mirror of
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Merge pull request #305 from simpeg/feat/sparse-regularization
Feat/sparse regularization
This commit is contained in:
Lindsey
+97
-55
@@ -169,7 +169,7 @@ def readUBC_DC2DModel(fileName):
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return model
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def plot_pseudoSection(DCsurvey, axs, stype='dpdp', dtype="appc", clim=None):
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def plot_pseudoSection(DCsurvey, axs, stype='dpdp', dtype="appc", clim=None, cblabel=True, axlabel = True, colorbar = True, contour = None):
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"""
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Read list of 2D tx-rx location and plot a speudo-section of apparent
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resistivity.
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@@ -192,9 +192,6 @@ def plot_pseudoSection(DCsurvey, axs, stype='dpdp', dtype="appc", clim=None):
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from scipy.interpolate import griddata
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import pylab as plt
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# Set depth to 0 for now
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z0 = 0.
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# Pre-allocate
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midx = []
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midz = []
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@@ -259,38 +256,53 @@ def plot_pseudoSection(DCsurvey, axs, stype='dpdp', dtype="appc", clim=None):
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midx = np.hstack([midx, ( Cmid + Pmid )/2 ])
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midz = np.hstack([midz, -np.abs(Cmid-Pmid)/2 + (Tx[0][2] + Tx[1][2])/2 ])
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ax = axs
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# Grid points
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grid_x, grid_z = np.mgrid[np.min(midx):np.max(midx), np.min(midz):np.max(midz)]
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grid_rho = griddata(np.c_[midx,midz], rho.T, (grid_x, grid_z), method='linear')
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# Scale the color scheme
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if clim == None:
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vmin, vmax = rho.min(), rho.max()
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else:
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vmin, vmax = clim[0], clim[1]
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# Plot data
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grid_rho = np.ma.masked_where(np.isnan(grid_rho), grid_rho)
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ph = plt.pcolormesh(grid_x[:,0],grid_z[0,:],grid_rho.T, clim=(vmin, vmax))
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cbar = plt.colorbar(format="$10^{%.1f}$",fraction=0.04,orientation="horizontal")
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cmin,cmax = cbar.get_clim()
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ticks = np.linspace(cmin,cmax,3)
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cbar.set_ticks(ticks)
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cbar.ax.tick_params(labelsize=10)
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ph = plt.pcolormesh(grid_x[:,0],grid_z[0,:],grid_rho.T, vmin = vmin, vmax = vmax)
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plt.gca().tick_params(axis='both', which='major', labelsize=8)
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if dtype == 'appc':
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cbar.set_label("App.Cond",size=12)
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elif dtype == 'appr':
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cbar.set_label("App.Res.",size=12)
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elif dtype == 'volt':
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cbar.set_label("Potential (V)",size=12)
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if contour is not None:
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plt.contour(grid_x,grid_z,grid_rho,levels = contour,colors = 'r', vmin = vmin, vmax = vmax)
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# Add scatter points
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axs.scatter(midx,midz,s=10,c=rho.T, vmin = vmin, vmax = vmax)
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if colorbar:
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if dtype == 'volt':
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cbar = plt.colorbar(ph, ax = axs, format="%4.1f",fraction=0.04,orientation="horizontal")
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# Plot apparent resistivity
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ax.scatter(midx,midz,s=10,c=rho.T, vmin =vmin, vmax = vmax, clim=(vmin, vmax))
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else:
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cbar = plt.colorbar(ph, ax = axs, format="$10^{%.1f}$",fraction=0.04,orientation="horizontal")
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cmin,cmax = cbar.get_clim()
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ticks = np.linspace(cmin,cmax,3)
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cbar.set_ticks(ticks)
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cbar.ax.tick_params(labelsize=10)
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if cblabel:
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if dtype == 'appc':
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cbar.set_label("App.Cond",size=12)
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elif dtype == 'appr':
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cbar.set_label("App.Res.",size=12)
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elif dtype == 'volt':
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cbar.set_label("Potential (V)",size=12)
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#ax.set_xticklabels([])
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#ax.set_yticklabels([])
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if not axlabel:
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axs.set_xticklabels([])
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axs.set_yticklabels([])
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plt.gca().set_aspect('equal', adjustable='box')
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@@ -448,15 +460,15 @@ def gen_DCIPsurvey(endl, mesh, stype, a, b, n):
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survey = DC.SurveyDC(SrcList)
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return survey, Tx, Rx
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def writeUBC_DCobs(fileName, DCsurvey, dtype, stype):
