Remove ccl_dict_operations.py
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import pyzebra.ccl_dict_operation
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from pyzebra.anatric import *
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from pyzebra.anatric import *
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from pyzebra.ccl_findpeaks import ccl_findpeaks
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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.fit2 import fitccl
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@ -1,513 +0,0 @@
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import numpy as np
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import uncertainties as u
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from .fit2 import create_uncertanities
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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["scan"]])
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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["scan"]]
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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["scan"], new_filenames):
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dict2["scan"][keys]["file_of_origin"] = str(dict2["meta"]["original_filename"])
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dict1["scan"][name] = dict2["scan"][keys]
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dict1[new_meta_name] = dict2["meta"]
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else:
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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["scan"]["NP"])
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d["om"] = dict2["scan"]["om"]
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d["Counts"] = dict2["scan"]["Counts"]
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d["monitor"] = dict2["scan"]["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["scan"][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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"""scans dictionary for duplicate hkl indexes
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:arg dict : dictionary to scan
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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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for i in dict["scan"]:
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for j in dict["scan"]:
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if dict["scan"][str(i)] != dict["scan"][str(j)]:
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itup = (
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dict["scan"][str(i)]["h_index"],
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dict["scan"][str(i)]["k_index"],
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dict["scan"][str(i)]["l_index"],
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)
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jtup = (
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dict["scan"][str(j)]["h_index"],
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dict["scan"][str(j)]["k_index"],
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dict["scan"][str(j)]["l_index"],
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)
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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)] = list()
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d[str(itup)].append((i, j))
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else:
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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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key and tuple with keys to same scan 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 scan 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["scan"]:
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for key in dict2["scan"]:
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if (
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dict1["scan"][str(keys)]["h_index"] == dict2["scan"][str(key)]["h_index"]
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and dict1["scan"][str(keys)]["k_index"] == dict2["scan"][str(key)]["k_index"]
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and dict1["scan"][str(keys)]["l_index"] == dict2["scan"][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["scan"][str(keys)]["h_index"])
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+ " "
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+ str(dict1["scan"][str(keys)]["k_index"])
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+ " "
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+ str(dict1["scan"][str(keys)]["l_index"])
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)
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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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str(dict1["scan"][str(keys)]["h_index"])
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+ " "
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+ str(dict1["scan"][str(keys)]["k_index"])
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+ " "
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+ str(dict1["scan"][str(keys)]["l_index"])
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)
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] = (str(keys), str(key))
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else:
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dupl = dupl + 1
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d[
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str(
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str(dict1["scan"][str(keys)]["h_index"])
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+ " "
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+ str(dict1["scan"][str(keys)]["k_index"])
