From 0819a3aea54a62387e53ed8abd8ad57220fb5516 Mon Sep 17 00:00:00 2001
From: woutdenolf <woutdenolf@users.sf.net>
Date: Wed, 5 Feb 2025 05:55:00 +0100
Subject: [PATCH] read_concatenated_xas: handle NaNs with masked arrays
---
src/est/io/concatenated.py | 8 ++++++--
1 file changed, 6 insertions(+), 2 deletions(-)
diff --git a/src/est/io/concatenated.py b/src/est/io/concatenated.py
index 21db1cb8..156f9bac 100644
--- a/src/est/io/concatenated.py
+++ b/src/est/io/concatenated.py
@@ -4,6 +4,7 @@ from typing import Tuple, Dict, Any
import pint
import numpy
+import numpy.ma
from est import settings
from est.io.information import InputInformation
@@ -40,7 +41,7 @@ def read_concatenated_xas(
if information.skip_concatenated_n_spectra:
ramp_slices = ramp_slices[information.skip_concatenated_n_spectra :]
- interpolated_spectra = numpy.zeros(
+ interpolated_spectra = numpy.ma.masked_all(
(len(energy), len(ramp_slices), 1), dtype=raw_spectra.dtype
)
for i, ramp_slice in enumerate(ramp_slices):
@@ -49,12 +50,15 @@ def read_concatenated_xas(
if information.skip_concatenated_n_points:
raw_spectrum_i[: information.skip_concatenated_n_points] = numpy.nan
raw_spectrum_i[-information.skip_concatenated_n_points :] = numpy.nan
- interpolated_spectra[:, i, 0] = numpy.interp(
+ spectrum_i = numpy.interp(
energy,
raw_energy_i,
raw_spectrum_i,
left=numpy.nan,
right=numpy.nan,
)
+ interpolated_spectra[:, i, 0] = numpy.ma.masked_array(
+ spectrum_i, mask=~numpy.isfinite(spectrum_i)
+ )
return interpolated_spectra, energy * information.energy_unit, config
--
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