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Update load_1D.py

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Added angles from meta to each scan, try except to try to get hkl from title
This commit is contained in:
JakHolzer 2020-10-21 14:46:03 +02:00 committed by GitHub
parent 31335b398b
commit f79553c1ba
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1 changed files with 53 additions and 72 deletions
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125
pyzebra/load_1D.py
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@ -57,40 +57,6 @@ META_VARS_FLOAT = (
)
META_UB_MATRIX = ("ub1j", "ub2j", "ub3j")
CCL_FIRST_LINE = (
# the first element is `measurement_number`, which we don't save to metadata
("h_index", float),
("k_index", float),
("l_index", float),
)
CCL_FIRST_LINE_BI = (
*CCL_FIRST_LINE,
("twotheta_angle", float),
("omega_angle", float),
("chi_angle", float),
("phi_angle", float),
)
CCL_FIRST_LINE_NB = (
*CCL_FIRST_LINE,
("gamma_angle", float),
("omega_angle", float),
("nu_angle", float),
("unkwn_angle", float),
)
CCL_SECOND_LINE = (
("number_of_measurements", int),
("angle_step", float),
("monitor", float),
("temperature", float),
("mag_field", float),
("date", str),
("time", str),
("scan_type", str),
)
def load_1D(filepath):
"""
@ -133,44 +99,51 @@ def parse_1D(fileobj, data_type):
measurements = {}
if data_type == ".ccl":
decimal = list()
if metadata["zebra_mode"] == "bi":
ccl_first_line = CCL_FIRST_LINE_BI
elif metadata["zebra_mode"] == "nb":
ccl_first_line = CCL_FIRST_LINE_NB
ccl_second_line = CCL_SECOND_LINE
for line in fileobj:
d = {}
# first line
measurement_number, *params = line.split()
for param, (param_name, param_type) in zip(params, ccl_first_line):
d[param_name] = param_type(param)
decimal.append(bool(Decimal(d["h_index"]) % 1 == 0))
decimal.append(bool(Decimal(d["k_index"]) % 1 == 0))
decimal.append(bool(Decimal(d["l_index"]) % 1 == 0))
# second line
next_line = next(fileobj)
params = next_line.split()
for param, (param_name, param_type) in zip(params, ccl_second_line):
d[param_name] = param_type(param)
d["om"] = np.linspace(
d["omega_angle"] - (d["number_of_measurements"] / 2) * d["angle_step"],
d["omega_angle"] + (d["number_of_measurements"] / 2) * d["angle_step"],
d["number_of_measurements"],
)
# subsequent lines with counts
counts = []
while len(counts) < d["number_of_measurements"]:
counts.extend(map(int, next(fileobj).split()))
d["Counts"] = counts
measurement_number = int(line.split()[0])
d = {}
d["h_index"] = float(line.split()[1])
decimal.append(bool(Decimal(d["h_index"]) % 1 == 0))
d["k_index"] = float(line.split()[2])
decimal.append(bool(Decimal(d["k_index"]) % 1 == 0))
d["l_index"] = float(line.split()[3])
decimal.append(bool(Decimal(d["l_index"]) % 1 == 0))
if metadata["zebra_mode"] == "bi":
d["twotheta_angle"] = float(line.split()[4]) # gamma
d["omega_angle"] = float(line.split()[5]) # omega
d["chi_angle"] = float(line.split()[6]) # nu
d["phi_angle"] = float(line.split()[7]) # doesnt matter
elif metadata["zebra_mode"] == "nb":
d["gamma_angle"] = float(line.split()[4]) # gamma
d["omega_angle"] = float(line.split()[5]) # omega
d["nu_angle"] = float(line.split()[6]) # nu
d["unkwn_angle"] = float(line.split()[7])
measurements[int(measurement_number)] = d
next_line = next(fileobj)
d["number_of_measurements"] = int(next_line.split()[0])
d["angle_step"] = float(next_line.split()[1])
d["monitor"] = float(next_line.split()[2])
d["temperature"] = float(next_line.split()[3])
d["mag_field"] = float(next_line.split()[4])
d["date"] = str(next_line.split()[5])
d["time"] = str(next_line.split()[6])
d["scan_type"] = str(next_line.split()[7])
for i in range(
int(int(next_line.split()[0]) / 10) + (int(next_line.split()[0]) % 10 > 0)
):
fileline = next(fileobj).split()
numbers = [int(w) for w in fileline]
counts = counts + numbers
d["om"] = np.linspace(
float(line.split()[5])
- (int(next_line.split()[0]) / 2) * float(next_line.split()[1]),
float(line.split()[5])
+ (int(next_line.split()[0]) / 2) * float(next_line.split()[1]),
int(next_line.split()[0]),
)
d["Counts"] = counts
measurements[measurement_number] = d
if all(decimal):
metadata["indices"] = "hkl"
@ -192,15 +165,23 @@ def parse_1D(fileobj, data_type):
for name, val in zip(col_names, line.split()):
data_cols[name].append(float(val))
data_cols['h_index'] = float(metadata['title'].split()[-3])
data_cols['k_index'] = float(metadata['title'].split()[-2])
data_cols['l_index'] = float(metadata['title'].split()[-1])
try:
data_cols['h_index'] = float(metadata['title'].split()[-3])
data_cols['k_index'] = float(metadata['title'].split()[-2])
data_cols['l_index'] = float(metadata['title'].split()[-1])
except (ValueError, IndexError):
print("seems hkl is not in title")
data_cols['temperature'] = metadata['temp']
data_cols['mag_field'] = metadata['mf']
data_cols['omega_angle'] = metadata['omega']
data_cols['number_of_measurements'] = len(data_cols['om'])
data_cols['monitor'] = data_cols['Monitor1'][0]
measurements[1] = dict(data_cols)
# add angles to scan from meta
data_cols["twotheta_angle"] = metadata['2-theta']
data_cols["chi_angle"] = metadata['chi']
data_cols["phi_angle"] = metadata['phi']
data_cols["nu_angle"] = metadata['nu']
else:
print("Unknown file extention")