The tool set is extensively documented using pydoc. To launch the graphical interface run:

    pydoc -g 

in the command line.

The main interface HRFAnalyseDirect allows for operations to be applied to files or directories (no subdirectories):

• Clean:

  Retrieve the hrf:

    ./HRFAnalyseDirect.py unittest_dataset clean
  

  Retrieve the timestamps and hrf from the first hour:

    ./HRFAnalyseDirect.py unittest_dataset clean -kt -s 3600
  

  Retrieve the valid hrf(50<=hrf<=250) for the last hour:

    ./HRFAnalyseDirect.py unittest_dataset clean -s 3600 --apply_limits --start-at-end
  

  Retrieve the hrf for the interval 1m--61m

    ./HRFAnalyseDirect.py unittest_dataset clean -ds 1 -s 3600 
  

  Retrieve the hrf from first 2000 lines:

    ./HRFAnalyseDirect.py unittest_dataset clean -s 2000 --use_lines
  

  Break the file into 5 minute blocks where the blocks don't overlap

    ./HRFAnalyseDirect.py unittest_dataset clean -s 300 --full-file
  

  Break the file into 5 minute blocks where the blocks start with a one minute difference

    ./HRFAnalyseDirect.py unittest_dataset clean -s 300 -g 60 --full-file
  

• Compress

  Compress using the gzip algorithm (maximum compression level will be used)

    ./HRFAnalyseDirectory.py unittest_dataset compress -c gzip
  

  Compress using the bzip2 algorithm with minimum compression(1 in this case):

    ./HRFAnalyseDirectory.py unittest_dataset -c bzip2 --level 1
  

• Entropy

  Calculate the entropy using Approximate entropy with tolerance 0.2 and matrix dimension 2 (reference values for the analysis of biological data)

    ./HRFAnalyseDirectory.py unittest_dataset entropy apen -t 0.2
  

The auxiliary interface HRFAnalyseFileBlocks does the partition and compression of the file blocks automatically.

• Compress

   Cut files into 5min blocks with no overlap and compress each one with the default compressor
    
    ./HRFAnalyseFileBlocks.py unittest_dataset/ -s 300 compress
    
    
   Cut files into blocks with 300 lines with no overlap and compress each one with the default compressor
    
    ./HRFAnalyseFileBlocks.py unittest_dataset/ -s 300 --use-lines compress
    
    
   Cut files into blocks with 5 min where one block starts 1 min later then the previous one did. Compress each one with the paq8l compressor
    
    ./HRFAnalyseFileBlocks.py unittest_dataset/ -s 300 -g 60 compress -c paq8l
  

• Entropy

   Cut files into blocks with 5 min where one block starts 1 min later then the previous one did. Calculte each files entropy using the Sample entropy.
    
    ./HRFAnalyseFileBlocks.py unittest_dataset/ -s 300 -g 60 entropy sampen
  

The last interface HRFAnalyseMultiScale is specific to calculate MultiScale entropy and compression:

• Multiscale entropy for all the files starting at scale 1(original files) and ending in scale 20

    ./HRFAnalyseMultiscale unittest_dataset entropy sampen
  

• Multiscale compression with rounded results for scale, since the scales are constructed by averaging a given number of point we are bound to have floats, this options rounds those numbers to an integer.

    ./HRFAnalyseMultiscale unittest_dataset --round-to-int compression
  

• Multiscale compression with rounded results for scale, multiplyed by 10, the scale point is multiplied by 10 and rounded.

    ./HRFAnalyseMultiscale unittest_dataset --round-to-int --multiply 10 compression -c paq8l
  

Copyright (C) 2012 Mara Matias

This file is part of HRFAnalyse.

HRFAnalyse is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published
by the Free Software Foundation, either version 3 of the License,
or (at your option) any later version.

HRFAnalyse is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with HRFAnalyse.  If not, see
<http://www.gnu.org/licenses/>.