remove Microscope object

README.md

@@ -30,7 +30,7 @@ classDiagram
         label : text
         description : text, optional
         manufacturer : text, optional
-        injection_location : text, optional
+        injection_brain_region : text, optional
         injection_coordinates_in_mm : numeric, length 3, optional
     }
     class Effector{
@@ -41,7 +41,7 @@ classDiagram
         label : text
         description : text, optional
         manufacturer : text, optional
-        injection_location : text, optional
+        injection_brain_region : text, optional
         injection_coordinates_in_mm : numeric, length 3, optional
     }
 ```
@@ -139,6 +139,7 @@ classDiagram
         detector_type : text, optional
         detected_wavelength_in_nm : numeric, optional
         gain : numeric, optional
+        gain_unit : text, false
     }
     class ObjectiveLens{
         <<DeviceModel>>
@@ -148,18 +149,10 @@ classDiagram
         numerical_aperture : numeric, optional
         magnification : numeric, optional
     }
-    class Microscope{
-        <<DeviceModel>>
-        --------------------------------------
-        attributes
-        --------------------------------------
-        microscopy_type : text, optional
-        doi : text, optional
-    }
+    
     ExcitationSource *-- DeviceModel : extends
     PulsedExcitationSource *-- ExcitationSource : extends
     Photodetector *-- DeviceModel : extends
-    Microscope *-- DeviceModel : extends
     ObjectiveLens *-- DeviceModel : extends
     OpticalFilter *-- DeviceModel : extends
     BandOpticalFilter *-- OpticalFilter : extends

spec/ndx-ophys-devices.extensions.yaml

@@ -16,13 +16,13 @@ groups:
         doc: Indicator standard notation.
       - name: description
         dtype: text
-        doc: Effector description.
+        doc: Indicator description.
         required: false
       - name: manufacturer
         dtype: text
-        doc: Effector manufacturer.
+        doc: Indicator manufacturer.
         required: false
-      - name: injection_location
+      - name: injection_brain_region
         dtype: text
         doc: Injection brain region name.
         required: false
@@ -101,6 +101,11 @@ groups:
       - name: gain
         dtype: float
         doc: Gain on the photodetector.
+        required: false
+      - name: gain_unit
+        dtype: text
+        doc: Gain on the photodetector.
+        required: false
   - neurodata_type_def: DichroicMirror
     neurodata_type_inc: DeviceModel
     doc: Extends DeviceModel to hold a Dichroic Mirror.
@@ -202,7 +207,7 @@ groups:
         dtype: text
         doc: Effector manufacturer.
         required: false
-      - name: injection_location
+      - name: injection_brain_region
         dtype: text
         doc: Injection brain region name.
         required: false
@@ -211,19 +216,7 @@ groups:
         shape:
           - 3
         doc:
-          Indicator injection location in stereotactic coordinates (AP, ML, DV) mm
+          Effector injection location in stereotactic coordinates (AP, ML, DV) mm
           relative to Bregma.
         required: false
-  - neurodata_type_def: Microscope
-    neurodata_type_inc: DeviceModel
-    doc: Extends DeviceModel to hold a Microscope.
-    attributes:
-      - name: microscopy_type
-        dtype: text
-        doc:
-          Type of microscope used to capture the image (e.g., inverted, upright, light
-          sheet, confocal, two photon).
-      - name: doi
-        dtype: text
-        doc: The publication link for custom-built microscope.
