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Enable Fit/Int area selector

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This commit is contained in:
usov_i 2021-05-20 12:00:53 +02:00
parent 09d22e7674
commit 0b6a58e160
4 changed files with 73 additions and 71 deletions
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30
pyzebra/app/panel_ccl_integrate.py
View File

@ -43,7 +43,7 @@ from bokeh.models import (
)
import pyzebra
from pyzebra.ccl_io import AREA_METHODS
from pyzebra.ccl_process import AREA_METHODS
javaScript = """
@ -467,6 +467,11 @@ def create():
pyzebra.fit_scan(
scan, fit_params, fit_from=fit_from_spinner.value, fit_to=fit_to_spinner.value
)
pyzebra.get_area(
scan,
area_method=AREA_METHODS[area_method_radiobutton.active],
lorentz=lorentz_checkbox.active,
)
_update_plot(_get_selected_scan())
_update_table()
@ -479,6 +484,11 @@ def create():
pyzebra.fit_scan(
scan, fit_params, fit_from=fit_from_spinner.value, fit_to=fit_to_spinner.value
)
pyzebra.get_area(
scan,
area_method=AREA_METHODS[area_method_radiobutton.active],
lorentz=lorentz_checkbox.active,
)
_update_plot(scan)
_update_table()
@ -486,19 +496,9 @@ def create():
fit_button = Button(label="Fit Current", width=145)
fit_button.on_click(fit_button_callback)
def area_method_radiobutton_callback(_handler):
_update_preview()
area_method_radiobutton = RadioButtonGroup(
labels=["Fit area", "Int area"], active=0, width=145, disabled=True
)
area_method_radiobutton.on_click(area_method_radiobutton_callback)
def lorentz_checkbox_callback(_handler):
_update_preview()
area_method_radiobutton = RadioButtonGroup(labels=["Fit area", "Int area"], active=0, width=145)
lorentz_checkbox = CheckboxGroup(labels=["Lorentz Correction"], width=145, margin=[13, 5, 5, 5])
lorentz_checkbox.on_click(lorentz_checkbox_callback)
export_preview_textinput = TextAreaInput(title="Export file preview:", width=500, height=400)
@ -511,11 +511,7 @@ def create():
export_data.append(s)
pyzebra.export_1D(
export_data,
temp_file,
area_method=AREA_METHODS[int(area_method_radiobutton.active)],
lorentz=bool(lorentz_checkbox.active),
hkl_precision=int(hkl_precision_select.value),
export_data, temp_file, hkl_precision=int(hkl_precision_select.value),
)
exported_content = ""

31
pyzebra/app/panel_param_study.py
View File

@ -48,7 +48,7 @@ from bokeh.palettes import Category10, Turbo256
from bokeh.transform import linear_cmap
import pyzebra
from pyzebra.ccl_io import AREA_METHODS
from pyzebra.ccl_process import AREA_METHODS
javaScript = """
for (let i = 0; i < js_data.data['fname'].length; i++) {
@ -557,6 +557,11 @@ def create():
pyzebra.fit_scan(
scan, fit_params, fit_from=fit_from_spinner.value, fit_to=fit_to_spinner.value
)
pyzebra.get_area(
scan,
area_method=AREA_METHODS[area_method_radiobutton.active],
lorentz=lorentz_checkbox.active,
)
_update_plot()
_update_table()
@ -569,6 +574,11 @@ def create():
pyzebra.fit_scan(
scan, fit_params, fit_from=fit_from_spinner.value, fit_to=fit_to_spinner.value
)
pyzebra.get_area(
scan,
area_method=AREA_METHODS[area_method_radiobutton.active],
lorentz=lorentz_checkbox.active,
)
_update_plot()
_update_table()
@ -576,19 +586,9 @@ def create():
fit_button = Button(label="Fit Current", width=145)
fit_button.on_click(fit_button_callback)
def area_method_radiobutton_callback(_handler):
_update_preview()
area_method_radiobutton = RadioButtonGroup(
labels=["Fit area", "Int area"], active=0, width=145, disabled=True
)
area_method_radiobutton.on_click(area_method_radiobutton_callback)
def lorentz_checkbox_callback(_handler):
_update_preview()
area_method_radiobutton = RadioButtonGroup(labels=["Fit area", "Int area"], active=0, width=145)
lorentz_checkbox = CheckboxGroup(labels=["Lorentz Correction"], width=145, margin=[13, 5, 5, 5])
lorentz_checkbox.on_click(lorentz_checkbox_callback)
export_preview_textinput = TextAreaInput(title="Export file preview:", width=450, height=400)
@ -600,12 +600,7 @@ def create():
if export:
export_data.append(s)
pyzebra.export_1D(
export_data,
temp_file,
area_method=AREA_METHODS[int(area_method_radiobutton.active)],
lorentz=bool(lorentz_checkbox.active),
)
pyzebra.export_1D(export_data, temp_file)
exported_content = ""
file_content = []

