datalab-platform 1.0.2__py3-none-any.whl → 1.0.4__py3-none-any.whl

datalab/gui/main.py

@@ -1360,6 +1360,10 @@ class DLMainWindow(QW.QMainWindow, AbstractDLControl, metaclass=DLMainWindowMeta
             title += f" [{datalab.__version__}]"
         self.setWindowTitle(title)
 
+    def is_modified(self) -> bool:
+        """Return True if mainwindow is modified"""
+        return self.__is_modified
+
     def __add_dockwidget(self, child, title: str) -> QW.QDockWidget:
         """Add QDockWidget and toggleViewAction"""
         dockwidget, location = child.create_dockwidget(title)
@@ -1559,9 +1563,7 @@ class DLMainWindow(QW.QMainWindow, AbstractDLControl, metaclass=DLMainWindowMeta
             if not filename:
                 return
         with qth.qt_try_loadsave_file(self, filename, "save"):
-            filename = self.__check_h5file(filename, "save")
-            self.h5inputoutput.save_file(filename)
-            self.set_modified(False)
+            self.save_h5_workspace(filename)
 
     @remote_controlled
     def open_h5_files(
@@ -1667,6 +1669,59 @@ class DLMainWindow(QW.QMainWindow, AbstractDLControl, metaclass=DLMainWindowMeta
             self.__check_h5file(filename, "load")
         self.h5inputoutput.import_files(filenames, False, reset_all)
 
+    @remote_controlled
+    def load_h5_workspace(self, h5files: list[str], reset_all: bool = False) -> None:
+        """Load native DataLab HDF5 workspace files without any GUI elements.
+
+        This method can be safely called from the internal console as it does not
+        create any Qt widgets, dialogs, or progress bars. It is designed for
+        programmatic use when loading DataLab workspace files.
+
+        .. warning::
+
+            This method only supports native DataLab HDF5 files. For importing
+            arbitrary HDF5 files (non-native), use the GUI menu or macros with
+            :class:`datalab.control.proxy.RemoteProxy`.
+
+        Args:
+            h5files: List of native DataLab HDF5 filenames
+            reset_all: Reset all application data before importing. Defaults to False.
+
+        Raises:
+            ValueError: If a file is not a valid native DataLab HDF5 file
+        """
+        for idx, filename in enumerate(h5files):
+            filename = self.__check_h5file(filename, "load")
+            success = self.h5inputoutput.open_file_headless(
+                filename, reset_all=(reset_all and idx == 0)
+            )
+            if not success:
+                raise ValueError(
+                    f"File '{filename}' is not a native DataLab HDF5 file. "
+                    f"Use the GUI menu or a macro with RemoteProxy to import "
+                    f"arbitrary HDF5 files."
+                )
+        # Refresh panel trees after loading
+        self.repopulate_panel_trees()
+
+    @remote_controlled
+    def save_h5_workspace(self, filename: str) -> None:
+        """Save current workspace to a native DataLab HDF5 file without GUI elements.
+
+        This method can be safely called from the internal console as it does not
+        create any Qt widgets, dialogs, or progress bars. It is designed for
+        programmatic use when saving DataLab workspace files.
+
+        Args:
+            filename: HDF5 filename to save to
+
+        Raises:
+            IOError: If file cannot be saved
+        """
+        filename = self.__check_h5file(filename, "save")
+        self.h5inputoutput.save_file(filename)
+        self.set_modified(False)
+
     @remote_controlled
     def import_h5_file(self, filename: str, reset_all: bool | None = None) -> None:
         """Import HDF5 file into DataLab
@@ -2027,7 +2082,7 @@ class DLMainWindow(QW.QMainWindow, AbstractDLControl, metaclass=DLMainWindowMeta
         Returns:
             True if closed properly, False otherwise
         """
-        if not env.execenv.unattended and self.__is_modified:
+        if not env.execenv.unattended and self.is_modified():
             answer = QW.QMessageBox.warning(
                 self,
                 _("Quit"),
@@ -2039,7 +2094,7 @@ class DLMainWindow(QW.QMainWindow, AbstractDLControl, metaclass=DLMainWindowMeta
             )
             if answer == QW.QMessageBox.Yes:
                 self.save_to_h5_file()
-                if self.__is_modified:
+                if self.is_modified():
                     return False
             elif answer == QW.QMessageBox.Cancel:
                 return False

datalab/gui/objectview.py

@@ -222,11 +222,26 @@ class SimpleObjectTree(QW.QTreeWidget):
             self.set_current_item_id(uuid)
 
     def update_tree(self) -> None:
-        """Update tree"""
+        """Update tree
+
+        Note: If an item is not found in the tree, the tree is repopulated to ensure
+        consistency between the tree and the model. This can happen in rare cases when
+        objects are added to the model but the tree was not properly updated.
+        """
         for group in self.objmodel.get_groups():
-            self.__update_item(self.get_item_from_id(get_uuid(group)), group)
+            group_item = self.get_item_from_id(get_uuid(group))
+            if group_item is None:
+                # Group item not found, repopulate tree to fix inconsistency
+                self.populate_tree()
+                return
+            self.__update_item(group_item, group)
             for obj in group:
-                self.__update_item(self.get_item_from_id(get_uuid(obj)), obj)
+                obj_item = self.get_item_from_id(get_uuid(obj))
+                if obj_item is None:
+                    # Object item not found, repopulate tree to fix inconsistency
+                    self.populate_tree()
+                    return
+                self.__update_item(obj_item, obj)
 
     def __add_to_group_item(
         self, obj: SignalObj | ImageObj, group_item: QW.QTreeWidgetItem

datalab/gui/panel/base.py

@@ -79,6 +79,7 @@ from datalab.gui.newobject import (
 from datalab.gui.processor.base import (
     PROCESSING_PARAMETERS_OPTION,
     ProcessingParameters,
+    clear_analysis_parameters,
     extract_processing_parameters,
     insert_processing_parameters,
 )
@@ -217,11 +218,11 @@ class ObjectProp(QW.QWidget):
         self.analysis_parameters.setFont(font)
 
         # Track newly created objects to show Creation tab only once
-        self._newly_created_obj_uuid: str | None = None
+        self.newly_created_obj_uuid: str | None = None
         # Track when analysis results were just computed
-        self._fresh_analysis_obj_uuid: str | None = None
+        self.fresh_analysis_obj_uuid: str | None = None
         # Track when object was just processed (1-to-1)
-        self._fresh_processing_obj_uuid: str | None = None
+        self.fresh_processing_obj_uuid: str | None = None
 
         self.tabwidget.addTab(
             self.processing_history, get_icon("history.svg"), _("History")
@@ -455,7 +456,7 @@ class ObjectProp(QW.QWidget):
         Args:
             obj: Object to mark
         """
-        self._newly_created_obj_uuid = get_uuid(obj)
+        self.newly_created_obj_uuid = get_uuid(obj)
 
     def mark_as_freshly_processed(self, obj: SignalObj | ImageObj) -> None:
         """Mark object to show Processing tab on next selection.
@@ -463,7 +464,7 @@ class ObjectProp(QW.QWidget):
         Args:
             obj: Object to mark
         """
-        self._fresh_processing_obj_uuid = get_uuid(obj)
+        self.fresh_processing_obj_uuid = get_uuid(obj)
 
     def mark_as_fresh_analysis(self, obj: SignalObj | ImageObj) -> None:
         """Mark object to show Analysis tab on next selection.
@@ -471,7 +472,7 @@ class ObjectProp(QW.QWidget):
         Args:
             obj: Object to mark
         """
-        self._fresh_analysis_obj_uuid = get_uuid(obj)
+        self.fresh_analysis_obj_uuid = get_uuid(obj)
 
     def get_changed_properties(self) -> dict[str, Any]:
         """Get dictionary of properties that have changed from original values.
@@ -1532,9 +1533,9 @@ class BaseDataPanel(AbstractPanel, Generic[TypeObj, TypeROI, TypeROIEditor]):
         # BUT: Don't overwrite if this object is already marked as freshly processed
         # or has fresh analysis results (those take precedence)
         obj_uuid = get_uuid(obj)
-        if (
-            obj_uuid != self.objprop._fresh_processing_obj_uuid
-            and obj_uuid != self.objprop._fresh_analysis_obj_uuid
+        if obj_uuid not in (
+            self.objprop.fresh_processing_obj_uuid,
+            self.objprop.fresh_analysis_obj_uuid,
         ):
             self.objprop.mark_as_newly_created(obj)
 
