def run_once(x0,x1):
sol = fmin_cg(rosen, [x0, x1], retall = True, full_output=1)
xy = numpy.asarray(sol[-1])
sam.putarray('xy',xy)
sam.eval("plot(xy(:,1),xy(:,2),'w-','LineWidth',2)")
sam.eval("plot(xy(:,1),xy(:,2),'wo','MarkerSize',6)")
return sol
def run_once(x0, x1):
sol = fmin_cg(rosen, [x0, x1], retall=True, full_output=1)
xy = numpy.asarray(sol[-1])
sam.putarray('xy', xy)
sam.eval("plot(xy(:,1),xy(:,2),'w-','LineWidth',2)")
sam.eval("plot(xy(:,1),xy(:,2),'wo','MarkerSize',6)")
return sol
def plot(self, contours=None):
"""Plots the isosurfaces for the field data, at corresponding contour values."""
import ExcitationSlicer
path = ExcitationSlicer.__file__
path = path.strip('__init__.pyc')
if contours is None:
contours = self._contvals
import sam
import numpy as np
try:
contourvalue = contours[0]
except:
raise ValueError, "contourvalues is empty."
#we first pass the data into Matlab as an array:
array = np.array(self._getArray())
(dim0, dim1, dim2) = array.shape
q0 = np.arange(1, dim0 + 1)
q1 = np.arange(1, dim1 + 1)
q2 = np.arange(1, dim2 + 1)
sam.put('dim0', [dim0])
sam.put('dim1', [dim1])
sam.put('dim2', [dim2])
sam.put('q0', q0)
sam.put('q1', q1)
sam.put('q2', q2)
sam.eval("[q0i, q1i, q2i] = meshgrid(q0, q1, q2);")
# this causes a segmentation fault for an array of 20x20x20 doubles:
#sam.putarray('array', array)
# here is a temporary ugly(!) fix:
array.shape = (dim0 * dim1 * dim2, )
sam.put('array', array)
sam.eval("earray = reshape(array', dim0, dim1, dim2)")
# end of fix
# pass the energy-value for which to draw the isosurface into matlab"
sam.put('contourvalue', [contourvalue])
# We use an M-file that gets called when we evaluate the name
# of the corresponding function in Matlab via SAM
print "path: ", path
sam.eval("cd('" + path + "')")
sam.eval(
"MlabPhonIsoSurfacePlotter(q0i,q1i,q2i, earray, contourvalue, 'blue')"
)
waitforentry = raw_input("Press any key.")
sam.eval("close")
return 0
def run_once():
simplex = Monitor()
solver = fmin(2)
solver.SetRandomInitialPoints([0, 0], [7, 7])
solver.SetGenerationMonitor(simplex)
solver.Solve(CostFunction, termination=CRT())
sol = solver.Solution()
for x in simplex.x:
sam.putarray('x', x)
sam.eval("plot(x([1,2,3,1],1),x([1,2,3,1],2),'k-')")
def run_once():
simplex = Monitor()
solver = fmin(2)
solver.SetRandomInitialPoints([0,0],[2,2])
solver.SetGenerationMonitor(simplex)
solver.Solve(Corana2, termination=CRT())
sol = solver.Solution()
for x in simplex.x:
sam.putarray('x',x)
sam.eval("plot(x([1,2,3,1],1),x([1,2,3,1],2),'w-')")
def plot(self,contours=None):
"""Plots the isosurfaces for the field data, at corresponding contour values."""
import ExcitationSlicer
path = ExcitationSlicer.__file__
path=path.strip('__init__.pyc')
if contours is None:
contours = self._contvals
import sam
import numpy as np
try:
contourvalue = contours[0]
except:
raise ValueError, "contourvalues is empty."
#we first pass the data into Matlab as an array:
array = np.array(self._getArray())
(dim0, dim1, dim2) = array.shape
q0 = np.arange(1, dim0 + 1)
q1 = np.arange(1, dim1 + 1)
q2 = np.arange(1, dim2 + 1)
sam.put('dim0', [dim0])
sam.put('dim1', [dim1])
sam.put('dim2', [dim2])
sam.put('q0', q0)
sam.put('q1', q1)
sam.put('q2', q2)
sam.eval("[q0i, q1i, q2i] = meshgrid(q0, q1, q2);")
# this causes a segmentation fault for an array of 20x20x20 doubles:
#sam.putarray('array', array)
# here is a temporary ugly(!) fix:
array.shape=(dim0*dim1*dim2,)
sam.put('array', array)
sam.eval("earray = reshape(array', dim0, dim1, dim2)")
# end of fix
# pass the energy-value for which to draw the isosurface into matlab"
sam.put('contourvalue', [contourvalue])
# We use an M-file that gets called when we evaluate the name
# of the corresponding function in Matlab via SAM
print "path: ", path
sam.eval("cd('"+path+"')")
sam.eval("MlabPhonIsoSurfacePlotter(q0i,q1i,q2i, earray, contourvalue, 'blue')")
waitforentry=raw_input("Press any key.")
sam.eval("close")
return 0
def run_once(x0,x1):
simplex = Monitor()
xinit = [x0, x1]
solver = fmin(len(xinit))
solver.SetInitialPoints(xinit)
solver.SetGenerationMonitor(simplex)
solver.Solve(rosen, termination=CRT())
sol = solver.Solution()
for x in simplex.x:
sam.putarray('x',x)
sam.eval("plot(x([1,2,3,1],1),x([1,2,3,1],2),'w-')")
def run_once(x0, x1):
simplex = Monitor()
xinit = [x0, x1]
solver = fmin(len(xinit))
solver.SetInitialPoints(xinit)
solver.SetGenerationMonitor(simplex)
solver.Solve(rosen, termination=CRT())
sol = solver.Solution()
for x in simplex.x:
sam.putarray('x', x)
sam.eval("plot(x([1,2,3,1],1),x([1,2,3,1],2),'w-')")
def run_once_xv():
simplex = Monitor()
y1 = y0*random.uniform(0.5,1.5)
z1 = z0*random.uniform(0.5,1.5)
xinit = [random.uniform(x0-40,x0+40), y1, z1, random.uniform(v0-0.1,v0+0.1)]
solver = fmin(len(xinit))
solver.SetInitialPoints(xinit)
solver.SetGenerationMonitor(simplex)
solver.Solve(cost_function, termination=CRT())
sol = solver.Solution()
print(sol)
for x in simplex.x:
sam.putarray('x',x)
sam.eval("plot(x([1,2,3,1],1),x([1,2,3,1],2),'w-','LineWidth',2)")
return sol
def draw_contour_xv():
import numpy
x, y = mgrid[-40:40:0.5, -0.1:0.3:.01]
x = x0 + x
y = v0 + y
s,t = x.shape
c = 0*x
s,t = x.shape
for i in range(s):
for j in range(t):
xx,yy = x[i,j], y[i,j]
c[i,j] = cost_function([xx, y0, z0, yy])
sam.putarray('X',x)
sam.putarray('Y',y)
sam.putarray('C',c)
sam.eval("[c,h]=contourf(X,Y,C,100);set(h,'EdgeColor','none')")
sam.eval('hold on')
def draw_contour_xv():
import numpy
x, y = mgrid[-40:40:0.5, -0.1:0.3:.01]
x = x0 + x
y = v0 + y
s, t = x.shape
c = 0 * x
s, t = x.shape
for i in range(s):
for j in range(t):
xx, yy = x[i, j], y[i, j]
c[i, j] = cost_function([xx, y0, z0, yy])
sam.putarray('X', x)
sam.putarray('Y', y)
sam.putarray('C', c)
sam.eval("[c,h]=contourf(X,Y,C,100);set(h,'EdgeColor','none')")
sam.eval('hold on')
def matlab(scriptdir,title,heading,imagefile,htmlfile='results.html'):
# use sam module to run a matlab session from python
import sam
sam.eval("") # initiate matlab session
# scriptdir should contain the amroc matlab scripts needed to process
# the hdf files. make sure this is in MATLABPATH
sam.eval("addpath %s" % scriptdir)
# run plothdf script, using local menu_automation.m script to make plot
sam.eval("plothdf")
sam.close() # end matlab session
# generate HTML web page with results
makeHTML(title,heading,imagefile,htmlfile)
return
def draw_contour():
import numpy
x, y = numpy.mgrid[0:7.5:0.05, 0:7.5:0.05]
c = 0 * x
s, t = x.shape
for i in range(s):
for j in range(t):
xx, yy = x[i, j], y[i, j]
c[i, j] = CostFunction([xx, yy])
sam.putarray('X', x)
sam.putarray('Y', y)
sam.putarray('C', c)
sam.verbose()
sam.eval("[c,h]=contourf(X,Y,log(C*20+1)+2,100);set(h,'EdgeColor','none')")
sam.eval("title('Zimmermann''s Corner. Min at 7,2')")
sam.eval('hold on')
def draw_contour():
import numpy
x, y = numpy.mgrid[0:2.1:0.02, 0:2.1:0.02]
c = 0 * x
s, t = x.shape
for i in range(s):
for j in range(t):
xx, yy = x[i, j], y[i, j]
c[i, j] = rosen([xx, yy])
sam.putarray('X', x)
sam.putarray('Y', y)
sam.putarray('C', c)
sam.verbose()
#sam.eval("[c,h]=contourf(X,Y,C,60);set(h,'EdgeColor','none')")
sam.eval("[c,h]=contourf(X,Y,log(C*20+1)+2,60);set(h,'EdgeColor','none')")
sam.eval("title('Rosenbrock''s function in 2D. Min at 1,1')")
