Enable Fit/Int area selector

pyzebra/app/panel_ccl_integrate.py

@@ -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):
+    area_method_radiobutton = RadioButtonGroup(labels=["Fit area", "Int area"], active=0, width=145)
-        _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()
 
     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,
+                export_data, temp_file, hkl_precision=int(hkl_precision_select.value),
-                temp_file,
-                area_method=AREA_METHODS[int(area_method_radiobutton.active)],
-                lorentz=bool(lorentz_checkbox.active),
-                hkl_precision=int(hkl_precision_select.value),
             )
 
             exported_content = ""

pyzebra/app/panel_param_study.py

@@ -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):
+    area_method_radiobutton = RadioButtonGroup(labels=["Fit area", "Int area"], active=0, width=145)
-        _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()
 
     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(
+            pyzebra.export_1D(export_data, temp_file)
-                export_data,
-                temp_file,
-                area_method=AREA_METHODS[int(area_method_radiobutton.active)],
-                lorentz=bool(lorentz_checkbox.active),
-            )
 
             exported_content = ""
             file_content = []

pyzebra/ccl_io.py

@@ -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():
+        area_n, area_s = scan["area"]
-            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_str = f"{area_n:10.2f}{area_s:10.2f}"
 
         ang_str = ""

pyzebra/ccl_process.py

@@ -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)