Vplants.sequenceprotect T1 extunderscore analysis Documentation

							Vplants.sequence_analysis
           Documentation
                 Release 0.6.2




            Vplants consortium




                      July 16, 2009
                                                                                     CONTENTS



1   Module description                                                                                              1

2   Documentation                                                                                                   3
    2.1 Sequence_analysis User Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .    3
    2.2 Sequence_analysis Reference Guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .     4

3   Authors                                                                                                         9

4   ChangeLog                                                                                                      11

5   20 May 2009                                                                                                    13

6   License                                                                                                        15

Module Index                                                                                                       17

Index                                                                                                              19




                                                                                                                    i
ii
                                                    CHAPTER

                                                      ONE



                                      MODULE DESCRIPTION

Summary

    Version 0.6
    Release 0.6.2
    Date July 16, 2009
    Author See Authors section
    ChangeLog See ChangeLog section




Overview




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2                                                        Chapter 1. Module description
                                                                                                       CHAPTER

                                                                                                           TWO



                                                                DOCUMENTATION

2.1 Sequence_analysis User Guide

      Version 0.6
      Release 0.6.2
      Date July 16, 2009

This manual details functions, modules, and objects included in VPlants.Sequence_analysis, describing what they are
and what they do. For learning how to use VPlants.Sequence_analysis see Sequence_analysis Reference Guide.

  Warning: This Guide is still very much in progress. Many aspects of VPlants.Sequence_analysis are not covered.
  More documentation can be found on the openalea wiki.



2.1.1 Current Developments


 Contents

     • Current Developments
          – documentation
          – Wrapper
          – Test
          – Questions



documentation

The sphinx documentation is now used to manage the documentation so as to include a reference guide as well as a
User guide (and this administration section).
docstrings need to be written.


Wrapper

See the wrapping section


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Test

Most of the functions have a test. The data structure such as Semi_markov, Sequences as well.
Remains to be done : clean the test and use a common data.py file to create common data sets.


Questions

     • do we want a specific extension for all different type of data: top for tops, seq for sequences and so on ? or just
       .dat ?

     • Discrete and sequences difference ?


2.1.2 WRAPPING

Todo
check all wrapper with optional arguments and switch to BOOST_OVERLOAD ?


wrapping to be done

     • Functions that remain to be done or check carefully: Estimation, Simulate and Extract*, Display, Save, Plot

     • Fully done : Compare and all other “simple” functions.
     • time_events: estimation ?
     • renewal: function to extct forward, backward and so on.
     • renewal_data: estimation ?


known issues

     • ComputeSelfTransition: the prototype is protected. Only the empty argument case has been wrapped in ex-
       port_markovian.cpp


2.2 Sequence_analysis Reference Guide

        Version 0.6
        Release 0.6.2
        Date July 16, 2009

This manual details functions, modules, and objects included in VPlants.Sequence_analysis, describing what they are
and what they do. For learning how to use VPlants.Sequence_analysis see Sequence_analysis User Guide.

    Warning: This Guide is still very much in progress. Many aspects of VPlants.Sequence_analysis are not covered.
    More documentation can be found on the openalea wiki.




4                                                                                        Chapter 2. Documentation
                                                       Vplants.sequence_analysis Documentation, Release 0.6.2



2.2.1 openalea.sequence_analysis.sequences API

      Revision $Id: vectors.py 6217 2009-04-08 12:40:15Z cokelaer $
      License


Reference

Sequences
uthor:/
Sequences(*args, **kargs)
     Construction of a set of sequences from multidimensional arrays of integers, from data generated by a renewal
     process or from an ASCII file.
      The data structure of type array(array(array(int))) should be constituted at the most internal level of arrays of
      constant size. If the optional argument IndexParameter is set at “Position” or “Time”, the data structure of type
      array(array(array(int))) is constituted at the most internal level of arrays of size 1+n (index parameter, n variables
      attached to the explicit index parameter). If the optional argument IndexParameter is set at “Position”, only the
      index parameter of the last array of size 1+n is considered and the first component of successive elementary
      arrays (representing the index parameter) should be increasing. If the optional argument IndexParameter is set
      at “Time”, the first component of successive elementary arrays should be strictly increasing.

