def _traj_file_load(fname, traj_axis='x'): #MR20160725
nLinesHead = 1
hlp = []
with open(fname, 'r') as f:
for i in range(nLinesHead):
hlp.append(f.readline())
data = uti_io.read_ascii_data_cols(fname, '\t', _i_col_start=0, _i_col_end=10, _n_line_skip=nLinesHead)
mode = 3
allrange = [
data[5][0], # z-coordinate begin
data[5][-1], # z-coordinate end
len(data[0]), # number of points
min(data[1]), # x-coordinate begin
max(data[1]), # x-coordinate end
1,
min(data[3]), # y-coordinate begin
max(data[3]), # y-coordinate end
1,
]
arLabels = ['Longitudinal Position', 'Horizontal Position', 'Vertical Position']
arUnits = ['m', 'm', 'm', 'm']
if traj_axis == 'x':
data = data[1]
arLabels.append('Horizontal Coordinate')
elif traj_axis == 'y':
data = data[3]
arLabels.append('Vertical Coordinate')
else:
raise ValueError('Parameter "axis" has wrong value: {}. Allowed values are "x" and "y"'.format(traj_axis))
return data, mode, allrange, arLabels, arUnits
def _file_load(_fname, _read_labels=1): #MR20160725
nLinesHead = 11
hlp = []
#with open(_fname,'r') as f: hlp = f.readlines(nLinesHead)
with open(_fname,'r') as f:
for i in range(nLinesHead):
hlp.append(f.readline())
#ne, nx, ny, ns = [ int(hlp[i].replace('#','').split()[0]) for i in [3,6,9,10] ]
ne, nx, ny = [int(hlp[i].replace('#','').split()[0]) for i in [3,6,9]]
ns = 1
testStr = hlp[nLinesHead - 1]
if testStr[0] == '#':
ns = int(testStr.replace('#','').split()[0])
else: nLinesHead -= 1
e0,e1,x0,x1,y0,y1 = [float(hlp[i].replace('#','').split()[0]) for i in [1,2,4,5,7,8]]
#data = np.squeeze(np.loadtxt(_fname, dtype=np.float64)) #get data from file (C-aligned flat)
data = uti_io.read_ascii_data_cols(_fname, '\t', _i_col_start=0, _i_col_end=0, _n_line_skip=nLinesHead)[0]
allrange = e0, e1, ne, x0, x1, nx, y0, y1, ny
arLabels = ['Photon Energy', 'Horizontal Position', 'Vertical Position', 'Intensity']
arUnits = ['eV', 'm', 'm', 'ph/s/.1%bw/mm^2']
if _read_labels:
arTokens = hlp[0].split(' [')
arLabels[3] = arTokens[0].replace('#','')
arUnits[3] = '';
if len(arTokens) > 1:
arUnits[3] = arTokens[1].split('] ')[0]
#print(arLabels[3], arUnits[3])
for i in range(3):
arTokens = hlp[i*3 + 1].split()
nTokens = len(arTokens)
nTokensLabel = nTokens - 3
nTokensLabel_mi_1 = nTokensLabel - 1
strLabel = ''
for j in range(nTokensLabel):
strLabel += arTokens[j + 2]
if j < nTokensLabel_mi_1: strLabel += ' '
arLabels[i] = strLabel
arUnits[i] = arTokens[nTokens - 1].replace('[','').replace(']','')
m = _enum('T','V','H','E','HV','EV','EH','EHV')
if ne==1 and nx==1 and ny==1 : mode = m.T
if ne==1 and nx==1 and ny>1 : mode = m.V
if ne==1 and nx>1 and ny==1 : mode = m.H
if ne>1 and nx==1 and ny==1 : mode = m.E
if ne==1 and nx>1 and ny>1 : mode = m.HV
if ne>1 and nx==1 and ny>1 : mode = m.EV
if ne>1 and nx>1 and ny==1 : mode = m.EH
if ne>1 and nx>1 and ny>1 : mode = m.EHV
#print(mode)
return data, mode, allrange, arLabels, arUnits
def file_load(_fname, _read_labels=1):
nLinesHead = 11
hlp = []
#with open(_fname,'r') as f: hlp = f.readlines(nLinesHead)
with open(_fname,'r') as f:
for i in range(nLinesHead):
hlp.append(f.readline())
#ne, nx, ny, ns = [ int(hlp[i].replace('#','').split()[0]) for i in [3,6,9,10] ]
ne, nx, ny = [int(hlp[i].replace('#','').split()[0]) for i in [3,6,9]]
ns = 1
testStr = hlp[nLinesHead - 1]
if testStr[0] == '#':
ns = int(testStr.replace('#','').split()[0])
else: nLinesHead -= 1
e0,e1,x0,x1,y0,y1 = [float(hlp[i].replace('#','').split()[0]) for i in [1,2,4,5,7,8]]
#data = np.squeeze(np.loadtxt(_fname, dtype=np.float64)) #get data from file (C-aligned flat)
