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codes/CS.py
240
codes/CS.py
@ -36,7 +36,6 @@ def mask_pdf_1d(n,norm,q,pf):
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npf = np.round(pf*n)
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klo = ks[n-npf]
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for k in range(int(kmax)):
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P = pdf(ks, k+1, klo, q)
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if np.sum(P) >= norm:
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@ -44,12 +43,6 @@ def mask_pdf_1d(n,norm,q,pf):
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P = np.fft.fftshift(P)
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#if np.mod(n,2)!=0:
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# P = np.concatenate(([1],P),axis=None)
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return P
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def mask_pdf_2d(dims, norm, q, pf):
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@ -64,7 +57,6 @@ def mask_pdf_2d(dims,norm,q,pf):
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Z = np.abs(Z - nz/2 - 0.5)
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Y = np.abs(Y - ny/2 - 0.5)
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for rw in range(1, int(rmax)+1):
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P = np.ones([ny, nz])/pf
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C = np.logical_and(Z <= rw, Y <= rw)
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@ -73,8 +65,6 @@ def mask_pdf_2d(dims,norm,q,pf):
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if np.sum(P) >= norm:
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break
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return [P, C]
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def GeneratePattern(dim, R):
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@ -95,7 +85,7 @@ def GeneratePattern(dim,R):
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break
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# remove partial Fourier plane and compensate sampling density
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M = M != 0
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M = np.tile(M,[nro,1]);
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M = np.tile(M, [nro, 1])
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#M = M.T
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# 4D CASE
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@ -128,14 +118,10 @@ def GeneratePattern(dim,R):
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idxy = outerOff[1][idxs[0:numToFlip]]
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M[idxx, idxy] = True
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M = np.rollaxis(np.tile(np.rollaxis(M, 1), [nro, 1, 1]), 2)
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M = np.fft.ifftshift(M)
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M = M.transpose((1, 0, 2))
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return M
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def get_norm_factor(MASK, uu):
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@ -177,9 +163,12 @@ def Dxyz(u):
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if np.ndim(u) == 3:
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dx = u[:,:,:]- np.vstack((u[-1,:,:][np.newaxis,:,:],u[0:-1,:,:]))
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dy = u[:,:,:]- np.hstack((u[:,-1,:][:,np.newaxis,:],u[:,0:-1,:]))
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dz = u[:,:,:]- np.dstack((u[:,:,-1][:,:,np.newaxis],u[:,:,0:-1]))
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dx = u[:, :, :] - \
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np.vstack((u[-1, :, :][np.newaxis, :, :], u[0:-1, :, :]))
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dy = u[:, :, :] - \
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np.hstack((u[:, -1, :][:, np.newaxis, :], u[:, 0:-1, :]))
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dz = u[:, :, :] - \
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np.dstack((u[:, :, -1][:, :, np.newaxis], u[:, :, 0:-1]))
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D = np.zeros([dx.shape[0], dx.shape[1], dx.shape[2], 3], dtype=complex)
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@ -201,8 +190,7 @@ def shrink(X,pgam):
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return ss*X
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def CSMETHOD(ITOT, R):
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''' Compressed Function.
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''' Compressed Sensing Function.
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Args:
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ITOT: a numpy matrix with the full sampled (3D or 4D) dynamical data
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@ -215,7 +203,6 @@ def CSMETHOD(ITOT,R):
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mu = 20
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gam = 1
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if np.ndim(ITOT) == 3:
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[row, col, numt2] = ITOT.shape
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elif np.ndim(ITOT) == 4:
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@ -223,15 +210,12 @@ def CSMETHOD(ITOT,R):
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else:
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raise Exception('Dynamical data is requested')
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MASK = GeneratePattern(ITOT.shape, R)
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CS1 = np.zeros(ITOT.shape, dtype=complex)
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nit = 0
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nit_tot = (numt2-1)/20
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if np.ndim(ITOT) == 3:
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for t in range(numt2):
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@ -256,8 +240,10 @@ def CSMETHOD(ITOT,R):
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murf = np.fft.ifft2(mu*mask*Kdata)*scale
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uker = np.zeros([row, col])
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uker[0, 0] = 4
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uker[0,1] = -1 ; uker[1,0] = -1
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uker[-1,0] = -1 ; uker[0,-1] = -1
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uker[0, 1] = -1
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uker[1, 0] = -1
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uker[-1, 0] = -1
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uker[0, -1] = -1
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uker = 1/(mu*mask + lmbda*np.fft.fftn(uker) + gam)
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@ -278,27 +264,15 @@ def CSMETHOD(ITOT,R):
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# undo the normalization so that results are scaled properly
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img = img / norm_factor / scale
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CS1[:, :, t] = img
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if np.ndim(ITOT) == 4:
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for t in range(numt2):
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if rank == 0:
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print('[4D CS] R = {re} t = {te}/{tef}'.format(re=R,te=t,tef=numt2))
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#if np.mod(t,nit_tot)<1:
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# sys.stdout.write('\r')
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# # Progress bar
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# if numt2==3:
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# sys.stdout.write("{4d-CS} [%-6s] %d%%" % ('=='*nit, 100*t/numt2))
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# else:
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# sys.stdout.write("{4d-CS} [%-40s] %d%%" % ('=='*nit, 100*t/numt2))
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# sys.stdout.flush()
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# nit = nit +1
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print(
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'[4D CS] R = {re} t = {te}/{tef}'.format(re=R, te=t, tef=numt2))
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Kdata_0 = np.fft.fftn(ITOT[:, :, :, t])
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Kdata = Kdata_0*MASK
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@ -317,8 +291,12 @@ def CSMETHOD(ITOT,R):
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murf = np.fft.ifftn(mu*mask*Kdata)*scale
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uker = np.zeros([row, col, dep])
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uker[0, 0, 0] = 8
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uker[1,0,0] = -1 ; uker[0,1,0] = -1 ; uker[0,0,1] = -1
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uker[-1,0,0] = -1 ; uker[0,-1,0] = -1 ; uker[0,0,-1] = -1
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uker[1, 0, 0] = -1
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uker[0, 1, 0] = -1
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uker[0, 0, 1] = -1
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uker[-1, 0, 0] = -1
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uker[0, -1, 0] = -1
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uker[0, 0, -1] = -1
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uker = 1/(mu*mask + lmbda*np.fft.fftn(uker) + gam)
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# Do the reconstruction
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@ -338,16 +316,12 @@ def CSMETHOD(ITOT,R):
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# undo the normalization so that results are scaled properly
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img = img / norm_factor / scale
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CS1[:, :, :, t] = img
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return CS1
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def CSMETHOD_SENSE(ITOT, R, R_SENSE):
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''' Compressed Function.
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''' Compressed sense algorith with SENSE... in contruction!.
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Args:
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ITOT: a numpy matrix with the full sampled (3D or 4D) dynamical data
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@ -375,7 +349,8 @@ def CSMETHOD_SENSE(ITOT,R,R_SENSE):
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for rs in range(R_SENSE):
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for t in range(numt2):
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if rank == 0:
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print('[4D CS] R = {re} t = {te}/{tef}'.format(re=R,te=t,tef=numt2))
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print(
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'[4D CS] R = {re} t = {te}/{tef}'.format(re=R, te=t, tef=numt2))
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Kdata_0 = np.fft.fftn(ITOT[:, :, :, t])
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Kdata_0 = Kdata_0*SenseMAP[rs]
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@ -397,8 +372,12 @@ def CSMETHOD_SENSE(ITOT,R,R_SENSE):
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murf = np.fft.ifftn(mu*mask*Kdata)*scale
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uker = np.zeros([row, col, dep])
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uker[0, 0, 0] = 8
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uker[1,0,0] = -1 ; uker[0,1,0] = -1 ; uker[0,0,1] = -1
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uker[-1,0,0] = -1 ; uker[0,-1,0] = -1 ; uker[0,0,-1] = -1
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uker[1, 0, 0] = -1
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uker[0, 1, 0] = -1
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uker[0, 0, 1] = -1
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uker[-1, 0, 0] = -1
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uker[0, -1, 0] = -1
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uker[0, 0, -1] = -1
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uker = 1/(mu*mask + lmbda*np.fft.fftn(uker) + gam)
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# Do the reconstruction
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@ -420,74 +399,8 @@ def CSMETHOD_SENSE(ITOT,R,R_SENSE):
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ITOTCS[rs][:, :, :, t] = img
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return [ITOTCS[0], ITOTCS[1]]
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def CSMETHOD_peaksystole(ITOT,R,tstar):
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''' Compressed Function.
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Args:
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ITOT: a numpy matrix with the full sampled (3D or 4D) dynamical data
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R: the acceleration factor
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tstar: the time when the flux in the inlet it's maximum
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'''
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# Method parameters
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ninner = 5
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nbreg = 10
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lmbda = 4
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mu = 20
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gam = 1
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[row,col,dep,numt2] = ITOT.shape
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MASK = GeneratePattern(ITOT.shape,R)
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CS1 = np.zeros([row,col,dep],dtype=complex)
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for t in range(tstar,tstar+1):
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Kdata = np.fft.fftn(ITOT[:,:,:,t])*MASK
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data_ndims = Kdata.ndim
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mask = Kdata!=0 # not perfect, but good enough
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# normalize the data so that standard parameter values work
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norm_factor = get_norm_factor(mask, Kdata)
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Kdata = Kdata*norm_factor
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# Reserve memory for the auxillary variables
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Kdata0 = Kdata
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img = np.zeros([row,col,dep],dtype=complex)
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X = np.zeros([row,col,dep, data_ndims])
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B = np.zeros([row,col,dep, data_ndims])
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# Build Kernels
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scale = np.sqrt(row*col*dep)
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murf = np.fft.ifftn(mu*mask*Kdata)*scale
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uker = np.zeros([row,col,dep])
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uker[0,0,0] = 8
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uker[1,0,0] = -1 ; uker[0,1,0] = -1 ; uker[0,0,1] = -1
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uker[-1,0,0] = -1 ; uker[0,-1,0] = -1 ; uker[0,0,-1] = -1
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uker = 1/(mu*mask + lmbda*np.fft.fftn(uker) + gam)
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# Do the reconstruction
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for outer in range(nbreg):
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for inner in range(ninner):
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# update u
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rhs = murf + lmbda*Dxyzt(X-B) + gam*img
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img = np.fft.ifft2(np.fft.fft2(rhs)*uker)
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# update x and y
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A = Dxyz(img) + B
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X = shrink(A, 1/lmbda)
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# update bregman parameters
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B = A - X
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Kdata = Kdata + Kdata0 - mask*np.fft.fftn(img)/scale
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murf = np.fft.ifftn(mu*mask*Kdata)*scale
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# undo the normalization so that results are scaled properly
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img = img / norm_factor / scale
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CS1[:,:,:] = img
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return CS1
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def phase_contrast(M1, M0, VENC, scantype='0G'):
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param = 1
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if scantype == '-G+G':
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@ -495,6 +408,9 @@ def phase_contrast(M1,M0,VENC,scantype='0G'):
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return VENC*param*(np.angle(M1) - np.angle(M0))/np.pi
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def GenerateMagnetization(Sq, VENC, noise, scantype='0G'):
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''' Simulation of a typical magnetization. A x-dependent plane is added into the
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reference phase.
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'''
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# MRI PARAMETERS
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gamma = 267.513e6 # rad/Tesla/sec Gyromagnetic ratio for H nuclei
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B0 = 1.5 # Tesla Magnetic Field Strenght
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@ -506,7 +422,8 @@ def GenerateMagnetization(Sq,VENC,noise,scantype='0G'):
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if np.ndim(Sq) == 3:
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[row, col, numt2] = Sq.shape
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[X,Y] = np.meshgrid(np.linspace(0,col,col),np.linspace(0,row,row))
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[X, Y] = np.meshgrid(np.linspace(0, col, col),
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np.linspace(0, row, row))
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for k in range(numt2):
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if noise:
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Drho = np.random.normal(0, 0.2, [row, col])
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@ -515,20 +432,26 @@ def GenerateMagnetization(Sq,VENC,noise,scantype='0G'):
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Drho = np.zeros([row, col])
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Drho2 = np.zeros([row, col])
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varPHASE0 = np.random.randint(-10,11,size=(row,col))*np.pi/180*(np.abs(Sq[:,:,k])<0.001) #Hugo's observation
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varPHASE0 = np.random.randint(-10, 11, size=(row, col))*np.pi/180*(
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np.abs(Sq[:, :, k]) < 0.001) # Hugo's observation
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modulus = 0.5 + 0.5*(np.abs(Sq[:, :, k]) > 0.001)
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if scantype == '0G':
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PHASE0[:,:,k] = (gamma*B0*TE+0.01*X)*(np.abs(Sq[:,:,k])>0.001) + 10*varPHASE0
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PHASE1[:,:,k] = (gamma*B0*TE+0.01*X)*(np.abs(Sq[:,:,k])>0.001) + 10*varPHASE0 + np.pi*Sq[:,:,k]/VENC
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PHASE0[:, :, k] = (gamma*B0*TE+0.01*X) * \
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(np.abs(Sq[:, :, k]) > 0.001) + 10*varPHASE0
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PHASE1[:, :, k] = (gamma*B0*TE+0.01*X)*(np.abs(Sq[:, :, k])
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> 0.001) + 10*varPHASE0 + np.pi*Sq[:, :, k]/VENC
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if scantype == '-G+G':
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PHASE0[:,:,k] = gamma*B0*TE*np.ones([row,col]) + 10*varPHASE0 - np.pi*Sq[:,:,k]/VENC
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PHASE1[:,:,k] = gamma*B0*TE*np.ones([row,col]) + 10*varPHASE0 + np.pi*Sq[:,:,k]/VENC
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RHO0[:,:,k] = modulus*np.cos(PHASE0[:,:,k]) + Drho + 1j*modulus*np.sin(PHASE0[:,:,k]) + 1j*Drho2
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RHO1[:,:,k] = modulus*np.cos(PHASE1[:,:,k]) + Drho + 1j*modulus*np.sin(PHASE1[:,:,k]) + 1j*Drho2
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PHASE0[:, :, k] = gamma*B0*TE * \
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np.ones([row, col]) + 10*varPHASE0 - np.pi*Sq[:, :, k]/VENC
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PHASE1[:, :, k] = gamma*B0*TE * \
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np.ones([row, col]) + 10*varPHASE0 + np.pi*Sq[:, :, k]/VENC
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RHO0[:, :, k] = modulus*np.cos(PHASE0[:, :, k]) + \
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Drho + 1j*modulus*np.sin(PHASE0[:, :, k]) + 1j*Drho2
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RHO1[:, :, k] = modulus*np.cos(PHASE1[:, :, k]) + \
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Drho + 1j*modulus*np.sin(PHASE1[:, :, k]) + 1j*Drho2
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if np.ndim(Sq) == 4:
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[row, col, dep, numt2] = Sq.shape
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@ -556,17 +479,17 @@ def GenerateMagnetization(Sq,VENC,noise,scantype='0G'):
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if scantype == '-G+G':
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PHASE0[:, :, :, k] = gamma*B0*TE * \
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np.ones([row, col, dep]) + varPHASE0 - np.pi*Sq[:, :, :, k]/VENC
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np.ones([row, col, dep]) + varPHASE0 - \
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np.pi*Sq[:, :, :, k]/VENC
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PHASE1[:, :, :, k] = gamma*B0*TE * \
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np.ones([row, col, dep]) + varPHASE0 + np.pi*Sq[:, :, :, k]/VENC
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np.ones([row, col, dep]) + varPHASE0 + \
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np.pi*Sq[:, :, :, k]/VENC
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RHO0[:, :, :, k] = modulus*np.cos(PHASE0[:, :, :, k]) + \
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Drho + 1j*modulus*np.sin(PHASE0[:, :, :, k]) + 1j*Drho2
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RHO1[:, :, :, k] = modulus*np.cos(PHASE1[:, :, :, k]) + \
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Drho + 1j*modulus*np.sin(PHASE1[:, :, :, k]) + 1j*Drho2
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return [RHO0, RHO1]
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def undersampling(Sqx, Sqy, Sqz, options, savepath):
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@ -579,8 +502,8 @@ def undersampling(Sqx,Sqy,Sqz,options,savepath):
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print('Using Acceleration Factor R = ' + str(r))
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print('Component x of M0')
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[M0,M1] = GenerateMagnetization(Sqx,options['cs']['VENC'],options['cs']['noise'])
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[M0, M1] = GenerateMagnetization(
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Sqx, options['cs']['VENC'], options['cs']['noise'])
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print('\n Component x of M0')
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M0_cs = CSMETHOD(M0, r)
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@ -591,21 +514,21 @@ def undersampling(Sqx,Sqy,Sqz,options,savepath):
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del M0, M1
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del M0_cs, M1_cs
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[M0,M1] = GenerateMagnetization(Sqy,options['cs']['VENC'],options['cs']['noise'])
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[M0, M1] = GenerateMagnetization(
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Sqy, options['cs']['VENC'], options['cs']['noise'])
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print('\n Component y of M0')
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M0_cs = CSMETHOD(M0, r)
|
||||
print('\n Component y of M1')
|
||||
M1_cs = CSMETHOD(M1, r)
|
||||
|
||||
|
||||
Sqy_cs = phase_contrast(M1_cs, M0_cs, options['cs']['VENC'])
|
||||
|
||||
del M0, M1
|
||||
del M0_cs, M1_cs
|
||||
|
||||
[M0,M1] = GenerateMagnetization(Sqz,options['cs']['VENC'],options['cs']['noise'])
|
||||
[M0, M1] = GenerateMagnetization(
|
||||
Sqz, options['cs']['VENC'], options['cs']['noise'])
|
||||
|
||||
if rank == 0:
|
||||
print('\n Component z of M0')
|
||||
@ -618,46 +541,20 @@ def undersampling(Sqx,Sqy,Sqz,options,savepath):
|
||||
|
||||
Sqz_cs = phase_contrast(M1_cs, M0_cs, options['cs']['VENC'])
|
||||
|
||||
|
||||
if rank == 0:
|
||||
print('saving the sequences in ' + savepath)
|
||||
seqname = options['cs']['name'] + '_R' + str(r) + '.npz'
|
||||
print('sequence name: ' + seqname)
|
||||
np.savez_compressed( savepath + seqname, x=Sqx_cs, y=Sqy_cs,z=Sqz_cs)
|
||||
np.savez_compressed(savepath + seqname,
|
||||
x=Sqx_cs, y=Sqy_cs, z=Sqz_cs)
|
||||
|
||||
del Sqx_cs, Sqy_cs, Sqz_cs
|
||||
|
||||
def undersampling_peakpv(Sqx,Sqy,Sqz,options,R):
|
||||
|
||||
Sqx_cs = {}
|
||||
Sqy_cs = {}
|
||||
Sqz_cs = {}
|
||||
[Mx0,Mx1] = GenerateMagnetization(Sqx,options['cs']['VENC'],options['cs']['noise'],scantype='0G')
|
||||
[My0,My1] = GenerateMagnetization(Sqy,options['cs']['VENC'],options['cs']['noise'],scantype='0G')
|
||||
[Mz0,Mz1] = GenerateMagnetization(Sqz,options['cs']['VENC'],options['cs']['noise'],scantype='0G')
|
||||
|
||||
|
||||
Mx0_cs = CSMETHOD(Mx0,R)
|
||||
Mx1_cs = CSMETHOD(Mx1,R)
|
||||
My0_cs = CSMETHOD(My0,R)
|
||||
My1_cs = CSMETHOD(My1,R)
|
||||
Mz0_cs = CSMETHOD(Mz0,R)
|
||||
Mz1_cs = CSMETHOD(Mz1,R)
|
||||
|
||||
Sqx_cs = phase_contrast(Mx1_cs,Mx0_cs,options['cs']['VENC'],scantype='0G')
|
||||
Sqy_cs = phase_contrast(My1_cs,My0_cs,options['cs']['VENC'],scantype='0G')
|
||||
Sqz_cs = phase_contrast(Mz1_cs,Mz0_cs,options['cs']['VENC'],scantype='0G')
|
||||
|
||||
|
||||
|
||||
return [Sqx_cs,Sqy_cs,Sqz_cs]
|
||||
|
||||
def undersampling_short(Mx, My, Mz, options):
|
||||
|
||||
R = options['cs']['R']
|
||||
savepath = options['cs']['savepath']
|
||||
|
||||
|
||||
R_SENSE = 1
|
||||
if 'R_SENSE' in options['cs']:
|
||||
R_SENSE = options['cs']['R_SENSE'][0]
|
||||
@ -666,7 +563,6 @@ def undersampling_short(Mx,My,Mz,options):
|
||||
if rank == 0:
|
||||
print('Using Acceleration Factor R = ' + str(r))
|
||||
|
||||
|
||||
if R_SENSE == 2:
|
||||
[MxS0_cs, MxS1_cs] = CSMETHOD_SENSE(Mx, r, 2)
|
||||
[MyS0_cs, MyS1_cs] = CSMETHOD_SENSE(My, r, 2)
|
||||
@ -676,9 +572,11 @@ def undersampling_short(Mx,My,Mz,options):
|
||||
seqname_s0 = options['cs']['name'] + 'S0_R' + str(r) + '.npz'
|
||||
seqname_s1 = options['cs']['name'] + 'S1_R' + str(r) + '.npz'
|
||||
print('sequence name: ' + seqname_s0)
|
||||
np.savez_compressed( savepath + seqname_s0, x=MxS0_cs, y=MyS0_cs,z=MzS0_cs)
|
||||
np.savez_compressed(savepath + seqname_s0,
|
||||
x=MxS0_cs, y=MyS0_cs, z=MzS0_cs)
|
||||
print('sequence name: ' + seqname_s1)
|
||||
np.savez_compressed( savepath + seqname_s1, x=MxS1_cs, y=MyS1_cs,z=MzS1_cs)
|
||||
np.savez_compressed(savepath + seqname_s1,
|
||||
x=MxS1_cs, y=MyS1_cs, z=MzS1_cs)
|
||||
del MxS0_cs, MyS0_cs, MzS0_cs
|
||||
del MxS1_cs, MyS1_cs, MzS1_cs
|
||||
elif R_SENSE == 1:
|
||||
@ -689,17 +587,11 @@ def undersampling_short(Mx,My,Mz,options):
|
||||
print('saving the sequences in ' + savepath)
|
||||
seqname = options['cs']['name'] + '_R' + str(r) + '.npz'
|
||||
print('sequence name: ' + seqname)
|
||||
np.savez_compressed( savepath + seqname, x=Mx_cs, y=My_cs,z=Mz_cs)
|
||||
np.savez_compressed(savepath + seqname,
|
||||
x=Mx_cs, y=My_cs, z=Mz_cs)
|
||||
del Mx_cs, My_cs, Mz_cs
|
||||
else:
|
||||
raise Exception('Only implemented for 2-fold SENSE!!')
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# THE END
|
||||
|
||||
|
||||
|
||||
|
||||
@ -586,25 +586,15 @@ def CenterComparison(A,B,C,R,center):
|
||||
|
||||
def VelocityChannel(M,repeat,recorder):
|
||||
[row,col,numt2] = M.shape
|
||||
|
||||
|
||||
[X,Y] = np.meshgrid(np.linspace(0,col,col),np.linspace(0,row,row))
|
||||
|
||||
plt.ion()
|
||||
|
||||
rown = row*6/row
|
||||
coln = col*6/row
|
||||
|
||||
fig = plt.figure()#figsize=(4, 6) , dpi=200)
|
||||
ax = fig.add_subplot(111, projection='3d')
|
||||
|
||||
|
||||
for rr in range(-1,repeat):
|
||||
|
||||
for t in range(numt2):
|
||||
|
||||
V = M[:,:,t]
|
||||
|
||||
#ax.plot_surface(X, Y, V, cmap=plt.cm.magma, vmin=-30, vmax=50, linewidth=0, antialiased=False)
|
||||
#ax.plot_wireframe(X, Y, V,rcount=20,ccount=20,linewidth=0.5)
|
||||
ax.plot_surface(X, Y, V,cmap='magma',vmin=-30, vmax=100, linewidth=0, antialiased=False)
|
||||
@ -615,7 +605,6 @@ def VelocityChannel(M,repeat,recorder):
|
||||
ax.set_xlabel('$x$')
|
||||
ax.set_ylabel('$y$')
|
||||
ax.set_zlabel('$v(r)$')
|
||||
|
||||
ax.set_title('phase ' + str(t))
|
||||
plt.pause(0.001)
|
||||
plt.draw()
|
||||
@ -633,115 +622,6 @@ def PlotTri(tri,pos,p):
|
||||
ax = fig.add_subplot(1, 1, 1, projection='3d')
|
||||
#ax.plot_trisurf(pos[:,0], pos[:,1], pos[:,2], triangles=tri.simplices, cmap=plt.cm.Spectral,linewidth=0.1,edgecolors='k')
|
||||
#ax.tripcolor(pos[:,0], pos[:,1], pos[:,2], triangles=tri.simplices, facecolors=p2.T, edgecolor='black')
|
||||
plt.show()
|
||||
|
||||
def PlotPressureDrop(mode):
|
||||
|
||||
barye2mmHg = 1/1333.22387415
|
||||
|
||||
CT = np.loadtxt('Pressure/DROPS/pd_NS_coarse.txt')
|
||||
CT2 = np.loadtxt('Pressure/DROPS/pd_NS_coarse2.txt')
|
||||
|
||||
ref_ao = np.loadtxt('Pressure/DROPS2/refPPE1_coarse.txt')
|
||||
ref = np.loadtxt('Pressure/DROPS2/refPPE1_coarse_leo1.txt')
|
||||
CS2 = np.loadtxt('Pressure/DROPS2/CSPPE2_coarse_leo1.txt')
|
||||
|
||||
|
||||
PPE_CT = np.loadtxt('Pressure/DROPS/pd_PPE_NS_coarse.txt')
|
||||
PPE_CT_leo = np.loadtxt('Pressure/DROPS/pd_PPE_NS_coarse_leo1.txt')
|
||||
|
||||
|
||||
STE_CT = np.loadtxt('Pressure/DROPS/test_STE_R1_coarse.txt')
|
||||
test_STE_CT = np.loadtxt('Pressure/DROPS/test2_STE_R1_coarse_leo1.txt')
|
||||
|
||||
STEint_CT = np.loadtxt('Pressure/DROPS/test_STEint_R1_coarse.txt')
|
||||
test_STEint_CT = np.loadtxt('Pressure/DROPS/test2_STEint_R1_coarse_leo1.txt')
|
||||
|
||||
|
||||
# UNDERSAMPLING
|
||||
PPE_R1_leo1 = np.loadtxt('Pressure/DROPS/test_PPE_R1_coarse_leo1.txt')
|
||||
|
||||
PPE_KT_R2_leo1 = np.loadtxt('Pressure/DROPS/KT_PPE_R2_coarse_leo1.txt')
|
||||
PPE_KT_R4_leo1 = np.loadtxt('Pressure/DROPS/KT_PPE_R4_coarse_leo1.txt')
|
||||
PPE_KT_R8_leo1 = np.loadtxt('Pressure/DROPS/KT_PPE_R8_coarse_leo1.txt')
|
||||
PPE_KT_R12_leo1 = np.loadtxt('Pressure/DROPS/KT_PPE_R12_coarse_leo1.txt')
|
||||
PPE_KT_R20_leo1 = np.loadtxt('Pressure/DROPS/KT_PPE_R20_coarse_leo1.txt')
|
||||
|
||||
PPE_CS_R2_leo1 = np.loadtxt('Pressure/DROPS/CS_PPE_R2_coarse_leo1.txt')
|
||||
PPE_CS_R4_leo1 = np.loadtxt('Pressure/DROPS/CS_PPE_R4_coarse_leo1.txt')
|
||||
PPE_CS_R8_leo1 = np.loadtxt('Pressure/DROPS/CS_PPE_R8_coarse_leo1.txt')
|
||||
PPE_CS_R12_leo1 = np.loadtxt('Pressure/DROPS/CS_PPE_R12_coarse_leo1.txt')
|
||||
PPE_CS_R20_leo1 = np.loadtxt('Pressure/DROPS/CS_PPE_R20_coarse_leo1.txt')
|
||||
|
||||
#CT_fine = np.loadtxt('Pressure/DROPS/pd_NS_fine.txt')
|
||||
#CT_fine_T = np.loadtxt('Pressure/DROPS/pd_NS_fine_T.txt')
|
||||
#PPE_CT_fine = np.loadtxt('Pressure/DROPS/pd_PPE_NS_fine.txt')
|
||||
#PPE_CT_fine_leo3 = np.loadtxt('Pressure/DROPS/pd_PPE_NS_fine_leo3.txt')
|
||||
|
||||
|
||||
tvec2 = np.linspace(0, 2.5 ,PPE_CT_leo.size)
|
||||
tvec = np.linspace(tvec2[1]*0.5 ,2.5+tvec2[1]*0.5 , CT.size)
|
||||
#tvec_T = np.linspace(0,2.5,CT_fine_T.size)
|
||||
|
||||
fig = plt.figure()
|
||||
|
||||
if mode=='KT':
|
||||
plt.plot(tvec,CT,'-k',linewidth=2,label='$ref$')
|
||||
plt.plot(tvec2,PPE_R1_leo1,'xkcd:red',linewidth=2,linestyle='-' , label='$R = 1$')
|
||||
plt.plot(tvec2,PPE_KT_R2_leo1,'xkcd:blue',linewidth=2,linestyle='-' ,label='$R = 2$')
|
||||
plt.plot(tvec2,PPE_KT_R4_leo1,'xkcd:green',linewidth=2,linestyle='-',label='$R = 4$')
|
||||
plt.plot(tvec2,PPE_KT_R8_leo1,'xkcd:orange',linewidth=2,linestyle='-',label='$R = 8$')
|
||||
plt.plot(tvec2,PPE_KT_R20_leo1,'xkcd:magenta',linewidth=2,linestyle='-', label='$R = 20$')
|
||||
plt.title('$kt-BLAST$',fontsize=20)
|
||||
|
||||
if mode=='CS':
|
||||
plt.plot(tvec,CT,'-k',linewidth=2,label='$ref$')
|
||||
plt.plot(tvec2,ref_ao,'xkcd:red',linewidth=2,linestyle='--' , label='$aorta$')
|
||||
plt.plot(tvec2,ref,'xkcd:red',linewidth=2,linestyle='-' , label='$leo$')
|
||||
plt.plot(tvec2,CS2,'xkcd:blue',linewidth=2,linestyle='-' ,label='$R = 2$')
|
||||
|
||||
#plt.plot(tvec2,PPE_R1_leo1,'xkcd:red',linewidth=2,linestyle='-' , label='$R = 1$')
|
||||
#plt.plot(tvec2,PPE_CS_R2_leo1,'xkcd:blue',linewidth=2,linestyle='-' ,label='$R = 2$')
|
||||
#plt.plot(tvec2,PPE_CS_R4_leo1,'xkcd:green',linewidth=2,linestyle='-',label='$R = 4$')
|
||||
#plt.plot(tvec2,PPE_CS_R8_leo1,'xkcd:orange',linewidth=2,linestyle='-',label='$R = 8$')
|
||||
#plt.plot(tvec2,PPE_CS_R20_leo1,'xkcd:magenta',linewidth=2,linestyle='-', label='$R = 20$')
|
||||
plt.title('$Compressed \ \ Sensing$',fontsize=20)
|
||||
|
||||
|
||||
|
||||
if mode=='STE':
|
||||
plt.plot(tvec,CT,'-k',linewidth=2,label='$ref$')
|
||||
plt.plot(tvec2,STE_CT , 'xkcd:purple' , label='STE-CT aorta')
|
||||
plt.plot(tvec2,test_STE_CT , 'xkcd:purple' , linestyle='--', marker='o', label='STE-CT leo')
|
||||
|
||||
|
||||
if mode=='STEint':
|
||||
plt.plot(tvec,CT,'-k',linewidth=2,label='$ref$')
|
||||
plt.plot(tvec2,STEint_CT, 'xkcd:aquamarine', label='STEint-CT aorta')
|
||||
plt.plot(tvec2,test_STEint_CT, 'xkcd:aquamarine', linestyle='--', marker='o',label='STEint-CT aorta')
|
||||
|
||||
|
||||
plt.ylim([-2,7])
|
||||
plt.xlabel(r'$time \ \ \ (s)$',fontsize=20)
|
||||
plt.ylabel(r'$\delta p \ \ \ (mmHg) $',fontsize=20)
|
||||
plt.legend(fontsize=16)
|
||||
##############################################################################################################################
|
||||
|
||||
|
||||
#fig = plt.figure()
|
||||
#plt.plot(tvec2,CT_fine,'-ok',label='CT')
|
||||
##plt.plot(tvec_T,CT_fine_T,'--k',label='CT T')
|
||||
#plt.plot(tvec2 ,PPE_CT_fine ,'-om',label='PPE-CT aorta')
|
||||
#plt.plot(tvec2 ,PPE_CT_fine_leo3,'-oc',label='PPE-CT leo3')
|
||||
#plt.title('aorta fine')
|
||||
#plt.xlabel(r'$time \ \ (s) $',fontsize=20)
|
||||
#plt.ylabel(r'$\delta p \ \ \ (mmHg) $',fontsize=20)
|
||||
#plt.legend(fontsize=14)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
plt.show()
|
||||
|
||||
def Plot_flux(masterpath,meshpath,options,mode,R):
|
||||
@ -1091,7 +971,6 @@ def Plot_dP(masterpath,options,mode,R):
|
||||
tcat = tcat+shift_t
|
||||
ax.plot(tcat[cstar[0]:tcat.size-cstar[1]],catheter[cstar[0]:tcat.size-cstar[1]],'white',linewidth=linesize,linestyle='--',label='$catheter$')
|
||||
|
||||
|
||||
tm = np.linspace(0,Dt*tend,tend)
|
||||
ax.set_xlim([-0.05,0.81])
|
||||
|
||||
@ -1130,225 +1009,6 @@ def Plot_dP(masterpath,options,mode,R):
|
||||
|
||||
|
||||
|
||||
plt.show()
|
||||
|
||||
def Plot_peaksystole(datapath,options,meshes,dt,R):
|
||||
import pickle
|
||||
barye2mmHg = 1/1333.22387415
|
||||
|
||||
|
||||
for mesh_size in meshes:
|
||||
t_star = 6
|
||||
|
||||
|
||||
PPE_MEAN = np.zeros([len(R)])
|
||||
PPE_STD = np.zeros([len(R)])
|
||||
STE_MEAN = np.zeros([len(R)])
|
||||
STE_STD = np.zeros([len(R)])
|
||||
V_MEAN = np.zeros([len(R)])
|
||||
V_STD = np.zeros([len(R)])
|
||||
|
||||
ref_P = 0
|
||||
ref_V = 0
|
||||
|
||||
|
||||
|
||||
|
||||
if mesh_size=='Ucoarse':
|
||||
ref_V = 326.95828118309191
|
||||
if mesh_size=='Ufine':
|
||||
ref_V = 232.95021682714497
|
||||
if mesh_size=='Uffine':
|
||||
ref_V = 234.66445211879045
|
||||
|
||||
|
||||
|
||||
|
||||
for l in range(len(R)):
|
||||
if R[l]==0:
|
||||
ref = np.loadtxt('/home/yeye/N_MRI/codes/pressure_drop/'+mesh_size+'/dt' + str(dt) + '/ref_'+mesh_size+'.txt')
|
||||
PPE0_raw = open('/home/yeye/N_MRI/codes/pressure_drop/'+mesh_size+'/dt' + str(dt) + '/R0/pdrop_PPE_impl_stan.dat','rb')
|
||||
STE0_raw = open('/home/yeye/N_MRI/codes/pressure_drop/'+mesh_size+'/dt' + str(dt) + '/R0/pdrop_STE_impl_stan.dat','rb')
|
||||
PPE0 = pickle.load(PPE0_raw)['pdrop']*(-barye2mmHg)
|
||||
STE0 = pickle.load(STE0_raw)['pdrop']*(-barye2mmHg)
|
||||
|
||||
curpath = datapath + 'sequences/aorta_'+mesh_size+'.npz'
|
||||
p = np.load(curpath)
|
||||
px = p['x']
|
||||
py = p['y']
|
||||
pz = p['z']
|
||||
v = np.sqrt(px[:,:,:,t_star]**2 + py[:,:,:,t_star]**2 + pz[:,:,:,t_star]**2)
|
||||
max0 = np.where(v==np.max(v))
|
||||
|
||||
ref_P = ref[6]
|
||||
V_MEAN[l] = ref_V
|
||||
V_STD[l] = 0
|
||||
PPE_MEAN[l] = PPE0[6]
|
||||
PPE_STD[l] = 0
|
||||
STE_MEAN[l] = STE0[6]
|
||||
STE_STD[l] = 0
|
||||
else:
|
||||
PPE_MEAN[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/ppemean_R'+ str(R[l]) +'.txt')
|
||||
PPE_STD[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/ppestd_R'+ str(R[l]) +'.txt')
|
||||
STE_MEAN[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/stemean_R'+ str(R[l]) +'.txt')
|
||||
STE_STD[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/stestd_R'+ str(R[l]) +'.txt')
|
||||
V_MEAN[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/vmean_R'+ str(R[l]) +'.txt')
|
||||
V_STD[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/vstd_R'+ str(R[l]) +'.txt')
|
||||
|
||||
|
||||
|
||||
plt.figure(figsize=(10, 6), dpi=100)
|
||||
Rvec = np.linspace(-10,R[-1]+5,100)
|
||||
hline = Rvec*0+ref_P
|
||||
plt.subplot(1,2,1)
|
||||
plt.plot([0],[ref_P],color='k',marker='o',label= '$ref$')
|
||||
plt.plot(Rvec,hline,color='k',linestyle='--')
|
||||
plt.errorbar(R,PPE_MEAN, yerr=PPE_STD,color=options['ppecol'],marker='o',label= '$PPE$')
|
||||
plt.errorbar(R,STE_MEAN, yerr=STE_STD,color=options['stecol'],marker='o',label= '$STE$')
|
||||
plt.xlim([-2,R[-1]+5])
|
||||
plt.ylim([-7,18])
|
||||
plt.xlabel(r'$R$',fontsize=20)
|
||||
plt.title('$Peak \ Systole \ pressure$',fontsize=18)
|
||||
plt.ylabel(r'$ max \ \big ( \delta P \big ) \ \ mmHg$',fontsize=16)
|
||||
|
||||
|
||||
plt.subplot(1,2,2)
|
||||
#plt.plot([0],[ref_V],color='k',marker='o',label= '$ref$')
|
||||
Rvec = np.linspace(-10,R[-1]+5,100)
|
||||
hline = Rvec*0+ref_V
|
||||
plt.plot(Rvec,hline,color='k',linestyle='--')
|
||||
plt.errorbar(R,V_MEAN, yerr=V_STD,color='royalblue',marker='o',label= '$' + mesh_size + '$')
|
||||
plt.xlim([-2,R[-1]+5])
|
||||
plt.ylim([0,350])
|
||||
plt.xlabel(r'$R$',fontsize=20)
|
||||
plt.ylabel(r'$ max \ \big ( v \big ) \ \ cm/s$',fontsize=16)
|
||||
plt.title('$Peak \ Systole \ velocity$',fontsize=18)
|
||||
#plt.legend(fontsize=15)
|
||||
|
||||
plt.annotate('$'+mesh_size+'$', xy=(-0.2, 1.1), xycoords='axes fraction',fontsize=15)
|
||||
|
||||
|
||||
plt.show()
|
||||
|
||||
def Plot_peaksystole_flux(datapath,options,meshes,dt,R):
|
||||
import pickle
|
||||
barye2mmHg = 1/1333.22387415
|
||||
|
||||
|
||||
for mesh_size in meshes:
|
||||
t_star = 6
|
||||
PPE_MEAN = np.zeros([len(R)])
|
||||
PPE_STD = np.zeros([len(R)])
|
||||
STE_MEAN = np.zeros([len(R)])
|
||||
STE_STD = np.zeros([len(R)])
|
||||
V_MEAN = np.zeros([len(R)])
|
||||
V_STD = np.zeros([len(R)])
|
||||
Q_MEAN = np.zeros([len(R)])
|
||||
Q_STD = np.zeros([len(R)])
|
||||
|
||||
ref_V = 0
|
||||
|
||||
if mesh_size=='Ucoarse':
|
||||
ref_V = 326.95828118309191
|
||||
if mesh_size=='Ufine':
|
||||
ref_V = 232.95021682714497
|
||||
if 'Uffine' in mesh_size:
|
||||
ref_V = 226.93523675462458
|
||||
maxv1 = 184.05091675316763
|
||||
ref_Q = 454.77517472437495
|
||||
maxq1 = 429.01393994253556
|
||||
|
||||
|
||||
for l in range(len(R)):
|
||||
if R[l]==0:
|
||||
ref = np.loadtxt('/home/yeye/N_MRI/codes/pressure_drop/'+mesh_size+'/dt' + str(dt) + '/ref_'+mesh_size+'.txt')
|
||||