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def writeUBC_DCobs(fileName, DCsurvey, dtype='3D', stype='SURFACE', iptype = 0):
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"""
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Write UBC GIF DCIP 2D or 3D observation file
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Input:
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:string fileName -> including path where the file is written out
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:DCsurvey -> DC survey class object
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:string dtype -> either '2D' | '3D'
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:string stype -> either 'SURFACE' | 'GENERAL'
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:string fileName -> including path where the file is written out
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:DCsurvey DC survey class object
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:string dtype -> either '2D' | '3D'
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:string stype -> either 'SURFACE' | 'GENERAL'
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Output:
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:param UBC2D-Data file
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@@ -471,10 +483,16 @@ def writeUBC_DCobs(fileName, DCsurvey, dtype, stype):
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assert (dtype=='2D') | (dtype=='3D'), "Data must be either '2D' | '3D'"
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assert (stype=='SURFACE') | (stype=='GENERAL') | (stype=='SIMPLE'), "Data must be either 'SURFACE' | 'GENERAL' | 'SIMPLE'"
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fid = open(fileName,'w')
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fid.write('! ' + stype + ' FORMAT\n')
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if iptype!=0:
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fid.write('IPTYPE=%i\n'%iptype)
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else:
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fid.write('! ' + stype + ' FORMAT\n')
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count = 0
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for ii in range(DCsurvey.nSrc):
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@@ -498,7 +516,7 @@ def writeUBC_DCobs(fileName, DCsurvey, dtype, stype):
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B = np.repeat(tx[0,1],M.shape[0],axis=0)
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M = M[:,0]
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N = N[:,0]
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np.savetxt(fid, np.c_[A, B, M, N , DCsurvey.dobs[count:count+nD], DCsurvey.std[count:count+nD] ], fmt='%e',delimiter=' ',newline='\n')
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@@ -506,18 +524,25 @@ def writeUBC_DCobs(fileName, DCsurvey, dtype, stype):
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if stype == 'SURFACE':
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fid.writelines("%e " % ii for ii in mkvc(tx[0,:]))
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fid.writelines("%f " % ii for ii in mkvc(tx[0,:]))
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M = M[:,0]
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N = N[:,0]
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if stype == 'GENERAL':
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# Flip sign for z-elevation to depth
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tx[2::2,:] = -tx[2::2,:]
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fid.writelines("%e " % ii for ii in mkvc(tx[::2,:]))
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M = M[:,0::2]
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N = N[:,0::2]
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# Flip sign for z-elevation to depth
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M[:,1::2] = -M[:,1::2]
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N[:,1::2] = -N[:,1::2]
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fid.write('%i\n'% nD)
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np.savetxt(fid, np.c_[ M, N , DCsurvey.dobs[count:count+nD], DCsurvey.std[count:count+nD] ], fmt='%e',delimiter=' ',newline='\n')
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np.savetxt(fid, np.c_[ M, N , DCsurvey.dobs[count:count+nD], DCsurvey.std[count:count+nD] ], fmt='%f',delimiter=' ',newline='\n')
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if dtype=='3D':
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@@ -529,11 +554,12 @@ def writeUBC_DCobs(fileName, DCsurvey, dtype, stype):
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if stype == 'GENERAL':
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fid.writelines("%e " % ii for ii in mkvc(tx))
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fid.writelines("%e " % ii for ii in mkvc(tx[0:3,:]))
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fid.write('%i\n'% nD)
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np.savetxt(fid, np.c_[ M, N , DCsurvey.dobs[count:count+nD], DCsurvey.std[count:count+nD] ], fmt='%e',delimiter=' ',newline='\n')
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fid.write('\n')
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count += nD
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fid.close()
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@@ -640,51 +666,59 @@ def convertObs_DC3D_to_2D(DCsurvey,lineID, flag = 'local'):
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DCsurvey2D.std = np.asarray(DCsurvey.std)
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return DCsurvey2D
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def readUBC_DC3Dobs(fileName):
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def readUBC_DC3Dobs(fileName, dtype = 'DC'):
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"""
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Read UBC GIF DCIP 3D observation file and generate survey
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Read UBC GIF IP 3D observation file and generate survey
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Input:
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:param fileName, path to the UBC GIF 3D obs file
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Output:
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:param DCIPsurvey
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:param IPsurvey
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:return
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Created on Mon April 6th, 2015
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@author: dominiquef
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"""
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zflag = True # Flag for z value provided
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# Load file
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obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='!')
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if dtype == 'IP':
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obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='IPTYPE')
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elif dtype == 'DC':
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obsfile = np.genfromtxt(fileName,delimiter=' \n',dtype=np.str,comments='!')
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else:
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print "dtype must be 'DC'(default) | 'IP'"
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# Pre-allocate
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srcLists = []
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Rx = []
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d = []
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wd = []
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zflag = True # Flag for z value provided
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# Countdown for number of obs/tx
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count = 0
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for ii in range(obsfile.shape[0]):
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# Skip if blank line
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if not obsfile[ii]:
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continue
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# First line is transmitter with number of receivers
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# First line or end of a transmitter block, read transmitter info
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if count==0:
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temp = (np.fromstring(obsfile[ii], dtype=float,sep=' ').T)
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# Read the line
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temp = (np.fromstring(obsfile[ii], dtype=float, sep=' ').T)
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count = int(temp[-1])
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# Check if z value is provided, if False -> nan
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if len(temp)==5:
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tx = np.r_[temp[0:2],np.nan,temp[0:2],np.nan]
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zflag = False
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tx = np.r_[temp[0:2],np.nan,temp[2:4],np.nan]
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zflag = False # Pass on the flag to the receiver loc
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else:
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tx = temp[:-1]
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@@ -692,8 +726,16 @@ def readUBC_DC3Dobs(fileName):
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rx = []
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continue
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temp = np.fromstring(obsfile[ii], dtype=float,sep=' ')
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temp = np.fromstring(obsfile[ii], dtype=float,sep=' ') # Get the string
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# Filter out negative IP
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# if temp[-2] < 0:
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# count = count -1
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# print "Negative!"
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#
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# else:
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# If the Z-location is provided, otherwise put nan
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if zflag:
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rx.append(temp[:-2])
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@@ -703,7 +745,7 @@ def readUBC_DC3Dobs(fileName):
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wd.append(temp[-1])
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else:
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rx.append(np.r_[temp[0:2],np.nan,temp[0:2],np.nan] )
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rx.append(np.r_[temp[0:2],np.nan,temp[2:4],np.nan] )
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# Check if there is data with the location
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if len(temp)==6:
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d.append(temp[-2])
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@@ -711,7 +753,7 @@ def readUBC_DC3Dobs(fileName):
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count = count -1
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# Reach the end of transmitter block
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# Reach the end of transmitter block, append the src, rx and continue
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if count == 0:
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rx = np.asarray(rx)
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Rx = DC.RxDipole(rx[:,:3],rx[:,3:])
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+43
-10
@@ -258,6 +258,7 @@ class Update_IRLS(InversionDirective):
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phi_m_last = None
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phi_d_last = None
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def initialize(self):
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# Scale the regularization for changes in norm
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@@ -275,7 +276,7 @@ class Update_IRLS(InversionDirective):
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self.phi_d_last = self.invProb.phi_d
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def endIter(self):
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# Cool the threshold parameter
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# Cool the threshold parameter if required
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if getattr(self, 'factor', None) is not None:
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eps = self.reg.eps / self.factor
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@@ -290,28 +291,44 @@ class Update_IRLS(InversionDirective):
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# Update the model used for the IRLS weights
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self.reg.curModel = self.invProb.curModel
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# Temporarely set gamma to 1.
