napari-spatialdata 0.7.1__tar.gz → 0.7.3__tar.gz

{napari_spatialdata-0.7.1 → napari_spatialdata-0.7.3}/.github/workflows/benchmarks.yml

@@ -66,7 +66,7 @@ jobs:
       - uses: actions/setup-python@v6
         name: Install Python
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           cache-dependency-path: pyproject.toml
 
       - uses: tlambert03/setup-qt-libs@v1
@@ -140,7 +140,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           PLATFORM: ${{ matrix.runs-on }}
-          PYTHON: "3.11"
+          PYTHON: "3.12"
           BACKEND: ${{ matrix.benchmark-name }}
           RUN_ID: ${{ github.run_id }}
           TITLE: "[test-bot] Benchmark tests failing"

{napari_spatialdata-0.7.1 → napari_spatialdata-0.7.3}/.github/workflows/test.yml

@@ -24,7 +24,7 @@ jobs:
       fail-fast: false
       matrix:
         platform: [ubuntu-latest, macos-latest] # [ubuntu-latest, windows-latest, macos-latest]
-        python-version: ["3.11", "3.13"]
+        python-version: ["3.12", "3.13", "3.14"]
 
     steps:
       - uses: actions/checkout@v6

{napari_spatialdata-0.7.1 → napari_spatialdata-0.7.3}/.pre-commit-config.yaml

@@ -7,13 +7,13 @@ default_stages:
 minimum_pre_commit_version: 2.9.3
 repos:
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.19.1
+    rev: v1.20.2
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.23]
         exclude: docs
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.12.0
+    rev: 26.3.1
     hooks:
       - id: black
         additional_dependencies: [toml]
@@ -49,7 +49,7 @@ repos:
     hooks:
       - id: blacken-docs
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.10
+    rev: v0.15.12
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]

{napari_spatialdata-0.7.1 → napari_spatialdata-0.7.3}/.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3.12"
 sphinx:
   configuration: docs/conf.py
   fail_on_warning: false

{napari_spatialdata-0.7.1 → napari_spatialdata-0.7.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: napari-spatialdata
-Version: 0.7.1
+Version: 0.7.3
 Summary: Interactive visualization of spatial omics data with napari
 Home-page: https://github.com/scverse/napari-spatialdata.git
 Author: giovanni palla
@@ -16,12 +16,12 @@ Classifier: Framework :: napari
 Classifier: Topic :: Software Development :: Testing
 Classifier: Programming Language :: Python
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Operating System :: OS Independent
 Classifier: License :: OSI Approved :: BSD License
-Requires-Python: >=3.11
+Requires-Python: >=3.12
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: anndata>=0.12.0
@@ -78,10 +78,10 @@ Requires-Dist: pydantic>2; extra == "readthedocs"
 Provides-Extra: pre
 Requires-Dist: spatialdata>=0.7.3a1; extra == "pre"
 Provides-Extra: all
-Requires-Dist: napari[pyqt5]; extra == "all"
+Requires-Dist: napari[pyqt6]; extra == "all"
 Dynamic: license-file
 
-![SpatialData banner](https://github.com/scverse/spatialdata/blob/main/docs/_static/img/spatialdata_horizontal.png?raw=true)
+![SpatialData banner](https://github.com/scverse/spatialdata/blob/main/docs/_static/img/spatialdata_horizontal.svg?raw=true)
 
 # napari-spatialdata: interactive exploration and annotation of spatial omics data
 
@@ -108,7 +108,7 @@ You can install `napari-spatialdata` via [pip]:
 
     pip install napari-spatialdata[all]
 
-The `all` command will install the qt bindings `PyQt5`.
+The `all` extra also installs the Qt bindings `PyQt6` (via `napari[pyqt6]`).
 
 Napari now also includes multiple triangulation backends. These improve the speed by which a napari 'Shapes' layer gets
 loaded (this does not improve the speed of editing large numbers of shapes yet!). See also the napari

{napari_spatialdata-0.7.1 → napari_spatialdata-0.7.3}/README.md

@@ -1,4 +1,4 @@
-![SpatialData banner](https://github.com/scverse/spatialdata/blob/main/docs/_static/img/spatialdata_horizontal.png?raw=true)
+![SpatialData banner](https://github.com/scverse/spatialdata/blob/main/docs/_static/img/spatialdata_horizontal.svg?raw=true)
 
 # napari-spatialdata: interactive exploration and annotation of spatial omics data
 
@@ -25,7 +25,7 @@ You can install `napari-spatialdata` via [pip]:
 
     pip install napari-spatialdata[all]
 
-The `all` command will install the qt bindings `PyQt5`.
+The `all` extra also installs the Qt bindings `PyQt6` (via `napari[pyqt6]`).
 