PPE0_raw = open('/home/yeye/N_MRI/codes/pressure_drop/'+mesh_size+'/dt' + str(dt) + '/R0/pdrop_PPE_impl_stan.dat','rb')
|
||||
STE0_raw = open('/home/yeye/N_MRI/codes/pressure_drop/'+mesh_size+'/dt' + str(dt) + '/R0/pdrop_STE_impl_stan.dat','rb')
|
||||
PPE0 = pickle.load(PPE0_raw)['pdrop']*(-barye2mmHg)
|
||||
STE0 = pickle.load(STE0_raw)['pdrop']*(-barye2mmHg)
|
||||
|
||||
curpath = datapath + 'sequences/aorta_'+mesh_size+'.npz'
|
||||
p = np.load(curpath)
|
||||
px = p['x']
|
||||
py = p['y']
|
||||
pz = p['z']
|
||||
v = np.sqrt(px[:,:,:,t_star]**2 + py[:,:,:,t_star]**2 + pz[:,:,:,t_star]**2)
|
||||
max0 = np.where(v==np.max(v))
|
||||
V_MEAN[l] = ref_V
|
||||
V_STD[l] = 0
|
||||
PPE_MEAN[l] = PPE0[6]
|
||||
PPE_STD[l] = 0
|
||||
STE_MEAN[l] = STE0[6]
|
||||
STE_STD[l] = 0
|
||||
elif R[l]==1:
|
||||
PPE_MEAN[l] = 0
|
||||
PPE_STD[l] = 0
|
||||
STE_MEAN[l] = 0
|
||||
STE_STD[l] = 0
|
||||
V_MEAN[l] = maxv1
|
||||
V_STD[l] = 0
|
||||
Q_MEAN[l] = maxq1
|
||||
Q_STD[l] = 0
|
||||
|
||||
else:
|
||||
PPE_MEAN[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/ppemean_R'+ str(R[l]) +'.txt')
|
||||
PPE_STD[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/ppestd_R'+ str(R[l]) +'.txt')
|
||||
STE_MEAN[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/stemean_R'+ str(R[l]) +'.txt')
|
||||
STE_STD[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/stestd_R'+ str(R[l]) +'.txt')
|
||||
V_MEAN[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/vmean_R'+ str(R[l]) +'.txt')
|
||||
V_STD[l] = np.loadtxt(datapath + 'maxpv/'+mesh_size + '/vstd_R'+ str(R[l]) +'.txt')
|
||||
Q_MEAN[l] = -np.loadtxt(datapath + 'maxpv/'+mesh_size + '/Q2_R'+ str(R[l]) +'.txt')
|
||||
Q_STD[l] = -np.loadtxt(datapath + 'maxpv/'+mesh_size + '/Qstd2_R'+ str(R[l]) +'.txt')
|
||||
|
||||
|
||||
|
||||
plt.figure(figsize=(15, 5), dpi=100)
|
||||
plt.annotate('$'+mesh_size+'$', xy=(-0.2, 1.1), xycoords='axes fraction',fontsize=15)
|
||||
|
||||
|
||||
Rvec = np.linspace(-10,R[-1]+5,100)
|
||||
plt.subplot(1,3,1)
|
||||
#plt.plot(Rvec,hline,color='k',linestyle='--')
|
||||
plt.errorbar(R,PPE_MEAN, yerr=PPE_STD,color=options['ppecol'],marker='o',label= '$PPE$')
|
||||
plt.errorbar(R,STE_MEAN, yerr=STE_STD,color=options['stecol'],marker='o',label= '$STE$')
|
||||
plt.xlim([-2,R[-1]+5])
|
||||
plt.ylim([-0.1,2.0])
|
||||
plt.xlabel(r'$R$',fontsize=20)
|
||||
plt.legend(fontsize=12,loc=2)
|
||||
plt.title('$ l_2 \ error \ in \ Peak \ pressure$',fontsize=16)
|
||||
plt.xticks(R)
|
||||
plt.ylabel(r'$ || p - p^{ref} ||/|| p^{ref} ||_{l2} $',fontsize=16)
|
||||
|
||||
|
||||
plt.subplot(1,3,2)
|
||||
#plt.plot([0],[ref_V],color='k',marker='o',label= '$ref$')
|
||||
Rvec = np.linspace(-10,R[-1]+7,100)
|
||||
hline = Rvec*0+ref_V
|
||||
plt.plot(Rvec,hline,color='royalblue',linestyle='--')
|
||||
plt.errorbar(R,V_MEAN, yerr=V_STD,color='royalblue',marker='o',label= '$' + mesh_size + '$')
|
||||
plt.xlim([-2,R[-1]+5])
|
||||
plt.ylim([0,350])
|
||||
plt.xlabel(r'$R$',fontsize=20)
|
||||
plt.ylabel(r'$ v \ \ cm/s$',fontsize=16)
|
||||
plt.xticks(R)
|
||||
plt.title('$Peak \ velocity$',fontsize=16)
|
||||
#plt.legend(fontsize=15)
|
||||
|
||||
plt.subplot(1,3,3)
|
||||
Rvec = np.linspace(-10,R[-1]+7,100)
|
||||
hline = Rvec*0+ref_Q
|
||||
plt.plot(Rvec,hline,color='mediumvioletred',linestyle='--')
|
||||
plt.errorbar(R,Q_MEAN, yerr=Q_STD,color='mediumvioletred',marker='o',label= '$' + mesh_size + '$')
|
||||
plt.xlim([-2,R[-1]+5])
|
||||
plt.xlabel(r'$R$',fontsize=20)
|
||||
plt.ylabel(r'$ Q \ \ ml/s$',fontsize=16)
|
||||
plt.xticks(R)
|
||||
plt.ylim([150,550])
|
||||
plt.title('$Peak \ Flux $',fontsize=16)
|
||||
|
||||
|
||||
|
||||
|
||||
plt.show()
|
||||
|
||||
def CLOCK(t1, t2):
|
||||
@ -1411,6 +1071,9 @@ def ROUTINE(options):
|
||||
if options['Error-curves']['apply']:
|
||||
print('--- Error-curves analysis ---')
|
||||
ratio = False
|
||||
fac=1
|
||||
if '11mm' in options['Error-curves']['subfolders']:
|
||||
fac=100
|
||||
for types in options['Error-curves']['type']:
|
||||
if types=='mean_ratio':
|
||||
types = 'mean'
|
||||
@ -1418,6 +1081,9 @@ def ROUTINE(options):
|
||||
if types=='max_ratio':
|
||||
types = 'max'
|
||||
ratio = True
|
||||
if types=='norm2_m':
|
||||
types='norm2'
|
||||
meas=True
|
||||
nc = 0
|
||||
if len(options['Error-curves']['subfolders'])==0:
|
||||
ucomp = []
|
||||
@ -1445,45 +1111,261 @@ def ROUTINE(options):
|
||||
for subf in options['Error-curves']['subfolders']:
|
||||
ucomp = []
|
||||
wcomp = []
|
||||
if 'colors' in options['Error-curves']:
|
||||
print('colors setted...')
|
||||
colorset = options['Error-curves']['colors']
|
||||
colorsetted = True
|
||||
else:
|
||||
colorsetted = False
|
||||
styles = options['Error-curves']['styles']
|
||||
labelset = options['Error-curves']['labels']
|
||||
path = options['Error-curves']['folder'] + subf + '/'
|
||||
try:
|
||||
ucomp = np.loadtxt(path + '/u'+types+'.txt')
|
||||
wcomp = np.loadtxt(path + '/w'+types+'.txt')
|
||||
times = np.loadtxt(path + '/times.txt')
|
||||
except IOError:
|
||||
print('no cError-curves for ' + subf)
|
||||
wcomp = np.loadtxt(path + 'w'+types+'.txt')
|
||||
times = np.loadtxt(path + 'times.txt')
|
||||
if types != 'grad':
|
||||
ucomp = np.loadtxt(path + 'u'+types+'.txt')
|
||||
|
||||
|
||||
if colorsetted:
|
||||
if not ratio:
|
||||
plt.plot(
|
||||
times, ucomp, color=colorset[nc], linestyle='-', label= '$u'+ subf +'$' )
|
||||
|
||||
plt.plot(
|
||||
times, wcomp, color=colorset[nc], linestyle='--', label='$w'+subf+'$')
|
||||
if types not in ['grad']:
|
||||
if meas:
|
||||
plt.plot(times, fac*ucomp, color=colorset[nc], linestyle='--', label= '$ u \ '+ labelset[nc] +'$',linewidth=2.5 )
|
||||
plt.plot(times, fac*wcomp, color=colorset[nc], linestyle=styles[nc], label= '$ w \ '+ labelset[nc] +'$',linewidth=2.5)
|
||||
else:
|
||||
wu = wcomp/ucomp
|
||||
plt.plot(
|
||||
times, wu, color=colorset[nc], linestyle='-', label= '$'+ labelset[nc] +'$' )
|
||||
times, wu, color=colorset[nc], linestyle=styles[nc], label= '$'+ labelset[nc] +'$' )
|
||||
nc +=1
|
||||
else:
|
||||
if not ratio:
|
||||
if types not in ['grad']:
|
||||
if meas:
|
||||
plt.plot(times, fac*ucomp, linestyle='--', label= '$'+ labelset[nc] +'$' )
|
||||
else:
|
||||
plt.plot(times, fac*ucomp, linestyle='--', label= '$'+ labelset[nc] +'$' )
|
||||
plt.plot(
|
||||
times, fac*wcomp, linestyle=styles[nc], label= '$'+ labelset[nc] +'$')
|
||||
else:
|
||||
wu = wcomp/ucomp
|
||||
plt.plot(
|
||||
times, wu, linestyle=styles[nc], label= '$'+ labelset[nc] +'$' )
|
||||
nc +=1
|
||||
|
||||
|
||||
|
||||
plt.xlabel('$time \ \ (s)$', fontsize=18)
|
||||
plt.legend(fontsize=14)
|
||||
if options['Error-curves']['title']:
|
||||
plt.title(options['Error-curves']['title'], fontsize=18)
|
||||
|
||||
if not ratio:
|
||||
if types == 'grad':
|
||||
plt.ylim([0, 230])
|
||||
plt.ylabel('$ |grad(w)|_2 \ \ (1/s)$', fontsize=18)
|
||||
elif types == 'norm2':
|
||||
plt.ylim([0, 52])
|
||||
plt.ylabel('$ |w|_2 \ \ (cm/s)$', fontsize=18)
|
||||
else:
|
||||
plt.ylabel('$velocity \ \ (cm/s)$', fontsize=18)
|
||||
plt.savefig(options['Error-curves']['outpath'] + types + '.png', dpi=500, bbox_inches='tight')
|
||||
else:
|
||||
plt.ylabel('$|w/u|$', fontsize=18)
|
||||
#if 'max' in types:
|
||||
#plt.ylim([0, 1.8])
|
||||
plt.savefig(options['Error-curves']['outpath'] + types + '_ratio.png', dpi=500, bbox_inches='tight')
|
||||
plt.show()
|
||||
|
||||
if 'Histograms_checkpoint' in options:
|
||||
if options['Histograms_checkpoint']['apply']:
|
||||
print('--- Histograms ---')
|
||||
path = options['Histograms_checkpoint']['path']
|
||||
freq = np.loadtxt(path + 'hist_freq.txt')
|
||||
edges = np.loadtxt(path + 'hist_edges.txt')
|
||||
fig, ax = plt.subplots()
|
||||
#ax.bar(edges[:-1], freq, width=np.diff(edges), edgecolor="black", align="edge")
|
||||
ax.bar(edges[:-1], freq, width=np.diff(edges), align="edge")
|
||||
plt.title(options['Histograms_checkpoint']['title'], fontsize=18)
|
||||
plt.xlim([0 , 50])
|
||||
plt.ylim([0 , 1.8])
|
||||
plt.savefig(path + 'hist.png', dpi=500, bbox_inches='tight')
|
||||
plt.show()
|
||||
|
||||
if 'Pressure_drops' in options:
|
||||
if options['Pressure_drops']['apply']:
|
||||
print('--- Pressure_drops ---')
|
||||
import pickle
|
||||
nc = 0
|
||||
tommhg = options['Pressure_drops']['convertor']
|
||||
|
||||
for subf in options['Pressure_drops']['subfolders']:
|
||||
ucomp = []
|
||||
wcomp = []
|
||||
if 'colors' in options['Pressure_drops']:
|
||||
colorset = options['Pressure_drops']['colors']
|
||||
colorsetted = True
|
||||
else:
|
||||
colorsetted = False
|
||||
styles = options['Pressure_drops']['styles']
|
||||
labelset = options['Pressure_drops']['labels']
|
||||
path = options['Pressure_drops']['folder'] + subf + '/'
|
||||
dataname = 'pdrop_COR_impl_stan.dat'
|
||||
if 'STE' in path:
|
||||
dataname = 'pdrop_STE_impl_stan.dat'
|
||||
if labelset[nc]=='ref':
|
||||
dataname = 'pdrop.dat'
|
||||
data = open(path+dataname, 'rb')
|
||||
p_drop = pickle.load(data)['pdrop']/tommhg
|
||||
data = open(path+dataname, 'rb')
|
||||
times = pickle.load(data)['time']
|
||||
|
||||
if labelset[nc] == 'ref':
|
||||
plt.plot(times, p_drop,color='black', linestyle='-', label= '$ref$' )
|
||||
else:
|
||||
|
||||
if colorsetted:
|
||||
plt.plot(
|
||||
times, p_drop, color=colorset[nc], linestyle=styles[nc], label= '$'+ labelset[nc] +'$' )
|
||||
else:
|
||||
plt.plot(times, p_drop, linestyle=styles[nc], label= '$'+ labelset[nc] +'$' )
|
||||
|
||||
if options['Pressure_drops']['catheter']:
|
||||
|
||||
c_path = '/home/yeye/Desktop/PhD/MEDICAL_DATA/Study_David/catheter_data/catheter_'+ labelset[nc]+'_rest_stats.csv'
|
||||
|
||||
|
||||
with open(c_path, 'r') as csvfile:
|
||||
mylist = [row[0] for row in csv.reader(csvfile, delimiter=';')]
|
||||
|
||||
Values = np.array(mylist)
|
||||
catheter = np.zeros([len(Values)-2])
|
||||
tcat = np.zeros([len(Values)-2])
|
||||
for l in range(2,len(Values)):
|
||||
row = Values[l].split(',')
|
||||
catheter[l-2] = float(row[5])
|
||||
tcat[l-2] = float(row[0])
|
||||
|
||||
|
||||
if '11mm' in subf:
|
||||
tdelay = 0.015
|
||||
elif '9mm' in subf:
|
||||
tdelay = -0.12
|
||||
elif '13mm' in subf:
|
||||
tdelay = 0.1
|
||||
elif 'Normal' in subf:
|
||||
tdelay = -0.01
|
||||
|
||||
plt.plot(tcat+tdelay,catheter,color=colorset[nc],linestyle='--')# ,label='$cat' + subf + '$')
|
||||
|
||||
nc +=1
|
||||
|
||||
|
||||
#plt.ylim([0, 170])
|
||||
plt.xlabel('$time \ \ (s)$', fontsize=18)
|
||||
plt.legend(fontsize=16)
|
||||
if options['Error-curves']['title']:
|
||||
plt.title(options['Error-curves']['title'], fontsize=18)
|
||||
|
||||
if not ratio:
|
||||
plt.ylabel('$velocity \ \ (cm/s)$', fontsize=18)
|
||||
plt.savefig(options['Error-curves']['outpath'] + types + '.png', dpi=500, bbox_inches='tight')
|
||||
else:
|
||||
plt.ylabel('$w/u$', fontsize=18)
|
||||
if 'max' in types:
|
||||
plt.ylim([0, 1.8])
|
||||
plt.savefig(options['Error-curves']['outpath'] + types + '_ratio.png', dpi=500, bbox_inches='tight')
|
||||
plt.legend(fontsize=14)
|
||||
if options['Pressure_drops']['title']:
|
||||
plt.title(options['Pressure_drops']['title'], fontsize=18)
|
||||
plt.ylabel('$ \delta P \ \ (mmHg)$', fontsize=18)
|
||||
plt.savefig(options['Pressure_drops']['outpath'] + 'pressure_drops.png', dpi=500, bbox_inches='tight')
|
||||
plt.show()
|
||||
|
||||
if 'l2_comp' in options:
|
||||
if options['l2_comp']['apply']:
|
||||
print('--- L2 component analysis ---')
|
||||
fig, ax = plt.subplots()
|
||||
for subf in options['l2_comp']['subfolder']:
|
||||
path = options['l2_comp']['folder'] + subf + '/'
|
||||
colors = options['l2_comp']['colors']
|
||||
mode = options['l2_comp']['mode']['type']
|
||||
|
||||
if mode in ['gain','gain_compressed']:
|
||||
gain = True
|
||||
path_to_comp = options['l2_comp']['mode']['comp']
|
||||
wx = np.loadtxt(path_to_comp + '/wx.txt')
|
||||
wy = np.loadtxt(path_to_comp + '/wy.txt')
|
||||
wz = np.loadtxt(path_to_comp + '/wz.txt')
|
||||
else:
|
||||
gain = False
|
||||
wx = np.loadtxt(path + '/wx.txt')
|
||||
wy = np.loadtxt(path + '/wy.txt')
|
||||
wz = np.loadtxt(path + '/wz.txt')
|
||||
|
||||
times = np.loadtxt(path + '/times.txt')
|
||||
if subf != 'SNRinfV120' and gain:
|
||||
varux = np.loadtxt(path + '/varux.txt')
|
||||
varuy = np.loadtxt(path + '/varuy.txt')
|
||||
varuz = np.loadtxt(path + '/varuz.txt')
|
||||
if 'SNRinfV120' in subf:
|
||||
lsty = '--'
|
||||
labels = ['','','','','']
|
||||
else:
|
||||
lsty = '-'
|
||||
lsty2 = '--'
|
||||
labels = ['$wx$','$wy$','$wz$','$div$']
|
||||
labels2 = ['$\delta u_x$','$\delta u_y$','$\delta u_z$']
|
||||
labels3 = ['$x$','$y$','$z$']
|
||||
|
||||
if mode == 'gain':
|
||||
plt.plot(times, varux, color = colors[0], linestyle=lsty2 , label= labels2[0] )
|
||||
plt.plot(times, varuy, color = colors[1], linestyle=lsty2 , label= labels2[1] )
|
||||
plt.plot(times, varuz, color = colors[2], linestyle=lsty2 , label= labels2[2] )
|
||||
plt.plot(times, wx, color = colors[0], linestyle=lsty, label= labels[0] )
|
||||
plt.plot(times, wy, color = colors[1], linestyle=lsty, label= labels[1] )
|
||||
plt.plot(times, wz, color = colors[2], linestyle=lsty, label= labels[2] )
|
||||
elif mode == 'gain_compressed':
|
||||
plt.plot(times, varux-wx, color = colors[0], linestyle=lsty, label= labels3[0] )
|
||||
plt.plot(times, varuy-wy, color = colors[1], linestyle=lsty, label= labels3[1] )
|
||||
plt.plot(times, varuz-wz, color = colors[2], linestyle=lsty, label= labels3[2] )
|
||||
else:
|
||||
plt.plot(times, wx, color = colors[0], linestyle=lsty, label= labels[0] )
|
||||
plt.plot(times, wy, color = colors[1], linestyle=lsty, label= labels[1] )
|
||||
plt.plot(times, wz, color = colors[2], linestyle=lsty, label= labels[2] )
|
||||
|
||||
plt.xlabel('$time \ \ (s)$', fontsize=18)
|
||||
|
||||
if options['l2_comp']['div']:
|
||||
div = np.loadtxt(path + 'div.txt')
|
||||
div_rescaled = div*0.01
|
||||
div_rescaled = div_rescaled + 0.1
|
||||
plt.plot(times, div_rescaled, color = 'indigo', linestyle=lsty, label= labels[3] )
|
||||
|
||||
if 'title' in options['l2_comp']:
|
||||
if options['l2_comp']['title']:
|
||||
plt.title(options['l2_comp']['title'], fontsize=18)
|
||||
|
||||
|
||||
|
||||
if options['l2_comp']['aliasing']:
|
||||
if 'Poiseuille' in options['l2_comp']['folder']:
|
||||
print('adding alaising color in Poiseuille')
|
||||
import matplotlib.transforms as mtransforms
|
||||
trans = mtransforms.blended_transform_factory(ax.transData, ax.transAxes)
|
||||
if 'SNR10' in subf:
|
||||
time_al = [0.15,0.78]
|
||||
elif 'SNRinf' in subf:
|
||||
time_al = [0.21,0.78]
|
||||
pm_al = 0.5*(time_al[1] + time_al[0])
|
||||
r_al = 0.5*(time_al[1] - time_al[0])
|
||||
ax.fill_between(times, 0, 1, where=np.abs(times -pm_al)<= r_al ,facecolor='gold', alpha=0.4, transform=trans)
|
||||
if mode == 'gain_compressed':
|
||||
ax.text(pm_al/times[-1], 0.55, '$aliasing$', horizontalalignment='center',verticalalignment='center', transform=ax.transAxes,fontsize=17)
|
||||
else:
|
||||
ax.text(pm_al/times[-1], 0.82, '$aliasing$', horizontalalignment='center',verticalalignment='center', transform=ax.transAxes,fontsize=17)
|
||||
|
||||
leg = plt.legend(fancybox=True,fontsize=16)
|
||||
leg.get_frame().set_linewidth(0.0)
|
||||
ax.tick_params(axis='both', which='major', labelsize=14)
|
||||
#plt.ylim([-0.005 , 0.235])
|
||||
|
||||
if mode == 'gain_compressed':
|
||||
plt.ylim([-0.25 , 1.75])
|
||||
plt.ylabel('$|| \delta u ||_{L2} - || w ||_{L2}$', fontsize=18)
|
||||
if not gain:
|
||||
plt.ylim([-0.005 , 0.5])
|
||||
plt.ylabel('$ \sqrt{\int w^2 dx /| \Omega|}/ venc$', fontsize=18)
|
||||
|
||||
plt.savefig(options['l2_comp']['folder'] + options['l2_comp']['name'] + '.png', dpi=500, bbox_inches='tight')
|
||||
plt.show()
|
||||
|
||||
|
||||
|
||||
|
||||
185
codes/MRI.py
185
codes/MRI.py
@ -3,13 +3,10 @@
|
||||
# Workspace for MRI analysis of the 4Dflow data
|
||||
#
|
||||
# written by Jeremias Garay L: j.e.garay.labra@rug.nl
|
||||
# Fernanda te amo
|
||||
# for autoreload in ipython3
|
||||
# %load_ext autoreload
|
||||
# %autoreload 2
|
||||
################################################################
|
||||
import h5py
|
||||
from dPdirectestim.dPdirectestim import *
|
||||
from dolfin import *
|
||||
import dolfin
|
||||
import numpy as np
|
||||
@ -999,14 +996,8 @@ def CLOCK(rank,t1,t2):
|
||||
print('Total time: ' + str(time_hour) + ' hrs, ' + str(time_min) + ' min, ' + str(time_sec) + ' s')
|
||||
|
||||
|
||||
|
||||
def SCANNER(options):
|
||||
|
||||
########################################
|
||||
#
|
||||
# Basic Tools
|
||||
#
|
||||
########################################
|
||||
if 'kspace_cib' in options:
|
||||
if options['kspace_cib']['apply']:
|
||||
print('--- kspace from CIB data ---')
|
||||
@ -1416,21 +1407,15 @@ def SCANNER(options):
|
||||
else:
|
||||
CIBtoH5(path_to_cib,times,dt,outpath,flip=flip)
|
||||
|
||||
########################################
|
||||
#
|
||||
# Undersampling
|
||||
#
|
||||
########################################
|
||||
if 'cs' in options:
|
||||
if options['cs']['apply']:
|
||||
if rank==0:
|
||||
print('Applying Compressed Sensing')
|
||||
|
||||
|
||||
[Sqx, Sqy, Sqz] = LOADsequences(options['cs']['seqpath'])
|
||||
|
||||
|
||||
import CS
|
||||
if 'short' in options['cs']:
|
||||
if options['cs']['short']:
|
||||
[Mx,My,Mz] = LOADsequences(options['cs']['Mpath'])
|
||||
CS.undersampling_short(Mx,My,Mz,options)
|
||||
@ -1457,12 +1442,6 @@ def SCANNER(options):
|
||||
print('saving the sequences' + options['SENSE']['savepath'])
|
||||
np.savez_compressed(options['SENSE']['savepath'], x=MxS,y=MyS,z=MzS)
|
||||
|
||||
########################################
|
||||
#
|
||||
# Writing Checkpoint from Sequence
|
||||
#
|
||||
########################################
|
||||
|
||||
if 'create_checkpoint' in options:
|
||||
if options['create_checkpoint']['apply']:
|
||||
print('--- Create Checkpoint ---')
|
||||
@ -1529,7 +1508,7 @@ def SCANNER(options):
|
||||
comm = MESH['mesh'].mpi_comm()
|
||||
dt = options['create_checkpoint']['dt']
|
||||
if options['create_checkpoint']['xdmf']:
|
||||
xdmf_u = XDMFFile(options['create_checkpoint']['savepath']+'u.xdmf')
|
||||
xdmf_u = XDMFFile(options['create_checkpoint']['savepath']+ 'R' + str(r) + '/u.xdmf')
|
||||
|
||||
for l in range(len(vel_seq)):
|
||||
if rank == 0:
|
||||
@ -1545,11 +1524,6 @@ def SCANNER(options):
|
||||
inout.write_HDF5_data(
|
||||
comm, path + '/u.h5', vel_seq[l], '/u', t=l*dt)
|
||||
|
||||
########################################
|
||||
#
|
||||
# Relative Pressure Estimators
|
||||
#
|
||||
########################################
|
||||
if 'reference' in options:
|
||||
if options['reference']['apply']:
|
||||
if rank == 0:
|
||||
@ -1688,157 +1662,6 @@ def SCANNER(options):
|
||||
if rank==0:
|
||||
print(' ')
|
||||
|
||||
if 'peak_pv' in options:
|
||||
|
||||
if options['peak_pv']['apply']:
|
||||
import CS
|
||||
import pickle
|
||||
import sys
|
||||
import logging
|
||||
# DPestim
|
||||
logging.getLogger().setLevel(logging.INFO)
|
||||
parameters['form_compiler']['optimize'] = True
|
||||
parameters['form_compiler']['cpp_optimize'] = True
|
||||
parameters['form_compiler']['cpp_optimize_flags'] = '-O3 -ffast-math -march=native'
|
||||
infile_dp = options['peak_pv']['infile_dp']
|
||||
estimator = DPDirectEstim(infile_dp)
|
||||
|
||||
barye2mmHg = 1/1333.22387415
|
||||
t_star = 0.185
|
||||
if rank==0:
|
||||
print('Computing Velocity and Pressure at Peak Systole')
|
||||
print('The inlet max occurs at ' + str(t_star) + ' sec')
|
||||
|
||||
|
||||
[BOX,AORTA,LEO] = CREATEmeshes(options)
|
||||
|
||||
if options['peak_pv']['mesh_into']=='leo':
|
||||
MESH = LEO
|
||||
del AORTA
|
||||
if options['peak_pv']['mesh_into']=='aorta':
|
||||
MESH = AORTA
|
||||
del LEO
|
||||
|
||||
if options['peak_pv']['p_comp']=='error':
|
||||
if rank==0:
|
||||
print('Reading Pressure Reference')
|
||||
P0_PPE = READcheckpoint(MESH,'p',options,options['checkpoint_path'],'p_PPE_impl_stan')
|
||||
P0_STE = READcheckpoint(MESH,'p',options,options['checkpoint_path'],'p_STE_impl_stan')
|
||||
|
||||
[Sqx,Sqy,Sqz] = LOADsequences(options['peak_pv']['orig_seq'])
|
||||
Nite = options['peak_pv']['N_CS']
|
||||
[row,col,dep,numt] = Sqz.shape
|
||||
frms_num = 3
|
||||
peakslice = options['peak_pv']['peak_slice']
|
||||
R = options['peak_pv']['R']
|
||||
|
||||
v0 = np.sqrt(Sqx[:,:,:,peakslice]**2 + Sqy[:,:,:,peakslice]**2 + Sqz[:,:,:,peakslice]**2)
|
||||
max0 = np.where(v0==np.max(v0))
|
||||
|
||||
qqvec = {}
|
||||
for ss in options['peak_pv']['flux_bnd']:
|
||||
qqvec[ss] = np.zeros([Nite])
|
||||
|
||||
ppemax = np.zeros([Nite])
|
||||
stemax = np.zeros([Nite])
|
||||
vmax = np.zeros([Nite])
|
||||
slrdmax = peakslice
|
||||
# Selecting around the max only
|
||||
slrdmax = 1
|
||||
Sqx = Sqx[:,:,:,peakslice-1:peakslice+2]
|
||||
Sqy = Sqy[:,:,:,peakslice-1:peakslice+2]
|
||||
Sqz = Sqz[:,:,:,peakslice-1:peakslice+2]
|
||||
|
||||
for l in range(len(R)):
|
||||
if rank==0:
|
||||
print('Peak Systole velocity and pressure at R = ' + str(R[l]))
|
||||
|
||||
sx_cs = np.zeros([row,col,dep,frms_num,Nite])
|
||||
sy_cs = np.zeros([row,col,dep,frms_num,Nite])
|
||||
sz_cs = np.zeros([row,col,dep,frms_num,Nite])
|
||||
|
||||
for k in range(Nite):
|
||||
if rank==0:
|
||||
print('CS iteration number ' + str(k+1))
|
||||
[xcs,ycs,zcs] = CS.undersampling_peakpv(Sqx,Sqy,Sqz,options,R[l])
|
||||
sx_cs[:,:,:,:,k] = xcs
|
||||
sy_cs[:,:,:,:,k] = ycs
|
||||
sz_cs[:,:,:,:,k] = zcs
|
||||
vk = np.sqrt(sx_cs[:,:,:,1,k]**2 + sy_cs[:,:,:,1,k]**2 + sz_cs[:,:,:,1,k]**2)
|
||||
vmax[k] = vk[max0]
|
||||
|
||||
if rank==0:
|
||||
print('\n CS done')
|
||||
|
||||
# To write the checkpoints
|
||||
vel_seq = SqtoH5(BOX,MESH,sx_cs[:,:,:,:,k],sy_cs[:,:,:,:,k],sz_cs[:,:,:,:,k])
|
||||
comm = MESH['mesh'].mpi_comm()
|
||||
|
||||
# Computing the Fluxes
|
||||
if rank==0:
|
||||
print('\n Computing the Flux')
|
||||
QQ = Fluxes(MESH,vel_seq,options,options['peak_pv']['flux_bnd'])
|
||||
|
||||
for ss in options['peak_pv']['flux_bnd']:
|
||||
qqvec[ss][k] = QQ[ss][slrdmax]
|
||||
|
||||
if rank==0:
|
||||
print('\n Writing checkpoints')
|
||||
|
||||
for ns in range(len(vel_seq)):
|
||||
pathss = options['peak_pv']['savepath'] + 'H5/checkpoint/{i}/'.format(i=ns)
|
||||
if l<10 and l>0:
|
||||
pathss = options['peak_pv']['savepath'] + 'H5/checkpoint/0{i}/'.format(i=ns)
|
||||
inout.write_HDF5_data(comm, pathss + '/u.h5', vel_seq[ns], '/u', t=0)
|
||||
if rank==0:
|
||||
print('\n The checkpoints were wrote')
|
||||
|
||||
# Computing the Pressure Drop
|
||||
estimator.estimate()
|
||||
# Reading the results
|
||||
if options['peak_pv']['p_comp']=='peak':
|
||||
ppe_raw = open(options['peak_pv']['savepath'] + '/H5/pdrop_PPE_impl_stan.dat','rb')
|
||||
ste_raw = open(options['peak_pv']['savepath'] + '/H5/pdrop_STE_impl_stan.dat','rb')
|
||||
ppe = pickle.load(ppe_raw)['pdrop']*(-barye2mmHg)
|
||||
ste = pickle.load(ste_raw)['pdrop']*(-barye2mmHg)
|
||||
p1max[k] = ppe[slrdmax]
|
||||
p2max[k] = ste[slrdmax]
|
||||
elif options['peak_pv']['p_comp']=='error':
|
||||
PPE = READcheckpoint(MESH,'p',options,options['peak_pv']['savepath']+'H5/checkpoint/','p_PPE_impl_stan')
|
||||
STE = READcheckpoint(MESH,'p',options,options['peak_pv']['savepath']+'H5/checkpoint/','p_STE_impl_stan')
|
||||
ppe_vec_0 = P0_PPE[peakslice].vector().get_local() - P0_PPE[peakslice].vector().get_local()[0]
|
||||
ppe_vec = PPE[slrdmax].vector().get_local() - PPE[slrdmax].vector().get_local()[0]
|
||||
ste_vec_0 = P0_STE[peakslice].vector().get_local() - P0_STE[peakslice].vector().get_local()[0]
|
||||
ste_vec = STE[slrdmax].vector().get_local() - STE[slrdmax].vector().get_local()[0]
|
||||
ppemax[k] = np.linalg.norm(ppe_vec_0 - ppe_vec)/np.linalg.norm(ppe_vec_0)
|
||||
stemax[k] = np.linalg.norm(ste_vec_0 - ste_vec)/np.linalg.norm(ste_vec_0)
|
||||
else:
|
||||
raise Exception('Pressure computation not recognize!')
