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= TISEAN Package Porting Project  =
 
= TISEAN Package Porting Project  =
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== Goal of the project ==
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The goal of this project is not to port the entire TISEAN package to octave. That would be a desired outcome though it might not be feasible within the time constraints. The goal of this project is to give the TISEAN package a solid start and to port as many functions as possible to create a solid foundation for the future.
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== General division ==
 
== General division ==
AS the TISEAN package consists of 74 programs it needs to be divided into subparts that can be tackled separately and create a entity in-and-of-themselves. I chose to work along the lines of the articles about implementations of nonlinear timeseries included in the documentation. This article discusses various algorithms and what certain programs mean. It can be found [http://www.mpipks-dresden.mpg.de/~tisean/Tisean_3.0.1/docs/chaospaper/TiseanHTML.html| here]. I will discuss in which order I would like to port various topics in this and where my work currently stands.
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As the TISEAN package consists of 74 programs I have divided the first part into three sub-parts:
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# FORTRAN ones that can be re-implemented easily in m-files (a good example of such a program is 'henon') -- there are 5 programs in this class
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# c programs which also need to be linked to oct files (an example is 'ghkss') -- there are 41 programs in this class
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# the FORTRAN ones that need to be linked to oct files (an example of such a program is 'project') -- there are 28 programs in this class
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They are ordered so that according to my estimates the difficulty rises with the number. This is because typecasting and implicit typing (which is included in most of the FORTRAN files in the TISEAN library) can be problematic sometimes.
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Apart from the qualitative division I propose a work oriented division, in which each subpart can be tackled separately and create an entity in-and-of-itself. I chose to work along the lines of the articles about implementations of nonlinear timeseries included in the documentation. This article discusses various algorithms and what certain programs mean. It can be found [http://www.mpipks-dresden.mpg.de/~tisean/Tisean_3.0.1/docs/chaospaper/TiseanHTML.html| here]. I will discuss in which order I would like to port various topics in this and where my work currently stands.
 
==== Nonlinear noise reduction ====
 
==== Nonlinear noise reduction ====
 
This is the first topic I chose. It is because it contains programs from all three categories. It is also relatively small -- it contains 3 programs: project, lazy, ghkss. I have chosen to further implement addnoise and henon, to demonstrate how project and ghkss work. Thus this topic contains programs from each category:  
 
This is the first topic I chose. It is because it contains programs from all three categories. It is also relatively small -- it contains 3 programs: project, lazy, ghkss. I have chosen to further implement addnoise and henon, to demonstrate how project and ghkss work. Thus this topic contains programs from each category:  
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* Linkable to FORTAN (surrogates, randomize , timerev)
 
* Linkable to FORTAN (surrogates, randomize , timerev)
 
This stage should take me about 3 days to complete.
 
This stage should take me about 3 days to complete.
=== Notes to time estimates ===
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=== Notes on time estimates ===
 
Totaling up the above estimates it should take me 6 weeks to complete my task as outlined above. I do think my time estimates are rather conservative, but I would rather work on other programs (the documentation contains another article located [http://www.mpipks-dresden.mpg.de/~tisean/Tisean_3.0.1/docs/surropaper/Surrogates.html| here]) than to be overwhelmed with the work and try to rush trough. As I am not fully familiar with the mathematical concepts discussed within these articles I want to make sure that I reduce the possibility of error when linking programs to octave to a minimum. If I vastly overestimated the time I will need to port those functions I intend to finish the 'Visualization, non-stationary' section of the work on nonlinear timeseries and then proceed to programs from the 'Surrogate time series article'.
 
Totaling up the above estimates it should take me 6 weeks to complete my task as outlined above. I do think my time estimates are rather conservative, but I would rather work on other programs (the documentation contains another article located [http://www.mpipks-dresden.mpg.de/~tisean/Tisean_3.0.1/docs/surropaper/Surrogates.html| here]) than to be overwhelmed with the work and try to rush trough. As I am not fully familiar with the mathematical concepts discussed within these articles I want to make sure that I reduce the possibility of error when linking programs to octave to a minimum. If I vastly overestimated the time I will need to port those functions I intend to finish the 'Visualization, non-stationary' section of the work on nonlinear timeseries and then proceed to programs from the 'Surrogate time series article'.
 
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== Details of work on each program ==
 
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* FORTRAN linking
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For each FORTRAN program that I intend to link to a oct-file I intend to:  
Porting of the TISEAN package has a couple parts. First part is making the FORTRAN and c programs accessible to Octave. Second part would be creating makefiles and putting all that code in a neat package.
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# Strip the program of its input validation and transform it into a subroutine
I have divided the first part into three sub-parts:  
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# Create a .cc program (compiled into an oct-file) that will launch the stripped FORTRAN subroutine; this .cc program will also not contain input validation, it will be for internal use only
# FORTRAN ones that can be re-implemented easily in m-files (a good example of such a program is 'henon') -- there are 5 programs in this class
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# Create a m-file that will perform input validation and launch the .cc and contain usage documentation
# c programs which also need to be linked to oct files (an example is 'ghkss') -- there are 41 programs in this class
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* C linking
# the FORTRAN ones that need to be linked to oct files (an example of such a program is 'project') -- there are 28 programs in this class
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I intend to do here something similar to the FORTRAN programs, although, it might be better to not create any extra m-files and incorporate the program's existing input validation into the .cc file. This might be a desired course of action. I will make a decision once I complete one such linking program.  
They are ordered so that my estimate of the difficulty rises with the number. This is because typecasting and implicit typing (which is included in most of the FORTRAN files in the TISEAN library) can be problematic sometimes.
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* Reimplementing in mfile
 
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This is quite straightforward, although it is important not to make a mistake while taking this approach.
 
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As linking FORTRAN code to oct code is most difficult of those three tasks, there are 28 in this category. If it is more difficult than I expect I will move some of the easier programs into the m-file category.  
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Next there are the programs in the Tisean package which can be ported to m-files easily. This is not as difficult a task as linking FORTRAN code to oct files. I have put 5 programs in this category.
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Last but not least, I have 41 programs in C that need to be linked to Oct files. There are 41 programs in this category.
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My plan is to try to work with sections of the library at the time. As described below, I intend to begin with the programs connected to Nonlinear noise reduction. The goal is to then document all those files and create a usable package. After finishing those functions I intend to move to another area of the TISEAN package and add programs that actually make a whole. As it is hard to precisely estimate how much time porting the entire TISEAN package will take, I can make small steps that will in-and-of-themselves form a whole.  
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Thus every milestone will be finishing each section of the TISEAN package.
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I would like to tackle them in the following order:
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* Nonlinear noise reduction
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* Testing for nonlinearity
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* Nonlinear prediction
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* Lapunov Exponents
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* Dimensions and entropies
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Once those are completed I will look at other programs to be ported. The idea though, is to focus on getting a solid start for porting this library.
      
== Where I intend to start ==
 
== Where I intend to start ==
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