Python arpfit Examples

Example #1

File: structured_nmf.py Project: ninehundred1/Constrained_NMF

    def init_rois(self, n_components=100, show=False):
        Ain, Cin, center = greedyROI2d(self.Y,
                                       nr=n_components,
                                       gSig=[2, 2],
                                       gSiz=[7, 7],
                                       use_median=False)
        Cn = np.mean(self.Y, axis=-1)

        if show:
            pl1 = pl.imshow(Cn, interpolation='none')
            pl.colorbar()
            pl.scatter(x=center[:, 1], y=center[:, 0], c='m', s=40)
            pl.axis((-0.5, self.Y.shape[1] - 0.5, -0.5, self.Y.shape[0] - 0.5))
            pl.gca().invert_yaxis()

        active_pixels = np.squeeze(np.nonzero(np.sum(Ain, axis=1)))
        Yr = np.reshape(self.Y,
                        (self.Y.shape[0] * self.Y.shape[1], self.Y.shape[2]),
                        order='F')
        P = arpfit(Yr, p=2, pixels=active_pixels)
        Y_res = Yr - np.dot(Ain, Cin)
        model = ProjectedGradientNMF(n_components=1,
                                     init='random',
                                     random_state=0)
        model.fit(np.maximum(Y_res, 0))
        fin = model.components_.squeeze()

        self.Yr, self.Cin, self.fin, self.Ain, self.P, self.Cn = Yr, Cin, fin, Ain, P, Cn

Example #2

File: structured_nmf.py Project: epnev/SOURCE_EXTRACTION_PYTHON

    def init_rois(self, n_components=100, show=False):
        Ain,Cin,center = greedyROI2d(self.Y, nr=n_components, gSig=[2,2], gSiz=[7,7], use_median=False)
        Cn = np.mean(self.Y, axis=-1)

        if show:
            pl1 = pl.imshow(Cn,interpolation='none')
            pl.colorbar()
            pl.scatter(x=center[:,1], y=center[:,0], c='m', s=40)
            pl.axis((-0.5,self.Y.shape[1]-0.5,-0.5,self.Y.shape[0]-0.5))
            pl.gca().invert_yaxis()

        active_pixels = np.squeeze(np.nonzero(np.sum(Ain,axis=1)))
        Yr = np.reshape(self.Y,(self.Y.shape[0]*self.Y.shape[1],self.Y.shape[2]),order='F')
        P = arpfit(Yr, p=2, pixels=active_pixels)
        Y_res = Yr - np.dot(Ain,Cin)
        model = ProjectedGradientNMF(n_components=1, init='random', random_state=0)
        model.fit(np.maximum(Y_res,0))
        fin = model.components_.squeeze()
        
        self.Yr,self.Cin,self.fin,self.Ain,self.P,self.Cn = Yr,Cin,fin,Ain,P,Cn

Example #3

File: demo_script.py Project: epnev/SOURCE_EXTRACTION_PYTHON

#%%
d1,d2,T = np.shape(Y)
#%% greedy initialization
nr = 30
t1 = time()
Ain,Cin,center = greedyROI2d(Y, nr = nr, gSig = [4,4], gSiz = [9,9])
t_elGREEDY = time()-t1

#%% arpfit


active_pixels = np.squeeze(np.nonzero(np.sum(Ain,axis=1)))
Yr = np.reshape(Y,(d1*d2,T),order='F')
p = 2;
P = arpfit(Yr,p=2,pixels = active_pixels)

#%% nmf

Y_res = Yr - np.dot(Ain,Cin)
model = ProjectedGradientNMF(n_components=1, init='random', random_state=0)
model.fit(np.maximum(Y_res,0)) 

fin = model.components_.squeeze()

#%% update spatial components

t1 = time()
A,b = update_spatial_components(Yr, Cin, fin, Ain, d1=d1, d2=d2, sn = P['sn'])
t_elSPATIAL = time() - t1

Example #4

File: demo_script_FLY.py Project: eschlaf2/SOURCE_EXTRACTION_PYTHON

#%% plot centers
Cn = local_correlations(Y)
plt1 = plt.imshow(Cn,interpolation='none')
plt.colorbar()

plt.scatter(x=center[:,1], y=center[:,0], c='m', s=40)
plt.axis((-0.5,d2-0.5,-0.5,d1-0.5))
plt.gca().invert_yaxis()
#%%
crd = plot_contours(coo_matrix(Ain[:,::-1]),Cn,thr=0.9)
#%%
active_pixels = np.squeeze(np.nonzero(np.sum(Ain,axis=1)))
Yr = np.reshape(Y,(d1*d2,T),order='F')
p = 2;
P = arpfit(Yr,p=1,pixels = active_pixels)
Y_res = Yr - np.dot(Ain,Cin)
model = ProjectedGradientNMF(n_components=1, init='random', random_state=0)
model.fit(np.maximum(Y_res,0))

fin = model.components_.squeeze()
#%%
t1 = time()
A,b,Cin = update_spatial_components(Yr, Cin, fin, Ain, d1=d1, d2=d2, sn = P['sn'],dist=2,max_size=8,min_size=3)
t_elSPATIAL = time() - t1
#%%
crd = plot_contours(A,Cn2,thr=0.9,cmap=pl.cm.gray)
#%%
t1 = time()
C,f,Y_res,Pnew = update_temporal_components(Yr,A,b,Cin,fin,ITER=2,deconv_method = 'spgl1')
t_elTEMPORAL2 = time() - t1