|
||||
|
||||
|
||||
# VELOCITIES
|
||||
vmean = np.mean(vmax)
|
||||
vstd = np.std(vmax)
|
||||
# PRESSURES
|
||||
ppemean = np.mean(ppemax)
|
||||
stemean = np.mean(stemax)
|
||||
ppestd = np.std(ppemax)
|
||||
stestd = np.std(stemax)
|
||||
|
||||
|
||||
if options['peak_pv']['save']:
|
||||
if rank==0:
|
||||
print('\n saving the files in ' + options['peak_pv']['savepath'])
|
||||
for ss in options['peak_pv']['flux_bnd']:
|
||||
np.savetxt( options['peak_pv']['savepath'] + 'Q'+str(ss) +'_R'+str(R[l])+'.txt', [np.mean(qqvec[ss])])
|
||||
np.savetxt( options['peak_pv']['savepath'] + 'Qstd'+str(ss) +'_R'+str(R[l])+'.txt', [np.std(qqvec[ss])])
|
||||
np.savetxt( options['peak_pv']['savepath'] + 'ppemean_R'+str(R[l])+'.txt', [ppemean] )
|
||||
np.savetxt( options['peak_pv']['savepath'] + 'stemean_R'+str(R[l])+'.txt', [stemean] )
|
||||
np.savetxt( options['peak_pv']['savepath'] + 'vmean_R'+str(R[l])+'.txt', [vmean] )
|
||||
np.savetxt( options['peak_pv']['savepath'] + 'ppestd_R'+str(R[l])+'.txt', [ppestd] )
|
||||
np.savetxt( options['peak_pv']['savepath'] + 'stestd_R'+str(R[l])+'.txt', [stestd] )
|
||||
np.savetxt( options['peak_pv']['savepath'] + 'vstd_R'+str(R[l])+'.txt', [vstd] )
|
||||
|
||||
if 'change_mesh' in options:
|
||||
if options['change_mesh']['apply']:
|
||||
if rank == 0:
|
||||
@ -1861,9 +1684,9 @@ def SCANNER(options):
|
||||
changed = {}
|
||||
#W = LEO['FEM'].sub(0).collapse()
|
||||
comm = MESH_out['mesh'].mpi_comm()
|
||||
v2 = Function(MESH_out['FEM'])
|
||||
|
||||
for k in range(len(list(origin))):
|
||||
v2 = Function(MESH_out['FEM'])
|
||||
if rank == 0:
|
||||
print('CHANGING: index', k)
|
||||
LagrangeInterpolator.interpolate(v2, origin[k])
|
||||
@ -1878,7 +1701,7 @@ def SCANNER(options):
|
||||
if rank == 0:
|
||||
print('saving checkpoint', l)
|
||||
path = options['change_mesh']['savepath'] + \
|
||||
'R1/checkpoint/{i}/'.format(i=l)
|
||||
'checkpoint/{i}/'.format(i=l)
|
||||
writepath = path + '/'+options['change_mesh']['mode']+'.h5'
|
||||
inout.write_HDF5_data(
|
||||
comm, writepath, changed[l] ,'/'+options['change_mesh']['mode'], t=l*dt)
|
||||
|
||||
@ -109,14 +109,10 @@ def WORKcheck(MESH, mode, output_path, checkpoint_path, filename, outname, optio
|
||||
|
||||
if mode == 'p' or mode == 'p_cib':
|
||||
xdmf_p = XDMFFile(output_path+outname+'.xdmf')
|
||||
for k in range(0, len(indexes), 1):
|
||||
dt = options['Pressure']['dt']
|
||||
for k in range(0, len(indexes), options['Pressure']['undersampling']):
|
||||
te = k*dt
|
||||
path = checkpoint_path + str(indexes[k]) + '/'+filename+'.h5'
|
||||
|
||||
if filename == 'p':
|
||||
if k < 10 and k > 0:
|
||||
path = checkpoint_path + '0' + \
|
||||
str(indexes[k]) + '/'+filename+'.h5'
|
||||
|
||||
p = Function(W)
|
||||
if mode == 'p':
|
||||
barye2mmHg = 1/1333.22387415
|
||||
@ -126,36 +122,10 @@ def WORKcheck(MESH, mode, output_path, checkpoint_path, filename, outname, optio
|
||||
hdf = HDF5File(MESH['mesh'].mpi_comm(), path, 'r')
|
||||
hdf.read(p, 'p/vector_0')
|
||||
hdf.close()
|
||||
|
||||
p1vec = p.vector().get_local()
|
||||
p1vec = p1vec - np.mean(p1vec)
|
||||
#p1vec = p1vec - np.mean(p1vec)
|
||||
p.vector()[:] = p1vec*barye2mmHg
|
||||
xdmf_p.write(p, te)
|
||||
te = te + dt
|
||||
numt = numt + 1
|
||||
|
||||
if mode == 'divu':
|
||||
xdmf_u = XDMFFile(output_path+outname+'.xdmf')
|
||||
for k in range(0, len(indexes), 1):
|
||||
path = checkpoint_path + str(indexes[k]) + '/'+filename+'.h5'
|
||||
|
||||
if indexes[k] < 10 and indexes[k] > 0:
|
||||
path = checkpoint_path + '0' + \
|
||||
str(indexes[k]) + '/'+filename+'.h5'
|
||||
|
||||
v = Function(V)
|
||||
dv = Function(W)
|
||||
|
||||
dv.rename('div', outname)
|
||||
comm = MPI.COMM_WORLD
|
||||
hdf = HDF5File(MESH['mesh'].mpi_comm(), path, 'r')
|
||||
hdf.read(v, 'u/vector_0')
|
||||
|
||||
hdf.close()
|
||||
dv.assign(project(div(v), W))
|
||||
xdmf_u.write(dv, te)
|
||||
te = te + dt
|
||||
numt = numt + 1
|
||||
|
||||
def READcheckpoint(MESH, mode, output_path, checkpoint_path, filename, outname, options, flow=False, bnds=None):
|
||||
|
||||
@ -203,7 +173,7 @@ def READcheckpoint(MESH, mode, output_path, checkpoint_path, filename, outname,
|
||||
freq,edges = np.histogram(ValuesPeak, bins=80, density=True)
|
||||
#Saving the histogram
|
||||
print('Saving at ' + output_path)
|
||||
np.savetxt(output_path + 'hist_frew.txt', freq)
|
||||
np.savetxt(output_path + 'hist_freq.txt', freq)
|
||||
np.savetxt(output_path + 'hist_edges.txt', edges)
|
||||
|
||||
if mode == 'perturbation':
|
||||
@ -235,6 +205,20 @@ def READcheckpoint(MESH, mode, output_path, checkpoint_path, filename, outname,
|
||||
|
||||
noise_in_coil = options['Perturbation']['type']['coil']
|
||||
|
||||
umaxima = []
|
||||
for k in indexes:
|
||||
path = checkpoint_path + str(k) + '/'+filename+'.h5'
|
||||
hdf = HDF5File(MESH['mesh'].mpi_comm(), path, 'r')
|
||||
hdf.read(u, 'u/vector_0')
|
||||
time = hdf.attributes('u/vector_0').to_dict()['timestamp']
|
||||
hdf.close()
|
||||
uvec = u.vector().get_local()
|
||||
umaxima.append(np.max(uvec))
|
||||
|
||||
ufactor = options['Perturbation']['type']['phase_contrast']/100
|
||||
VENC = np.floor(np.ceil(np.max(umaxima))*ufactor)
|
||||
print('VENC chosen = ',VENC)
|
||||
|
||||
for k in indexes:
|
||||
path = checkpoint_path + str(k) + '/'+filename+'.h5'
|
||||
hdf = HDF5File(MESH['mesh'].mpi_comm(), path, 'r')
|
||||
@ -244,9 +228,7 @@ def READcheckpoint(MESH, mode, output_path, checkpoint_path, filename, outname,
|
||||
uvec = u.vector().get_local()
|
||||
|
||||
if Phase_Contrast:
|
||||
ufactor = options['Perturbation']['type']['phase_contrast']/100
|
||||
VENC = np.max(np.abs(uvec))*ufactor
|
||||
gamma = 267.513e6 # rad/Tesla/sec Gyromagnetic ratio for H nuclei
|
||||
#gamma = 267.513e6 # rad/Tesla/sec Gyromagnetic ratio for H nuclei
|
||||
B0 = 1.5 # Tesla Magnetic Field Strenght
|
||||
TE = 5e-3 # Echo-time
|
||||
Phi1 = 1*B0*TE + 0*uvec
|
||||
@ -474,7 +456,11 @@ def ERRORmap(MESH, mode, outpath, reference_path, checkpoint_path, refname,comna
|
||||
|
||||
from dolfin import HDF5File
|
||||
V = MESH['FEM']
|
||||
V1 = MESH['FEM'].sub(1).collapse()
|
||||
W = MESH['FEM'].sub(0).collapse()
|
||||
DGs = FunctionSpace( MESH['mesh'], 'DG',0)
|
||||
cellv = CellVolume(MESH['mesh'])
|
||||
h = CellDiameter(MESH['mesh'])
|
||||
unsort_indexes = os.listdir(checkpoint_path)
|
||||
indexes = [int(x) for x in unsort_indexes]
|
||||
indexes.sort()
|
||||
@ -486,6 +472,80 @@ def ERRORmap(MESH, mode, outpath, reference_path, checkpoint_path, refname,comna
|
||||
if len(indexes)!=len(indexes0):
|
||||
raise Exception('The lengh of the checkpoints are not the same!')
|
||||
|
||||
if mode == 'algebra':
|
||||
outname = options['Algebra']['outname']
|
||||
output = XDMFFile(outpath+outname+'.xdmf')
|
||||
checkpoint = options['Algebra']['checkpoint']
|
||||
v1 = Function(W)
|
||||
v2 = Function(W)
|
||||
vout = Function(W)
|
||||
vout.rename('velocity','velocity')
|
||||
vout_vec = np.zeros(vout.vector().get_local().size)
|
||||
times_vec = np.zeros(len(indexes0))
|
||||
vdict1 = {}
|
||||
vdict2 = {}
|
||||
if options['Algebra']['mode'] == 'aliasing':
|
||||
print('Assuming the corrector in the second path entered')
|
||||
|
||||
# Reading all the timestamps first
|
||||
for k in range(len(indexes)):
|
||||
path_v1 = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
|
||||
path_v2 = checkpoint_path + str(indexes[k]) + '/'+comname+'.h5'
|
||||
hdf_v1 = HDF5File(MESH['mesh'].mpi_comm(), path_v1, 'r')
|
||||
|
||||
if 'w' in refname:
|
||||
hdf_v1.read(v1, 'w/vector_0')
|
||||
time = hdf_v1.attributes('w/vector_0').to_dict()['timestamp']
|
||||
else:
|
||||
hdf_v1.read(v1, 'u/vector_0')
|
||||
time = hdf_v1.attributes('u/vector_0').to_dict()['timestamp']
|
||||
times_vec[k] = time
|
||||
hdf_v2 = HDF5File(MESH['mesh'].mpi_comm(), path_v2, 'r')
|
||||
if 'w' in comname:
|
||||
hdf_v2.read(v2, 'w/vector_0')
|
||||
else:
|
||||
hdf_v2.read(v2, 'u/vector_0')
|
||||
|
||||
print('computing algebra for the time',time)
|
||||
hdf_v1.close()
|
||||
hdf_v2.close()
|
||||
vdict1[k] = v1.vector().get_local()
|
||||
vdict2[k] = v2.vector().get_local()
|
||||
|
||||
|
||||
for k in range(len(indexes)):
|
||||
if options['Algebra']['mode'] == '+':
|
||||
vout.vector()[:] = vdict1[k] + vdict2[k]
|
||||
elif options['Algebra']['mode'] == '-':
|
||||
vout.vector()[:] = vdict1[k] - vdict2[k]
|
||||
elif options['Algebra']['mode'] == 'aliasing':
|
||||
VENC = options['Algebra']['VENC']
|
||||
aliasing = False
|
||||
for l in range(len(vout_vec)):
|
||||
if k>0:
|
||||
#mean1 = abs(np.mean(vdict2[0][:]))
|
||||
#mean2 = abs(np.mean(vdict2[1][:]))
|
||||
#mean3 = abs(np.mean(vdict2[2][:]))
|
||||
#treshold = 10*max(mean1,mean2,mean3)
|
||||
#if abs(np.mean(vdict2[k][:]))>treshold:
|
||||
# vout_vec[l] = 0
|
||||
if vdict1[k][l]-vdict1[k-1][l] < -VENC:
|
||||
vdict1[k][l] = vdict1[k][l] + 2*VENC
|
||||
vout_vec[l] = vdict1[k][l]
|
||||
else:
|
||||
vout_vec[l] = vdict1[k][l]
|
||||
else:
|
||||
vout_vec[l] = vdict1[k][l] # first case is suppouse to be aliasing-free
|
||||
|
||||
vout.vector()[:] = vout_vec
|
||||
else:
|
||||
raise Exception('Not supported operation between vectors!')
|
||||
|
||||
output.write(vout, times_vec[k])
|
||||
if checkpoint:
|
||||
path = outpath + 'checkpoint/' + str(indexes[k]) + '/' + 'u.h5'
|
||||
inout.write_HDF5_data(MESH['mesh'].mpi_comm(), path , vout, '/u', t=times_vec[k])
|
||||
|
||||
if mode =='curves':
|
||||
|
||||
if options['Error-curves']['undersampling']>1:
|
||||
@ -495,27 +555,54 @@ def ERRORmap(MESH, mode, outpath, reference_path, checkpoint_path, refname,comna
|
||||
|
||||
u = Function(W)
|
||||
w = Function(W)
|
||||
ones = interpolate(Constant(1), V.sub(1).collapse())
|
||||
L_sys = assemble(ones*dx)
|
||||
VENC = options['Error-curves']['VENC']
|
||||
|
||||
for typs in options['Error-curves']['type']:
|
||||
ucomp = []
|
||||
wcomp = []
|
||||
div_array = []
|
||||
varu = []
|
||||
times = []
|
||||
dt = options['Error-curves']['dt']
|
||||
for k in range(1,len(indexes)):
|
||||
path_w = checkpoint_path + str(indexes[k]) + '/'+comname+'.h5'
|
||||
path_u = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
|
||||
|
||||
if typs == 'l2_comp':
|
||||
wy = Function(V1)
|
||||
wz = Function(V1)
|
||||
comname2 = comname
|
||||
wx_array = []
|
||||
wy_array = []
|
||||
wz_array = []
|
||||
|
||||
if typs == 'utrue-uobs':
|
||||
u_path = options['Error-curves']['true_check'] + 'checkpoint/'
|
||||
w_path = options['Error-curves']['ref_check'] + 'checkpoint/'
|
||||
comname2 = 'u'
|
||||
varux_array = []
|
||||
varuy_array = []
|
||||
varuz_array = []
|
||||
else:
|
||||
u_path = reference_path
|
||||
w_path = checkpoint_path
|
||||
|
||||
dt = options['Error-curves']['dt']
|
||||
|
||||
for k in range(1,len(indexes)):
|
||||
path_w = w_path + str(indexes[k]) + '/'+comname2+'.h5'
|
||||
path_u = u_path + str(indexes0[k]) + '/'+refname+'.h5'
|
||||
u.rename('meas', 'meas')
|
||||
w.rename('w', 'w')
|
||||
hdf_w = HDF5File(MESH['mesh'].mpi_comm(),path_w,'r')
|
||||
if 'w' in comname:
|
||||
if 'w' in comname2:
|
||||
hdf_w.read(w, 'w/vector_0')
|
||||
else:
|
||||
hdf_w.read(w, 'u/vector_0')
|
||||
if typs != 'l2_comp':
|
||||
hdf_u = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
|
||||
hdf_u.read(u, 'u/vector_0')
|
||||
hdf_u.close()
|
||||
hdf_w.close()
|
||||
u_vec = u.vector().get_local()
|
||||
hdf_w.close()
|
||||
w_vec = w.vector().get_local()
|
||||
print('computing error in timestep numer',k)
|
||||
|
||||
@ -525,59 +612,53 @@ def ERRORmap(MESH, mode, outpath, reference_path, checkpoint_path, refname,comna
|
||||
elif typs == 'max':
|
||||
ucomp.append(np.max(abs(u_vec)))
|
||||
wcomp.append(np.max(abs(w_vec)))
|
||||
elif typs == 'norm2':
|
||||
ucomp.append(np.sqrt(assemble(dot(u,u)*dx)/L_sys))
|
||||
wcomp.append(np.sqrt(assemble(dot(w,w)*dx)/L_sys))
|
||||
elif typs == 'grad':
|
||||
wcomp.append(np.sqrt(assemble(inner(grad(w),grad(w))*dx)/L_sys))
|
||||
elif typs == 'l2_comp':
|
||||
wx = w.sub(0,deepcopy=True)
|
||||
wy = w.sub(1,deepcopy=True)
|
||||
wz = w.sub(2,deepcopy=True)
|
||||
wx_array.append(np.sqrt(assemble(wx*wx*dx)/L_sys)/VENC)
|
||||
wy_array.append(np.sqrt(assemble(wy*wy*dx)/L_sys)/VENC)
|
||||
wz_array.append(np.sqrt(assemble(wz*wz*dx)/L_sys)/VENC)
|
||||
elif typs == 'div':
|
||||
div_array.append(np.sqrt(assemble(div(u)**2/h*dx)/L_sys)/VENC)
|
||||
elif typs == 'utrue-uobs':
|
||||
wx = w.sub(0,deepcopy=True)
|
||||
wy = w.sub(1,deepcopy=True)
|
||||
wz = w.sub(2,deepcopy=True)
|
||||
ux = u.sub(0,deepcopy=True)
|
||||
uy = u.sub(1,deepcopy=True)
|
||||
uz = u.sub(2,deepcopy=True)
|
||||
varux_array.append(np.sqrt(assemble((ux-wx)**2*dx)/L_sys)/VENC)
|
||||
varuy_array.append(np.sqrt(assemble((uy-wy)**2*dx)/L_sys)/VENC)
|
||||
varuz_array.append(np.sqrt(assemble((uz-wz)**2*dx)/L_sys)/VENC)
|
||||
else:
|
||||
raise Exception('No defined type for curve printing!')
