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Merge branch 'det1d' of https://github.com/paulscherrerinstitute/pyzebra into det1d

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usov_i 2020-10-06 16:59:03 +02:00
commit 01ac35f93d
2 changed files with 205 additions and 112 deletions
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304
pyzebra/ccl_dict_operation.py
View File

@ -1,6 +1,73 @@
import numpy as np import numpy as np
import uncertainties as u import uncertainties as u
from fitvol2 import create_uncertanities 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): 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 :return dictionary with matching scans, if there are none, the dict is empty
note: can be checked by "not d", true if empty note: can be checked by "not d", true if empty
""" """
d = {} d = {}
dupl = 0
for i in dict["Measurements"]: for i in dict["Measurements"]:
for j in dict["Measurements"]: for j in dict["Measurements"]:
if dict["Measurements"][str(i)] != dict["Measurements"][str(j)]: if dict["Measurements"][str(i)] != dict["Measurements"][str(j)]:
@ -27,11 +94,12 @@ def scan_dict(dict):
if itup != jtup: if itup != jtup:
pass pass
else: else:
if str(itup) not in d: if str(itup) not in d:
d[str(itup)] = (i, j) d[str(itup)] = list()
d[str(itup)].append((i, j))
else: else:
dupl = dupl + 1 d[str(itup)].append((i, j))
d[str(itup) + "_" + str(dupl)] = (i, j)
else: else:
continue continue
return d return d
@ -50,25 +118,25 @@ def compare_hkl(dict1, dict2):
for keys in dict1["Measurements"]: for keys in dict1["Measurements"]:
for key in dict2["Measurements"]: for key in dict2["Measurements"]:
if ( if (
dict1["Measurements"][str(keys)]["h_index"] dict1["Measurements"][str(keys)]["h_index"]
== dict2["Measurements"][str(key)]["h_index"] == dict2["Measurements"][str(key)]["h_index"]
and dict1["Measurements"][str(keys)]["k_index"] and dict1["Measurements"][str(keys)]["k_index"]
== dict2["Measurements"][str(key)]["k_index"] == dict2["Measurements"][str(key)]["k_index"]
and dict1["Measurements"][str(keys)]["l_index"] and dict1["Measurements"][str(keys)]["l_index"]
== dict2["Measurements"][str(key)]["l_index"] == dict2["Measurements"][str(key)]["l_index"]
): ):
if ( if (
str( str(
( (
str(dict1["Measurements"][str(keys)]["h_index"]) str(dict1["Measurements"][str(keys)]["h_index"])
+ " " + " "
+ str(dict1["Measurements"][str(keys)]["k_index"]) + str(dict1["Measurements"][str(keys)]["k_index"])
+ " " + " "
+ str(dict1["Measurements"][str(keys)]["l_index"]) + str(dict1["Measurements"][str(keys)]["l_index"])
)
) )
) not in d
not in d
): ):
d[ d[
str( str(
@ -103,7 +171,7 @@ def create_tuples(x, y, y_err):
Counts need to be normalized to monitor before""" Counts need to be normalized to monitor before"""
t = list() t = list()
for i in range(len(x)): for i in range(len(x)):
tup = (x[i], y[i], y_err) tup = (x[i], y[i], y_err[i])
t.append(tup) t.append(tup)
return t 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) cor_y2, y_err2 = normalize(dict2, keys[1], monitor=monitor)
# creates touples (om, Counts, sigma) for sorting and further processing # 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) 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 = sorted(tuple_list, key=lambda tup: tup[0])
sorted_t.append((0, 0, 0)) sorted_t.append((0, 0, 0))
om, Counts, sigma = [], [], [] 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]]["Counts"] = Counts
dict1["Measurements"][keys[0]]["sigma"] = sigma dict1["Measurements"][keys[0]]["sigma"] = sigma
dict1["Measurements"][keys[0]]["monitor"] = monitor dict1["Measurements"][keys[0]]["monitor"] = monitor
print('merging done')
return dict1 return dict1
@ -219,10 +288,17 @@ def substract_measurement(dict1, dict2, keys, auto=True, monitor=100000):
for k in range(len(res)): for k in range(len(res)):
res_nom = np.append(res_nom, res[k].n) res_nom = np.append(res_nom, res[k].n)
