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 ctr_menu(ctr,
scans=None,
I=None,
Inorm=None,
Ierr=None,
corr_params=None,
scan_type=None):
"""
Interactively inspect/integrate CtrData
Parameters:
-----------
* ctr is a ctr data object
* scans is a [list] of scan data objects
* I, Inorm, Ierr are string tags corresponding to
the values from the scandata object to used in computing
structure factors
* corr_params is a (optional) dictionary of correction parameters
* scan_type is the type of scan (e.g. 'image')
"""
#if not isinstance(ctr,ctr_data.CtrData):
# print "Error CtrData object required"
# return
prompt = 'Select option >'
ret = ''
point = 0
set = []
npts = len(ctr.L)
# append new data
if scans != None:
ctr.append_scans(scans,
I=I,
Inorm=Inorm,
Ierr=Ierr,
corr_params=corr_params,
scan_type=scan_type)
set = range(npts, len(ctr.L))
point = npts
npts = len(ctr.L)
# make menu
m = Menu(labels=CTR_LABELS, descr=CTR_DESCR, sort=False, matchidx=True)
# make a plot
def _ctr_plot(ctr, I=False):
#pyplot.close(0)
pyplot.figure(0)
pyplot.clf()
if I == False:
ctr.plot(fig=0, spnt=point)
else:
ctr.plot_I(fig=0, spnt=point)
_ctr_plot(ctr)
# loop
while ret != 'done':
if point in ctr.bad:
bad_flag = True
else:
bad_flag = False
header = CTR_HEADER % (
str(npts), str(set), str(point), str(ctr.scan_type[point]),
str(ctr.labels['I'][point]), str(ctr.labels['Inorm'][point]),
str(ctr.labels['Ierr'][point]), str(ctr.labels['Ibgr'][point]),
str(ctr.corr_params[point].get('geom')),
str(ctr.corr_params[point].get('beam_slits')),
str(ctr.corr_params[point].get('det_slits')),
str(ctr.corr_params[point].get('sample')),
str(ctr.corr_params[point].get('scale')), str(bad_flag),
ctr.H[point], ctr.K[point], ctr.L[point], ctr.I[point],
ctr.Ierr[point], ctr.Ibgr[point], ctr.ctot[point], ctr.F[point],
ctr.Ferr[point])
m.header = header
ret = m.prompt(prompt)
#
if ret == 'plot':
_ctr_plot(ctr)
elif ret == 'iplot':
_ctr_plot(ctr, I=True)
elif ret == 'labels':
(scan, spnt) = ctr.get_scan(point)
lbls = scan.scalers.keys()
if scan.image:
lbls.extend(scan.image.peaks.keys())
print "Labels: \n", lbls
Ilbl = get_str(prompt='Enter Intensity lbl',
default=ctr.labels['I'][point],
valid=lbls)
Ierrlbl = get_str(prompt='Enter Intensity error lbl',
default=ctr.labels['Ierr'][point],
valid=lbls)
Inormlbl = get_str(prompt='Enter Intensity norm lbl',
default=ctr.labels['Inorm'][point],
valid=lbls)
Ibgrlbl = get_str(prompt='Enter Intensity background lbl',
default=ctr.labels['Ibgr'][point],
valid=lbls)
pp = "Apply to 'p' current point, 's' to set, "
pp = pp + "'a' to all, 'n' for none"
app = get_str(prompt=pp, default='p', valid=['p', 'a', 's', 'n'])
if app == 'p':
ctr.labels['I'][point] = Ilbl
ctr.labels['Ierr'][point] = Ierrlbl
ctr.labels['Inorm'][point] = Inormlbl
ctr.labels['Ibgr'][point] = Ibgrlbl
print "Integrate point index %i" % point
ctr.integrate_point(point)
elif app == 's':
for j in set:
ctr.labels['I'][j] = Ilbl
ctr.labels['Ierr'][j] = Ierrlbl
ctr.labels['Inorm'][j] = Inormlbl
ctr.labels['Ibgr'][j] = Ibgrlbl
print "Integrate point index %i" % j
ctr.integrate_point(j)
elif app == 'a':
for j in range(npts):
ctr.labels['I'][j] = Ilbl
ctr.labels['Ierr'][j] = Ierrlbl
ctr.labels['Inorm'][j] = Inormlbl
ctr.labels['Ibgr'][j] = Ibgrlbl
print "Integrate point index %i" % j
ctr.integrate_point(j)
elif app == 'n':
print "Ignoring updates"
_ctr_plot(ctr)
elif ret == 'correction':
corr_params = {}
#
check = get_yn(prompt='Edit geometry', default='y')
if check == 'yes':
geom = get_str(prompt='Enter geometry',
default=ctr.corr_params[point]['geom'],
valid=['psic'])
corr_params['geom'] = geom
#
check = get_yn(prompt='Edit beam slits', default='y')
if check == 'yes':
beam_slits = ctr.corr_params[point]['beam_slits']
if beam_slits == None: beam_slits = {'horz': 1., 'vert': 1.}
print "Horizontal = total slit width in lab-z,or horizontal scatt plane"
beam_slits['horz'] = get_flt('Beam horizontal slit (mm)',
default=beam_slits['horz'])
print "Vertical = total slit width in lab-x,or vertical scatt plane"
beam_slits['vert'] = get_flt('Beam vertical slit (mm)',
default=beam_slits['vert'])
corr_params['beam_slits'] = beam_slits
#
check = get_yn(prompt='Edit detector slits', default='y')
if check == 'yes':
det_slits = ctr.corr_params[point]['det_slits']
if det_slits == None: det_slits = {'horz': 1., 'vert': 1.}
print "Horizontal = total slit width in lab-z,or horizontal scatt plane"
det_slits['horz'] = get_flt('Det horizontal slit (mm)',
default=det_slits['horz'])
print "Vertical = total slit width in lab-x,or vertical scatt plane"
det_slits['vert'] = get_flt('Det vertical slit (mm)',
default=det_slits['vert'])
corr_params['det_slits'] = det_slits
#
check = get_yn(prompt='Edit sample shape/size', default='y')
if check == 'yes':
sample = ctr.corr_params[point]['sample']
check2 = get_str(
prompt="Sample described by diameter 'd' or polygon 'p'?",
default='d',
valid=['d', 'p'])
if check2 == 'd':
if type(sample) == types.DictType: sample = 1.
sample = get_flt('Sample diameter (mm)', default=sample)
elif check2 == 'p':
xx = "Sample is described by a polygon which is a collection \n"
xx = xx + "of [x,y,(z)] points (minimum of three points);\n"
xx = xx + "x is lab frame vertical, y is along ki, z is horizontal.\n"
xx = xx + "These points need to be specified along with the set of\n"
xx = xx + "gonio angles at the time of the polygon determination.\n"
xx = xx + "If phi and chi are at the 'flat' values, and the sample is\n"
xx = xx + "on the beam center, then z = 0 (and only [x,y] points are needed).\n"
print xx
sample = {
'polygon': [],
'angles': {
'phi': 0.0,
'chi': 0.0
}
}
while 1:
xx = "Enter a sample polygon point, '[]' to end"
sp = get_flt_list(prompt=xx, default=[])
if sp == []:
break
else:
sample['polygon'].append(sp)
xx = "Enter gonio angles"
sample['angles']['phi'] = get_flt(
'phi', default=sample['angles']['phi'])
sample['angles']['chi'] = get_flt(
'chi', default=sample['angles']['chi'])
print 'Sample: ', sample
corr_params['sample'] = sample
#
check = get_yn(prompt='Edit scale', default='y')
if check == 'yes':
scale = get_flt(prompt='Enter scale factor',
default=ctr.corr_params[point]['scale'])
corr_params['scale'] = scale
#
pp = "Apply to 'p' current point, 's' to set, 'a' to all, 'n' for none"
app = get_str(prompt=pp, default='p', valid=['p', 'a', 's', 'n'])