|
||||
|
||||
times.append(k*dt)
|
||||
|
||||
if typs == 'grad':
|
||||
np.savetxt(outpath+'w' +typs+'.txt',wcomp)
|
||||
elif typs == 'l2_comp':
|
||||
np.savetxt(outpath+'wx.txt',wx_array)
|
||||
np.savetxt(outpath+'wy.txt',wy_array)
|
||||
np.savetxt(outpath+'wz.txt',wz_array)
|
||||
elif typs == 'div':
|
||||
np.savetxt(outpath+'div.txt',div_array)
|
||||
elif typs == 'utrue-uobs':
|
||||
np.savetxt(outpath+'varux.txt',varux_array)
|
||||
np.savetxt(outpath+'varuy.txt',varuy_array)
|
||||
np.savetxt(outpath+'varuz.txt',varuz_array)
|
||||
else:
|
||||
np.savetxt(outpath+'u' +typs+'.txt',ucomp)
|
||||
np.savetxt(outpath+'w' +typs+'.txt',wcomp)
|
||||
|
||||
np.savetxt(outpath+'times.txt',times)
|
||||
|
||||
if mode == 'histogram':
|
||||
from pathlib import Path
|
||||
import pickle
|
||||
u = Function(V)
|
||||
w = Function(V)
|
||||
errors = {}
|
||||
|
||||
for k in range(len(indexes)):
|
||||
path_w = checkpoint_path + str(indexes[k]) + '/'+comname+'.h5'
|
||||
path_u = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
|
||||
|
||||
if indexes0[k] < 10:
|
||||
path_u = reference_path + '0' + \
|
||||
str(indexes0[k]) + '/'+refname+'.h5'
|
||||
|
||||
u.rename('meas', 'meas')
|
||||
w.rename('w', 'w')
|
||||
hdf_w = HDF5File(MESH['mesh'].mpi_comm(),path_w,'r')
|
||||
hdf_w.read(w, 'w/vector_0')
|
||||
hdf_u = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
|
||||
hdf_u.read(u, 'u/vector_0')
|
||||
hdf_u.close()
|
||||
hdf_w.close()
|
||||
|
||||
u_vec = u.vector().get_local()
|
||||
w_vec = w.vector().get_local()
|
||||
errors[k] = np.zeros(u_vec.size)
|
||||
|
||||
for l in range(len(errors[k])):
|
||||
#errors[k][l] = np.nan
|
||||
if u_vec[l]<1e-9:
|
||||
errors[k][l] = -1
|
||||
else:
|
||||
eta = np.abs(w_vec[l]/u_vec[l])
|
||||
if np.abs(eta)>50:
|
||||
errors[k][l] = -1
|
||||
else:
|
||||
errors[k][l] = eta
|
||||
|
||||
|
||||
write_path = Path(outpath)
|
||||
fpath = write_path.joinpath('errors.dat')
|
||||
pickle.dump(errors, fpath.open('wb'))
|
||||
|
||||
if mode == 'h5':
|
||||
xdmf_u = XDMFFile(outpath+'meas.xdmf')
|
||||
#xdmf_ucor = XDMFFile(output_path+'ucor.xdmf')
|
||||
@ -592,10 +673,6 @@ def ERRORmap(MESH, mode, outpath, reference_path, checkpoint_path, refname,comna
|
||||
path_w = checkpoint_path + str(indexes[k]) + '/'+comname+'.h5'
|
||||
path_u = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
|
||||
|
||||
if indexes0[k] < 10:
|
||||
path_u = reference_path + '0' + \
|
||||
str(indexes0[k]) + '/'+refname+'.h5'
|
||||
|
||||
u.rename('meas', 'meas')
|
||||
w.rename('w', 'w')
|
||||
#ucor.rename('ucor', 'ucor')
|
||||
@ -612,34 +689,173 @@ def ERRORmap(MESH, mode, outpath, reference_path, checkpoint_path, refname,comna
|
||||
#ucor.vector()[:] = u_vec + w_vec
|
||||
|
||||
xdmf_u.write(u, k)
|
||||
#xdmf_ucor.write(ucor, k)
|
||||
xdmf_w.write(w, k)
|
||||
|
||||
if mode == 'colormap':
|
||||
colormap = XDMFFile(outpath+'colormap.xdmf')
|
||||
if mode == 'u':
|
||||
colormap = XDMFFile(outpath+'u.xdmf')
|
||||
#ds = Measure("ds", subdomain_data=MESH['boundaries'])
|
||||
u = Function(W)
|
||||
#P2 = FunctionSpace( MESH['mesh'], 'P',1)
|
||||
cm = Function(DGs)
|
||||
vs = TestFunction(DGs)
|
||||
|
||||
for k in range(len(indexes)):
|
||||
path_u = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
|
||||
u.rename('meas', 'meas')
|
||||
cm.rename('vel','vel')
|
||||
hdf_u = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
|
||||
hdf_u.read(u, 'u/vector_0')
|
||||
time = hdf_u.attributes('u/vector_0').to_dict()['timestamp']
|
||||
print('making the colormap in the time',time)
|
||||
hdf_u.close()
|
||||
r = assemble(dot(u,u)*vs/cellv*dx).get_local()
|
||||
cm.vector()[:] = np.sqrt(np.abs(r))
|
||||
#cm.vector()[:] = np.sqrt(r)
|
||||
colormap.write(cm, time)
|
||||
|
||||
if mode == 'w':
|
||||
colormap = XDMFFile(outpath+'w.xdmf')
|
||||
#ds = Measure("ds", subdomain_data=MESH['boundaries'])
|
||||
w = Function(W)
|
||||
#P2 = FunctionSpace( MESH['mesh'], 'P',2)
|
||||
cm = Function(DGs)
|
||||
vs = TestFunction(DGs)
|
||||
|
||||
for k in range(len(indexes)):
|
||||
path_w = checkpoint_path + str(indexes0[k]) + '/'+comname+'.h5'
|
||||
w.rename('cor', 'cor')
|
||||
cm.rename('w','w')
|
||||
hdf_w = HDF5File(MESH['mesh'].mpi_comm(), path_w, 'r')
|
||||
hdf_w.read(w, 'w/vector_0')
|
||||
time = hdf_w.attributes('w/vector_0').to_dict()['timestamp']
|
||||
print('making the colormap in the time',time)
|
||||
hdf_w.close()
|
||||
r = assemble(dot(w,w)*vs/cellv*dx).get_local()
|
||||
cm.vector()[:] = np.sqrt(np.abs(r))
|
||||
colormap.write(cm, time)
|
||||
|
||||
if mode == 'w/u':
|
||||
colormap = XDMFFile(outpath+'w_u.xdmf')
|
||||
#ds = Measure("ds", subdomain_data=MESH['boundaries'])
|
||||
u = Function(W)
|
||||
w = Function(W)
|
||||
cm = Function(W)
|
||||
dt = options['Corrector']['dt']
|
||||
cm = Function(DGs)
|
||||
vs = TestFunction(DGs)
|
||||
|
||||
for k in range(len(indexes)):
|
||||
print('making the colormap in the time',np.round(k*dt,2))
|
||||
path_w = checkpoint_path + str(indexes[k]) + '/'+comname+'.h5'
|
||||
path_u = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
|
||||
u.rename('meas', 'meas')
|
||||
w.rename('w', 'w')
|
||||
cm.rename('color','color')
|
||||
cm.rename('w_u','w_u')
|
||||
hdf_w = HDF5File(MESH['mesh'].mpi_comm(),path_w,'r')
|
||||
hdf_w.read(w, 'w/vector_0')
|
||||
hdf_u = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
|
||||
hdf_u.read(u, 'u/vector_0')
|
||||
time = hdf_u.attributes('u/vector_0').to_dict()['timestamp']
|
||||
print('making the colormap in the time',time)
|
||||
hdf_u.close()
|
||||
hdf_w.close()
|
||||
uvec = u.vector().get_local()
|
||||
wvec = w.vector().get_local()
|
||||
cm.vector()[:] = np.sqrt((uvec - wvec)**2)
|
||||
colormap.write(cm, k*dt)
|
||||
rw = assemble(dot(w,w)*vs/cellv*dx).get_local()
|
||||
ru = assemble(dot(u,u)*vs/cellv*dx).get_local()
|
||||
cm.vector()[:] = np.sqrt(rw)/np.sqrt(ru)
|
||||
colormap.write(cm, time)
|
||||
|
||||
if mode == 'dot':
|
||||
colormap = XDMFFile(outpath+'dot.xdmf')
|
||||
#ds = Measure("ds", subdomain_data=MESH['boundaries'])
|
||||
u = Function(W)
|
||||
w = Function(W)
|
||||
cm = Function(V1)
|
||||
u.rename('meas', 'meas')
|
||||
w.rename('w', 'w')
|
||||
|
||||
for k in range(len(indexes)):
|
||||
path_w = checkpoint_path + str(indexes[k]) + '/'+comname+'.h5'
|
||||
path_u = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
|
||||
hdf_w = HDF5File(MESH['mesh'].mpi_comm(),path_w,'r')
|
||||
hdf_w.read(w, 'w/vector_0')
|
||||
hdf_u = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
|
||||
hdf_u.read(u, 'u/vector_0')
|
||||
time = hdf_u.attributes('u/vector_0').to_dict()['timestamp']
|
||||
print('making the colormap in the time',time)
|
||||
hdf_u.close()
|
||||
hdf_w.close()
|
||||
cm = project(inner(u,w),V1)
|
||||
cm.rename('dot','dot')
|
||||
colormap.write(cm, time)
|
||||
|
||||
if mode == 'div(u)':
|
||||
|
||||
colormap = XDMFFile(outpath+'divu.xdmf')
|
||||
#ds = Measure("ds", subdomain_data=MESH['boundaries'])
|
||||
u = Function(W)
|
||||
cm = Function(DGs)
|
||||
vs = TestFunction(DGs)
|
||||
|
||||
for k in range(len(indexes)):
|
||||
path_u = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
|
||||
u.rename('meas', 'meas')
|
||||
cm.rename('divu','divu')
|
||||
hdf_u = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
|
||||
hdf_u.read(u, 'u/vector_0')
|
||||
time = hdf_u.attributes('u/vector_0').to_dict()['timestamp']
|
||||
print('making the colormap in the time',time)
|
||||
hdf_u.close()
|
||||
r = assemble(div(u)**2*vs/cellv*dx).get_local()
|
||||
cm.vector()[:] = np.sqrt(r)
|
||||
colormap.write(cm, time)
|
||||
|
||||
if mode == 'div(u)/u':
|
||||
|
||||
colormap = XDMFFile(outpath+'divu_u.xdmf')
|
||||
#ds = Measure("ds", subdomain_data=MESH['boundaries'])
|
||||
u = Function(W)
|
||||
cm = Function(DGs)
|
||||
vs = TestFunction(DGs)
|
||||
|
||||
surface = np.zeros(cm.vector().get_local().size)
|
||||
volume = np.zeros(cm.vector().get_local().size)
|
||||
Cells = MESH['mesh'].cells()
|
||||
Points = MESH['mesh'].coordinates()
|
||||
for k in range(MESH['mesh'].num_cells()):
|
||||
A = Points[Cells[k]][0]
|
||||
B = Points[Cells[k]][1]
|
||||
C = Points[Cells[k]][2]
|
||||
D = Points[Cells[k]][3]
|
||||
# volume
|
||||
Vol = 1/6*np.abs(np.inner(A-D, np.cross(B-D, C-D)))
|
||||
volume[k] = Vol
|
||||
# surface area
|
||||
SA = 0
|
||||
for l in range(4):
|
||||
if l == 0:
|
||||
[P1, P2, P3, P4] = [A, B, C, D]
|
||||
if l == 1:
|
||||
[P1, P2, P3, P4] = [D, A, B, C]
|
||||
if l == 2:
|
||||
[P1, P2, P3, P4] = [C, D, A, B]
|
||||
if l == 3:
|
||||
[P1, P2, P3, P4] = [B, C, D, A]
|
||||
|
||||
SA += 0.5*np.linalg.norm(np.cross(P2-P1, P3-P1))
|
||||
surface[k] = SA
|
||||
|
||||
|
||||
|
||||
for k in range(len(indexes)):
|
||||
path_u = reference_path + str(indexes0[k]) + '/'+refname+'.h5'
|
||||
u.rename('meas', 'meas')
|
||||
cm.rename('divu','divu')
|
||||
hdf_u = HDF5File(MESH['mesh'].mpi_comm(), path_u, 'r')
|
||||
hdf_u.read(u, 'u/vector_0')
|
||||
time = hdf_u.attributes('u/vector_0').to_dict()['timestamp']
|
||||
print('making the colormap in the time',time)
|
||||
hdf_u.close()
|
||||
rdiv = assemble(div(u)**2*vs*dx).get_local()
|
||||
ru = assemble(dot(u,u)*vs*dx).get_local()
|
||||
cm.vector()[:] = np.sqrt(rdiv)/np.sqrt(ru)*volume/surface/np.sqrt(120)
|
||||
colormap.write(cm, time)
|
||||
|
||||
if mode == 'error_u':
|
||||
xdmf_u = XDMFFile(output_path+'error_u.xdmf')
|
||||
@ -874,6 +1090,11 @@ def ESTIMpressure(MESH, outpath, checkpoint_path, filename, options):
|
||||
#from dolfin import HDF5File
|
||||
V = MESH['FEM']
|
||||
W = MESH['FEM'].sub(1).collapse()
|
||||
p = Function(W)
|
||||
one_mesh = interpolate(Constant(1), W)
|
||||
dt = options['Estim_Pressure']['dt']
|
||||
p_drop_lst = []
|
||||
time_ = []
|
||||
# Checkpoints folders
|
||||
unsort_indexes = os.listdir(checkpoint_path)
|
||||
indexes = [int(x) for x in unsort_indexes]
|
||||
@ -897,22 +1118,25 @@ def ESTIMpressure(MESH, outpath, checkpoint_path, filename, options):
|
||||
sphere1 = mshr.Sphere(x1, radius1)
|
||||
mesh_s1 = mshr.generate_mesh(sphere0, Npts0)
|
||||
mesh_s2 = mshr.generate_mesh(sphere1, Npts1)
|
||||
|
||||
# New elements
|
||||
VS1 = FunctionSpace(mesh_s1, FiniteElement('P', mesh_s1.ufl_cell(), 1))
|
||||
VS2 = FunctionSpace(mesh_s2, FiniteElement('P', mesh_s2.ufl_cell(), 1))
|
||||
s1 = Function(VS1)
|
||||
s2 = Function(VS2)
|
||||
p = Function(W)
|
||||
|
||||
one_mesh = interpolate(Constant(1), W)
|
||||
LagrangeInterpolator.interpolate(s1, one_mesh)
|
||||
LagrangeInterpolator.interpolate(s2, one_mesh)
|
||||
vol1 = assemble(s1*dx)
|
||||
vol2 = assemble(s1*dx)
|
||||
|
||||
dt = options['Estim_Pressure']['dt']
|
||||
p_drop_lst = []
|
||||
time_ = []
|
||||
if options['Estim_Pressure']['method'] == 'boundaries':
|
||||
boundaries = MESH['boundaries']
|
||||
ds = Measure("ds", subdomain_data=boundaries)
|
||||
bnd1 = options['Estim_Pressure']['boundaries'][0]
|
||||
bnd2 = options['Estim_Pressure']['boundaries'][1]
|
||||
area1 = assemble(one_mesh*ds(bnd1))
|
||||
area2 = assemble(one_mesh*ds(bnd2))
|
||||
|
||||
|
||||
|
||||
for k in range(0, len(indexes)):
|
||||
path = checkpoint_path + str(indexes[k]) + '/'+filename+'.h5'
|
||||
@ -920,11 +1144,14 @@ def ESTIMpressure(MESH, outpath, checkpoint_path, filename, options):
|
||||
hdf.read(p, 'p/vector_0')
|
||||
hdf.close()
|
||||
|
||||
if options['Estim_Pressure']['method'] == 'spheres':
|
||||
LagrangeInterpolator.interpolate(s1, p)
|
||||
LagrangeInterpolator.interpolate(s2, p)
|
||||
|
||||
P1 = assemble(s1*dx)/vol1
|
||||
P2 = assemble(s2*dx)/vol2
|
||||
if options['Estim_Pressure']['method'] == 'boundaries':
|
||||
P1 = assemble(p*ds(bnd1))/area1
|
||||
P2 = assemble(p*ds(bnd2))/area2
|
||||
|
||||
p_drop_lst.append(P2-P1)
|
||||
time_.append(k*dt)
|
||||
@ -1012,41 +1239,60 @@ def OUTLETwind(MESH, output_path, checkpoint_path, filename, bnds):
|
||||
|
||||
def ROUTINE(options):
|
||||
|
||||
if 'Algebra' in options:
|
||||
if options['Algebra']['apply']:
|
||||
|
||||
if rank == 0:
|
||||
print('Applying Algebra')
|
||||
print('Choosen mode: ' + options['Algebra']['mode'])
|
||||
|
||||
MESH = LOADmesh(options['Algebra']['meshpath'])
|
||||
v1path = options['Algebra']['v1']['path'] + 'checkpoint/'
|
||||
v1name = options['Algebra']['v1']['name']
|
||||
v2path = options['Algebra']['v2']['path'] + 'checkpoint/'
|
||||
v2name = options['Algebra']['v2']['name']
|
||||
outpath = options['Algebra']['outpath']
|
||||
|
||||
ERRORmap(MESH, 'algebra', outpath, v1path,
|
||||
v2path, v1name, v2name, options)
|
||||
|
||||
if 'Outlet_Wind' in options:
|
||||
if options['Outlet_Wind']['apply']:
|
||||
if rank == 0:
|
||||
print('--- Outlet Windkessel ---')
|
||||
|
||||