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# Temporarely set gamma to 1. to get raw phi_m
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self.reg.gamma = 1.
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# Compute change in model objective function and update scaling
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# Compute new model objective function value
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phim_new = self.reg.eval(self.invProb.curModel)
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# Update gamma to scale the regularization between IRLS iterations
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self.reg.gamma = self.phi_m_last / phim_new
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self.invProb.beta = self.invProb.beta * self.survey.nD*0.5 / self.invProb.phi_d
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# Set the weighting matrix to None so that it is recomputed next time
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# it is called in the inversion
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self.reg._W = None
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class Update_lin_PreCond(InversionDirective):
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"""
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Create a Jacobi preconditioner for the linear problem
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"""
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onlyOnStart=False
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def initialize(self):
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if getattr(self.opt, 'approxHinv', None) is None:
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# Update the pre-conditioner
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diagA = np.sum(self.prob.G**2.,axis=0) + self.invProb.beta*(self.reg.W.T*self.reg.W).diagonal() #* (self.reg.mapping * np.ones(self.reg.curModel.size))**2.
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PC = Utils.sdiag((self.prob.mapping.deriv(None).T *diagA)**-1.)
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self.opt.approxHinv = PC
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def endIter(self):
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# Cool the threshold parameter
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if self.onlyOnStart==True:
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return
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if getattr(self.opt, 'approxHinv', None) is not None:
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# Update the pre-conditioner
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diagA = np.sum(self.prob.G**2.,axis=0) + self.invProb.beta*(self.reg.W.T*self.reg.W).diagonal() * (self.reg.mapping * np.ones(self.reg.curModel.size))**2.
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PC = Utils.sdiag(diagA**-1.)
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diagA = np.sum(self.prob.G**2.,axis=0) + self.invProb.beta*(self.reg.W.T*self.reg.W).diagonal() #* (self.reg.mapping * np.ones(self.reg.curModel.size))**2.
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PC = Utils.sdiag((self.prob.mapping.deriv(None).T *diagA)**-1.)
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self.opt.approxHinv = PC
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print 'Updated pre-cond'
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class Update_Wj(InversionDirective):
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"""
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@@ -338,3 +355,19 @@ class Update_Wj(InversionDirective):
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JtJdiag = JtJdiag / max(JtJdiag)
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self.reg.wght = JtJdiag
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class Scale_Beta(InversionDirective):
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"""
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Instead of a linear cooling schedule, beta is allowed to change based
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on the ratio between the target misfit and the current data misfit. The
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update is done only if the misfit is outside some threshold bounds.
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"""
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tol = 0.05
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def endIter(self):
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# Check if misfit is within the tolerance, otherwise adjust beta
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val = self.invProb.phi_d / (self.survey.nD*0.5)
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if np.abs(1.-val) > self.tol:
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self.invProb.beta = self.invProb.beta * self.survey.nD*0.5 / self.invProb.phi_d
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@@ -86,12 +86,12 @@ def run(N=200, plotIt=True):
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#reg.recModel = mrec
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reg.wght = np.ones(mesh.nC)
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reg.mref = np.zeros(mesh.nC)
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reg.eps_p = 2e-3
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reg.eps_q = 2e-3
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reg.eps_p = 5e-2
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reg.eps_q = 1e-2
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reg.norms = [0., 0., 2., 2.]
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reg.wght = wr
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opt = Optimization.ProjectedGNCG(maxIter=5 ,lower=-2.,upper=2., maxIterCG= 100, tolCG = 1e-3)
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opt = Optimization.ProjectedGNCG(maxIter=10 ,lower=-2.,upper=2., maxIterLS = 20, maxIterCG= 20, tolCG = 1e-3)
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invProb = InvProblem.BaseInvProblem(dmis, reg, opt, beta = invProb.beta*2.)
