def image_menu(imdata,scan_pnt=None):
"""
Interactively inspect/integrate images in ScanData or a
ImageScan object
Parameters:
-----------
* imdata is either an ImageScan or ScanData object
* scan_pnt is an integer value for a point to integrate
None indicates start at the first point
"""
#if isinstance(imdata,data.ScanData):
if hasattr(imdata,'get_positioner'):
imdata = imdata.image
#elif isinstance(imdata,image_data.ImageScan):
elif hasattr(imdata,'image'):
pass
else:
print "Invalid image data"
prompt = 'Select option >'
ret = ''
roi = []
#bad_points = []
im_max = None
# make menu
if scan_pnt == None:
short = False
npts = len(imdata.image)
scan_pnt = 0
m = Menu(labels=IMG_LABELS,
descr=IMG_DESCR,
sort=False,matchidx=True)
else:
short = True
npts = 1
scan_pnt = int(scan_pnt)
m = Menu(labels=IMG_LABELS_SHORT,
descr=IMG_DESCR_SHORT,
sort=False,matchidx=True)
# local plot fun
def _implot(imdata,scan_pnt):
rotangle = imdata.rotangle[scan_pnt]
im_max = imdata.im_max[scan_pnt]
roi = imdata.rois[scan_pnt]
figtitle = "Scan Point = %i" % (scan_pnt)
image_data.image_plot(imdata.image[scan_pnt],fig=1,verbose=True,
figtitle=figtitle,im_max=im_max,
rotangle=rotangle,roi=roi)
# check init and plot first
if imdata._is_init() == False:
imdata._init_image()
_implot(imdata,scan_pnt)
# loop
while ret != 'done':
roi = imdata.rois[scan_pnt]
rotangle = imdata.rotangle[scan_pnt]
if short:
header = IMG_HEADER_SHORT % (str(roi),str(rotangle))
else:
header = IMG_HEADER % (str(npts),str(scan_pnt),
str(roi),str(rotangle))
m.header = header
ret = m.prompt(prompt)
if ret == 'display':
_implot(imdata,scan_pnt)
elif ret == 'imax':
print 'Image max intensity = ', imdata.image[scan_pnt].max()
im_max = get_int(prompt='Enter maximum intensity value for image plot',
default=imdata.im_max[scan_pnt],min=-1)
imdata.im_max[scan_pnt] = im_max
_implot(imdata,scan_pnt)
elif ret == "rotangle":
rotangle = get_flt(prompt='Enter rotation angle in degrees ccw',
default=imdata.rotangle[scan_pnt],
min=-360.,max=360.)
imdata.rotangle[scan_pnt] = rotangle
_implot(imdata,scan_pnt)
elif ret == 'setroi':
pyplot.figure(1)
(x1,x2,y1,y2) = pyplot.axis()
roi = [int(x1),int(y1),int(x2),int(y2)]
imdata.rois[scan_pnt] = roi
elif ret == 'plotsums':
roi = imdata.rois[scan_pnt]
rotangle = imdata.rotangle[scan_pnt]
image = image_data.clip_image(imdata.image[scan_pnt],roi,
rotangle=rotangle)
bgr_par = imdata.bgrpar[scan_pnt]
image_data.sum_plot(image,fig=2,**bgr_par)
elif ret == 'selectroi':
image = imdata.image[scan_pnt]
bgr_par = imdata.bgrpar[scan_pnt]
image_data.sum_plot(image,fig=2,**bgr_par)
c = cursor(fig=2)
(c1,y) = c.get_click(msg="Select left col sum")
(c2,y) = c.get_click(msg="Select right col sum")
(r1,y) = c.get_click(msg="Select left row sum")
(r2,y) = c.get_click(msg="Select right row sum")
roi = [int(c1),int(r1),int(c2),int(r2)]
imdata.rois[scan_pnt] = roi
elif ret == 'background':
bgr_par = imdata.bgrpar[scan_pnt]
bgr_par = bgr_menu(bgr_par)
imdata.bgrpar[scan_pnt] = bgr_par
elif ret == 'copyall':
roi = imdata.rois[scan_pnt]
rotangle = imdata.rotangle[scan_pnt]
bgr_par = imdata.bgrpar[scan_pnt]
#
imdata.rois = []
imdata.rotangle = []
imdata.bgrpar = []
#
for j in range(npts):
imdata.rois.append(copy.copy(roi))
imdata.rotangle.append(rotangle)
imdata.bgrpar.append(copy.copy(bgr_par))
elif ret == 'integrate':
imdata.integrate(idx=[scan_pnt],
plot=True,fig=3)
elif ret == 'intall':
yn = get_tf("Plot all images",default=False)
imdata.integrate(plot=yn)
#
pyplot.figure(5, figsize = [5,4])
pyplot.clf()
#
x = num.arange(len(imdata.image))
pyplot.plot(x,imdata.peaks['I'],'b',label='image sum')
pyplot.errorbar(x,imdata.peaks['I'],imdata.peaks['Ierr'],fmt='bo')
#
pyplot.plot(x,imdata.peaks['I_c'],'r',label='col sum')
pyplot.errorbar(x,imdata.peaks['I_c'],imdata.peaks['Ierr_c'],fmt='ro')
#
pyplot.plot(x,imdata.peaks['I_r'],'g',label='row sum')
pyplot.errorbar(x,imdata.peaks['I_r'],imdata.peaks['Ierr_r'],fmt='go')
#
pyplot.semilogy()
pyplot.legend(loc = 9)
pyplot.xlabel('Point')
pyplot.ylabel('Integrated Intensity')
#elif ret == 'flag':
# if int(scan_pnt) in bad_points:
# bad_points.remove(scan_pnt)
# print "Data point removed from bad list"
# else:
# bad_points.append(int(scan_pnt))
# print "Data point added to bad list"
elif ret == 'point':
scan_pnt = get_int(prompt='Enter scan point',
default=scan_pnt,min=0,max = npts-1)
_implot(imdata,scan_pnt)
elif ret == 'next':
if scan_pnt + 1 < npts:
scan_pnt = scan_pnt + 1
_implot(imdata,scan_pnt)
elif ret == 'previous':
if scan_pnt - 1 > -1:
scan_pnt = scan_pnt - 1
_implot(imdata,scan_pnt)
else:
pass
def rasd_menu(rasddata, cell = None, bulk_file = None, sur_file = None, f1f2_file = None, E0 = 0.):
"""
Interactively create RasdList object and inspect/analyze data in it
"""
if cell == None:
ok = False
while not ok:
cell = get_flt_list(prompt='Enter unit cell [a,b,c,alpha,beta,gamma,delta1,delta2]')
if len(cell) != 8:
print 'invalid unit cell'
else: ok = True
if bulk_file == None:
ok = False
while not ok:
bulk_file = get_str(prompt='Enter path and\or name of your bulk file (ROD .bul file without header and cell definition)')
if not os.path.exists(bulk_file):
print bulk_file+' not found'
else:
ok = True
bulk = []
f = file(bulk_file,'r')
data = f.readlines()
f.close()
for i in range(len(data)):
if '#' not in data[i]:
tmp = str.rsplit(data[i])
bulk.append([tmp[0],float(tmp[1]),float(tmp[2]),float(tmp[3]),float(tmp[4])])
if sur_file == None:
ok = False
while not ok:
sur_file = get_str(prompt='Enter path and\or name of your surface file (ROD .sur file without header and cell definition)')
if not os.path.exists(sur_file):
print sur_file+' not found'
else:
ok = True
surface = []
f = file(sur_file,'r')
data = f.readlines()
f.close()
for i in range(len(data)):
if '#' not in data[i]:
tmp = str.rsplit(data[i])
surface.append([tmp[0],float(tmp[1]),float(tmp[2]),float(tmp[3]),float(tmp[4]),float(tmp[5])])
if f1f2_file == None:
ok = False
while not ok:
f1f2_file = get_str(prompt='Enter path and\or name of your f1f2 file (HEPHAESTUS or experimental f1f2 file)')
if not os.path.exists(f1f2_file):
print f1f2_file+' not found'
else:
ok = True
f = file(f1f2_file, 'r')
data = f.readlines()
f.close()
f1f2 = num.ndarray((0,3),float)
for i in range(len(data)):
if '#' not in data[i]:
tmp = str.rsplit(data[i])
f1f2 = num.append(f1f2, [[int(float(tmp[0])),float(tmp[1]),float(tmp[2])]], axis = 0)
f1f2 = f1f2.transpose()
if E0 == 0:
E0 = get_flt(prompt='Enter E0 in eV')
allrasd = rasd_ana.read_RSD(cell, bulk, surface, database, rasddata, f1f2, E0)
prompt = 'Select option >'