mesh_path = options['Outlet_Wind']['mesh_path']
|
||||
meshpath = options['Outlet_Wind']['meshpath']
|
||||
out_path = options['Outlet_Wind']['out_path']
|
||||
filename = options['Outlet_Wind']['filename']
|
||||
checkpoint = options['Outlet_Wind']['checkpoint'] + 'checkpoint/'
|
||||
bnds = options['Outlet_Wind']['bnds']
|
||||
MESH = LOADmesh(mesh_path)
|
||||
MESH = LOADmesh(meshpath)
|
||||
OUTLETwind(MESH, out_path, checkpoint, filename, bnds)
|
||||
|
||||
if 'Corrector' in options:
|
||||
if options['Corrector']['apply']:
|
||||
if 'Colormap' in options:
|
||||
if options['Colormap']['apply']:
|
||||
|
||||
for mode in options['Colormap']['mode']:
|
||||
if rank == 0:
|
||||
print('Applying Corrector')
|
||||
print('Applying Colormap')
|
||||
print('Choosen mode: ' + mode)
|
||||
|
||||
MESH = LOADmesh(options['Corrector']['mesh_path'])
|
||||
u_path = options['Corrector']['u_path'] + 'checkpoint/'
|
||||
w_path = options['Corrector']['w_path'] + 'checkpoint/'
|
||||
wname = options['Corrector']['wname']
|
||||
uname = options['Corrector']['uname']
|
||||
mode = options['Corrector']['mode']
|
||||
outpath = options['Corrector']['outpath']
|
||||
MESH = LOADmesh(options['Colormap']['meshpath'])
|
||||
upath = options['Colormap']['upath'] + 'checkpoint/'
|
||||
wpath = options['Colormap']['wpath'] + 'checkpoint/'
|
||||
wname = options['Colormap']['wname']
|
||||
uname = options['Colormap']['uname']
|
||||
outpath = options['Colormap']['outpath']
|
||||
|
||||
ERRORmap(MESH, mode, outpath, u_path,
|
||||
w_path, uname, wname, options)
|
||||
ERRORmap(MESH, mode, outpath, upath,
|
||||
wpath, uname, wname, options)
|
||||
|
||||
if 'Velocity' in options:
|
||||
if options['Velocity']['apply']:
|
||||
if rank == 0:
|
||||
print('--- Reading Velocity ---')
|
||||
|
||||
MESH = LOADmesh(options['Velocity']['mesh_path'])
|
||||
MESH = LOADmesh(options['Velocity']['meshpath'])
|
||||
filename = options['Velocity']['filename']
|
||||
checkpoint_path = options['Velocity']['checkpoint'] + 'checkpoint/'
|
||||
outpath = options['Velocity']['checkpoint']
|
||||
@ -1067,7 +1313,7 @@ def ROUTINE(options):
|
||||
if options['W_map']['apply']:
|
||||
if rank == 0:
|
||||
print('Applying W--MAP')
|
||||
MESH = LOADmesh(options['mesh_path'])
|
||||
MESH = LOADmesh(options['meshpath'])
|
||||
filename = options['W_map']['filename']
|
||||
outname = options['W_map']['out_name']
|
||||
mode = 'w'
|
||||
@ -1078,7 +1324,7 @@ def ROUTINE(options):
|
||||
if options['GradW_map']['apply']:
|
||||
if rank == 0:
|
||||
print('Applying Grad W--MAP')
|
||||
MESH = LOADmesh(options['mesh_path'])
|
||||
MESH = LOADmesh(options['meshpath'])
|
||||
filename = options['GradW_map']['filename']
|
||||
outname = options['GradW_map']['out_name']
|
||||
mode = 'gradw'
|
||||
@ -1088,21 +1334,21 @@ def ROUTINE(options):
|
||||
if 'Pressure' in options:
|
||||
if options['Pressure']['apply']:
|
||||
if rank == 0:
|
||||
print('Applying Pressure-MAP')
|
||||
print('---Applying Pressure---')
|
||||
|
||||
MESH = LOADmesh(options['mesh_path'])
|
||||
MESH = LOADmesh(options['meshpath'])
|
||||
outpath = options['Pressure']['checkpoint']
|
||||
checkpoint_path = options['Pressure']['checkpoint'] + 'checkpoint/'
|
||||
filename = options['Pressure']['filename']
|
||||
outname = options['Pressure']['out_name']
|
||||
mode = 'p'
|
||||
WORKcheck(MESH, mode, output_path, checkpoint_path,
|
||||
filename, outname, options)
|
||||
WORKcheck(MESH, 'p', outpath, checkpoint_path,
|
||||
filename, filename, options)
|
||||
|
||||
if 'Error_P' in options:
|
||||
if options['Error_P']['apply']:
|
||||
if rank == 0:
|
||||
print('Applying L2 error to Pressure')
|
||||
|
||||
MESH = LOADmesh(options['mesh_path'])
|
||||
MESH = LOADmesh(options['meshpath'])
|
||||
refname = options['Error_P']['refname']
|
||||
reference_path = options['Error_P']['refpath']
|
||||
filename = options['Error_P']['filename']
|
||||
@ -1115,10 +1361,13 @@ def ROUTINE(options):
|
||||
if options['Estim_Pressure']['apply']:
|
||||
if rank == 0:
|
||||
print('Applying Pressure Estimator')
|
||||
print('Method choosed: '+options['Estim_Pressure']['method'])
|
||||
|
||||
MESH = LOADmesh(options['mesh_path'])
|
||||
MESH = LOADmesh(options['Estim_Pressure']['meshpath'])
|
||||
filename = options['Estim_Pressure']['filename']
|
||||
outpath = options['Estim_Pressure']['outpath']
|
||||
outpath = options['Estim_Pressure']['checkpath']
|
||||
checkpoint_path = options['Estim_Pressure']['checkpath'] + 'checkpoint/'
|
||||
|
||||
ESTIMpressure(MESH, outpath, checkpoint_path, filename, options)
|
||||
|
||||
if 'Error-curves' in options:
|
||||
@ -1162,7 +1411,11 @@ def ROUTINE(options):
|
||||
|
||||
MESH = LOADmesh(options['Perturbation']['meshpath'])
|
||||
checkpath = options['Perturbation']['checkpath'] + 'checkpoint/'
|
||||
if type(options['Perturbation']['type']['SNR'])=='str':
|
||||
name_folder = 'SNR' +options['Perturbation']['type']['SNR'] + 'V' + str(options['Perturbation']['type']['phase_contrast'])
|
||||
else:
|
||||
name_folder = 'SNR' +str(options['Perturbation']['type']['SNR']) + 'V' + str(options['Perturbation']['type']['phase_contrast'])
|
||||
|
||||
out_check = options['Perturbation']['checkpath'] + name_folder + '/'
|
||||
READcheckpoint(MESH,'perturbation', out_check,checkpath,'u','u',options)
|
||||
|
||||
|
||||
Binary file not shown.
Binary file not shown.
@ -1,5 +1,4 @@
|
||||
from dolfin import *
|
||||
import matplotlib.pyplot as plt
|
||||
import numpy as np
|
||||
from common import inout
|
||||
from mpi4py import MPI
|
||||
@ -23,7 +22,6 @@ def solv_NavierStokes(options):
|
||||
theta = Constant(options['theta'])
|
||||
Tf = options['Tf']
|
||||
dt = options['dt']
|
||||
dt_w = options['dt_write']
|
||||
|
||||
# CREATING THE FILES
|
||||
xdmf_u = XDMFFile(options['savepath']+'u.xdmf')
|
||||
@ -53,7 +51,6 @@ def solv_NavierStokes(options):
|
||||
BCS = []
|
||||
bc = options['boundary_conditions']
|
||||
# For Windkessel implementation
|
||||
flows = {}
|
||||
pii0 = {}
|
||||
pii = {}
|
||||
press = {}
|
||||
@ -63,6 +60,23 @@ def solv_NavierStokes(options):
|
||||
Windkvar = {}
|
||||
windkessel = False
|
||||
|
||||
u, p = TrialFunctions(W)
|
||||
w = Function(W)
|
||||
h = CellDiameter(mesh)
|
||||
|
||||
u0, p0 = w.split()
|
||||
u_ = theta*u + otheta*u0
|
||||
p_ = theta*p + otheta*p0
|
||||
# The variational formulation
|
||||
# Mass matrix
|
||||
F = (
|
||||
(rho/dt)*dot(u - u0, v)*dx
|
||||
+ mu*inner(grad(u_), grad(v))*dx
|
||||
- p_*div(v)*dx + q*div(u)*dx
|
||||
+ rho*dot(grad(u_)*u0, v)*dx
|
||||
)
|
||||
|
||||
|
||||
for nbc in range(len(bc)):
|
||||
nid = bc[nbc]['id']
|
||||
if bc[nbc]['type'] == 'dirichlet':
|
||||
@ -82,43 +96,27 @@ def solv_NavierStokes(options):
|
||||
windkessel = True
|
||||
if rank==0:
|
||||
print('Adding Windkessel BC at boundary ',nid)
|
||||
[R_p,C,R_d] = bc[nbc]['value']
|
||||
[R_p,R_d,C] = bc[nbc]['value']
|
||||
# coeficients
|
||||
alpha[nid] = R_d*C/(R_d*C + dt)
|
||||
beta[nid] = R_d*(1-alpha[nid])
|
||||
gamma[nid] = R_p + beta[nid]
|
||||
# dynamical terms
|
||||
if C ==0:
|
||||
flows[nid] = Constant(0)
|
||||
press[nid] = Constant(R_p*0)
|
||||
print('no capacitance C for boundary',nid)
|
||||
press[nid] = Constant(0)
|
||||
else:
|
||||
flows[nid] = Constant(0)
|
||||
pii0[nid] = Constant(bc[nbc]['p0'][0]*bc[nbc]['p0'][1])
|
||||
pii[nid] = Constant(alpha[nid]*pii0[nid] + beta[nid]*flows[nid])
|
||||
press[nid] = Constant(gamma[nid]*flows[nid] + alpha[nid]*pii0[nid])
|
||||
pii[nid] = Constant(bc[nbc]['p0'][0]*bc[nbc]['p0'][1])
|
||||
press[nid] = Constant(bc[nbc]['p0'][0]*bc[nbc]['p0'][1])
|
||||
|
||||
Windkvar[nid] = dt*press[nid]*dot(v,n)*ds(nid)
|
||||
Windkvar[nid] = press[nid]*dot(v,n)*ds(nid)
|
||||
|
||||
u, p = TrialFunctions(W)
|
||||
w = Function(W)
|
||||
h = CellDiameter(mesh)
|
||||
|
||||
u0, p0 = w.split()
|
||||
u_ = theta*u + otheta*u0
|
||||
p_ = theta*p + otheta*p0
|
||||
# The variational formulation
|
||||
# Mass matrix
|
||||
F = (
|
||||
(rho/dt)*dot(u - u0, v)*dx
|
||||
+ mu*inner(grad(u_), grad(v))*dx
|
||||
- p_*div(v)*dx + q*div(u)*dx
|
||||
+ rho*dot(grad(u_)*u0, v)*dx
|
||||
)
|
||||
|
||||
# Stabilization Terms
|
||||
if options['stabilization']['temam']:
|
||||
if rank==0:
|
||||
print('Addint Temam stabilization term')
|
||||
print('Adding Temam stabilization term')
|
||||
F += 0.5*rho*div(u0)*dot(u_, v)*dx
|
||||
|
||||
if pspg:
|
||||
@ -132,7 +130,7 @@ def solv_NavierStokes(options):
|
||||
for nid in options['stabilization']['forced_normal']['boundaries']:
|
||||
if rank==0:
|
||||
print('Forcing normal velocity in border ', nid)
|
||||
ut = u - n*dot(u,n)
|
||||
ut = u - n*dot(u0,n)
|
||||
vt = v - n*dot(v,n)
|
||||
F += gparam*dot(ut,vt)*ds(nid)
|
||||
|
||||
@ -145,52 +143,67 @@ def solv_NavierStokes(options):
|
||||
print('adding backflow stabilization in border number:' + str(nk))
|
||||
F -= 0.5*rho*abs_n(dot(u0, n))*dot(u_, v)*ds(nk)
|
||||
|
||||
a = lhs(F)
|
||||
L = rhs(F)
|
||||
|
||||
if windkessel:
|
||||
for nid in Windkvar.keys():
|
||||
L = L - Windkvar[nid]
|
||||
F += Windkvar[nid]
|
||||
|
||||
a = lhs(F)
|
||||
L = rhs(F)
|
||||
|
||||
# The static part of the matrix
|
||||
A = assemble(a)
|
||||
u, p = w.split()
|
||||
uwrite = Function(W.sub(0).collapse())
|
||||
pwrite = Function(W.sub(1).collapse())
|
||||
uwrite.rename('velocity', 'u')
|
||||
pwrite.rename('pressure', 'p')
|
||||
u.rename('velocity', 'u')
|
||||
p.rename('pressure', 'p')
|
||||
ind = 0
|
||||
t = dt
|
||||
checkcicle = int(options['checkpoint_dt']/options['dt'])
|
||||
writecicle = int(options['checkpoint_dt']/options['dt_write'])
|
||||
writecicle = int(options['xdmf_dt']/options['dt'])
|
||||
|
||||
while t<=Tf+dt:
|
||||
if windkessel:
|
||||
for k in flows.keys():
|
||||
flows[k].assign(assemble(dot(u0,n)*ds(k)))
|
||||
pii0[k].assign(pii[k])
|
||||
pii[k].assign(alpha[k]*pii0[k] + beta[k]*flows[k])
|
||||
press[k].assign(gamma[k]*flows[k] + alpha[k]*pii0[k])
|
||||
|
||||
# To solve
|
||||
assemble(a, tensor=A)
|
||||
b = assemble(L)
|
||||
[bcs.apply(A, b) for bcs in BCS]
|
||||
solve(A, w.vector(), b , 'lu')
|
||||
print('solving for t = ' + str(np.round(t,4)))
|
||||
solve(A, w.vector(), b )
|
||||
ind += 1
|
||||
|
||||
if options['write_xdmf']:
|
||||
if np.mod(ind,writecicle)<0.1 or ind==1:
|
||||
xdmf_u.write(u, t)
|
||||
xdmf_p.write(p, t)
|
||||
|
||||
assign(uwrite, w.sub(0))
|
||||
assign(pwrite, w.sub(1))
|
||||
|
||||
if np.mod(ind,checkcicle)<0.1 or ind==1:
|
||||
if options['write_checkpoint']:
|
||||
checkpath = options['savepath'] +'checkpoint/{i}/'.format(i=ind)
|
||||
comm = u.function_space().mesh().mpi_comm()
|
||||
inout.write_HDF5_data(comm, checkpath + '/u.h5', u, '/u', t=t)
|
||||
inout.write_HDF5_data(comm, checkpath + '/p.h5', p, '/p', t=t)
|
||||
comm = uwrite.function_space().mesh().mpi_comm()
|
||||
inout.write_HDF5_data(comm, checkpath + '/u.h5', uwrite, '/u', t=t)
|
||||
inout.write_HDF5_data(comm, checkpath + '/p.h5', pwrite, '/p', t=t)
|
||||
|
||||
inflow.t = t
|
||||
t += dt
|
||||
inflow.t = t
|
||||
assign(u0, w.sub(0))
|
||||
|
||||
if windkessel:
|
||||
for nid in Windkvar.keys():
|
||||
qq = assemble(dot(u0,n)*ds(nid))
|
||||
pii0[nid].assign(pii[nid])
|
||||
pii[nid].assign(Constant(alpha[nid]*float(pii0[nid]) + beta[nid]*qq))
|
||||
pp = Constant(gamma[nid]*qq + alpha[nid]*float(pii0[nid]))
|
||||
press[nid].assign(pp)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
|
||||
@ -3,12 +3,6 @@
|
||||
# Input file for Graphics
|
||||
#
|
||||
#################################################
|
||||
ppecol: 'coral'
|
||||
stecol: 'yellowgreen'
|
||||
daecol: 'cyan'
|
||||
corcol: 'indigo'
|
||||
refcol: 'black'
|
||||
|
||||
dP:
|
||||
apply: false
|
||||
data: '/home/yeye/Desktop/dP/results/11AoCoPhantomRest2/R1/testBF/'
|
||||
@ -23,7 +17,7 @@ dP:
|
||||
save: True
|
||||
name: '/home/yeye/Desktop/11AoCoPhantomRest2_BF.png'
|
||||
|
||||
Histograms:
|
||||
Histograms_meshes:
|
||||
apply: false
|
||||
outpath: '/home/yeye/Desktop/'
|
||||
colors:
|
||||
@ -44,20 +38,45 @@ HistCorrector:
|
||||
errors: '/home/yeye/Desktop/testH/H2/errors.dat'
|
||||
outpath: '/home/yeye/Desktop/h2_160.png'
|
||||
|
||||
Histograms_checkpoint:
|
||||
apply: false
|
||||
path: '/home/yeye/Desktop/Corrector_2019/mono2/dt10ms_SUPGcon/'
|
||||
title: '$dt = 10 \ ms$'
|
||||
|
||||
Error-curves:
|
||||
apply: false
|
||||
norm: 2
|
||||
folder: '/home/yeye/Desktop/First/'
|
||||
resol: ['H2']
|
||||
mode: ['meas','corrs']
|
||||
times: ['30ms']
|
||||
colors: ['orangered','lime','dodgerblue']
|
||||
outpath: '/home/yeye/Desktop/'
|
||||
folder: '/home/yeye/Desktop/Corrector_2019/Perturbation/'
|
||||
type: ['norm2_m']
|
||||
subfolders: ['SNRinfV120','SNR10V120','SNRinfV80','SNR10V80']
|
||||