sam.eval('hold on')
def draw_contour():
import numpy
x, y = numpy.mgrid[0:2.1:0.05, 0:2.1:0.05]
c = 0 * x
s, t = x.shape
for i in range(s):
for j in range(t):
xx, yy = x[i, j], y[i, j]
c[i, j] = Corana2([xx, yy])
sam.putarray('X', x)
sam.putarray('Y', y)
sam.putarray('C', c)
sam.verbose()
sam.eval("[c,h]=contourf(X,Y,C,100);set(h,'EdgeColor','none')")
#sam.eval("[c,h]=contourf(X,Y,log(C*20+1)+2,100);set(h,'EdgeColor','none')")
sam.eval("title('Corana''s Parabola in 2D. Min at 0,0')")
sam.eval('hold on')
def draw_contour():
import numpy
x, y = numpy.mgrid[0:7.5:0.05,0:7.5:0.05]
c = 0*x
s,t = x.shape
for i in range(s):
for j in range(t):
xx,yy = x[i,j], y[i,j]
c[i,j] = CostFunction([xx,yy])
sam.putarray('X',x)
sam.putarray('Y',y)
sam.putarray('C',c)
sam.verbose()
sam.eval("[c,h]=contourf(X,Y,log(C*20+1)+2,100);set(h,'EdgeColor','none')")
sam.eval("title('Zimmermann''s Corner. Min at 7,2')")
sam.eval('hold on')
def draw_contour():
import numpy
x, y = numpy.mgrid[0:2.1:0.05,0:2.1:0.05]
c = 0*x
s,t = x.shape
for i in range(s):
for j in range(t):
xx,yy = x[i,j], y[i,j]
c[i,j] = Corana2([xx,yy])
sam.putarray('X',x)
sam.putarray('Y',y)
sam.putarray('C',c)
sam.verbose()
sam.eval("[c,h]=contourf(X,Y,C,100);set(h,'EdgeColor','none')")
#sam.eval("[c,h]=contourf(X,Y,log(C*20+1)+2,100);set(h,'EdgeColor','none')")
sam.eval("title('Corana''s Parabola in 2D. Min at 0,0')")
sam.eval('hold on')
def draw_contour():
import numpy
x, y = numpy.mgrid[0:2.1:0.02,0:2.1:0.02]
c = 0*x
s,t = x.shape
for i in range(s):
for j in range(t):
xx,yy = x[i,j], y[i,j]
c[i,j] = rosen([xx,yy])
sam.putarray('X',x)
sam.putarray('Y',y)
sam.putarray('C',c)
sam.verbose()
#sam.eval("[c,h]=contourf(X,Y,C,60);set(h,'EdgeColor','none')")
sam.eval("[c,h]=contourf(X,Y,log(C*20+1)+2,60);set(h,'EdgeColor','none')")
sam.eval("title('Rosenbrock''s function in 2D. Min at 1,1')")
sam.eval('hold on')
def draw_contour_xy():
import numpy
x, y = mgrid[-40:40:0.5, -40:40:0.5]
x = x0 + x
y = y0 + y
s, t = x.shape
c = 0 * x
s, t = x.shape
for i in range(s):
for j in range(t):
xx, yy = x[i, j], y[i, j]
c[i, j] = cost_function([xx, yy, z0, v0])
sam.putarray('X', x)
sam.putarray('Y', y)
sam.putarray('C', c)
sam.verbose()
sam.eval("[c,h]=contourf(X,Y,C,100);set(h,'EdgeColor','none')")
sam.eval("title('Mogi Fitting')")
sam.eval('hold on')
def draw_contour_xy():
import numpy
x, y = mgrid[-40:40:0.5, -40:40:0.5]
x = x0 + x
y = y0 + y
s,t = x.shape
c = 0*x
s,t = x.shape
for i in range(s):
for j in range(t):
xx,yy = x[i,j], y[i,j]
c[i,j] = cost_function([xx,yy, z0, v0])
sam.putarray('X',x)
sam.putarray('Y',y)
sam.putarray('C',c)
sam.verbose()
sam.eval("[c,h]=contourf(X,Y,C,100);set(h,'EdgeColor','none')")
sam.eval("title('Mogi Fitting')")
sam.eval('hold on')
def run_once(x0, x1):
simplex = Monitor()
xinit = [x0, x1]
solver = fmin(len(xinit))
solver.SetInitialPoints(xinit)
solver.SetGenerationMonitor(simplex)
solver.Solve(rosen, termination=CRT())
sol = solver.Solution()
for x in simplex.x:
sam.putarray('x', x)
sam.eval("plot(x([1,2,3,1],1),x([1,2,3,1],2),'w-')")
draw_contour()
run_once(0.5, 0.1)
sam.eval("figure(2)")
draw_contour()
run_once(1.5, 0.1)
sam.eval("figure(3)")
draw_contour()
run_once(0.5, 1.8)
#run_once(1.5,1.8)
getch("Press any key to quit")
# end of file
Testing the Corana parabola in 1D. Requires sam.
