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Refactor get_scale()
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@pietsjoh
pietsjoh committed Sep 27, 2022
1 parent 2012e20 commit f1194fc
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Showing 2 changed files with 64 additions and 55 deletions.
84 changes: 38 additions & 46 deletions rsciio/jobin_yvon/api.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@
from copy import deepcopy

import numpy as np
from numpy.polynomial.polynomial import polyfit

_logger = logging.getLogger(__name__)

Expand Down Expand Up @@ -325,38 +326,6 @@ def _set_signal_type(self, xml_element):
"signal units"
] = child.text

def _get_scale(self, array, name):
"""Get scale for navigation/signal axes.
Furthermore, checks whether the axis is uniform. Throws warning when this not the case.
This check is performed by comparing the difference between the first 2 and last 2 values.
The decision to use a non-uniform/uniform data-axis is left to the user
(use_uniform_wavelength_axis).
Parameters
----------
array: np.ndarray
Contains the axes data points.
name: Str
Name of the axis.
"""
scale = np.abs(array[0] - array[-1]) / (array.size - 1)
if array.size >= 3:
abs_diff_begin = np.abs(array[0] - array[1])
abs_diff_end = np.abs(array[-1] - array[-2])
rel_diff_compare = np.abs(abs_diff_begin - abs_diff_end) / scale
if rel_diff_compare > 0.01 and self._use_uniform_signal_axis:
_logger.warning(
f"The relative variation of the {name}-axis-scale ({rel_diff_compare:.3f}%) exceeds 1%.\n"
" "
f"Difference between first 2 entrys: {abs_diff_begin:.3f}.\n"
" "
f"Difference between last 2 entrys: {abs_diff_end:.3f}.\n"
" "
"Using a non-uniform-axis is recommended."
)
return scale

def _set_nav_axis(self, xml_element, tag):
"""Helper method for setting navigation axes.
Expand All @@ -381,7 +350,7 @@ def _set_nav_axis(self, xml_element, tag):
if nav_size < 2:
has_nav = False
else:
nav_dict["scale"] = self._get_scale(nav_array, tag)
nav_dict["scale"] = nav_array[1] - nav_array[0]
nav_dict["offset"] = nav_array[0]
nav_dict["size"] = nav_size
nav_dict["navigate"] = True
Expand All @@ -405,17 +374,38 @@ def _set_signal_axis(self, xml_element):
id = self._get_id(child)
if id == "0x7D6CD4DB":
signal_array = np.fromstring(child.text.strip(), sep=" ")
if signal_array[0] > signal_array[1]:
signal_array = signal_array[::-1]
self._reverse_signal = True
else:
self._reverse_signal = False
if self._use_uniform_signal_axis:
signal_dict["scale"] = self._get_scale(signal_array, "signal")
signal_dict["offset"] = signal_array[0]
signal_dict["size"] = signal_array.size
else:
signal_dict["axis"] = signal_array
if signal_array.size > 1:
if signal_array[0] > signal_array[1]:
signal_array = signal_array[::-1]
self._reverse_signal = True
else:
self._reverse_signal = False
if self._use_uniform_signal_axis:
offset, scale = polyfit(
np.arange(signal_array.size), signal_array, deg=1
)
signal_dict["offset"] = offset
signal_dict["scale"] = scale
signal_dict["size"] = signal_array.size
scale_compare = 100 * np.max(
np.abs(np.diff(signal_array) - scale) / scale
)
if scale_compare > 1:
_logger.warning(
f"The relative variation of the signal-axis-scale ({scale_compare:.2f}%) exceeds 1%.\n"
" "
"Using a non-uniform-axis is recommended."
)
else:
signal_dict["axis"] = signal_array
else: # pragma: no cover
if self._use_uniform_signal_axis: # pragma: no cover
_logger.warning( # pragma: no cover
"Signal only contains one entry.\n" # pragma: no cover
" " # pragma: no cover
"Using non-uniform-axis independent of use_uniform_signal_axis setting" # pragma: no cover
) # pragma: no cover
signal_dict["axis"] = signal_array # pragma: no cover
if id == "0x7C696E75":
units = child.text
if "/" in units and units[-3:] == "abs":
Expand Down Expand Up @@ -683,8 +673,10 @@ def file_reader(filename, use_uniform_signal_axis=False, **kwds):
Parameters
----------
use_uniform_signal_axis: bool, default=True
Can be specified to choose between non-uniform or uniform signal-axis.
use_uniform_signal_axis: bool, default=False
Can be specified to choose between non-uniform or uniform signal axis.
If `True`, the ``scale`` attribute is calculated from the average delta along the signal axis
and a warning is raised in case the delta varies by more than 1%.
"""
if not isinstance(filename, Path):
filename = Path(filename)
Expand Down
35 changes: 26 additions & 9 deletions rsciio/tests/test_jobin_yvon.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -192,8 +192,6 @@ def test_axes(self):
"navigate": False,
"is_binned": False,
"size": 34,
"scale": 0.44809090909091015,
"offset": 522.574,
}
}