ret = ''
# make menu
m = Menu(labels=RASD_LABELS,
descr=RASD_DESCR,
sort=False, matchidx=True)
scan_pnt = 0
norm = True
# loop
while ret != 'done':
allrasd.list[scan_pnt] = rasd_ana.RASD_Fourier(allrasd,scan_pnt)
header = RASD_HEADER % (str(allrasd.dims),str(scan_pnt),
str(allrasd.list[scan_pnt].AR),str(allrasd.list[scan_pnt].PR),
str(allrasd.list[scan_pnt].e0shift))
m.header = header
allrasd.list[scan_pnt].plot(norm = norm, fig = 1)
ret = m.prompt(prompt)
if ret == 'plot_norm':
norm = get_tf(prompt = 'Plot normalized or not (True/False)', default = norm)
elif ret == 'setE0shift':
allrasd.list[scan_pnt].e0shift = get_flt(prompt = 'Enter e0 shift for this scan',
default = allrasd.list[scan_pnt].e0shift)
allrasd.list[scan_pnt].E = allrasd.list[scan_pnt].Eorig + allrasd.list[scan_pnt].e0shift
allrasd.list[scan_pnt].E0 = allrasd.E0 + allrasd.list[scan_pnt].e0shift
elif ret == 'setPRstart':
allrasd.list[scan_pnt].PR = get_flt(prompt = 'Enter PR start (0-1)', default = allrasd.list[scan_pnt].PR,
min = 0, max = 1)
elif ret == 'useInFourier':
allrasd.list[scan_pnt].use_in_Fourier = get_tf(prompt= 'Use this scan in Fourier synthesis (True/False)?',
default = allrasd.list[scan_pnt].use_in_Fourier)
elif ret == 'useInRefine':
allrasd.list[scan_pnt].use_in_Refine = get_tf(prompt= 'Use this scan for Structure Refinement (True/False)?',
default = allrasd.list[scan_pnt].use_in_Refine)
elif ret == 'FourierParams':
allrasd.ZR = get_int(prompt= 'Atomic number of resonant element', default = allrasd.ZR)
allrasd.xf = get_flt(prompt= 'number of unit cells along a', default = allrasd.xf)
allrasd.yf = get_flt(prompt= 'number of unit cells along b', default = allrasd.yf)
allrasd.zf = get_flt(prompt= 'number of unit cells along c', default = allrasd.zf)
allrasd.an = get_int(prompt= 'number of datapoints along a', default = allrasd.an)
allrasd.bn = get_int(prompt= 'number of datapoints along b', default = allrasd.bn)
allrasd.cn = get_int(prompt= 'number of datapoints along c', default = allrasd.cn)
allrasd.Plusminus = get_tf(prompt= 'calculate rho(e-) above and below surface', default = allrasd.Plusminus)
elif ret == 'runFourier':
allrasd.Fourier = []
data = []
for rasd in allrasd.list:
if rasd.use_in_Fourier:
allrasd.Fourier.append([rasd.Q[0],rasd.Q[1],rasd.Q[2],rasd.AR,rasd.PR])
data.append(rasd.file)
if allrasd.Fourier == []: print 'No scans specified for use in Fourier'
else:
rasd_ana.Fourier_synthesis(allrasd.Fourier, allrasd.cell, allrasd.ZR,allrasd.xf,allrasd.yf,allrasd.zf,
allrasd.an,allrasd.bn,allrasd.cn,allrasd.Plusminus)
print 'Scans used for Fourier synthesis: \n'+str(data)
elif ret == 'RefinementParams':
allrasd.natoms = get_int(prompt = 'How many atoms in structure model?', default = allrasd.natoms)
if allrasd.Rmin == None or len(allrasd.thetamin) != allrasd.natoms:
allrasd.Rmin = num.zeros((allrasd.natoms,3),float)
allrasd.Rmax = num.ndarray((0,3),float)
for i in range(allrasd.natoms):
allrasd.Rmax = num.append(allrasd.Rmax, [[allrasd.cell[0],allrasd.cell[1],allrasd.cell[2]]],axis = 0)
allrasd.thetamin = num.ones((allrasd.natoms),float) *0.05
allrasd.thetamax = num.ones((allrasd.natoms),float) *0.999
allrasd.DWmin = num.zeros((allrasd.natoms,6),float)
for i in range(allrasd.natoms):
allrasd.DWmin[i] = [0.001,0.001,0.001,0.,0.,0.]
allrasd.DWmax = num.zeros((allrasd.natoms,6),float)
for i in range(allrasd.natoms):
allrasd.DWmax[i] = [1.,1.,1.,0.,0.,0.]
for i in range(allrasd.natoms):
allrasd.Rmin[i] = get_flt_list(prompt = ('Rmin of atom '+str(i+1)+' [xmin,ymin,zmin] (Angstroem)'), default = allrasd.Rmin[i])
for i in range(allrasd.natoms):
allrasd.Rmax[i] = get_flt_list(prompt = ('Rmax of atom '+str(i+1)+' [xmax,ymax,zmax] (Angstroem)'), default = allrasd.Rmax[i])
for i in range(allrasd.natoms):
allrasd.thetamin[i] = get_flt(prompt = ('min. occupancy of atom '+str(i+1)), default = allrasd.thetamin[i])
for i in range(allrasd.natoms):
allrasd.thetamax[i] = get_flt(prompt = ('max. occupancy of atom '+str(i+1)), default = allrasd.thetamax[i])
for i in range(allrasd.natoms):
allrasd.DWmin[i] = get_flt_list(prompt = ('min. DW-factor for atom '+str(i+1)+' [b11,b22,b33,b12,b13,b23]'), default = allrasd.DWmin[i])
for i in range(allrasd.natoms):
allrasd.DWmax[i] = get_flt_list(prompt = ('max. DW-factor for atom '+str(i+1)+' [b11,b22,b33,b12,b13,b23]'), default = allrasd.DWmax[i])
allrasd.Tstart = get_flt(prompt = 'Startimg Temperature for simmulated annealing', default = allrasd.Tstart)
allrasd.Tend = get_flt(prompt = 'End Temperature for simmulated annealing', default = allrasd.Tend)
allrasd.cool = get_flt(prompt = 'cooling factor for simmulated annealing (usually 0.7 - 0.95)', default = allrasd.cool, min = 0.1, max = 0.99)
allrasd.maxrun = get_flt(prompt = 'max. repeats at one Temp.', default = allrasd.maxrun)
allrasd.MC = get_flt(prompt = 'max fractional parameter change at T = 100', default = allrasd.MC)
allrasd.RMS_count_max = get_flt(prompt = 'max. annealing (T) steps without improvement', default = allrasd.RMS_count_max)
allrasd.factor = get_flt(prompt = 'some factor (Boltz. = exp(d(RMS)*factor/T)) in decision process (~1e4 - 1e7)', default = allrasd.factor)
def bgr_menu(bgr_params=IMG_BGR_PARAMS):
"""
Get background options
"""
prompt = 'Select option >'
# make menu
m = Menu(labels=BGR_LABELS,descr=BGR_DESCR,sort=False,matchidx=True)
ret = ''
while ret != 'done':
header = BGR_HEADER % (bgr_params['bgrflag'],
bgr_params['cnbgr'],bgr_params['cwidth'],
bgr_params['cpow'],str(bgr_params['ctan']),
bgr_params['rnbgr'],bgr_params['rwidth'],
bgr_params['rpow'],str(bgr_params['rtan']))
m.header = header
ret = m.prompt(prompt)
#
if ret == 'bgrflag':
bgr_params['bgrflag'] = get_int(prompt='Enter bgrflag',
default=bgr_params['bgrflag'],
valid=[0,1,2,3])
#
elif ret == 'cnbgr':
bgr_params['cnbgr'] = get_int(prompt='Enter col nbgr',
default=bgr_params['cnbgr'],
min=0)
elif ret == 'cwidth':
# could use flt??
bgr_params['cwidth'] = get_int(prompt='Enter col width',
default=bgr_params['cwidth'],
min=0)
elif ret == 'cpow':
bgr_params['cpow'] = get_flt(prompt='Enter col pow',
default=bgr_params['cpow'],
min=0.)
elif ret == 'ctan':
bgr_params['ctan'] = get_tf(prompt='Enter col tan flag',
default=bgr_params['ctan'])
#
elif ret == 'rnbgr':
bgr_params['rnbgr'] = get_int(prompt='Enter row nbgr',
default=bgr_params['rnbgr'],
min=0)
elif ret == 'rwidth':
# could use flt??
bgr_params['rwidth'] = get_int(prompt='Enter row width',
default=bgr_params['rwidth'],
min=0)
elif ret == 'rpow':
bgr_params['rpow'] = get_flt(prompt='Enter row pow',
default=bgr_params['rpow'],
min=0.)
elif ret == 'rtan':
bgr_params['rtan'] = get_tf(prompt='Enter row tan flag',
default=bgr_params['rtan'])
elif ret == 'info':
show_more(BGR_INFO)
get_yn(prompt="Continue",default='y')
return bgr_params
def rasd_menu(rasddata,
cell=None,
bulk_file=None,
sur_file=None,
f1f2_file=None,
E0=0.):
"""
Interactively create RasdList object and inspect/analyze data in it
"""
if cell == None:
ok = False
while not ok:
cell = get_flt_list(
prompt='Enter unit cell [a,b,c,alpha,beta,gamma,delta1,delta2]'
)
if len(cell) != 8:
print 'invalid unit cell'
else:
ok = True
if bulk_file == None:
ok = False
while not ok:
bulk_file = get_str(
prompt=
'Enter path and\or name of your bulk file (ROD .bul file without header and cell definition)'
)
if not os.path.exists(bulk_file):
print bulk_file + ' not found'
else:
ok = True
bulk = []
f = file(bulk_file, 'r')
data = f.readlines()
f.close()
for i in range(len(data)):
if '#' not in data[i]:
tmp = str.rsplit(data[i])
bulk.append([
tmp[0],
float(tmp[1]),
float(tmp[2]),
float(tmp[3]),
float(tmp[4])
])
if sur_file == None:
ok = False
while not ok:
sur_file = get_str(
prompt=
'Enter path and\or name of your surface file (ROD .sur file without header and cell definition)'
)
if not os.path.exists(sur_file):
print sur_file + ' not found'
else:
ok = True
surface = []
f = file(sur_file, 'r')
data = f.readlines()
f.close()
for i in range(len(data)):
if '#' not in data[i]:
tmp = str.rsplit(data[i])
surface.append([
tmp[0],
float(tmp[1]),
float(tmp[2]),
float(tmp[3]),
float(tmp[4]),
float(tmp[5])
])
if f1f2_file == None:
ok = False
while not ok:
f1f2_file = get_str(
prompt=
'Enter path and\or name of your f1f2 file (HEPHAESTUS or experimental f1f2 file)'
)
if not os.path.exists(f1f2_file):
print f1f2_file + ' not found'
else:
ok = True
f = file(f1f2_file, 'r')
data = f.readlines()
f.close()
f1f2 = num.ndarray((0, 3), float)
for i in range(len(data)):
if '#' not in data[i]:
tmp = str.rsplit(data[i])
f1f2 = num.append(
f1f2, [[int(float(tmp[0])),
float(tmp[1]),
float(tmp[2])]],
axis=0)
f1f2 = f1f2.transpose()
if E0 == 0:
E0 = get_flt(prompt='Enter E0 in eV')
allrasd = rasd_ana.read_RSD(cell, bulk, surface, database, rasddata, f1f2,
E0)
prompt = 'Select option >'
ret = ''
# make menu
m = Menu(labels=RASD_LABELS, descr=RASD_DESCR, sort=False, matchidx=True)
scan_pnt = 0
norm = True
# loop
while ret != 'done':
allrasd.list[scan_pnt] = rasd_ana.RASD_Fourier(allrasd, scan_pnt)
