Beispiel #1
0
def setup():
    create_files('myexperiment', dir=DIRPATH, prm=prm, prb=prb)

    # Open the files.
    files = open_files('myexperiment', dir=DIRPATH, mode='a')

    # Add data.
    add_recording(files,
                  sample_rate=sample_rate,
                  nchannels=nchannels)
    add_cluster_group(files, channel_group_id='0', id='0', name='Noise')
    add_cluster(files, channel_group_id='0',)

    # Close the files
    close_files(files)
def create_files_Experiment(filename, DIRPATH, prm, prb):
    #files_exist is a function in SD2.dataio.kwik
    if not files_exist(filename, dir=DIRPATH):
        create_files(filename, dir=DIRPATH, prm=prm, prb=prb)
    
        # Open the files.
        files = open_files(filename, dir=DIRPATH, mode='a')
    
        # Add data.
        add_recording(files, 
                  sample_rate=prm['sample_rate'],
                  nchannels=prm['nchannels'])
        add_cluster_group(files, channel_group_id='0', id='0', name='Noise')
        add_cluster(files, channel_group_id='0',)
    
        # Close the files
        close_files(files)
def learn_data_grid_general(hybdatadict, SDparams,prb,detectioncrit,supervised_params,addtokwik):  
    '''
       If addtokwik == True, then the clusterings are also stored in the .kwik file
       
       
            
       calls learn_data() for various values of the
       grids and also the function compute_errors()
    
       Writes output as clusterings labelled by Hash(svmparams) of the grid in 
       Hash(hybdatadict)_Hash(sdparams)_Hash(detectioncrit)_Hash(supervised_params).kwik
       using write_kwik(hybdatadict,sdparams,detectioncrit,svmparams,confusion_test,confusion_train)
       the new .kwik format can store multiple clusterings.
    
       supervised_params consists of the following quantities: 
       supervised_params = {'numfirstspikes': 200000,'kernel': 'rbf','grid_C': [1,100000,0.00001], 'grid_weights': listofweights
       ,gammagrid : [1e-5, 0.001, 0.1, 1, 10, 1000, 100000], cross_param :  2, 
       PCAS : 3, subvector: None}
    '''
    #----------------------------------------------------------
    
    argPLDG = [hybdatadict, SDparams,prb,detectioncrit,supervised_params]
    if ju.is_cached(pre_learn_data_grid,*argPLDG):
        print 'Yes, pre_learn_data_grid has been run \n'    
    else:
        print 'Running pre_learn_data_grid(hybdatadict, SDparams,prb,detectioncrit,supervised_params), \n you have not run it yet' 
        
    hash_hyb_SD,classweights,scaled_fets, target = pre_learn_data_grid(hybdatadict, SDparams,prb,detectioncrit,supervised_params)
    
    DIRPATH = hybdatadict['output_path']
    
    number_of_weights = len(classweights)
    
    numspikes = scaled_fets.shape[0]
    cross_valid = do_cross_validation_shuffle(numspikes,supervised_params['cross_param'])
    
    #print cross_valid
    
    #do_supervised(supervised_params,

    #'grid_C': [1,100000,0.00001], number_cvalues = 3
    number_cvalues = len(supervised_params['grid_C'])
    
    #number_support_vectors = {}
    weights_clu_test = np.zeros((number_cvalues,number_of_weights,numspikes,2),dtype=np.int32)
    weights_clu_train = np.zeros((number_cvalues,number_of_weights, numspikes,2),dtype=np.int32)
    cludict= {(0,0):1, (0,1):2, (1,0):3, (1,1):4}
    # (prediction, groundtruth)
    #(0,0) TN, (0,1) FN ,(1,0) FP ,(1,1) TP
    testclu = np.zeros((number_cvalues,number_of_weights,numspikes),dtype=np.int32)
    trainclu = np.zeros((number_cvalues,number_of_weights,numspikes),dtype=np.int32)
    
    
    
    for c, Cval in enumerate(supervised_params['grid_C']):
        preds = {}
        preds_train = {}
                    ##Defined to avoid: TypeError: unhashable type: 'numpy.ndarray', something about dictionaries
                    #testclu_pre = np.zeros((number_of_weights,numspikes),dtype=np.int32)
                    #trainclu_pre = np.zeros((number_of_weights,numspikes),dtype=np.int32)
        for i, (weights) in enumerate(classweights):
            for j, (train, test) in enumerate(cross_valid):
                if supervised_params['kernel'] == 'poly':
                    preds[i,j], preds_train[i,j]= do_supervised_learning(test, train,Cval, supervised_params['kernel'], scaled_fets, target,classweights[i])
                else:#radial kernel, only allow a single gamma value at a time
                    preds[i,j], preds_train[i,j]= do_supervised_learning_radial(test, train,Cval, supervised_params['kernel'],supervised_params['gamma'], scaled_fets, target,classweights[i])    
                