if app == 'p':
ctr.corr_params[point].update(corr_params)
print "Integrate point index %i" % point
ctr.integrate_point(point)
elif app == 's':
for j in set:
ctr.corr_params[j].update(corr_params)
print "Integrate point index %i" % j
ctr.integrate_point(j)
elif app == 'a':
for j in range(npts):
ctr.corr_params[j].update(corr_params)
print "Integrate point index %i" % j
ctr.integrate_point(j)
elif app == 'n':
print "Ignoring updates"
#
_ctr_plot(ctr)
elif ret == 'cplot':
(scan, spnt) = ctr.get_scan(point)
corr_params = ctr.corr_params[point]
corr = ctr_data._get_corr(scan, spnt, corr_params)
if ctr.scan_type[point] == 'image':
corr.ctot_stationary(plot=True, fig=2)
elif ret == 'integrate':
if ctr.scan_type[point] == 'image':
(sc_idx, scan_pnt) = ctr.scan_index[point]
scan = ctr.scan[sc_idx]
image_menu.image_menu(scan, scan_pnt)
#
pp = "Apply / copy integration parameters to\n"
pp = pp + "(note image max is not copied)\n"
pp = pp + "'p' current point only, 's' to set, 'a' to all"
app = get_str(prompt=pp, default='p', valid=['p', 'a', 's'])
if app == 'p':
print "Integrate point index %i" % point
ctr.integrate_point(point)
elif app == 's':
roi = scan.image.rois[scan_pnt]
rotangle = scan.image.rotangle[scan_pnt]
bgrpar = scan.image.bgrpar[scan_pnt]
for j in set:
print "Integrate point index %i" % j
ctr.integrate_point(j,
roi=roi,
rotangle=rotangle,
bgrpar=bgrpar)
elif app == 'a':
roi = scan.image.rois[scan_pnt]
rotangle = scan.image.rotangle[scan_pnt]
bgrpar = scan.image.bgrpar[scan_pnt]
for j in range(npts):
print "Integrate point index %i" % j
ctr.integrate_point(j,
roi=roi,
rotangle=rotangle,
bgrpar=bgrpar)
_ctr_plot(ctr)
elif ret == 'copyint':
idx = get_int(prompt='Enter point index to copy FROM',
default=point,
min=0,
max=npts - 1)
if ctr.scan_type[idx] == 'image':
(sc_idx, scan_pnt) = ctr.scan_index[idx]
scan = ctr.scan[sc_idx]
#
roi = scan.image.rois[scan_pnt]
rotangle = scan.image.rotangle[scan_pnt]
bgrpar = scan.image.bgrpar[scan_pnt]
#
pp = "Apply / copy integration parameters to\n"
pp = pp + "(note image max is not copied)\n"
pp = pp + "'p' current point only, 's' to set, 'a' to all"
app = get_str(prompt=pp, default='p', valid=['p', 'a', 's'])
if app == 'p':
print "Integrate point index %i" % point
ctr.integrate_point(point,
roi=roi,
rotangle=rotangle,
bgrpar=bgrpar)
elif app == 's':
for j in set:
print "Integrate point index %i" % j
ctr.integrate_point(j,
roi=roi,
rotangle=rotangle,
bgrpar=bgrpar)
elif app == 'a':
for j in range(npts):
print "Integrate point index %i" % j
ctr.integrate_point(j,
roi=roi,
rotangle=rotangle,
bgrpar=bgrpar)
_ctr_plot(ctr)
elif ret == 'pointselect':
idx = ctr.get_idx()
point = idx[0]
elif ret == 'pplot':
idx = ctr.get_idx()
point = idx[0]
ctr.plot_point(idx=point, fig=3, show_int=True)
elif ret == 'zoomselect':
set = ctr.get_points()
point = set[0]
elif ret == 'selpoint':
point = get_int(prompt='Enter point',
default=point,
min=0,
max=npts - 1)
elif ret == 'next':
if point + 1 < npts:
point = point + 1
elif ret == 'previous':
if point - 1 > -1:
point = point - 1
elif ret == 'flag':
if point in ctr.bad:
ctr.bad.remove(point)
else:
