Merge branch 'det1d' of https://github.com/paulscherrerinstitute/pyzebra into det1d
This commit is contained in:
commit
01ac35f93d
@ -1,6 +1,73 @@
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import numpy as np
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import uncertainties as u
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from fitvol2 import create_uncertanities
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import matplotlib.pyplot as plt
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def add_dict(dict1, dict2):
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"""adds two dictionaries, meta of the new is saved as meata+original_filename and
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measurements are shifted to continue with numbering of first dict
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:arg dict1 : dictionarry to add to
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:arg dict2 : dictionarry from which to take the measurements
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:return dict1 : combined dictionary
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Note: dict1 must be made from ccl, otherwise we would have to change the structure of loaded
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dat file"""
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max_measurement_dict1 = max([int(str(keys)[1:]) for keys in dict1["Measurements"]])
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if dict2['meta']['data_type'] == '.ccl':
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new_filenames = ['M' + str(x + max_measurement_dict1) for x in
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[int(str(keys)[1:]) for keys in dict2["Measurements"]]]
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new_meta_name = 'meta' + str(dict2["meta"]['original_filename'])
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if new_meta_name not in dict1:
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for keys, name in zip(dict2["Measurements"], new_filenames):
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dict2["Measurements"][keys]['file_of_origin'] = str(dict2["meta"]['original_filename'])
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dict1["Measurements"][name] = dict2["Measurements"][keys]
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dict1[new_meta_name] = dict2["meta"]
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else:
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raise KeyError(str('The file %s has alredy been added to %s' % (dict2["meta"][
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'original_filename'],
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dict1["meta"][
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'original_filename'])))
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elif dict2['meta']['data_type'] == '.dat':
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d = {}
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new_name = 'M' + str(max_measurement_dict1+1)
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hkl = dict2['meta']['title']
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d['h_index'] = float(hkl.split()[-3])
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d['k_index'] = float(hkl.split()[-2])
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d['l_index'] = float(hkl.split()[-1])
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d['number_of_measurements'] = len(dict2['Measurements']['NP'])
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d['om'] = dict2['Measurements']['om']
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d['Counts'] = dict2['Measurements']['Counts']
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d['monitor'] = dict2['Measurements']['Monitor1'][0]
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d['temperature'] = dict2['meta']['temp']
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d['mag_field'] = dict2['meta']['mf']
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d['omega_angle'] = dict2['meta']['omega']
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dict1["Measurements"][new_name] = d
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print(hkl.split())
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for keys in d:
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print(keys)
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print('s')
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return dict1
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def auto(dict):
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"""takes just unique tuples from all tuples in dictionary returend by scan_dict
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intendet for automatic merge if you doesent want to specify what scans to merge together
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args: dict - dictionary from scan_dict function
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:return dict - dict without repetitions"""
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for keys in dict:
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tuple_list = dict[keys]
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new = list()
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for i in range(len(tuple_list)):
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if tuple_list[0][0] == tuple_list[i][0]:
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new.append(tuple_list[i])
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dict[keys] = new
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return dict
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def scan_dict(dict):
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@ -9,8 +76,8 @@ def scan_dict(dict):
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:return dictionary with matching scans, if there are none, the dict is empty
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note: can be checked by "not d", true if empty
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"""
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d = {}
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dupl = 0
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for i in dict["Measurements"]:
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for j in dict["Measurements"]:
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if dict["Measurements"][str(i)] != dict["Measurements"][str(j)]:
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@ -27,48 +94,49 @@ def scan_dict(dict):
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if itup != jtup:
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pass
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else:
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if str(itup) not in d:
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d[str(itup)] = (i, j)
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d[str(itup)] = list()
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d[str(itup)].append((i, j))
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else:
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dupl = dupl + 1
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d[str(itup) + "_" + str(dupl)] = (i, j)
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d[str(itup)].append((i, j))
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else:
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continue
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return d
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def compare_hkl(dict1, dict2):
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"""Compares two dictionaries based on hkl indexes and return dictionary with str(h k l) as
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"""Compares two dictionaries based on hkl indexes and return dictionary with str(h k l) as
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key and tuple with keys to same measurement in dict1 and dict2
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:arg dict1 : first dictionary
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:arg dict2 : second dictionary
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:return d : dict with matches
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example of one key: '0.0 0.0 -1.0 : ('M1', 'M9')' meaning that 001 hkl measurement is M1 in
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example of one key: '0.0 0.0 -1.0 : ('M1', 'M9')' meaning that 001 hkl measurement is M1 in
