From eae8a1bde4f05229edaae6bcc6694ae775a8948e Mon Sep 17 00:00:00 2001
From: Ivan Usov <ivan.usov@psi.ch>
Date: Fri, 29 Sep 2023 17:17:14 +0200
Subject: [PATCH] Handle NaNs in magnetic_field/temp for hdf data
Fix #58
---
pyzebra/h5.py | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/pyzebra/h5.py b/pyzebra/h5.py
index 743ab97..394f3c5 100644
--- a/pyzebra/h5.py
+++ b/pyzebra/h5.py
@@ -147,11 +147,17 @@ def read_detector_data(filepath, cami_meta=None):
# optional parameters
if "/entry1/sample/magnetic_field" in h5f:
scan["mf"] = h5f["/entry1/sample/magnetic_field"][:]
+ # TODO: NaNs are not JSON compliant, so replace them with None
+ # this is not a great solution, but makes it safe to use the array in bokeh
+ scan["mf"] = np.where(np.isnan(scan["mf"]), None, scan["mf"])
if "/entry1/sample/temperature" in h5f:
scan["temp"] = h5f["/entry1/sample/temperature"][:]
elif "/entry1/sample/Ts/value" in h5f:
scan["temp"] = h5f["/entry1/sample/Ts/value"][:]
+ # TODO: NaNs are not JSON compliant, so replace them with None
+ # this is not a great solution, but makes it safe to use the array in bokeh
+ scan["temp"] = np.where(np.isnan(scan["temp"]), None, scan["temp"])
# overwrite metadata from .cami
if cami_meta is not None:
--
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