Fix imports and apply formatter
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@ -5,3 +5,4 @@ from pyzebra.load_1D import load_1D, parse_1D
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from pyzebra.ccl_findpeaks import ccl_findpeaks
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from pyzebra.fit2 import fitccl
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from pyzebra.comm_export import export_comm
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import pyzebra.ccl_dict_operation
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@ -1,7 +1,6 @@
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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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from .fit2 import create_uncertanities
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def add_dict(dict1, dict2):
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@ -13,48 +12,52 @@ def add_dict(dict1, dict2):
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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 dict2["meta"]["data_type"] == ".ccl":
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new_filenames = [
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"M" + str(x + max_measurement_dict1)
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for x in [int(str(keys)[1:]) for keys in dict2["Measurements"]]
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]
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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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dict2["Measurements"][keys]["file_of_origin"] = str(
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dict2["meta"]["original_filename"]
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)
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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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raise KeyError(
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str(
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"The file %s has alredy been added to %s"
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% (dict2["meta"]["original_filename"], dict1["meta"]["original_filename"])
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)
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)
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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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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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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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@ -118,25 +121,25 @@ def compare_hkl(dict1, dict2):
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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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)
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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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not in d
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)
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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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@ -244,8 +247,10 @@ def merge(dict1, dict2, keys, auto=True, monitor=100000):
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if dict1 == dict2:
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del dict1["Measurements"][keys[1]]
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note = f'This measurement was merged with measurement {keys[1]} from ' \
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f'file {dict2["meta"]["original_filename"]} \n'
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note = (
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f"This measurement was merged with measurement {keys[1]} from "
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f'file {dict2["meta"]["original_filename"]} \n'
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)
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if "notes" not in dict1["Measurements"][str(keys[0])]:
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dict1["Measurements"][str(keys[0])]["notes"] = note
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else:
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@ -255,7 +260,7 @@ 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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print("merging done")
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return dict1
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@ -288,22 +293,20 @@ 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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# 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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print(
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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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)
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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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note = f'Measurement {keys[1]} from file {dict2["meta"]["original_filename"]} ' \
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f'was substracted from this measurement \n'
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note = (
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f'Measurement {keys[1]} from file {dict2["meta"]["original_filename"]} '
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f"was substracted from this measurement \n"
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)
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if "notes" not in dict1["Measurements"][str(keys[0])]:
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dict1["Measurements"][str(keys[0])]["notes"] = note
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else:
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@ -384,7 +387,7 @@ 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", "date", 'notes']
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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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@ -392,8 +395,8 @@ def compare_dict(dict1, dict2):
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if key2 not in select_set:
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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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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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):
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S.append(
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"Measurement value "
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@ -417,19 +420,19 @@ def compare_dict(dict1, dict2):
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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)]))
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conflicts[key2]["measurements"] + " " + (str(comp[str(keys1)]))
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)
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except KeyError as e:
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print('Missing keys, some files were probably merged or substracted')
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print("Missing keys, some files were probably merged or substracted")
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print(e.args)
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else:
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try:
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comparison = list(dict1["Measurements"][comp[str(keys1)][0]][str(key2)]) == list(
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dict2["Measurements"][comp[str(keys1)][1]][str(key2)]
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)
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comparison = list(
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dict1["Measurements"][comp[str(keys1)][0]][str(key2)]
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) == list(dict2["Measurements"][comp[str(keys1)][1]][str(key2)])
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if len(list(dict1["Measurements"][comp[str(keys1)][0]][str(key2)])) != len(
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list(dict2["Measurements"][comp[str(keys1)][1]][str(key2)])
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list(dict2["Measurements"][comp[str(keys1)][1]][str(key2)])
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):
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if str("different length of %s" % key2) not in warnings:
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warnings[str("different length of %s" % key2)] = list()
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@ -462,10 +465,10 @@ def compare_dict(dict1, dict2):
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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)]))
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conflicts[key2]["measurements"] + " " + (str(comp[str(keys1)]))
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)
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except KeyError as e:
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print('Missing keys, some files were probably merged or substracted')
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print("Missing keys, some files were probably merged or substracted")
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print(e.args)
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for keys in conflicts:
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@ -483,22 +486,22 @@ def guess_next(dict1, dict2, comp):
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threshold = 0.05
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for keys in comp:
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if (
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abs(
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(
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dict1["Measurements"][str(comp[keys][0])]["temperature"]
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- dict2["Measurements"][str(comp[keys][1])]["temperature"]
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)
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/ dict2["Measurements"][str(comp[keys][1])]["temperature"]
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abs(
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(
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dict1["Measurements"][str(comp[keys][0])]["temperature"]
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- dict2["Measurements"][str(comp[keys][1])]["temperature"]
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)
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< threshold
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and abs(
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(
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/ dict2["Measurements"][str(comp[keys][1])]["temperature"]
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)
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< threshold
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and abs(
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(
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dict1["Measurements"][str(comp[keys][0])]["mag_field"]
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- dict2["Measurements"][str(comp[keys][1])]["mag_field"]
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)
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/ dict2["Measurements"][str(comp[keys][1])]["mag_field"]
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)
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/ dict2["Measurements"][str(comp[keys][1])]["mag_field"]
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)
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< threshold
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< threshold
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):
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comp[keys] = comp[keys] + tuple("m")
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else:
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