"""
import sam, numpy, mystic
#from test_corana import *
from mystic.solvers import fmin
from mystic.tools import getch
from mystic.models.corana import corana1d as Corana1
x = numpy.arange(-2., 2., 0.01)
y = [Corana1([c]) for c in x]
sam.put('x', x)
sam.put('y', y)
sam.eval("plot(x,y,'LineWidth',1); hold on")
for xinit in numpy.arange(0.1,2,0.1):
sol = fmin(Corana1, [xinit], full_output=1, retall=1)
xx = mystic.flatten_array(sol[-1])
yy = [Corana1([c]) for c in xx]
sam.put('xx', xx)
sam.put('yy', yy)
sam.eval("plot(xx,yy,'r-',xx,yy,'ko','LineWidth',2)")
sam.eval("axis([0 2 0 4])")
getch('press any key to exit')
# end of file
def run_once(x0,x1):
simplex = Monitor()
xinit = [x0, x1]
solver = fmin(len(xinit))
solver.SetInitialPoints(xinit)
solver.SetGenerationMonitor(simplex)
solver.Solve(rosen, termination=CRT())
sol = solver.Solution()
for x in simplex.x:
sam.putarray('x',x)
sam.eval("plot(x([1,2,3,1],1),x([1,2,3,1],2),'w-')")
draw_contour()
run_once(0.5,0.1)
sam.eval("figure(2)")
draw_contour()
run_once(1.5,0.1)
sam.eval("figure(3)")
draw_contour()
run_once(0.5,1.8)
#run_once(1.5,1.8)
getch("Press any key to quit")
# end of file
solver = fmin(len(xinit))
solver.SetInitialPoints(xinit)
solver.SetGenerationMonitor(simplex)
solver.Solve(cost_function, termination=CRT())
sol = solver.Solution()
print(sol)
for x in simplex.x:
sam.putarray('x',x)
sam.eval("plot(x([1,2,3,1],1),x([1,2,3,1],2),'w-','LineWidth',2)")
return sol
draw_contour_xv()
xysol = run_once_xy()
sam.eval("figure(2)")
draw_contour_xy()
xvsol = run_once_xv()
sam.eval("figure(3)")
plot_noisy_data()
sam.eval("hold on")
plot_sol(xysol)
plot_sol(xvsol)
getch()
# end of file
def renderOnSurface(self, surface):
"""Renders the scattering intensity on given detector surface in reciprocal space."""