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first dict and M9 in second"""
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d = {}
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dupl = 0
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for keys in dict1["Measurements"]:
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for key in dict2["Measurements"]:
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if (
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dict1["Measurements"][str(keys)]["h_index"]
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== dict2["Measurements"][str(key)]["h_index"]
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and dict1["Measurements"][str(keys)]["k_index"]
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== dict2["Measurements"][str(key)]["k_index"]
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and dict1["Measurements"][str(keys)]["l_index"]
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== dict2["Measurements"][str(key)]["l_index"]
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dict1["Measurements"][str(keys)]["h_index"]
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== dict2["Measurements"][str(key)]["h_index"]
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and dict1["Measurements"][str(keys)]["k_index"]
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== dict2["Measurements"][str(key)]["k_index"]
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and dict1["Measurements"][str(keys)]["l_index"]
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== dict2["Measurements"][str(key)]["l_index"]
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):
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if (
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str(
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(
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str(dict1["Measurements"][str(keys)]["h_index"])
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+ " "
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+ str(dict1["Measurements"][str(keys)]["k_index"])
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+ " "
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+ str(dict1["Measurements"][str(keys)]["l_index"])
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str(
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(
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str(dict1["Measurements"][str(keys)]["h_index"])
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+ " "
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+ str(dict1["Measurements"][str(keys)]["k_index"])
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+ " "
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+ str(dict1["Measurements"][str(keys)]["l_index"])
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)
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)
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)
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not in d
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not in d
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):
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d[
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str(
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@ -103,7 +171,7 @@ def create_tuples(x, y, y_err):
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Counts need to be normalized to monitor before"""
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t = list()
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for i in range(len(x)):
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tup = (x[i], y[i], y_err)
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tup = (x[i], y[i], y_err[i])
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t.append(tup)
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return t
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@ -149,7 +217,7 @@ def merge(dict1, dict2, keys, auto=True, monitor=100000):
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cor_y2, y_err2 = normalize(dict2, keys[1], monitor=monitor)
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# creates touples (om, Counts, sigma) for sorting and further processing
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tuple_list = create_tuples(x1, cor_y1, y_err1) + create_tuples(x2, cor_y2, y_err2)
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# Sort the list on om and add 0 0 0 tuple to the last postion
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# Sort the list on om and add 0 0 0 tuple to the last position
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sorted_t = sorted(tuple_list, key=lambda tup: tup[0])
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sorted_t.append((0, 0, 0))
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om, Counts, sigma = [], [], []
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@ -187,6 +255,7 @@ def merge(dict1, dict2, keys, auto=True, monitor=100000):
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dict1["Measurements"][keys[0]]["Counts"] = Counts
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dict1["Measurements"][keys[0]]["sigma"] = sigma
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dict1["Measurements"][keys[0]]["monitor"] = monitor
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print('merging done')
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return dict1
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@ -219,10 +288,17 @@ def substract_measurement(dict1, dict2, keys, auto=True, monitor=100000):
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for k in range(len(res)):
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res_nom = np.append(res_nom, res[k].n)
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res_err = np.append(res_err, res[k].s)
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if len([num for num in res_nom if num < 0]) >= 0.3*len(res_nom):
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# plt.plot(res_nom, 'r', label='final')
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# plt.plot(cor_y1, 'g', label='dict1')
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# plt.plot(cor_y2, 'b', label='dict2')
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# plt.legend()
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# plt.title(str(keys))
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# plt.show()
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if len([num for num in res_nom if num < 0]) >= 0.3 * len(res_nom):
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print(f'Warning! percentage of negative numbers in measurement subsracted {keys[0]} is '
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f'{len([num for num in res_nom if num < 0])/len(res_nom)}')
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f'{len([num for num in res_nom if num < 0]) / len(res_nom)}')
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dict1["Measurements"][str(keys[0])]["Counts"] = res_nom
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dict1["Measurements"][str(keys[0])]["sigma"] = res_err
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dict1["Measurements"][str(keys[0])]["monitor"] = monitor
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@ -243,7 +319,7 @@ def compare_dict(dict1, dict2):
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information of how many measurement differ and which ones differ
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:returns report_string string comparing all different values respecively of measurements"""
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if dict1["file_type"] != dict2["file_type"]:
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if dict1["meta"]["data_type"] != dict2["meta"]["data_type"]:
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print("select two dicts")
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return
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S = []
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@ -283,16 +359,19 @@ def compare_dict(dict1, dict2):
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for k in dict1["meta"]
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if k in dict2["meta"] and dict1["meta"][k] != dict2["meta"][k]
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}
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exlude_meta_set = ["original_filename", "date", "title"]
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for keys in different_meta:
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if keys not in conflicts:
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conflicts[keys] = 1
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if keys in exlude_meta_set:
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continue
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else:
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conflicts[keys] = conflicts[keys] + 1
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if keys not in conflicts:
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conflicts[keys] = 1
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else:
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conflicts[keys] = conflicts[keys] + 1
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S.append(" Different values in %s \n" % str(keys))
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S.append(" dict1: %s \n" % str(dict1["meta"][str(keys)]))
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S.append(" dict2: %s \n" % str(dict2["meta"][str(keys)]))
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S.append(" Different values in %s \n" % str(keys))
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S.append(" dict1: %s \n" % str(dict1["meta"][str(keys)]))
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S.append(" dict2: %s \n" % str(dict2["meta"][str(keys)]))
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# compare Measurements
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S.append(
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@ -305,80 +384,89 @@ def compare_dict(dict1, dict2):
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)
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S.append("Different values in Measurements:\n")
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select_set = ["om", "Counts", "sigma"]
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exlude_set = ["time", "Counts"]
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exlude_set = ["time", "Counts", "date", 'notes']
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for keys1 in comp:
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for key2 in dict1["Measurements"][str(comp[str(keys1)][0])]:
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if key2 in exlude_set:
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continue
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if key2 not in select_set:
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if (
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dict1["Measurements"][comp[str(keys1)][0]][str(key2)]
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!= dict2["Measurements"][str(comp[str(keys1)][0])][str(key2)]
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):
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S.append(
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"Measurement value "
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"%s"
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", with hkl %s differs in meausrements %s and %s \n"
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% (key2, keys1, comp[str(keys1)][0], comp[str(keys1)][1])
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)
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S.append(
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" dict1: %s \n"
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% str(dict1["Measurements"][comp[str(keys1)][0]][str(key2)])
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)
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S.append(
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" dict2: %s \n"
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% str(dict2["Measurements"][comp[str(keys1)][1]][str(key2)])
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)
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if key2 not in conflicts:
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conflicts[key2] = {}
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conflicts[key2]["amount"] = 1
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conflicts[key2]["measurements"] = str(comp[str(keys1)][0])
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else:
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conflicts[key2]["amount"] = conflicts[key2]["amount"] + 1
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conflicts[key2]["measurements"] = (
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conflicts[key2]["measurements"] + " " + (str(comp[str(keys1)][0]))
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try:
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if (
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dict1["Measurements"][comp[str(keys1)][0]][str(key2)]
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!= dict2["Measurements"][str(comp[str(keys1)][1])][str(key2)]
|
||||
):
|
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S.append(
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"Measurement value "
|
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"%s"
|
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", with hkl %s differs in meausrements %s and %s \n"
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% (key2, keys1, comp[str(keys1)][0], comp[str(keys1)][1])
|
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)
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S.append(
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" dict1: %s \n"
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% str(dict1["Measurements"][comp[str(keys1)][0]][str(key2)])
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)
|
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S.append(
|
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" dict2: %s \n"
|
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% str(dict2["Measurements"][comp[str(keys1)][1]][str(key2)])
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||||
)
|
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if key2 not in conflicts:
|
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conflicts[key2] = {}
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conflicts[key2]["amount"] = 1
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conflicts[key2]["measurements"] = str(comp[str(keys1)])
|
||||
else:
|
||||
|
||||
conflicts[key2]["amount"] = conflicts[key2]["amount"] + 1
|
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conflicts[key2]["measurements"] = (
|
||||
conflicts[key2]["measurements"] + " " + (str(comp[str(keys1)]))
|
||||
)
|
||||
except KeyError as e:
|
||||
print('Missing keys, some files were probably merged or substracted')
|
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print(e.args)
|
||||
|
||||
else:
|
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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])
|
||||
try:
|
||||
comparison = list(dict1["Measurements"][comp[str(keys1)][0]][str(key2)]) == list(
|
||||
dict2["Measurements"][comp[str(keys1)][1]][str(key2)]
|
||||
)
|
||||
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)][0])
|
||||
else:
|
||||
conflicts[key2]["amount"] = conflicts[key2]["amount"] + 1
|
||||
conflicts[key2]["measurements"] = (
|
||||
conflicts[key2]["measurements"] + " " + (str(comp[str(keys1)][1]))
|
||||
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(
|
||||
" 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:
|
||||
try:
|
||||
@ -390,27 +478,27 @@ def compare_dict(dict1, dict2):
|
||||
|
||||
|
||||
def guess_next(dict1, dict2, comp):
|
||||
"""iterates thorough the scans and tries to decide if the scans should be
|
||||
"""iterates thorough the scans and tries to decide if the scans should be
|
||||
substracted or merged"""
|
||||
threshold = 0.05
|
||||
for keys in comp:
|
||||
if (
|
||||
abs(
|
||||
(
|
||||
dict1["Measurements"][str(comp[keys][0])]["temperature"]
|
||||
- dict2["Measurements"][str(comp[keys][1])]["temperature"]
|
||||
abs(
|
||||
(
|
||||
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"]
|
||||
)
|
||||
< threshold
|
||||
and abs(
|
||||
(
|
||||
< threshold
|
||||
and abs(
|
||||
(
|
||||
dict1["Measurements"][str(comp[keys][0])]["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")
|
||||
else:
|
||||
|
||||
@ -142,6 +142,11 @@ def fitccl(
|
||||
# u.ufloat to work with uncertanities
|
||||
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
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user