ctr.bad.append(point)
else:
pass
def ctr_menu(ctr,scans=None,I=None,Inorm=None,Ierr=None,
corr_params=None,scan_type=None):
"""
Interactively inspect/integrate CtrData
Parameters:
-----------
* ctr is a ctr data object
* scans is a [list] of scan data objects
* I, Inorm, Ierr are string tags corresponding to
the values from the scandata object to used in computing
structure factors
* corr_params is a (optional) dictionary of correction parameters
* scan_type is the type of scan (e.g. 'image')
"""
#if not isinstance(ctr,ctr_data.CtrData):
# print "Error CtrData object required"
# return
prompt = 'Select option >'
ret = ''
point = 0
set = []
npts = len(ctr.L)
# append new data
if scans!=None:
ctr.append_scans(scans,I=I,Inorm=Inorm,Ierr=Ierr,
corr_params=corr_params,scan_type=scan_type)
set = range(npts,len(ctr.L))
point = npts
npts = len(ctr.L)
# make menu
m = Menu(labels=CTR_LABELS,descr=CTR_DESCR,sort=False,matchidx=True)
# make a plot
def _ctr_plot(ctr,I=False):
#pyplot.close(0)
pyplot.figure(0)
pyplot.clf()
if I == False:
ctr.plot(fig=0,spnt=point)
else:
ctr.plot_I(fig=0,spnt=point)
_ctr_plot(ctr)
# loop
while ret != 'done':
if point in ctr.bad:
bad_flag = True
else:
bad_flag = False
header = CTR_HEADER % (str(npts),str(set),str(point),
str(ctr.scan_type[point]),
str(ctr.labels['I'][point]),
str(ctr.labels['Inorm'][point]),
str(ctr.labels['Ierr'][point]),
str(ctr.labels['Ibgr'][point]),
str(ctr.corr_params[point].get('geom')),
str(ctr.corr_params[point].get('beam_slits')),
str(ctr.corr_params[point].get('det_slits')),
str(ctr.corr_params[point].get('sample')),
str(ctr.corr_params[point].get('scale')),
str(bad_flag),
ctr.H[point],ctr.K[point],ctr.L[point],
ctr.I[point],ctr.Ierr[point],ctr.Ibgr[point],
ctr.ctot[point],ctr.F[point],ctr.Ferr[point])
m.header = header
ret = m.prompt(prompt)
#
if ret == 'plot':
_ctr_plot(ctr)
elif ret == 'iplot':
_ctr_plot(ctr,I=True)
elif ret == 'labels':
(scan,spnt) = ctr.get_scan(point)
lbls = scan.scalers.keys()
if scan.image:
lbls.extend(scan.image.peaks.keys())
print "Labels: \n", lbls
Ilbl = get_str(prompt='Enter Intensity lbl',
default=ctr.labels['I'][point],valid=lbls)
Ierrlbl = get_str(prompt='Enter Intensity error lbl',
default=ctr.labels['Ierr'][point],valid=lbls)
Inormlbl = get_str(prompt='Enter Intensity norm lbl',
default=ctr.labels['Inorm'][point],valid=lbls)
Ibgrlbl = get_str(prompt='Enter Intensity background lbl',
default=ctr.labels['Ibgr'][point],valid=lbls)
pp = "Apply to 'p' current point, 's' to set, "
pp = pp + "'a' to all, 'n' for none"
app = get_str(prompt=pp,default='p',
valid=['p','a','s','n'])
if app == 'p':
ctr.labels['I'][point] = Ilbl
ctr.labels['Ierr'][point] = Ierrlbl
ctr.labels['Inorm'][point] = Inormlbl
ctr.labels['Ibgr'][point] = Ibgrlbl
print "Integrate point index %i" % point
ctr.integrate_point(point)
elif app == 's':
for j in set:
ctr.labels['I'][j] = Ilbl
ctr.labels['Ierr'][j] = Ierrlbl
ctr.labels['Inorm'][j] = Inormlbl
ctr.labels['Ibgr'][j] = Ibgrlbl
print "Integrate point index %i" % j
ctr.integrate_point(j)
elif app == 'a':
for j in range(npts):
ctr.labels['I'][j] = Ilbl
ctr.labels['Ierr'][j] = Ierrlbl