 Napari now also includes multiple triangulation backends. These improve the speed by which a napari 'Shapes' layer gets
 loaded (this does not improve the speed of editing large numbers of shapes yet!). See also the napari

{napari_spatialdata-0.7.1 → napari_spatialdata-0.7.3}/asv.conf.json

@@ -35,7 +35,7 @@
   "show_commit_url": "http://github.com/napari/napari/commit/",
 
   // The Pythons you'd like to test against.
-  "pythons": ["3.11"],
+  "pythons": ["3.12"],
 
   // The directory (relative to the current directory) to cache the Python
   // environments in.

{napari_spatialdata-0.7.1 → napari_spatialdata-0.7.3}/setup.cfg

@@ -19,16 +19,16 @@ classifiers =
 	Topic :: Software Development :: Testing
 	Programming Language :: Python
 	Programming Language :: Python :: 3
-	Programming Language :: Python :: 3.11
 	Programming Language :: Python :: 3.12
 	Programming Language :: Python :: 3.13
+	Programming Language :: Python :: 3.14
 	Operating System :: OS Independent
 	License :: OSI Approved :: BSD License
 
 [options]
 packages = find:
 include_package_data = True
-python_requires = >=3.11
+python_requires = >=3.12
 setup_requires = setuptools_scm
 install_requires = 
 	anndata>=0.12.0
@@ -89,7 +89,7 @@ readthedocs =
 pre = 
 	spatialdata>=0.7.3a1
 all = 
-	napari[pyqt5]
+	napari[pyqt6]
 
 [options.packages.find]
 where = src

{napari_spatialdata-0.7.1 → napari_spatialdata-0.7.3}/src/napari_spatialdata/_model.py

@@ -28,8 +28,6 @@ class DataModel:
     _layer: Layer = field(init=False, default=None, repr=True)
     _adata: AnnData | None = field(init=False, default=None, repr=True)
     _adata_layer: str | None = field(init=False, default=None, repr=False)
-    _region_key: str | None = field(default=None, repr=True)
-    _instance_key: str | None = field(default=None, repr=True)
     _color_by: str = field(default="", repr=True, init=False)
     _system_name: str | None = field(default=None, repr=True)
 
@@ -138,7 +136,8 @@ class DataModel:
         except KeyError:
             raise KeyError(f"Key `{name}` not found in `adata.var_names`.") from None
 
-        column = self.adata._get_X(layer=self.adata_layer)[ix]
+        X = self.adata.X if self.adata_layer is None else self.adata.layers[self.adata_layer]
+        column = X[ix]
         index = self.adata.obs[[self.instance_key]].set_index(self.instance_key).index
         return column, self._format_key(name, adata_layer=True), index
 

{napari_spatialdata-0.7.1 → napari_spatialdata-0.7.3}/src/napari_spatialdata/_scatterwidgets.py

@@ -251,14 +251,12 @@ class DiscreteColorWidget(GraphicsWidget):
             color_button = ColorButton(color=color)
             color_button.setMinimumSize(60, 30)
             color_button.setMaximumSize(60, 30)
-            color_button.setStyleSheet(
-                """
+            color_button.setStyleSheet("""
             QPushButton {
                 background-color: transparent;
                 border: none;
             }
-            """
-            )
+            """)
 
             self.color_buttons[obj_category] = color_button
 
@@ -384,8 +382,7 @@ class PlotWidget(GraphicsLayoutWidget):
         self.drawing_mode_button = QPushButton(self)
         self.drawing_mode_button.setIcon(QIcon(str(Path(__file__).parent / "resources/icons8-polygon-80.png")))
         self.drawing_mode_button.setIconSize(QSize(24, 24))
-        self.drawing_mode_button.setStyleSheet(
-            f"""
+        self.drawing_mode_button.setStyleSheet(f"""
             QPushButton {{
                 background-color: transparent;
                 border: none;
@@ -393,8 +390,7 @@ class PlotWidget(GraphicsLayoutWidget):
             QPushButton:checked {{
                 border: 1px solid rgb{self.color};
             }}
-        """
-        )
+        """)
         self.drawing_mode_button.setCheckable(True)
         self.drawing_mode_button.clicked.connect(self.toggle_drawing_mode)
         self.drawing_mode_button.setToolTip("Add freehand ROIs.")
@@ -405,8 +401,7 @@ class PlotWidget(GraphicsLayoutWidget):
         self.rectangle_mode_button = QPushButton(self)
         self.rectangle_mode_button.setIcon(QIcon(str(Path(__file__).parent / "resources/icons8-rectangle-48.png")))
         self.rectangle_mode_button.setIconSize(QSize(24, 24))
-        self.rectangle_mode_button.setStyleSheet(
-            f"""
+        self.rectangle_mode_button.setStyleSheet(f"""
             QPushButton {{
                 background-color: transparent;
                 border: none;
@@ -414,8 +409,7 @@ class PlotWidget(GraphicsLayoutWidget):
             QPushButton:checked {{
                 border: 1px solid rgb{self.color};
             }}
-        """
-        )
+        """)
         self.rectangle_mode_button.setCheckable(True)
         self.rectangle_mode_button.clicked.connect(self.toggle_rectangle_mode)
         self.rectangle_mode_button.setToolTip("Add rectangular ROIs.")
@@ -873,14 +867,12 @@ class PlotWidget(GraphicsLayoutWidget):
         # view.setVerticalScrollBarPolicy(QtCore.Qt.ScrollBarAlwaysOn)
         # sets stle of the vertical slider
         view.setStyleSheet(get_current_stylesheet())
-        view.setStyleSheet(
-            """
+        view.setStyleSheet("""
             QGraphicsView {
             border: none;
             background: rgb(0, 0, 0);
             }
-            """
-        )
+            """)
 
         view.setSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Preferred)
 
@@ -931,11 +923,11 @@ class PlotWidget(GraphicsLayoutWidget):
             logger.debug("Left press detected")
 
             # Get the position of the click in the scene
-            scene_pos = event.pos()
+            scene_pos = self.mapToScene(event.pos())
 
             # Check if the click is within the scatter plot view box
             if not self.scatter_plot.vb.sceneBoundingRect().contains(scene_pos):
-                logger.debug("Click outside scatter plot view box, scene position: {scene_pos}")
+                logger.debug(f"Click outside scatter plot view box, scene position: {scene_pos}")
                 return
 
             pen = pg.mkPen(color="gray", width=2)
@@ -946,7 +938,7 @@ class PlotWidget(GraphicsLayoutWidget):
 
             if self.drawing:
 
-                plot_pos = self.scatter_plot.vb.mapSceneToView(event.pos())
+                plot_pos = self.scatter_plot.vb.mapSceneToView(scene_pos)
 
                 self.current_roi = pg.PolyLineROI(
                     [], closed=True, removable=True, pen=pen, handlePen=handlePen, hoverPen=hoverPen
@@ -954,7 +946,7 @@ class PlotWidget(GraphicsLayoutWidget):
                 self.scatter_plot.addItem(self.current_roi)
 
                 self.current_points = [(plot_pos.x(), plot_pos.y())]
-                self.last_pos = (event.pos().x(), event.pos().y())
+                self.last_pos = (scene_pos.x(), scene_pos.y())
 
                 event.accept()
 
@@ -962,7 +954,7 @@ class PlotWidget(GraphicsLayoutWidget):
 
                 logger.info("Rectangle")
 
-                plot_pos = self.scatter_plot.vb.mapSceneToView(event.pos())
+                plot_pos = self.scatter_plot.vb.mapSceneToView(scene_pos)
                 self.current_roi = pg.RectROI(
                     pos=(plot_pos.x(), plot_pos.y()),
                     size=(0, 0),
@@ -987,16 +979,17 @@ class PlotWidget(GraphicsLayoutWidget):
         if self.drawing and self.current_roi is not None:
 
             if self.last_pos is not None:
-                dist = np.sqrt((event.pos().x() - self.last_pos[0]) ** 2 + (event.pos().y() - self.last_pos[1]) ** 2)
+                scene_pos = self.mapToScene(event.pos())
+                dist = np.sqrt((scene_pos.x() - self.last_pos[0]) ** 2 + (scene_pos.y() - self.last_pos[1]) ** 2)
 
                 if dist > self.vertex_add_threshold:
 
-                    plot_pos = self.scatter_plot.vb.mapSceneToView(event.pos())
+                    plot_pos = self.scatter_plot.vb.mapSceneToView(scene_pos)
                     self.current_points.append((plot_pos.x(), plot_pos.y()))
 
                     self.current_roi.setPoints(self.current_points)
 
-                    self.last_pos = (event.pos().x(), event.pos().y())
+                    self.last_pos = (scene_pos.x(), scene_pos.y())
 
                     logger.debug(f"Updated points for PolyLineROI: {self.current_points}")
 
@@ -1004,7 +997,7 @@ class PlotWidget(GraphicsLayoutWidget):
 
         elif self.rectangle and self.current_roi is not None and self.initial_pos is not None:
 
-            plot_pos = self.scatter_plot.vb.mapSceneToView(event.pos())
+            plot_pos = self.scatter_plot.vb.mapSceneToView(self.mapToScene(event.pos()))
             width = plot_pos.x() - self.initial_pos.x()  # type: ignore[attr-defined]
             height = plot_pos.y() - self.initial_pos.y()  # type: ignore[attr-defined]
             self.current_roi.setSize([width, height])
@@ -1018,7 +1011,7 @@ class PlotWidget(GraphicsLayoutWidget):
             super().mouseMoveEvent(event)
 
         # Get cursor position
-        scene_pos = event.pos()
+        scene_pos = self.mapToScene(event.pos())
         plot_pos = self.scatter_plot.vb.mapSceneToView(scene_pos)
 
         # Update the cursor position label
@@ -1029,7 +1022,10 @@ class PlotWidget(GraphicsLayoutWidget):
 
     def mouseReleaseEvent(self, event: Any) -> None:
 
-        logger.debug(f"Mouse release event detected at {self.scatter_plot.vb.mapSceneToView(event.pos())}")
+        # also called by scene().sigMouseClicked with a pyqtgraph MouseClickEvent, whose pos() mapToScene can't take
+        if isinstance(event, QtGui.QMouseEvent):
+            scene_pos = self.mapToScene(event.pos())
+            logger.debug(f"Mouse release event detected at {self.scatter_plot.vb.mapSceneToView(scene_pos)}")
 
         if self.drawing and event.button() == Qt.LeftButton:
 
@@ -1057,7 +1053,7 @@ class PlotWidget(GraphicsLayoutWidget):
     def mouseDoubleClickEvent(self, event: Any) -> None:
         if event.button() == Qt.LeftButton:
 
-            plot_pos = self.scatter_plot.vb.mapSceneToView(event.pos())
+            plot_pos = self.scatter_plot.vb.mapSceneToView(self.mapToScene(event.pos()))
             point = Point(plot_pos.x(), plot_pos.y())
 
             self.remove_roi(point=point)

{napari_spatialdata-0.7.1 → napari_spatialdata-0.7.3}/src/napari_spatialdata/_sdata_widgets.py

@@ -5,7 +5,7 @@ from collections.abc import Iterable
 from importlib.metadata import version
 from operator import itemgetter
 from pathlib import Path
-from typing import TYPE_CHECKING, cast
+from typing import TYPE_CHECKING
 
 import numpy as np
 import shapely
@@ -15,11 +15,20 @@ from napari.utils.notifications import show_info
 from packaging.version import parse as parse_version
 from qtpy.QtCore import QThread, Signal
 from qtpy.QtGui import QIcon
-from qtpy.QtWidgets import QLabel, QListWidget, QListWidgetItem, QProgressBar, QVBoxLayout, QWidget
+from qtpy.QtWidgets import (
+    QCheckBox,
+    QLabel,
+    QListWidget,
+    QListWidgetItem,
+    QProgressBar,
+    QVBoxLayout,
+    QWidget,
+)
 from spatialdata import SpatialData
 from spatialdata.models._utils import DEFAULT_COORDINATE_SYSTEM
 
 from napari_spatialdata._viewer import SpatialDataViewer
+from napari_spatialdata.constants import config
 from napari_spatialdata.constants.config import N_CIRCLES_WARNING_THRESHOLD, N_SHAPES_WARNING_THRESHOLD
 from napari_spatialdata.utils._utils import _get_sdata_key, get_duplicate_element_names, get_elements_meta_mapping
 
