Source Code for Package mvpa.base

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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 mvpa.base.config import ConfigManager 
 27  from mvpa.base.verbosity import LevelLogger, OnceLogger 
 28   
 29  # 
 30  # Setup verbose and debug outputs 
 31  # 
 32 -class _SingletonType(type): 
 33      """Simple singleton implementation adjusted from 
 34      http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/412551 
 35      """ 
 36 -    def __init__(mcs, *args): 
 37          type.__init__(mcs, *args) 
 38          mcs._instances = {} 
 39   
 40 -    def __call__(mcs, sid, instance, *args): 
 41          if not sid in mcs._instances: 
 42              mcs._instances[sid] = instance 
 43          return mcs._instances[sid] 
 44   
 45 -class __Singleton: 
 46      """To ensure single instance of a class instantiation (object) 
 47   
 48      """ 
 49   
 50      __metaclass__ = _SingletonType 
 51 -    def __init__(self, *args): 
 52          pass 
 53      # Provided __call__ just to make silly pylint happy 
 54 -    def __call__(self): 
 55          raise NotImplementedError 
 56   
 57  # 
 58  # As the very first step: Setup configuration registry instance and 
 59  # read all configuration settings from files and env variables 
 60  # 
 61  cfg = __Singleton('cfg', ConfigManager()) 
 62   
 63  verbose = __Singleton("verbose", LevelLogger( 
 64      handlers = cfg.get('verbose', 'output', default='stdout').split(','))) 
 65   
 66  # Not supported/explained/used by now since verbose(0, is to print errors 
 67  #error = __Singleton("error", LevelLogger( 
 68  #    handlers=environ.get('MVPA_ERROR_OUTPUT', 'stderr').split(','))) 
 69   
 70  # Levels for verbose 
 71  # 0 -- nothing besides errors 
 72  # 1 -- high level stuff -- top level operation or file operations 
 73  # 2 -- cmdline handling 
 74  # 3 -- 
 75  # 4 -- computation/algorithm relevant thingies 
 76   
 77  # Lets check if environment can tell us smth 
 78  if cfg.has_option('general', 'verbose'): 
 79      verbose.level = cfg.getint('general', 'verbose') 
 80   
 81   
 82 -class WarningLog(OnceLogger): 
 83      """Logging class of messsages to be printed just once per each message 
 84   
 85      """ 
 86   
 87 -    def __init__(self, btlevels=10, btdefault=False, 
 88                   maxcount=1, *args, **kwargs): 
 89          """Define Warning logger. 
 90   
 91          It is defined by 
 92            btlevels : int 
 93              how many levels of backtrack to print to give a hint on WTF 
 94            btdefault : bool 
 95              if to print backtrace for all warnings at all 
 96            maxcount : int 
 97              how many times to print each warning 
 98          """ 
 99          OnceLogger.__init__(self, *args, **kwargs) 
100          self.__btlevels = btlevels 
101          self.__btdefault = btdefault 
102          self.__maxcount = maxcount 
103          self.__explanation_seen = False 
104   
105   
106 -    def __call__(self, msg, bt=None): 
107          import traceback 
108          if bt is None: 
109              bt = self.__btdefault 
110          tb = traceback.extract_stack(limit=2) 
111          msgid = repr(tb[-2])         # take parent as the source of ID 
112          fullmsg = "WARNING: %s" % msg 
113          if not self.__explanation_seen: 
114              self.__explanation_seen = True 
115              fullmsg += "\n * Please note: warnings are "  + \ 
116                    "printed only once, but underlying problem might " + \ 
117                    "occur many times *" 
118          if bt and self.__btlevels > 0: 
119              fullmsg += "Top-most backtrace:\n" 
120              fullmsg += reduce(lambda x, y: x + "\t%s:%d in %s where '%s'\n" % \ 
121                                y, 
122                                traceback.extract_stack(limit=self.__btlevels), 
123                                "") 
124   
125          OnceLogger.__call__(self, msgid, fullmsg, self.__maxcount) 
126   
127   
128 -    def _setMaxCount(self, value): 
129          """Set maxcount for the warning""" 
130          self.__maxcount = value 
131   
132      maxcount = property(fget=lambda x:x.__maxcount, fset=_setMaxCount) 
133   
134  # XXX what is 'bt'? Maybe more verbose name? 
