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Extract fit controls

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This commit is contained in:
usov_i 2022-12-23 19:22:03 +01:00
parent 0b340d0bb9
commit 200e5d0a13
5 changed files with 244 additions and 451 deletions
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1
pyzebra/app/__init__.py
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@ -0,0 +1 @@
from pyzebra.app.fit_controls import FitControls

169
pyzebra/app/fit_controls.py Normal file
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@ -0,0 +1,169 @@
import types
from bokeh.models import (
Button,
CellEditor,
CheckboxEditor,
CheckboxGroup,
ColumnDataSource,
DataTable,
Dropdown,
MultiSelect,
NumberEditor,
RadioGroup,
Spinner,
TableColumn,
TextAreaInput,
)
import pyzebra
def _params_factory(function):
if function == "linear":
param_names = ["slope", "intercept"]
elif function == "gaussian":
param_names = ["amplitude", "center", "sigma"]
elif function == "voigt":
param_names = ["amplitude", "center", "sigma", "gamma"]
elif function == "pvoigt":
param_names = ["amplitude", "center", "sigma", "fraction"]
elif function == "pseudovoigt1":
param_names = ["amplitude", "center", "g_sigma", "l_sigma", "fraction"]
else:
raise ValueError("Unknown fit function")
n = len(param_names)
params = dict(
param=param_names, value=[None] * n, vary=[True] * n, min=[None] * n, max=[None] * n
)
if function == "linear":
params["value"] = [0, 1]
params["vary"] = [False, True]
params["min"] = [None, 0]
elif function == "gaussian":
params["min"] = [0, None, None]
return params
class FitControls:
def __init__(self):
self.params = {}
def add_function_button_callback(click):
# bokeh requires (str, str) for MultiSelect options
new_tag = f"{click.item}-{function_select.tags[0]}"
function_select.options.append((new_tag, click.item))
self.params[new_tag] = _params_factory(click.item)
function_select.tags[0] += 1
add_function_button = Dropdown(
label="Add fit function",
menu=[
("Linear", "linear"),
("Gaussian", "gaussian"),
("Voigt", "voigt"),
("Pseudo Voigt", "pvoigt"),
# ("Pseudo Voigt1", "pseudovoigt1"),
],
width=145,
)
add_function_button.on_click(add_function_button_callback)
self.add_function_button = add_function_button
def function_list_callback(_attr, old, new):
# Avoid selection of multiple indicies (via Shift+Click or Ctrl+Click)
if len(new) > 1:
# drop selection to the previous one
function_select.value = old
return
if len(old) > 1:
# skip unnecessary update caused by selection drop
return
if new:
params_table_source.data.update(self.params[new[0]])
else:
params_table_source.data.update(dict(param=[], value=[], vary=[], min=[], max=[]))
function_select = MultiSelect(options=[], height=120, width=145)
function_select.tags = [0]
function_select.on_change("value", function_list_callback)
self.function_select = function_select
def remove_function_button_callback():
if function_select.value:
sel_tag = function_select.value[0]
del self.params[sel_tag]
for elem in function_select.options:
if elem[0] == sel_tag:
function_select.options.remove(elem)
break
function_select.value = []
remove_function_button = Button(label="Remove fit function", width=145)
remove_function_button.on_click(remove_function_button_callback)
self.remove_function_button = remove_function_button
params_table_source = ColumnDataSource(dict(param=[], value=[], vary=[], min=[], max=[]))
self.params_table = DataTable(
source=params_table_source,