-        required: false
+

src/pynwb/ndx_ophys_devices/testing/__init__.py

@@ -11,7 +11,6 @@
     mock_ObjectiveLens,
     mock_ExcitationSource,
     mock_PulsedExcitationSource,
-    mock_Microscope,
 )
 
 __all__ = [
@@ -27,5 +26,4 @@
     "mock_ObjectiveLens",
     "mock_ExcitationSource",
     "mock_PulsedExcitationSource",
-    "mock_Microscope",
 ]

src/pynwb/ndx_ophys_devices/testing/_mock.py

@@ -27,15 +27,15 @@ def mock_Indicator(
     description: str = "This is a mock instance of a Indicator type to be used for rapid testing.",
     manufacturer: str = "A fake manufacturer of the mock indicator.",
     label: str = "A fake label of the indicator.",
-    injection_location: str = "A fake injection location of the indicator.",
+    injection_brain_region: str = "A fake injection brain region of the indicator.",
     injection_coordinates_in_mm: list = [3.0, 2.0, 1.0],
 ) -> ndx_ophys_devices.Indicator:
     indicator = ndx_ophys_devices.Indicator(
         name=name or name_generator("Indicator"),
         description=description,
         manufacturer=manufacturer,
         label=label,
-        injection_location=injection_location,
+        injection_brain_region=injection_brain_region,
         injection_coordinates_in_mm=injection_coordinates_in_mm,
     )
     return indicator
@@ -47,15 +47,15 @@ def mock_Effector(
     description: str = "This is a mock instance of a Effector type to be used for rapid testing.",
     manufacturer: str = "A fake manufacturer of the mock effector.",
     label: str = "A fake label of the effector.",
-    injection_location: str = "A fake injection location of the effector.",
+    injection_brain_region: str = "A fake injection brain region of the effector.",
     injection_coordinates_in_mm: list = [3.0, 2.0, 1.0],
 ) -> ndx_ophys_devices.Effector:
     effector = ndx_ophys_devices.Effector(
         name=name or name_generator("Effector"),
         description=description,
         manufacturer=manufacturer,
         label=label,
-        injection_location=injection_location,
+        injection_brain_region=injection_brain_region,
         injection_coordinates_in_mm=injection_coordinates_in_mm,
     )
     return effector
@@ -90,6 +90,7 @@ def mock_Photodetector(
     detector_type: str = "PMT",
     detected_wavelength_in_nm: float = 520.0,
     gain: float = 100.0,
+    gain_unit: str = "A/W",
 ) -> ndx_ophys_devices.Photodetector:
     photodetector = ndx_ophys_devices.Photodetector(
         name=name or name_generator("Photodetector"),
@@ -99,6 +100,7 @@ def mock_Photodetector(
         detector_type=detector_type,
         detected_wavelength_in_nm=detected_wavelength_in_nm,
         gain=gain,
+        gain_unit=gain_unit,
     )
     return photodetector
 
@@ -215,24 +217,6 @@ def mock_ObjectiveLens(
     return objective_lens
 
 
-def mock_Microscope(
-    *,
-    name: Optional[str] = None,
-    description: str = "This is a mock instance of a Microscope type to be used for rapid testing.",
-    manufacturer: str = "A fake manufacturer of the mock microscope.",
-    model: str = "A fake model of the mock microscope.",
-    microscopy_type: str = "Two photon.",
-) -> ndx_ophys_devices.Microscope:
-    microscope = ndx_ophys_devices.Microscope(
-        name=name or name_generator("Microscope"),
-        description=description,
-        manufacturer=manufacturer,
-        model=model,
-        microscopy_type=microscopy_type,
-    )
-    return microscope
-
-
 def mock_ExcitationSource(
     *,
     name: Optional[str] = None,

src/pynwb/tests/test_constructors.py

@@ -15,7 +15,6 @@
     mock_ObjectiveLens,
     mock_ExcitationSource,
     mock_PulsedExcitationSource,
-    mock_Microscope,
 )
 
 
@@ -59,10 +58,6 @@ def test_constructor_objective_lens():
     mock_ObjectiveLens()
 
 
-def test_constructor_microscope():
-    mock_Microscope()
-
-
 def test_constructor_excitation_source():
     mock_ExcitationSource()
 

src/pynwb/tests/test_ophysdevices.py

@@ -15,7 +15,6 @@
     mock_ObjectiveLens,
     mock_ExcitationSource,
     mock_PulsedExcitationSource,
-    mock_Microscope,
 )
 
 
@@ -59,10 +58,6 @@ def test_constructor_objective_lens():
     mock_ObjectiveLens()
 
 
-def test_constructor_microscope():
-    mock_Microscope()
-
-
 def test_constructor_excitation_source():
     mock_ExcitationSource()
 
@@ -72,7 +67,7 @@ def test_constructor_pulsed_excitation_source():
 
 
 @pytest.fixture(scope="module")
-def nwbfile_with_microscopy():
+def nwbfile_with_ophys_devices():
     nwbfile = mock_NWBFile()
 
     mock_DeviceModel()
@@ -87,7 +82,6 @@ def nwbfile_with_microscopy():
     mock_EdgeOpticalFilter()
     mock_Effector()
     mock_ObjectiveLens()
-    mock_Microscope()
 
     return nwbfile