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Overwrite metadata from .cami

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Fix #32, fix #31
This commit is contained in:
usov_i 2021-06-29 12:00:50 +02:00
parent 57e503fc3d
commit cf6527af13
2 changed files with 34 additions and 9 deletions
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5
pyzebra/app/panel_hdf_viewer.py
View File

@ -188,10 +188,7 @@ def create():
# skip unnecessary update caused by selection drop
return
det_data = pyzebra.read_detector_data(new[0])
if cami_meta and "crystal" in cami_meta:
det_data["ub"] = cami_meta["crystal"]["UB"]
det_data = pyzebra.read_detector_data(new[0], cami_meta)
index_spinner.value = 0
index_spinner.high = det_data["data"].shape[0] - 1

38
pyzebra/h5.py
View File

@ -3,6 +3,7 @@ import numpy as np
META_MATRIX = ("UB")
META_CELL = ("cell")
META_STR = ("name")
def read_h5meta(filepath):
@ -43,19 +44,21 @@ def parse_h5meta(file):
value = value.strip()
if variable in META_STR:
content[section][variable] = value
pass
elif variable in META_CELL:
value = np.array(value.split(",")[:6], dtype=np.float)
elif variable in META_MATRIX:
ub_matrix = np.array(value.split(",")[:9], dtype=np.float).reshape(3, 3)
content[section][variable] = ub_matrix
value = np.array(value.split(",")[:9], dtype=np.float).reshape(3, 3)
else: # default is a single float number
content[section][variable] = float(value)
value = float(value)
content[section][variable] = value
else:
content[section].append(line)
return content
def read_detector_data(filepath):
def read_detector_data(filepath, cami_meta=None):
"""Read detector data and angles from an h5 file.
Args:
@ -78,6 +81,11 @@ def read_detector_data(filepath):
else:
det_data["zebra_mode"] = "nb"
# overwrite zebra_mode from cami
if cami_meta is not None:
if "zebra_mode" in cami_meta:
det_data["zebra_mode"] = cami_meta["zebra_mode"][0]
# om, sometimes ph
if det_data["zebra_mode"] == "nb":
det_data["omega"] = h5f["/entry1/area_detector2/rotation_angle"][:]
@ -91,6 +99,8 @@ def read_detector_data(filepath):
det_data["chi"] = h5f["/entry1/sample/chi"][:] # ch
det_data["phi"] = h5f["/entry1/sample/phi"][:] # ph
det_data["ub"] = h5f["/entry1/sample/UB"][:].reshape(3, 3)
det_data["name"] = h5f["/entry1/sample/name"][0].decode()
det_data["cell"] = h5f["/entry1/sample/cell"][:]
for var in ("omega", "gamma", "nu", "chi", "phi"):
if abs(det_data[var][0] - det_data[var][-1]) > 0.1:
@ -106,4 +116,22 @@ def read_detector_data(filepath):
if "/entry1/sample/temperature" in h5f:
det_data["temp"] = h5f["/entry1/sample/temperature"][:]
# overwrite metadata from .cami
if cami_meta is not None:
if "crystal" in cami_meta:
cami_meta_crystal = cami_meta["crystal"]
if "name" in cami_meta_crystal:
det_data["name"] = cami_meta_crystal["name"]
if "UB" in cami_meta_crystal:
det_data["ub"] = cami_meta_crystal["UB"]
if "cell" in cami_meta_crystal:
det_data["cell"] = cami_meta_crystal["cell"]
if "lambda" in cami_meta_crystal:
det_data["wave"] = cami_meta_crystal["lambda"]
if "detector parameters" in cami_meta:
cami_meta_detparam = cami_meta["detector parameters"]
if "dist1" in cami_meta_detparam:
det_data["ddist"] = cami_meta_detparam["dist1"]
return det_data