def load_BL7_XAS_files(file_name_filter):
"""helper function to load a bunch of spectra from ALS BL 7.0.1.1 XAS text files in the current dir"""
files = os.listdir('.')
spectra = {}
for f in files:
m = re.search('(' + file_name_filter + '.*)\d\.txt$', f)
if (m):
filename = f
print filename
name = filename
nametey = name + 'TEY'
nametfy = name + 'TFY'
spectra[nametey] = Spectrum()
spectra[nametey].name = nametey
spectra[nametfy] = Spectrum()
spectra[nametfy].name = nametfy
data = read_bl7011_xas(filename)
spectra[nametey].EE = data['MonoEnergy']
spectra[nametey].data = data['Counter1'] / data['Izero']
spectra[nametfy].EE = data['MonoEnergy']
spectra[nametfy].data = data['Counter2'] / data['Izero']
return spectra
def load_BL7_XAS_files(file_name_filter):
"""helper function to load a bunch of spectra from ALS BL 7.0.1.1 XAS text files in the current dir"""
files = os.listdir('.')
spectra = {}
for f in files:
m = re.search('('+file_name_filter+'.*)\d\.txt$',f)
if (m):
filename = f
print filename
name = filename
nametey = name+'TEY'
nametfy = name+'TFY'
spectra[nametey] = Spectrum()
spectra[nametey].name = nametey
spectra[nametfy] = Spectrum()
spectra[nametfy].name = nametfy
data = read_bl7011_xas(filename)
spectra[nametey].EE = data['MonoEnergy']
spectra[nametey].data = data['Counter1']/data['Izero']
spectra[nametfy].EE = data['MonoEnergy']
spectra[nametfy].data = data['Counter2']/data['Izero']
return spectra
def load_AugerScan_text_files(file_name_filter):
"""helper function to load a bunch of spectra from AugerScan text files in the current dir"""
files = os.listdir('.')
special_chars = r'[ \t\(\"\(\)\*\&\^\%\$\#\@\!\_\+\-\=\[\]\{\}\|\;\'\"\:\/\.\,\<\>\\\?]'
spectra = {}
EE = []
data = []
i = 0
for spec_file in files:
m = re.search('(' + file_name_filter + ')\.txt', spec_file)
if (m):
filename = spec_file
print filename
f = open(filename, 'r')
name = m.group(1)
header = True
for line in f:
if (re.search('Element', line)):
print '+e'
header = False
m = re.search(
'Element\s(.*);.*;\sDepth Cycle (\d+).*;\sTime Per Step (\d+);\sSweeps (\d+);.*',
line)
#print m.group(0)
label = i #name+'-'+line
i = i + 1
#print '+' + label
spectrum = Spectrum()
spectrum.element = m.group(1)
spectrum.depth_cycle = double(m.group(2))
spectrum.time_per_step = double(m.group(3))
spectrum.sweeps = double(m.group(4))
spectrum.name = name
spectrum.EE = array([])
spectrum.data = array([])
spectra[label] = spectrum
elif header:
continue
elif (re.search('^[\d\.]+\s\d+\s*$', line)):
m = re.search('^([\d\.]+)\s(\d+)', line)
#print m.group(0)
spectra[label].EE = append(spectra[label].EE,
double(m.group(1)))
spectra[label].data = append(spectra[label].data,
double(m.group(2)))
return spectra
def load_AugerScan_text_files(file_name_filter):
"""helper function to load a bunch of spectra from AugerScan text files in the current dir"""
files = os.listdir('.')
special_chars = r'[ \t\(\"\(\)\*\&\^\%\$\#\@\!\_\+\-\=\[\]\{\}\|\;\'\"\:\/\.\,\<\>\\\?]'
spectra = {}
EE=[]
data=[]
i = 0;
for spec_file in files:
m = re.search('('+file_name_filter+')\.txt',spec_file)
if (m):
filename = spec_file
print filename
f = open(filename, 'r')
name = m.group(1)
header = True
for line in f:
if (re.search('Element',line)):
print '+e'
header = False
m = re.search('Element\s(.*);.*;\sDepth Cycle (\d+).*;\sTime Per Step (\d+);\sSweeps (\d+);.*',line)
#print m.group(0)
label = i#name+'-'+line
i = i+1
#print '+' + label
spectrum = Spectrum()
spectrum.element = m.group(1)
spectrum.depth_cycle = double(m.group(2))
spectrum.time_per_step = double(m.group(3))
spectrum.sweeps = double(m.group(4))
spectrum.name = name
spectrum.EE=array([])
spectrum.data=array([])
spectra[label] = spectrum
elif header:
continue
elif (re.search('^[\d\.]+\s\d+\s*$',line)):
m = re.search('^([\d\.]+)\s(\d+)',line)
#print m.group(0)
spectra[label].EE = append(spectra[label].EE, double(m.group(1)))
spectra[label].data = append(spectra[label].data, double(m.group(2)))
return spectra
def load_BL62_text_files(file_name_filter):
"""helper function to load a bunch of spectra from SSRL BL6-2 text files in the current dir"""
files = os.listdir('.')
