fix(gui): pre-beta-5 review findings (shortcuts help, collada, shuffle, z-trace)

PyReconstruct/modules/backend/autoseg/palette.py

@@ -163,7 +163,7 @@ def palette_color(label_id, palette=None, seed: int = 0) -> tuple:
     return tuple(int(c) for c in palette[index])
 
 
-def next_shuffle_seed(current_seed: int, palette=None, rng=None) -> int:
+def next_shuffle_seed(current_seed: int, palette=None, ids=None, rng=None) -> int:
     """Pick a new seed whose color arrangement differs from the current one.
 
     This backs the "Shuffle colors" button: each click must visibly change the
@@ -174,10 +174,20 @@ def next_shuffle_seed(current_seed: int, palette=None, rng=None) -> int:
     option, so determinism and preview==import are preserved exactly as with a
     hand-entered seed.
 
+    The guarantee is enforced over ``ids``: the label ids the caller can
+    actually see. With only a few labels on screen, a generic 1..63 fingerprint
+    can "change" while none of the *visible* labels move color -- a no-op click
+    for the user. Passing the overlay's present ids ties the guarantee to what
+    is on screen. When ``ids`` is None (or has no usable entries) it falls back
+    to the 1..63 range, which reaches every palette entry.
+
         Params:
             current_seed (int): the seed currently in effect
             palette: list of (R, G, B) entries; falls back to the shipped
                 default when None or empty
+            ids: optional iterable of label ids to fingerprint the arrangement
+                over (the visible/present ids); None uses the default 1..63
+                range
             rng: an optional random.Random (injectable for deterministic tests);
                 a fresh default source is used when None
         Returns:
@@ -196,10 +206,16 @@ def next_shuffle_seed(current_seed: int, palette=None, rng=None) -> int:
     if len(palette) < 2:
         return int(current_seed)
 
-    # A small id sample fingerprints the arrangement. Reaching every entry over
-    # ~64 ids is near-certain, so two seeds agreeing across all of them means
-    # the visible mapping is identical.
-    sample = range(1, 64)
+    # Fingerprint the arrangement over the visible ids when supplied (id 0 is
+    # background, not a segment, so it is dropped); otherwise a 1..63 sample,
+    # which reaches every entry so two seeds agreeing across all of them means
+    # the mapping is identical.
+    if ids is None:
+        sample = range(1, 64)
+    else:
+        sample = [int(i) for i in ids if i]
+        if not sample:
+            sample = range(1, 64)
 
     def arrangement(seed):
         return tuple(palette_color(i, palette, seed) for i in sample)

PyReconstruct/modules/backend/view/zarr_layer.py

@@ -118,6 +118,25 @@ def selectID(self, pix_x : int, pix_y : int):
             return True
         return False
 
+    def getPresentIds(self):
+        """Return the label ids visible on the current section.
+
+        These are the unique non-zero ids in the current section's slice of the
+        label overlay -- i.e. the labels the user actually sees colored (the
+        whole crop is colored, not just ``selected_ids``). Used to tie the
+        shuffle-colors guarantee to what is on screen. Returns an empty list
+        when this is not a label overlay or the current section falls outside
+        the overlay's z-range.
+        """
+        if not self.is_labels:
+            return []
+        bz = self.zarr.shape[0]
+        z = round(self.section.n - self.zarr_s)
+        if not 0 <= z < bz:
+            return []
+        present = np.unique(self.zarr[z])
+        return [int(v) for v in present.tolist() if v != 0]
+
     def deselectAll(self):
         """Deselect all the IDs."""
         self.selected_ids = []

PyReconstruct/modules/backend/volume/export_volumes.py

@@ -1,5 +1,6 @@
 """Export 3D objects."""
 
+import importlib.util
 from pathlib import Path
 from typing import List, Union
 
@@ -12,6 +13,18 @@
 from PyReconstruct.modules.gui.utils import notify
 
 
+def collada_available() -> bool:
+    """Return True when the optional 'pycollada' package is importable.
+
+    Collada (.dae) export goes through trimesh's Collada writer, which imports
+    'pycollada' lazily. That package is NOT bundled by PyInstaller, so a frozen
+    ("packaged") build never has it available. Callers use this to grey out the
+    .dae menu item up front instead of offering an export that can only fail.
+    Uses ``find_spec`` so it merely checks importability without importing.
+    """
+    return importlib.util.find_spec("collada") is not None
+
+
 def export3DObjects(series: Series, obj_names : list, output_dir : str, export_type: str, notify_user: bool = True) -> None:
     """Export 3D objects.
 
@@ -26,18 +39,22 @@ def export3DObjects(series: Series, obj_names : list, output_dir : str, export_t
 
     ## Collada (.dae) export needs the optional 'pycollada' package (trimesh's
     ## Collada writer imports it lazily and otherwise raises a bare
-    ## ModuleNotFoundError). Surface the requirement here, before any work, so
-    ## the user gets a clear message instead of an unhandled traceback.
+    ## ModuleNotFoundError). The menu normally disables .dae when it is absent
+    ## (see collada_available), but keep this as a backstop -- surface the
+    ## requirement here, before any work, so the user gets a clear message
+    ## instead of an unhandled traceback.
     if export_type == "dae":
         try:
             import collada  # noqa: F401  (provided by the 'pycollada' package)
         except ImportError:
             if notify_user:
                 notify(
-                    "Collada (.dae) export requires the 'pycollada' package, "
-                    "which is not installed.\n\n"
-                    "Install it (e.g. 'pip install pycollada') and try again, "
-                    "or choose another export format."
+                    "Collada (.dae) export needs the optional 'pycollada' "
+                    "package, which is not available in this installation.\n\n"
+                    "In a pip/uv environment you can install it (e.g. "
+                    "'pip install pycollada'); packaged (frozen) builds do not "
+                    "include Collada support. Otherwise choose another export "
+                    "format."
                 )
             return
 

PyReconstruct/modules/datatypes/default_settings.py

@@ -94,6 +94,7 @@ def get_username() -> str:
     "deccon_act": "[",
     "inccon_act": "]",
     "blend_act": "Space",
+    "toggleztraces_act": "",  # checkable "Show z-traces"; no default key
     "homeview_act": "Home",
     "selectall_act": "Ctrl+A",
     "deselect_act": "Ctrl+D",

PyReconstruct/modules/gui/dialog/shortcuts.py

@@ -146,15 +146,15 @@ def getStaticShortcuts(w : QWidget) -> list[QKeySequence]:
     ("flicker_act", "Switch between current and last viewed section"),
     None,
     "View",
-    ("focus_act", "Toggle focus mode"),
-    ("hideall_act", "Toggle hide all traces (regardless of trace's hide status)"),
-    ("showall_act", "Toggle show all traces (regardless of trace's hide status)"),
-    ("hideimage_act", "Toggle hide images"),
+    ("focus_act", "Focus mode"),
+    ("hideall_act", "Hide trace layer"),
+    ("showall_act", "Show all traces (ignore hidden)"),
+    ("hideimage_act", "Hide image"),
     ("decbr_act", "Decrease brightness"),
     ("incbr_act", "Increase brightness"),
     ("deccon_act", "Decrease contrast"),
     ("inccon_act", "Increase contrast"),
-    ("blend_act", "Blend current and last viwed section"),
+    ("blend_act", "Section blend"),
     ("homeview_act", "Set view to image"),
     None,
     "Field Interactions",

PyReconstruct/modules/gui/main/context_menu_list.py

@@ -4,6 +4,49 @@
 from PyReconstruct.modules.gui.utils import getUserColsMenu, getAlignmentsMenu
 
 
+def collada_menu_label(available=None):
+    """Label for the Collada (.dae) export item, flagged when unavailable.
+
+    Collada export needs the optional 'pycollada' package, which frozen
+    (PyInstaller) builds never bundle. When it is unavailable the label gains a
+    "(not installed)" suffix so the (disabled) item explains itself. Pass
+    ``available`` explicitly to keep the string logic pure/testable; when None
+    the live availability is queried (import kept local so this menu module
+    doesn't pull in the heavy export backend at import time).
+
+        Params:
+            available (bool | None): whether pycollada is importable; None to
+                query it live
+        Returns:
+            (str): the menu label
+    """
+    if available is None:
+        from PyReconstruct.modules.backend.volume.export_volumes import (
+            collada_available,
+        )
+        available = collada_available()
+    return "Collada (.dae)" if available else "Collada (.dae) (not installed)"
+
+
+def disable_unavailable_export_formats(widget):
+    """Grey out 3D-export formats whose optional dependency is missing.
+
+    Currently only Collada (.dae), which needs 'pycollada' (absent from frozen
+    builds). Disabling the menu item up front means a packaged user is never
+    offered an export that can only fail; the runtime guard in
+    ``export3DObjects`` remains a backstop. Call once, right after the object
+    menu is populated onto ``widget`` (both the field context menu and the
+    object-list table build it). No-op when the action isn't on this widget or
+    Collada IS available.
+    """
+    from PyReconstruct.modules.backend.volume.export_volumes import (
+        collada_available,
+    )
+    act = getattr(widget, "export3D_dae_act", None)
+    if act is not None and not collada_available():
+        act.setEnabled(False)
+
+
 def edit_selected_label(active):
     """Resolve the Q8 top-level edit action's (label, enabled) for a selection.
 
@@ -146,7 +189,11 @@ def get_context_menu_list_obj(self):
                 ("editobjradius_act", "Edit radius...", "", self.editRadius),
                 ("editobjshape_act", "Edit shape...", "", self.editShape),
                 None,
-                ("smoothtraces_act", "Smooth traces", "", self.smoothObject),
+                # Distinct attr_name from the field Trace submenu's
+                # "smoothtraces_act": both menus are populated onto the same
+                # widget, so a shared name meant one silently shadowed the
+                # other (same class of bug as the old export3D_act).
+                ("smoothobj_act", "Smooth traces", "", self.smoothObject),
                 ("splitobj_act", "Split into separate objects", "", self.splitObject),
                 None,
                 ("removealltags_act", "Remove all tags", "", self.removeAllTags),
@@ -177,15 +224,16 @@ def get_context_menu_list_obj(self):
                     [
                         # unique attr_names per format (previously all "export3D_act",
                         # so four of five silently shadowed the last on the widget).
-                        # Collada requires the optional 'pycollada' package; the
-                        # export handler surfaces that requirement gracefully
-                        # (export_volumes.export3DObjects), so the dependency note
-                        # is no longer crammed into the label.
+                        # Collada needs the optional 'pycollada' package (never
+                        # bundled in frozen builds): its label is flagged when
+                        # unavailable and the item is disabled after build (see
+                        # disable_unavailable_export_formats); export3DObjects
+                        # keeps a runtime guard as a backstop.
                         ("export3D_obj_act", "Wavefront (.obj)", "", lambda : self.exportAs3D("obj")),
                         ("export3D_off_act", "Object File Format (.off)", "", lambda : self.exportAs3D("off")),
                         ("export3D_ply_act", "Stanford PLY (.ply)", "", lambda : self.exportAs3D("ply")),
                         ("export3D_stl_act", "STL (.stl)", "", lambda : self.exportAs3D("stl")),
-                        ("export3D_dae_act", "Collada (.dae)", "", lambda : self.exportAs3D("dae")),
+                        ("export3D_dae_act", collada_menu_label(), "", lambda : self.exportAs3D("dae")),
                     ]
 
                     },

PyReconstruct/modules/gui/main/field_widget_2_trace.py

@@ -1183,7 +1183,7 @@ def editTraceShape(self, traces : list):
     def getZtraceMenu(self):
         """Get the context menu list for interacting with ztraces."""
         context_menu_list = [
-            ("editztracce_act", "Edit Z-trace attributes...", "", self.editZtraceAttributes),
+            ("editztracce_act", "Edit z-trace attributes...", "", self.editZtraceAttributes),
             ("smoothztrace_act", "Smooth", "", self.smoothZtrace),
             None,
             {
@@ -1207,7 +1207,7 @@ def getZtraceMenu(self):
             },
             ("setztracealignment_act", "Edit alignment...", "", self.editZtraceAlignment),
             None,
-            ("deleteztrace_act", "Delete Z-traces", "", self.deleteZtrace)
+            ("deleteztrace_act", "Delete z-traces", "", self.deleteZtrace)
         ]
         return context_menu_list
 

PyReconstruct/modules/gui/main/main_imports.py

@@ -172,4 +172,8 @@
 
 from .menubar import return_menubar
 
-from .context_menu_list import get_field_menu_list, edit_selected_label
+from .context_menu_list import (
+    get_field_menu_list,
+    edit_selected_label,
+    disable_unavailable_export_formats,
+)

PyReconstruct/modules/gui/main/main_window.py

@@ -143,13 +143,26 @@ def createMenuBar(self):
         ## Populate menu bar with menus and options
         populateMenuBar(self, self.menubar, menu)
 
+        ## Seed menubar checkables that have no aboutToShow resync hook from the
+        ## live option, so they are correct on first show. checkActions keeps
+        ## them synced thereafter (see its View-toggle block). NOTE: the menubar
+        ## has no per-open resync, so an external change to show_ztraces (e.g.
+        ## the all-options dialog) is only reflected on the next checkActions
+        ## pass (field interactions) or menubar rebuild -- an accepted
+        ## limitation for a rarely-out-of-band toggle.
+        self.toggleztraces_act.setChecked(bool(self.series.getOption("show_ztraces")))
+
     def createContextMenus(self):
         """Create right-click menus used in the field."""
         ## Create user columns options
         field_menu_list = get_field_menu_list(self)
         self.field_menu = QMenu(self)
         populateMenu(self, self.field_menu, field_menu_list)
 
+        ## Grey out export formats whose optional dependency is missing
+        ## (e.g. Collada/.dae without 'pycollada', as in frozen builds).
+        disable_unavailable_export_formats(self)
+
         ## Organize actions
         self.trace_actions = [
             self.tracemenu,
@@ -296,6 +309,17 @@ def checkActions(self, context_menu=False, clicked_trace=None, clicked_label=Non
         self.hideimage_act.setChecked(self.field.hide_image)
         self.blend_act.setChecked(self.field.blend_sections)
 
+        ## Focus mode needs a selection to turn ON (it focuses the selected
+        ## object); disabling the checkbox when nothing is selected avoids the
+        ## "Please select at least one trace" error from a menu click. Stays
+        ## enabled while already in focus mode so it can always be turned off.
+        self.focus_act.setEnabled(bool(self.field.focus_mode) or bool(selected_traces))
+
+        ## Menubar "Show z-traces" checkbox: same live-state resync as the
+        ## field View toggles above (setChecked emits `toggled`, not
+        ## `triggered`, so it never re-fires the handler).
+        self.toggleztraces_act.setChecked(bool(self.series.getOption("show_ztraces")))
+
         ## Group visibility
         for group, viz in self.series.groups_visibility.items():
             try:
@@ -2468,8 +2492,16 @@ def shuffleAutosegColors(self):
 
         current = self.series.getOption("autoseg_color_seed") or 0
         palette = self.series.getOption("autoseg_color_palette") or None
+        # Enforce the "always reshuffles" guarantee over the labels actually
+        # visible on this section, not a fixed 1..63 range: with only a few
+        # labels on screen a new seed could recolor ids the user can't see and
+        # leave the visible ones unchanged (a no-op click). Fall back to the
+        # default range when the overlay can't supply present ids.
+        zarr_layer = self.field.zarr_layer
+        present_ids = zarr_layer.getPresentIds() if zarr_layer else None
         self.series.setOption(
-            "autoseg_color_seed", next_shuffle_seed(current, palette)
+            "autoseg_color_seed",
+            next_shuffle_seed(current, palette, ids=present_ids)
         )
         self.field.generateView()
 

PyReconstruct/modules/gui/main/menubar.py

@@ -356,7 +356,11 @@ def return_view_menu(self):
             ("viewmag_act", "View magnification...", "", self.field.setViewMagnification),
             ("findview_act", "Set zoom when finding contours...", "", self.setFindZoom),
             None,
-            ("toggleztraces_act", "Toggle show Z-traces", "", self.toggleZtraces),
+            # Checkable, mirroring the live show_ztraces option (see
+            # MainWindow.checkActions / createMenuBar for the resync). The
+            # (series, "checkbox") form keeps it configurable-shortcut-capable
+            # like the field View toggles; its option default is "" (no key).
+            ("toggleztraces_act", "Show z-traces", (self.series, "checkbox"), self.toggleZtraces),
             None,
             {
                 "attr_name": "palettemenu",

PyReconstruct/modules/gui/table/object.py

@@ -239,6 +239,13 @@ def getCall(col_name, opt_name):
         self.context_menu = QMenu(self)
         populateMenu(self, self.context_menu, context_menu_list)
 
+        # Grey out export formats whose optional dependency is missing
+        # (e.g. Collada/.dae without 'pycollada', as in frozen builds).
+        from PyReconstruct.modules.gui.main.context_menu_list import (
+            disable_unavailable_export_formats,
+        )
+        disable_unavailable_export_formats(self)
+
     def updateTitle(self):
         """Update the title of the table."""
         is_regex = tuple(self.re_filters) != (".*",)

PyReconstruct/modules/gui/table/trace.py

@@ -275,7 +275,7 @@ def createMenus(self):
         populateMenuBar(self, self.menubar, menubar_list)
 
         # create the right-click menu -- prepend the list-only table ops
-        # (invert selection + copy row text) whose handlers belong to THIS
+        # (invert selection + copy trace values) whose handlers belong to THIS
         # table, then the shared trace menu built by the field.
         context_menu_list = [
             ("inverttraceselection_act", "Invert selection", "", self.invertSelection),

PyReconstruct/modules/gui/table/ztrace.py

@@ -115,7 +115,7 @@ def createMenus(self):
         populateMenuBar(self, self.menubar, menubar_list)
 
         # create the right-click menu -- prepend the list-only table ops
-        # (invert selection + copy row text) whose handlers belong to THIS
+        # (invert selection + copy z-trace values) whose handlers belong to THIS
         # table, then the shared z-trace menu (also used in the field).
         context_menu_list = [
             ("invertztraceselection_act", "Invert selection", "", self.invertSelection),