Source Code for Package mvpa.base

  1  #emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*- 
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  4  # 
  5  #   See COPYING file distributed along with the PyMVPA package for the 
  6  #   copyright and license terms. 
  7  # 
  8  ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ## 
  9  """Base functionality of PyMVPA 
 10   
 11  Module Organization 
 12  =================== 
 13   
 14  mvpa.base module contains various modules which are used through out 
 15  PyMVPA code, and are generic building blocks 
 16   
 17  .. packagetree:: 
 18     :style: UML 
 19   
 20  :group Basic: externals, config, verbosity, dochelpers 
 21  """ 
 22   
 23  __docformat__ = 'restructuredtext' 
 24   
 25   
 26  from sys import stdout, stderr 
 27   
 28  from mvpa.base.config import ConfigManager 
 29  from mvpa.base.verbosity import LevelLogger, OnceLogger, Logger 
 30   
 31  # 
 32  # Setup verbose and debug outputs 
 33  # 
 34 -class _SingletonType(type): 
 35      """Simple singleton implementation adjusted from 
 36      http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/412551 
 37      """ 
 38 -    def __init__(mcs, *args): 
 39          type.__init__(mcs, *args) 
 40          mcs._instances = {} 
 41   
 42 -    def __call__(mcs, sid, instance, *args): 
 43          if not sid in mcs._instances: 
 44              mcs._instances[sid] = instance 
 45          return mcs._instances[sid] 
 46   
 47 -class __Singleton: 
 48      """To ensure single instance of a class instantiation (object) 
 49   
 50      """ 
 51   
 52      __metaclass__ = _SingletonType 
 53 -    def __init__(self, *args): 
 54          pass 
 55      # Provided __call__ just to make silly pylint happy 
 56 -    def __call__(self): 
 57          raise NotImplementedError 
 58   
 59  # 
 60  # As the very first step: Setup configuration registry instance and 
 61  # read all configuration settings from files and env variables 
 62  # 
 63  cfg = __Singleton('cfg', ConfigManager()) 
 64   
 65  verbose = __Singleton("verbose", LevelLogger( 
 66      handlers = cfg.get('verbose', 'output', default='stdout').split(','))) 
 67   
 68  # Not supported/explained/used by now since verbose(0, is to print errors 
 69  #error = __Singleton("error", LevelLogger( 
 70  #    handlers=environ.get('MVPA_ERROR_OUTPUT', 'stderr').split(','))) 
 71   
 72  # Levels for verbose 
 73  # 0 -- nothing besides errors 
 74  # 1 -- high level stuff -- top level operation or file operations 
 75  # 2 -- cmdline handling 
 76  # 3 -- 
 77  # 4 -- computation/algorithm relevant thingies 
 78   
 79  # Lets check if environment can tell us smth 
 80  if cfg.has_option('general', 'verbose'): 
 81      verbose.level = cfg.getint('general', 'verbose') 
 82   
 83   
 84 -class WarningLog(OnceLogger): 
 85      """Logging class of messsages to be printed just once per each message 
 86   
 87      """ 
 88   
 89 -    def __init__(self, btlevels=10, btdefault=False, 
 90                   maxcount=1, *args, **kwargs): 
 91          """Define Warning logger. 
 92   
 93          It is defined by 
 94            btlevels : int 
 95              how many levels of backtrack to print to give a hint on WTF 
 96            btdefault : bool 
 97              if to print backtrace for all warnings at all 
 98            maxcount : int 
 99              how many times to print each warning 
100          """ 
101          OnceLogger.__init__(self, *args, **kwargs) 
102          self.__btlevels = btlevels 
103          self.__btdefault = btdefault 
104          self.__maxcount = maxcount 
105          self.__explanation_seen = False 
106   
107   
108 -    def __call__(self, msg, bt=None): 
109          import traceback 
110          if bt is None: 
111              bt = self.__btdefault 
112          tb = traceback.extract_stack(limit=2) 
113          msgid = repr(tb[-2])         # take parent as the source of ID 
114          fullmsg = "WARNING: %s" % msg 
115          if not self.__explanation_seen: 
116              self.__explanation_seen = True 
117              fullmsg += "\n * Please note: warnings are "  + \ 
118                    "printed only once, but underlying problem might " + \ 
119                    "occur many times *" 
120          if bt and self.__btlevels > 0: 
121              fullmsg += "Top-most backtrace:\n" 
122              fullmsg += reduce(lambda x, y: x + "\t%s:%d in %s where '%s'\n" % \ 
123                                y, 
124                                traceback.extract_stack(limit=self.__btlevels), 
125                                "") 
126   
127          OnceLogger.__call__(self, msgid, fullmsg, self.__maxcount) 
128   
129   
130 -    def _setMaxCount(self, value): 
131          """Set maxcount for the warning""" 
132          self.__maxcount = value 
133   
134      maxcount = property(fget=lambda x:x.__maxcount, fset=_setMaxCount) 
135   
136  # XXX what is 'bt'? Maybe more verbose name? 