38
pyzebra/ccl_io.py
View File

@ -3,7 +3,6 @@ import re
from collections import defaultdict
import numpy as np
from scipy.integrate import simpson, trapezoid
META_VARS_STR = (
"instrument",
@ -77,8 +76,6 @@ CCL_SECOND_LINE = (
("scan_motor", str),
)
AREA_METHODS = ("fit_area", "int_area")
def load_1D(filepath):
"""
@ -244,7 +241,7 @@ def parse_1D(fileobj, data_type):
return scan
def export_1D(data, path, area_method=AREA_METHODS[0], lorentz=False, hkl_precision=2):
def export_1D(data, path, hkl_precision=2):
"""Exports data in the .comm/.incomm format
Scans with integer/real hkl values are saved in .comm/.incomm files correspondingly. If no scans
@ -266,38 +263,7 @@ def export_1D(data, path, area_method=AREA_METHODS[0], lorentz=False, hkl_precis
else:
hkl_str = f"{h:8.{hkl_precision}f}{k:8.{hkl_precision}f}{l:8.{hkl_precision}f}"
for name, param in scan["fit"].params.items():
if "amplitude" in name:
if param.stderr is None:
area_n = np.nan
area_s = np.nan
else:
area_n = param.value
area_s = param.stderr
# TODO: take into account multiple peaks
break
else:
# no peak functions in a fit model
# assume this is a background fit, so do numeric integration
y_val = scan["Counts"]
x_val = scan[scan["scan_motor"]]
y_bkg = scan["fit"].eval(x=x_val)
area_n = simpson(y_val, x=x_val) - trapezoid(y_bkg, x=x_val)
area_s = np.sqrt(area_n)
# apply lorentz correction to area
if lorentz:
if zebra_mode == "bi":
twotheta = np.deg2rad(scan["twotheta"])
corr_factor = np.sin(twotheta)
else: # zebra_mode == "nb":
gamma = np.deg2rad(scan["gamma"])
nu = np.deg2rad(scan["nu"])
corr_factor = np.sin(gamma) * np.cos(nu)
area_n = np.abs(area_n * corr_factor)
area_s = np.abs(area_s * corr_factor)
area_n, area_s = scan["area"]
area_str = f"{area_n:10.2f}{area_s:10.2f}"
ang_str = ""

45
pyzebra/ccl_process.py
View File

@ -3,6 +3,7 @@ import os
import numpy as np
from lmfit.models import GaussianModel, LinearModel, PseudoVoigtModel, VoigtModel
from scipy.integrate import simpson, trapezoid
from .ccl_io import CCL_ANGLES
@ -22,6 +23,8 @@ MAX_RANGE_GAP = {
"omega": 0.5,
}
AREA_METHODS = ("fit_area", "int_area")
def normalize_dataset(dataset, monitor=100_000):
for scan in dataset:
@ -148,3 +151,45 @@ def fit_scan(scan, model_dict, fit_from=None, fit_to=None):
weights = [1 / np.sqrt(val) if val != 0 else 1 for val in y_fit]
scan["fit"] = model.fit(y_fit, x=x_fit, weights=weights)
def get_area(scan, area_method, lorentz):
if area_method not in AREA_METHODS:
raise ValueError(f"Unknown area method: {area_method}.")
if area_method == "fit_area":
for name, param in scan["fit"].params.items():
if "amplitude" in name:
if param.stderr is None:
area_n = np.nan
area_s = np.nan
else:
area_n = param.value
area_s = param.stderr
# TODO: take into account multiple peaks
break
else:
area_n = np.nan
area_s = np.nan
else: # area_method == "int_area"
y_val = scan["Counts"]
x_val = scan[scan["scan_motor"]]
y_bkg = scan["fit"].eval_components(x=x_val)["f0_"]
area_n = simpson(y_val, x=x_val) - trapezoid(y_bkg, x=x_val)
area_s = np.sqrt(area_n)
if lorentz:
# lorentz correction to area
if scan["zebra_mode"] == "bi":
twotheta = np.deg2rad(scan["twotheta"])
corr_factor = np.sin(twotheta)
else: # zebra_mode == "nb":
gamma = np.deg2rad(scan["gamma"])
nu = np.deg2rad(scan["nu"])
corr_factor = np.sin(gamma) * np.cos(nu)
area_n = np.abs(area_n * corr_factor)
area_s = np.abs(area_s * corr_factor)
scan["area"] = (area_n, area_s)