data = uti_io.read_ascii_data_cols(_fname, '\t', _i_col_start=0, _i_col_end=0, _n_line_skip=nLinesHead)[0]
allrange = e0, e1, ne, x0, x1, nx, y0, y1, ny
arLabels = ['Photon Energy', 'Horizontal Position', 'Vertical Position', 'Intensity']
arUnits = ['eV', 'm', 'm', 'ph/s/.1%bw/mm^2']
if _read_labels:
arTokens = hlp[0].split(' [')
arLabels[3] = arTokens[0].replace('#','')
arUnits[3] = '';
if len(arTokens) > 1:
arUnits[3] = arTokens[1].split('] ')[0]
#print(arLabels[3], arUnits[3])
for i in range(3):
arTokens = hlp[i*3 + 1].split()
nTokens = len(arTokens)
nTokensLabel = nTokens - 3
nTokensLabel_mi_1 = nTokensLabel - 1
strLabel = ''
for j in range(nTokensLabel):
strLabel += arTokens[j + 2]
if j < nTokensLabel_mi_1: strLabel += ' '
arLabels[i] = strLabel
arUnits[i] = arTokens[nTokens - 1].replace('[','').replace(']','')
m = _enum('T','V','H','E','HV','EV','EH','EHV')
if ne==1 and nx==1 and ny==1 : mode = m.T
if ne==1 and nx==1 and ny>1 : mode = m.V
if ne==1 and nx>1 and ny==1 : mode = m.H
if ne>1 and nx==1 and ny==1 : mode = m.E
if ne==1 and nx>1 and ny>1 : mode = m.HV
if ne>1 and nx==1 and ny>1 : mode = m.EV
if ne>1 and nx>1 and ny==1 : mode = m.EH
if ne>1 and nx>1 and ny>1 : mode = m.EHV
#print(mode)
return data, mode, allrange, arLabels, arUnits
def _traj_file_load(fname, traj_axis='x'): #MR20160725
nLinesHead = 1
hlp = []
with open(fname, 'r') as f:
for i in range(nLinesHead):
hlp.append(f.readline())
data = uti_io.read_ascii_data_cols(fname, '\t', _i_col_start=0, _i_col_end=10, _n_line_skip=nLinesHead)
mode = 3
allrange = [
data[5][0], # z-coordinate begin
data[5][-1], # z-coordinate end
len(data[0]), # number of points
min(data[1]), # x-coordinate begin
max(data[1]), # x-coordinate end
1,
min(data[3]), # y-coordinate begin
max(data[3]), # y-coordinate end
1,
]
arLabels = ['Longitudinal Position', 'Horizontal Position', 'Vertical Position']
arUnits = ['m', 'm', 'm', 'm']
if traj_axis == 'x':
data = data[1]
arLabels.append('Horizontal Coordinate')
elif traj_axis == 'y':
data = data[3]
arLabels.append('Vertical Coordinate')
else:
raise ValueError('Parameter "axis" has wrong value: {}. Allowed values are "x" and "y"'.format(traj_axis))
return data, mode, allrange, arLabels, arUnits
def _check_finite(file_path):
try:
import numpy as np
NUMPY = True
except ImportError:
NUMPY = False
if NUMPY:
with open(file_path) as f:
data = np.loadtxt(f)
condition = np.isfinite(data).all()
else:
import math
import uti_io
data = uti_io.read_ascii_data_cols(file_path,
'\t',
_i_col_start=0,
_i_col_end=0,
_n_line_skip=10)[0]
first_value = data[0]
condition = math.isinf(first_value) and not math.isnan(first_value)
assert condition, \
'data is not finite: [{}, ...]'.format(', '.join([str(x) for x in data[:10]]))
return data
def get_att_len(material, E=8000):
"""
by LW 07/04/2011
function gets the attenuation length from stored data file,
attenuation length is a .dat file from http://henke.lbl.gov/optical_constants/getdb2.html
(energy range: 2-30keV,delete the header lines or comment with '%', name the file n_material.dat)
calling sequence: mu=get_mu(material,E) where mu [meter] is the 1/e attenuation length, E: X-ray energy in eV, default: 8000eV'
"""
#get list_of supported materials from data file directory:
#xdatafiles = [ f for f in listdir(datapath) if isfile(join(datapath,f)) ]
xdatafiles = [
f for f in os.listdir(datapath)
if os.path.isfile(os.path.join(datapath, f))
] #OC150715
name = []
#for i in range(0, np.size(xdatafiles)):
for i in range(0, len(xdatafiles)): #OC100915
mm = re.search('(?<=mu_)\w+', xdatafiles[i])
if mm is not None:
name.append(mm.group(0))
#E=np.array(E)
if material in name:
#loadn=datapath+'mu_'+material+'.dat'
loadm = os.path.join(datapath, 'mu_' + material + '.dat') #OC100915
#m=pl.loadtxt(loadn,comments='%')
m = uti_io.read_ascii_data_cols(loadm,
' ',
_i_col_start=0,
_i_col_end=1,
_n_line_skip=2) #OC100915
#if np.min(E)>=np.min(m[:,0]) and np.max(E)<=np.max(m[:,0]):
# mu=np.interp(E,m[:,0],m[:,1])
# return mu*1e-6
#else: raise xfuncs_Exception ('error: energy '+"%3.4f" %E +'[keV] out of range ('+"%3.4f" % np.min(m[:,0])+'=<E<='+"%3.4f" % np.max(m[:,0])+'eV)')
arE = m[0]
arAttLen = m[1]
attLen = (1e-6) * uti_math.interp_1d_var(E, arE, arAttLen)
nE_mi_1 = len(arE) - 1
if ((E < arE[0]) or (E > arE[nE_mi_1])):
print('Warning: energy ' + "%3.4f" % E + '[keV] out of range (' +
"%3.4f" % arE[0] + '=<E<=' + "%3.4f" % arE[nE_mi_1] + 'eV)')
return attLen
elif material == 'material?':
#print 'list of supported materials (based on data files in directory '+datapath+':'
#print name
print(
'list of supported materials (based on data files in directory ' +
datapath + ':')
print(name)
else:
raise xfuncs_Exception(
'error: non recognized material, please create index of refraction file first. Type get_mu("?") for instructions; type get_n("material?") for list of supported materials'
)
def get_ac(material, E=8000):
"""
by LW 10/03/2010
function calculates the critical angle for total external reflection as a function of
the material and the X-ray energy according to ac=sqrt(2*delta)
index of refraction is a .dat file from http://henke.lbl.gov/optical_constants/getdb2.html
(energy range: 2-30keV,delete the header % lines, name the file n_material.dat) %
calling sequence: ac=get_ac(material,E) where ac: critial angle in degrees, E [eV] (default: 8000eV)
type get_ac(\'materilal?\') to show list of supported materials"
"""
#get list_of supported materials from data file directory:
#xdatafiles = [ f for f in listdir(datapath) if isfile(join(datapath,f)) ]
xdatafiles = [
f for f in os.listdir(datapath)
if os.path.isfile(os.path.join(datapath, f))
] #OC150715
name = []
#for i in range(0, np.size(xdatafiles)):
for i in range(0, len(xdatafiles)): #OC150715
m = re.search('(?<=n_)\w+', xdatafiles[i])
if m is not None:
name.append(m.group(0))
#E=np.array(E)
if material in name:
#loadn=datapath+'n_'+material+'.dat'
#n=pl.loadtxt(loadn,comments='%')
loadn = os.path.join(datapath, 'n_' + material + '.dat') #OC150715
n = uti_io.read_ascii_data_cols(loadn,
' ',
_i_col_start=0,
_i_col_end=1,
_n_line_skip=2) #OC150715
#if np.min(E)>=np.min(n[:,0]) and np.max(E)<=np.max(n[:,0]):
# d=np.interp(E,n[:,0],n[:,1])
# return np.degrees(np.sqrt(2*d))
#else: raise xfuncs_Exception ('error: energy '+"%3.4f" %E +'[eV] out of range ('+"%3.4f" % np.min(n[:,0])+'=<E<='+"%3.4f" % np.max(n[:,0])+'eV)')
arE = n[0]
arDelta = n[1]
####################################################
elif material == 'material?':
#print 'list of supported materials (based on data files in directory '+datapath+':'
#print name
print(
'list of supported materials (based on data files in directory ' +
datapath + ':')
print(name)
else:
raise xfuncs_Exception(
'error: non recognized material, please create index of refraction file first. Type "get_ac?" for instructions; type get_ac("material?") for list of supported materials'
)
def _multicolumn_file_load(fname): #MR31102017
with open(fname, 'r') as f:
header = f.readline().split(',')
header = [x.replace('#', '').strip() for x in header]
data = uti_io.read_ascii_data_cols(fname, '\t', _i_col_start=0, _i_col_end=-1, _n_line_skip=1)
d = {}
for i, k in enumerate(header):
k_no_units = k.split('[')[0].strip()
units = k.split('[')[1].split(']')[0].strip()
