Difference between revisions of "User:Josiah425:TISEAN Package"

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# the FORTRAN ones that need to be linked to oct files (an example of such a program is 'project')
 
# the FORTRAN ones that need to be linked to oct files (an example of such a program is 'project')
 
# c programs which also need to be linked to oct files.  
 
# c programs which also need to be linked to oct files.  
As linking FORTRAN code to oct code is most difficult of those three tasks I assume in my estimates that it will take me around 3 hours for each program, there are 28 in this category. Thus I assume it will take me about 2-3 to complete this task.  
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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.  
  
Next there are the programs in the Tisean package which can be ported to m-files easily. As this is not as difficult a task as linking FORTRAN code to oct files I have allotted 2 hr for each program. I have put 5 programs in this category thus it should only take me about 2 days to complete this task.
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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.
Last but not least, I have 41 programs in C that need to be linked to Oct files. As this task seems fairly straightforward I have allotted 2 hours for each program. There are 41 programs in this category, therefore this task should also take me 2-3 weeks.  
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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.
  
I plan to allot another 2 weeks for cleaning the code up. Therefore, the a grand total is about 7 weeks.  
+
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.  
  
My plan is to tackle the hardest task first, that is to work on the FORTRAN programs that need to be linked to oct files.  
+
Thus every milestone will be finishing each section of the TISEAN package.
 +
 
 +
I would like to tackle them in the following order:
 +
* Nonlinear noise reduction
 +
* Testing for nonlinearity
 +
* Nonlinear prediction
 +
* Lapunov Exponents
 +
* Dimensions and entropies
 +
 
 +
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 ==
 +
 
 +
I will start with a small step of porting all of the functions needed for [http://www.mpipks-dresden.mpg.de/~tisean/Tisean_3.0.1/index.html| Nonlinear noise reduction]. The functions I will need is: henon (for generating data), addnoise, ghkss and project. They cover all of the three categories I talked about in the first section. I have already reimplemented henon in m-file, it is accessible [http://agora.octave.org/snippet/hOzw/ here]. Both addnoise and project are in FORTRAN and need to be linked to C++ files and compiled into oct files. Lastly, ghkss is implemented in c and needs to be linked to a C++ oct file.
  
There are 9 weeks designated for GSoC so I hope the extra room will allow me easily finish on time.
 
 
== Explanation of what I want to do with each file ==
 
== Explanation of what I want to do with each file ==
 
Each FORTRAN file that need to be linked to an Oct file needs work done on it. I plan to take the following steps with each FORTRAN program:
 
Each FORTRAN file that need to be linked to an Oct file needs work done on it. I plan to take the following steps with each FORTRAN program:
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I plan to do similar steps for the c files. I believe this stage will be easier as the c code is much better organized and eliminating input validation & parsing, file inputs and outputs should be a much easier task.
 
I plan to do similar steps for the c files. I believe this stage will be easier as the c code is much better organized and eliminating input validation & parsing, file inputs and outputs should be a much easier task.
 
== Where I intend to start ==
 
 
I will start with a small step of porting all of the functions needed for [http://www.mpipks-dresden.mpg.de/~tisean/Tisean_3.0.1/index.html| Nonlinear noise reduction]. The functions I will need is: henon (for generating data), addnoise, ghkss and project. They cover all of the three categories I talked about in the first section. I have already reimplemented henon in m-file, it is accessible [http://agora.octave.org/snippet/hOzw/ here]. Both addnoise and project are in FORTRAN and need to be linked to C++ files and compiled into oct files. Lastly, ghkss is implemented in c and needs to be linked to a C++ oct file.
 

Revision as of 16:50, 27 March 2015

TISEAN Package Porting Project

General division and time estimation

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. I have divided the first part into three sub-parts:

  1. FORTRAN ones that can be re-implemented easily in m-files (a good example of such a program is 'henon')
  2. the FORTRAN ones that need to be linked to oct files (an example of such a program is 'project')
  3. c programs which also need to be linked to oct files.

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.

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. 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.

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.

Thus every milestone will be finishing each section of the TISEAN package.

I would like to tackle them in the following order:

  • Nonlinear noise reduction
  • Testing for nonlinearity
  • Nonlinear prediction
  • Lapunov Exponents
  • Dimensions and entropies

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

I will start with a small step of porting all of the functions needed for Nonlinear noise reduction. The functions I will need is: henon (for generating data), addnoise, ghkss and project. They cover all of the three categories I talked about in the first section. I have already reimplemented henon in m-file, it is accessible here. Both addnoise and project are in FORTRAN and need to be linked to C++ files and compiled into oct files. Lastly, ghkss is implemented in c and needs to be linked to a C++ oct file.

Explanation of what I want to do with each file

Each FORTRAN file that need to be linked to an Oct file needs work done on it. I plan to take the following steps with each FORTRAN program:

  1. Change the FORTRAN program into a subroutine. The arguments of this subroutine will be the parameters that this program would have normally read from the user during execution.
  2. Move input parsing and validation from the FORTRAN files to the .cc file which will link the respective fortran file to it. This will make the fortran subroutines 'dumb' and unable to distinguish between good and bad data.
  3. Eliminate all file inputs and outputs. The fortran programs write and read data to/from files. This is unnecessary in Octave, as data can be supplied and retrieved to/from these subroutines directly via oct files.
  4. Test the oct file against the original library to ensure I didn't make mistakes.

I plan to do similar steps for the c files. I believe this stage will be easier as the c code is much better organized and eliminating input validation & parsing, file inputs and outputs should be a much easier task.