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beta = Directives.BetaSchedule(coolingFactor=1, coolingRate=1)
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#betaest = Directives.BetaEstimate_ByEig()
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@@ -21,10 +21,9 @@ class TensorMeshIO(object):
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if '*' in seg:
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st = seg
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sp = seg.split('*')
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re = np.array(sp[0],dtype=int)*(' ' + sp[1])
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re = int(sp[0])*(' ' + sp[1])
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line = line.replace(st,re.strip())
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return np.array(line.split(),dtype=float)
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# Read the file as line strings, remove lines with comment = !
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msh = np.genfromtxt(fileName,delimiter='\n',dtype=np.str,comments='!')
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@@ -731,14 +731,14 @@ class Sparse(Simple):
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@property
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def W(self):
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"""Full regularization matrix W"""
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#if getattr(self, '_W', None) is None:
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wlist = (self.Wsmall, self.Wsmooth)
|
||||
#self._W = sp.vstack(wlist)
|
||||
return sp.vstack(wlist)
|
||||
if getattr(self, '_W', None) is None:
|
||||
wlist = (self.Wsmall, self.Wsmooth)
|
||||
self._W = sp.vstack(wlist)
|
||||
return self._W
|
||||
|
||||
def R(self, f_m , eps, exponent):
|
||||
|
||||
eta = (eps**(1-exponent/2.))**0.5
|
||||
r = eta / (f_m**2.+ eps**2.)**((1-exponent/2.)/2.)
|
||||
eta = (eps**(1.-exponent/2.))**0.5
|
||||
r = eta / (f_m**2.+ eps**2.)**((1.-exponent/2.)/2.)
|
||||
|
||||
return r
|
||||
|
||||
@@ -0,0 +1,137 @@
|
||||
from SimPEG import np, Mesh
|
||||
import time as tm
|
||||
import vtk, vtk.util.numpy_support as npsup
|
||||
import re
|
||||
|
||||
def read_GOCAD_ts(tsfile):
|
||||
"""
|
||||
|
||||
Read GOCAD triangulated surface (*.ts) file
|
||||
INPUT:
|
||||
tsfile: Triangulated surface
|
||||
|
||||
OUTPUT:
|
||||
vrts : Array of vertices in XYZ coordinates [n x 3]
|
||||
trgl : Array of index for triangles [m x 3]. The order of the vertices
|
||||
is important and describes the normal
|
||||
n = cross( (P2 - P1 ) , (P3 - P1) )
|
||||
|
||||
Author: @fourndo
|
||||
|
||||
|
||||
.. note::
|
||||
|
||||
Remove all attributes from the GoCAD surface before exporting it!
|
||||
|
||||
"""
|
||||
|
||||
|
||||
fid = open(tsfile,'r')
|
||||
line = fid.readline()
|
||||
|
||||
# Skip all the lines until the vertices
|
||||
while re.match('TFACE',line)==None:
|
||||
line = fid.readline()
|
||||
|
||||
line = fid.readline()
|
||||
vrtx = []
|
||||
|
||||
# Run down all the vertices and save in array
|
||||
while re.match('VRTX',line):
|
||||
l_input = re.split('[\s*]',line)
|
||||
temp = np.array(l_input[2:5])
|
||||
vrtx.append(temp.astype(np.float))
|
||||
|
||||
# Read next line
|
||||
line = fid.readline()
|
||||
|
||||
vrtx = np.asarray(vrtx)
|
||||
|
||||
# Skip lines to the triangles
|
||||
while re.match('TRGL',line)==None:
|
||||
line = fid.readline()
|
||||
|
||||
# Run down the list of triangles
|
||||
trgl = []
|
||||
|
||||
# Run down all the vertices and save in array
|
||||
while re.match('TRGL',line):
|
||||
l_input = re.split('[\s*]',line)
|
||||
temp = np.array(l_input[1:4])
|
||||
trgl.append(temp.astype(np.int))
|
||||
|
||||
# Read next line
|
||||
line = fid.readline()
|
||||
|
||||
trgl = np.asarray(trgl)
|
||||
|
||||
return vrtx, trgl
|
||||
|
||||
def surface2inds(vrtx, trgl, mesh, boundaries=True, internal=True):
|
||||
""""
|
||||
Function to read gocad polystructure file and output indexes of mesh with in the structure.
