Merge pull request #90 from hanjinliu/fix-inspector

Fix inspector

cylindra/widgets/subwidgets/measure.py

@@ -24,7 +24,7 @@
 from cylindra.widgets.subwidgets._child_widget import ChildWidget
 
 if TYPE_CHECKING:
-    from cylindra.components.tomogram._cyl_tomo import ImageWithPeak
+    from cylindra.components.tomogram._misc import ImageWithPeak
 
 
 class MouseMode(Enum):
@@ -56,15 +56,16 @@ def __init__(self):
         self._power_spectra = list[ip.ImgArray | None]()
         self._image = np.zeros((1, 1))
         self._is_log_scale = False
+        self._current_spline_index = 0
         self._current_binsize = 1
         self._last_upsample_params = {}
 
     def __post_init__(self):
         self._upsampled_image_item = pg.ImageItem()
         self.canvas._viewbox.addItem(self._upsampled_image_item)
         self._upsampled_image_item.setVisible(False)
-        self._infline_x = self.canvas.add_infline(1, 0, color="yellow")
-        self._infline_y = self.canvas.add_infline(1, 90, color="yellow")
+        self._infline_x = self.canvas.add_infline((0, 0), 0, color="yellow")
+        self._infline_y = self.canvas.add_infline((0, 0), 90, color="yellow")
         self._layer_axial = self.canvas.add_scatter(
             [], [], color="cyan", symbol="+", size=12
         )
@@ -90,11 +91,14 @@ def _set_spline(self, i: int, binsize: int | None = None):
                 self._power_spectra = []
                 self._peaks = None
                 self._image = np.zeros((1, 1))
-            return None
+                return None
+            else:
+                raise ValueError(f"Invalid spline index: {i}")
         spl = main.splines[i]
         self._layer_axial.data = [], []
         self._layer_angular.data = [], []
         self._upsampled_image_item.setVisible(False)
+        self._current_spline_index = i
         if self.show_what == "Local-CFT":
             if spl.props.has_loc(H.twist) and spl.has_anchors:
                 # has local-CFT results
@@ -110,6 +114,10 @@ def _set_spline(self, i: int, binsize: int | None = None):
             self["pos"].visible = True
             self["pos"].max = len(self._power_spectra) - 1
         else:
+            if self._may_show_text_overlay(
+                spl.radius is None, "No CFT available (radius not set)"
+            ):
+                return
             if spl.props.has_glob(H.twist):
                 # has global-CFT results
                 if binsize is None:
@@ -203,12 +211,8 @@ def _pos_changed(self, pos: int):
         if len(self._power_spectra) == 0:
             return None
         _next_image = self._power_spectra[pos]
-        if _next_image is None:
-            self.canvas.text_overlay.text = "No CFT available"
-            self.canvas.text_overlay.visible = True
-            self.canvas.text_overlay.color = "lime"
-            return
-        self.canvas.text_overlay.visible = False
+        if self._may_show_text_overlay(_next_image is None, "No CFT available"):
+            return None
         self._image = np.asarray(_next_image)
         self._update_image()
         if self._peaks is None:
@@ -225,7 +229,19 @@ def _pos_changed(self, pos: int):
     @show_what.connect
     def _show_what_changed(self, value: str):
         if len(self._power_spectra) > 0:
-            self._set_spline(self.pos, binsize=None)
+            self._set_spline(self._current_spline_index, binsize=None)
+
+    def _may_show_text_overlay(self, when: bool, text: str) -> bool:
+        if when:
+            self.canvas.text_overlay.text = text
+            self.canvas.text_overlay.visible = True
+            self.canvas.text_overlay.color = "lime"
+            del self.canvas.image
+            self._markers.visible = False
+            self._image = np.zeros((1, 1))
+        else:
+            self.canvas.text_overlay.visible = False
+        return when
 
 
 @magicclass(widget_type="groupbox", record=False)

docs/index.md

@@ -16,6 +16,7 @@ structures are implemented.
 - [Open an image](open_image.md)
 - [Fit splines](fit_splines.md)
 - [Measure lattice parameters](lattice_params.md)
+- [Inspect CFT Results](inspect_results.md)
 - [Load & Save Projects](project_io.md)
 - [Custom Workflows](workflows.md)
 - [Spline](spline/index.md)

docs/inspect_results.md

@@ -1,19 +1,26 @@
 # Inspect CFT Results
 
 To clarify if the analysis is done correctly or to determine the parameters, you may
-sometimes want to inspect the results of the CFT.
+sometimes want to inspect the results of the CFT. This can be done by the spectra
+inspector widget.
 
 :material-arrow-right-thin-circle-outline: GUI: `Analysis > Open spectra inspector` or ++ctrl+k++ → ++ctrl+v++
 
 In this window, you can see the local- and global-CFT power spectra of the existing
-splines, and the estimated peak positions (red markers) if available.
+splines, and the estimated peak positions (red markers) if available. By clicking the
+"Load spline" button, you can set other splines in the tomogram for inspection.
 
-![Inspect Results](images/inspect_local_cft.png){ loading=lazy, width=500px }
+![Inspection result](images/inspect_local_cft.png){ loading=lazy, width=570px }
 
 After clicking "Upsample spectrum" to enable the upsampling mode, you can upsample the
 local power spectrum interactively by clicking the canvas.
 
-![Inspect Results](images/inspect_local_cft_upsampled.png){ loading=lazy, width=500px }
+![Upsampled Result](images/inspect_local_cft_upsampled.png){ loading=lazy, width=570px }
+
+If the spline is not well fitted to the image, the peaks of the local power spectrum are
+blurred, especially in the x (angular) direction.
+
+![Bad result](images/inspect_local_cft_bad.png){ loading=lazy, width=570px }
 
 !!! note
     This widget is also used to measure the lattice parameters of unknown structures.

docs/scripts/_screenshots.py

@@ -82,7 +82,7 @@ def _workflow_gui(path: Path, tilt_range: tuple[float, float] = (-60, 60)):
 
     ui._runner.run(interval=12, n_refine=0, map_monomers=True)
 
-    # inspect local CFT
+    ### inspect local CFT ###
     ui.spectra_inspector.show()
     ui.spectra_inspector.load_spline(0)
     ui.spectra_inspector.peak_viewer.show_what = "Local-CFT"
@@ -99,7 +99,22 @@ def _workflow_gui(path: Path, tilt_range: tuple[float, float] = (-60, 60)):
     QtW.QApplication.processEvents()
     _imsave(ui.spectra_inspector.native, "inspect_local_cft_upsampled")
     ui.spectra_inspector.peak_viewer.show_what = "Global-CFT"  # will be used later
+    ui.copy_spline(0)
+    ui.spline_fitter.fit(1, [[1, 0.5], [-0.2, 0.8], [1, 0.3]])
+    ui.measure_radius(1)
+    ui.local_cft_analysis(1, interval=50)
+    ui.spectra_inspector.load_spline(1)
+    ui.spectra_inspector.peak_viewer.show_what = "Local-CFT"
+    ui.spectra_inspector.width = 500
+    ui.spectra_inspector.height = 525
+    QtW.QApplication.processEvents()
+    ui.spectra_inspector.peak_viewer._upsample_and_update_image(45, 23)
+    ui.spectra_inspector.peak_viewer.canvas.xlim = (41, 49)
+    ui.spectra_inspector.peak_viewer.canvas.ylim = (18, 28)
+    QtW.QApplication.processEvents()
+    _imsave(ui.spectra_inspector.native, "inspect_local_cft_bad")
 
+    ### magicgui widgets ###
     for meth in [
         ui.load_project,
         # fit, CFT, etc.
@@ -142,10 +157,12 @@ def _workflow_gui(path: Path, tilt_range: tuple[float, float] = (-60, 60)):
         _imsave(gui.native, method)
         gui.close()
 
+    ### canvas with monomers ###
     ui.parent_viewer.dims.ndisplay = 3
     _viewer_screenshot(ui, "viewer_01_monomer_mapped", canvas_only=True)
     ui.parent_viewer.dims.ndisplay = 2
 
+    ### magicgui widgets ###
     for meth in [
         ui.sta.average_all,
         ui.sta.calculate_fsc,
@@ -171,6 +188,7 @@ def _workflow_gui(path: Path, tilt_range: tuple[float, float] = (-60, 60)):
         _imsave(gui.native, meth.__name__)
         gui.close()
 
+    ### Bigger widgets ###
     # Runner
     ui._runner.show()
     _imsave(ui._runner.native, "run_workflow_dialog")