ctr.labels['Inorm'][j] = Inormlbl
ctr.labels['Ibgr'][j] = Ibgrlbl
print "Integrate point index %i" % j
ctr.integrate_point(j)
elif app == 'n':
print "Ignoring updates"
_ctr_plot(ctr)
elif ret == 'correction':
corr_params = {}
#
check = get_yn(prompt='Edit geometry',default='y')
if check=='yes':
geom = get_str(prompt='Enter geometry',
default=ctr.corr_params[point]['geom'],
valid=['psic'])
corr_params['geom'] = geom
#
check = get_yn(prompt='Edit beam slits',default='y')
if check=='yes':
beam_slits = ctr.corr_params[point]['beam_slits']
if beam_slits == None: beam_slits = {'horz':1.,'vert':1.}
print "Horizontal = total slit width in lab-z,or horizontal scatt plane"
beam_slits['horz'] = get_flt('Beam horizontal slit (mm)',
default=beam_slits['horz'])
print "Vertical = total slit width in lab-x,or vertical scatt plane"
beam_slits['vert'] = get_flt('Beam vertical slit (mm)',default=beam_slits['vert'])
corr_params['beam_slits'] = beam_slits
#
check = get_yn(prompt='Edit detector slits',default='y')
if check=='yes':
det_slits = ctr.corr_params[point]['det_slits']
if det_slits == None: det_slits = {'horz':1.,'vert':1.}
print "Horizontal = total slit width in lab-z,or horizontal scatt plane"
det_slits['horz'] = get_flt('Det horizontal slit (mm)',
default=det_slits['horz'])
print "Vertical = total slit width in lab-x,or vertical scatt plane"
det_slits['vert'] = get_flt('Det vertical slit (mm)',
default=det_slits['vert'])
corr_params['det_slits'] = det_slits
#
check = get_yn(prompt='Edit sample shape/size',default='y')
if check=='yes':
sample = ctr.corr_params[point]['sample']
check2 = get_str(prompt="Sample described by diameter 'd' or polygon 'p'?",
default='d',valid=['d','p'])
if check2 == 'd':
if type(sample) == types.DictType: sample = 1.
sample = get_flt('Sample diameter (mm)',default=sample)
elif check2 == 'p':
xx = "Sample is described by a polygon which is a collection \n"
xx = xx + "of [x,y,(z)] points (minimum of three points);\n"
xx = xx + "x is lab frame vertical, y is along ki, z is horizontal.\n"
xx = xx + "These points need to be specified along with the set of\n"
xx = xx + "gonio angles at the time of the polygon determination.\n"
xx = xx + "If phi and chi are at the 'flat' values, and the sample is\n"
xx = xx + "on the beam center, then z = 0 (and only [x,y] points are needed).\n"
print xx
sample = {'polygon':[],'angles':{'phi':0.0,'chi':0.0}}
while 1:
xx = "Enter a sample polygon point, '[]' to end"
sp = get_flt_list(prompt=xx,default=[])
if sp == []:
break
else:
sample['polygon'].append(sp)
xx = "Enter gonio angles"
sample['angles']['phi'] = get_flt('phi',default=sample['angles']['phi'])
sample['angles']['chi'] = get_flt('chi',default=sample['angles']['chi'])
print 'Sample: ', sample
corr_params['sample'] = sample
#
check = get_yn(prompt='Edit scale',default='y')
if check=='yes':
scale = get_flt(prompt='Enter scale factor',default=ctr.corr_params[point]['scale'])
corr_params['scale'] = scale
#
pp = "Apply to 'p' current point, 's' to set, 'a' to all, 'n' for none"
app = get_str(prompt=pp, default='p',
valid=['p','a','s','n'])
if app == 'p':
ctr.corr_params[point].update(corr_params)
