minor fixes

cylindra/widgets/batch/sta.py

@@ -220,6 +220,8 @@ def filter_loader(
     @nogui
     def get_loader(self, name: str) -> BatchLoader:
         """Return the acryo.BatchLoader object with the given name"""
+        if not isinstance(name, str):
+            raise TypeError(f"Name must be a string, got {type(name).__name__}")
         return self._get_parent().loader_infos[name].loader
 
     @set_design(text="Average all molecules", location=BatchSubtomogramAnalysis)
@@ -545,7 +547,7 @@ def show_template_original(self):
     @do_not_record
     def show_mask(self):
         """Load and show mask image in the scale of the tomogram."""
-        loader = self._get_parent().loader_infos[self.loader_name].loader
+        loader = self.get_loader(self.loader_name)
         _, mask = loader.normalize_input(
             self.params._norm_template_param(
                 self.params._get_template_input(allow_multiple=False),
@@ -572,7 +574,7 @@ def _get_shape_in_px(
             return (roundint(default / loader.scale),) * 3
 
     def _get_template_image(self) -> ip.ImgArray:
-        scale = self._get_parent().loader_infos[self.loader_name].loader.scale
+        scale = self.get_loader(self.loader_name).scale
 
         template = self.params._norm_template_param(
             self.params._get_template_input(allow_multiple=True),

cylindra/widgets/sta.py

@@ -200,7 +200,7 @@ def _get_choice(self: "SubtomogramAveraging", w=None) -> list[str]:
             return features.columns
         return [c for c in features.columns if features[c].dtype.kind in dtype_kind]
 
-    _get_choice.__qualname__ = "CylindraMainWidget.sta._get_choice"
+    _get_choice.__qualname__ = "SubtomogramAveraging._get_choice"
     return _get_choice
 
 
@@ -1629,7 +1629,7 @@ def seam_search_by_feature(
             Name of the feature that will be used for seam search.
         """
         layer = assert_layer(layer, self.parent_viewer)
-        feat = layer.features
+        feat = layer.molecules.features
         if by not in feat.columns:
             raise ValueError(f"Column {by} does not exist.")
         npf = utils.roundint(layer.molecules.features[Mole.pf].max() + 1)
@@ -1648,14 +1648,16 @@ def seam_search_manually(
         """
         Search for seams manually.
 
+        Seam location is represented by a number in the range [0, 2 * npf - 1].
+
         Parameters
         ----------
         {layer}
         location : int
             Seam location.
         """
         layer = assert_layer(layer, self.parent_viewer)
-        feat = layer.features
+        feat = layer.molecules.features
         npf = utils.roundint(layer.molecules.features[Mole.pf].max() + 1)
         seam_searcher = ManualSeamSearcher(npf)
         result = seam_searcher.search(location)

docs/alignment/index.md

@@ -5,7 +5,7 @@ cryo-ET analysis workflows. `cylindra` provides methods to perform the analyses.
 GUI, these methods are all in a separate dock widget titled "STA widget". You can open
 via `Analysis > Open STA widget` (++ctrl+k++ → ++s++).
 
-![STA widget](../images/sta_widget.png)
+![STA widget](../images/sta_widget.png){ loading=lazy, width=480px }
 
 Since many methods share the same parameters, the STA widget uses the same widget for
 these parameters.

pyproject.toml

@@ -24,7 +24,7 @@ dependencies = [
     "acryo>=0.4.7",
     "macro-kit>=0.4.6",
     "magicgui>=0.8.1",
-    "magic-class>=0.7.6",
+    "magic-class>=0.7.7",
     "psygnal>=0.9.1",
     "superqt[iconify]>=0.6.1",
     "pyqtgraph>=0.12.4",

tests/test_gui_0.py

@@ -57,11 +57,14 @@ def assert_orientation(ui: CylindraMainWidget, ori: str):
 
 def test_click_buttons(ui: CylindraMainWidget):
     mcls_testing.check_function_gui_buildable(ui)
+    mcls_testing.check_function_gui_buildable(ui.sta)
     mcls_testing.check_function_gui_buildable(ui.simulator)
 
 
 def test_tooltip(ui: CylindraMainWidget):
     mcls_testing.check_tooltip(ui)
+    mcls_testing.check_tooltip(ui.sta)
+    mcls_testing.check_tooltip(ui.simulator)
 
 
 def test_misc_actions(ui: CylindraMainWidget):
@@ -561,7 +564,7 @@ def test_sub_widgets(ui: CylindraMainWidget):
 @pytest.mark.parametrize("bin_size", [1, 2])
 def test_sta(ui: CylindraMainWidget, bin_size: int):
     ui.load_project(PROJECT_DIR_13PF, filter=None)
-    ui.AnalysisMenu.open_subtomogram_analyzer()
+    ui.AnalysisMenu.open_sta_widget()
     ui.sta.average_all("Mole-0", size=12.0, bin_size=bin_size)
     ui.sta.average_all("Mole-0", size=12.0, bin_size=bin_size)  # check coerce name
     for method in ["steps", "first", "last", "random"]: