.0   "
-#define TF_POLESNZEROES_CC_CVSID \
-  "$Id$"
 
 #include <fourier/polesnzeroes.h>
 

contrib/fourier/polesnzeroes.h

@@ -3,7 +3,6 @@
  * 
  * ----------------------------------------------------------------------------
  * 
- * $Id$
  * \author Thomas Forbriger
  * \date 05/01/2003
  * 
@@ -38,8 +37,6 @@
 
 #define TF_POLESNZEROES_H_VERSION \
   "TF_POLESNZEROES_H   V1.0   "
-#define TF_POLESNZEROES_H_CVSID \
-  "$Id$"
 
 #include<cmath>
 #include<complex>

contrib/fourier/polesnzeros.inc

 c this is <polesnzeros.inc>
 cS
 c ----------------------------------------------------------------------------
-c   ($Id$)
 c
 c Copyright (c) 2002 by Thomas Forbriger (IMG Frankfurt) 
 c

contrib/libcseife/README

 this is <README>
 ============================================================================
 SEIFE --- seismic waveform filters
-----------------------------------
-$Id$
 ============================================================================
 
-For compilation instructions see README.1st in the root directory of the tar-ball or
-http://gpitrsvn.gpi.uni-karlsruhe.de:8000/TFSoftware/wiki/docs/installation
+For compilation instructions see README.1st in the root directory.
 
 libseife is a collection of Fortran 77 functions and subroutines for time
 series analysis and digital filters. It is a full-grown signal processing
@@ -37,5 +34,15 @@ Dependencies
   external dependencies: -
   internal dependencies: -
 
+Arrays in C version
+-------------------
+
+The proper definition of arrays and parameters to be passed to the C-API of
+libseife becomes obvious in function seife_first, which is defined in cseife.c
+A call
+
+  seife_first(x, n);
+
+will address elements x[0] to x[n-1] in C-array x.
 
 ----- END OF README ----- 

contrib/stfinv/README

@@ -70,7 +70,7 @@ documentation.
 
 User documentation
 ------------------
-The theory behind the Fourier domain least squares engine is outlined by
+The theory behind the Fourier domain least squares procedure is outlined by
 Lisa Groos (2013, Appendix F, page 146). She also describes a way to find an
 approrpiate water level by application of the L-curve criterion (Groos, 2013,
 Appendix G, page 148).
@@ -87,6 +87,9 @@ tests/onlinehelp Provides access to these texts. Just issue
 
 to get access.
 
+A toy example and a step-by-step introduction are provided in subdirectory
+src/ts/wf/testcases in README.soutifu
+
 A short descrpition of the library and the accompanying program soutifu is
 provided on the OpenTOAST web-page:
 http://www.opentoast.de/Data_analysis_code_soutifu_and_libstfinv.php

contrib/stfinv/debug.h

@@ -40,7 +40,7 @@
   "STFINV_DEBUG_H   V1.0"
 
 /*! \brief produce debug output
- * \ingroup misc_h
+ * \ingroup group_debug
  *
  * \param C output will be generated if C == true
  * \param N name of function 
@@ -54,8 +54,15 @@
     std::cerr.flush(); \
   }
 
+/*! \brief report value in a sequence of output operators
+ * \ingroup group_debug
+ *
+ * \param P parameter to dump
+ */
+#define STFINV_value( P ) #P << "=" << P
+
 /*! \brief report value of expression
- * \ingroup misc_h
+ * \ingroup group_debug
  *
  * \param P parameter to dump
  */

contrib/stfinv/doxygen.txt

@@ -104,7 +104,7 @@ processing are described in the \ref page_help.
 
 /*! \brief Engines implemented in libstfinv
 
-\defgroup engines Engines
+\defgroup group_engines Engines
 
 \todo
   A detailed description for implementers is still missing
@@ -116,7 +116,7 @@ processing are described in the \ref page_help.
 
 /*! \brief Tools and utilities used by the libstfinv engines
 
-\defgroup tools Internal tools and utilities
+\defgroup group_tools Internal tools and utilities
 
 \todo
   A detailed description for implementers is still missing
@@ -136,4 +136,18 @@ processing are described in the \ref page_help.
 \date 04.10.2015
  */
 
+/*======================================================================*/
+
+/*! \brief Debug tools
+
+\defgroup group_debug Debugging module
+
+\todo
+  Selection of debug statements in most parts of the code is done by bits in
+  the value of the debug variable. E.g∵ The value 16 (bit 4) selects debugging
+  of the taper function. This is not yet properly documented.
+
+\date 04.10.2015
+ */
+
 // ----- END OF doxygen.txt ----- 

contrib/stfinv/doxygen_library_users.txt

@@ -94,9 +94,9 @@
   Programs using this library will require the following libraries in
   addition:
 
-    - libfourierxx (available from TFSoftware)
+    - libfourierxx (available from Seitosh)
     - libfftw3
-    - libaff (available from TFSoftware)
+    - libaff (available from Seitosh)
 
   C programs will further be required to link against
 

contrib/stfinv/parameterhandler.h

@@ -45,12 +45,12 @@
 namespace stfinv {
 
   /*! \brief Namespace for internal tools
-   * \ingroup tools
+   * \ingroup group_tools
    */
   namespace tools {
 
     /*! strip substring
-     * \ingroup tools
+     * \ingroup group_tools
      *
      * Strips off first substring up to given delimiter.
      * The string is passed as a reference and will be modified (i.e. the
@@ -65,14 +65,14 @@ namespace stfinv {
     /*----------------------------------------------------------------------*/
 
     /*! \brief A map to store parameters.
-     * \ingroup tools
+     * \ingroup group_tools
      */
     typedef std::map<std::string,std::string> Tparamap;
 
     /*----------------------------------------------------------------------*/
 
     /*! \brief Create a parameter map from a parameter string
-     * \ingroup tools
+     * \ingroup group_tools
      *
      * \param p parameter string
      * \param delimiter delimiter which separates two parameters
@@ -86,7 +86,7 @@ namespace stfinv {
     /*----------------------------------------------------------------------*/
 
     /*! replace comma by whitespace
-     * \ingroup tools
+     * \ingroup group_tools
      *
      * \param s input string
      * \return input string with all commas replaced by whitespace
@@ -96,7 +96,7 @@ namespace stfinv {
     /*----------------------------------------------------------------------*/
 
     /*! \brief remove leading and trailing whitespace
-     * \ingroup tools
+     * \ingroup group_tools
      *
      * \param s any string