Exemple #1
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 def set(self, address):
     """
     This parameter stores a biovars.Address object.
      
     """
     if isinstance(address, basestring):
         address = self._p._dataset.experiment.variables.get(address)
     
     if address is None or isaddress(address):
         Param.set(self, address)
     else:
         Param.set(self, asaddress(address))
Exemple #2
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    def initWithSegments_over_(self, segments, over, exclude=None,
                               func=None, mp=False, **kwargs):
        """
        kwargs:
         func=None:     is initially applied to the whole data cube; can be string
                        'phase'--> x/abs(x)
                        else: eval
         mp=True:       use multiprocessing
         v=False        verbose mode
         
         """
        raise NotImplementedError("TODO: get this method out of here!")
        # interpret func
        if func == None:
            def func(x):
                return x
        elif func=='phase':
            def func(x):
                return x/abs(x)
        elif type(func)==str:
            func = eval(func)
        #logging.debug( 'func'+str(func) )
            
        # start
        t0 = time.time()
        
        self._properties.update(kwargs)
        kwargs['out']='data'
        
        if exclude:
            over = over!=exclude
        else:
            over = asaddress(over)
        
        segs_sorted = over.sort(segments)
        
        slist = segs_sorted.keys()
        slist.sort()
        self._properties.update({'slist':slist,
                                'svar':over,
                                'avars': '???',
                                'address': '???'})
        
        # determine shape 
        seg1 = segs_sorted[slist[0]][0]
        data1 = seg1.subdata(**kwargs)
        shape = data1.shape
        
        # create empty array
        self._data = np.empty(shape + (len(slist),))
        
        # collect data
        for i, s in enumerate(slist):
            segs = segs_sorted[s]
            assert len(segs) > 0, "No data for %s"%str(s)
            data = np.empty(shape + (len(segs),))
            for j, seg in enumerate(segs):
                segdata = seg.subdata(**kwargs)
                if shape == segdata.shape:
                    data[...,j] = segdata
                else:
                    msg = "'{n}' shape {s1} does not match the shape {s}"
                    msg.format(n=seg.name, s1=segdata.shape, s=shape)
                    raise ValueError(msg)

            self._data[...,i] = data.mean(-1)
        

        # info
        #segInfo = ' '.join(['%s:%s'%(k, str(len(v)).rjust(3)) for k,v in segments.iteritems()])
        print ' '.join([self.name[:10], 'over', over.name[:10], 
                        ": time %.1f s"%(time.time()-t0)])
        return self
Exemple #3
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    def collectstats(self, cells, over, mask=None, mp=False, pool=None, 
                     save='ask', **kwargs):
        """
        cells: address; statistics are extracted for each valid combination of
               values in this address
        over: variable specifying the cases within the cells (usually subject)
        
        - adds statistics segment for all values of cells in address to self.stats
        - forwards statsForAddress_over_ kwargs
        
        kwargs:
        mp  False
            'outer' Spawn one process for each StatsSegment 
            True    do statsSegments serially but use multiple processes in
                    StatsSegment.initWithSegments_over_
                    
        **kwargs: 
                    
        """
        t0=time.time()
        msg = "--> Collecting Statistics for {0} over {1}, mp={2}"
        print msg.format(cells.name, over.name, str(mp))
        
        if len(self.stats) > 0:
            msg = "self.stats currently contains the following statistics: %s"%str(self.stats.keys())
            if ui.ask(title="Clear existing statistics?",
                      message=msg):
                self.stats = {}
        
        cells = biovars.asaddress(cells)
        if mask == None:
            all_segments = self.segments
        else:
            all_segments = mask.filter(self.segments)
        segs_sorted = cells.sort(all_segments)
        
        # progress bar
#        n = len(segs_sorted)
#        i = 0
#        prog_ttl = "Collecting statistics for {n} cells".format(n=n)
#        prog_msg = "{name} ({i} of {n}) done...".format(name='{name}', n=n, i='{i}')
#        prog = ui.progress(i_max=n,
#                           title=prog_ttl,
#                           message=prog_msg.format(name='', i=0))
        
        label_dic = cells.short_labels()
        
        for address, segs in segs_sorted.iteritems():
            label = label_dic[address]
#            color = cells.color_for_value(key)
            s = StatsSegment(self.properties, name=label)#, color=color)
            s.initWithSegments_over_(segs, over, **kwargs)

            # make sure label is a valid name
            if label[0].isalpha():
                valid_label = label
            else:
                valid_label = 'c' + label
            
            self.stats[valid_label] = s
            
            # close all files
            self._store.close()
        
#        # progress bar
#            if prog:
#                i += 1
#                prog.advance(prog_msg.format(name=valid_label, i=i))
#        if prog:
#            prog.terminate()


#        if mp=='outer':
#            for key, label in cells.dictionary.iteritems():
#                self.stats[label] = self.stats[label].recv()
        print '\n'.join(["---",
                         "Finished after %s"%(time.time()-t0),
                         "Dataset now contains stats: %s"%self.stats.keys()])
        
        # save the experiment
        if save == 'ask':
            msg = "Save Experiment with newly added statistics segments?"
            save = ui.ask(title="Save Experiment?", message=msg)
        if save:
            self.experiment.save()
Exemple #4
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 def set_cov(self, covs):
     "list of variables"
     if covs:
         self._covs = _vars.asaddress(covs).keys()
     else:
         self._covs = []