135  if cfg.has_option('warnings', 'bt'): 
136      warnings_btlevels = cfg.getint('warnings', 'bt') 
137      warnings_bt = True 
138  else: 
139      warnings_btlevels = 10 
140      warnings_bt = False 
141   
142  if cfg.has_option('warnings', 'count'): 
143      warnings_maxcount = cfg.getint('warnings', 'count') 
144  else: 
145      warnings_maxcount = 1 
146   
147  warning = WarningLog( 
148      handlers={ 
149          False: cfg.get('warnings', 'output', default='stdout').split(','), 
150          True: []}[cfg.getboolean('warnings', 'suppress', default=False)], 
151      btlevels=warnings_btlevels, 
152      btdefault=warnings_bt, 
153      maxcount=warnings_maxcount 
154      ) 
155   
156   
157  if __debug__: 
158      from mvpa.base.verbosity import DebugLogger 
159      # NOTE: all calls to debug must be preconditioned with 
160      # if __debug__: 
161   
162      debug = __Singleton("debug", DebugLogger( 
163          handlers=cfg.get('debug', 'output', default='stdout').split(','))) 
164   
165      # set some debugging matricses to report 
166      # debug.registerMetric('vmem') 
167   
168      # List agreed sets for debug 
169      debug.register('PY',   "No suppression of various warnings (numpy, scipy) etc.") 
170      debug.register('DBG',  "Debug output itself") 
171      debug.register('DOCH', "Doc helpers") 
172      debug.register('INIT', "Just sequence of inits") 
173      debug.register('RANDOM', "Random number generation") 
174      debug.register('EXT',  "External dependencies") 
175      debug.register('EXT_', "External dependencies (verbose)") 
176      debug.register('TEST', "Debug unittests") 
177      debug.register('MODULE_IN_REPR', "Include module path in __repr__") 
178      debug.register('ID_IN_REPR', "Include id in __repr__") 
179      debug.register('CMDLINE', "Handling of command line parameters") 
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('SOM',  "Self-organizing-maps (SOM)") 
188      debug.register('IRELIEF', "Various I-RELIEFs") 
189      debug.register('SA_',  "Sensitivity analyzers (verbose)") 
190      debug.register('PSA',  "Perturbation analyzer call") 
191      debug.register('RFEC', "Recursive Feature Elimination call") 
192      debug.register('RFEC_', "Recursive Feature Elimination call (verbose)") 
193      debug.register('IFSC', "Incremental Feature Search call") 
194      debug.register('DS',   "*Dataset") 
195      debug.register('DS_NIFTI', "NiftiDataset(s)") 
196      debug.register('DS_',  "*Dataset (verbose)") 
197      debug.register('DS_ID',   "ID Datasets") 
198      debug.register('DS_STATS',"Datasets statistics") 
199      debug.register('SPL',   "*Splitter") 
200   
201      debug.register('TRAN',  "Transformers") 
202      debug.register('TRAN_', "Transformers (verbose)") 
203   
204      # CHECKs 
205      debug.register('CHECK_DS_SELECT', 
206                     "Check in dataset.select() for sorted and unique indexes") 
207      debug.register('CHECK_DS_SORTED', "Check in datasets for sorted") 
208      debug.register('CHECK_IDS_SORTED', 
209                     "Check for ids being sorted in mappers") 
210      debug.register('CHECK_TRAINED', 
211                     "Checking in checking if clf was trained on given dataset") 
212      debug.register('CHECK_RETRAIN', "Checking in retraining/retesting") 
213      debug.register('CHECK_STABILITY', "Checking for numerical stability") 
214   
215      debug.register('MAP',   "*Mapper") 
216      debug.register('MAP_',  "*Mapper (verbose)") 
217   
218      debug.register('COL',  "Generic Collectable") 
219      debug.register('UATTR', "Attributes with unique") 
220      debug.register('ST',   "State") 
221      debug.register('STV',  "State Variable") 