columns=[
TableColumn(field="param", title="Parameter", editor=CellEditor()),
TableColumn(field="value", title="Value", editor=NumberEditor()),
TableColumn(field="vary", title="Vary", editor=CheckboxEditor()),
TableColumn(field="min", title="Min", editor=NumberEditor()),
TableColumn(field="max", title="Max", editor=NumberEditor()),
],
height=200,
width=350,
index_position=None,
editable=True,
auto_edit=True,
)
# start with `background` and `gauss` fit functions added
add_function_button_callback(types.SimpleNamespace(item="linear"))
add_function_button_callback(types.SimpleNamespace(item="gaussian"))
function_select.value = ["gaussian-1"] # put selection on gauss
self.from_spinner = Spinner(title="Fit from:", width=145)
self.to_spinner = Spinner(title="to:", width=145)
self.area_method_radiogroup = RadioGroup(labels=["Function", "Area"], active=0, width=145)
self.lorentz_checkbox = CheckboxGroup(
labels=["Lorentz Correction"], width=145, margin=(13, 5, 5, 5)
)
self.result_textarea = TextAreaInput(title="Fit results:", width=750, height=200)
def _process_scan(self, scan):
pyzebra.fit_scan(
scan, self.params, fit_from=self.from_spinner.value, fit_to=self.to_spinner.value
)
pyzebra.get_area(
scan,
area_method=pyzebra.AREA_METHODS[self.area_method_radiogroup.active],
lorentz=self.lorentz_checkbox.active,
)
def fit_scan(self, scan):
self._process_scan(scan)
def fit_dataset(self, dataset):
for scan in dataset:
if scan["export"]:
self._process_scan(scan)
def update_result_textarea(self, scan):
fit = scan.get("fit")
if fit is None:
self.result_textarea.value = ""
else:
self.result_textarea.value = fit.fit_report()

174
pyzebra/app/panel_ccl_compare.py
View File

@ -2,7 +2,6 @@ import base64
import io
import os
import tempfile
import types
import numpy as np
from bokeh.io import curdoc
@ -11,15 +10,12 @@ from bokeh.models import (
Button,
CellEditor,
CheckboxEditor,
CheckboxGroup,
ColumnDataSource,
CustomJS,
DataTable,
Div,
Dropdown,
FileInput,
MultiSelect,
NumberEditor,
Panel,
RadioGroup,
Select,
@ -33,7 +29,7 @@ from bokeh.models import (
from bokeh.plotting import figure
import pyzebra
from pyzebra import AREA_METHODS, EXPORT_TARGETS
from pyzebra import EXPORT_TARGETS, app
javaScript = """
let j = 0;
@ -61,7 +57,6 @@ def create():
doc = curdoc()
dataset1 = []
dataset2 = []
fit_params = {}
js_data = ColumnDataSource(data=dict(content=["", ""], fname=["", ""], ext=["", ""]))
def file_select_update_for_proposal():
@ -244,7 +239,7 @@ def create():
xs_peak = []
ys_peak = []
comps = fit.eval_components(x=x_fit)
for i, model in enumerate(fit_params):
for i, model in enumerate(app_fitctrl.params):
if "linear" in model:
x_bkg = x_fit
y_bkg = comps[f"f{i}_"]
@ -264,7 +259,7 @@ def create():
bkg_source.data.update(x=[], y=[])
peak_source.data.update(xs=[], ys=[])
fit_output_textinput.value = fit_output
app_fitctrl.result_textarea.value = fit_output
# Main plot
plot = figure(
@ -425,136 +420,21 @@ def create():
restore_button = Button(label="Restore scan", width=145)
restore_button.on_click(restore_button_callback)
app_fitctrl = app.FitControls()
def fit_from_spinner_callback(_attr, _old, new):
fit_from_span.location = new
fit_from_spinner = Spinner(title="Fit from:", width=145)
fit_from_spinner.on_change("value", fit_from_spinner_callback)
app_fitctrl.from_spinner.on_change("value", fit_from_spinner_callback)
def fit_to_spinner_callback(_attr, _old, new):
fit_to_span.location = new
fit_to_spinner = Spinner(title="to:", width=145)
fit_to_spinner.on_change("value", fit_to_spinner_callback)
def fitparams_add_dropdown_callback(click):
# bokeh requires (str, str) for MultiSelect options
new_tag = f"{click.item}-{fitparams_select.tags[0]}"
fitparams_select.options.append((new_tag, click.item))
fit_params[new_tag] = fitparams_factory(click.item)
fitparams_select.tags[0] += 1
fitparams_add_dropdown = Dropdown(
label="Add fit function",
menu=[
("Linear", "linear"),
("Gaussian", "gaussian"),
("Voigt", "voigt"),
("Pseudo Voigt", "pvoigt"),
# ("Pseudo Voigt1", "pseudovoigt1"),
],
width=145,
)
fitparams_add_dropdown.on_click(fitparams_add_dropdown_callback)
def fitparams_select_callback(_attr, old, new):
# Avoid selection of multiple indicies (via Shift+Click or Ctrl+Click)
if len(new) > 1:
# drop selection to the previous one
fitparams_select.value = old
return
if len(old) > 1:
# skip unnecessary update caused by selection drop
return
if new:
fitparams_table_source.data.update(fit_params[new[0]])
else:
fitparams_table_source.data.update(dict(param=[], value=[], vary=[], min=[], max=[]))
fitparams_select = MultiSelect(options=[], height=120, width=145)
fitparams_select.tags = [0]
fitparams_select.on_change("value", fitparams_select_callback)
def fitparams_remove_button_callback():
if fitparams_select.value:
sel_tag = fitparams_select.value[0]
del fit_params[sel_tag]
for elem in fitparams_select.options:
if elem[0] == sel_tag:
fitparams_select.options.remove(elem)
break
fitparams_select.value = []
fitparams_remove_button = Button(label="Remove fit function", width=145)
fitparams_remove_button.on_click(fitparams_remove_button_callback)
def fitparams_factory(function):
if function == "linear":
params = ["slope", "intercept"]
elif function == "gaussian":
params = ["amplitude", "center", "sigma"]
elif function == "voigt":
params = ["amplitude", "center", "sigma", "gamma"]
elif function == "pvoigt":
params = ["amplitude", "center", "sigma", "fraction"]
elif function == "pseudovoigt1":
params = ["amplitude", "center", "g_sigma", "l_sigma", "fraction"]
else:
raise ValueError("Unknown fit function")
n = len(params)
fitparams = dict(
param=params, value=[None] * n, vary=[True] * n, min=[None] * n, max=[None] * n
)
if function == "linear":
fitparams["value"] = [0, 1]
fitparams["vary"] = [False, True]
fitparams["min"] = [None, 0]
elif function == "gaussian":
fitparams["min"] = [0, None, None]
return fitparams
fitparams_table_source = ColumnDataSource(dict(param=[], value=[], vary=[], min=[], max=[]))
fitparams_table = DataTable(
source=fitparams_table_source,
columns=[
TableColumn(field="param", title="Parameter", editor=CellEditor()),
TableColumn(field="value", title="Value", editor=NumberEditor()),
TableColumn(field="vary", title="Vary", editor=CheckboxEditor()),
TableColumn(field="min", title="Min", editor=NumberEditor()),
TableColumn(field="max", title="Max", editor=NumberEditor()),
],
height=200,
width=350,
index_position=None,
editable=True,
auto_edit=True,
)
# start with `background` and `gauss` fit functions added
fitparams_add_dropdown_callback(types.SimpleNamespace(item="linear"))
fitparams_add_dropdown_callback(types.SimpleNamespace(item="gaussian"))
fitparams_select.value = ["gaussian-1"] # add selection to gauss
fit_output_textinput = TextAreaInput(title="Fit results:", width=750, height=200)
app_fitctrl.to_spinner.on_change("value", fit_to_spinner_callback)
def proc_all_button_callback():
for scan in [*dataset1, *dataset2]:
if scan["export"]:
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,
)
app_fitctrl.fit_dataset(dataset1)
app_fitctrl.fit_dataset(dataset2)
_update_plot()
_update_table()
@ -563,15 +443,9 @@ def create():
proc_all_button.on_click(proc_all_button_callback)
def proc_button_callback():
for scan in _get_selected_scan():
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,
)
scan1, scan2 = _get_selected_scan()
app_fitctrl.fit_scan(scan1)
app_fitctrl.fit_scan(scan2)
_update_plot()
_update_table()
@ -579,16 +453,11 @@ def create():
proc_button = Button(label="Process Current", width=145)
proc_button.on_click(proc_button_callback)
area_method_div = Div(text="Intensity:", margin=(5, 5, 0, 5))
area_method_radiobutton = RadioGroup(labels=["Function", "Area"], active=0, width=145)
intensity_diff_div = Div(text="Intensity difference:", margin=(5, 5, 0, 5))
intensity_diff_radiobutton = RadioGroup(
labels=["file1 - file2", "file2 - file1"], active=0, width=145
)
lorentz_checkbox = CheckboxGroup(labels=["Lorentz Correction"], width=145, margin=(13, 5, 5, 5))
export_preview_textinput = TextAreaInput(title="Export file(s) preview:", width=500, height=400)
def _update_preview():
@ -648,19 +517,24 @@ def create():
save_button = Button(label="Download File(s)", button_type="success", width=200)
save_button.js_on_click(CustomJS(args={"js_data": js_data}, code=javaScript))
area_method_div = Div(text="Intensity:", margin=(5, 5, 0, 5))
fitpeak_controls = row(
column(fitparams_add_dropdown, fitparams_select, fitparams_remove_button),
fitparams_table,
column(
app_fitctrl.add_function_button,
app_fitctrl.function_select,
app_fitctrl.remove_function_button,
),
app_fitctrl.params_table,
Spacer(width=20),
column(
fit_from_spinner,
lorentz_checkbox,
app_fitctrl.from_spinner,
app_fitctrl.lorentz_checkbox,
area_method_div,
area_method_radiobutton,
app_fitctrl.area_method_radiogroup,
intensity_diff_div,
intensity_diff_radiobutton,
),
column(fit_to_spinner, proc_button, proc_all_button),
column(app_fitctrl.to_spinner, proc_button, proc_all_button),
)
scan_layout = column(
@ -680,7 +554,7 @@ def create():
tab_layout = column(
row(import_layout, scan_layout, plot, Spacer(width=30), export_layout),
row(fitpeak_controls, fit_output_textinput),
row(fitpeak_controls, app_fitctrl.result_textarea),
)
return Panel(child=tab_layout, title="ccl compare")

176
pyzebra/app/panel_ccl_integrate.py
View File

@ -2,7 +2,6 @@ import base64
import io
import os
import tempfile
import types
import numpy as np
from bokeh.io import curdoc
@ -11,17 +10,13 @@ from bokeh.models import (
Button,
CellEditor,
CheckboxEditor,
CheckboxGroup,
ColumnDataSource,
CustomJS,
DataTable,
Div,
Dropdown,
FileInput,
MultiSelect,
NumberEditor,
Panel,
RadioGroup,
Select,
Spacer,
Span,
@ -33,7 +28,7 @@ from bokeh.models import (
from bokeh.plotting import figure
import pyzebra
from pyzebra import AREA_METHODS, EXPORT_TARGETS
from pyzebra import EXPORT_TARGETS, app
javaScript = """
let j = 0;
@ -60,7 +55,6 @@ for (let i = 0; i < js_data.data['fname'].length; i++) {
def create():
doc = curdoc()
dataset = []
fit_params = {}
js_data = ColumnDataSource(data=dict(content=["", ""], fname=["", ""], ext=["", ""]))
def file_select_update_for_proposal():
@ -259,7 +253,7 @@ def create():
xs_peak = []
ys_peak = []
comps = fit.eval_components(x=x_fit)
for i, model in enumerate(fit_params):
for i, model in enumerate(app_fitctrl.params):
if "linear" in model:
x_bkg = x_fit
y_bkg = comps[f"f{i}_"]
@ -271,13 +265,12 @@ def create():
bkg_source.data.update(x=x_bkg, y=y_bkg)
peak_source.data.update(xs=xs_peak, ys=ys_peak)
fit_output_textinput.value = fit.fit_report()
else:
fit_source.data.update(x=[], y=[])
bkg_source.data.update(x=[], y=[])
peak_source.data.update(xs=[], ys=[])
fit_output_textinput.value = ""
app_fitctrl.update_result_textarea(scan)
# Main plot
plot = figure(
@ -403,136 +396,20 @@ def create():
restore_button = Button(label="Restore scan", width=145)
restore_button.on_click(restore_button_callback)
app_fitctrl = app.FitControls()
def fit_from_spinner_callback(_attr, _old, new):
fit_from_span.location = new
fit_from_spinner = Spinner(title="Fit from:", width=145)
fit_from_spinner.on_change("value", fit_from_spinner_callback)
app_fitctrl.from_spinner.on_change("value", fit_from_spinner_callback)
def fit_to_spinner_callback(_attr, _old, new):
fit_to_span.location = new
fit_to_spinner = Spinner(title="to:", width=145)
fit_to_spinner.on_change("value", fit_to_spinner_callback)
def fitparams_add_dropdown_callback(click):
# bokeh requires (str, str) for MultiSelect options
new_tag = f"{click.item}-{fitparams_select.tags[0]}"
fitparams_select.options.append((new_tag, click.item))
fit_params[new_tag] = fitparams_factory(click.item)
fitparams_select.tags[0] += 1
fitparams_add_dropdown = Dropdown(
label="Add fit function",
menu=[
("Linear", "linear"),
("Gaussian", "gaussian"),
("Voigt", "voigt"),
("Pseudo Voigt", "pvoigt"),
# ("Pseudo Voigt1", "pseudovoigt1"),
],
width=145,
)
fitparams_add_dropdown.on_click(fitparams_add_dropdown_callback)
def fitparams_select_callback(_attr, old, new):
# Avoid selection of multiple indicies (via Shift+Click or Ctrl+Click)
if len(new) > 1:
# drop selection to the previous one
fitparams_select.value = old
return
if len(old) > 1:
# skip unnecessary update caused by selection drop
return
if new:
fitparams_table_source.data.update(fit_params[new[0]])
else:
fitparams_table_source.data.update(dict(param=[], value=[], vary=[], min=[], max=[]))
fitparams_select = MultiSelect(options=[], height=120, width=145)
fitparams_select.tags = [0]
fitparams_select.on_change("value", fitparams_select_callback)
def fitparams_remove_button_callback():
if fitparams_select.value:
sel_tag = fitparams_select.value[0]
del fit_params[sel_tag]
for elem in fitparams_select.options:
if elem[0] == sel_tag:
fitparams_select.options.remove(elem)
break
fitparams_select.value = []
fitparams_remove_button = Button(label="Remove fit function", width=145)
fitparams_remove_button.on_click(fitparams_remove_button_callback)
def fitparams_factory(function):
if function == "linear":
params = ["slope", "intercept"]
elif function == "gaussian":
params = ["amplitude", "center", "sigma"]
elif function == "voigt":
params = ["amplitude", "center", "sigma", "gamma"]
elif function == "pvoigt":
params = ["amplitude", "center", "sigma", "fraction"]
elif function == "pseudovoigt1":
params = ["amplitude", "center", "g_sigma", "l_sigma", "fraction"]
else:
raise ValueError("Unknown fit function")
n = len(params)
fitparams = dict(
param=params, value=[None] * n, vary=[True] * n, min=[None] * n, max=[None] * n
)
if function == "linear":
fitparams["value"] = [0, 1]
fitparams["vary"] = [False, True]
fitparams["min"] = [None, 0]
elif function == "gaussian":
fitparams["min"] = [0, None, None]
return fitparams
fitparams_table_source = ColumnDataSource(dict(param=[], value=[], vary=[], min=[], max=[]))
fitparams_table = DataTable(
source=fitparams_table_source,
columns=[
TableColumn(field="param", title="Parameter", editor=CellEditor()),
TableColumn(field="value", title="Value", editor=NumberEditor()),
TableColumn(field="vary", title="Vary", editor=CheckboxEditor()),
TableColumn(field="min", title="Min", editor=NumberEditor()),
TableColumn(field="max", title="Max", editor=NumberEditor()),
],
height=200,
width=350,
index_position=None,
editable=True,
auto_edit=True,
)
# start with `background` and `gauss` fit functions added
fitparams_add_dropdown_callback(types.SimpleNamespace(item="linear"))
fitparams_add_dropdown_callback(types.SimpleNamespace(item="gaussian"))
fitparams_select.value = ["gaussian-1"] # add selection to gauss
fit_output_textinput = TextAreaInput(title="Fit results:", width=750, height=200)
app_fitctrl.to_spinner.on_change("value", fit_to_spinner_callback)
def proc_all_button_callback():
for scan in dataset:
if scan["export"]:
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,
)
app_fitctrl.fit_dataset(dataset)
_update_plot()
_update_table()
@ -541,15 +418,7 @@ def create():
proc_all_button.on_click(proc_all_button_callback)
def proc_button_callback():
scan = _get_selected_scan()
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,
)
app_fitctrl.fit_scan(_get_selected_scan())
_update_plot()
_update_table()
@ -557,11 +426,6 @@ def create():
proc_button = Button(label="Process Current", width=145)
proc_button.on_click(proc_button_callback)
area_method_div = Div(text="Intensity:", margin=(5, 5, 0, 5))
area_method_radiobutton = RadioGroup(labels=["Function", "Area"], active=0, width=145)
lorentz_checkbox = CheckboxGroup(labels=["Lorentz Correction"], width=145, margin=(13, 5, 5, 5))
export_preview_textinput = TextAreaInput(title="Export file(s) preview:", width=500, height=400)
def _update_preview():
@ -615,12 +479,22 @@ def create():
save_button = Button(label="Download File(s)", button_type="success", width=200)
save_button.js_on_click(CustomJS(args={"js_data": js_data}, code=javaScript))
area_method_div = Div(text="Intensity:", margin=(5, 5, 0, 5))
fitpeak_controls = row(
column(fitparams_add_dropdown, fitparams_select, fitparams_remove_button),
fitparams_table,
column(
app_fitctrl.add_function_button,
app_fitctrl.function_select,
app_fitctrl.remove_function_button,
),
app_fitctrl.params_table,
Spacer(width=20),
column(fit_from_spinner, lorentz_checkbox, area_method_div, area_method_radiobutton),
column(fit_to_spinner, proc_button, proc_all_button),
column(
app_fitctrl.from_spinner,
app_fitctrl.lorentz_checkbox,
area_method_div,
app_fitctrl.area_method_radiogroup,
),
column(app_fitctrl.to_spinner, proc_button, proc_all_button),
)
scan_layout = column(
@ -647,7 +521,7 @@ def create():
tab_layout = column(
row(import_layout, scan_layout, plot, Spacer(width=30), export_layout),
row(fitpeak_controls, fit_output_textinput),
row(fitpeak_controls, app_fitctrl.result_textarea),
)
return Panel(child=tab_layout, title="ccl integrate")

175
pyzebra/app/panel_param_study.py
View File

@ -3,7 +3,6 @@ import io
import itertools
import os
import tempfile
import types
import numpy as np
from bokeh.io import curdoc
@ -12,19 +11,16 @@ from bokeh.models import (
Button,
CellEditor,
CheckboxEditor,
CheckboxGroup,
ColumnDataSource,
CustomJS,
DataTable,
Div,
Dropdown,
FileInput,
HoverTool,
LinearColorMapper,
MultiSelect,
NumberEditor,
Panel,
RadioGroup,
Range1d,
Select,
Spacer,
@ -40,7 +36,7 @@ from bokeh.plotting import figure
from scipy import interpolate
import pyzebra
from pyzebra import AREA_METHODS
from pyzebra import app
javaScript = """
let j = 0;
@ -72,7 +68,6 @@ def color_palette(n_colors):
def create():
doc = curdoc()
dataset = []
fit_params = {}
js_data = ColumnDataSource(data=dict(content=[""], fname=[""], ext=[""]))
def file_select_update_for_proposal():
@ -281,7 +276,7 @@ def create():
xs_peak = []
ys_peak = []
comps = fit.eval_components(x=x_fit)
for i, model in enumerate(fit_params):
for i, model in enumerate(app_fitctrl.params):
if "linear" in model:
x_bkg = x_fit
y_bkg = comps[f"f{i}_"]
@ -293,13 +288,12 @@ def create():
bkg_source.data.update(x=x_bkg, y=y_bkg)
peak_source.data.update(xs=xs_peak, ys=ys_peak)
fit_output_textinput.value = fit.fit_report()
else:
fit_source.data.update(x=[], y=[])
bkg_source.data.update(x=[], y=[])
peak_source.data.update(xs=[], ys=[])
fit_output_textinput.value = ""
app_fitctrl.update_result_textarea(scan)
def _update_overview():
xs = []
@ -562,136 +556,20 @@ def create():
)
param_select.on_change("value", param_select_callback)
app_fitctrl = app.FitControls()
def fit_from_spinner_callback(_attr, _old, new):
fit_from_span.location = new
fit_from_spinner = Spinner(title="Fit from:", width=145)
fit_from_spinner.on_change("value", fit_from_spinner_callback)
app_fitctrl.from_spinner.on_change("value", fit_from_spinner_callback)
def fit_to_spinner_callback(_attr, _old, new):
fit_to_span.location = new
fit_to_spinner = Spinner(title="to:", width=145)
fit_to_spinner.on_change("value", fit_to_spinner_callback)
def fitparams_add_dropdown_callback(click):
# bokeh requires (str, str) for MultiSelect options
new_tag = f"{click.item}-{fitparams_select.tags[0]}"
fitparams_select.options.append((new_tag, click.item))
fit_params[new_tag] = fitparams_factory(click.item)
fitparams_select.tags[0] += 1
fitparams_add_dropdown = Dropdown(
label="Add fit function",
menu=[
("Linear", "linear"),
("Gaussian", "gaussian"),
("Voigt", "voigt"),
("Pseudo Voigt", "pvoigt"),
# ("Pseudo Voigt1", "pseudovoigt1"),
],
width=145,
)
fitparams_add_dropdown.on_click(fitparams_add_dropdown_callback)
def fitparams_select_callback(_attr, old, new):
# Avoid selection of multiple indicies (via Shift+Click or Ctrl+Click)
if len(new) > 1:
# drop selection to the previous one
fitparams_select.value = old
return
if len(old) > 1:
# skip unnecessary update caused by selection drop
return
if new:
fitparams_table_source.data.update(fit_params[new[0]])
else:
fitparams_table_source.data.update(dict(param=[], value=[], vary=[], min=[], max=[]))
fitparams_select = MultiSelect(options=[], height=120, width=145)
fitparams_select.tags = [0]
fitparams_select.on_change("value", fitparams_select_callback)
def fitparams_remove_button_callback():
if fitparams_select.value:
sel_tag = fitparams_select.value[0]
del fit_params[sel_tag]
for elem in fitparams_select.options:
if elem[0] == sel_tag:
fitparams_select.options.remove(elem)
break
fitparams_select.value = []
fitparams_remove_button = Button(label="Remove fit function", width=145)
fitparams_remove_button.on_click(fitparams_remove_button_callback)
def fitparams_factory(function):
if function == "linear":
params = ["slope", "intercept"]
elif function == "gaussian":
params = ["amplitude", "center", "sigma"]
elif function == "voigt":
params = ["amplitude", "center", "sigma", "gamma"]
elif function == "pvoigt":
params = ["amplitude", "center", "sigma", "fraction"]
elif function == "pseudovoigt1":
params = ["amplitude", "center", "g_sigma", "l_sigma", "fraction"]
else:
raise ValueError("Unknown fit function")
n = len(params)
fitparams = dict(
param=params, value=[None] * n, vary=[True] * n, min=[None] * n, max=[None] * n
)
if function == "linear":
fitparams["value"] = [0, 1]
fitparams["vary"] = [False, True]
fitparams["min"] = [None, 0]
elif function == "gaussian":
fitparams["min"] = [0, None, None]
return fitparams
fitparams_table_source = ColumnDataSource(dict(param=[], value=[], vary=[], min=[], max=[]))
fitparams_table = DataTable(
source=fitparams_table_source,
columns=[
TableColumn(field="param", title="Parameter", editor=CellEditor()),
TableColumn(field="value", title="Value", editor=NumberEditor()),
TableColumn(field="vary", title="Vary", editor=CheckboxEditor()),
TableColumn(field="min", title="Min", editor=NumberEditor()),
TableColumn(field="max", title="Max", editor=NumberEditor()),
],
height=200,
width=350,
index_position=None,
editable=True,
auto_edit=True,
)
# start with `background` and `gauss` fit functions added
fitparams_add_dropdown_callback(types.SimpleNamespace(item="linear"))
fitparams_add_dropdown_callback(types.SimpleNamespace(item="gaussian"))
fitparams_select.value = ["gaussian-1"] # add selection to gauss
fit_output_textinput = TextAreaInput(title="Fit results:", width=750, height=200)
app_fitctrl.to_spinner.on_change("value", fit_to_spinner_callback)
def proc_all_button_callback():
for scan in dataset:
if scan["export"]:
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,
)
app_fitctrl.fit_dataset(dataset)
_update_single_scan_plot()
_update_overview()
@ -708,15 +586,7 @@ def create():
proc_all_button.on_click(proc_all_button_callback)
def proc_button_callback():
scan = _get_selected_scan()
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,
)
app_fitctrl.fit_scan(_get_selected_scan())
_update_single_scan_plot()
_update_overview()
@ -732,11 +602,6 @@ def create():
proc_button = Button(label="Process Current", width=145)
proc_button.on_click(proc_button_callback)
area_method_div = Div(text="Intensity:", margin=(5, 5, 0, 5))
area_method_radiobutton = RadioGroup(labels=["Function", "Area"], active=0, width=145)
lorentz_checkbox = CheckboxGroup(labels=["Lorentz Correction"], width=145, margin=(13, 5, 5, 5))
export_preview_textinput = TextAreaInput(title="Export file preview:", width=450, height=400)
def _update_preview():
@ -769,12 +634,22 @@ def create():
save_button = Button(label="Download File", button_type="success", width=220)
save_button.js_on_click(CustomJS(args={"js_data": js_data}, code=javaScript))
area_method_div = Div(text="Intensity:", margin=(5, 5, 0, 5))
fitpeak_controls = row(
column(fitparams_add_dropdown, fitparams_select, fitparams_remove_button),
fitparams_table,
column(
app_fitctrl.add_function_button,
app_fitctrl.function_select,
app_fitctrl.remove_function_button,
),
app_fitctrl.params_table,
Spacer(width=20),
column(fit_from_spinner, lorentz_checkbox, area_method_div, area_method_radiobutton),
column(fit_to_spinner, proc_button, proc_all_button),
column(
app_fitctrl.from_spinner,
app_fitctrl.lorentz_checkbox,
area_method_div,
app_fitctrl.area_method_radiogroup,
),
column(app_fitctrl.to_spinner, proc_button, proc_all_button),
)
scan_layout = column(
@ -796,7 +671,7 @@ def create():
tab_layout = column(
row(import_layout, scan_layout, plots, Spacer(width=30), export_layout),
row(fitpeak_controls, fit_output_textinput),
row(fitpeak_controls, app_fitctrl.result_textarea),
)
return Panel(child=tab_layout, title="param study")