spectra = {}
for spec_file in files:
m = re.search('('+file_name_filter+'.*)\.dat',spec_file)
if (m):
name = spec_file
spectra[name] = Spectrum()
spectra[name].name = name
data = np.genfromtxt(name,skip_header=37)
#print data
spectra[name].EE = data[:,1]
spectra[name].data = data[:,1:]
return spectra
def load_BL62_text_files(file_name_filter):
"""helper function to load a bunch of spectra from SSRL BL6-2 text files in the current dir"""
files = os.listdir('.')
spectra = {}
for spec_file in files:
m = re.search('(' + file_name_filter + '.*)\.dat', spec_file)
if (m):
name = spec_file
spectra[name] = Spectrum()
spectra[name].name = name
data = np.genfromtxt(name, skip_header=37)
#print data
spectra[name].EE = data[:, 1]
spectra[name].data = data[:, 1:]
return spectra
def load_BL7_XES_files(file_name_filter):
"""helper function to load a bunch of spectra from ALS BL 7.0.1.1 XES text files in the current dir"""
files = os.listdir('.')
spectra = {}
for spec_file in files:
m = re.search('('+file_name_filter+'.*)\_spec.txt',spec_file)
if (m):
filename = spec_file
name = filename
spectra[name] = Spectrum()
spectra[name].name = name
data = np.genfromtxt(filename,skip_header=0)
#print data
spectra[name].EE = data[:-1,0]
spectra[name].data = data[:-1,1]
return spectra
def load_SUPER_text_files(file_name_filter):
"""helper function to load a bunch of spectra from AugerScan text files in the current dir"""
files = os.listdir('.')
spectra = {}
for spec_file in files:
m = re.search('('+file_name_filter+'.*)\.\d\d\d',spec_file)
if (m):
filename = spec_file
name = filename
spectra[name] = Spectrum()
spectra[name].name = name
data = np.genfromtxt(filename,skip_header=12)
#print data
spectra[name].EE = data[:,0]
spectra[name].data = data[:,1:]
return spectra
def load_BL7_XES_files(file_name_filter):
"""helper function to load a bunch of spectra from ALS BL 7.0.1.1 XES text files in the current dir"""
files = os.listdir('.')
spectra = {}
for spec_file in files:
m = re.search('(' + file_name_filter + '.*)\_spec.txt', spec_file)
if (m):
filename = spec_file
name = filename
spectra[name] = Spectrum()
spectra[name].name = name
data = np.genfromtxt(filename, skip_header=0)
#print data
spectra[name].EE = data[:-1, 0]
spectra[name].data = data[:-1, 1]
return spectra
def load_SUPER_text_files(file_name_filter):
"""helper function to load a bunch of spectra from AugerScan text files in the current dir"""
files = os.listdir('.')
spectra = {}
for spec_file in files:
m = re.search('(' + file_name_filter + '.*)\.\d\d\d', spec_file)
if (m):
filename = spec_file
name = filename
spectra[name] = Spectrum()
spectra[name].name = name
data = np.genfromtxt(filename, skip_header=12)
#print data
spectra[name].EE = data[:, 0]
spectra[name].data = data[:, 1:]
return spectra
def load_from_file(self, filename=None, filefilter=None):
## fix reload behavoir to maintain existing Spectrum objects
self.spectra = []
self.names = []
if filename:
if filefilter == 'VAMAS (*.vms)':
experiment = VAMASExperiment(filename)
i = 1
for block in experiment.blocks: #VAMAS file may contain multiple spectra
treename = 'B-' + str(i) + '-' + block.comment
treename = treename.replace('Not Specified', '') #DFO
treename = treename.strip()
spectrum = Spectrum()
spectrum.EE = block.abscissa()
spectrum.name = os.path.basename(filename) + '-' + treename
spectrum.data = block.ordinate(0) / (
block.number_of_scans_to_compile_this_block *
block.signal_collection_time)
spectrum.raw_data = spectrum.data.copy() #keep a copy
if block.analyser_mode in ('FAT', 'FRR'):
spectrum.spec_mode = block.analyser_mode
spectrum.pass_energy_ratio = block.analyser_pass_energy_of_retard_ratio_or_mass_resolution
self.spectra.append(spectrum)
self.names.append(treename)
i += 1
elif filefilter == 'SSRL (*.dat)':
experiment = np.genfromtxt(filename, skip_header=37)
spectrum = Spectrum()
spectrum.EE = experiment[:, 1]
spectrum.data = experiment[:, 2]
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'I0'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment[:, 1]
spectrum.data = experiment[:, 3]
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'I1'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment[:, 1]
spectrum.data = experiment[:, 2] / experiment[:, 1]
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'I1/I0'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment[:, 1]
spectrum.data = experiment[:, 6]
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'ICR'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment[:, 1]
spectrum.data = experiment[:, 7]
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'FF1'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment[:, 1]
spectrum.data = experiment[:, 6] / experiment[:, 1]
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'ICR/I0'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
elif filefilter == 'BL7.0.1.1 XAS (*.txt)':