@@ -2474,17 +2475,17 @@ class BaseDataPanel(AbstractPanel, Generic[TypeObj, TypeROI, TypeROIEditor]):
         if current_obj is not None:
             obj_uuid = get_uuid(current_obj)
             # Show Creation tab for newly created objects (only once)
-            if obj_uuid == self.objprop._newly_created_obj_uuid:
+            if obj_uuid == self.objprop.newly_created_obj_uuid:
                 force_tab = "creation"
-                self.objprop._newly_created_obj_uuid = None
+                self.objprop.newly_created_obj_uuid = None
             # Show Processing tab for freshly processed objects (only once)
-            elif obj_uuid == self.objprop._fresh_processing_obj_uuid:
+            elif obj_uuid == self.objprop.fresh_processing_obj_uuid:
                 force_tab = "processing"
-                self.objprop._fresh_processing_obj_uuid = None
+                self.objprop.fresh_processing_obj_uuid = None
             # Show Analysis tab for objects with fresh analysis results
-            elif obj_uuid == self.objprop._fresh_analysis_obj_uuid:
+            elif obj_uuid == self.objprop.fresh_analysis_obj_uuid:
                 force_tab = "analysis"
-                self.objprop._fresh_analysis_obj_uuid = None
+                self.objprop.fresh_analysis_obj_uuid = None
 
         self.objprop.update_properties_from(current_obj, force_tab=force_tab)
         self.acthandler.selected_objects_changed(selected_groups, selected_objects)
@@ -2921,9 +2922,11 @@ class BaseDataPanel(AbstractPanel, Generic[TypeObj, TypeROI, TypeROIEditor]):
             dialog was accepted or not.
         """
         obj = self.objview.get_sel_objects(include_groups=True)[-1]
-        item = create_adapter_from_object(obj).make_item(
-            update_from=self.plothandler[get_uuid(obj)]
-        )
+        # Use get() instead of [] to avoid KeyError if the plot item doesn't exist
+        # (can happen when "auto refresh" is disabled or in "show first only" mode
+        # where not all objects have plot items created yet)
+        existing_item = self.plothandler.get(get_uuid(obj))
+        item = create_adapter_from_object(obj).make_item(update_from=existing_item)
         roi_editor_class = self.get_roieditor_class()  # pylint: disable=not-callable
         roi_editor = roi_editor_class(
             parent=self.parentWidget(),
@@ -3274,6 +3277,9 @@ class BaseDataPanel(AbstractPanel, Generic[TypeObj, TypeROI, TypeROIEditor]):
                     # Remove all table and geometry results using adapter methods
                     TableAdapter.remove_all_from(obj)
                     GeometryAdapter.remove_all_from(obj)
+                    # Clear analysis parameters to prevent auto-recompute from
+                    # attempting to recompute deleted analyses when ROI changes
+                    clear_analysis_parameters(obj)
                     if obj is self.objview.get_current_object():
                         self.objprop.update_properties_from(obj)
                 # Update action states to reflect the removal

datalab/gui/panel/macro.py

@@ -204,6 +204,10 @@ class MacroPanel(AbstractPanel, DockableWidgetMixin):
             self.addWidget(widget)
         self.setStretchFactor(0, 2)
         self.setStretchFactor(1, 1)
+        # Set initial sizes: give more space to editor (70%) than console (30%)
+        # This ensures proper layout on first open
+        total_height = 600  # Default reasonable height
+        self.setSizes([int(total_height * 0.7), int(total_height * 0.3)])
 
         self.run_action = None
         self.stop_action = None
@@ -252,6 +256,8 @@ class MacroPanel(AbstractPanel, DockableWidgetMixin):
                 #  in a group but directly in the root of the HDF5 file
                 obj = self.deserialize_object_from_hdf5(reader, name, reset_all)
                 self.add_object(obj)
+        # Update untitled number counter to prevent duplicate names
+        self.update_untitled_counter()
 
     def __len__(self) -> int:
         """Return number of objects"""
@@ -298,6 +304,8 @@ class MacroPanel(AbstractPanel, DockableWidgetMixin):
         self.tabwidget.clear()
         self.__macros.clear()
         super().remove_all_objects()
+        # Reset untitled counter when clearing all macros
+        Macro.set_untitled_number(0)
 
     # ---- Macro panel API -------------------------------------------------------------
     def setup_actions(self) -> None:
@@ -572,9 +580,27 @@ class MacroPanel(AbstractPanel, DockableWidgetMixin):
                 Conf.main.base_dir.set(filename)
                 macro = self.add_macro()
                 macro.from_file(filename)
+            # Update untitled number counter to prevent duplicate names
+            self.update_untitled_counter()
             return self.get_number_from_macro(macro)
         return -1
 
+    def update_untitled_counter(self) -> None:
+        """Update the untitled counter based on existing macro titles
+
+        This scans all macro titles to find the highest "macro_XX" number
+        and updates the global counter to prevent duplicate names.
+        """
+        max_untitled = 0
+        for macro in self.__macros:
+            # Match titles like "macro_01", "macro_02", etc.
+            match = re.match(r"macro_(\d+)", macro.title)
+            if match:
+                number = int(match.group(1))
+                max_untitled = max(max_untitled, number)
+        # Set the counter to the highest found number
+        Macro.set_untitled_number(max_untitled)
+
     def remove_macro(self, number_or_title: int | str | None = None) -> None:
         """Remove macro
 

datalab/gui/plothandler.py

@@ -162,6 +162,7 @@ class BasePlotHandler(Generic[TypeObj, TypePlotItem]):  # type: ignore
         self.__merged_result_adapters = {}
         self.cleanup_dataview()
         self.remove_all_shape_items()
+        self.plot.replot()
 
     def add_shapes(self, oid: str, do_autoscale: bool = False) -> None:
         """Add geometric shape items associated to computed results and annotations,
@@ -391,7 +392,10 @@ class BasePlotHandler(Generic[TypeObj, TypePlotItem]):  # type: ignore
         if what == "selected":
             # Refresh selected objects
             oids = self.panel.objview.get_sel_object_uuids(include_groups=True)
-            if len(oids) == 1:
+            if len(oids) <= 1:
+                # Cleanup data view when there is 0 or 1 selected object.
+                # This removes stray plot items (like XRangeSelection, DataInfoLabel)
+                # that were created by PlotPy tools but are not managed by DataLab.
                 self.cleanup_dataview()
             self.remove_all_shape_items()
             for item in self:
@@ -806,4 +810,9 @@ class ImagePlotHandler(BasePlotHandler[ImageObj, MaskedXYImageItem]):
         options = super().get_plot_options()
         options.zlabel = self.plot.get_axis_title("right")
         options.zunit = self.plot.get_axis_unit("right")
+        # Include aspect ratio configuration so that separate plot dialogs
+        # (e.g. "View in a new window", ROI editors, profile dialogs) use the same
+        # settings as the integrated plot handler:
+        options.aspect_ratio = self.plot.get_aspect_ratio()
+        options.lock_aspect_ratio = self.plot.lock_aspect_ratio
         return options

datalab/gui/processor/base.py

@@ -195,6 +195,21 @@ def insert_processing_parameters(
         obj.set_metadata_option(PROCESSING_PARAMETERS_OPTION, pp.to_dict())
 
 
+def clear_analysis_parameters(obj: SignalObj | ImageObj) -> None:
+    """Clear analysis parameters from object metadata.
+
+    This removes the stored analysis parameters (1-to-0 operations) from the object.
+    Should be called when all analysis results are deleted to prevent the
+    auto_recompute_analysis function from attempting to recompute deleted analyses.
+
+    Args:
+        obj: Signal or Image object
+    """
+    key = f"__{ANALYSIS_PARAMETERS_OPTION}"
+    if key in obj.metadata:
+        del obj.metadata[key]
+
+
 def run_with_env(func: Callable, args: tuple, env_json: str) -> CompOut:
     """Wrapper to apply environment config before calling func
 
@@ -945,7 +960,9 @@ class BaseProcessor(QC.QObject, Generic[TypeROI, TypeROIParam]):
             TableAdapter.remove_all_from(result_obj)
             GeometryAdapter.remove_all_from(result_obj)
 
-    def auto_recompute_analysis(self, obj: SignalObj | ImageObj) -> None:
+    def auto_recompute_analysis(
+        self, obj: SignalObj | ImageObj, refresh_plot: bool = True
+    ) -> None:
         """Automatically recompute analysis (1-to-0) operations after data changes.
 
         This method checks if the object has 1-to-0 analysis parameters (analysis
@@ -962,6 +979,7 @@ class BaseProcessor(QC.QObject, Generic[TypeROI, TypeROIParam]):
 
         Args:
             obj: The object whose data was modified
+            refresh_plot: Whether to refresh the plot after recomputation
         """
         # Check if object has 1-to-0 analysis parameters (analysis operations)
         proc_params = extract_analysis_parameters(obj)
@@ -974,14 +992,16 @@ class BaseProcessor(QC.QObject, Generic[TypeROI, TypeROIParam]):
         # Get the actual function from the function name
         feature = self.get_feature(proc_params.func_name)
 