137  if cfg.has_option('warnings', 'bt'): 
138      warnings_btlevels = cfg.getint('warnings', 'bt') 
139      warnings_bt = True 
140  else: 
141      warnings_btlevels = 10 
142      warnings_bt = False 
143   
144  if cfg.has_option('warnings', 'count'): 
145      warnings_maxcount = cfg.getint('warnings', 'count') 
146  else: 
147      warnings_maxcount = 1 
148   
149  warning = WarningLog( 
150      handlers={ 
151          False: cfg.get('warnings', 'output', default='stdout').split(','), 
152          True: []}[cfg.getboolean('warnings', 'suppress', default=False)], 
153      btlevels=warnings_btlevels, 
154      btdefault=warnings_bt, 
155      maxcount=warnings_maxcount 
156      ) 
157   
158   
159  if __debug__: 
160      from mvpa.base.verbosity import DebugLogger 
161      # NOTE: all calls to debug must be preconditioned with 
162      # if __debug__: 
163   
164      debug = __Singleton("debug", DebugLogger( 
165          handlers=cfg.get('debug', 'output', default='stdout').split(','))) 
166   
167      # set some debugging matricses to report 
168      # debug.registerMetric('vmem') 
169   
170      # List agreed sets for debug 
171      debug.register('DBG',  "Debug output itself") 
172      debug.register('DOCH', "Doc helpers") 
173      debug.register('INIT', "Just sequence of inits") 
174      debug.register('RANDOM', "Random number generation") 
175      debug.register('EXT',  "External dependencies") 
176      debug.register('EXT_', "External dependencies (verbose)") 
177      debug.register('TEST', "Debug unittests") 
178      debug.register('MODULE_IN_REPR', "Include module path in __repr__") 
179      debug.register('ID_IN_REPR', "Include id in __repr__") 
180   
181      debug.register('DG',   "Data generators") 
182      debug.register('LAZY', "Miscelaneous 'lazy' evaluations") 
183      debug.register('LOOP', "Support's loop construct") 
184      debug.register('PLR',  "PLR call") 
185      debug.register('SLC',  "Searchlight call") 
186      debug.register('SA',   "Sensitivity analyzers") 
187      debug.register('IRELIEF', "Various I-RELIEFs") 
188      debug.register('SA_',  "Sensitivity analyzers (verbose)") 
189      debug.register('PSA',  "Perturbation analyzer call") 
190      debug.register('RFEC', "Recursive Feature Elimination call") 
191      debug.register('RFEC_', "Recursive Feature Elimination call (verbose)") 
192      debug.register('IFSC', "Incremental Feature Search call") 
193      debug.register('DS',   "*Dataset") 
194      debug.register('DS_NIFTI', "NiftiDataset(s)") 
195      debug.register('DS_',  "*Dataset (verbose)") 
196      debug.register('DS_ID',   "ID Datasets") 
197      debug.register('DS_STATS',"Datasets statistics") 
198      debug.register('SPL',   "*Splitter") 
199   
200      debug.register('TRAN',  "Transformers") 
201      debug.register('TRAN_', "Transformers (verbose)") 
202   
203      # CHECKs 
204      debug.register('CHECK_DS_SELECT', 
205                     "Check in dataset.select() for sorted and unique indexes") 
206      debug.register('CHECK_DS_SORTED', "Check in datasets for sorted") 
207      debug.register('CHECK_IDS_SORTED', 
208                     "Check for ids being sorted in mappers") 
209      debug.register('CHECK_TRAINED', 
210                     "Checking in checking if clf was trained on given dataset") 
211      debug.register('CHECK_RETRAIN', "Checking in retraining/retesting") 
212      debug.register('CHECK_STABILITY', "Checking for numerical stability") 
213   
214      debug.register('MAP',   "*Mapper") 
215      debug.register('MAP_',  "*Mapper (verbose)") 
216   
217      debug.register('COL',  "Generic Collectable") 