|
||||
|
||||
"""
|
||||
# Adjust the index
|
||||
trgl = trgl - 1
|
||||
|
||||
# Make vtk pts
|
||||
ptsvtk = vtk.vtkPoints()
|
||||
ptsvtk.SetData(npsup.numpy_to_vtk(vrtx,deep=1))
|
||||
|
||||
# Make the polygon connection
|
||||
polys = vtk.vtkCellArray()
|
||||
for face in trgl:
|
||||
poly = vtk.vtkPolygon()
|
||||
poly.GetPointIds().SetNumberOfIds(len(face))
|
||||
for nrv, vert in enumerate(face):
|
||||
poly.GetPointIds().SetId(nrv,vert)
|
||||
polys.InsertNextCell(poly)
|
||||
|
||||
# Make the polydata, structure of connections and vrtx
|
||||
polyData = vtk.vtkPolyData()
|
||||
polyData.SetPoints(ptsvtk)
|
||||
polyData.SetPolys(polys)
|
||||
|
||||
# Make implicit func
|
||||
ImpDistFunc = vtk.vtkImplicitPolyDataDistance()
|
||||
ImpDistFunc.SetInput(polyData)
|
||||
|
||||
# Convert the mesh
|
||||
vtkMesh = vtk.vtkRectilinearGrid()
|
||||
vtkMesh.SetDimensions(mesh.nNx,mesh.nNy,mesh.nNz)
|
||||
vtkMesh.SetXCoordinates(npsup.numpy_to_vtk(mesh.vectorNx, deep=1))
|
||||
vtkMesh.SetYCoordinates(npsup.numpy_to_vtk(mesh.vectorNy, deep=1))
|
||||
vtkMesh.SetZCoordinates(npsup.numpy_to_vtk(mesh.vectorNz, deep=1))
|
||||
# Add indexes
|
||||
vtkInd = npsup.numpy_to_vtk(np.arange(mesh.nC), deep=1)
|
||||
vtkInd.SetName('Index')
|
||||
vtkMesh.GetCellData().AddArray(vtkInd)
|
||||
|
||||
extractImpDistRectGridFilt = vtk.vtkExtractGeometry() # Object constructor
|
||||
extractImpDistRectGridFilt.SetImplicitFunction(ImpDistFunc) #
|
||||
extractImpDistRectGridFilt.SetInputData(vtkMesh)
|
||||
|
||||
if boundaries is True:
|
||||
extractImpDistRectGridFilt.ExtractBoundaryCellsOn()
|
||||
|
||||
else:
|
||||
extractImpDistRectGridFilt.ExtractBoundaryCellsOff()
|
||||
|
||||
if internal is True:
|
||||
extractImpDistRectGridFilt.ExtractInsideOn()
|
||||
|
||||
else:
|
||||
extractImpDistRectGridFilt.ExtractInsideOff()
|
||||
|
||||
print "Extracting indices from grid..."
|
||||
# Executing the pipe
|
||||
extractImpDistRectGridFilt.Update()
|
||||
|
||||
# Get index inside
|
||||
insideGrid = extractImpDistRectGridFilt.GetOutput()
|
||||
insideGrid = npsup.vtk_to_numpy(insideGrid.GetCellData().GetArray('Index'))
|
||||
|
||||
|
||||
# Return the indexes inside
|
||||
return insideGrid
|
||||
Reference in New Issue
Block a user