@@ -174,11 +183,39 @@ class SdataWidget(QWidget):
         self.slider.setRange(0, 0)
         self.slider.setVisible(False)
 
+        self.discard_z_points = QCheckBox("Discard z for 3D points")
+        self.discard_z_points.setChecked(config.PROJECT_3D_POINTS_TO_2D)
+        self.discard_z_points.setToolTip(
+            "When checked, the z coordinate of new points layers is discarded so they are loaded in 2D. "
+            "Only applies to new layers; layers already displayed are not affected."
+        )
+        self.discard_z_points.toggled.connect(self._on_discard_z_points_toggled)
+
+        self.discard_z_shapes = QCheckBox("Discard z for 2.5D shapes")
+        self.discard_z_shapes.setChecked(config.PROJECT_2_5D_SHAPES_TO_2D)
+        self.discard_z_shapes.setToolTip(
+            "When checked, the z coordinate of new shapes layers is discarded so they are loaded in 2D. "
+            "Only applies to new layers; layers already displayed are not affected."
+        )
+        self.discard_z_shapes.toggled.connect(self._on_discard_z_shapes_toggled)
+
+        # The 3D toggles only matter when at least one element across the loaded
+        # SpatialData objects has a z axis. Otherwise we hide them to save screen
+        # real estate for users working with 2D-only data.
+        self._has_z_data = self._sdatas_have_z_axis(self._sdata)
+        self._three_d_settings_label = QLabel("3D Settings:")
+        self._three_d_settings_label.setVisible(self._has_z_data)
+        self.discard_z_points.setVisible(self._has_z_data)
+        self.discard_z_shapes.setVisible(self._has_z_data)
+
         self.layout().addWidget(self.slider)
         self.layout().addWidget(QLabel("Coordinate System:"))
         self.layout().addWidget(self.coordinate_system_widget)
         self.layout().addWidget(QLabel("Elements:"))
         self.layout().addWidget(self.elements_widget)
+        self.layout().addWidget(self._three_d_settings_label)
+        self.layout().addWidget(self.discard_z_points)
+        self.layout().addWidget(self.discard_z_shapes)
         self.elements_widget.itemDoubleClicked.connect(self._on_click_item)
         self.coordinate_system_widget.currentItemChanged.connect(
             lambda item: self.elements_widget._onItemChange(item.text())
@@ -219,8 +256,6 @@ class SdataWidget(QWidget):
             }:
                 return
 
-            type_ = cast(str, type_)
-
             self.worker_thread.load_data(type_, text, sdata, selected_cs, multi)
             if not PROBLEMATIC_NUMPY_MACOS:
                 self.slider.setVisible(True)
@@ -258,6 +293,24 @@ class SdataWidget(QWidget):
                         layer.metadata["_active_in_cs"].add(coordinate_system)
                         layer.metadata["_current_cs"] = coordinate_system
 
+    def _on_discard_z_points_toggled(self, checked: bool) -> None:
+        config.PROJECT_3D_POINTS_TO_2D = checked
+
+    def _on_discard_z_shapes_toggled(self, checked: bool) -> None:
+        config.PROJECT_2_5D_SHAPES_TO_2D = checked
+
+    @staticmethod
+    def _sdatas_have_z_axis(sdatas: EventedList) -> bool:
+        """Return ``True`` if any element across the given ``SpatialData`` objects has a z axis.
+
+        Used to decide whether to expose the 3D / 2.5D projection toggles in the widget.
+        """
+        for sdata in sdatas:
+            for _, _, element in sdata._gen_elements():
+                if SpatialDataViewer._has_z_axis(element):
+                    return True
+        return False
+
     def _get_shapes(self, sdata: SpatialData, key: str, selected_cs: str, multi: bool) -> Shapes | Points:
         original_name = key[: key.rfind("_")] if multi else key
 