222      debug.register('COLR', "Collector for states and classifier parameters") 
223      debug.register('ES',   "Element selectors") 
224   
225      debug.register('CLF',    "Base Classifiers") 
226      debug.register('CLF_',   "Base Classifiers (verbose)") 
227      #debug.register('CLF_TB', 
228      #    "Report traceback in train/predict. Helps to resolve WTF calls it") 
229      debug.register('CLFBST', "BoostClassifier") 
230      #debug.register('CLFBST_TB', "BoostClassifier traceback") 
231      debug.register('CLFBIN', "BinaryClassifier") 
232      debug.register('CLFMC',  "MulticlassClassifier") 
233      debug.register('CLFSPL', "SplitClassifier") 
234      debug.register('CLFFS',  "FeatureSelectionClassifier") 
235      debug.register('CLFFS_', "FeatureSelectionClassifier (verbose)") 
236   
237      debug.register('STAT',   "Statistics estimates") 
238      debug.register('STAT_',  "Statistics estimates (verbose)") 
239      debug.register('STAT__', "Statistics estimates (very verbose)") 
240   
241      debug.register('FS',     "FeatureSelections") 
242      debug.register('FS_',    "FeatureSelections (verbose)") 
243      debug.register('FSPL',   "FeatureSelectionPipeline") 
244   
245      debug.register('SVM',    "SVM") 
246      debug.register('SVM_',   "SVM (verbose)") 
247      debug.register('LIBSVM', "Internal libsvm output") 
248   
249      debug.register('SMLR',    "SMLR") 
250      debug.register('SMLR_',   "SMLR verbose") 
251   
252      debug.register('LARS',    "LARS") 
253      debug.register('LARS_',   "LARS (verbose)") 
254   
255      debug.register('ENET',    "ENET") 
256      debug.register('ENET_',   "ENET (verbose)") 
257   
258      debug.register('GLMNET',    "GLMNET") 
259      debug.register('GLMNET_',   "GLMNET (verbose)") 
260   
261      debug.register('GPR',     "GPR") 
262      debug.register('GPR_WEIGHTS', "Track progress of GPRWeights computation") 
263      debug.register('KERNEL',  "Kernels module") 
264      debug.register('MOD_SEL', "Model Selector (also makes openopt's iprint=0)") 
265      debug.register('OPENOPT', "OpenOpt toolbox verbose (iprint=1)") 
266   
267      debug.register('SG',  "PyMVPA SG wrapping") 
268      debug.register('SG_', "PyMVPA SG wrapping verbose") 
269      debug.register('SG__', "PyMVPA SG wrapping debug") 
270      debug.register('SG_SVM', "Internal shogun debug output for SVM itself") 
271      debug.register('SG_FEATURES', "Internal shogun debug output for features") 
272      debug.register('SG_LABELS', "Internal shogun debug output for labels") 
273      debug.register('SG_KERNELS', "Internal shogun debug output for kernels") 
274      debug.register('SG_PROGRESS', 
275                     "Internal shogun progress bar during computation") 
276   
277      debug.register('IOH',    "IO Helpers") 
278      debug.register('IO_HAM', "Hamster") 
279      debug.register('CM',   "Confusion matrix computation") 
280      debug.register('ROC',  "ROC analysis") 
281      debug.register('CROSSC', "Cross-validation call") 
282      debug.register('CERR', "Various ClassifierErrors") 
283   
284      debug.register('ATL',    "Atlases") 
285      debug.register('ATL_',   "Atlases (verbose)") 
286      debug.register('ATL__',  "Atlases (very verbose)") 
287   
288      # Lets check if environment can tell us smth 
289      if cfg.has_option('general', 'debug'): 
290          debug.setActiveFromString(cfg.get('general', 'debug')) 
291   
292      # Lets check if environment can tell us smth 
293      if cfg.has_option('debug', 'metrics'): 
294          debug.registerMetric(cfg.get('debug', 'metrics').split(",")) 
295   
296   
297   
298  if __debug__: 
299      debug('INIT', 'mvpa.base end') 
300