Merge pull request #56 from zoccoler/draw_fixed_shapes

Draw fixed shapes

Author: zoccoler

.github/workflows/test_and_deploy.yml

@@ -23,7 +23,7 @@ jobs:
     strategy:
       matrix:
         platform: [windows-latest, macos-latest, ubuntu-latest]
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
       - uses: actions/checkout@v3
@@ -36,27 +36,32 @@ jobs:
       # these libraries enable testing on Qt on linux
       - uses: tlambert03/setup-qt-libs@v1
 
+      # strategy borrowed from vispy for installing opengl libs on windows
+      - name: Install Windows OpenGL
+        if: runner.os == 'Windows'
+        run: |
+          git clone --depth 1 https://github.com/pyvista/gl-ci-helpers.git
+          powershell gl-ci-helpers/appveyor/install_opengl.ps1
+
       # note: if you need dependencies from conda, considering using
       # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
       # and
       # tox-conda: https://github.com/tox-dev/tox-conda
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          python -m pip install setuptools tox tox-gh-actions pytest-qt pytest-xvfb
+          python -m pip install setuptools tox tox-gh-actions
 
       # this runs the platform-specific tests declared in tox.ini
       - name: Test with tox
-        uses: GabrielBB/xvfb-action@v1
+        uses: aganders3/headless-gui@v2
         with:
           run: python -m tox
         env:
           PLATFORM: ${{ matrix.platform }}
 
       - name: Coverage
-        uses: codecov/codecov-action@v2
-        with:
-          token: ${{ secrets.CODECOV_TOKEN }}
+        uses: codecov/codecov-action@v3
 
   deploy:
     # this will run when you have tagged a commit, starting with "v*"
@@ -66,20 +71,20 @@ jobs:
     runs-on: ubuntu-latest
     if: contains(github.ref, 'tags')
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: "3.x"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -U setuptools setuptools_scm wheel twine
+          pip install -U setuptools setuptools_scm wheel twine build
       - name: Build and publish
         env:
           TWINE_USERNAME: __token__
           TWINE_PASSWORD: ${{ secrets.TWINE_API_KEY }}
         run: |
           git tag
-          python setup.py sdist bdist_wheel
+          python -m build .
           twine upload dist/*

README.md

@@ -7,8 +7,9 @@
 [![codecov](https://codecov.io/gh/BiAPoL/napari-crop/branch/main/graph/badge.svg)](https://codecov.io/gh/BiAPoL/napari-crop)
 [![DOI](https://zenodo.org/badge/419822240.svg)](https://zenodo.org/badge/latestdoi/419822240)
 
-## Currently, this repository is not guaranteed to be actively maintained.
-If you are interested in further developing it, feel free to fork it.
+🚨🚨🚨 **Call for maintainers** 🚨🚨🚨
+
+If you are interested in further developing it, please get in touch or create a fork.
 
 Crop regions in napari manually
 
@@ -28,12 +29,16 @@ Cut a volume using a plane
 
 ![](https://github.com/BiAPoL/napari-crop/raw/main/images/napari_crop_cut_with_plane_demo.gif)
 
+Draw shapes of fixed size at given coordinates for later cropping
+
+![](https://github.com/BiAPoL/napari-crop/raw/main/images/napari_crop_draw_shapes.gif)
+
 ## Usage
 Create a new shapes layer to annotate the region you would like to crop:
 
 ![](https://github.com/BiAPoL/napari-crop/raw/main/images/shapes.png)
 
-Use the rectangle tool to annotate a region. Start the `crop` tool from the `Tools > Utilities > Crop region` menu. 
+Use the rectangle tool to annotate a region. Start the `crop` tool from the `Plugins > napari-crop > Crop region` or, if available, `Tools > Utilities > Crop region` menu. 
 Click the `Run` button to crop the region.
 