header = RASD_HEADER % (str(
allrasd.dims), str(scan_pnt), str(
allrasd.list[scan_pnt].AR), str(allrasd.list[scan_pnt].PR),
str(allrasd.list[scan_pnt].e0shift))
m.header = header
allrasd.list[scan_pnt].plot(norm=norm, fig=1)
ret = m.prompt(prompt)
if ret == 'plot_norm':
norm = get_tf(prompt='Plot normalized or not (True/False)',
default=norm)
elif ret == 'setE0shift':
allrasd.list[scan_pnt].e0shift = get_flt(
prompt='Enter e0 shift for this scan',
default=allrasd.list[scan_pnt].e0shift)
allrasd.list[scan_pnt].E = allrasd.list[
scan_pnt].Eorig + allrasd.list[scan_pnt].e0shift
allrasd.list[
scan_pnt].E0 = allrasd.E0 + allrasd.list[scan_pnt].e0shift
elif ret == 'setPRstart':
allrasd.list[scan_pnt].PR = get_flt(
prompt='Enter PR start (0-1)',
default=allrasd.list[scan_pnt].PR,
min=0,
max=1)
elif ret == 'useInFourier':
allrasd.list[scan_pnt].use_in_Fourier = get_tf(
prompt='Use this scan in Fourier synthesis (True/False)?',
default=allrasd.list[scan_pnt].use_in_Fourier)
elif ret == 'useInRefine':
allrasd.list[scan_pnt].use_in_Refine = get_tf(
prompt='Use this scan for Structure Refinement (True/False)?',
default=allrasd.list[scan_pnt].use_in_Refine)
elif ret == 'FourierParams':
allrasd.ZR = get_int(prompt='Atomic number of resonant element',
default=allrasd.ZR)
allrasd.xf = get_flt(prompt='number of unit cells along a',
default=allrasd.xf)
allrasd.yf = get_flt(prompt='number of unit cells along b',
default=allrasd.yf)
allrasd.zf = get_flt(prompt='number of unit cells along c',
default=allrasd.zf)
allrasd.an = get_int(prompt='number of datapoints along a',
default=allrasd.an)
allrasd.bn = get_int(prompt='number of datapoints along b',
default=allrasd.bn)
allrasd.cn = get_int(prompt='number of datapoints along c',
default=allrasd.cn)
allrasd.Plusminus = get_tf(
prompt='calculate rho(e-) above and below surface',
default=allrasd.Plusminus)
elif ret == 'runFourier':
allrasd.Fourier = []
data = []
for rasd in allrasd.list:
if rasd.use_in_Fourier:
allrasd.Fourier.append(
[rasd.Q[0], rasd.Q[1], rasd.Q[2], rasd.AR, rasd.PR])
data.append(rasd.file)
if allrasd.Fourier == []:
print 'No scans specified for use in Fourier'
else:
rasd_ana.Fourier_synthesis(allrasd.Fourier, allrasd.cell,
allrasd.ZR, allrasd.xf, allrasd.yf,
allrasd.zf, allrasd.an, allrasd.bn,
allrasd.cn, allrasd.Plusminus)
print 'Scans used for Fourier synthesis: \n' + str(data)
elif ret == 'RefinementParams':
allrasd.natoms = get_int(
prompt='How many atoms in structure model?',
default=allrasd.natoms)
if allrasd.Rmin == None or len(allrasd.thetamin) != allrasd.natoms:
allrasd.Rmin = num.zeros((allrasd.natoms, 3), float)
allrasd.Rmax = num.ndarray((0, 3), float)
for i in range(allrasd.natoms):
allrasd.Rmax = num.append(
allrasd.Rmax,
[[allrasd.cell[0], allrasd.cell[1], allrasd.cell[2]]],
axis=0)
allrasd.thetamin = num.ones((allrasd.natoms), float) * 0.05
allrasd.thetamax = num.ones((allrasd.natoms), float) * 0.999
allrasd.DWmin = num.zeros((allrasd.natoms, 6), float)
for i in range(allrasd.natoms):
allrasd.DWmin[i] = [0.001, 0.001, 0.001, 0., 0., 0.]