218      debug.register('UATTR', "Attributes with unique") 
219      debug.register('ST',   "State") 
220      debug.register('STV',  "State Variable") 
221      debug.register('COLR', "Collector for states and classifier parameters") 
222      debug.register('ES',   "Element selectors") 
223   
224      debug.register('CLF',    "Base Classifiers") 
225      debug.register('CLF_',   "Base Classifiers (verbose)") 
226      #debug.register('CLF_TB', 
227      #    "Report traceback in train/predict. Helps to resolve WTF calls it") 
228      debug.register('CLFBST', "BoostClassifier") 
229      #debug.register('CLFBST_TB', "BoostClassifier traceback") 
230      debug.register('CLFBIN', "BinaryClassifier") 
231      debug.register('CLFMC',  "MulticlassClassifier") 
232      debug.register('CLFSPL', "SplitClassifier") 
233      debug.register('CLFFS',  "FeatureSelectionClassifier") 
234      debug.register('CLFFS_', "FeatureSelectionClassifier (verbose)") 
235   
236      debug.register('STAT',   "Statistics estimates") 
237      debug.register('STAT_',  "Statistics estimates (verbose)") 
238      debug.register('STAT__', "Statistics estimates (very verbose)") 
239   
240      debug.register('FS',     "FeatureSelections") 
241      debug.register('FS_',    "FeatureSelections (verbose)") 
242      debug.register('FSPL',   "FeatureSelectionPipeline") 
243   
244      debug.register('SVM',    "SVM") 
245      debug.register('SVM_',   "SVM (verbose)") 
246      debug.register('LIBSVM', "Internal libsvm output") 
247   
248      debug.register('SMLR',    "SMLR") 
249      debug.register('SMLR_',   "SMLR verbose") 
250   
251      debug.register('LARS',    "LARS") 
252      debug.register('LARS_',   "LARS (verbose)") 
253   
254      debug.register('GPR',     "GPR") 
255      debug.register('GPR_WEIGHTS', "Track progress of GPRWeights computation") 
256      debug.register('KERNEL',  "Kernels module") 
257      debug.register('MOD_SEL', "Model Selector (also makes openopt's iprint=0)") 
258      debug.register('OPENOPT', "OpenOpt toolbox verbose (iprint=1)") 
259   
260      debug.register('SG',  "PyMVPA SG wrapping") 
261      debug.register('SG_', "PyMVPA SG wrapping verbose") 
262      debug.register('SG__', "PyMVPA SG wrapping debug") 
263      debug.register('SG_SVM', "Internal shogun debug output for SVM itself") 
264      debug.register('SG_FEATURES', "Internal shogun debug output for features") 
265      debug.register('SG_LABELS', "Internal shogun debug output for labels") 
266      debug.register('SG_KERNELS', "Internal shogun debug output for kernels") 
267      debug.register('SG_PROGRESS', 
268                     "Internal shogun progress bar during computation") 
269   
270      debug.register('IOH',    "IO Helpers") 
271      debug.register('IO_HAM', "Hamster") 
272      debug.register('CM',   "Confusion matrix computation") 
273      debug.register('ROC',  "ROC analysis") 
274      debug.register('CROSSC',"Cross-validation call") 
275      debug.register('CERR', "Various ClassifierErrors") 
276   
277      debug.register('ATL',    "Atlases") 
278      debug.register('ATL_',   "Atlases (verbose)") 
279      debug.register('ATL__',  "Atlases (very verbose)") 
280   
281      # Lets check if environment can tell us smth 
282      if cfg.has_option('general', 'debug'): 
283          debug.setActiveFromString(cfg.get('general', 'debug')) 
284   
285      # Lets check if environment can tell us smth 
286      if cfg.has_option('debug', 'metrics'): 
287          debug.registerMetric(cfg.get('debug', 'metrics').split(",")) 
288   
289   
290   
291  if __debug__: 
292      debug('INIT', 'mvpa.base end') 
293