Update PlaneAcquisition attribute from plane_thickness_in_um to point_spread_function_in_um across documentation and tests (#60)

Author: alessandratrapani

README.md

@@ -229,7 +229,7 @@ classDiagram
         --------------------------------------
         attributes
         --------------------------------------
-        plane_thickness_in_um : float64, optional
+        point_spread_function_in_um : text, optional
         illumination_angle_in_degrees : float64, optional
         plane_rate_in_Hz : float64, optional
     }

docs/source/examples.rst

@@ -731,7 +731,7 @@ Example of multi-plane imaging with an electrically tunable lens:
     plane_acquisition = PlaneAcquisition(
         name=f'plane_acquisition',
         description=f'Plane acquisition',
-        plane_thickness_in_um=2.0
+        point_spread_function_in_um="32 um ± 1.6 um"
     )
 
     for depth in depths:

docs/source/format.rst

@@ -281,9 +281,9 @@ Whole plane acquisition method for microscopy.
         neurodata_type_inc: IlluminationPattern
         doc: Whole plane acquisition, common for light sheet techniques.
         attributes:
-          - name: plane_thickness_in_um
-            dtype: float64
-            doc: Thickness of the plane in micrometers.
+          - name: point_spread_function_in_um
+            dtype: text
+            doc: Estimated plane spatial profile or point spread function, expressed as mean [um] ± s.d [um].
             required: false
           - name: illumination_angle_in_degrees
             dtype: float64

docs/source/user_guide.rst

@@ -101,7 +101,7 @@ Illumination patterns define how the microscope scans or illuminates the sample:
        plane_acquisition = PlaneAcquisition(
            name='plane_acquisition',
            description='Widefield fluorescence imaging',
-           plane_thickness_in_um=5.0,
+           point_spread_function_in_um="32 um ± 1.6 um",
            illumination_angle_in_degrees=45.0,  # for light sheet
            plane_rate_in_Hz=100.0               # planes per second
        )
@@ -156,7 +156,7 @@ Imaging spaces define the physical region being imaged:
        plane_acquisition = PlaneAcquisition(
            name='plane_acquisition',
            description='Light sheet imaging',
-           plane_thickness_in_um=5.0,
+           point_spread_function_in_um="32 um ± 1.6 um",
            illumination_angle_in_degrees=45.0,
            plane_rate_in_Hz=100.0
        )
@@ -260,7 +260,7 @@ Workflow for one-photon widefield imaging:
     plane_acquisition = PlaneAcquisition(
         name='plane_acquisition',
         description='Widefield fluorescence imaging',
-        plane_thickness_in_um=5.0,
+        point_spread_function_in_um="32 um ± 1.6 um",
         plane_rate_in_Hz=30.0
     )
 

examples/one-photon_calcium_imaging_example.ipynb

@@ -250,7 +250,7 @@
     "illumination_pattern = PlaneAcquisition(\n",
     "    name=\"plane_acquisition\",\n",
     "    description=\"Widefield fluorescence imaging\",\n",
-    "    plane_thickness_in_um=5.0,\n",
+    "    point_spread_function_in_um=\"32 um ± 1.6 um\",\n",
     ")\n",
     "imaging_space = PlanarImagingSpace(\n",
     "    name=\"hippo_plane1\",\n",

spec/ndx-microscopy.extensions.yaml

@@ -110,9 +110,11 @@ groups:
     neurodata_type_inc: IlluminationPattern
     doc: Whole plane acquisition, common for light sheet techniques.
     attributes:
-      - name: plane_thickness_in_um
-        dtype: float64
-        doc: Thickness of the plane in micrometers.
+      - name: point_spread_function_in_um
+        dtype: text
+        doc:
+          Estimated plane spatial profile or point spread function, expressed as
+          mean [um] ± s.d [um].
         required: false
       - name: illumination_angle_in_degrees
         dtype: float64

src/pynwb/ndx_microscopy/testing/_mock.py

@@ -126,15 +126,15 @@ def mock_PlaneAcquisition(
     *,
     name: Optional[str] = None,
     description: str = "A mock instance of a PlaneAcquisition type to be used for rapid testing.",
-    plane_thickness_in_um: Optional[float] = 5.0,
+    point_spread_function_in_um: Optional[str] = "32 um ± 1.6 um",
     illumination_angle_in_degrees: Optional[float] = 45.0,
     plane_rate_in_Hz: Optional[float] = 100.0,
 ) -> ndx_microscopy.PlaneAcquisition:
     """Light sheet method."""
     plane_acquisition = ndx_microscopy.PlaneAcquisition(
         name=name or name_generator("PlaneAcquisition"),
         description=description,
-        plane_thickness_in_um=plane_thickness_in_um,
+        point_spread_function_in_um=point_spread_function_in_um,
         illumination_angle_in_degrees=illumination_angle_in_degrees,
         plane_rate_in_Hz=plane_rate_in_Hz,
     )

src/pynwb/tests/test_constructors.py

@@ -86,7 +86,7 @@ def test_constructor_plane_acquisition():
     """Test constructor for PlaneAcquisition class."""
     plane_acquisition = mock_PlaneAcquisition()
     assert plane_acquisition.description == "A mock instance of a PlaneAcquisition type to be used for rapid testing."
-    assert plane_acquisition.plane_thickness_in_um == 5.0
+    assert plane_acquisition.point_spread_function_in_um == "32 um ± 1.6 um"
     assert plane_acquisition.illumination_angle_in_degrees == 45.0
     assert plane_acquisition.plane_rate_in_Hz == 100.0
     assert isinstance(plane_acquisition, PlaneAcquisition)