-        # Recompute the analysis operation silently
+        # Recompute the analysis operation silently, only for this specific object
+        # (not all selected objects, to avoid O(n²) behavior when called in a loop)
         with Conf.proc.show_result_dialog.temp(False):
-            self.compute_1_to_0(feature.function, param, edit=False)
+            self.compute_1_to_0(feature.function, param, edit=False, target_objs=[obj])
 
         # Update the view
         obj_uuid = get_uuid(obj)
         self.panel.objview.update_item(obj_uuid)
-        self.panel.refresh_plot(obj_uuid, update_items=True, force=True)
+        if refresh_plot:
+            self.panel.refresh_plot(obj_uuid, update_items=True, force=True)
 
     def __exec_func(
         self,
@@ -1332,12 +1352,14 @@ class BaseProcessor(QC.QObject, Generic[TypeROI, TypeROIParam]):
         title: str | None = None,
         comment: str | None = None,
         edit: bool | None = None,
+        target_objs: list[SignalObj | ImageObj] | None = None,
     ) -> ResultData:
         """Generic processing method: 1 object in → no object out.
 
-        Applies a function to each selected object, returning metadata or measurement
-        results (e.g. peak coordinates, statistical properties) without generating
-        new objects. Results are stored in the object's metadata and returned as a
+        Applies a function to each selected object (or specified target objects),
+        returning metadata or measurement results (e.g. peak coordinates, statistical
+        properties) without generating new objects. Results are stored in the object's
+        metadata and returned as a
         ResultData instance.
 
         Args:
@@ -1349,6 +1371,8 @@ class BaseProcessor(QC.QObject, Generic[TypeROI, TypeROIParam]):
             title: Optional progress bar title.
             comment: Optional comment for parameter dialog.
             edit: Whether to open the parameter editor before execution.
+            target_objs: Optional list of specific objects to process. If None,
+             processes all currently selected objects.
 
         Returns:
             ResultData instance containing the results for all processed objects.
@@ -1365,7 +1389,11 @@ class BaseProcessor(QC.QObject, Generic[TypeROI, TypeROIParam]):
         if param is not None:
             if edit and not param.edit(parent=self.mainwindow):
                 return None
-        objs = self.panel.objview.get_sel_objects(include_groups=True)
+        objs = (
+            target_objs
+            if target_objs is not None
+            else self.panel.objview.get_sel_objects(include_groups=True)
+        )
         current_obj = self.panel.objview.get_current_object()
         title = func.__name__ if title is None else title
         refresh_needed = False
@@ -2381,8 +2409,13 @@ class BaseProcessor(QC.QObject, Generic[TypeROI, TypeROIParam]):
                 )
                 # Auto-recompute analysis operations for objects with modified ROIs
                 if mode == "apply":
-                    for obj_i in objs:
-                        self.auto_recompute_analysis(obj_i)
+                    with create_progress_bar(
+                        self.panel, _("Recomputing..."), max_=len(objs)
+                    ) as progress:
+                        for idx, obj_i in enumerate(objs):
+                            progress.setValue(idx)
+                            self.auto_recompute_analysis(obj_i, refresh_plot=False)
+                    self.panel.manual_refresh()
         return edited_roi
 
     def edit_roi_numerically(self) -> TypeROI:

datalab/gui/processor/image.py

@@ -779,7 +779,8 @@ class ImageProcessor(BaseProcessor[ImageROI, ROI2DParam]):
                 == QW.QMessageBox.No
             ):
                 return
-        editor = ImageGridROIEditor(parent=self.parent(), obj=obj0)
+        options = self.panel.plothandler.get_plot_options()
+        editor = ImageGridROIEditor(parent=self.parent(), obj=obj0, options=options)
         if exec_dialog(editor):
             for obj in self.panel.objview.get_sel_objects():
                 obj.roi = editor.get_roi()
@@ -1014,7 +1015,10 @@ class ImageProcessor(BaseProcessor[ImageROI, ROI2DParam]):
         with :py:func:`sigima.proc.image.offset_correction`"""
         obj = self.panel.objview.get_sel_objects(include_groups=True)[0]
         if param is None:
-            dlg = imagebackground.ImageBackgroundDialog(obj, parent=self.mainwindow)
+            options = self.panel.plothandler.get_plot_options()
+            dlg = imagebackground.ImageBackgroundDialog(
+                obj, parent=self.mainwindow, options=options
+            )
             if exec_dialog(dlg):
                 x0, y0, x1, y1 = dlg.get_rect_coords()
                 param = ROI2DParam.create(