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+ " "
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+ str(dict1["scan"][str(keys)]["l_index"])
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+ "_dupl"
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+ str(dupl)
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)
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] = (str(keys), str(key))
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else:
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continue
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return d
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def create_tuples(x, y, y_err):
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"""creates tuples for sorting and merginng of the data
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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[i])
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t.append(tup)
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return t
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def normalize(dict, key, monitor):
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"""Normalizes the scan to monitor, checks if sigma exists, otherwise creates it
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:arg dict : dictionary to from which to tkae the scan
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:arg key : which scan to normalize from dict1
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:arg monitor : final monitor
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:return counts - normalized counts
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:return sigma - normalized sigma"""
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counts = np.array(dict["scan"][key]["Counts"])
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sigma = np.sqrt(counts) if "sigma" not in dict["scan"][key] else dict["scan"][key]["sigma"]
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monitor_ratio = monitor / dict["scan"][key]["monitor"]
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scaled_counts = counts * monitor_ratio
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scaled_sigma = np.array(sigma) * monitor_ratio
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return scaled_counts, scaled_sigma
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def merge(dict1, dict2, keys, auto=True, monitor=100000):
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"""merges the two tuples and sorts them, if om value is same, Counts value is average
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averaging is propagated into sigma if dict1 == dict2, key[1] is deleted after merging
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:arg dict1 : dictionary to which scan will be merged
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:arg dict2 : dictionary from which scan will be merged
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:arg keys : tuple with key to dict1 and dict2
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:arg auto : if true, when monitors are same, does not change it, if flase, takes monitor always
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:arg monitor : final monitor after merging
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note: dict1 and dict2 can be same dict
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:return dict1 with merged scan"""
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if auto:
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if dict1["scan"][keys[0]]["monitor"] == dict2["scan"][keys[1]]["monitor"]:
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monitor = dict1["scan"][keys[0]]["monitor"]
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# load om and Counts
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x1, x2 = dict1["scan"][keys[0]]["om"], dict2["scan"][keys[1]]["om"]
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cor_y1, y_err1 = normalize(dict1, keys[0], monitor=monitor)
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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 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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seen = list()
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for i in range(len(sorted_t) - 1):
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if sorted_t[i][0] not in seen:
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if sorted_t[i][0] != sorted_t[i + 1][0]:
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om = np.append(om, sorted_t[i][0])
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Counts = np.append(Counts, sorted_t[i][1])
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sigma = np.append(sigma, sorted_t[i][2])
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else:
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om = np.append(om, sorted_t[i][0])
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counts1, counts2 = sorted_t[i][1], sorted_t[i + 1][1]
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sigma1, sigma2 = sorted_t[i][2], sorted_t[i + 1][2]
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count_err1 = u.ufloat(counts1, sigma1)
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count_err2 = u.ufloat(counts2, sigma2)
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avg = (count_err1 + count_err2) / 2
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Counts = np.append(Counts, avg.n)
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sigma = np.append(sigma, avg.s)
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seen.append(sorted_t[i][0])
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else:
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continue
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if dict1 == dict2:
