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Handle NaNs in magnetic_field/temp for hdf data

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Fix #58
This commit is contained in:
usov_i 2023-09-29 17:17:14 +02:00
parent a1c1de4adf
commit eae8a1bde4
1 changed files with 6 additions and 0 deletions
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6
pyzebra/h5.py
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@ -147,11 +147,17 @@ def read_detector_data(filepath, cami_meta=None):
# optional parameters # optional parameters
if "/entry1/sample/magnetic_field" in h5f: if "/entry1/sample/magnetic_field" in h5f:
scan["mf"] = h5f["/entry1/sample/magnetic_field"][:] 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: if "/entry1/sample/temperature" in h5f:
scan["temp"] = h5f["/entry1/sample/temperature"][:] scan["temp"] = h5f["/entry1/sample/temperature"][:]
elif "/entry1/sample/Ts/value" in h5f: elif "/entry1/sample/Ts/value" in h5f:
scan["temp"] = h5f["/entry1/sample/Ts/value"][:] 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 # overwrite metadata from .cami
if cami_meta is not None: if cami_meta is not None: