fix: fitall button and clicking per file should output identical results

CHANGELOG

@@ -1,4 +1,5 @@
 0.16.4
+ - fix: ensure identical results when clicking per file and compute button (#47, #48)
  - setup: support latest python versions (#32, #46)
  - setup: support latest matplotlib versions (#32, #46)
  - fix: remember user's choice upon curve open (#44, #45)

pyjibe/fd/main.py

@@ -83,6 +83,7 @@ def __init__(self, *args, **kwargs):
             self.on_cb_rating_scheme)
         self.btn_rater.clicked.connect(self.on_user_rate)
         # plotting parameters
+        self.cb_show_fit_line.stateChanged.connect(self.on_mpl_curve_update)
         self.cb_mpl_rescale_plot_x.stateChanged.connect(
             self.on_mpl_curve_update)
         self.cb_mpl_rescale_plot_x_min.valueChanged.connect(
@@ -512,6 +513,8 @@ def on_fit_all(self):
             try:
                 # preprocessing could fail for bad data
                 self.tab_preprocess.apply_preprocessing(fdist)
+                # update model key and ancillary parameters before fitting
+                self.tab_fit.fit_update_parameters(fdist)
                 # external fitting model could fail
                 self.tab_fit.fit_approach_retract(fdist, update_ui=False)
             except BaseException as e:

pyjibe/fd/main.ui

@@ -138,6 +138,16 @@
           <item>
            <widget class="QWidget" name="plot_prefs" native="true">
             <layout class="QVBoxLayout" name="verticalLayout_8">
+             <item>
+              <widget class="QCheckBox" name="cb_show_fit_line">
+               <property name="text">
+                <string>Show fit line</string>
+               </property>
+               <property name="checked">
+                <bool>true</bool>
+               </property>
+              </widget>
+             </item>
              <item>
               <widget class="QCheckBox" name="cb_mpl_rescale_plot_x">
                <property name="text">

pyjibe/fd/mpl_indent.py

@@ -50,6 +50,11 @@ def __init__(self):
                                                      range(2),
                                                      label="residuals")[0]
 
+        self.ann_r2 = self.axis_main.text(
+            0.98, 0.05, "", transform=self.axis_main.transAxes,
+            ha="right", va="bottom", fontsize=9,
+            bbox=dict(boxstyle="round,pad=0.2", fc="white", alpha=0.7))
+
         self.canvas = FigureCanvas(self.figure)
 
         self.canvas.draw()
@@ -67,7 +72,7 @@ def add_toolbar(self, widget):
     def save_data_callback(self, filename):
         self.fdist.export(filename)
 
-    def update(self, fdist, rescale_x=None, rescale_y=None):
+    def update(self, fdist, rescale_x=None, rescale_y=None, show_fit=True):
         self.fdist = fdist
         xaxis = "tip position"
         yaxis = "force"
@@ -96,13 +101,22 @@ def update(self, fdist, rescale_x=None, rescale_y=None):
 
         if "fit" in fdist and np.sum(fdist["fit range"]):
             self.plots["residuals"].set_visible(True)
-            self.plots["fit"].set_visible(True)
+            self.plots["fit"].set_visible(show_fit)
             self.plots["fit range"].set_visible(True)
 
             self.plots["fit"].set_data(fdist["tip position"]*xscale,
                                        fdist["fit"]*yscale)
             self.plots["residuals"].set_data(fdist["tip position"]*xscale,
                                              (fdist["fit residuals"])*yscale)
+
+            fit_mask = fdist["fit range"]
+            y_true = fdist["force"][fit_mask]
+            y_pred = fdist["fit"][fit_mask]
+            ss_res = np.sum((y_true - y_pred) ** 2)
+            ss_tot = np.sum((y_true - np.mean(y_true)) ** 2)
+            r2 = 1 - ss_res / ss_tot if ss_tot != 0 else np.nan
+            self.ann_r2.set_text(f"R² = {r2:.4f}")
+            self.ann_r2.set_visible(True)
             # fit range
             fitrange = (fdist[xaxis]*xscale)[fdist["fit range"]]
             fitmin = np.min(fitrange)
@@ -132,6 +146,8 @@ def update(self, fdist, rescale_x=None, rescale_y=None):
             self.plots["residuals"].set_visible(False)
             self.plots["fit"].set_visible(False)
             self.plots["fit range"].set_visible(False)
+            self.ann_r2.set_text("")
+            self.ann_r2.set_visible(False)
             self.canvas.draw()
 
     def update_plot(self, rescale_x=None, rescale_y=None):

pyjibe/fd/widget_plot_fd.py

@@ -36,6 +36,8 @@ def mpl_curve_update(self, fdist):
             rescale_y = (self.fd.cb_mpl_rescale_plot_y_min.value(),
                          self.fd.cb_mpl_rescale_plot_y_max.value())
 
