IO write module

The io_write submodule offers the following functions to write files:

Function	Description
write_xmu()	Writes a XAFS group in xmu format.
write_lcf()	Writes LCF data to a file.
write_lcf_report()	Writes a LCF report to a file.
write_file()	Utility function to write an array to a file.
set_header()	Utility function to write a file header.

araucaria.io.io_write.write_xmu(fpath, group, fmt='%12.8g', replace=False)

Writes a file in xmu format.

Parameters

• fpath (Path) – Path to file.

• group (Group) – Group dataset to write in file.

• fmt (str) – Format for numbers. The default is ‘%12.8g’.

• replace (bool) – Indicates if a previous file should be replaced. The detault is False.

Return type

str

Returns

Confirmation message.

Raises

TypeError – If group is not a valid Group instance.

Notes

By default the operation will be cancelled if the file already exists. The previous file can be overwritten with the option replace=True.

See also

write_file

Writes an array to a file.

Example

>>> from araucaria.testdata import get_testpath
>>> from araucaria.io import read_xmu, write_xmu
>>> fpath = get_testpath('xmu_testfile.xmu')
>>> # extracting mu and mu_ref scans
>>> group_mu = read_xmu(fpath, scan='mu')
>>> # saving a new xmu file
>>> write_xmu('new_file.xmu', group_mu)
'xmu_testfile.xmu written to new_file.xmu.'

araucaria.io.io_write.write_lcf(fpath, out, fmt='%12.8g', replace=False)

Writes LCF data to a file.

Parameters

• fpath (Path) – Path to file.

• out (Dataset) – Valid Dataset from lcf().

• fmt (str) – Format for numbers. The default is ‘%12.8g’.

• replace (bool) – Replace previous file. The detault is False.

Return type

str

Returns

Confirmation message.

Raises

• TypeError – If out is not a valid Dataset instance.

• AttributeError – If attribute min_pars, scangroup, or refgroups does not exist in out.

Notes

The returned file will contain in the header the output from lcf_report(), in addition to the following columns:

• energy : array with energy values. Returned only if fit_region='xanes' or fit_region='dxanes'.

• k : array with wavenumber values. Returned only if fit_region='exafs'.

• scan : array with values of the fitted spectrum.

• ref : array with interpolated values for each reference spectrum.

• fit : array with fit result.

• residual : fit residuals.

See also

write_file()

Writes an array to a file.

Example

>>> from numpy.random import seed, normal
>>> from numpy import arange, sin, pi
>>> from araucaria import Group, Collection
>>> from araucaria.fit import lcf
>>> from araucaria.io import write_lcf
>>> seed(1234)  # seed of random values
>>> k    = arange(0,  12,   0.05)
>>> eps  = normal(0, 0.1, len(k))
>>> f1   = 1.2  # freq 1
>>> f2   = 2.6  # freq 2
>>> amp1 = 0.4  # amp 1
>>> amp2 = 0.6  # amp 2
>>> group1 = Group(**{'name': 'group1', 'k': k, 'chi': sin(2*pi*f1*k)})
>>> group2 = Group(**{'name': 'group2', 'k': k, 'chi': sin(2*pi*f2*k)})
>>> group3 = Group(**{'name': 'group3', 'k': k,
...                   'chi' : amp1 * group1.chi + amp2 * group2.chi + eps})
>>> collection = Collection()
>>> tags = ['ref', 'ref', 'scan']
>>> for i,group in enumerate((group1,group2, group3)):
...     collection.add_group(group, tag=tags[i])
>>> # performing lcf
>>> out = lcf(collection, fit_region='exafs', fit_range=[3,10],
...           kweight=0, sum_one=False)
>>> # saving lcf to a file
>>> write_lcf('new_fit.lcf', out)
'lcf data written to new_fit.lcf.'

araucaria.io.io_write.write_lcf_report(fpath, out, replace=False)

Writes a LCF report to a file.

Parameters

• fpath (Path) – Path to file.

• out (Dataset) – Valid Dataset from lcf().

• replace (bool) – Replace previous file. The detault is False.

Return type

str

Returns

Confirmation message.

Raises

• TypeError – If out is not a valid Dataset instance.

• AttributeError – If attribute min_pars, lcf_pars, scangroup, or refgroups does not exist in out.

Example

>>> from numpy.random import seed, normal
>>> from numpy import arange, sin, pi
>>> from araucaria import Group, Collection
>>> from araucaria.fit import lcf
>>> from araucaria.io import write_lcf_report
>>> seed(1234)  # seed of random values
>>> k    = arange(0,  12,   0.05)
>>> eps  = normal(0, 0.1, len(k))
>>> f1   = 1.2  # freq 1
>>> f2   = 2.6  # freq 2
>>> amp1 = 0.4  # amp 1
>>> amp2 = 0.6  # amp 2
>>> group1 = Group(**{'name': 'group1', 'k': k, 'chi': sin(2*pi*f1*k)})
>>> group2 = Group(**{'name': 'group2', 'k': k, 'chi': sin(2*pi*f2*k)})
>>> group3 = Group(**{'name': 'group3', 'k': k,
...                   'chi' : amp1 * group1.chi + amp2 * group2.chi + eps})
>>> collection = Collection()
>>> tags = ['ref', 'ref', 'scan']
>>> for i,group in enumerate((group1,group2, group3)):
...     collection.add_group(group, tag=tags[i])
>>> # performing lcf
>>> out = lcf(collection, fit_region='exafs', fit_range=[3,10],
...           kweight=0, sum_one=False)
>>> # saving lcf report to a file
>>> write_lcf_report('lcf_report.log', out)
'lcf report written to lcf_report.log.'

araucaria.io.io_write.write_file(fpath, data, name, fmt='%12.8g', header='', replace=False)

Utility function to write a data array to a file.

Parameters

• fpath (Path) – Path to file.

• data (ndarray) – array to write in file.

• name (str) – Name of object to write.

• fmt (str) – Format for numbers. The default is ‘%12.8g’.

• header (str) – Header for the file.

• replace (bool) – Replace previous file. The detault is False.

Return type

None

Returns

Confirmation message.

Raises

IOError – If the file already exists and replace=False.

araucaria.io.io_write.set_header(fpath, file_type)

Utility function for write a file header.

Parameters

• fpath – Path to file.

• file_type (str) – Short descriptor for type of file.

Return type

str

Returns

Header for file.

Example

>>> from araucaria.io import set_header
>>> from araucaria import Group
>>> header = set_header('testdata.xmu', 'xmu')
>>> header.splitlines()[0]
'xmu file created by araucaria'
>>> header.splitlines()[2]
'name: testdata.xmu'