                
                
                print 'Computed ', classweights[i]
                #Used later to make equivalent to 4 seasons clu file
                weights_clu_test[c,i,test,0] = preds[i,j]
                weights_clu_test[c,i,test,1] = target[test]
                
                
                #Used later to make equivalent to 4 seasons clu file but for the training set
                weights_clu_train[c,i,train,0] = preds_train[i,j]
                weights_clu_train[c,i,train,1] = target[train]
                
    
            #Make 4 seasons clu file equivalent
            for k in np.arange(numspikes):
                testclu[c,i,k] = cludict[tuple(weights_clu_test[c,i,k,:])]
                trainclu[c,i,k] = cludict[tuple(weights_clu_train[c,i,k,:])]
            
#            supervisedinputdict = {'test':test, 'train':train, 'Cval': Cval, 'kernel': supervised_params['kernel'], 'scaled_fets':scaled_fets, 'target', target, 'classweights': classweigths
            
            
            #Add clusterings to .kwik file
            supervisedparamshash = None #if addtokwik = False otherwise crashes
            if addtokwik:
                kwikfiles = open_files(hash_hyb_SD,dir=DIRPATH, mode='a')
                supervisedparamshash = hash_utils.hash_dictionary_md5(supervised_params)
                supervisedhashname = supervisedparamshash + '_' + repr(c) + '_' + repr(i) 
                add_clustering(kwikfiles,name = supervisedhashname + 'test', spike_clusters=testclu[c,i,:] )    
                add_clustering(kwikfiles,name = supervisedhashname + 'train', spike_clusters=trainclu[c,i,:] )     
                close_files(kwikfiles)
                #print 'testclu[',c,',',i,',',k,']=',testclu[c,i,k]
    
   # for c, Cval in enumerate(supervised_params['grid_C']):                    
   #     kwikfilename = DIRPATH + hash_hyb_SD + '.kwik'
   #     supervisedhashname = hash_utils.hash_dictionary_md5(detectioncrit)
   #     add_clustering_kwik(kwikfilename, detectedgroundtruth, detectionhashname)        
   
      
                
   ####Train and test look like this for 2-fold cross validation and 200 spikes
  
   #         j =  0  train =  [100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117
   #      118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135
   #      136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153
   #      154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171
   #      172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189
   #      190 191 192 193 194 195 196 197 198 199]  
   #      test =  [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
   #      25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
   #      50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74
   #      75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99]
   #     j =  1  train =  [ 0  1  2  3  4  5  6  7  8  9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
   #      25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49
   #      50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74
   #      75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99]  
   #      test =  [100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117
   #      118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135
   #      136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153
   #      154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171
   #      172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189
   #      190 191 192 193 194 195 196 197 198 199] 
    
        
    return supervisedparamshash, classweights, testclu, trainclu
def test_detection_algorithm(hybdatadict, SDparams,prb, detectioncrit):
    '''
     It will query whether the cached function: 
    hybridata_creation_lib.create_hybrid_kwdfile(hybdatadict), 
    has been called already with those arguments using `joblib_utils.is_cached`,
     If it has, it calls it to obtain creation_groundtruth.
     else if the hybrid dataset does not exist, it will raise an Error. 
       creation_groundtruth consists of the equivalent to the old: 
     GroundtruthResfile,GroundtruthClufile,... (i.e. the times and the cluster labels for the
     added hybrid spikes.
     detection criteria include: 
      allowed_discrepancy,CSthreshold
       This function will call SpikeSimilarityMeasure(a,b)
         and output the file: Hash(hybdatadict)_Hash(sdparams)_Hash(detectioncrit).kwik  
       It will return detcrit_groundtruth, the groundtruth relative to the criteria, detectioncrit. 
       This will be an ordered dictionary so that hashing can work!'''
    
    
    if ju.is_cached(hcl.create_hybrid_kwdfile,hybdatadict):
        print 'Yes, this hybrid dataset exists, I shall now check if you have run SD \n'
    
    meanwaveform,kwdoutputname, creation_groundtruth, amplitude = hcl.create_hybrid_kwdfile(hybdatadict)
    
