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Rename "Measurements" to "meas"

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This commit is contained in:
usov_i 2020-10-16 15:30:52 +02:00
parent 306958b02a
commit 3f8900bf87
5 changed files with 111 additions and 122 deletions
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20
pyzebra/app/panel_ccl_integrate.py
View File

@ -75,7 +75,7 @@ def create():
_, ext = os.path.splitext(new)
det_data = pyzebra.parse_1D(file, ext)
meas_list = list(det_data["Measurements"].keys())
meas_list = list(det_data["meas"].keys())
meas_table_source.data.update(measurement=meas_list, peaks=[0] * len(meas_list))
meas_table_source.selected.indices = []
meas_table_source.selected.indices = [0]
@ -89,7 +89,7 @@ def create():
_, ext = os.path.splitext(upload_button.filename)
det_data = pyzebra.parse_1D(file, ext)
meas_list = list(det_data["Measurements"].keys())
meas_list = list(det_data["meas"].keys())
meas_table_source.data.update(measurement=meas_list, peaks=[0] * len(meas_list))
meas_table_source.selected.indices = []
meas_table_source.selected.indices = [0]
@ -98,14 +98,14 @@ def create():
upload_button.on_change("value", upload_button_callback)
def _update_table():
num_of_peaks = [meas.get("num_of_peaks", 0) for meas in det_data["Measurements"].values()]
num_of_peaks = [meas.get("num_of_peaks", 0) for meas in det_data["meas"].values()]
meas_table_source.data.update(peaks=num_of_peaks)
def _update_plot(ind):
nonlocal peak_pos_textinput_lock
peak_pos_textinput_lock = True
meas = det_data["Measurements"][ind]
meas = det_data["meas"][ind]
y = meas["Counts"]
x = meas["om"]
@ -223,7 +223,7 @@ def create():
if new is not None and not peak_pos_textinput_lock:
sel_ind = meas_table_source.selected.indices[-1]
meas_name = meas_table_source.data["measurement"][sel_ind]
meas = det_data["Measurements"][meas_name]
meas = det_data["meas"][meas_name]
meas["num_of_peaks"] = 1
peak_ind = (np.abs(meas["om"] - float(new))).argmin()
@ -296,7 +296,7 @@ def create():
fit_output_textinput = TextAreaInput(title="Fit results:", width=450, height=400)
def peakfind_all_button_callback():
for meas in det_data["Measurements"].values():
for meas in det_data["meas"].values():
pyzebra.ccl_findpeaks(
meas,
int_threshold=peak_int_ratio_spinner.value,
@ -318,7 +318,7 @@ def create():
sel_ind = meas_table_source.selected.indices[-1]
meas = meas_table_source.data["measurement"][sel_ind]
pyzebra.ccl_findpeaks(
det_data["Measurements"][meas],
det_data["meas"][meas],
int_threshold=peak_int_ratio_spinner.value,
prominence=peak_prominence_spinner.value,
smooth=smooth_toggle.active,
@ -333,7 +333,7 @@ def create():
peakfind_button.on_click(peakfind_button_callback)
def fit_all_button_callback():
for meas in det_data["Measurements"].values():
for meas in det_data["meas"].values():
num_of_peaks = meas.get("num_of_peaks")
if num_of_peaks is not None and num_of_peaks == 1:
pyzebra.fitccl(
@ -380,10 +380,10 @@ def create():
sel_ind = meas_table_source.selected.indices[-1]
meas = meas_table_source.data["measurement"][sel_ind]
num_of_peaks = det_data["Measurements"][meas].get("num_of_peaks")
num_of_peaks = det_data["meas"][meas].get("num_of_peaks")
if num_of_peaks is not None and num_of_peaks == 1:
pyzebra.fitccl(
det_data["Measurements"][meas],
det_data["meas"][meas],
guess=[
centre_guess.value,
sigma_guess.value,

175
pyzebra/ccl_dict_operation.py
View File

@ -12,19 +12,17 @@ def add_dict(dict1, dict2):
: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"]])
max_measurement_dict1 = max([int(str(keys)[1:]) for keys in dict1["meas"]])
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"]]
for x in [int(str(keys)[1:]) for keys in dict2["meas"]]
]
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]
for keys, name in zip(dict2["meas"], new_filenames):
dict2["meas"][keys]["file_of_origin"] = str(dict2["meta"]["original_filename"])
dict1["meas"][name] = dict2["meas"][keys]
dict1[new_meta_name] = dict2["meta"]
@ -42,14 +40,14 @@ def add_dict(dict1, dict2):
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["number_of_measurements"] = len(dict2["meas"]["NP"])
d["om"] = dict2["meas"]["om"]
d["Counts"] = dict2["meas"]["Counts"]
d["monitor"] = dict2["meas"]["Monitor1"][0]
d["temperature"] = dict2["meta"]["temp"]
d["mag_field"] = dict2["meta"]["mf"]
d["omega_angle"] = dict2["meta"]["omega"]
dict1["Measurements"][new_name] = d
dict1["meas"][new_name] = d
print(hkl.split())
for keys in d:
print(keys)
@ -82,18 +80,18 @@ def scan_dict(dict):
"""
d = {}
for i in dict["Measurements"]:
for j in dict["Measurements"]:
if dict["Measurements"][str(i)] != dict["Measurements"][str(j)]:
for i in dict["meas"]:
for j in dict["meas"]:
if dict["meas"][str(i)] != dict["meas"][str(j)]:
itup = (
dict["Measurements"][str(i)]["h_index"],
dict["Measurements"][str(i)]["k_index"],
dict["Measurements"][str(i)]["l_index"],
dict["meas"][str(i)]["h_index"],
dict["meas"][str(i)]["k_index"],
dict["meas"][str(i)]["l_index"],
)
jtup = (
dict["Measurements"][str(j)]["h_index"],
dict["Measurements"][str(j)]["k_index"],
dict["Measurements"][str(j)]["l_index"],
dict["meas"][str(j)]["h_index"],
dict["meas"][str(j)]["k_index"],
dict["meas"][str(j)]["l_index"],
)
if itup != jtup:
pass
@ -119,47 +117,44 @@ def compare_hkl(dict1, dict2):
first dict and M9 in second"""
d = {}
dupl = 0
for keys in dict1["Measurements"]:
for key in dict2["Measurements"]:
for keys in dict1["meas"]:
for key in dict2["meas"]:
if (
dict1["Measurements"][str(keys)]["h_index"]
== dict2["Measurements"][str(key)]["h_index"]
and dict1["Measurements"][str(keys)]["k_index"]
== dict2["Measurements"][str(key)]["k_index"]
and dict1["Measurements"][str(keys)]["l_index"]
== dict2["Measurements"][str(key)]["l_index"]
dict1["meas"][str(keys)]["h_index"] == dict2["meas"][str(key)]["h_index"]
and dict1["meas"][str(keys)]["k_index"] == dict2["meas"][str(key)]["k_index"]
and dict1["meas"][str(keys)]["l_index"] == dict2["meas"][str(key)]["l_index"]
):
if (
str(
(
str(dict1["Measurements"][str(keys)]["h_index"])
str(dict1["meas"][str(keys)]["h_index"])
+ " "
+ str(dict1["Measurements"][str(keys)]["k_index"])
+ str(dict1["meas"][str(keys)]["k_index"])
+ " "
+ str(dict1["Measurements"][str(keys)]["l_index"])
+ str(dict1["meas"][str(keys)]["l_index"])
)
)
not in d
):
d[
str(
str(dict1["Measurements"][str(keys)]["h_index"])
str(dict1["meas"][str(keys)]["h_index"])
+ " "
+ str(dict1["Measurements"][str(keys)]["k_index"])
+ str(dict1["meas"][str(keys)]["k_index"])
+ " "
+ str(dict1["Measurements"][str(keys)]["l_index"])
+ str(dict1["meas"][str(keys)]["l_index"])
)
] = (str(keys), str(key))
else:
dupl = dupl + 1
d[
str(
str(dict1["Measurements"][str(keys)]["h_index"])
str(dict1["meas"][str(keys)]["h_index"])
+ " "
+ str(dict1["Measurements"][str(keys)]["k_index"])
+ str(dict1["meas"][str(keys)]["k_index"])
+ " "
+ str(dict1["Measurements"][str(keys)]["l_index"])
+ str(dict1["meas"][str(keys)]["l_index"])
+ "_dupl"
+ str(dupl)
)
@ -188,13 +183,9 @@ def normalize(dict, key, monitor):
:return counts - normalized counts
:return sigma - normalized sigma"""
counts = np.array(dict["Measurements"][key]["Counts"])
sigma = (
np.sqrt(counts)
if "sigma" not in dict["Measurements"][key]
else dict["Measurements"][key]["sigma"]
)
monitor_ratio = monitor / dict["Measurements"][key]["monitor"]
counts = np.array(dict["meas"][key]["Counts"])
sigma = np.sqrt(counts) if "sigma" not in dict["meas"][key] else dict["meas"][key]["sigma"]
monitor_ratio = monitor / dict["meas"][key]["monitor"]
scaled_counts = counts * monitor_ratio
scaled_sigma = np.array(sigma) * monitor_ratio
@ -212,11 +203,11 @@ def merge(dict1, dict2, keys, auto=True, monitor=100000):
note: dict1 and dict2 can be same dict
:return dict1 with merged scan"""
if auto:
if dict1["Measurements"][keys[0]]["monitor"] == dict2["Measurements"][keys[1]]["monitor"]:
monitor = dict1["Measurements"][keys[0]]["monitor"]
if dict1["meas"][keys[0]]["monitor"] == dict2["meas"][keys[1]]["monitor"]:
monitor = dict1["meas"][keys[0]]["monitor"]
# load om and Counts
x1, x2 = dict1["Measurements"][keys[0]]["om"], dict2["Measurements"][keys[1]]["om"]
x1, x2 = dict1["meas"][keys[0]]["om"], dict2["meas"][keys[1]]["om"]
cor_y1, y_err1 = normalize(dict1, keys[0], monitor=monitor)
cor_y2, y_err2 = normalize(dict2, keys[1], monitor=monitor)
# creates touples (om, Counts, sigma) for sorting and further processing
@ -246,21 +237,21 @@ def merge(dict1, dict2, keys, auto=True, monitor=100000):
continue
if dict1 == dict2:
del dict1["Measurements"][keys[1]]
del dict1["meas"][keys[1]]
note = (
f"This measurement was merged with measurement {keys[1]} from "
f'file {dict2["meta"]["original_filename"]} \n'
)
if "notes" not in dict1["Measurements"][str(keys[0])]:
dict1["Measurements"][str(keys[0])]["notes"] = note
if "notes" not in dict1["meas"][str(keys[0])]:
dict1["meas"][str(keys[0])]["notes"] = note
else:
dict1["Measurements"][str(keys[0])]["notes"] += note
dict1["meas"][str(keys[0])]["notes"] += note
dict1["Measurements"][keys[0]]["om"] = om
dict1["Measurements"][keys[0]]["Counts"] = Counts
dict1["Measurements"][keys[0]]["sigma"] = sigma
dict1["Measurements"][keys[0]]["monitor"] = monitor
dict1["meas"][keys[0]]["om"] = om
dict1["meas"][keys[0]]["Counts"] = Counts
dict1["meas"][keys[0]]["sigma"] = sigma
dict1["meas"][keys[0]]["monitor"] = monitor
print("merging done")
return dict1
@ -274,12 +265,12 @@ def substract_measurement(dict1, dict2, keys, auto=True, monitor=100000):
:arg monitor : final monitor after merging
:returns d : dict1 with substracted Counts from dict2 and sigma that comes from the substraction"""
if len(dict1["Measurements"][keys[0]]["om"]) != len(dict2["Measurements"][keys[1]]["om"]):
if len(dict1["meas"][keys[0]]["om"]) != len(dict2["meas"][keys[1]]["om"]):
raise ValueError("Omegas have different lengths, cannot be substracted")
if auto:
if dict1["Measurements"][keys[0]]["monitor"] == dict2["Measurements"][keys[1]]["monitor"]:
monitor = dict1["Measurements"][keys[0]]["monitor"]
if dict1["meas"][keys[0]]["monitor"] == dict2["meas"][keys[1]]["monitor"]:
monitor = dict1["meas"][keys[0]]["monitor"]
cor_y1, y_err1 = normalize(dict1, keys[0], monitor=monitor)
cor_y2, y_err2 = normalize(dict2, keys[1], monitor=monitor)
@ -301,17 +292,17 @@ def substract_measurement(dict1, dict2, keys, auto=True, monitor=100000):
f"{len([num for num in res_nom if num < 0]) / len(res_nom)}"
)
dict1["Measurements"][str(keys[0])]["Counts"] = res_nom
dict1["Measurements"][str(keys[0])]["sigma"] = res_err
dict1["Measurements"][str(keys[0])]["monitor"] = monitor
dict1["meas"][str(keys[0])]["Counts"] = res_nom
dict1["meas"][str(keys[0])]["sigma"] = res_err
dict1["meas"][str(keys[0])]["monitor"] = monitor
note = (
f'Measurement {keys[1]} from file {dict2["meta"]["original_filename"]} '
f"was substracted from this measurement \n"
)
if "notes" not in dict1["Measurements"][str(keys[0])]:
dict1["Measurements"][str(keys[0])]["notes"] = note
if "notes" not in dict1["meas"][str(keys[0])]:
dict1["meas"][str(keys[0])]["notes"] = note
else:
dict1["Measurements"][str(keys[0])]["notes"] += note
dict1["meas"][str(keys[0])]["notes"] += note
return dict1
@ -380,24 +371,24 @@ def compare_dict(dict1, dict2):
# compare Measurements
S.append(
"Number of measurements in %s = %s \n"
% (dict1["meta"]["original_filename"], len(dict1["Measurements"]))
% (dict1["meta"]["original_filename"], len(dict1["meas"]))
)
S.append(
"Number of measurements in %s = %s \n"
% (dict2["meta"]["original_filename"], len(dict2["Measurements"]))
% (dict2["meta"]["original_filename"], len(dict2["meas"]))
)
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["Measurements"][str(comp[str(keys1)][0])]:
for key2 in dict1["meas"][str(comp[str(keys1)][0])]:
if key2 in exlude_set:
continue
if key2 not in select_set:
try:
if (
dict1["Measurements"][comp[str(keys1)][0]][str(key2)]
!= dict2["Measurements"][str(comp[str(keys1)][1])][str(key2)]
dict1["meas"][comp[str(keys1)][0]][str(key2)]
!= dict2["meas"][str(comp[str(keys1)][1])][str(key2)]
):
S.append(
"Measurement value "
@ -407,21 +398,21 @@ def compare_dict(dict1, dict2):
)
S.append(
" dict1: %s \n"
% str(dict1["Measurements"][comp[str(keys1)][0]][str(key2)])
% str(dict1["meas"][comp[str(keys1)][0]][str(key2)])
)
S.append(
" dict2: %s \n"
% str(dict2["Measurements"][comp[str(keys1)][1]][str(key2)])
% str(dict2["meas"][comp[str(keys1)][1]][str(key2)])
)
if key2 not in conflicts:
conflicts[key2] = {}
conflicts[key2]["amount"] = 1
conflicts[key2]["measurements"] = str(comp[str(keys1)])
conflicts[key2]["meas"] = str(comp[str(keys1)])
else:
conflicts[key2]["amount"] = conflicts[key2]["amount"] + 1
conflicts[key2]["measurements"] = (
conflicts[key2]["measurements"] + " " + (str(comp[str(keys1)]))
conflicts[key2]["meas"] = (
conflicts[key2]["meas"] + " " + (str(comp[str(keys1)]))
)
except KeyError as e:
print("Missing keys, some files were probably merged or substracted")
@ -429,11 +420,11 @@ def compare_dict(dict1, dict2):
else:
try:
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)])
comparison = list(dict1["meas"][comp[str(keys1)][0]][str(key2)]) == list(
dict2["meas"][comp[str(keys1)][1]][str(key2)]
)
if len(list(dict1["meas"][comp[str(keys1)][0]][str(key2)])) != len(
list(dict2["meas"][comp[str(keys1)][1]][str(key2)])
):
if str("different length of %s" % key2) not in warnings:
warnings[str("different length of %s" % key2)] = list()
@ -453,20 +444,20 @@ def compare_dict(dict1, dict2):
)
S.append(
" dict1: %s \n"
% str(list(dict1["Measurements"][comp[str(keys1)][0]][str(key2)]))
% str(list(dict1["meas"][comp[str(keys1)][0]][str(key2)]))
)
S.append(
" dict2: %s \n"
% str(list(dict2["Measurements"][comp[str(keys1)][1]][str(key2)]))
% str(list(dict2["meas"][comp[str(keys1)][1]][str(key2)]))
)
if key2 not in conflicts:
conflicts[key2] = {}
conflicts[key2]["amount"] = 1
conflicts[key2]["measurements"] = str(comp[str(keys1)])
conflicts[key2]["meas"] = str(comp[str(keys1)])
else:
conflicts[key2]["amount"] = conflicts[key2]["amount"] + 1
conflicts[key2]["measurements"] = (
conflicts[key2]["measurements"] + " " + (str(comp[str(keys1)]))
conflicts[key2]["meas"] = (
conflicts[key2]["meas"] + " " + (str(comp[str(keys1)]))
)
except KeyError as e:
print("Missing keys, some files were probably merged or substracted")
@ -474,7 +465,7 @@ def compare_dict(dict1, dict2):
for keys in conflicts:
try:
conflicts[str(keys)]["measurements"] = conflicts[str(keys)]["measurements"].split(" ")
conflicts[str(keys)]["meas"] = conflicts[str(keys)]["meas"].split(" ")
except:
continue
report_string = "".join(S)
@ -489,18 +480,18 @@ def guess_next(dict1, dict2, comp):
if (
abs(
(
dict1["Measurements"][str(comp[keys][0])]["temperature"]
- dict2["Measurements"][str(comp[keys][1])]["temperature"]
dict1["meas"][str(comp[keys][0])]["temperature"]
- dict2["meas"][str(comp[keys][1])]["temperature"]
)
/ dict2["Measurements"][str(comp[keys][1])]["temperature"]
/ dict2["meas"][str(comp[keys][1])]["temperature"]
)
< threshold
and abs(
(
dict1["Measurements"][str(comp[keys][0])]["mag_field"]
- dict2["Measurements"][str(comp[keys][1])]["mag_field"]
dict1["meas"][str(comp[keys][0])]["mag_field"]
- dict2["meas"][str(comp[keys][1])]["mag_field"]
)
/ dict2["Measurements"][str(comp[keys][1])]["mag_field"]
/ dict2["meas"][str(comp[keys][1])]["mag_field"]
)
< threshold
):

2
pyzebra/comm_export.py
View File

@ -30,7 +30,7 @@ def export_comm(data, path, lorentz=False):
padding = [4, 6, 10, 8]
with open(str(path + extension), "w") as out_file:
for keys, meas in data["Measurements"].items():
for keys, meas in data["meas"].items():
if "fit" not in meas:
print("Measurement skipped - no fit value for:", keys)
continue

2
pyzebra/load_1D.py
View File

@ -183,4 +183,4 @@ def parse_1D(fileobj, data_type):
metadata["data_type"] = data_type
metadata["area_method"] = "fit"
return {"meta": metadata, "Measurements": measurements}
return {"meta": metadata, "meas": measurements}

34
pyzebra/param_study_moduls.py
View File

@ -38,12 +38,12 @@ def load_dats(filepath):
dict1 = add_dict(dict1, load_1D(file_list[i][0]))
else:
dict1 = add_dict(dict1, load_1D(file_list[i]))
dict1["Measurements"][str("M" + str(i + 1))]["params"] = {}
dict1["meas"][str("M" + str(i + 1))]["params"] = {}
if data_type == "txt":
for x in range(len(col_names) - 1):
dict1["Measurements"][str("M" + str(i + 1))]["params"][
col_names[x + 1]
] = file_list[i][x + 1]
dict1["meas"][str("M" + str(i + 1))]["params"][col_names[x + 1]] = file_list[i][
x + 1
]
return dict1
@ -55,7 +55,7 @@ def create_dataframe(dict1):
# create dictionary to which we pull only wanted items before transforming it to pd.dataframe
pull_dict = {}
pull_dict["filenames"] = list()
for key in dict1["Measurements"]["M1"]["params"]:
for key in dict1["meas"]["M1"]["params"]:
pull_dict[key] = list()
pull_dict["temperature"] = list()
pull_dict["mag_field"] = list()
@ -65,21 +65,19 @@ def create_dataframe(dict1):
pull_dict["Counts"] = list()
# populate the dict
for keys in dict1["Measurements"]:
if "file_of_origin" in dict1["Measurements"][keys]:
pull_dict["filenames"].append(
dict1["Measurements"][keys]["file_of_origin"].split("/")[-1]
)
for keys in dict1["meas"]:
if "file_of_origin" in dict1["meas"][keys]:
pull_dict["filenames"].append(dict1["meas"][keys]["file_of_origin"].split("/")[-1])
else:
pull_dict["filenames"].append(dict1["meta"]["original_filename"].split("/")[-1])
for key in dict1["Measurements"][keys]["params"]:
pull_dict[str(key)].append(float(dict1["Measurements"][keys]["params"][key]))
pull_dict["temperature"].append(dict1["Measurements"][keys]["temperature"])
pull_dict["mag_field"].append(dict1["Measurements"][keys]["mag_field"])
pull_dict["fit_area"].append(dict1["Measurements"][keys]["fit"]["fit_area"])
pull_dict["int_area"].append(dict1["Measurements"][keys]["fit"]["int_area"])
pull_dict["om"].append(dict1["Measurements"][keys]["om"])
pull_dict["Counts"].append(dict1["Measurements"][keys]["Counts"])
for key in dict1["meas"][keys]["params"]:
pull_dict[str(key)].append(float(dict1["meas"][keys]["params"][key]))
pull_dict["temperature"].append(dict1["meas"][keys]["temperature"])
pull_dict["mag_field"].append(dict1["meas"][keys]["mag_field"])
pull_dict["fit_area"].append(dict1["meas"][keys]["fit"]["fit_area"])
pull_dict["int_area"].append(dict1["meas"][keys]["fit"]["int_area"])
pull_dict["om"].append(dict1["meas"][keys]["om"])
pull_dict["Counts"].append(dict1["meas"][keys]["Counts"])
return pd.DataFrame(data=pull_dict)