+        show_fit = self.fd.cb_show_fit_line.isChecked()
         self.mpl_curve.update(fdist,
                               rescale_x=rescale_x,
-                              rescale_y=rescale_y)
+                              rescale_y=rescale_y,
+                              show_fit=show_fit)

tests/test_fd_fit.py

@@ -262,3 +262,121 @@ def test_set_indentation_depth_manually_infdoublespinbox(qtbot):
         qtbot.keyClicks(war.tab_fit.sp_range_1, text_entered)
         assert war.tab_fit.sp_range_1.value() == resulting_value
     main_window.close()
+
+
+def test_fit_all_matches_single_fit(qtbot):
+    """on_fit_all must produce the same fitted params as fitting one-by-one.
+
+    Regression test for issue #47: fit-all skipped fit_update_parameters(),
+    so ancillary parameters were not recomputed, leading to different TSV
+    output compared to the single-curve path.
+    """
+    main_window = pyjibe.head.PyJibe()
+    qtbot.addWidget(main_window)
+    main_window.load_data(files=make_directory_with_data(2))
+    war = main_window.subwindows[0].widget()
+    war.cb_autosave.setChecked(0)
+    war.tab_preprocess.set_preprocessing(["compute_tip_position"])
+    war.tab_fit.cb_weight_cp.setCheckState(QtCore.Qt.CheckState.Unchecked)
+
+    # Fit first curve via the single-curve path (on_curve_list triggers this)
+    war.on_tab_changed()
+    fdist0 = war.data_set[0]
+    assert fdist0.fit_properties.get("success", False), (
+        "single fit must succeed")
+    single_E = fdist0.fit_properties["params_fitted"]["E"].value
+
+    # Now re-fit everything via fit-all
+    war.on_fit_all()
+    fitall_E = fdist0.fit_properties["params_fitted"]["E"].value
+
+    assert single_E == pytest.approx(fitall_E, rel=1e-6), (
+        f"fit-all gave E={fitall_E:.4g} but single-fit gave E={single_E:.4g}")
+    main_window.close()
+
+
+def test_fit_all_matches_single_fit_kvm(qtbot):
+    """fit-all must match single-fit for the KVM model (issue #47).
+
+    KVM has ancillary parameters (eta, time_ind) that are derived by fitting
+    a preliminary Hertz model to each curve. Before the fix, on_fit_all()
+    skipped fit_update_parameters(), so those ancillaries were never
+    recomputed and the fitted Eu values differed from the single-curve path.
+
+    The KVM model is loaded via PyJibe's extension system at startup.
+    """
+    main_window = pyjibe.head.PyJibe()
+    qtbot.addWidget(main_window)
+    main_window.load_data(files=make_directory_with_data(2))
+    war = main_window.subwindows[0].widget()
+    war.cb_autosave.setChecked(0)
+    war.tab_preprocess.set_preprocessing(["compute_tip_position"])
+    war.tab_fit.cb_weight_cp.setCheckState(QtCore.Qt.CheckState.Unchecked)
+
+    # Switch to the KVM model (loaded via PyJibe's extension system)
+    idx = war.tab_fit.cb_model.findData("hertz_corr_visco_KVM")
+    if idx < 0:
+        pytest.skip("KVM model extension not installed in this environment")
+    war.tab_fit.cb_model.setCurrentIndex(idx)
+
+    # Fit first curve via the single-curve path
+    war.on_tab_changed()
+    fdist0 = war.data_set[0]
+    assert fdist0.fit_properties.get("success", False), "single KVM fit failed"
+    single_Eu = fdist0.fit_properties["params_fitted"]["Eu"].value
+
+    # Re-fit everything via fit-all
+    war.on_fit_all()
+    fitall_Eu = fdist0.fit_properties["params_fitted"]["Eu"].value
+
+    assert single_Eu == pytest.approx(fitall_Eu, rel=1e-6), (
+        f"fit-all gave Eu={fitall_Eu:.4g} but single-fit "
+        f"gave Eu={single_Eu:.4g}")
+    main_window.close()
+
+
+def test_show_fit_line_toggle(qtbot):
+    """Toggle cb_show_fit_line hides/shows the fit line on the plot."""
+    main_window = pyjibe.head.PyJibe()
+    qtbot.addWidget(main_window)
+    main_window.load_data(files=make_directory_with_data(1))
+    war = main_window.subwindows[0].widget()
+    war.cb_autosave.setChecked(0)
+    war.tab_preprocess.set_preprocessing(["compute_tip_position"])
+    war.tab_fit.cb_weight_cp.setCheckState(QtCore.Qt.CheckState.Unchecked)
+    war.on_tab_changed()
+
+    mpl = war.widget_plot_fd.mpl_curve
+    # fit line should be visible by default after fitting
+    assert mpl.plots["fit"].get_visible()
+
+    # uncheck the toggle — fit line should disappear
+    war.cb_show_fit_line.setChecked(False)
+    war.on_mpl_curve_update()
+    assert not mpl.plots["fit"].get_visible()
+
+    # re-check — fit line should reappear
+    war.cb_show_fit_line.setChecked(True)
+    war.on_mpl_curve_update()
+    assert mpl.plots["fit"].get_visible()
+    main_window.close()
+
+
+def test_r2_annotation_shown_after_fit(qtbot):
+    """R² annotation is visible and well-formed after a successful fit."""
+    main_window = pyjibe.head.PyJibe()
+    qtbot.addWidget(main_window)
+    main_window.load_data(files=make_directory_with_data(1))
+    war = main_window.subwindows[0].widget()
+    war.cb_autosave.setChecked(0)
+    war.tab_preprocess.set_preprocessing(["compute_tip_position"])
+    war.tab_fit.cb_weight_cp.setCheckState(QtCore.Qt.CheckState.Unchecked)
+    war.on_tab_changed()
+
+    mpl = war.widget_plot_fd.mpl_curve
+    assert mpl.ann_r2.get_visible()
+    text = mpl.ann_r2.get_text()
+    assert text.startswith("R²")
+    r2_value = float(text.split("=")[1].strip())
+    assert 0.0 <= r2_value <= 1.0
+    main_window.close()