{napari_spatialdata-0.7.1 → napari_spatialdata-0.7.3}/src/napari_spatialdata/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.7.1'
-__version_tuple__ = version_tuple = (0, 7, 1)
+__version__ = version = '0.7.3'
+__version_tuple__ = version_tuple = (0, 7, 3)
 
-__commit_id__ = commit_id = 'g3a8b87fb6'
+__commit_id__ = commit_id = 'g2cb4e2ca7'

{napari_spatialdata-0.7.1 → napari_spatialdata-0.7.3}/src/napari_spatialdata/_view.py

@@ -65,9 +65,7 @@ class QtAdataScatterWidget(QWidget):
             self._viewer = napari_viewer
 
             self._model = (
-                model
-                if model is not None
-                else self._viewer.window._dock_widgets["SpatialData"].widget().viewer_model._model
+                model if model is not None else self._viewer.window.dock_widgets["SpatialData"].viewer_model._model
             )
 
             self._select_layer()
@@ -241,9 +239,8 @@ class QtAdataScatterWidget(QWidget):
 
                     # check that the view widget is present
                     # and trigger its update
-                    if "View (napari-spatialdata)" in dict(self._viewer.window._dock_widgets.items()):
-                        view_widget = dict(self._viewer.window._dock_widgets.items())["View (napari-spatialdata)"]
-                        qtAdataViewWidget = [x for x in view_widget.children() if isinstance(x, QtAdataViewWidget)][0]
+                    if "View (napari-spatialdata)" in self._viewer.window.dock_widgets:
+                        qtAdataViewWidget = self._viewer.window.dock_widgets["View (napari-spatialdata)"]
                         qtAdataViewWidget._on_layer_update()
 
                 # new annotation - update options
@@ -306,9 +303,7 @@ class QtAdataScatterWidget(QWidget):
             selected_table = self.table_name_widget.currentText()
 
             # trigger saving of the table
-            # TODO: have to find another way to pass this as this is deprecated from 0.5.0 onwards
-            # it's used in the save_sdata method
-            self._viewer_model = self._viewer.window._dock_widgets["SpatialData"].widget().viewer_model
+            self._viewer_model = self._viewer.window.dock_widgets["SpatialData"].viewer_model
             self._viewer_model._write_element_to_disk(
                 selected_layer.metadata["sdata"],
                 selected_table,
@@ -611,8 +606,6 @@ class QtAdataViewWidget(QWidget):
         if self.model.adata.shape == (0, 0):
             return
 
-        self.model._region_key = layer.metadata["region_key"] if isinstance(layer, Labels) else None
-        self.model._instance_key = layer.metadata["instance_key"] if isinstance(layer, Labels) else None
         self.model.system_name = layer.metadata.get("name", None)
 
         if hasattr(
@@ -695,8 +688,7 @@ class QtAdataAnnotationWidget(QWidget):
     def __init__(self, napari_viewer: Viewer):
         super().__init__()
         self._viewer = napari_viewer
-        # TODO: have to find another way to pass this as this is deprecated from 0.5.0 onwards
-        self._viewer_model = self._viewer.window._dock_widgets["SpatialData"].widget().viewer_model
+        self._viewer_model = self._viewer.window.dock_widgets["SpatialData"].viewer_model
 
         self.setLayout(QGridLayout())
         self._current_color = "#FFFFFF"

{napari_spatialdata-0.7.1 → napari_spatialdata-0.7.3}/src/napari_spatialdata/_viewer.py

@@ -189,9 +189,6 @@ class SpatialDataViewer(QObject):
             raise ValueError("Cannot export a points element with no points")
         transformed_data = np.array([layer_to_save.data_to_world(xy) for xy in layer_to_save.data])
         swap_data = np.fliplr(transformed_data)
-        # ignore z axis if present
-        if swap_data.shape[1] == 3:
-            swap_data = swap_data[:, :2]
         parsed = PointsModel.parse(swap_data, transformations=transformation)
 
         # saving to disk of points temporarily disabled until the interface update that will unify the view widget,
@@ -261,14 +258,21 @@ class SpatialDataViewer(QObject):
             for shape in layer_to_save._data_view.shapes
         ]
 
-        def _fix_coords(coords: ArrayLike) -> ArrayLike:
-            remove_z = coords.shape[1] == 3
-            first_index = 1 if remove_z else 0
-            coords = coords[:, first_index::]
-            return np.fliplr(coords)
+        has_z = coords[0].shape[1] == 3
 