             Parameters

            •array1 (array(array(int))): input data for univariate sequences
            •arrayn (array(array(array(int)))): input data for multivariate sequences,
            •timev (renewal_data),
            •file_name (string).

             Optional parameters

            •Identifiers (array(int)): explicit identifiers of sequences. This optional argument can only be used if the
             first argument is of type array(array(int/array(int))).
            •IndexParameter (string): type of the explicit index parameter: “Position” or “Time” (the default: implicit
             discrete index parameter starting at 0). This optional argument can only be used if the first argument is of
             type array(array(int/array(int))).

             Returns

      If the construction succeeds, an object of type sequences or discrete_sequences is returned, otherwise no object
      is returned. The returned object is of type discrete_sequences if all the variables are of type STATE, if the
      possible values for each variable are consecutive from 0 and if the number of possible values for each variable
      is <= 15.

             Examples

      >>>   Sequences(array1, Identifiers=[1, 8, 12])
      >>>   Sequences(arrayn, Identifiers=[1, 8, 12],
      >>>   IndexParameter="Position")
      >>>   Sequences(timev)
      >>>   Sequences(file_name)




2.2. Sequence_analysis Reference Guide                                                                                    5
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       See Also:
       Save, AddAbsorbingRun(), Cluster(), Cumulate(), Difference(), IndexParameterExtract(),
       LengthSelect(), Merge(), MergeVariable(), MovingAverage(), RecurrenceTimeSequences(),
       RemoveRun(), Reverse(), SegmentationExtract(), SelectIndividual(), SelectVariable(),
       Shift(),   Transcode(),    ValueSelect(),   VariableScaling().       ExtractHistogram(),
       ExtractVectors(),         ComputeCorrelation(),         ComputePartialAutoCorrelation(),
       ComputeSelfTransition(), Compare(), Estimate(), ComputeStateSequences(), Simulate().
       Todo
       refactoring using AML original code
LumpabilityTest(obj, *args, **kargs)

       Todo
       documenation
RemoveIndexParameter(obj)

       Todo
       documenation
       input can be sequence, markovian_sequences, nonhomogeneous_markov, variable_order_markov
TransformPosition(obj, step=None)

       Todo
       documenation
       input is a sequence only


Source

Show Source file


2.2.2 openalea.sequence_analysis.tops API

       Revision $Id: vectors.py 6217 2009-04-08 12:40:15Z cokelaer $
       License


Reference

Tops
Tops(*args, **kargs)
     Construction of a set of sequences from multidimensional arrays of integers, from data generated by a renewal
     process or from an ASCII file.
       The data structure of type array(array(array(int))) should be constituted at the most internal level of arrays of
       constant size. If the optional argument IndexParameter is set at “Position” or “Time”, the data structure of type
       array(array(array(int))) is constituted at the most internal level of arrays of size 1+n (index parameter, n variables
       attached to the explicit index parameter). If the optional argument IndexParameter is set at “Position”, only the
       index parameter of the last array of size 1+n is considered and the first component of successive elementary
       arrays (representing the index parameter) should be increasing. If the optional argument IndexParameter is set
       at “Time”, the first component of successive elementary arrays should be strictly increasing.


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                                                      Vplants.sequence_analysis Documentation, Release 0.6.2



            Parameters

           •array1 (array(array(int))): input data for univariate sequences
           •arrayn (array(array(array(int)))): input data for multivariate sequences,
           •timev (renewal_data), file_name (string).

