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modified scan_reader
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@bingli621
bingli621 committed Sep 3, 2024
1 parent fb5273d commit 9891e0b
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171 changes: 85 additions & 86 deletions src/tavi/data/scan_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -124,120 +124,119 @@ class ScanData(NamedTuple):
persistent_field: Optional[tuple[float, ...]] = None


def get_string(nexus_entry, entry_string):
try:
return str(nexus_entry[entry_string].asstr()[...])
except KeyError:
return None

def nexus_entry_to_scan(nexus_entry):

def get_data(nexus_entry, entry_string):
try:
return nexus_entry[entry_string][...]
except KeyError:
return None
def get_string(entry_string):
try:
return str(nexus_entry[entry_string].asstr()[...])
except KeyError:
return None

def get_data(entry_string):
try:
return nexus_entry[entry_string][...]
except KeyError:
return None

def nexus_entry_to_scan(nexus_entry):
scan_name = nexus_entry.filename.split("/")[-1] # e.g. "scan0001"
scan_info = ScanInfo(
scan_num=int(scan_name[4:-3]),
start_time=get_string(nexus_entry, "start_time"),
end_time=get_string(nexus_entry, "end_time"),
scan_title=get_string(nexus_entry, "title"),
start_time=get_string("start_time"),
end_time=get_string("end_time"),
scan_title=get_string("title"),
# preset_type="normal",
preset_channel=get_string(nexus_entry, "monitor/mode"),
preset_channel=get_string("monitor/mode"),
preset_value=float(nexus_entry["monitor/preset"][...]),
def_y=nexus_entry["data"].attrs["signal"],
def_x=nexus_entry["data"].attrs["axes"],
)
sample_ub_info = SampleUBInfo(
sample_name=get_string(nexus_entry, "sample/name"),
lattice_constants=np.array(get_data(nexus_entry, "sample/unit_cell")),
ub_matrix=np.array(get_data(nexus_entry, "sample/orientation_matrix")).reshape(3, 3),
sample_name=get_string("sample/name"),
lattice_constants=np.array(get_data("sample/unit_cell")),
ub_matrix=np.array(get_data("sample/orientation_matrix")).reshape(3, 3),
# ub_mode=0,
# angle_mode=0,
plane_normal=get_data(nexus_entry, "sample/plane_normal"),
plane_normal=get_data("sample/plane_normal"),
# in_plane_ref=None,
ubconf=get_string(nexus_entry, "sample/ub_conf"),
ubconf=get_string("sample/ub_conf"),
)
instrument_info = InstrumentInfo()

scan_data = ScanData(
detector=get_data(nexus_entry, "instrument/detector/data"),
detector=get_data("instrument/detector/data"),
# monitor
time=get_data(nexus_entry, "monitor/time"),
monitor=get_data(nexus_entry, "monitor/monitor"),
mcu=get_data(nexus_entry, "monitor/mcu"),
time=get_data("monitor/time"),
monitor=get_data("monitor/monitor"),
mcu=get_data("monitor/mcu"),
# monochromator
m1=get_data(nexus_entry, "instrument/monochromator/m1"),
m2=get_data(nexus_entry, "instrument/monochromator/m2"),
ei=get_data(nexus_entry, "instrument/monochromator/ei"),
focal_length=get_data(nexus_entry, "instrument/monochromator/focal_length"),
mfocus=get_data(nexus_entry, "instrument/monochromator/mfocus"),
marc=get_data(nexus_entry, "instrument/monochromator/marc"),
mtrans=get_data(nexus_entry, "instrument/monochromator/mtrans"),
m1=get_data("instrument/monochromator/m1"),
m2=get_data("instrument/monochromator/m2"),
ei=get_data("instrument/monochromator/ei"),
focal_length=get_data("instrument/monochromator/focal_length"),
mfocus=get_data("instrument/monochromator/mfocus"),
marc=get_data("instrument/monochromator/marc"),
mtrans=get_data("instrument/monochromator/mtrans"),
# analyzer
ef=get_data(nexus_entry, "instrument/analyser/ef"),
a1=get_data(nexus_entry, "instrument/analyser/a1"),
a2=get_data(nexus_entry, "instrument/analyser/a2"),
afocus=get_data(nexus_entry, "instrument/analyser/afocus"),
ef=get_data("instrument/analyser/ef"),
a1=get_data("instrument/analyser/a1"),
a2=get_data("instrument/analyser/a2"),
afocus=get_data("instrument/analyser/afocus"),
# ctax double-focused analyzer
qm=np.array([get_data(nexus_entry, f"instrument/analyser/qm{i}") for i in range(1, 9, 1)]),
xm=np.array([get_data(nexus_entry, f"instrument/analyser/xm{i}") for i in range(1, 9, 1)]),
qm=np.array([get_data(f"instrument/analyser/qm{i}") for i in range(1, 9, 1)]),
xm=np.array([get_data(f"instrument/analyser/xm{i}") for i in range(1, 9, 1)]),
# goiometer motor angles
s1=get_data(nexus_entry, "sample/s1"),
s2=get_data(nexus_entry, "sample/s2"),
sgl=get_data(nexus_entry, "sample/sgl"),
sgu=get_data(nexus_entry, "sample/sgu"),
stl=get_data(nexus_entry, "sample/stl"),
stu=get_data(nexus_entry, "sample/stu"),
chi=get_data(nexus_entry, "sample/chi"),
phi=get_data(nexus_entry, "sample/phi"),
s1=get_data("sample/s1"),
s2=get_data("sample/s2"),
sgl=get_data("sample/sgl"),
sgu=get_data("sample/sgu"),
stl=get_data("sample/stl"),
stu=get_data("sample/stu"),
chi=get_data("sample/chi"),
phi=get_data("sample/phi"),
# slits
bat=get_data(nexus_entry, "instrument/slit/bat"),
bab=get_data(nexus_entry, "instrument/slit/bab"),
bal=get_data(nexus_entry, "instrument/slit/bal"),
bar=get_data(nexus_entry, "instrument/slit/bar"),
bbt=get_data(nexus_entry, "instrument/slit/bbt"),
bbb=get_data(nexus_entry, "instrument/slit/bbb"),
bbl=get_data(nexus_entry, "instrument/slit/bbl"),
bbr=get_data(nexus_entry, "instrument/slit/bbr"),
slita_bt=get_data(nexus_entry, "instrument/slit/slita_bt"),
slita_tp=get_data(nexus_entry, "instrument/slit/slita_tp"),
slita_lf=get_data(nexus_entry, "instrument/slit/slita_lf"),
slita_rt=get_data(nexus_entry, "instrument/slit/slita_rt"),
slitb_bt=get_data(nexus_entry, "instrument/slit/slitb_bt"),
slitb_tp=get_data(nexus_entry, "instrument/slit/slitb_tp"),
slitb_lf=get_data(nexus_entry, "instrument/slit/slitb_lf"),
slitb_rt=get_data(nexus_entry, "instrument/slit/slitb_rt"),
slit_pre_bt=get_data(nexus_entry, "instrument/slit/slit_pre_bt"),
slit_pre_tp=get_data(nexus_entry, "instrument/slit/slit_pre_tp"),
slit_pre_lf=get_data(nexus_entry, "instrument/slit/slit_pre_lf"),
slit_pre_rt=get_data(nexus_entry, "instrument/slit/slit_pre_rt"),
bat=get_data("instrument/slit/bat"),
bab=get_data("instrument/slit/bab"),
bal=get_data("instrument/slit/bal"),
bar=get_data("instrument/slit/bar"),
bbt=get_data("instrument/slit/bbt"),
bbb=get_data("instrument/slit/bbb"),
bbl=get_data("instrument/slit/bbl"),
bbr=get_data("instrument/slit/bbr"),
slita_bt=get_data("instrument/slit/slita_bt"),
slita_tp=get_data("instrument/slit/slita_tp"),
slita_lf=get_data("instrument/slit/slita_lf"),
slita_rt=get_data("instrument/slit/slita_rt"),
slitb_bt=get_data("instrument/slit/slitb_bt"),
slitb_tp=get_data("instrument/slit/slitb_tp"),
slitb_lf=get_data("instrument/slit/slitb_lf"),
slitb_rt=get_data("instrument/slit/slitb_rt"),
slit_pre_bt=get_data("instrument/slit/slit_pre_bt"),
slit_pre_tp=get_data("instrument/slit/slit_pre_tp"),
slit_pre_lf=get_data("instrument/slit/slit_pre_lf"),
slit_pre_rt=get_data("instrument/slit/slit_pre_rt"),
# Q-E space
q=get_data(nexus_entry, "sample/q"),
qh=get_data(nexus_entry, "sample/qh"),
qk=get_data(nexus_entry, "sample/qk"),
ql=get_data(nexus_entry, "sample/ql"),
en=get_data(nexus_entry, "sample/en"),
q=get_data("sample/q"),
qh=get_data("sample/qh"),
qk=get_data("sample/qk"),
ql=get_data("sample/ql"),
en=get_data("sample/en"),
# temperature
temp=get_data(nexus_entry, "sample/temp"),
temp_a=get_data(nexus_entry, "sample/temp_a"),
temp_2=get_data(nexus_entry, "sample/temp_2"),
coldtip=get_data(nexus_entry, "sample/coldtip"),
tsample=get_data(nexus_entry, "sample/tsample"),
sample=get_data(nexus_entry, "sample/sample"),
vti=get_data(nexus_entry, "sample/vti"),
dr_tsample=get_data(nexus_entry, "sample/dr_tsample"),
dr_temp=get_data(nexus_entry, "sample/dr_temp"),
lt=get_data(nexus_entry, "sample/lt"),
ht=get_data(nexus_entry, "sample/ht"),
sorb_temp=get_data(nexus_entry, "sample/sorb_temp"),
sorb=get_data(nexus_entry, "sample/sorb"),
sample_ht=get_data(nexus_entry, "sample/sample_ht"),
temp=get_data("sample/temp"),
temp_a=get_data("sample/temp_a"),
temp_2=get_data("sample/temp_2"),
coldtip=get_data("sample/coldtip"),
tsample=get_data("sample/tsample"),
sample=get_data("sample/sample"),
vti=get_data("sample/vti"),
dr_tsample=get_data("sample/dr_tsample"),
dr_temp=get_data("sample/dr_temp"),
lt=get_data("sample/lt"),
ht=get_data("sample/ht"),
sorb_temp=get_data("sample/sorb_temp"),
sorb=get_data("sample/sorb"),
sample_ht=get_data("sample/sample_ht"),
# field
persistent_field=get_data(nexus_entry, "sample/persistent_field"),
persistent_field=get_data("sample/persistent_field"),
)

return (scan_info, sample_ub_info, instrument_info, scan_data)
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