From 917c34ff0f8972aad2d642a441e50761937c314e Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Thu, 10 Oct 2024 15:09:47 +1100
Subject: [PATCH 01/16] Add shape selector widget

---
 plugin/napari_lattice/fields.py         |   6 +-
 plugin/napari_lattice/shape_selector.py | 121 ++++++++++++++++++++++++
 2 files changed, 125 insertions(+), 2 deletions(-)
 create mode 100644 plugin/napari_lattice/shape_selector.py

diff --git a/plugin/napari_lattice/fields.py b/plugin/napari_lattice/fields.py
index 2360c69f..b2fc7a3b 100644
--- a/plugin/napari_lattice/fields.py
+++ b/plugin/napari_lattice/fields.py
@@ -20,7 +20,7 @@
 from lls_core.models.deskew import DefinedPixelSizes
 from lls_core.models.output import SaveFileType
 from lls_core.workflow import workflow_from_path
-from magicclass import FieldGroup, MagicTemplate, field, magicclass, set_design
+from magicclass import FieldGroup, MagicTemplate, field, magicclass, set_design, vfield
 from magicclass.fields import MagicField
 from magicclass.widgets import ComboBox, Label, Widget
 from napari.layers import Image, Shapes
@@ -32,6 +32,7 @@
 from qtpy.QtWidgets import QTabWidget
 from strenum import StrEnum
 from napari_lattice.parent_connect import connect_parent
+from plugin.napari_lattice.shape_selector import ShapeSelector
 
 if TYPE_CHECKING:
     from magicgui.widgets.bases import RangedWidget
@@ -429,7 +430,8 @@ class CroppingFields(NapariFieldGroup):
         This is to support the workflow of performing a preview deskew and using that to calculate the cropping coordinates.
     """), widget_type="Label")
     fields_enabled = field(False, label="Enabled")
-    shapes= field(List[Shapes], widget_type="Select", label = "ROI Shape Layers").with_options(choices=lambda _x, _y: get_layers(Shapes))
+
+    shapes= vfield(ShapeSelector)
     z_range = field(Tuple[int, int]).with_options(
         label = "Z Range",
         value = (0, 1),
diff --git a/plugin/napari_lattice/shape_selector.py b/plugin/napari_lattice/shape_selector.py
new file mode 100644
index 00000000..81e966e0
--- /dev/null
+++ b/plugin/napari_lattice/shape_selector.py
@@ -0,0 +1,121 @@
+from __future__ import annotations
+from dataclasses import dataclass
+from typing import Iterator, Tuple, TYPE_CHECKING
+from magicclass import field, magicclass
+from magicgui.widgets import Select
+from napari.layers import Shapes
+from napari.components.layerlist import LayerList
+
+from plugin.napari_lattice.utils import get_viewer
+
+if TYPE_CHECKING:
+    from napari.utils.events.event import Event
+    from numpy.typing import NDArray
+
+@dataclass
+class Shape:
+    """
+    Holds data about a single shape within a Shapes layer
+    """
+    layer: Shapes
+    index: int
+
+    def __str__(self) -> str:
+        return f"{self.layer.name} {self.index}"
+
+    def get_array(self) -> NDArray:
+        return self.layer.data[self.index]
+
+@magicclass
+class ShapeSelector:
+    def __init__(self, *args, **kwargs) -> None:
+        # Needed to handle extra kwargs
+        pass
+
+    def _get_shape_choices(self, widget: Select | None = None) -> Iterator[Tuple[str, Shape]]:
+        """
+        Returns the choices to use for the Select box
+        """
+        viewer = get_viewer()
+        for layer in viewer.layers:
+            if isinstance(layer, Shapes):
+                for index in layer.features.index:
+                    result = Shape(layer=layer, index=index)
+                    yield str(result), result
+
+    def _on_selection_change(self, event: Event) -> None:
+        """
+        Triggered when the user clicks on one or more shapes.
+        The widget is then updated to synchronise
+        """
+        source: Shapes = event.source
+        selection: list[Shape] = []
+        for index in source.selected_data:
+            selection.append(Shape(layer=source, index=index))
+        self.shapes.value = selection
+
+    def _connect_shapes(self, shapes: Shapes) -> None:
+        """
+        Called on a newly discovered `Shapes` layer.
+        Listens to events on that layer that we are interested in.
+        """
+        shapes.events.data.connect(self._on_shape_change)
+        shapes.events.highlight.connect(self._on_selection_change)
+        # shapes.events.current_properties.connect(self._on_selection_change)
+
+    def _on_shape_change(self, event: Event) -> None:
+        """
+        Triggered whenever a shape layer changes.
+        Resets the select box options
+        """
+        if isinstance(event.source, Shapes):
+            self.shapes.reset_choices()
+
+    def _on_layer_add(self, event: Event) -> None:
+        """
+        Triggered whenever a new layer is inserted.
+        Ensures we listen for shape changes to that new layer
+        """
+        if isinstance(event.source, LayerList):
+            for layer in event.source:
+                if isinstance(layer, Shapes):
+                    self._connect_shapes(layer)
+                
+    def __post_init__(self) -> None:
+        """
+        Whenever a new layer is inserted
+        """
+        viewer = get_viewer()
+
+        # Listen for new layers
+        viewer.layers.events.inserted.connect(self._on_layer_add)
+
+        # Watch current layers
+        for layer in viewer.layers:
+            if isinstance(layer, Shapes):
+                self._connect_shapes(layer)
+
+    shapes = field(Select, options={"choices": _get_shape_choices})
+
+    # values is a list[Shape], but if we use the correct annotation it breaks magicclass
+    @shapes.connect
+    def _widget_changed(self, values: list) -> None:
+        """
+        Triggered when the plugin widget is changed.
+        We then synchronise the Napari shape selection with it.
+        """
+        layers: set[Shapes] = set()
+        indices: set[int] = set()
+        value: Shape
+
+        for value in values:
+            layers.add(value.layer)
+            indices.add(value.index)
+
+        if len(layers) > 1:
+            raise Exception("Shapes from multiple layers selected. This shouldn't be possible")
+
+        if layers:
+            layer = layers.pop()
+            layer.selected_data = indices
+            layer.refresh()

From 6dd6be3a6c623ecbc71d124aeb0fa4e18daa443d Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Thu, 10 Oct 2024 16:31:47 +1100
Subject: [PATCH 02/16] Fixes for multiple shape layers

---
 plugin/napari_lattice/shape_selector.py | 71 +++++++++++++++++--------
 1 file changed, 48 insertions(+), 23 deletions(-)

diff --git a/plugin/napari_lattice/shape_selector.py b/plugin/napari_lattice/shape_selector.py
index 81e966e0..732e2e53 100644
--- a/plugin/napari_lattice/shape_selector.py
+++ b/plugin/napari_lattice/shape_selector.py
@@ -5,6 +5,8 @@
 from magicgui.widgets import Select
 from napari.layers import Shapes
 from napari.components.layerlist import LayerList
+from collections import defaultdict
+from contextlib import contextmanager
 
 from plugin.napari_lattice.utils import get_viewer
 
@@ -12,7 +14,7 @@
     from napari.utils.events.event import Event
     from numpy.typing import NDArray
 
-@dataclass
+@dataclass(frozen=True, eq=True)
 class Shape:
     """
     Holds data about a single shape within a Shapes layer
@@ -21,16 +23,32 @@ class Shape:
     index: int
 
     def __str__(self) -> str:
-        return f"{self.layer.name} {self.index}"
+        return f"{self.layer.name}: Shape {self.index}"
 
     def get_array(self) -> NDArray:
         return self.layer.data[self.index]
 
 @magicclass
 class ShapeSelector:
+
+    _blocked: bool
+
     def __init__(self, *args, **kwargs) -> None:
         # Needed to handle extra kwargs
-        pass
+        self._blocked = False
+
+    @contextmanager
+    def _block(self):
+        """
+        Context manager that prevents event handlers recursively calling each other.
+        Yields a boolean, which means functions should proceed if `True`, or return immediately if `False`
+        """
+        if self._blocked:
+            yield False
+        else:
+            self._blocked = True
+            yield True
+            self._blocked = False
 
     def _get_shape_choices(self, widget: Select | None = None) -> Iterator[Tuple[str, Shape]]:
         """
@@ -48,11 +66,16 @@ def _on_selection_change(self, event: Event) -> None:
         Triggered when the user clicks on one or more shapes.
         The widget is then updated to synchronise
         """
-        source: Shapes = event.source
-        selection: list[Shape] = []
-        for index in source.selected_data:
-            selection.append(Shape(layer=source, index=index))
-        self.shapes.value = selection
+        # Prevent recursion
+        with self._block() as execute:
+            if not execute:
+                return
+
+            source: Shapes = event.source
+            selection: list[Shape] = []
+            for index in source.selected_data:
+                selection.append(Shape(layer=source, index=index))
+            self.shapes.value = selection
 
     def _connect_shapes(self, shapes: Shapes) -> None:
         """
@@ -104,18 +127,20 @@ def _widget_changed(self, values: list) -> None:
         Triggered when the plugin widget is changed.
         We then synchronise the Napari shape selection with it.
         """
-        layers: set[Shapes] = set()
-        indices: set[int] = set()
-        value: Shape
-
-        for value in values:
-            layers.add(value.layer)
-            indices.add(value.index)
-
-        if len(layers) > 1:
-            raise Exception("Shapes from multiple layers selected. This shouldn't be possible")
-
-        if layers:
-            layer = layers.pop()
-            layer.selected_data = indices
-            layer.refresh()
+        with self._block() as execute:
+            if not execute:
+                return
+            layers: dict[Shapes, list[int]] = {layer: [] for layer in get_viewer().layers if isinstance(layer, Shapes)}
+            value: Shape
+
+            # Find the current selection for each layer
+            for value in values:
+                layers[value.layer].append(value.index)
+
+            # For each layer, set the appropriate selection (this can't be done incrementally)
+            for layer, shapes in layers.items():
+                layer.selected_data = shapes
+
+            # Re-calculate the selections for all Shapes layers (since some have been deselected)
+            for layer in layers.keys():
+                    layer.refresh()

From 056ad2ee7749c632b7a67b6766ff5ca3d3e7fe9d Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Thu, 10 Oct 2024 18:19:10 +1100
Subject: [PATCH 03/16] Better comments

---
 plugin/napari_lattice/shape_selector.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/plugin/napari_lattice/shape_selector.py b/plugin/napari_lattice/shape_selector.py
index 732e2e53..4acaf810 100644
--- a/plugin/napari_lattice/shape_selector.py
+++ b/plugin/napari_lattice/shape_selector.py
@@ -41,7 +41,7 @@ def __init__(self, *args, **kwargs) -> None:
     def _block(self):
         """
         Context manager that prevents event handlers recursively calling each other.
-        Yields a boolean, which means functions should proceed if `True`, or return immediately if `False`
+        Yields a boolean which means functions should proceed if `True`, or return immediately if `False`
         """
         if self._blocked:
             yield False
@@ -83,8 +83,9 @@ def _connect_shapes(self, shapes: Shapes) -> None:
         Listens to events on that layer that we are interested in.
         """
         shapes.events.data.connect(self._on_shape_change)
+        # There is no shape selection event. This is the closest thing.
+        # See: https://github.com/napari/napari/issues/6886
         shapes.events.highlight.connect(self._on_selection_change)
-        # shapes.events.current_properties.connect(self._on_selection_change)
 
     def _on_shape_change(self, event: Event) -> None:
         """

From 02a0c5642285bf5ca8df8f9093e2a366dfd515a9 Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Thu, 10 Oct 2024 18:20:44 +1100
Subject: [PATCH 04/16] Fix import

---
 plugin/napari_lattice/shape_selector.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugin/napari_lattice/shape_selector.py b/plugin/napari_lattice/shape_selector.py
index 4acaf810..d51e7fc8 100644
--- a/plugin/napari_lattice/shape_selector.py
+++ b/plugin/napari_lattice/shape_selector.py
@@ -8,7 +8,7 @@
 from collections import defaultdict
 from contextlib import contextmanager
 
-from plugin.napari_lattice.utils import get_viewer
+from napari_lattice.utils import get_viewer
 
 if TYPE_CHECKING:
     from napari.utils.events.event import Event

From a678a3d43ea205521fc83cb7da65fe795049976e Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Thu, 10 Oct 2024 18:44:07 +1100
Subject: [PATCH 05/16] Rename shapes field

---
 plugin/napari_lattice/shape_selector.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/plugin/napari_lattice/shape_selector.py b/plugin/napari_lattice/shape_selector.py
index d51e7fc8..e8362092 100644
--- a/plugin/napari_lattice/shape_selector.py
+++ b/plugin/napari_lattice/shape_selector.py
@@ -33,10 +33,10 @@ class ShapeSelector:
 
     _blocked: bool
 
-    def __init__(self, *args, **kwargs) -> None:
-        # Needed to handle extra kwargs
+    def __init__(self, enabled: bool, *args, **kwargs) -> None:
         self._blocked = False
-
+        self.enabled = enabled
+    
     @contextmanager
     def _block(self):
         """
@@ -119,7 +119,7 @@ def __post_init__(self) -> None:
             if isinstance(layer, Shapes):
                 self._connect_shapes(layer)
 
-    shapes = field(Select, options={"choices": _get_shape_choices})
+    shapes = field(Select, options={"choices": _get_shape_choices, "label": "ROIs"})
 
     # values is a list[Shape], but if we use the correct annotation it breaks magicclass
     @shapes.connect
@@ -144,4 +144,4 @@ def _widget_changed(self, values: list) -> None:
 
             # Re-calculate the selections for all Shapes layers (since some have been deselected)
             for layer in layers.keys():
-                    layer.refresh()
+                layer.refresh()

From 8146b9ac0d61de1c074bfbefe1af9a3e4b0000ce Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Fri, 11 Oct 2024 14:24:42 +1100
Subject: [PATCH 06/16] Integrate shape selector into rest of plugin

---
 core/lls_core/models/results.py         | 36 ++++++++++++++++++------
 plugin/napari_lattice/dock_widget.py    | 15 +++++-----
 plugin/napari_lattice/fields.py         | 24 ++++++++--------
 plugin/napari_lattice/shape_selector.py | 37 +++++++++++++++----------
 4 files changed, 68 insertions(+), 44 deletions(-)

diff --git a/core/lls_core/models/results.py b/core/lls_core/models/results.py
index 2fb07a9b..3e7943d6 100644
--- a/core/lls_core/models/results.py
+++ b/core/lls_core/models/results.py
@@ -2,7 +2,7 @@
 from itertools import groupby
 from pathlib import Path
 
-from typing import Iterable, Optional, Tuple, Union, cast, TYPE_CHECKING, overload
+from typing import Iterable, Iterator, Optional, Tuple, TypeAlias, Union, cast, TYPE_CHECKING, overload
 from typing_extensions import Generic, TypeVar
 from pydantic.v1 import BaseModel, NonNegativeInt, Field
 from lls_core.types import ArrayLike, is_arraylike
@@ -75,6 +75,19 @@ class ImageSlices(ProcessedSlices[ArrayLike]):
     # This re-definition of the type is helpful for `mkdocs`
     slices: Iterable[ProcessedSlice[ArrayLike]] = Field(description="Iterable of result slices. For a given slice, you can access the image data through the `slice.data` property, which is a numpy-like array.")
 
+    def roi_previews(self) -> Iterable[ArrayLike]:
+        """
+        Extracts a single 3D image for each ROI
+        """
+        import numpy as np
+        def _preview(slices: Iterable[ProcessedSlice[ArrayLike]]) -> ArrayLike:
+            for slice in slices:
+                return slice.data
+            raise Exception("This ROI has no images. This shouldn't be possible")
+
+        for roi_index, slices in groupby(self.slices, key=lambda slice: slice.roi_index):
+            yield _preview(slices)
+
     def save_image(self):
         """
         Saves result slices to disk
@@ -96,7 +109,8 @@ def save_image(self):
 If a `DataFrame`, then it contains non-image data returned by your workflow.
 """
 
-class WorkflowSlices(ProcessedSlices[Union[Tuple[RawWorkflowOutput], RawWorkflowOutput]]):
+MaybeTupleRawWorkflowOutput: TypeAlias = Union[Tuple[RawWorkflowOutput], RawWorkflowOutput]
+class WorkflowSlices(ProcessedSlices[MaybeTupleRawWorkflowOutput]):
     """
     The counterpart of `ImageSlices`, but for workflow outputs.
     This is needed because workflows have vastly different outputs that may include regular
@@ -159,16 +173,20 @@ def process(self) -> Iterable[Tuple[RoiIndex, ProcessedWorkflowOutput]]:
                 else:
                     yield roi, pd.DataFrame(element)
 
-    def extract_preview(self) -> NDArray:
+    def roi_previews(self) -> Iterable[NDArray]:
         """
-        Extracts a single 3D image for previewing purposes
+        Extracts a single 3D image for each ROI
         """
         import numpy as np
-        for slice in self.slices:
-            for value in slice.as_tuple():
-                if is_arraylike(value):
-                    return np.asarray(value)
-        raise Exception("No image was returned from this workflow")
+        def _preview(slices: Iterable[ProcessedSlice[MaybeTupleRawWorkflowOutput]]) -> NDArray:
+            for slice in slices:
+                for value in slice.as_tuple():
+                    if is_arraylike(value):
+                        return np.asarray(value)
+            raise Exception("This ROI has no images. This shouldn't be possible")
+
+        for roi_index, slices in groupby(self.slices, key=lambda slice: slice.roi_index):
+            yield _preview(slices)
 
     def save(self) -> Iterable[Path]:
         """
diff --git a/plugin/napari_lattice/dock_widget.py b/plugin/napari_lattice/dock_widget.py
index c57ef838..7cf0aa69 100644
--- a/plugin/napari_lattice/dock_widget.py
+++ b/plugin/napari_lattice/dock_widget.py
@@ -149,20 +149,19 @@ def preview(self, header: str, time: int, channel: int):
             lattice.dy,
             lattice.dx
         )
-        preview: ArrayLike
+        previews: Iterable[ArrayLike]
 
         # We extract the first available image to use as a preview
         # This works differently for workflows and non-workflows
         if lattice.workflow is None:
-            for slice in lattice.process().slices:
-                preview = slice.data
-                break
+            previews = lattice.process().roi_previews()
         else:
-            preview = lattice.process_workflow().extract_preview()
+            previews = lattice.process_workflow().roi_previews()
 
-        self.parent_viewer.add_image(preview, scale=scale, name="Napari Lattice Preview")
-        max_z = np.argmax(np.sum(preview, axis=(1, 2)))
-        self.parent_viewer.dims.set_current_step(0, max_z)
+        for preview in previews:
+            self.parent_viewer.add_image(preview, scale=scale, name="Napari Lattice Preview")
+            max_z = np.argmax(np.sum(preview, axis=(1, 2)))
+            self.parent_viewer.dims.set_current_step(0, max_z)
 
 
     @set_design(text="Save")
diff --git a/plugin/napari_lattice/fields.py b/plugin/napari_lattice/fields.py
index b2fc7a3b..aa4e5df1 100644
--- a/plugin/napari_lattice/fields.py
+++ b/plugin/napari_lattice/fields.py
@@ -432,14 +432,6 @@ class CroppingFields(NapariFieldGroup):
     fields_enabled = field(False, label="Enabled")
 
     shapes= vfield(ShapeSelector)
-    z_range = field(Tuple[int, int]).with_options(
-        label = "Z Range",
-        value = (0, 1),
-        options = dict(
-            min = 0,
-        ),
-    )
-    errors = field(Label).with_options(label="Errors")
 
     @set_design(text="Import ROI")
     def import_roi(self, path: Path):
@@ -457,7 +449,16 @@ def new_crop_layer(self):
         from napari_lattice.utils import get_viewer
         shapes = get_viewer().add_shapes(name="Napari Lattice Crop")
         shapes.mode = "ADD_RECTANGLE"
-        self.shapes.value += [shapes]
+        # self.shapes.value += [shapes]
+
+    z_range = field(Tuple[int, int]).with_options(
+        label = "Z Range",
+        value = (0, 1),
+        options = dict(
+            min = 0,
+        ),
+    )
+    errors = field(Label).with_options(label="Errors")
 
     @connect_parent("deskew_fields.img_layer")
     def _on_image_changed(self, field: MagicField):
@@ -488,9 +489,8 @@ def _make_model(self) -> Optional[CropParams]:
         if self.fields_enabled.value:
             deskew = self._get_deskew()
             rois = []
-            for shape_layer in self.shapes.value:
-                for x in shape_layer.data:
-                    rois.append(Roi.from_array(x / deskew.dy))
+            for shape in self.shapes.shapes.value:
+                rois.append(Roi.from_array(shape.get_array() / deskew.dy))
 
             return CropParams(
                 # Convert from the input image space to the deskewed image space
diff --git a/plugin/napari_lattice/shape_selector.py b/plugin/napari_lattice/shape_selector.py
index e8362092..86258eec 100644
--- a/plugin/napari_lattice/shape_selector.py
+++ b/plugin/napari_lattice/shape_selector.py
@@ -1,8 +1,8 @@
 from __future__ import annotations
 from dataclasses import dataclass
 from typing import Iterator, Tuple, TYPE_CHECKING
-from magicclass import field, magicclass
-from magicgui.widgets import Select
+from magicclass import field, magicclass, set_design
+from magicgui.widgets import Select, Button
 from napari.layers import Shapes
 from napari.components.layerlist import LayerList
 from collections import defaultdict
@@ -31,7 +31,27 @@ def get_array(self) -> NDArray:
 @magicclass
 class ShapeSelector:
 
+    def _get_shape_choices(self, widget: Select | None = None) -> Iterator[Tuple[str, Shape]]:
+        """
+        Returns the choices to use for the Select box
+        """
+        viewer = get_viewer()
+        for layer in viewer.layers:
+            if isinstance(layer, Shapes):
+                for index in layer.features.index:
+                    result = Shape(layer=layer, index=index)
+                    yield str(result), result
+
     _blocked: bool
+    shapes = field(Select, options={"choices": _get_shape_choices, "label": "ROIs"})
+
+    @set_design(text="Select All")
+    def select_all(self) -> None:
+        self.shapes.value = self.shapes.choices
+
+    @set_design(text="Deselect All")
+    def deselect_all(self) -> None:
+        self.shapes.value = []
 
     def __init__(self, enabled: bool, *args, **kwargs) -> None:
         self._blocked = False
@@ -50,17 +70,6 @@ def _block(self):
             yield True
             self._blocked = False
 
-    def _get_shape_choices(self, widget: Select | None = None) -> Iterator[Tuple[str, Shape]]:
-        """
-        Returns the choices to use for the Select box
-        """
-        viewer = get_viewer()
-        for layer in viewer.layers:
-            if isinstance(layer, Shapes):
-                for index in layer.features.index:
-                    result = Shape(layer=layer, index=index)
-                    yield str(result), result
-
     def _on_selection_change(self, event: Event) -> None:
         """
         Triggered when the user clicks on one or more shapes.
@@ -119,8 +128,6 @@ def __post_init__(self) -> None:
             if isinstance(layer, Shapes):
                 self._connect_shapes(layer)
 
-    shapes = field(Select, options={"choices": _get_shape_choices, "label": "ROIs"})
-
     # values is a list[Shape], but if we use the correct annotation it breaks magicclass
     @shapes.connect
     def _widget_changed(self, values: list) -> None:

From 17e9ff2c584a12c757c3cd9fc80e99081445aa06 Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Mon, 14 Oct 2024 13:10:56 +1100
Subject: [PATCH 07/16] Fix plugin import

---
 plugin/napari_lattice/fields.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugin/napari_lattice/fields.py b/plugin/napari_lattice/fields.py
index aa4e5df1..3c8928b0 100644
--- a/plugin/napari_lattice/fields.py
+++ b/plugin/napari_lattice/fields.py
@@ -32,7 +32,7 @@
 from qtpy.QtWidgets import QTabWidget
 from strenum import StrEnum
 from napari_lattice.parent_connect import connect_parent
-from plugin.napari_lattice.shape_selector import ShapeSelector
+from napari_lattice.shape_selector import ShapeSelector
 
 if TYPE_CHECKING:
     from magicgui.widgets.bases import RangedWidget

From ea1957cd0493d2ec66f91d86265f6e11f3f9e417 Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Fri, 18 Oct 2024 12:15:08 +1100
Subject: [PATCH 08/16] Fix for shapes with > 2 dimensions

---
 plugin/napari_lattice/fields.py         | 7 ++++++-
 plugin/napari_lattice/shape_selector.py | 3 ++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/plugin/napari_lattice/fields.py b/plugin/napari_lattice/fields.py
index 3c8928b0..a6bbebfc 100644
--- a/plugin/napari_lattice/fields.py
+++ b/plugin/napari_lattice/fields.py
@@ -36,6 +36,7 @@
 
 if TYPE_CHECKING:
     from magicgui.widgets.bases import RangedWidget
+    from numpy.typing import NDArray
 
 logger = logging.getLogger(__name__)
 logger.setLevel(logging.INFO)
@@ -490,7 +491,11 @@ def _make_model(self) -> Optional[CropParams]:
             deskew = self._get_deskew()
             rois = []
             for shape in self.shapes.shapes.value:
-                rois.append(Roi.from_array(shape.get_array() / deskew.dy))
+                # The Napari shape is an array with 2 dimensions.
+                # Each column is an axis and each row is a point defining the shape
+                # We drop all but the last two axes, giving us a 2D shape with XY coordinates
+                array: NDArray = shape.get_array()[..., -2:] / deskew.dy
+                rois.append(Roi.from_array(array))
 
             return CropParams(
                 # Convert from the input image space to the deskewed image space
diff --git a/plugin/napari_lattice/shape_selector.py b/plugin/napari_lattice/shape_selector.py
index 86258eec..522ea90e 100644
--- a/plugin/napari_lattice/shape_selector.py
+++ b/plugin/napari_lattice/shape_selector.py
@@ -2,6 +2,7 @@
 from dataclasses import dataclass
 from typing import Iterator, Tuple, TYPE_CHECKING
 from magicclass import field, magicclass, set_design
+from magicclass.fields._fields import MagicField
 from magicgui.widgets import Select, Button
 from napari.layers import Shapes
 from napari.components.layerlist import LayerList
@@ -43,7 +44,7 @@ def _get_shape_choices(self, widget: Select | None = None) -> Iterator[Tuple[str
                     yield str(result), result
 
     _blocked: bool
-    shapes = field(Select, options={"choices": _get_shape_choices, "label": "ROIs"})
+    shapes: MagicField[Select] = field(Select, options={"choices": _get_shape_choices, "label": "ROIs"})
 
     @set_design(text="Select All")
     def select_all(self) -> None:

From 2f9b5eafccb88a317f46a99ce77ea0753793e922 Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Fri, 18 Oct 2024 12:17:55 +1100
Subject: [PATCH 09/16] Fix preview test

---
 core/tests/test_workflows.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/core/tests/test_workflows.py b/core/tests/test_workflows.py
index 9c1f2cfb..aceb5a96 100644
--- a/core/tests/test_workflows.py
+++ b/core/tests/test_workflows.py
@@ -107,8 +107,9 @@ def test_sum_preview(rbc_tiny: Path):
             workflow = "core/tests/workflows/binarisation/workflow.yml",
             save_dir = tmpdir
         )
-        preview = params.process_workflow().extract_preview()
-        np.sum(preview, axis=(1, 2))
+        previews = list(params.process_workflow().roi_previews())
+        assert len(previews) == 1, "There should be 1 preview when cropping is disabled"
+        assert previews[0].ndim == 3, "A preview should be a 3D image"
 
 def test_crop_workflow(rbc_tiny: Path):
     # Tests that crop workflows only process each ROI lazily

From 90cf7a2a5d5f2c62b8a806e9068491849824d1a9 Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Fri, 18 Oct 2024 12:24:18 +1100
Subject: [PATCH 10/16] Import TypeAlias from typing_extensions

---
 core/lls_core/models/results.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/core/lls_core/models/results.py b/core/lls_core/models/results.py
index 98d95b94..d8781646 100644
--- a/core/lls_core/models/results.py
+++ b/core/lls_core/models/results.py
@@ -2,8 +2,8 @@
 from itertools import groupby
 from pathlib import Path
 
-from typing import Iterable, Iterator, Optional, Tuple, TypeAlias, Union, cast, TYPE_CHECKING, overload
-from typing_extensions import Generic, TypeVar
+from typing import Iterable, Optional, Tuple, Union, cast, TYPE_CHECKING, overload
+from typing_extensions import Generic, TypeVar, TypeAlias
 from pydantic.v1 import BaseModel, NonNegativeInt, Field
 from lls_core.types import ArrayLike, is_arraylike
 from lls_core.utils import make_filename_suffix

From 69c68cbccb2cae21802145a16fe467465fd023c7 Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Fri, 18 Oct 2024 13:20:00 +1100
Subject: [PATCH 11/16] Fix for ShapeSelector when no viewer is present (in
 tests)

---
 plugin/napari_lattice/shape_selector.py | 36 ++++++++++++++-----------
 1 file changed, 21 insertions(+), 15 deletions(-)

diff --git a/plugin/napari_lattice/shape_selector.py b/plugin/napari_lattice/shape_selector.py
index 522ea90e..d0b62c20 100644
--- a/plugin/napari_lattice/shape_selector.py
+++ b/plugin/napari_lattice/shape_selector.py
@@ -8,8 +8,7 @@
 from napari.components.layerlist import LayerList
 from collections import defaultdict
 from contextlib import contextmanager
-
-from napari_lattice.utils import get_viewer
+from napari.viewer import current_viewer
 
 if TYPE_CHECKING:
     from napari.utils.events.event import Event
@@ -36,12 +35,13 @@ def _get_shape_choices(self, widget: Select | None = None) -> Iterator[Tuple[str
         """
         Returns the choices to use for the Select box
         """
-        viewer = get_viewer()
-        for layer in viewer.layers:
-            if isinstance(layer, Shapes):
-                for index in layer.features.index:
-                    result = Shape(layer=layer, index=index)
-                    yield str(result), result
+        viewer = current_viewer()
+        if viewer is not None:
+            for layer in viewer.layers:
+                if isinstance(layer, Shapes):
+                    for index in layer.features.index:
+                        result = Shape(layer=layer, index=index)
+                        yield str(result), result
 
     _blocked: bool
     shapes: MagicField[Select] = field(Select, options={"choices": _get_shape_choices, "label": "ROIs"})
@@ -119,15 +119,17 @@ def __post_init__(self) -> None:
         """
         Whenever a new layer is inserted
         """
-        viewer = get_viewer()
+        viewer = current_viewer()
+
+        if viewer is not None:
 
-        # Listen for new layers
-        viewer.layers.events.inserted.connect(self._on_layer_add)
+            # Listen for new layers
+            viewer.layers.events.inserted.connect(self._on_layer_add)
 
-        # Watch current layers
-        for layer in viewer.layers:
-            if isinstance(layer, Shapes):
-                self._connect_shapes(layer)
+            # Watch current layers
+            for layer in viewer.layers:
+                if isinstance(layer, Shapes):
+                    self._connect_shapes(layer)
 
     # values is a list[Shape], but if we use the correct annotation it breaks magicclass
     @shapes.connect
@@ -136,6 +138,10 @@ def _widget_changed(self, values: list) -> None:
         Triggered when the plugin widget is changed.
         We then synchronise the Napari shape selection with it.
         """
+        viewer = current_viewer()
+        if viewer is None:
+            return
+
         with self._block() as execute:
             if not execute:
                 return

From e9472f13d935f23222717ea820a33415ce4ca01e Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Fri, 18 Oct 2024 14:07:40 +1100
Subject: [PATCH 12/16] Fix type error

---
 plugin/napari_lattice/shape_selector.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/plugin/napari_lattice/shape_selector.py b/plugin/napari_lattice/shape_selector.py
index d0b62c20..3a1a5a05 100644
--- a/plugin/napari_lattice/shape_selector.py
+++ b/plugin/napari_lattice/shape_selector.py
@@ -145,7 +145,7 @@ def _widget_changed(self, values: list) -> None:
         with self._block() as execute:
             if not execute:
                 return
-            layers: dict[Shapes, list[int]] = {layer: [] for layer in get_viewer().layers if isinstance(layer, Shapes)}
+            layers: dict[Shapes, list[int]] = {layer: [] for layer in viewer.layers if isinstance(layer, Shapes)}
             value: Shape
 
             # Find the current selection for each layer

From 67a93cd9d4c9390fde1adf54357914cdb7683838 Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Tue, 12 Nov 2024 16:31:22 +1100
Subject: [PATCH 13/16] Refactor shape event listener into separate class

---
 plugin/napari_lattice/shape_selection.py | 57 ++++++++++++++++++++++++
 plugin/napari_lattice/shape_selector.py  |  4 +-
 2 files changed, 59 insertions(+), 2 deletions(-)
 create mode 100644 plugin/napari_lattice/shape_selection.py

diff --git a/plugin/napari_lattice/shape_selection.py b/plugin/napari_lattice/shape_selection.py
new file mode 100644
index 00000000..bf0d3eee
--- /dev/null
+++ b/plugin/napari_lattice/shape_selection.py
@@ -0,0 +1,57 @@
+from napari.utils.events import EventEmitter, Event
+from napari.layers import Shapes
+
+class ShapeLayerChangedEvent(Event):
+    """
+    Event triggered when the shape layer selection changes.
+    """
+
+class ShapeSelectionListener(EventEmitter):
+    """
+    Manages shape selection events for a given Shapes layer.
+
+    Examples:
+        This example code will open the viewer with an empty shape layer.
+        Any selection changes to that layer will trigger a notification popup.
+        >>> from napari import Viewer
+        >>> from napari.layers import Shapes
+        >>> viewer = Viewer()
+        >>> shapes = viewer.add_shapes()
+        >>> shape_selection = ShapeSelection(shapes)
+        >>> shape_selection.connect(lambda event: print("Shape selection changed!"))
+    """
+    last_selection: set[int]
+    layer: Shapes
+
+    def __init__(self, layer) -> None:
+        """
+        Initializes the ShapeSelection with the given Shapes layer.
+
+        Parameters:
+            layer: The Shapes layer to listen to.
+        """
+        super().__init__(source=layer, event_class=ShapeLayerChangedEvent, type_name="shape_layer_selection_changed")
+        self.layer = layer
+        self.last_selection = set()
+        layer.events.highlight.connect(self._on_highlight)
+
+    def _on_highlight(self, event) -> None:
+        new_selection = self.layer.selected_data
+        if new_selection != self.last_selection:
+            self()
+        self.last_selection = set(new_selection)
+
+def test_script():
+    """
+    Demo for testing the event behaviour.
+    """
+    from napari import run, Viewer
+    from napari.utils.notifications import show_info
+    viewer = Viewer()
+    shapes = viewer.add_shapes()
+    event = ShapeSelectionListener(shapes)
+    event.connect(lambda x: show_info("Shape selection changed!"))
+    run()
+
+if __name__ == "__main__":
+    test_script()
diff --git a/plugin/napari_lattice/shape_selector.py b/plugin/napari_lattice/shape_selector.py
index 3a1a5a05..a87bf7d1 100644
--- a/plugin/napari_lattice/shape_selector.py
+++ b/plugin/napari_lattice/shape_selector.py
@@ -9,6 +9,7 @@
 from collections import defaultdict
 from contextlib import contextmanager
 from napari.viewer import current_viewer
+from napari_lattice.shape_selection import ShapeSelectionListener
 
 if TYPE_CHECKING:
     from napari.utils.events.event import Event
@@ -93,8 +94,7 @@ def _connect_shapes(self, shapes: Shapes) -> None:
         Listens to events on that layer that we are interested in.
         """
         shapes.events.data.connect(self._on_shape_change)
-        # There is no shape selection event. This is the closest thing.
-        # See: https://github.com/napari/napari/issues/6886
+        ShapeSelectionListener(shapes).connect(self._on_selection_change)
         shapes.events.highlight.connect(self._on_selection_change)
 
     def _on_shape_change(self, event: Event) -> None:

From 5d6f68f484f24aeaf7e7717c1175f517519c90d7 Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Tue, 12 Nov 2024 17:05:33 +1100
Subject: [PATCH 14/16] Cache the ShapeSelectionListener objects

---
 plugin/napari_lattice/shape_selector.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/plugin/napari_lattice/shape_selector.py b/plugin/napari_lattice/shape_selector.py
index a87bf7d1..fee94b34 100644
--- a/plugin/napari_lattice/shape_selector.py
+++ b/plugin/napari_lattice/shape_selector.py
@@ -45,6 +45,7 @@ def _get_shape_choices(self, widget: Select | None = None) -> Iterator[Tuple[str
                         yield str(result), result
 
     _blocked: bool
+    _listeners: list[ShapeSelectionListener] = []
     shapes: MagicField[Select] = field(Select, options={"choices": _get_shape_choices, "label": "ROIs"})
 
     @set_design(text="Select All")
@@ -94,8 +95,9 @@ def _connect_shapes(self, shapes: Shapes) -> None:
         Listens to events on that layer that we are interested in.
         """
         shapes.events.data.connect(self._on_shape_change)
-        ShapeSelectionListener(shapes).connect(self._on_selection_change)
-        shapes.events.highlight.connect(self._on_selection_change)
+        listener = ShapeSelectionListener(shapes)
+        self._listeners.append(listener)
+        listener.connect(self._on_selection_change)
 
     def _on_shape_change(self, event: Event) -> None:
         """

From b8d4440530283183c1f319a78835fd2d22505639 Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Tue, 12 Nov 2024 17:16:07 +1100
Subject: [PATCH 15/16] Attempted fix for Windows

---
 plugin/napari_lattice/shape_selector.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/plugin/napari_lattice/shape_selector.py b/plugin/napari_lattice/shape_selector.py
index fee94b34..1cd63084 100644
--- a/plugin/napari_lattice/shape_selector.py
+++ b/plugin/napari_lattice/shape_selector.py
@@ -86,7 +86,12 @@ def _on_selection_change(self, event: Event) -> None:
             source: Shapes = event.source
             selection: list[Shape] = []
             for index in source.selected_data:
-                selection.append(Shape(layer=source, index=index))
+                shape = Shape(layer=source, index=index)
+                if shape not in self.shapes.choices:
+                    # If we ever encounter a shape that isn't a legal choice, we have to terminate to avoid an error
+                    # This seems to happen on Windows only due to the order of events firing
+                    return
+                selection.append(shape)
             self.shapes.value = selection
 
     def _connect_shapes(self, shapes: Shapes) -> None:

From 523e2ba353366002ed02d4bb9137876238e3edd3 Mon Sep 17 00:00:00 2001
From: Michael Milton <michael.r.milton@gmail.com>
Date: Wed, 13 Nov 2024 13:13:36 +1100
Subject: [PATCH 16/16] Use future annotations

---
 plugin/napari_lattice/shape_selection.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/plugin/napari_lattice/shape_selection.py b/plugin/napari_lattice/shape_selection.py
index bf0d3eee..0a1fa6e3 100644
--- a/plugin/napari_lattice/shape_selection.py
+++ b/plugin/napari_lattice/shape_selection.py
@@ -1,3 +1,4 @@
+from __future__ import annotations
 from napari.utils.events import EventEmitter, Event
 from napari.layers import Shapes