Add a Measurements reference tab to the in-app help

probeflow/gui/dialogs/image_viewer_chrome_mixin.py

@@ -241,7 +241,7 @@ def _build_viewer_menu_bar(self) -> None:
         processing_menu.addSeparator()
         self._add_combo_menu(
             processing_menu, "Align rows", self._processing_panel._align_combo,
-            ["None", "Median", "Mean"],
+            ["None", "Median", "Mean", "Linear"],
         )
         self._add_combo_menu(
             processing_menu, "Bad line correction", self._processing_panel._bad_lines_combo,
@@ -506,6 +506,11 @@ def _build_viewer_menu_bar(self) -> None:
             self._show_viewer_definitions,
         )
         help_menu.insertAction(github_action, definitions_action)
+        measurements_help_action = self._viewer_action(
+            "help.measurements",
+            self._show_viewer_measurements,
+        )
+        help_menu.insertAction(github_action, measurements_help_action)
         roi_reference_help_action = self._viewer_action(
             "help.roi_reference",
             self._show_viewer_roi_reference,

probeflow/gui/processing.py

@@ -129,10 +129,11 @@ def _col_lbl(text: str, target):
         line_lbl.setAlignment(Qt.AlignCenter)
         lay.addWidget(line_lbl)
 
-        self._align_combo = _combo_row("Align rows:", ["None", "Median", "Mean"])
+        self._align_combo = _combo_row("Align rows:", ["None", "Median", "Mean", "Linear"])
         self._align_combo.setToolTip(
             "Level each scan line by subtracting its median or mean, removing "
-            "row-to-row offsets and slow tilt along the slow-scan direction."
+            "row-to-row offsets and slow tilt along the slow-scan direction. "
+            "'Linear' also fits and removes a straight slope within each row."
         )
 
         self._bad_lines_combo = _combo_row(
@@ -340,7 +341,7 @@ def _col_lbl(text: str, target):
         lay.addWidget(self._filter_section)
 
     def state(self) -> dict:
-        align_map = {0: None, 1: "median", 2: "mean"}
+        align_map = {0: None, 1: "median", 2: "mean", 3: "linear"}
         bad_map = {0: None, 1: "step", 2: "mad"}
         cfg = {
             "align_rows": align_map[self._align_combo.currentIndex()],
@@ -382,7 +383,7 @@ def set_state(self, state: dict | None) -> None:
         state = state or {}
         old_block = self._align_combo.blockSignals(True)
         self._align_combo.setCurrentIndex(
-            {None: 0, "median": 1, "mean": 2}.get(state.get("align_rows"), 0))
+            {None: 0, "median": 1, "mean": 2, "linear": 3}.get(state.get("align_rows"), 0))
         self._align_combo.blockSignals(old_block)
         self._bad_lines_combo.setCurrentIndex(
             {None: 0, "step": 1, "step_segments": 1,

probeflow/gui/viewer/image_viewer_toolbar_mixin.py

@@ -39,6 +39,17 @@ def _show_viewer_definitions(self) -> None:
         dlg.raise_()
         dlg.activateWindow()
 
+    def _show_viewer_measurements(self) -> None:
+        dlg = getattr(self, "_definitions_dialog", None)
+        if dlg is None:
+            dlg = _DefinitionsDialog(self._t, self, initial_tab="measurements")
+            self._definitions_dialog = dlg
+        else:
+            dlg.set_reference_tab("measurements")
+        dlg.show()
+        dlg.raise_()
+        dlg.activateWindow()
+
     def _show_viewer_roi_reference(self) -> None:
         dlg = getattr(self, "_definitions_dialog", None)
         if dlg is None:

probeflow/gui/viewer/shortcuts.py

@@ -133,6 +133,11 @@ class ViewerCommand:
     ViewerCommand("help.shortcuts", "Image viewer shortcuts", "Help", status_tip="Show image-viewer shortcut help.", aliases=("keyboard", "keys")),
     ViewerCommand("help.howto", "How-to guides", "Help", status_tip="Show step-by-step how-to walkthroughs for common tasks.", aliases=("tutorial", "guide", "walkthrough", "getting started")),
     ViewerCommand("help.definitions", "Definitions", "Help", status_tip="Show processing definitions and equations.", aliases=("reference", "math", "algorithms")),
+    ViewerCommand(
+        "help.measurements", "Measurements Reference", "Help",
+        status_tip="Show what each measurement computes (distance, step height, roughness, …).",
+        aliases=("measure", "measurement", "stats", "step height", "roughness"),
+    ),
     ViewerCommand(
         "help.roi_reference", "ROI Reference", "Help",
         status_tip="Show ROI actions, selection rules, and tool interactions.",

tests/test_definitions_dialog.py

@@ -38,6 +38,7 @@ def test_definitions_reference_has_equations_and_light_theme_contrast():
         "STM background subtraction",
         "Gaussian high-pass",
         "Periodic notch filtering",
+        "Advanced edge detection (Canny",
         "Manual zero reference",
         "Image arithmetic",
         "Thresholding and bit-depth conversion",
@@ -46,6 +47,9 @@ def test_definitions_reference_has_equations_and_light_theme_contrast():
         "Forward/backward scan blending",
     ):
         assert operation in html
+    # Advanced edge detection explains hysteresis and the mask/ROI outputs.
+    assert "hysteresis" in html
+    assert "Sobel / Scharr" in html
 
     assert "color: #111827" in html
     assert "#cdd6f4" not in lowered
@@ -120,25 +124,62 @@ def test_howto_reference_has_numbered_steps_and_key_workflows():
         assert expected in html, expected
 
