Merge branch 'det1d' of https://github.com/paulscherrerinstitute/pyzebra into det1d
This commit is contained in:
commit
01ac35f93d
@ -1,6 +1,73 @@
|
||||
import numpy as np
|
||||
import uncertainties as u
|
||||
from fitvol2 import create_uncertanities
|
||||
import matplotlib.pyplot as plt
|
||||
|
||||
|
||||
def add_dict(dict1, dict2):
|
||||
"""adds two dictionaries, meta of the new is saved as meata+original_filename and
|
||||
measurements are shifted to continue with numbering of first dict
|
||||
:arg dict1 : dictionarry to add to
|
||||
:arg dict2 : dictionarry from which to take the measurements
|
||||
:return dict1 : combined dictionary
|
||||
Note: dict1 must be made from ccl, otherwise we would have to change the structure of loaded
|
||||
dat file"""
|
||||
max_measurement_dict1 = max([int(str(keys)[1:]) for keys in dict1["Measurements"]])
|
||||
if dict2['meta']['data_type'] == '.ccl':
|
||||
new_filenames = ['M' + str(x + max_measurement_dict1) for x in
|
||||
[int(str(keys)[1:]) for keys in dict2["Measurements"]]]
|
||||
new_meta_name = 'meta' + str(dict2["meta"]['original_filename'])
|
||||
if new_meta_name not in dict1:
|
||||
for keys, name in zip(dict2["Measurements"], new_filenames):
|
||||
dict2["Measurements"][keys]['file_of_origin'] = str(dict2["meta"]['original_filename'])
|
||||
dict1["Measurements"][name] = dict2["Measurements"][keys]
|
||||
|
||||
dict1[new_meta_name] = dict2["meta"]
|
||||
|
||||
|
||||
else:
|
||||
raise KeyError(str('The file %s has alredy been added to %s' % (dict2["meta"][
|
||||
'original_filename'],
|
||||
dict1["meta"][
|
||||
'original_filename'])))
|
||||
elif dict2['meta']['data_type'] == '.dat':
|
||||
d = {}
|
||||
new_name = 'M' + str(max_measurement_dict1+1)
|
||||
hkl = dict2['meta']['title']
|
||||
d['h_index'] = float(hkl.split()[-3])
|
||||
d['k_index'] = float(hkl.split()[-2])
|
||||
d['l_index'] = float(hkl.split()[-1])
|
||||
d['number_of_measurements'] = len(dict2['Measurements']['NP'])
|
||||
d['om'] = dict2['Measurements']['om']
|
||||
d['Counts'] = dict2['Measurements']['Counts']
|
||||
d['monitor'] = dict2['Measurements']['Monitor1'][0]
|
||||
d['temperature'] = dict2['meta']['temp']
|
||||
d['mag_field'] = dict2['meta']['mf']
|
||||
d['omega_angle'] = dict2['meta']['omega']
|
||||
dict1["Measurements"][new_name] = d
|
||||
print(hkl.split())
|
||||
for keys in d:
|
||||
print(keys)
|
||||
|
||||
|
||||
|
||||
print('s')
|
||||
|
||||
return dict1
|
||||
|
||||
def auto(dict):
|
||||
"""takes just unique tuples from all tuples in dictionary returend by scan_dict
|
||||
intendet for automatic merge if you doesent want to specify what scans to merge together
|
||||
args: dict - dictionary from scan_dict function
|
||||
:return dict - dict without repetitions"""
|
||||
for keys in dict:
|
||||
tuple_list = dict[keys]
|
||||
new = list()
|
||||
for i in range(len(tuple_list)):
|
||||
if tuple_list[0][0] == tuple_list[i][0]:
|
||||
new.append(tuple_list[i])
|
||||
dict[keys] = new
|
||||
return dict
|
||||
|
||||
|
||||
def scan_dict(dict):
|
||||
@ -9,8 +76,8 @@ def scan_dict(dict):
|
||||
:return dictionary with matching scans, if there are none, the dict is empty
|
||||
note: can be checked by "not d", true if empty
|