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del dict1["scan"][keys[1]]
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note = (
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f"This scan was merged with scan {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["scan"][str(keys[0])]:
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dict1["scan"][str(keys[0])]["notes"] = note
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else:
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dict1["scan"][str(keys[0])]["notes"] += note
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dict1["scan"][keys[0]]["om"] = om
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dict1["scan"][keys[0]]["Counts"] = Counts
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dict1["scan"][keys[0]]["sigma"] = sigma
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dict1["scan"][keys[0]]["monitor"] = monitor
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print("merging done")
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return dict1
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def substract_measurement(dict1, dict2, keys, auto=True, monitor=100000):
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"""Substracts two scan (scan key2 from dict2 from measurent key1 in dict1), expects om to be same
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:arg dict1 : dictionary to which scan will be merged
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:arg dict2 : dictionary from which scan will be merged
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:arg keys : tuple with key to dict1 and dict2
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:arg auto : if true, when monitors are same, does not change it, if flase, takes monitor always
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:arg monitor : final monitor after merging
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:returns d : dict1 with substracted Counts from dict2 and sigma that comes from the substraction"""
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if len(dict1["scan"][keys[0]]["om"]) != len(dict2["scan"][keys[1]]["om"]):
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raise ValueError("Omegas have different lengths, cannot be substracted")
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if auto:
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if dict1["scan"][keys[0]]["monitor"] == dict2["scan"][keys[1]]["monitor"]:
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monitor = dict1["scan"][keys[0]]["monitor"]
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cor_y1, y_err1 = normalize(dict1, keys[0], monitor=monitor)
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cor_y2, y_err2 = normalize(dict2, keys[1], monitor=monitor)
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dict1_count_err = create_uncertanities(cor_y1, y_err1)
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dict2_count_err = create_uncertanities(cor_y2, y_err2)
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res = np.subtract(dict1_count_err, dict2_count_err)
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res_nom = []
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res_err = []
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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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print(
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f"Warning! percentage of negative numbers in scan 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["scan"][str(keys[0])]["Counts"] = res_nom
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dict1["scan"][str(keys[0])]["sigma"] = res_err
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dict1["scan"][str(keys[0])]["monitor"] = monitor
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note = (
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f'Scan {keys[1]} from file {dict2["meta"]["original_filename"]} '
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f"was substracted from this scan \n"
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)
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if "notes" not in dict1["scan"][str(keys[0])]:
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dict1["scan"][str(keys[0])]["notes"] = note
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else:
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dict1["scan"][str(keys[0])]["notes"] += note
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return dict1
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def compare_dict(dict1, dict2):
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"""takes two ccl dictionaries and compare different values for each key
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:arg dict1 : dictionary 1 (ccl)
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:arg dict2 : dictionary 2 (ccl)
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:returns warning : dictionary with keys from primary files (if they differ) with
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information of how many scan 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["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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conflicts = {}
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warnings = {}
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comp = compare_hkl(dict1, dict2)
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d1 = scan_dict(dict1)
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d2 = scan_dict(dict2)
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if not d1:
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S.append("There are no duplicates in %s (dict1) \n" % dict1["meta"]["original_filename"])
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else:
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S.append(