print "Integrate point index %i" % point
ctr.integrate_point(point)
elif app == 's':
for j in set:
ctr.corr_params[j].update(corr_params)
print "Integrate point index %i" % j
ctr.integrate_point(j)
elif app == 'a':
for j in range(npts):
ctr.corr_params[j].update(corr_params)
print "Integrate point index %i" % j
ctr.integrate_point(j)
elif app == 'n':
print "Ignoring updates"
#
_ctr_plot(ctr)
elif ret == 'cplot':
(scan,spnt) = ctr.get_scan(point)
corr_params = ctr.corr_params[point]
corr = ctr_data._get_corr(scan,spnt,corr_params)
if ctr.scan_type[point] == 'image':
corr.ctot_stationary(plot=True,fig=2)
elif ret == 'integrate':
if ctr.scan_type[point] == 'image':
(sc_idx,scan_pnt) = ctr.scan_index[point]
scan = ctr.scan[sc_idx]
image_menu.image_menu(scan,scan_pnt)
#
pp = "Apply / copy integration parameters to\n"
pp = pp + "(note image max is not copied)\n"
pp = pp + "'p' current point only, 's' to set, 'a' to all"
app = get_str(prompt=pp,
default='p',valid=['p','a','s'])
if app == 'p':
print "Integrate point index %i" % point
ctr.integrate_point(point)
elif app == 's':
roi = scan.image.rois[scan_pnt]
rotangle = scan.image.rotangle[scan_pnt]
bgrpar = scan.image.bgrpar[scan_pnt]
for j in set:
print "Integrate point index %i" % j
ctr.integrate_point(j,roi=roi,rotangle=rotangle,bgrpar=bgrpar)
elif app == 'a':
roi = scan.image.rois[scan_pnt]
rotangle = scan.image.rotangle[scan_pnt]
bgrpar = scan.image.bgrpar[scan_pnt]
for j in range(npts):
print "Integrate point index %i" % j
ctr.integrate_point(j,roi=roi,rotangle=rotangle,bgrpar=bgrpar)
_ctr_plot(ctr)
elif ret == 'copyint':
idx = get_int(prompt='Enter point index to copy FROM',
default=point,min=0,max = npts-1)
if ctr.scan_type[idx] == 'image':
(sc_idx,scan_pnt) = ctr.scan_index[idx]
scan = ctr.scan[sc_idx]
#
roi = scan.image.rois[scan_pnt]
rotangle = scan.image.rotangle[scan_pnt]
bgrpar = scan.image.bgrpar[scan_pnt]
#
pp = "Apply / copy integration parameters to\n"
pp = pp + "(note image max is not copied)\n"
pp = pp + "'p' current point only, 's' to set, 'a' to all"
app = get_str(prompt=pp,
default='p',valid=['p','a','s'])
if app == 'p':
print "Integrate point index %i" % point
ctr.integrate_point(point,roi=roi,rotangle=rotangle,bgrpar=bgrpar)
elif app == 's':
for j in set:
print "Integrate point index %i" % j
ctr.integrate_point(j,roi=roi,rotangle=rotangle,bgrpar=bgrpar)
elif app == 'a':
for j in range(npts):
print "Integrate point index %i" % j
ctr.integrate_point(j,roi=roi,rotangle=rotangle,bgrpar=bgrpar)
_ctr_plot(ctr)
elif ret == 'pointselect':
idx = ctr.get_idx()
point = idx[0]
elif ret == 'pplot':
idx = ctr.get_idx()
point = idx[0]
ctr.plot_point(idx=point,fig=3,show_int=True)
elif ret == 'zoomselect':
set = ctr.get_points()
point = set[0]
elif ret == 'selpoint':
point = get_int(prompt='Enter point',
default=point,min=0,max = npts-1)
elif ret == 'next':
if point + 1 < npts:
point = point + 1
elif ret == 'previous':
if point - 1 > -1:
point = point - 1
elif ret == 'flag':
if point in ctr.bad:
ctr.bad.remove(point)
else:
ctr.bad.append(point)
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)
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