Expand Down Expand Up @@ -246,15 +244,22 @@ def test_axes(self):
]
)

uniform_axis_manager = deepcopy(self.s.axes_manager.as_dictionary())
non_uniform_axis_manager = deepcopy(
self.s_non_uniform.axes_manager.as_dictionary()
)
np.testing.assert_allclose(
uniform_axis_manager["axis-0"].pop("scale"), 0.4481, atol=0.0001
)
np.testing.assert_allclose(
uniform_axis_manager["axis-0"].pop("offset"), 522.6, atol=0.05
)

np.testing.assert_allclose(
non_uniform_axis_values[::-1],
non_uniform_axis_manager["axis-0"].pop("axis"),
)
assert spec_axes == self.s.axes_manager.as_dictionary()
assert spec_axes == uniform_axis_manager
assert spec_axes_non_uniform == non_uniform_axis_manager

def test_original_metadata(self):
Expand Down Expand Up @@ -597,8 +602,6 @@ def test_axes(self):
"navigate": False,
"is_binned": False,
"size": 34,
"scale": 0.44809090909091015,
"offset": 522.574,
},
}

Expand Down Expand Up @@ -661,16 +664,23 @@ def test_axes(self):
]
)

uniform_axis_manager = deepcopy(self.s.axes_manager.as_dictionary())
non_uniform_axis_manager = deepcopy(
self.s_non_uniform.axes_manager.as_dictionary()
)

np.testing.assert_allclose(
uniform_axis_manager["axis-1"].pop("scale"), 0.4481, atol=0.0001
)
np.testing.assert_allclose(
uniform_axis_manager["axis-1"].pop("offset"), 522.6, atol=0.05
)
np.testing.assert_allclose(
non_uniform_axis_values[::-1],
non_uniform_axis_manager["axis-1"].pop("axis"),
)
assert linescan_axes_non_uniform == non_uniform_axis_manager
assert linescan_axes == self.s.axes_manager.as_dictionary()
assert linescan_axes == uniform_axis_manager


class TestMap:
Expand Down Expand Up @@ -965,12 +975,19 @@ def test_axes(self):
"navigate": False,
"is_binned": False,
"size": 34,
"scale": 1.541606060606062,
"offset": 720.924,
},
}

assert map_axes == self.s.axes_manager.as_dictionary()
uniform_axis_manager = deepcopy(self.s.axes_manager.as_dictionary())

np.testing.assert_allclose(
uniform_axis_manager["axis-2"].pop("scale"), 1.5416, atol=0.0001
)
np.testing.assert_allclose(
uniform_axis_manager["axis-2"].pop("offset"), 720.967, atol=0.05
)

assert map_axes == uniform_axis_manager


class TestGlue:
Expand Down

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