Révision 78fcb188

b/modules/clustering.py
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clustering: Directs the clustering process by calling the relevant functions.
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"""
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import logging
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import warnings
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import hdbscan


  		





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import numpy as np


  		





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    exemplars = []


  		





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    for i, mtx in enumerate(clust_affty_mtcs):


  		





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        pref = -1e6 * np.max(np.abs(mtx))


  		





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        warnings.filterwarnings("error")


  		





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        try:


  		





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            af = AffinityPropagation(affinity='precomputed', preference=pref,


  		





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                                     damping=0.95, max_iter=2000,


  		





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                                     random_state=None).fit(mtx)


  		





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        except UserWarning as w:


  		





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            logger.warning(str(w))


  		





  
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        af = AffinityPropagation(affinity='precomputed', preference=pref,


  		





  
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                                 damping=0.95, max_iter=2000,


  		





  
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                                 random_state=None).fit(mtx)


  		





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        exemplars.append(clusters[i][af.cluster_centers_indices_[0]])


  		





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    return exemplars


  		





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      b/modules/config_log.py
    
  






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def config_log(label):  # TODO Format log to break line after column 80.


  		





  
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    logging.captureWarnings(True)


  		





  
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    warnings_logger = logging.getLogger("py.warnings")


  		





  
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    logger = logging.getLogger(label)


  		





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    logger.setLevel(logging.INFO)


  		





  
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    log_handler = logging.FileHandler('dockonsurf.log', mode='w')


  		





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    log_handler.setLevel(logging.INFO)


  		





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    log_format = logging.Formatter(fmt='%(asctime)s-%(levelname)s: %(message)s',


  		





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                                   datefmt='%d-%b-%y %H:%M:%S')


  		





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    log_handler.setFormatter(log_format)


  		





  
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    logger.addHandler(log_handler)


  		





  
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    warnings_logger.addHandler(log_handler)


  		





  
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    return logger


  		












  

    
      b/modules/utilities.py
    
  






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import logging


  		





  
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logger = logging.getLogger('DockOnSurf')


  		





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        return return_val


  		





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    finally:


  		





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        if isinstance(err, BaseException):


  		





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            raise err


  		





  
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            raise err


  		












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