||||
"""
|
||||
|
||||
d = {}
|
||||
dupl = 0
|
||||
for i in dict["Measurements"]:
|
||||
for j in dict["Measurements"]:
|
||||
if dict["Measurements"][str(i)] != dict["Measurements"][str(j)]:
|
||||
@ -27,11 +94,12 @@ def scan_dict(dict):
|
||||
if itup != jtup:
|
||||
pass
|
||||
else:
|
||||
|
||||
if str(itup) not in d:
|
||||
d[str(itup)] = (i, j)
|
||||
d[str(itup)] = list()
|
||||
d[str(itup)].append((i, j))
|
||||
else:
|
||||
dupl = dupl + 1
|
||||
d[str(itup) + "_" + str(dupl)] = (i, j)
|
||||
d[str(itup)].append((i, j))
|
||||
else:
|
||||
continue
|
||||
return d
|
||||
@ -103,7 +171,7 @@ def create_tuples(x, y, y_err):
|
||||
Counts need to be normalized to monitor before"""
|
||||
t = list()
|
||||
for i in range(len(x)):
|
||||
tup = (x[i], y[i], y_err)
|
||||
tup = (x[i], y[i], y_err[i])
|
||||
t.append(tup)
|
||||
return t
|
||||
|
||||
@ -149,7 +217,7 @@ def merge(dict1, dict2, keys, auto=True, monitor=100000):
|
||||
cor_y2, y_err2 = normalize(dict2, keys[1], monitor=monitor)
|
||||
# creates touples (om, Counts, sigma) for sorting and further processing
|
||||
tuple_list = create_tuples(x1, cor_y1, y_err1) + create_tuples(x2, cor_y2, y_err2)
|
||||
# Sort the list on om and add 0 0 0 tuple to the last postion
|
||||
# Sort the list on om and add 0 0 0 tuple to the last position
|
||||
sorted_t = sorted(tuple_list, key=lambda tup: tup[0])
|
||||
sorted_t.append((0, 0, 0))
|
||||
om, Counts, sigma = [], [], []
|
||||
@ -187,6 +255,7 @@ def merge(dict1, dict2, keys, auto=True, monitor=100000):
|
||||
dict1["Measurements"][keys[0]]["Counts"] = Counts
|
||||
dict1["Measurements"][keys[0]]["sigma"] = sigma
|
||||
dict1["Measurements"][keys[0]]["monitor"] = monitor
|
||||
print('merging done')
|
||||
return dict1
|
||||
|
||||
|
||||
@ -219,10 +288,17 @@ def substract_measurement(dict1, dict2, keys, auto=True, monitor=100000):
|
||||
for k in range(len(res)):
|
||||
res_nom = np.append(res_nom, res[k].n)
|
||||
res_err = np.append(res_err, res[k].s)
|
||||
# plt.plot(res_nom, 'r', label='final')
|
||||
# plt.plot(cor_y1, 'g', label='dict1')
|
||||
# plt.plot(cor_y2, 'b', label='dict2')
|
||||
# plt.legend()
|
||||
# plt.title(str(keys))
|
||||
# plt.show()
|
||||
|
||||
if len([num for num in res_nom if num < 0]) >= 0.3 * len(res_nom):
|
||||
print(f'Warning! percentage of negative numbers in measurement subsracted {keys[0]} is '
|
||||
f'{len([num for num in res_nom if num < 0]) / len(res_nom)}')
|
||||
|
||||
dict1["Measurements"][str(keys[0])]["Counts"] = res_nom
|
||||
dict1["Measurements"][str(keys[0])]["sigma"] = res_err
|
||||
dict1["Measurements"][str(keys[0])]["monitor"] = monitor
|
||||
@ -243,7 +319,7 @@ def compare_dict(dict1, dict2):
|
||||
information of how many measurement differ and which ones differ
|
||||
:returns report_string string comparing all different values respecively of measurements"""
|
||||
|
||||
if dict1["file_type"] != dict2["file_type"]:
|
||||
if dict1["meta"]["data_type"] != dict2["meta"]["data_type"]:
|
||||
print("select two dicts")
|
||||
return
|
||||
S = []
|
||||
@ -283,8 +359,11 @@ def compare_dict(dict1, dict2):
|
||||
for k in dict1["meta"]
|
||||
if k in dict2["meta"] and dict1["meta"][k] != dict2["meta"][k]
|
||||
}
|
||||
|
||||