 ![](https://github.com/BiAPoL/napari-crop/raw/main/images/draw_rectangle.png)

images/napari_crop_draw_shapes.gif

@@ -1,6 +1,7 @@
+try:
+    from ._version import version as __version__
+except ImportError:
+    __version__ = "unknown"
 
-__version__ = "0.1.9"
-
-
-from ._dock_widgets import napari_experimental_provide_dock_widget
-from ._function import crop_region, cut_with_plane
+from ._dock_widgets import CutWithPlane
+from ._function import crop_region, cut_with_plane, draw_fixed_shapes

napari_crop/__init__.py

@@ -2,23 +2,16 @@
 
 from magicgui.widgets import Container, PushButton, ComboBox, CheckBox
 from typing import TYPE_CHECKING
-from napari_plugin_engine import napari_hook_implementation
 from skimage.segmentation import relabel_sequential
 from napari_tools_menu import register_dock_widget
-from magicgui import magic_factory
 
 from ._utils import array_allclose_in_list, find_array_allclose_position_in_list
-from ._function import cut_with_plane, crop_region, trim_zeros, get_nonzero_slices
+from ._function import cut_with_plane, trim_zeros, get_nonzero_slices
 import napari.layers
 if TYPE_CHECKING:
     import napari.viewer
 
 
-@napari_hook_implementation
-def napari_experimental_provide_dock_widget():
-    return [magic_factory(crop_region), CutWithPlane]
-
-
 @register_dock_widget(menu="Utilities > Cut volume with plane (napari-crop)")
 class CutWithPlane(Container):
     input_layer_types = (
@@ -136,7 +129,8 @@ def _get_layers_to_be_cut(self, combo_box):
         '''Get layers of type image or labels and excludes the plane layer'''
         # Currently accepts only 3D data
         return [layer for layer in self._viewer.layers if isinstance(
-            layer, self.input_layer_types) and layer != self._plane_layer and layer.rgb is False and layer.ndim == 3]
+            layer, self.input_layer_types) and layer != self._plane_layer and 
+            (not isinstance(layer, napari.layers.Image) or layer.rgb is False) and layer.ndim == 3]
 
     def _on_plane_data_source_changed(self, new_value: str):
         '''Update plane data source and plane layer data'''

napari_crop/_dock_widgets.py

@@ -1,12 +1,12 @@
 import warnings
 
 import numpy as np
-from magicgui import magic_factory
 from napari_tools_menu import register_function
 import napari
 from napari.types import LayerDataTuple
 from typing import List
 from ._utils import compute_combined_slices
+from magicgui import magic_factory
 
 # This is the actual plugin function, where we export our function
 # (The functions themselves are defined below)
@@ -16,9 +16,29 @@
 def crop_region(
     layer: napari.layers.Layer,
     shapes_layer: napari.layers.Shapes,
+    as_numpy: bool = False,
+    translate: bool = True,
     viewer: 'napari.viewer.Viewer' = None,
 ) -> List[LayerDataTuple]:
-    """Crop regions in napari defined by shapes."""
+    """Crop regions in napari defined by shapes.
+    
+    Parameters
+    ----------
+    layer : napari.layers.Layer
+        Layer to crop. Can be an image or labels layer.
+    shapes_layer : napari.layers.Shapes
+        Shapes layer defining the regions to crop.
+    as_numpy : bool, optional
+        If True, return the cropped data as numpy arrays. Default is False.
+    translate : bool, optional
+        If True, apply translation to the cropped data. Default is True.
+    viewer : napari.viewer.Viewer, optional
+        Viewer instance to use for the dimensions order.
+
+    Returns
+    -------
+
+    """
     if shapes_layer is None:
         shapes_layer.mode = "add_rectangle"
         warnings.warn("Please annotate a region to crop.")
@@ -126,7 +146,8 @@ def crop_region(
         # Pixels belonging to the bounding box are in the half-open interval [min_row; max_row) and [min_col; max_col).
         new_layer_props['metadata'] = {'bbox': tuple(start + stop)}
         # apply layer translation scaled by layer scaling factor
-        new_layer_props['translate'] = tuple(np.asarray(tuple(start)) * np.asarray(layer_props['scale']))
+        if translate:
+            new_layer_props['translate'] = tuple(np.asarray(tuple(start)) * np.asarray(layer_props['scale']))
 
         # If layer name is in viewer or is about to be added,
         # increment layer name until it has a different name
@@ -139,6 +160,8 @@ def crop_region(
                 new_layer_index += 1
         new_layer_props["name"] = new_name
         names_list.append(new_name)
+        if as_numpy:
+            cropped_data = np.asarray(cropped_data)
         cropped_list.append((cropped_data, new_layer_props, layer_type))
     return cropped_list
 
@@ -203,3 +226,67 @@ def cut_with_plane(image_to_be_cut, plane_normal, plane_position, positive_cut=T
     if crop:
         image_cut = trim_zeros(image_cut)
     return image_cut
+
+@magic_factory(
+    call_button="Draw",
+    shape_type={"choices": ["rectangle", "ellipse"]},  # Dropdown for shape type
+    shape_size_x={"widget_type": "SpinBox", "min": 1, "max": 5000, "step": 1},
+    shape_size_y={"widget_type": "SpinBox", "min": 1, "max": 5000, "step": 1},
+)
+def draw_fixed_shapes(
+    points: napari.types.PointsData,
+    shape_type: str = "rectangle",
+    shape_size_x: int = 256,
+    shape_size_y: int = 256,
+    viewer: napari.Viewer = None,
+) -> napari.layers.Shapes:
+    """Create shapes of fixed size at points layer coordinates.
+    
+    Parameters
+    ----------
+    points : napari.types.PointsData
+        Coordinates of the points layer.
+    shape_type : str
+        Type of shape to create. Can be 'rectangle' or 'ellipse'.
+    shape_size_x : int
+        Width of the shape.
+    shape_size_y : int
+        Height of the shape.
+    viewer : napari.Viewer, optional
+        Viewer instance to use for the dimensions order.
+        
+    Returns
+    -------
+    Shapes
+        Shapes layer with the created shapes."""
+    if points is None:
+        raise ValueError("No points provided. Please select a points layer.")
+    dims_order = tuple(range(points.ndim))
+    if viewer is not None:
+        dims_order = viewer.dims.order
+    shape_size = (shape_size_y, shape_size_x)
+    odd_shape = [size % 2 for size in shape_size]
+    
+    shapes_data = []
+    for coord in points:
+        shape_data = np.array([
+            [coord[dims_order[-2]] - (shape_size[-2] // 2), coord[dims_order[-1]] - (shape_size[-1] // 2)],  # Top-left
+            [coord[dims_order[-2]] - (shape_size[-2] // 2), coord[dims_order[-1]] + (shape_size[-1] // 2) + odd_shape[-1]],  # Bottom-left
+            [coord[dims_order[-2]] + (shape_size[-2] // 2) + odd_shape[-2], coord[dims_order[-1]] + (shape_size[-1] // 2) + odd_shape[-1]],  # Bottom-right
+            [coord[dims_order[-2]] + (shape_size[-2] // 2) + odd_shape[-2], coord[dims_order[-1]] - (shape_size[-1] // 2)],  # Top-right
+        ])
+        # Insert extra coordinates for higher dimensions
+        # For example, if the shape is 3D, we need to add the z-coordinates
+        extra_coords = np.take(coord, indices=dims_order[:-2], axis=0)
+        for i, ec in enumerate(extra_coords):
+            shape_data = np.insert(shape_data, 0, round(ec), axis=-1)
+        shape_data = shape_data[:, np.argsort(dims_order)]
+        shapes_data.append(shape_data)
+    
+    return napari.layers.Shapes(
+        data=shapes_data,
+        shape_type=[shape_type for _ in points],
+        edge_color='magenta',
+        face_color='#ffff0080', # semi-transparent yellow
+        edge_width=2,
+    )

napari_crop/_function.py

@@ -1,4 +1,4 @@
-from napari_crop._function import crop_region, cut_with_plane
+from napari_crop._function import crop_region, cut_with_plane, draw_fixed_shapes
 import pytest
 import numpy as np
 