import sam
import numpy as np
########################
###
### this is to be implemented using the 'slice()' method of Matlab.
###
########################
#we first pass the data into Matlab as an array:
array = np.array(self._getArray())
(dim0, dim1, dim2) = array.shape
q0 = np.arange(1, dim0 + 1)
q1 = np.arange(1, dim1 + 1)
q2 = np.arange(1, dim2 + 1)
# set up the ranges for the grid in reciprocal space
# these are some dummy ranges for now ([-0.5,0.5])
q0 = (q0 - (dim0 + 1) / 2.0) / dim0
q1 = (q1 - (dim1 + 1) / 2.0) / dim1
q2 = (q2 - (dim2 + 1) / 2.0) / dim2
sam.put('dim0', [dim0])
sam.put('dim1', [dim1])
sam.put('dim2', [dim2])
sam.put('q0', q0)
sam.put('q1', q1)
sam.put('q2', q2)
sam.eval("[qxi, qyi, qzi] = meshgrid(q0, q1, q2);")
# this causes a segmentation fault for an array of 20x20x20 doubles:
#sam.putarray('array', array)
# here is a temporary ugly(!) fix:
array.shape = (dim0 * dim1 * dim2, )
sam.put('array', array)
sam.eval("scattarray = reshape(array', dim0, dim1, dim2)")
# end of fix
# we need to pass the detector surface into Matlab:
sam.eval("[sxi,syi] = meshgrid(q0,q1);")
sam.eval("szi = sqrt(1.0-(sxi.^2))-0.75 ;")
# We use an M-file that gets called when we evaluate the name
# of the corresponding function in Matlab via SAM
sam.eval(
"MlabScatteringIntensitySurfaceSlicer(qxi,qyi,qzi,scattarray, sxi, syi,szi)"
)
waitforentry = raw_input("Press any key.")
sam.eval("close")
return 0
solver = fmin(len(xinit))
solver.SetInitialPoints(xinit)
solver.SetGenerationMonitor(simplex)
solver.Solve(cost_function, termination=CRT())
sol = solver.Solution()
print sol
for x in simplex.x:
sam.putarray('x', x)
sam.eval("plot(x([1,2,3,1],1),x([1,2,3,1],2),'w-','LineWidth',2)")
return sol
draw_contour_xv()
xysol = run_once_xy()
sam.eval("figure(2)")
draw_contour_xy()
xvsol = run_once_xv()
sam.eval("figure(3)")
plot_noisy_data()
sam.eval("hold on")
plot_sol(xysol)
plot_sol(xvsol)
getch()
# end of file
# The dual problem verification begins here.
npt = xy.shape[0]
Q = dot(xy, transpose(xy))
#Q = zeros((npt,npt))
#for i in range(npt):
# for j in range(npt):
## Q[i,j] = dot(xy[i,:],xy[j,:])
#Q = array(Q)
f = -diag(Q)+10
H = Q*2
A = ones((1,npt))
b = ones(1)
sam.putarray('H',H);
sam.putarray('f',f);
sam.eval("npt = %d;" % npt);
sam.eval("al = quadprog(H,f,[],[],ones(1,npt),1,zeros(npt,1),ones(npt,1));")
alpha = sam.getarray('al').flatten()
def getobj(H,f, x):
return 0.5 * dot(dot(x,H),x) + dot(f,x)
def chop(x):
if abs(x) > 1e-6:
return x
else:
return 0
x = array([chop(y) for y in alpha])
center = dot(alpha,xy)
def renderOnSurface(self, surface):
"""Renders the scattering intensity on given detector surface in reciprocal space."""
import sam
import numpy as np
########################
###
### this is to be implemented using the 'slice()' method of Matlab.
###
########################
#we first pass the data into Matlab as an array:
array = np.array(self._getArray())
(dim0, dim1, dim2) = array.shape
q0 = np.arange(1, dim0 + 1)
q1 = np.arange(1, dim1 + 1)
q2 = np.arange(1, dim2 + 1)
# set up the ranges for the grid in reciprocal space
# these are some dummy ranges for now ([-0.5,0.5])
q0 = (q0 - (dim0+1)/2.0) / dim0
q1 = (q1 - (dim1+1)/2.0) / dim1
q2 = (q2 - (dim2+1)/2.0) / dim2
sam.put('dim0', [dim0])
sam.put('dim1', [dim1])
sam.put('dim2', [dim2])
sam.put('q0', q0)
sam.put('q1', q1)
sam.put('q2', q2)
sam.eval("[qxi, qyi, qzi] = meshgrid(q0, q1, q2);")
# this causes a segmentation fault for an array of 20x20x20 doubles:
#sam.putarray('array', array)
# here is a temporary ugly(!) fix:
array.shape=(dim0*dim1*dim2,)
sam.put('array', array)
sam.eval("scattarray = reshape(array', dim0, dim1, dim2)")
# end of fix
# we need to pass the detector surface into Matlab:
sam.eval("[sxi,syi] = meshgrid(q0,q1);")
sam.eval("szi = sqrt(1.0-(sxi.^2))-0.75 ;")
# We use an M-file that gets called when we evaluate the name
# of the corresponding function in Matlab via SAM
sam.eval("MlabScatteringIntensitySurfaceSlicer(qxi,qyi,qzi,scattarray, sxi, syi,szi)")
waitforentry=raw_input("Press any key.")
sam.eval("close")
return 0