ruff fixes

src/pynwb/ndx_microscopy/ndx_microscopy.py

@@ -1,37 +1,50 @@
 from hdmf.utils import docval, popargs
-from pynwb import get_class, register_class
-from pynwb.core import MultiContainerInterface
+from pynwb import get_class
 import numpy as np
 
 extension_name = "ndx-microscopy"
 
 MicroscopyPlaneSegmentation = get_class("MicroscopyPlaneSegmentation", extension_name)
 
-@docval({'name': 'pixel_mask', 'type': 'array_data', 'default': None,
-            'doc': 'pixel mask for 2D ROIs: [(x1, y1, weight1), (x2, y2, weight2), ...]',
-            'shape': (None, 3)},
-        {'name': 'voxel_mask', 'type': 'array_data', 'default': None,
-            'doc': 'voxel mask for 3D ROIs: [(x1, y1, z1, weight1), (x2, y2, z2, weight2), ...]',
-            'shape': (None, 4)},
-        {'name': 'image_mask', 'type': 'array_data', 'default': None,
-            'doc': 'image with the same size of image where positive values mark this ROI',
-            'shape': [[None]*2, [None]*3]},
-        {'name': 'id', 'type': int, 'doc': 'the ID for the ROI', 'default': None},
-        allow_extra=True)
 
+@docval(
+    {
+        "name": "pixel_mask",
+        "type": "array_data",
+        "default": None,
+        "doc": "pixel mask for 2D ROIs: [(x1, y1, weight1), (x2, y2, weight2), ...]",
+        "shape": (None, 3),
+    },
+    {
+        "name": "voxel_mask",
+        "type": "array_data",
+        "default": None,
+        "doc": "voxel mask for 3D ROIs: [(x1, y1, z1, weight1), (x2, y2, z2, weight2), ...]",
+        "shape": (None, 4),
+    },
+    {
+        "name": "image_mask",
+        "type": "array_data",
+        "default": None,
+        "doc": "image with the same size of image where positive values mark this ROI",
+        "shape": [[None] * 2, [None] * 3],
+    },
+    {"name": "id", "type": int, "doc": "the ID for the ROI", "default": None},
+    allow_extra=True,
+)
 def add_roi(self, **kwargs):
     """Add a Region Of Interest (ROI) data to this"""
-    pixel_mask, voxel_mask, image_mask = popargs('pixel_mask', 'voxel_mask', 'image_mask', kwargs)
+    pixel_mask, voxel_mask, image_mask = popargs("pixel_mask", "voxel_mask", "image_mask", kwargs)
     if image_mask is None and pixel_mask is None and voxel_mask is None:
         raise ValueError("Must provide 'image_mask' and/or 'pixel_mask'")
     rkwargs = dict(kwargs)
     if image_mask is not None:
-        rkwargs['image_mask'] = image_mask
+        rkwargs["image_mask"] = image_mask
     if pixel_mask is not None:
-        rkwargs['pixel_mask'] = pixel_mask
+        rkwargs["pixel_mask"] = pixel_mask
     if voxel_mask is not None:
-        rkwargs['voxel_mask'] = voxel_mask
-    return super(MicroscopyPlaneSegmentation,self).add_row(**rkwargs)
+        rkwargs["voxel_mask"] = voxel_mask
+    return super(MicroscopyPlaneSegmentation, self).add_row(**rkwargs)
 
 
 @staticmethod
@@ -45,11 +58,12 @@ def pixel_to_image(pixel_mask):
     image_matrix[y_coords, x_coords] = weights
     return image_matrix
 
+
 @staticmethod
 def image_to_pixel(image_mask):
     """Converts an image_mask of a ROI into a pixel_mask"""
     pixel_mask = []
-    it = np.nditer(image_mask, flags=['multi_index'])
+    it = np.nditer(image_mask, flags=["multi_index"])
     while not it.finished:
         weight = it[0][()]
         if weight > 0:
@@ -59,14 +73,19 @@ def image_to_pixel(image_mask):
         it.iternext()
     return pixel_mask
 
+
 MicroscopyPlaneSegmentation.add_roi = add_roi
 MicroscopyPlaneSegmentation.pixel_to_image = pixel_to_image
 MicroscopyPlaneSegmentation.image_to_pixel = image_to_pixel
 
-@docval({'name': 'description', 'type': str, 'doc': 'a brief description of what the region is'},
-        {'name': 'region', 'type': (slice, list, tuple), 'doc': 'the indices of the table', 'default': slice(None)},
-        {'name': 'name', 'type': str, 'doc': 'the name of the ROITableRegion', 'default': 'rois'})
+
+@docval(
+    {"name": "description", "type": str, "doc": "a brief description of what the region is"},
+    {"name": "region", "type": (slice, list, tuple), "doc": "the indices of the table", "default": slice(None)},
+    {"name": "name", "type": str, "doc": "the name of the ROITableRegion", "default": "rois"},
+)
 def create_roi_table_region(self, **kwargs):
-    return super(MicroscopyPlaneSegmentation,self).create_region(**kwargs)
+    return super(MicroscopyPlaneSegmentation, self).create_region(**kwargs)
+
 
 MicroscopyPlaneSegmentation.create_roi_table_region = create_roi_table_region

src/pynwb/tests/test_api_functions.py

@@ -2,29 +2,28 @@
 
 import numpy as np
 import pytest
-from pynwb import NWBFile
-from datetime import datetime
 from ndx_microscopy.testing import (
     mock_PlanarImagingSpace,
     mock_MicroscopyPlaneSegmentation,
-    mock_MicroscopySegmentations,
 )
 from ndx_microscopy import MicroscopyPlaneSegmentation
 
+
 def test_add_roi_with_pixel_mask():
     """Test adding ROI with pixel mask."""
 
     pixel_mask = [[1, 2, 1.0], [3, 4, 1.0], [5, 6, 1.0], [7, 8, 2.0], [9, 10, 2.0]]
 
     imaging_space = mock_PlanarImagingSpace()
-    name="MicroscopyPlaneSegmentation"
-    description="A mock instance of a MicroscopyPlaneSegmentation type to be used for rapid testing."
-   
+    name = "MicroscopyPlaneSegmentation"
+    description = "A mock instance of a MicroscopyPlaneSegmentation type to be used for rapid testing."
+
     plane_seg = MicroscopyPlaneSegmentation(name=name, description=description, imaging_space=imaging_space)
 
     plane_seg.add_roi(pixel_mask=pixel_mask)
     assert plane_seg.pixel_mask[:] == pixel_mask
-
+
+
 def test_add_roi_with_voxel_mask():
     """Test adding ROI with voxel mask."""
     voxel_mask = [[1, 2, 3, 1.0], [3, 4, 5, 1.0], [5, 6, 7, 1.0], [7, 8, 9, 2.0], [9, 10, 11, 2.0]]
@@ -38,6 +37,7 @@ def test_add_roi_with_voxel_mask():
     plane_seg.add_roi(voxel_mask=voxel_mask)
     assert plane_seg.voxel_mask[:] == voxel_mask
 
+
 def test_add_roi_with_image_mask():
     """Test adding ROI with image mask."""
     w, h = 5, 5
@@ -52,14 +52,16 @@ def test_add_roi_with_image_mask():
 
     assert plane_seg.image_mask[0] == image_mask
 
+
 def test_add_roi_without_masks():
     """Test adding ROI without any masks raises ValueError."""
     imaging_space = mock_PlanarImagingSpace()
     plane_seg = mock_MicroscopyPlaneSegmentation(imaging_space=imaging_space)
-    
+
     with pytest.raises(ValueError, match="Must provide 'image_mask' and/or 'pixel_mask"):
         plane_seg.add_roi(id=4)
 
