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remove tests at end of readers
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@lukaspie
lukaspie committed Nov 24, 2023
1 parent ae6b820 commit 3bcec38
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Showing 2 changed files with 22 additions and 177 deletions.
177 changes: 22 additions & 155 deletions pynxtools/dataconverter/readers/xps/txt/txt_vamas_export.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -24,11 +24,13 @@
import operator
import copy
from abc import ABC, abstractmethod
from scipy.interpolate import interp1d
import xarray as xr
import numpy as np

from pynxtools.dataconverter.readers.xps.reader_utils import (
check_uniform_step_width,
get_minimal_step,
interpolate_arrays,
construct_entry_name,
construct_data_key,
construct_detector_data_key,
Expand Down Expand Up @@ -134,6 +136,7 @@ def construct_data(self):
'region_name',
'start_energy',
'stop_energy',
'step_size'
],
}

Expand Down Expand Up @@ -195,60 +198,13 @@ def _update_xps_dict_with_spectrum(self, spectrum, key_map):

self._xps_dict[detector_data_key] = spectrum["data"]['intensity']

def safe_arange_with_edges(start, stop, step):
"""
In order to avoid float point errors in the division by step.
Parameters
----------
start : float
Smallest value.
stop : float
Biggest value.
step : float
Step size between points.
Returns
-------
ndarray
1D array with values in the interval (start, stop),
incremented by step.
"""
return step * np.arange(start / step, (stop + step) / step)


def _resample_array(y, x0, x1):
"""
Resample an array (y) which has the same initial spacing
of another array(x0), based on the spacing of a new
array(x1).
Parameters
----------
y : array
Lineshape array.
x0 : array
x array with old spacing.
x1 : array
x array with new spacing.
Returns
-------
TYPE
DESCRIPTION.
"""
fn = interp1d(x0, y, axis=0, fill_value="extrapolate")
return fn(x1)


class TextParser(ABC):
"""
Parser for ASCI files exported from CasaXPS.
"""

def __init__(self, **kwargs):
def __init__(self):
self.lines = []
self.data_dict = []
self.n_headerlines = 7
Expand Down Expand Up @@ -359,85 +315,6 @@ def _separate_header_and_data(self, block):

return header, data

def _check_uniform_step_width(self, x):
"""
Check to see if a non-uniform step width is used in the spectrum
Parameters
----------
x : list
List of data points.
Returns
-------
bool
False if list is non-uniformally spaced.
"""
start = x[0]
stop = x[-1]
step = self._get_minimal_step(x)

if step != 0.0 and np.abs((stop - start) / step) > len(x):
return False
return True

def _get_minimal_step(self, x):
"""
Return the minimal difference between two consecutive values
in a list. Used for extracting minimal difference in a
list with non-uniform spacing.
Parameters
----------
x : list
List of data points.
Returns
-------
step : float
Non-zero, minimal distance between consecutive data
points in x.
"""
x1 = np.roll(x, -1)
diff = np.abs(np.subtract(x, x1))
step = round(np.min(diff[diff != 0]), 2)

return step


def _interpolate(self, x, array_list):
"""
Interpolate data points in case a non-uniform step width was used.
Parameters
----------
x : list
List of non-uniformally spaced data points.
array_list : list
List of arrays to be interpolated according to new x axis.
Returns
-------
x, array_list
Interpolated x axis and list of arrays
"""
if not isinstance(array_list, list):
array_list = [array_list]
start = x[0]
stop = x[-1]
step = self._get_minimal_step(x)
if start > stop:
new_x = np.flip(safe_arange_with_edges(stop, start, step))
else:
new_x = safe_arange_with_edges(start, stop, step)

output_list = [_resample_array(arr, x, new_x) for arr in array_list]

return new_x, output_list


class TextParserRows(TextParser):
"""
Expand Down Expand Up @@ -550,20 +427,22 @@ def _parse_data(self, data_lines):
x_bin, y = np.array(x_bin), np.array(y)

if (self.uniform_energy_steps and
not self._check_uniform_step_width(x_bin)):
x_bin, y = self._interpolate(x_bin, y)
not check_uniform_step_width(x_bin)):
x_bin, y = interpolate_arrays(x_bin, y)

spectrum = {
"binding_energy": np.array(x_bin),
"intensity": np.array(y).squeeze(),
}

data += [{
"data": spectrum,
"step_size": self._check_uniform_step_width(x_bin),
"data": {
"binding_energy": np.array(x_bin),
"intensity": np.array(y).squeeze(),
},
"start_energy": x_bin[0],
"stop_energy": x_bin[-1],
}]
}

if check_uniform_step_width(x_bin):
spectrum["step_size"] = get_minimal_step(x_bin)

data += [spectrum]

return data

Expand Down Expand Up @@ -649,8 +528,8 @@ def _parse_block_data(self, block_data):
y = lines[:, 1]

if (self.uniform_energy_steps and
not self._check_uniform_step_width(x_kin)):
x_kin, (x_bin, y) = self._interpolate(x_kin, [x_bin, y])
not check_uniform_step_width(x_kin)):
x_kin, (x_bin, y) = interpolate_arrays(x_kin, [x_bin, y])

return {
"kinetic_energy": np.array(x_kin),
Expand Down Expand Up @@ -682,26 +561,14 @@ def _build_list_of_dicts(self, blocks):
block_data = {"data": self._parse_block_data(block_data_lines)}
kinetic_energy = block_data["data"]["kinetic_energy"]
block_settings.update({
"step_size": self._check_uniform_step_width(kinetic_energy),
"start_energy": kinetic_energy[0],
"stop_energy": kinetic_energy[-1],
})
if check_uniform_step_width(kinetic_energy):
block_settings["step_size"] = get_minimal_step(kinetic_energy)

spectra += [block_settings|block_data]

return spectra


if __name__ == "__main__":
filepaths = [
r"C:\Users\pielsticker\Downloads\vm_test_rows_r.txt",
r"C:\Users\pielsticker\Downloads\vm_test_rows_irr.txt",
r"C:\Users\pielsticker\Downloads\vm_test_cols_r.txt",
r"C:\Users\pielsticker\Downloads\vm_test_cols_irr.txt",
]

l = []

for file in filepaths:
p = TxtParserVamasExport()
new_dict = p.parse_file(file=file, uniform_energy_steps=True)
l.append(new_dict)
22 changes: 0 additions & 22 deletions pynxtools/dataconverter/readers/xps/xy/xy_specs.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -218,9 +218,7 @@ def __init__(self, **kwargs):
"""
self.lines = []
self.spectra = {}
self.prefix = "#"
self.file = file
self.n_headerlines = 14
self.export_settings = {}

Expand Down Expand Up @@ -776,23 +774,3 @@ def _reformat_y_units(self, y_units):
}

return unit_map[y_units]

if __name__ == "__main__":
import os
folder = r"C:\Users\pielsticker\Lukas\FAIRMat\user_cases\Pielsticker_XPS_MPI-CEC\EX889_S1110_MgFe2O4_spent\xy"
files = [
# "EX889_S1110_MgFe2O4_spent.xy",
# "EX889_S1110_MgFe2O4_spent_channels.xy",
"EX889_S1110_MgFe2O4_spent_channels_shortened.xy",
# "EX889_S1110_MgFe2O4_spent_tf.xy",
]

data = []

for file in files:
file = os.path.join(folder, file)
p = XyParserSpecs()
d = p.parse_file(file=file)
raw_data = p.raw_data

data.append(d)

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