d[k_no_units] = {
'data': data[i],
'label': k,
'units': units,
}
# data, mode, allrange, arLabels, arUnits
return d, None, [], [], []
def _multicolumn_file_load(fname): #MR31102017
with open(fname, 'r') as f:
header = f.readline().split(',')
header = [x.replace('#', '').strip() for x in header]
data = uti_io.read_ascii_data_cols(fname, '\t', _i_col_start=0, _i_col_end=-1, _n_line_skip=1)
d = {}
for i, k in enumerate(header):
k_no_units = k.split('[')[0].strip()
units = k.split('[')[1].split(']')[0].strip()
d[k_no_units] = {
'data': data[i],
'label': k,
'units': units,
}
# data, mode, allrange, arLabels, arUnits
return d, None, [], [], []
def _check_finite(file_path):
try:
import numpy as np
NUMPY = True
except ImportError:
NUMPY = False
if NUMPY:
with open(file_path) as f:
data = np.loadtxt(f)
condition = np.isfinite(data).all()
else:
import math
import uti_io
data = uti_io.read_ascii_data_cols(file_path, '\t', _i_col_start=0, _i_col_end=0, _n_line_skip=10)[0]
first_value = data[0]
condition = math.isinf(first_value) and not math.isnan(first_value)
assert condition, \
'data is not finite: [{}, ...]'.format(', '.join([str(x) for x in data[:10]]))
return data
def get_refr(material, E=8000):
"""
"by LW 07/04/2011 function get the complex index of refraction from stored data file,
index of refraction is a .dat file from http://henke.lbl.gov/optical_constants/getdb2.html
(energy range: 2-30keV,delete the header lines, name the file n_material.dat)
calling sequence: n=get_n(material,E) where n is the complex refractive index detlta-i*beta, E: X-ray energy in eV, default: 8000eV"
"""
#get list_of supported materials from data file directory:
#xdatafiles = [ f for f in listdir(datapath) if isfile(join(datapath,f)) ]
xdatafiles = [
f for f in os.listdir(datapath)
if os.path.isfile(os.path.join(datapath, f))
] #OC150715
name = []
#for i in range(0, np.size(xdatafiles)):
for i in range(0, len(xdatafiles)): #OC160715
m = re.search('(?<=n_)\w+', xdatafiles[i])
if m is not None:
name.append(m.group(0))
#E=np.array(E)
if material in name:
#loadn=datapath+'n_'+material+'.dat'
#n=pl.loadtxt(loadn,comments='%')
loadn = os.path.join(datapath, 'n_' + material + '.dat') #OC160715
n = uti_io.read_ascii_data_cols(loadn,
' ',
_i_col_start=0,
_i_col_end=2,
_n_line_skip=2) #OC160715
#if np.min(E)>=np.min(n[:,0]) and np.max(E)<=np.max(n[:,0]):
# d=np.interp(E,n[:,0],n[:,1])
# b=np.interp(E,n[:,0],n[:,2])
# return d-1j*b
#else: raise xfuncs_Exception ('error: energy '+"%3.4f" %E +'[keV] out of range ('+"%3.4f" % np.min(n[:,0])+'=<E<='+"%3.4f" % np.max(n[:,0])+'eV)')
arE = n[0]
arDelta = n[1]
arBeta = n[2]
d = uti_math.interp_1d_var(E, arE, arDelta)
b = uti_math.interp_1d_var(E, arE, arBeta)
nE_mi_1 = len(arE) - 1
if ((E < arE[0]) or (E > arE[nE_mi_1])):
print('Warning: energy ' + "%3.4f" % E + '[keV] out of range (' +
"%3.4f" % arE[0] + '=<E<=' + "%3.4f" % arE[nE_mi_1] + 'eV)')
return d - 1j * b #Check the sign of imaginary part!
elif material == 'material?':
#print 'list of supported materials (based on data files in directory '+datapath+':'
#print name
print(
'list of supported materials (based on data files in directory ' +
datapath + ':')
print(name)
#else: raise xfuncs_Exception ( 'error: non recognized material, please create index of refraction file first. Type "get_n?" for instructions; type get_n("material?") for list of supported materials')
else:
raise uti_xray_mat_Exception(
'error: non recognized material, please create index of refraction file first. Type "get_n?" for instructions; type get_n("material?") for list of supported materials'
)