labels: ['SNRinfV120','SNR10V120','SNRinfV80','SNR10V80']
|
||||
#subfolders: ['BA_p2p1','BAA','BBA']
|
||||
#labels: ['BA_{P2P1}','BAA','BBA']
|
||||
colors: ['indigo','limegreen','dodgerblue','orangered','yellow']
|
||||
styles: ['-','-','-','-','-','-','-','-']
|
||||
title: '$leo2.0$'
|
||||
outpath: '/home/yeye/Desktop/Corrector_2019/Perturbation/'
|
||||
|
||||
Components:
|
||||
Pressure_drops:
|
||||
apply: false
|
||||
folder: '/home/yeye/Desktop/Corrector_2019/Perturbation/STE/'
|
||||
convertor: -1333.22387415
|
||||
#convertor: -133.322
|
||||
catheter: false
|
||||
subfolders: ['SNRinfV120','SNR15V120','SNRinfV80','SNR15V80','dt10ms']
|
||||
labels: ['SNRinfV120','SNR15V120','SNRinfV80','SNR15V80','ref']
|
||||
colors: ['indigo','limegreen','dodgerblue','orangered','yellow']
|
||||
styles: ['-','-','-','-','-','-','-','-','-','-']
|
||||
title: '$STE \ leo2.0$'
|
||||
outpath: '/home/yeye/Desktop/Corrector_2019/Perturbation/STE/'
|
||||
|
||||
l2_comp:
|
||||
apply: True
|
||||
folder: '/home/yeye/Desktop/Corrector_2019/figures/Errorcurves/'
|
||||
subfolders: ['11mm','13mm','Normal']
|
||||
type: ['mean','max']
|
||||
colors: ['orangered','lime','dodgerblue']
|
||||
outpath: '/home/yeye/Desktop/'
|
||||
colors: ['dodgerblue','orangered','limegreen']
|
||||
div: false
|
||||
aliasing: false
|
||||
folder: '/home/yeye/Desktop/Poiseuille/curves/'
|
||||
subfolder: ['SNR10V80']
|
||||
name: 'SNR10V120_gain'
|
||||
mode:
|
||||
type: 'gain_compressed'
|
||||
comp: '/home/yeye/Desktop/Poiseuille/curves/SNR10V120/'
|
||||
@ -3,63 +3,95 @@
|
||||
# Input file for the checkpoint postprocessing
|
||||
#
|
||||
#################################################
|
||||
Corrector:
|
||||
Algebra:
|
||||
apply: false
|
||||
mode: 'colormap' # h5 , histogram, colormap
|
||||
outpath: '/home/yeye/Desktop/Corrector_2019/figure3/11mm/'
|
||||
mesh_path: '/home/yeye/Desktop/Corrector_2019/meshes/11AoCoPhantomRest2.h5'
|
||||
u_path: '/home/yeye/Desktop/Corrector_2019/First/meas/11mmAoCo2/'
|
||||
w_path: '/home/yeye/Desktop/Corrector_2019/First/corrector/11mmAoCo2/'
|
||||
wname: 'w_COR_impl_stan'
|
||||
mode: '+'
|
||||
VENC: 97
|
||||
outname: 'ucor'
|
||||
outpath: '/home/yeye/Desktop/Corrector_2019/Perturbation/gain/SNR10V60/'
|
||||
checkpoint: true
|
||||
#meshpath: '/home/yeye/Desktop/Poiseuille/Meas_leo/poiseuille.h5'
|
||||
meshpath: '/home/yeye/Desktop/Corrector_2019/Meshes/leoH3_2.0.h5'
|
||||
v1:
|
||||
name: 'u'
|
||||
path: '/home/yeye/Desktop/Corrector_2019/Perturbation/Meas/SNR10V60/'
|
||||
v2:
|
||||
name: 'w_COR_impl_stan'
|
||||
path: '/home/yeye/Desktop/Corrector_2019/Perturbation/COR/SNR10V60/'
|
||||
|
||||
Colormap:
|
||||
apply: false
|
||||
#mode: ['u','w','w/u','div(u)','div(u)/u']
|
||||
mode: ['dot']
|
||||
outpath: '/home/yeye/Desktop/Poiseuille/H5/leo2mm/SNRinfV80/'
|
||||
meshpath: '/home/yeye/Desktop/Poiseuille/Meas_leo/poiseuille.h5'
|
||||
upath: '/home/yeye/Desktop/Poiseuille/Meas_leo/SNRinfV80/'
|
||||
wpath: '/home/yeye/Desktop/Poiseuille/Corrector/leo2mm/SNRinfV80/'
|
||||
uname: 'u'
|
||||
dt: 0.03072
|
||||
wname: 'w_COR_impl_stan'
|
||||
|
||||
Velocity:
|
||||
apply: false
|
||||
mesh_path: '/home/yeye/Desktop/Corrector_2019/meshes/NormalAoCoPhantomRest2.h5'
|
||||
checkpoint: '/home/yeye/Desktop/Corrector_2019/First/meas/NormalAoCo2/'
|
||||
meshpath: '/home/yeye/Desktop/Corrector_2019/Poiseuille/poiseuille.h5'
|
||||
checkpoint: '/home/yeye/Desktop/Corrector_2019/Poiseuille/COR/SNR15V120/'
|
||||
undersampling: 1
|
||||
dt: 0.03072
|
||||
filename: 'u'
|
||||
dt: 0.03
|
||||
filename: 'w_COR_impl_stan'
|
||||
|
||||
Estim_Pressure:
|
||||
apply: false
|
||||
meshpath: '/home/yeye/Desktop/Corrector_2019/Meshes/9mmRest2.0.h5'
|
||||
filename: 'p_COR_impl_stan'
|
||||
outpath: '/home/yeye/Desktop/dP/results/11AoCoPhantomRest2/R1/testBF/'
|
||||
checkpath: '/home/yeye/Desktop/Corrector_2019/AoCo/9mm_pspg/'
|
||||
method: spheres # slices, boundaries, spheres
|
||||
dt: 0.03072
|
||||
boundaries: [2,3]
|
||||
spheres:
|
||||
- center: [0.09, 0.093, 0.08] # 11mm
|
||||
#- center : [0.08, 0.09, 0.08]
|
||||
#- center : [0.093, 0.09, 0.085] # Normal
|
||||
- center: [0.0980092, 0.0909768, 0.0802258] # 9mm
|
||||
#- center: [0.110266, 0.086805, 0.0794744] # 11mm
|
||||
#- center : [0.0940797, 0.0766444, 0.080433] #13mm
|
||||
#- center: [0.0870168, 0.0901715, 0.0883529] # Normal
|
||||
radius: 0.005
|
||||
Npts: 32
|
||||
- center: [0.134, 0.135, 0.026] # 11mm
|
||||
#- center : [0.125, 0.135, 0.025] # 13 mm
|
||||
#- center : [0.13, 0.14, 0.03] # Normal
|
||||
- center: [0.0980092, 0.135047, 0.0252659] # 9mm
|
||||
#- center: [0.110266, 0.133002, 0.0263899] # 11mm
|
||||
#- center : [0.0940573, 0.123321, 0.0260755] # 13 mm
|
||||
#- center: [0.0869949, 0.12838, 0.0269889] # Normal
|
||||
radius: 0.005
|
||||
Npts: 32
|
||||
|
||||
Outlet_Wind:
|
||||
apply: false
|
||||
mesh_path: '/home/yeye/NavierStokes/examples/meshes/aorta.h5'
|
||||
checkpoint: '/home/yeye/NavierStokes/examples/results/aorta/'
|
||||
mesh_path: '/home/yeye/Desktop/aorta/mesh/aorta_coarse_marked.h5'
|
||||
checkpoint: '/home/yeye/Desktop/aorta/results/mono/'
|
||||
filename: ['u','p']
|
||||
bnds: [3,4,5,6]
|
||||
out_path: '/home/yeye/NavierStokes/examples/results/aorta/'
|
||||
out_path: '/home/yeye/Desktop/aorta/results/mono/'
|
||||
|
||||
Error-curves:
|
||||
apply: true
|
||||
dt: 0.03072
|
||||
type: ['mean','max']
|
||||
meshpath: '/home/yeye/Desktop/Corrector_2019/meshes/NormalAoCoPhantomRest1.4.h5'
|
||||
ref_check: '/home/yeye/Desktop/Corrector_2019/I/meas/NormalRest1.4/R1/'
|
||||
dt: 0.03
|
||||
VENC: 204 #194/129/113/97 for aorta(120,80,70,60)/ 204/136
|
||||
type: ['utrue-uobs']
|
||||
#type: ['l2_comp','div']
|
||||
meshpath: '/home/yeye/Desktop/Poiseuille/Meas_leo/poiseuille.h5'
|
||||
#meshpath: '/home/yeye/Desktop/Corrector_2019/Meshes/leoH3_2.0.h5'
|
||||
true_check: '/home/yeye/Desktop/Poiseuille/Meas_leo/SNRinfV120/'
|
||||
true_name: 'u'
|
||||
ref_check: '/home/yeye/Desktop/Poiseuille/Meas_leo/SNR10V120/'
|
||||
ref_name: 'u'
|
||||
undersampling: 1
|
||||
com_check: '/home/yeye/Desktop/Corrector_2019/I/corrector/NormalRest1.4/'
|
||||
com_check: '/home/yeye/Desktop/Poiseuille/Corrector/leo2mm/SNR10V120/'
|
||||
com_name: 'w_COR_impl_stan'
|
||||
outpath: '/home/yeye/Desktop/Corrector_2019/figures/Errorcurves/Normal/'
|
||||
outpath: '/home/yeye/Desktop/Poiseuille/curves/SNR10V120/'
|
||||
|
||||
Histograms:
|
||||
apply: false
|
||||
type: ['normal','grad']
|
||||
meshpath: '/home/yeye/Desktop/Corrector_2019/meshes/11AoCoPhantomRest1.4.h5'
|
||||
checkpath: '/home/yeye/Desktop/Corrector_2019/I/corrector/11mmRest1.4/'
|
||||
field_name: 'w_COR_impl_stan'
|
||||
outpath: '/home/yeye/Desktop/Corrector_2019/I/corrector/11mmRest1.4/'
|
||||
|
||||
Temporal-Average:
|
||||
apply: false
|
||||
@ -78,3 +110,14 @@ Temporal-Interpolation:
|
||||
dt: 0.03072
|
||||
dt_new: 0.015
|
||||
out_check: '/home/yeye/Desktop/Corrector_2019/I/meas/11mmRest1.4/dt15ms/'
|
||||
|
||||
Perturbation:
|
||||
apply: false
|
||||
undersampling: 1
|
||||
type:
|
||||
SNR: 10 # dB signal to noise ratio
|
||||
coil: true
|
||||
phase_contrast: 80 # venc % respect u max
|
||||
meshpath: '/home/yeye/Desktop/Poiseuille/Meas_leo/poiseuille.h5'
|
||||
checkpath: '/home/yeye/Desktop/Poiseuille/Meas_leo/original/'
|
||||
xdmf: true
|
||||
@ -1,50 +0,0 @@
|
||||
#################################################
|
||||
#
|
||||
# Input file for CFD Monolithic Solver
|
||||
#
|
||||
#################################################
|
||||
mesh_path : '/home/p283370/Desktop/PhD/AORTA/MESH/aorta_fine/aorta_fine_marked.h5'
|
||||
write_xdmf : False
|
||||
savepath : '/home/yeye/Desktop/PhD/AORTA/DATA/monolithic/'
|
||||
write_checkpoint : False
|
||||
checkpoint_path : '/home/yeye/Desktop/PhD/AORTA/DATA/monolithic/checkpoint/'
|
||||
write_outlets : False
|
||||
outlets_path : '/home/yeye/Desktop/PhD/AORTA/DATA/monolithic/outlets/'
|
||||
|
||||
Tf : 0.9 # seg
|
||||
density : 1.2 # gr/cm3
|
||||
dynamic_viscosity : 0.035
|
||||
dt : 0.005
|
||||
dt_write : 0.01
|
||||
checkpoint_dt : 0.02
|
||||
|
||||
|
||||
stab:
|
||||
pspg : 1
|
||||
epsilon : 0.01
|
||||
backflow : 1
|
||||
back_id : [3,4,5,6]
|
||||
temam : 1
|
||||
supg : 0
|
||||
pssu : 0
|
||||
|
||||
param:
|
||||
U : 60
|
||||
period : 0.7
|
||||
Nvel : 1
|
||||
Npress : 1
|
||||
theta : 1
|
||||
|
||||
windkessel:
|
||||
id : [3,4,5,6]
|
||||
R_p : {'3':100 , '4':250, '5':250 , '6':250 }
|
||||
R_d : {'3':1000, '4':8000, '5':8000 , '6':8000}
|
||||
C : {'3':0.01, '4':0.0001, '5':0.00001, '6':0.0001}
|
||||
alpha : {'3':0 , '4':0 , '5':0 , '6':0}
|
||||
beta : {'3':0 , '4':0 , '5':0 , '6':0}
|
||||
gamma : {'3':0 , '4':0 , '5':0 , '6':0}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -32,15 +32,16 @@ magnetization:
|
||||
savepath: '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/MAG/Mag9AoCoE1.npz'
|
||||
|
||||
sequence:
|
||||
apply: False
|
||||
checkpoint_path: '/home/yeye/Desktop/First/H1/dt5ms/coaorta/'
|
||||
meshpath: '/home/yeye/Desktop/PhD/AORTA/MESH/coaorta/H1/coaortaH1.h5'
|
||||
apply: false
|
||||
checkpoint_path: '/home/yeye/Desktop/Poiseuille/Meas/'
|
||||
meshpath: '/home/yeye/Desktop/Poiseuille/Meas/poiseuille.h5'
|
||||
sampling_rate: 1
|
||||
boxtype: 'fix_resolution'
|
||||
ranges: {'x': [10.8,21] , 'y': [13,19] , 'z': [-0.1,11.5] }
|
||||
resol: [0.14,0.14,0.14]
|
||||
boxsize: [80,80,80]
|
||||
name: 'SH1_5ms'
|
||||
#ranges: {'x': [10.8,21] , 'y': [13,19] , 'z': [-0.1,11.5] }
|
||||
ranges: {'x': [-1,1] , 'y': [-1,1] , 'z': [0,6] }
|
||||
resol: [0.2,0.2,0.2]
|
||||
boxsize: [100,100,100]
|
||||
name: 'seq'
|
||||
|
||||
cs:
|
||||
apply: false
|
||||
@ -76,11 +77,6 @@ reference:
|
||||
save : True
|
||||
name : 'ref'
|
||||
|
||||
norms:
|
||||
apply : False
|
||||
field_path : '/home/yeye/Desktop/PhD/AORTA/DATA/ct/aorta_coarse/'
|
||||
plot : True
|
||||
|
||||
create_checkpoint:
|
||||
apply: false
|
||||
loadseq: '/home/yeye/Desktop/Corrector_2019/Second/Vol2/dicom/mod/'
|
||||
@ -100,28 +96,15 @@ create_checkpoint:
|
||||
savepath: '/home/yeye/Desktop/Corrector_2019/Second/Vol2/dicom/'
|
||||
xdmf: true
|
||||
|
||||
peak_pv:
|
||||
apply : False
|
||||
orig_seq : '/home/yeye/Desktop/PhD/AORTA/DATA/sequences/aorta_Ucoarse.npz'
|
||||
peak_slice : 6
|
||||
R : [1,2]
|
||||
p_comp : 'error' # 'peak' or 'error'
|
||||
flux_bnd : [2]
|
||||
N_CS : 1
|
||||
mesh_into : 'leo'
|
||||
save : True
|
||||
savepath : '/home/yeye/Desktop/PhD/AORTA/DATA/maxpv/Ucoarse_test/'
|
||||
infile_dp : '/home/yeye/Desktop/dP/input/all_points.yaml'
|
||||
|
||||
change_mesh:
|
||||
apply: false
|
||||
mode: 'u'
|
||||
dt: 0.005
|
||||
checkpoint_path: '/home/yeye/Desktop/R1/checkpoint/'
|
||||
dt: 0.03
|
||||
checkpoint_path: '/home/yeye/Desktop/Poiseuille/Meas/checkpoint/'
|
||||
under_rate: 1
|
||||
mesh_in: '/home/yeye/Desktop/PhD/AORTA/MESH/coaorta/H1/coaortaH1.h5'
|
||||
mesh_out: '/home/yeye/Desktop/meshes/leo_1.42.h5'
|
||||
savepath: '/home/yeye/Desktop/test/'
|
||||
mesh_in: '/home/yeye/Desktop/Poiseuille/Meas/poiseuille.h5'
|
||||
mesh_out: '/home/yeye/Desktop/Poiseuille/Meas_leo/poiseuille.h5'
|
||||
savepath: '/home/yeye/Desktop/Poiseuille/Meas_leo/'
|
||||
xdmf: True
|
||||
|
||||
SENSE:
|
||||
@ -133,8 +116,9 @@ SENSE:
|
||||
|
||||
create_leo:
|
||||
apply: false
|
||||
velseq: '/home/yeye/Desktop/Corrector_2019/Second/Vol2/dicom/mod_nocoro/u_R1.mat'
|
||||
resol: [0.09,0.09,0.09]
|
||||
velseq: '/home/yeye/Desktop/Corrector_2019/Meshes/SH3_2.0_R1.npz'
|
||||
resol: [0.2,0.2,0.2]
|
||||
#ranges: {'x': [-1.2,1.2] , 'y': [-1.2,1.2] , 'z': [-0.2,6.2] }
|
||||
ranges: {'x': [10.8,21] , 'y': [13,19] , 'z': [-0.1,11.5] }
|
||||
masked: false
|
||||
segmentation: '/home/yeye/Desktop/PhD/MEDICAL_DATA/Phantom/With_AoCo_9mm/MATLAB_FILES/Segmented_Aorta.mat'
|
||||
@ -148,13 +132,13 @@ kspace_cib:
|
||||
|
||||
CIBtoH5:
|
||||
apply: false
|
||||
data_path: '/home/yeye/Desktop/PhD/MEDICAL_DATA/AoCo/9AoCoPhantomRest0.9/'
|
||||
interpolate: true
|
||||
flip: false
|
||||
dt: 0.03072
|
||||
mesh_path: '/home/yeye/Desktop/PhD/MEDICAL_DATA/AoCo/9AoCoPhantomRest1.4/'
|
||||
times: [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]
|
||||
outpath: '/home/yeye/Desktop/9mmRest1.4/R1/'
|
||||
data_path: '/home/yeye/Desktop/PhD/MEDICAL_DATA/Study_David/Patients/Study_14_GM/velmesh_from_velmat/'
|
||||
interpolate: false
|
||||
flip: false # Set it True for AoCo = 13mm
|
||||
dt: 0.03831417624521074
|
||||
mesh_path: '/home/yeye/Desktop/PhD/MEDICAL_DATA/Study_David/Patients/Study_14_GM/velmesh_from_velmat/'
|
||||
times: [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]
|
||||
outpath: '/home/yeye/Desktop/Patient_GM/'
|
||||
|
||||
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user