res_err = np.append(res_err, res[k].s) 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): 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 ' 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)}') 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])]["Counts"] = res_nom
dict1["Measurements"][str(keys[0])]["sigma"] = res_err dict1["Measurements"][str(keys[0])]["sigma"] = res_err
dict1["Measurements"][str(keys[0])]["monitor"] = monitor 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 information of how many measurement differ and which ones differ
:returns report_string string comparing all different values respecively of measurements""" :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") print("select two dicts")
return return
S = [] S = []
@ -283,16 +359,19 @@ def compare_dict(dict1, dict2):
for k in dict1["meta"] for k in dict1["meta"]
if k in dict2["meta"] and dict1["meta"][k] != dict2["meta"][k] if k in dict2["meta"] and dict1["meta"][k] != dict2["meta"][k]
} }
exlude_meta_set = ["original_filename", "date", "title"]
for keys in different_meta: for keys in different_meta:
if keys not in conflicts: if keys in exlude_meta_set:
conflicts[keys] = 1 continue
else: else:
conflicts[keys] = conflicts[keys] + 1 if keys not in conflicts:
conflicts[keys] = 1
else:
conflicts[keys] = conflicts[keys] + 1
S.append(" Different values in %s \n" % str(keys)) S.append(" Different values in %s \n" % str(keys))
S.append(" dict1: %s \n" % str(dict1["meta"][str(keys)])) S.append(" dict1: %s \n" % str(dict1["meta"][str(keys)]))
S.append(" dict2: %s \n" % str(dict2["meta"][str(keys)])) S.append(" dict2: %s \n" % str(dict2["meta"][str(keys)]))
# compare Measurements # compare Measurements
S.append( S.append(
@ -305,80 +384,89 @@ def compare_dict(dict1, dict2):
) )
S.append("Different values in Measurements:\n") S.append("Different values in Measurements:\n")
select_set = ["om", "Counts", "sigma"] select_set = ["om", "Counts", "sigma"]
exlude_set = ["time", "Counts"] exlude_set = ["time", "Counts", "date", 'notes']
for keys1 in comp: for keys1 in comp:
for key2 in dict1["Measurements"][str(comp[str(keys1)][0])]: for key2 in dict1["Measurements"][str(comp[str(keys1)][0])]:
if key2 in exlude_set: if key2 in exlude_set:
continue continue
if key2 not in select_set: if key2 not in select_set:
if ( try:
dict1["Measurements"][comp[str(keys1)][0]][str(key2)] if (
!= dict2["Measurements"][str(comp[str(keys1)][0])][str(key2)] dict1["Measurements"][comp[str(keys1)][0]][str(key2)]
): != dict2["Measurements"][str(comp[str(keys1)][1])][str(key2)]
S.append( ):
"Measurement value " S.append(
"%s" "Measurement value "
", with hkl %s differs in meausrements %s and %s \n" "%s"
% (key2, keys1, comp[str(keys1)][0], comp[str(keys1)][1]) ", with hkl %s differs in meausrements %s and %s \n"
) % (key2, keys1, comp[str(keys1)][0], comp[str(keys1)][1])
S.append(
" dict1: %s \n"
% str(dict1["Measurements"][comp[str(keys1)][0]][str(key2)])
)
S.append(
" dict2: %s \n"
% str(dict2["Measurements"][comp[str(keys1)][1]][str(key2)])
)
if key2 not in conflicts:
conflicts[key2] = {}
conflicts[key2]["amount"] = 1
conflicts[key2]["measurements"] = str(comp[str(keys1)][0])
else:
conflicts[key2]["amount"] = conflicts[key2]["amount"] + 1
conflicts[key2]["measurements"] = (
conflicts[key2]["measurements"] + " " + (str(comp[str(keys1)][0]))
) )
S.append(
" dict1: %s \n"
% str(dict1["Measurements"][comp[str(keys1)][0]][str(key2)])
)
S.append(
" dict2: %s \n"
% str(dict2["Measurements"][comp[str(keys1)][1]][str(key2)])
)
if key2 not in conflicts:
conflicts[key2] = {}
conflicts[key2]["amount"] = 1
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)]))
)
except KeyError as e:
print('Missing keys, some files were probably merged or substracted')
print(e.args)
else: else:
comparison = list(dict1["Measurements"][comp[str(keys1)][0]][str(key2)]) == list( try:
dict2["Measurements"][comp[str(keys1)][1]][str(key2)] comparison = list(dict1["Measurements"][comp[str(keys1)][0]][str(key2)]) == list(
) dict2["Measurements"][comp[str(keys1)][1]][str(key2)]
if len(list(dict1["Measurements"][comp[str(keys1)][0]][str(key2)])) != len(
list(dict2["Measurements"][comp[str(keys1)][1]][str(key2)])
):
if str("different length of %s" % key2) not in warnings:
warnings[str("different length of %s" % key2)] = list()
warnings[str("different length of %s" % key2)].append(
(str(comp[keys1][0]), str(comp[keys1][1]))
)
else:
warnings[str("different length of %s" % key2)].append(
(str(comp[keys1][0]), str(comp[keys1][1]))
)
if not comparison:
S.append(
"Measurement value "
"%s"
" differs in measurement %s and %s \n"
% (key2, comp[str(keys1)][0], comp[str(keys1)][1])
) )
S.append( if len(list(dict1["Measurements"][comp[str(keys1)][0]][str(key2)])) != len(
" dict1: %s \n" list(dict2["Measurements"][comp[str(keys1)][1]][str(key2)])
% str(list(dict1["Measurements"][comp[str(keys1)][0]][str(key2)])) ):
) if str("different length of %s" % key2) not in warnings:
S.append( warnings[str("different length of %s" % key2)] = list()
" dict2: %s \n" warnings[str("different length of %s" % key2)].append(
% str(list(dict2["Measurements"][comp[str(keys1)][1]][str(key2)])) (str(comp[keys1][0]), str(comp[keys1][1]))
) )
if key2 not in conflicts: else:
conflicts[key2] = {} warnings[str("different length of %s" % key2)].append(
conflicts[key2]["amount"] = 1 (str(comp[keys1][0]), str(comp[keys1][1]))
conflicts[key2]["measurements"] = str(comp[str(keys1)][0]) )
else: if not comparison:
conflicts[key2]["amount"] = conflicts[key2]["amount"] + 1 S.append(
conflicts[key2]["measurements"] = ( "Measurement value "
conflicts[key2]["measurements"] + " " + (str(comp[str(keys1)][1])) "%s"
" differs in measurement %s and %s \n"
% (key2, comp[str(keys1)][0], comp[str(keys1)][1])
) )
S.append(
" dict1: %s \n"
% str(list(dict1["Measurements"][comp[str(keys1)][0]][str(key2)]))
)
S.append(
" dict2: %s \n"
% str(list(dict2["Measurements"][comp[str(keys1)][1]][str(key2)]))
)
if key2 not in conflicts:
conflicts[key2] = {}
conflicts[key2]["amount"] = 1
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)]))
)
except KeyError as e:
print('Missing keys, some files were probably merged or substracted')
print(e.args)
for keys in conflicts: for keys in conflicts:
try: try:
@ -395,22 +483,22 @@ def guess_next(dict1, dict2, comp):
threshold = 0.05 threshold = 0.05
for keys in comp: for keys in comp:
if ( if (
abs( abs(
( (
dict1["Measurements"][str(comp[keys][0])]["temperature"] dict1["Measurements"][str(comp[keys][0])]["temperature"]
- dict2["Measurements"][str(comp[keys][1])]["temperature"] - dict2["Measurements"][str(comp[keys][1])]["temperature"]
)
/ dict2["Measurements"][str(comp[keys][1])]["temperature"]
) )
/ dict2["Measurements"][str(comp[keys][1])]["temperature"] < threshold
) and abs(
< threshold (
and abs(
(
dict1["Measurements"][str(comp[keys][0])]["mag_field"] dict1["Measurements"][str(comp[keys][0])]["mag_field"]
- dict2["Measurements"][str(comp[keys][1])]["mag_field"] - dict2["Measurements"][str(comp[keys][1])]["mag_field"]
)
/ dict2["Measurements"][str(comp[keys][1])]["mag_field"]
) )
< threshold / dict2["Measurements"][str(comp[keys][1])]["mag_field"]
)
< threshold
): ):
comp[keys] = comp[keys] + tuple("m") comp[keys] = comp[keys] + tuple("m")
else: else:

5
pyzebra/fit2.py
View File

@ -143,6 +143,11 @@ def fitccl(
fit_area = u.ufloat(result.params["g_amp"].value, result.params["g_amp"].stderr) fit_area = u.ufloat(result.params["g_amp"].value, result.params["g_amp"].stderr)
comps = result.eval_components() 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: if len(meas["peak_indexes"]) == 0:
# for case of no peak, there is no reason to integrate, therefore fit and int are equal # for case of no peak, there is no reason to integrate, therefore fit and int are equal
int_area = fit_area int_area = fit_area