            Optional parameters

     Identifiers (array(int)): explicit identifiers of sequences. This optional argument can only be used if the first
     argument is of type array(array(int/array(int))). IndexParameter (string): type of the explicit index parameter:
     “Position” or “Time” (the default: implicit discrete index parameter starting at 0). This optional argument can
     only be used if the first argument is of type array(array(int/array(int))).
            Returns
     If the construction succeeds, an object of type sequences or discrete_sequences is returned, otherwise no object
     is returned. The returned object is of type discrete_sequences if all the variables are of type STATE, if the
     possible values for each variable are consecutive from 0 and if the number of possible values for each variable
     is <= 15.
            Examples

     >>>   Tops(array1, Identifiers=[1, 8, 12])
     >>>   Tops(arrayn, Identifiers=[1, 8, 12], IndexParameter="Position")
     >>>   Tops(timev)
     >>>   Tops(file_name)

     See Also:
     Save, AddAbsorbingRun(), Cluster(), Cumulate(), Difference(), IndexParameterExtract(),
     LengthSelect(), Merge(), MergeVariable(), MovingAverage(), RecurrenceTimeSequences(),
     RemoveRun(), Reverse(), SegmentationExtract(), SelectIndividual(), SelectVariable(),
     Shift(),   Transcode(),    ValueSelect(),   VariableScaling().        ExtractHistogram(),
     ExtractVectors(),         ComputeCorrelation(),         ComputePartialAutoCorrelation(),
     ComputeSelfTransition(), Compare(), Estimate(), ComputeStateTops(), Simulate().
RemoveApicalInternodes(obj, internode)
     RemoveApicalInternodes
     Removal of the apical internodes of the parent shoot of a ‘top’.
            Usage

     >>> RemoveApicalInternodes(top, nb_internode)


            Arguments

           •top (tops),
           •nb_internode (int): number of removed internodes.

            Returned object

     If nb_internode > 0 and if the removed internodes do not bear offspring shoots, an object of type tops is returned,
     otherwise no object is returned.
     See Also:
     SelectIndividual(), Merge(), Reverse().


2.2. Sequence_analysis Reference Guide                                                                               7
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Source

Show Source file

    • A PDF version of VPlants.Sequence_analysis documentation is available.

See Also:
More documentation can be found on the openalea wiki.




8                                                                              Chapter 2. Documentation
                                                                     CHAPTER

                                                                     THREE



                                                                 AUTHORS

Yann Guédon (Original code ; AML)
Thomas Cokelaer (Boost python wrapping, python modules, tests)




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10                                                       Chapter 3. Authors
      CHAPTER

       FOUR



CHANGELOG




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12                                                       Chapter 4. ChangeLog
                                                                                CHAPTER

                                                                                  FIVE



                                                                         20 MAY 2009

• Sequence Analysis major update to wrap CPP classes with boost python
• Add python modules

• add Tests




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14                                                       Chapter 5. 20 May 2009
                                                                     CHAPTER

                                                                        SIX



                                                                  LICENSE

VPlants.Sequence_analysis is released under a Cecill-C License.
Note: Cecill-C license is a LGPL compatible license.




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16                                                       Chapter 6. License
                                          MODULE INDEX


O
openalea.sequence_analysis.sequences, 5
openalea.sequence_analysis.tops, 6

S
sequence_analysis, 1
sequences, 4

T
tops, 6




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18                                                       Module Index
                                                          INDEX


L
LumpabilityTest()      (in        module           ope-
        nalea.sequence_analysis.sequences), 6

O
openalea.sequence_analysis.sequences (module), 5
openalea.sequence_analysis.tops (module), 6

R
RemoveApicalInternodes()     (in      module       ope-
        nalea.sequence_analysis.tops), 7
RemoveIndexParameter()      (in      module        ope-
        nalea.sequence_analysis.sequences), 6

S
sequence_analysis (module), 1
sequences (module), 4
Sequences()          (in         module            ope-
         nalea.sequence_analysis.sequences), 5

T
tops (module), 6
Tops() (in module openalea.sequence_analysis.tops), 6
TransformPosition()       (in        module        ope-
          nalea.sequence_analysis.sequences), 6




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