+
 def test_pixel_to_image():
     """Test conversion from pixel mask to image mask."""
     imaging_space = mock_PlanarImagingSpace()
@@ -70,9 +72,8 @@ def test_pixel_to_image():
     pixel_mask = [[0, 0, 1.0], [1, 0, 2.0], [2, 0, 2.0]]
 
     img_mask = plane_seg.pixel_to_image(pixel_mask)
-    np.testing.assert_allclose(img_mask, np.asarray([[1, 2, 2.0],
-                                                     [0, 0, 0.0],
-                                                     [0, 0, 0.0]]))
+    np.testing.assert_allclose(img_mask, np.asarray([[1, 2, 2.0], [0, 0, 0.0], [0, 0, 0.0]]))
+
 
 def test_image_to_pixel():
     """Test conversion from image mask to pixel mask."""
@@ -81,33 +82,32 @@ def test_image_to_pixel():
     description = "A mock instance of a MicroscopyPlaneSegmentation type to be used for rapid testing."
     plane_seg = MicroscopyPlaneSegmentation(name=name, description=description, imaging_space=imaging_space)
 
-    image_mask = np.asarray([[1.0, 0.0, 0.0],
-                             [0.0, 1.0, 0.0],
-                             [0.0, 0.0, 1.0]])
+    image_mask = np.asarray([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]])
 
     pixel_mask = plane_seg.image_to_pixel(image_mask)
     np.testing.assert_allclose(pixel_mask, np.asarray([[0, 0, 1.0], [1, 1, 1.0], [2, 2, 1.0]]))
 
+
 def test_create_roi_table_region():
     """Test creating ROI table region."""
     imaging_space = mock_PlanarImagingSpace()
     name = "MicroscopyPlaneSegmentation"
     description = "A mock instance of a MicroscopyPlaneSegmentation type to be used for rapid testing."
     plane_seg = MicroscopyPlaneSegmentation(name=name, description=description, imaging_space=imaging_space)
-    
+
     # Add some ROIs first
     pixel_mask = [[0, 0, 1.0], [1, 0, 2.0], [2, 0, 2.0]]
 
     plane_seg.add_roi(pixel_mask=pixel_mask)
     plane_seg.add_roi(pixel_mask=pixel_mask)
-    
+
     # Test with specific region indices
     region = plane_seg.create_roi_table_region(
         description="Test region",
         name="test_region",
-        region=[0]  # Only include first ROI
+        region=[0],  # Only include first ROI
     )
-    
+
     assert region.name == "test_region"
     assert region.description == "Test region"
     assert len(region.data) == 1

src/pynwb/tests/test_constructors.py

@@ -59,7 +59,7 @@ def test_constructor_volumetric_image_space():
 
 def test_constructor_microscopy_segmentations():
     microscopy_segmentations = mock_MicroscopySegmentations()
-    assert "MicroscopySegmentations" in microscopy_segmentations.name  
+    assert "MicroscopySegmentations" in microscopy_segmentations.name
 
 
 def test_constructor_microscopy_plane_segmentation():
@@ -90,13 +90,13 @@ def test_constructor_microscopy_image_segmentation_with_plane_segmentation():
 def test_constructor_planar_microscopy_series():
     microscope = mock_Microscope()
     excitation_light_path = mock_ExcitationLightPath()
-    planar_imaging_space = mock_PlanarImagingSpace() 
+    planar_imaging_space = mock_PlanarImagingSpace()
     emission_light_path = mock_EmissionLightPath()
 
     planar_microscopy_series = mock_PlanarMicroscopySeries(
         microscope=microscope,
         excitation_light_path=excitation_light_path,
-        planar_imaging_space=planar_imaging_space ,
+        planar_imaging_space=planar_imaging_space,
         emission_light_path=emission_light_path,
     )
     assert (
@@ -108,13 +108,13 @@ def test_constructor_planar_microscopy_series():
 def test_constructor_variable_depth_microscopy_series():
     microscope = mock_Microscope()
     excitation_light_path = mock_ExcitationLightPath()
-    planar_imaging_space = mock_PlanarImagingSpace() 
+    planar_imaging_space = mock_PlanarImagingSpace()
     emission_light_path = mock_EmissionLightPath()
 
     variable_depth_microscopy_series = mock_VariableDepthMicroscopySeries(
         microscope=microscope,
         excitation_light_path=excitation_light_path,
-        planar_imaging_space =planar_imaging_space ,
+        planar_imaging_space=planar_imaging_space,
         emission_light_path=emission_light_path,
     )
     assert (