    #Take the means of the binary donor masks of the donor cluster 
    binmeanmask = hcl.make_average_datamask_from_mean(hybdatadict, fmask= False)
    
    argSD = [hybdatadict,SDparams,prb]
    if ju.is_cached(rsd.run_spikedetekt,*argSD):
        print 'Yes, SD has been run \n'
        hash_hyb_SD = rsd.run_spikedetekt(hybdatadict,SDparams,prb)
    else:
        print 'You need to run Spikedetekt before attempting to analyse results ' 
    
    DIRPATH = hybdatadict['output_path']
    with Experiment(hash_hyb_SD, dir= DIRPATH, mode='a') as expt:
        res_int= expt.channel_groups[0].spikes.time_samples
        res_frac  = expt.channel_groups[0].spikes.time_fractional
        res_int_arr = res_int[:] 
        res_frac_arr = res_frac[:]
        detected_times = res_int_arr + res_frac_arr
        #Masks
        fmask = expt.channel_groups[0].spikes.features_masks
        
        #Spikes within time window
        existencewin = np.zeros_like(creation_groundtruth)
        
        #Mean binary mask for hybrid cluster
        if 'manual_meanmask' in detectioncrit.keys():
            binmeanmask = detectioncrit['manual_meanmask']
        else:    
            binmeanmask = hcl.make_average_datamask_from_mean(hybdatadict, fmask= False)
        
        indices_in_timewindow = hash_utils.order_dictionary({})
        #indices_in_timewindow = {0 (this is the 1st hybrid spike): (array([0, 1, 3]),),
        #1: (array([89, 90]),),
        #2: (array([154, 156, 157]),),
        #3: (array([191]),),
        #4: (array([259, 260, 261]),),
        
        num_spikes_in_timewindow = hash_utils.order_dictionary({})
        
        CauchySchwarz = hash_utils.order_dictionary({})
        detected = hash_utils.order_dictionary({})
        NumHybSpikes = creation_groundtruth.shape[0]
        trivialmainclustering = np.zeros_like(detected_times)
        detectedgroundtruth = np.zeros_like(detected_times)
        print detectedgroundtruth.shape
        for k in np.arange(NumHybSpikes):
            list_of_differences = np.zeros((detected_times.shape[0]))
            list_of_differences[:]= detected_times[:] - creation_groundtruth[k] 
            
            indices_in_timewindow[k] = np.nonzero(np.absolute(list_of_differences)<=detectioncrit['allowed_discrepancy'])
            num_spikes_in_timewindow[k] = indices_in_timewindow[k][0].shape[0]
            for j in np.arange(num_spikes_in_timewindow[k]):
                CauchySchwarz[k,j] = SpikeSimilarityMeasure(fmask[indices_in_timewindow[k][0][j],:,1],binmeanmask[0:3*hybdatadict['numchannels']])
                if CauchySchwarz[k,j] > detectioncrit['CSthreshold']:
                    detected[k,j] = 1    
                else:
                    detected[k,j] = 0       
                detectedgroundtruth[indices_in_timewindow[k][0][j]]= detected[k,j]
    #Store detectedgroundtruth in a clustering
    
    detectionhashname = hash_utils.hash_dictionary_md5(detectioncrit)
    #kwikfilename = DIRPATH + hash_hyb_SD 
    #+ '.kwik'
    #add_clustering_kwik(kwikfilename, detectedgroundtruth, detectionhashname)
    kwikfiles = open_files(hash_hyb_SD,dir=DIRPATH, mode='a')
    add_clustering(kwikfiles,name = detectionhashname, spike_clusters=detectedgroundtruth,overwrite = True )
    print 'Added a clustering called ', detectionhashname
    add_clustering(kwikfiles,name = 'main', spike_clusters= trivialmainclustering, overwrite = True)
    close_files(kwikfiles)
    #clusters = '/channel_groups[0]/spikes/clusters'
    #detectionhash = hash_dictionary_md5(detectioncrit)
    #expt.createEArray(clusters, detectionhash, tb.UInt32Atom(), (0,),
    #                      expectedrows=1000000)
        
        #percentage_detected = float(sum(detected.values()))/NumHybSpikes
        
    
    
    detcrit_groundtruth_pre ={'detection_hashname':
    detectionhashname,'binmeanmask': binmeanmask,'indices_in_timewindow':indices_in_timewindow, 'numspikes_in_timeswindow': num_spikes_in_timewindow,
    'Cauchy_Schwarz':CauchySchwarz,'detected': detected,'detected_groundtruth': detectedgroundtruth}
    detcrit_groundtruth = hash_utils.order_dictionary(detcrit_groundtruth_pre)
    return detcrit_groundtruth