 
+def test_measurements_reference_has_entries_and_formulas():
+    from probeflow.gui.dialogs.definitions import (
+        _MEASUREMENT_ENTRIES,
+        render_measurements_html,
+    )
+    from probeflow.gui.styling import THEMES
+
+    html = render_measurements_html(THEMES["light"])
+
+    # Every measurement entry renders an equation block and an "In practice" lead.
+    assert html.count('class="equation"') >= len(_MEASUREMENT_ENTRIES)
+    assert html.count("In practice:") >= len(_MEASUREMENT_ENTRIES)
+
+    for expected in (
+        "Measurements Reference",
+        "Distance",
+        "Angle",
+        "Line profile",
+        "Line periodicity",
+        "ROI statistics",
+        "Step height",
+        "Feature maxima",
+        "Pair correlation",
+        "Feature → lattice",
+        # A couple of formulas must match the implementation.
+        "rms_roughness = sqrt(mean((z - mean(z))^2))",
+        "height_difference = mean_b - mean_a",
+        # The line tool's drawing/editing is cross-referenced to the ROI tab.
+        "Line ROI actions",
+    ):
+        assert expected in html, expected
+
+
 def test_definitions_dialog_tabs_can_focus_howto_processing_and_roi(qapp):
     from probeflow.gui.dialogs.definitions import _DefinitionsDialog
     from probeflow.gui.styling import THEMES
 
     default = _DefinitionsDialog(THEMES["light"])
     roi_first = _DefinitionsDialog(THEMES["light"], initial_tab="roi")
     howto_first = _DefinitionsDialog(THEMES["light"], initial_tab="howto")
+    measure_first = _DefinitionsDialog(THEMES["light"], initial_tab="measurements")
     try:
         assert default.current_reference_tab() == "processing"
         default.set_reference_tab("roi")
         assert default.current_reference_tab() == "roi"
+        default.set_reference_tab("measurements")
+        assert default.current_reference_tab() == "measurements"
         default.set_reference_tab("howto")
         assert default.current_reference_tab() == "howto"
         default.set_reference_tab("processing")
         assert default.current_reference_tab() == "processing"
         assert roi_first.current_reference_tab() == "roi"
         assert howto_first.current_reference_tab() == "howto"
+        assert measure_first.current_reference_tab() == "measurements"
     finally:
-        for dlg in (default, roi_first, howto_first):
+        for dlg in (default, roi_first, howto_first, measure_first):
             dlg.close()
             dlg.deleteLater()
         qapp.processEvents()

tests/test_gui_processing_panel.py

@@ -145,6 +145,20 @@ def test_browse_quick_panel_emits_only_thumbnail_corrections(qapp):
     assert panel.state() == {"align_rows": "median", "remove_bad_lines": None}
 
 
+def test_align_rows_exposes_linear_option(qapp):
+    # The backend align_rows supports median/mean/linear; the GUI must offer all
+    # three so the documented 'linear' option is actually reachable.
+    from probeflow.gui import ProcessingControlPanel
+
+    panel = ProcessingControlPanel("viewer_full")
+    items = [panel._align_combo.itemText(i) for i in range(panel._align_combo.count())]
+    assert items == ["None", "Median", "Mean", "Linear"]
+
+    panel.set_state({"align_rows": "linear"})
+    assert panel._align_combo.currentIndex() == 3
+    assert panel.state()["align_rows"] == "linear"
+
+
 def test_viewer_full_panel_round_trips_standard_processing_state(qapp):
     from PySide6.QtWidgets import QCheckBox, QLabel, QPushButton
     from probeflow.gui import ProcessingControlPanel

tests/test_viewer_shortcuts.py

@@ -54,6 +54,7 @@ def test_command_finder_shortcut_and_visible_commands_are_high_level():
     assert "fft.periodic_filter" in finder_ids
     assert "measure.clear_lattice_grid" in finder_ids
     assert "help.definitions" in finder_ids
+    assert "help.measurements" in finder_ids
     assert "help.roi_reference" in finder_ids
     assert viewer_command("help.roi_reference").shortcuts == ()
     assert not any(command_id.startswith("roi.tool.") for command_id in finder_ids)