allrasd.DWmax = num.zeros((allrasd.natoms, 6), float)
for i in range(allrasd.natoms):
allrasd.DWmax[i] = [1., 1., 1., 0., 0., 0.]
for i in range(allrasd.natoms):
allrasd.Rmin[i] = get_flt_list(
prompt=('Rmin of atom ' + str(i + 1) +
' [xmin,ymin,zmin] (Angstroem)'),
default=allrasd.Rmin[i])
for i in range(allrasd.natoms):
allrasd.Rmax[i] = get_flt_list(
prompt=('Rmax of atom ' + str(i + 1) +
' [xmax,ymax,zmax] (Angstroem)'),
default=allrasd.Rmax[i])
for i in range(allrasd.natoms):
allrasd.thetamin[i] = get_flt(
prompt=('min. occupancy of atom ' + str(i + 1)),
default=allrasd.thetamin[i])
for i in range(allrasd.natoms):
allrasd.thetamax[i] = get_flt(
prompt=('max. occupancy of atom ' + str(i + 1)),
default=allrasd.thetamax[i])
for i in range(allrasd.natoms):
allrasd.DWmin[i] = get_flt_list(
prompt=('min. DW-factor for atom ' + str(i + 1) +
' [b11,b22,b33,b12,b13,b23]'),
default=allrasd.DWmin[i])
for i in range(allrasd.natoms):
allrasd.DWmax[i] = get_flt_list(
prompt=('max. DW-factor for atom ' + str(i + 1) +
' [b11,b22,b33,b12,b13,b23]'),
default=allrasd.DWmax[i])
allrasd.Tstart = get_flt(
prompt='Startimg Temperature for simmulated annealing',
default=allrasd.Tstart)
allrasd.Tend = get_flt(
prompt='End Temperature for simmulated annealing',
default=allrasd.Tend)
allrasd.cool = get_flt(
prompt=
'cooling factor for simmulated annealing (usually 0.7 - 0.95)',
default=allrasd.cool,
min=0.1,
max=0.99)
allrasd.maxrun = get_flt(prompt='max. repeats at one Temp.',
default=allrasd.maxrun)
allrasd.MC = get_flt(
prompt='max fractional parameter change at T = 100',
default=allrasd.MC)
allrasd.RMS_count_max = get_flt(
prompt='max. annealing (T) steps without improvement',
default=allrasd.RMS_count_max)
allrasd.factor = get_flt(
prompt=
'some factor (Boltz. = exp(d(RMS)*factor/T)) in decision process (~1e4 - 1e7)',
default=allrasd.factor)
elif ret == 'runRefine':
if allrasd.Rmin == None:
print 'Please define simmulated annealing parameters first'
else:
allrasd.reflist = []
for rasd in allrasd.list:
if rasd.use_in_Refine:
allrasd.reflist.append(rasd)
if allrasd.reflist == []:
print 'No scans specified for use in refinement'
else:
rasd_ana.simulated_annealing(allrasd)
elif ret == 'select':
scan_pnt = get_int(prompt='Enter scan number',
default=scan_pnt,
min=0,
max=allrasd.dims - 1)
elif ret == 'next':
if scan_pnt + 1 < allrasd.dims:
scan_pnt = scan_pnt + 1
elif ret == 'previous':
if scan_pnt - 1 > -1:
scan_pnt = scan_pnt - 1
else:
pass