experiment = read_bl7011_xas(filename)
spectrum = Spectrum()
spectrum.EE = experiment['MonoEnergy']
spectrum.data = experiment['Izero']
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'I0'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment['MonoEnergy']
spectrum.data = experiment['Counter1']
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'TEY'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment['MonoEnergy']
spectrum.data = experiment['Counter2']
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'TFY'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment['MonoEnergy']
spectrum.data = experiment['Counter1'] / experiment['Izero']
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'TEY/I0'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment['MonoEnergy']
spectrum.data = experiment['Counter2'] / experiment['Izero']
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'TFY/I0'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
elif filefilter == 'AugerScan (*.txt)':
experiment = read_augerscan(filename)
spectrum = Spectrum()
spectrum.EE = -experiment['Energy']
#print spectrum.EE
spectrum.data = experiment['Counts']
spectrum.raw_data = spectrum.data.copy() #keep a copy
#print spectrum.data
spectrum.name = 'Region 1'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
elif filefilter == 'SUPER (*)':
pass
def load_from_file(self, filename=None, filefilter=None):
## fix reload behavoir to maintain existing Spectrum objects
self.spectra = []
self.names = []
if filename:
if filefilter == 'VAMAS (*.vms)':
experiment = VAMASExperiment(filename)
i=1
for block in experiment.blocks: #VAMAS file may contain multiple spectra
treename = 'B-' + str(i) + '-' + block.comment
treename = treename.replace('Not Specified','') #DFO
treename = treename.strip()
spectrum = Spectrum()
spectrum.EE = block.abscissa()
spectrum.name = os.path.basename(filename) + '-' + treename
spectrum.data = block.ordinate(0)/(block.number_of_scans_to_compile_this_block * block.signal_collection_time)
spectrum.raw_data = spectrum.data.copy() #keep a copy
if block.analyser_mode in ('FAT','FRR') :
spectrum.spec_mode = block.analyser_mode
spectrum.pass_energy_ratio = block.analyser_pass_energy_of_retard_ratio_or_mass_resolution
self.spectra.append(spectrum)
self.names.append(treename)
i += 1
elif filefilter == 'SSRL (*.dat)':
experiment = np.genfromtxt(filename,skip_header=37)
spectrum = Spectrum()
spectrum.EE = experiment[:,1]
spectrum.data = experiment[:,2]
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'I0'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment[:,1]
spectrum.data = experiment[:,3]
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'I1'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment[:,1]
spectrum.data = experiment[:,2]/experiment[:,1]
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'I1/I0'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment[:,1]
spectrum.data = experiment[:,6]
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'ICR'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment[:,1]
spectrum.data = experiment[:,7]
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'FF1'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment[:,1]
spectrum.data = experiment[:,6]/experiment[:,1]
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'ICR/I0'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
elif filefilter == 'BL7.0.1.1 XAS (*.txt)':
experiment = read_bl7011_xas(filename)
spectrum = Spectrum()
spectrum.EE = experiment['MonoEnergy']
spectrum.data = experiment['Izero']
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'I0'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment['MonoEnergy']
spectrum.data = experiment['Counter1']
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'TEY'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment['MonoEnergy']
spectrum.data = experiment['Counter2']
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'TFY'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment['MonoEnergy']
spectrum.data = experiment['Counter1']/experiment['Izero']
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'TEY/I0'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
spectrum = Spectrum()
spectrum.EE = experiment['MonoEnergy']
spectrum.data = experiment['Counter2']/experiment['Izero']
spectrum.raw_data = spectrum.data.copy() #keep a copy
spectrum.name = 'TFY/I0'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
elif filefilter == 'AugerScan (*.txt)':
experiment = read_augerscan(filename)
spectrum = Spectrum()
spectrum.EE = -experiment['Energy']
#print spectrum.EE
spectrum.data = experiment['Counts']
spectrum.raw_data = spectrum.data.copy() #keep a copy
#print spectrum.data
spectrum.name = 'Region 1'
self.spectra.append(spectrum)
self.names.append(spectrum.name)
elif filefilter == 'SUPER (*)':
pass