exlude_meta_set = ["original_filename", "date", "title"]
|
||||
for keys in different_meta:
|
||||
if keys in exlude_meta_set:
|
||||
continue
|
||||
else:
|
||||
if keys not in conflicts:
|
||||
conflicts[keys] = 1
|
||||
else:
|
||||
@ -305,16 +384,16 @@ def compare_dict(dict1, dict2):
|
||||
)
|
||||
S.append("Different values in Measurements:\n")
|
||||
select_set = ["om", "Counts", "sigma"]
|
||||
exlude_set = ["time", "Counts"]
|
||||
|
||||
exlude_set = ["time", "Counts", "date", 'notes']
|
||||
for keys1 in comp:
|
||||
for key2 in dict1["Measurements"][str(comp[str(keys1)][0])]:
|
||||
if key2 in exlude_set:
|
||||
continue
|
||||
if key2 not in select_set:
|
||||
try:
|
||||
if (
|
||||
dict1["Measurements"][comp[str(keys1)][0]][str(key2)]
|
||||
!= dict2["Measurements"][str(comp[str(keys1)][0])][str(key2)]
|
||||
!= dict2["Measurements"][str(comp[str(keys1)][1])][str(key2)]
|
||||
):
|
||||
S.append(
|
||||
"Measurement value "
|
||||
@ -333,13 +412,19 @@ def compare_dict(dict1, dict2):
|
||||
if key2 not in conflicts:
|
||||
conflicts[key2] = {}
|
||||
conflicts[key2]["amount"] = 1
|
||||
conflicts[key2]["measurements"] = str(comp[str(keys1)][0])
|
||||
conflicts[key2]["measurements"] = str(comp[str(keys1)])
|
||||
else:
|
||||
|
||||
conflicts[key2]["amount"] = conflicts[key2]["amount"] + 1
|
||||
conflicts[key2]["measurements"] = (
|
||||
conflicts[key2]["measurements"] + " " + (str(comp[str(keys1)][0]))
|
||||
conflicts[key2]["measurements"] + " " + (str(comp[str(keys1)]))
|
||||
)
|
||||
except KeyError as e:
|
||||
print('Missing keys, some files were probably merged or substracted')
|
||||
print(e.args)
|
||||
|
||||
else:
|
||||
try:
|
||||
comparison = list(dict1["Measurements"][comp[str(keys1)][0]][str(key2)]) == list(
|
||||
dict2["Measurements"][comp[str(keys1)][1]][str(key2)]
|
||||
)
|
||||
@ -373,12 +458,15 @@ def compare_dict(dict1, dict2):
|
||||
if key2 not in conflicts:
|
||||
conflicts[key2] = {}
|
||||
conflicts[key2]["amount"] = 1
|
||||
conflicts[key2]["measurements"] = str(comp[str(keys1)][0])
|
||||
conflicts[key2]["measurements"] = str(comp[str(keys1)])
|
||||
else:
|
||||
conflicts[key2]["amount"] = conflicts[key2]["amount"] + 1
|
||||
conflicts[key2]["measurements"] = (
|
||||
conflicts[key2]["measurements"] + " " + (str(comp[str(keys1)][1]))
|
||||
conflicts[key2]["measurements"] + " " + (str(comp[str(keys1)]))
|
||||
)
|
||||
except KeyError as e:
|
||||
print('Missing keys, some files were probably merged or substracted')
|
||||
print(e.args)
|
||||
|
||||
for keys in conflicts:
|
||||
try:
|
||||
|
||||
@ -143,6 +143,11 @@ def fitccl(
|
||||
fit_area = u.ufloat(result.params["g_amp"].value, result.params["g_amp"].stderr)
|
||||
comps = result.eval_components()
|
||||
|
||||
if result.params["g_amp"].stderr is None:
|
||||
result.params["g_amp"].stderr = result.params["g_amp"].value
|
||||
elif result.params["g_amp"].stderr > result.params["g_amp"].value:
|
||||
result.params["g_amp"].stderr = result.params["g_amp"].value
|
||||
|
||||
if len(meas["peak_indexes"]) == 0:
|
||||
# for case of no peak, there is no reason to integrate, therefore fit and int are equal
|
||||
int_area = fit_area
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user