@@ -258,3 +258,66 @@ def test_cut_with_plane_position(plane_position, output_expected_position):
 def test_cut_with_plane_negative():
     image_cut = cut_with_plane(volume_data, plane_normal_z, plane_position_1, positive_cut=False)
     assert np.array_equal(output_expected_normal_z_position_1_negative, image_cut)
+
+
+# Tests for draw_fixed_shapes function
+points_2d = np.array([[2, 2], [1, 4]])  # 2D points
+points_3d = np.array([[1, 2, 2], [1, 1, 4]])  # 3D points with z=1
+shape_types_fixed = ["rectangle", "ellipse"]
+shape_sizes = [(100, 50), (256, 256)]  # (x, y) sizes
+
+
+@pytest.mark.parametrize("shape_type", shape_types_fixed)
+@pytest.mark.parametrize("shape_size_x,shape_size_y", shape_sizes)
+def test_draw_fixed_shapes_2d(make_napari_viewer, shape_type, shape_size_x, shape_size_y):
+    """Test drawing fixed shapes in 2D with different types and sizes."""
+    viewer = make_napari_viewer()
+    points_layer = viewer.add_points(points_2d)
+    
+    widget = draw_fixed_shapes()
+    widget.shape_type.value = shape_type
+    widget.shape_size_x.value = shape_size_x
+    widget.shape_size_y.value = shape_size_y
+
+    shapes_layer = widget()
+    
+    # Check that we get the correct number of shapes
+    assert len(shapes_layer.data) == len(points_2d)
+    
+    # Check that all shapes have the correct type
+    assert all(st == shape_type for st in shapes_layer.shape_type)
+    
+    # Check that shapes are rectangles with 4 vertices each
+    for shape_data in shapes_layer.data:
+        assert shape_data.shape == (4, 2)  # 4 vertices, 2D coordinates
+
+
+def test_draw_fixed_shapes_3d(make_napari_viewer):
+    """Test drawing fixed shapes in 3D."""
+    viewer = make_napari_viewer()
+    points_layer = viewer.add_points(points_3d)
+
+    widget = draw_fixed_shapes()
+    widget.shape_type.value = "rectangle"
+    widget.shape_size_x.value = 100
+    widget.shape_size_y.value = 100
+
+    shapes_layer = widget()
+
+    # Check that we get the correct number of shapes
+    assert len(shapes_layer.data) == len(points_3d)
+
+    # Check that shapes have 3D coordinates (z, y, x)
+    for shape_data in shapes_layer.data:
+        assert shape_data.shape == (4, 3)  # 4 vertices, 3D coordinates
+        shape_size_y=100,
+        viewer=viewer
+    
+    
+    # Check that we get the correct number of shapes
+    assert len(shapes_layer.data) == len(points_3d)
+    
+    # Check that shapes have 3D coordinates (z, y, x)
+    for shape_data in shapes_layer.data:
+        assert shape_data.shape == (4, 3)  # 4 vertices, 3D coordinates
+

napari_crop/_tests/test_function.py

@@ -0,0 +1,21 @@
+name: napari-crop
+schema_version: 0.2.1
+contributions:
+  commands:
+  - id: napari-crop.crop_region
+    title: Crop Region(s) with Shapes layer
+    python_name: napari_crop._function:crop_region
+  - id: napari-crop.CutWithPlane
+    title: Create Cut With Plane
+    python_name: napari_crop._dock_widgets:CutWithPlane
+  - id: napari-crop.draw_fixed_shapes
+    title: Draw shapes of fixed dimensions
+    python_name: napari_crop._function:draw_fixed_shapes
+  widgets:
+  - command: napari-crop.CutWithPlane
+    display_name: Cut With Plane
+  - command: napari-crop.crop_region
+    display_name: Crop Region(s)
+    autogenerate: true
+  - command: napari-crop.draw_fixed_shapes
+    display_name: Draw Fixed Shapes