Python update_spatial_components_parallel 예제들

예제 #1

파일: demo.py 프로젝트: ninehundred1/Constrained_NMF

#%% PREPROCESS DATA
t1 = time()
Yr,sn,g=cse.preprocess_data(Yr,**preprocess_params)
Ain, Cin, b_in, f_in, center=cse.initialize_components(Y, **init_params)                                                    
print time() - t1  
plt2 = plt.imshow(Cn,interpolation='None')
plt.colorbar()
plt.scatter(x=center[:,1], y=center[:,0], c='m', s=40)
crd = cse.plot_contours(coo_matrix(Ain[:,::-1]),Cn,thr=0.9)
plt.axis((-0.5,d2-0.5,-0.5,d1-0.5))
plt.gca().invert_yaxis()
pl.show()
  
#%%
t1 = time()
A,b,Cin = cse.update_spatial_components_parallel(Yr, Cin, f_in, Ain, sn=sn, **spatial_params)
t_elSPATIAL = time() - t1
print t_elSPATIAL 
crd = cse.plot_contours(A,Cn,thr=0.9)
#%% update_temporal_components
t1 = time()
C,f,Y_res,S,bl,c1,neurons_sn,g = cse.update_temporal_components_parallel(Yr,A,b,Cin,f_in,bl=None,c1=None,sn=None,g=None,**temporal_params)
t_elTEMPORAL2 = time() - t1
print t_elTEMPORAL2 # took 98 sec   
#%% merge components corresponding to the same neuron
t1 = time()
A_m,C_m,nr_m,merged_ROIs,S_m,bl_m,c1_m,sn_m,g_m=cse.mergeROIS_parallel(Y_res,A,b,C,f,S,sn,temporal_params, spatial_params, bl=bl, c1=c1, sn=neurons_sn, g=g, thr=0.8, mx=50)
t_elMERGE = time() - t1
print t_elMERGE  
#%% view results. Notice that in order to scroll components you need to click on the plot
A_or, C_or, srt = cse.order_components(A_m,C_m)

예제 #2

        'noise_method': 'logmexp',
        'lags': 5,
        'fudge_factor': 1.,
        'verbosity': False
    }
    #%% PREPROCESS DATA
    t1 = time()
    Yr, sn, g = cse.preprocess_data(Yr, **preprocess_params)
    Ain, Cin, b_in, f_in, center = cse.initialize_components(Y, **init_params)
    print time() - t1

    #%%
    t1 = time()
    A, b, Cin = cse.update_spatial_components_parallel(Yr,
                                                       Cin,
                                                       f_in,
                                                       Ain,
                                                       sn=sn,
                                                       **spatial_params)
    t_elSPATIAL = time() - t1
    print t_elSPATIAL
    #%% update_temporal_components
    t1 = time()
    C, f, Y_res, S, bl, c1, neurons_sn, g = cse.update_temporal_components_parallel(
        Yr,
        A,
        b,
        Cin,
        f_in,
        bl=None,
        c1=None,
        sn=None,

예제 #3

파일: check_up.py 프로젝트: ninehundred1/Constrained_NMF

                        'memory_efficient':False,                                
                        'bas_nonneg':True,  
                        'noise_range':[.25,.5], 'noise_method':'logmexp', 
                        'lags':5, 'fudge_factor':1., 
                        'verbosity':False
                    }
    #%% PREPROCESS DATA
    t1 = time()
    Yr,sn,g=cse.preprocess_data(Yr,**preprocess_params)
    Ain, Cin, b_in, f_in, center=cse.initialize_components(Y, **init_params)                                                    
    print time() - t1  
    
      
    #%%
    t1 = time()
    A,b,Cin = cse.update_spatial_components_parallel(Yr, Cin, f_in, Ain, sn=sn, **spatial_params)
    t_elSPATIAL = time() - t1
    print t_elSPATIAL 
    #%% update_temporal_components
    t1 = time()
    C,f,Y_res,S,bl,c1,neurons_sn,g = cse.update_temporal_components_parallel(Yr,A,b,Cin,f_in,bl=None,c1=None,sn=None,g=None,**temporal_params)
    t_elTEMPORAL2 = time() - t1
    print t_elTEMPORAL2 # took 98 sec   
    #%% merge components corresponding to the same neuron
    t1 = time()
    A_m,C_m,nr_m,merged_ROIs,S_m,bl_m,c1_m,sn_m,g_m=cse.mergeROIS_parallel(Y_res,A,b,C,f,S,sn,temporal_params, spatial_params, bl=bl, c1=c1, sn=neurons_sn, g=g, thr=0.8, mx=50)
    t_elMERGE = time() - t1
    print t_elMERGE  
except:
    print 'test failed'
    raise