-        polygons: list[Polygon] = [Polygon(_fix_coords(p)) for p in coords]
-        gdf = GeoDataFrame({"geometry": polygons})
+        def _fix_coords(coords: ArrayLike) -> tuple[ArrayLike, float | None]:
+            if coords.shape[1] == 3:
+                z_val = float(coords[0, 0])
+                yx = coords[:, 1:]
+                return np.fliplr(yx), z_val
+            return np.fliplr(coords), None
+
+        fixed = [_fix_coords(p) for p in coords]
+        polygons: list[Polygon] = [Polygon(xy) for xy, _ in fixed]
+        gdf_dict: dict[str, Any] = {"geometry": polygons}
+        if has_z:
+            gdf_dict["z"] = [z_val for _, z_val in fixed]
+        gdf = GeoDataFrame(gdf_dict)
 
         force_2d(gdf)
         parsed = ShapesModel.parse(gdf, transformations=transformation)
@@ -514,11 +518,15 @@ class SpatialDataViewer(QObject):
             original_name = original_name[: original_name.rfind("_")]
 
         df = sdata.shapes[original_name]
-        affine = _get_transform(sdata.shapes[original_name], selected_cs)
+        axes = get_axes_names(df)
+        include_z = "z" in axes and not config.PROJECT_2_5D_SHAPES_TO_2D
+        affine = _get_transform(sdata.shapes[original_name], selected_cs, include_z=include_z)
 
-        # 2.5D circles not supported yet
         xy = np.array([df.geometry.x, df.geometry.y]).T
         yx = np.fliplr(xy)
+        if include_z:
+            z_vals = df["z"].to_numpy()
+            yx = np.column_stack([z_vals, yx])
         radii = df.radius.to_numpy()
 
         adata, table_name, table_names = self._get_table_data(sdata, original_name)
@@ -561,7 +569,7 @@ class SpatialDataViewer(QObject):
             else:
                 kwargs |= {"border_color": "white"}
             # useful code to have readily available to debug the correct radius of circles when represented as points
-            ellipses = _get_ellipses_from_circles(yx=yx, radii=radii)
+            ellipses = _get_ellipses_from_circles(coords=yx, radii=radii)
             layer = Shapes(
                 ellipses,
                 shape_type="ellipse",
@@ -804,8 +812,43 @@ class SpatialDataViewer(QObject):
                 sdata = metadata["sdata"]
                 element_name = metadata["name"]
                 element_data = sdata[element_name]
-                affine = _get_transform(element_data, coordinate_system)
+                include_z = self._should_include_z(element_data)
+                affine = _get_transform(element_data, coordinate_system, include_z=include_z)
                 if affine is not None:
                     layer.affine = affine
                     if layer._type_string == "points":
                         self._adjust_radii_of_points_layer(layer, affine)
+
+    @staticmethod
+    def _has_z_axis(element: Any) -> bool:
+        """Return ``True`` if ``element`` exposes a ``z`` axis.
+
+        For raster elements (images / labels) the ``z`` axis is reported by
+        :func:`spatialdata.models.get_axes_names`. For vector elements (points
+        as :class:`~dask.dataframe.DataFrame`, shapes as
+        :class:`~geopandas.GeoDataFrame`) the same helper is used.
+        """
+        from xarray import DataArray, DataTree
+
+        if not isinstance(element, DataArray | DataTree | DaskDataFrame | GeoDataFrame):
+            return False
+        return "z" in get_axes_names(element)
+
+    @staticmethod
+    def _should_include_z(element: DaskDataFrame | GeoDataFrame) -> bool:
+        """Determine whether to include the z axis for a given spatial element.
+
+        For raster data (images, labels) z is always included when present.
+        For vector data (points, shapes) z inclusion depends on the user-facing
+        projection config flags.
+        """
+        from xarray import DataArray, DataTree
+
+        if isinstance(element, DataArray | DataTree):
+            return True
+        axes = get_axes_names(element)
+        if "z" not in axes:
+            return False
+        if isinstance(element, DaskDataFrame):
+            return not config.PROJECT_3D_POINTS_TO_2D
+        return not config.PROJECT_2_5D_SHAPES_TO_2D