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"There are %d duplicates in %s (dict1) \n"
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% (len(d1), dict1["meta"]["original_filename"])
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)
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warnings["Duplicates in dict1"] = list()
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for keys in d1:
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S.append("Measurements %s with hkl %s \n" % (d1[keys], keys))
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warnings["Duplicates in dict1"].append(d1[keys])
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if not d2:
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S.append("There are no duplicates in %s (dict2) \n" % dict2["meta"]["original_filename"])
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else:
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S.append(
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|
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"There are %d duplicates in %s (dict2) \n"
|
|
||||||
% (len(d2), dict2["meta"]["original_filename"])
|
|
||||||
)
|
|
||||||
warnings["Duplicates in dict2"] = list()
|
|
||||||
for keys in d2:
|
|
||||||
S.append("Measurements %s with hkl %s \n" % (d2[keys], keys))
|
|
||||||
warnings["Duplicates in dict2"].append(d2[keys])
|
|
||||||
|
|
||||||
# compare meta
|
|
||||||
S.append("Different values in meta: \n")
|
|
||||||
different_meta = {
|
|
||||||
k: dict1["meta"][k]
|
|
||||||
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:
|
|
||||||
conflicts[keys] = conflicts[keys] + 1
|
|
||||||
|
|
||||||
S.append(" Different values in %s \n" % str(keys))
|
|
||||||
S.append(" dict1: %s \n" % str(dict1["meta"][str(keys)]))
|
|
||||||
S.append(" dict2: %s \n" % str(dict2["meta"][str(keys)]))
|
|
||||||
|
|
||||||
# compare Measurements
|
|
||||||
S.append(
|
|
||||||
"Number of measurements in %s = %s \n"
|
|
||||||
% (dict1["meta"]["original_filename"], len(dict1["scan"]))
|
|
||||||
)
|
|
||||||
S.append(
|
|
||||||
"Number of measurements in %s = %s \n"
|
|
||||||
% (dict2["meta"]["original_filename"], len(dict2["scan"]))
|
|
||||||
)
|
|
||||||
S.append("Different values in Measurements:\n")
|
|
||||||
select_set = ["om", "Counts", "sigma"]
|
|
||||||
exlude_set = ["time", "Counts", "date", "notes"]
|
|
||||||
for keys1 in comp:
|
|
||||||
for key2 in dict1["scan"][str(comp[str(keys1)][0])]:
|
|
||||||
if key2 in exlude_set:
|
|
||||||
continue
|
|
||||||
if key2 not in select_set:
|
|
||||||
try:
|
|
||||||
if (
|
|
||||||
dict1["scan"][comp[str(keys1)][0]][str(key2)]
|
|
||||||
!= dict2["scan"][str(comp[str(keys1)][1])][str(key2)]
|
|
||||||
):
|
|
||||||
S.append(
|
|
||||||
"Scan value "
|
|
||||||
"%s"
|
|
||||||
", 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["scan"][comp[str(keys1)][0]][str(key2)])
|
|
||||||
)
|
|
||||||
S.append(
|
|
||||||
" dict2: %s \n"
|
|
||||||
% str(dict2["scan"][comp[str(keys1)][1]][str(key2)])
|
|
||||||
)
|
|
||||||
if key2 not in conflicts:
|
|
||||||
conflicts[key2] = {}
|
|
||||||
conflicts[key2]["amount"] = 1
|
|
||||||
conflicts[key2]["scan"] = str(comp[str(keys1)])
|
|
||||||
else:
|
|
||||||
|
|
||||||
conflicts[key2]["amount"] = conflicts[key2]["amount"] + 1
|
|
||||||
conflicts[key2]["scan"] = (
|
|
||||||
conflicts[key2]["scan"] + " " + (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["scan"][comp[str(keys1)][0]][str(key2)]) == list(
|
|
||||||
dict2["scan"][comp[str(keys1)][1]][str(key2)]
|
|
||||||
)
|
|
||||||
if len(list(dict1["scan"][comp[str(keys1)][0]][str(key2)])) != len(
|
|
||||||
list(dict2["scan"][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(
|
|
||||||
"Scan value "
|
|
||||||
"%s"
|
|
||||||
" differs in scan %s and %s \n"
|
|
||||||
% (key2, comp[str(keys1)][0], comp[str(keys1)][1])
|
|
||||||
)
|
|
||||||
S.append(
|
|
||||||
" dict1: %s \n"
|
|
||||||
% str(list(dict1["scan"][comp[str(keys1)][0]][str(key2)]))
|
|
||||||
)
|
|
||||||
S.append(
|
|
||||||
" dict2: %s \n"
|
|
||||||
% str(list(dict2["scan"][comp[str(keys1)][1]][str(key2)]))
|
|
||||||
)
|
|
||||||
if key2 not in conflicts:
|
|
||||||
conflicts[key2] = {}
|
|
||||||
conflicts[key2]["amount"] = 1
|
|
||||||
conflicts[key2]["scan"] = str(comp[str(keys1)])
|
|
||||||
else:
|
|
||||||
conflicts[key2]["amount"] = conflicts[key2]["amount"] + 1
|
|
||||||
conflicts[key2]["scan"] = (
|
|
||||||
conflicts[key2]["scan"] + " " + (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:
|
|
||||||
conflicts[str(keys)]["scan"] = conflicts[str(keys)]["scan"].split(" ")
|
|
||||||
except:
|
|
||||||
continue
|
|
||||||
report_string = "".join(S)
|
|
||||||
return warnings, conflicts, report_string
|
|
||||||
|
|
||||||
|
|
||||||
def guess_next(dict1, dict2, comp):
|
|
||||||
"""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["scan"][str(comp[keys][0])]["temperature"]
|
|
||||||
- dict2["scan"][str(comp[keys][1])]["temperature"]
|
|
||||||
)
|
|
||||||
/ dict2["scan"][str(comp[keys][1])]["temperature"]
|
|
||||||
)
|
|
||||||
< threshold
|
|
||||||
and abs(
|
|
||||||
(
|
|
||||||
dict1["scan"][str(comp[keys][0])]["mag_field"]
|
|
||||||
- dict2["scan"][str(comp[keys][1])]["mag_field"]
|
|
||||||
)
|
|
||||||
/ dict2["scan"][str(comp[keys][1])]["mag_field"]
|
|
||||||
)
|
|
||||||
< threshold
|
|
||||||
):
|
|
||||||
comp[keys] = comp[keys] + tuple("m")
|
|
||||||
else:
|
|
||||||
comp[keys] = comp[keys] + tuple("s")
|
|
||||||
|
|
||||||
return comp
|
|
||||||
|
|
||||||
|
|
||||||
def process_dict(dict1, dict2, comp):
|
|
||||||
"""substracts or merges scans, guess_next function must run first """
|
|
||||||
for keys in comp:
|
|
||||||
if comp[keys][2] == "s":
|
|
||||||
substract_measurement(dict1, dict2, comp[keys])
|
|
||||||
elif comp[keys][2] == "m":
|
|
||||||
merge(dict1, dict2, comp[keys])
|
|
||||||
|
|
||||||
return dict1
|
|
||||||
Loading…
x
Reference in New Issue
Block a user