Refactor attribute names to add um

Author: alessandratrapani

spec/ndx-microscopy.extensions.yaml

@@ -68,13 +68,13 @@ groups:
     attributes:
       - name: scan_direction
         dtype: text
-        doc: Direction of line scanning (horizontal, vertical, or diagonal).
+        doc: Direction of line scanning (horizontal or vertical).
         required: false
-      - name: line_rate
+      - name: line_rate_in_Hz
         dtype: float64
         doc: Rate of line scanning in lines per second.
         required: false
-      - name: dwell_time
+      - name: dwell_time_in_s
         dtype: float64
         doc: Average time spent at each scanned point.
         required: false
@@ -87,7 +87,7 @@ groups:
         dtype: text
         doc: Specific raster scanning pattern (e.g., bidirectional, unidirectional).
         required: false
-      - name: dwell_time
+      - name: dwell_time_in_s
         dtype: float64
         doc: Average time spent at each scanned point.
         required: false
@@ -96,7 +96,7 @@ groups:
     neurodata_type_inc: ImagingModality
     doc: Resonant scanning method using a rapidly oscillating mirror for high-speed imaging.
     attributes:
-      - name: resonant_frequency
+      - name: resonant_frequency_in_Hz
         dtype: float64
         doc: Frequency of the resonant scanner in Hz.
         required: false
@@ -115,7 +115,7 @@ groups:
       - name: axial_point_spread_function_in_um
         dtype: text
         doc: Estimated axial spatial profile or point spread function, expressed as mean [um] ± s.d [um].
-      - name: pulse_duration
+      - name: pulse_duration_in_s
         dtype: float64
         doc: Duration of excitation pulses in seconds.
         required: false
@@ -128,7 +128,7 @@ groups:
         dtype: float64
         doc: Thickness of the light sheet in micrometers.
         required: false
-      - name: illumination_angle
+      - name: illumination_angle_in_degrees
         dtype: float64
         doc: Angle of light sheet illumination in degrees.
         required: false
@@ -141,7 +141,7 @@ groups:
         dtype: numeric
         doc: Maximum number of points that can be scanned in a single frame.
         required: false
-      - name: dwell_time
+      - name: dwell_time_in_s
         dtype: float64
         doc: Average time spent at each scanned point.
         required: false

src/pynwb/ndx_microscopy/testing/_mock.py

@@ -88,16 +88,16 @@ def mock_LineScanning(
     name: Optional[str] = None,
     description: str = "A mock instance of a LineScanning type to be used for rapid testing.",
     scan_direction: Optional[str] = "horizontal",
-    line_rate: Optional[float] = 500.0,
-    dwell_time: Optional[float] = 0.001,
+    line_rate_in_Hz: Optional[float] = 1000.0,
+    dwell_time_in_s: Optional[float] = 1.0e-6,
 ) -> ndx_microscopy.LineScanning:
     """Line scanning method used in microscopy, particularly common in two-photon imaging."""
     line_scanning = ndx_microscopy.LineScanning(
         name=name or name_generator("LineScanning"),
         description=description,
         scan_direction=scan_direction,
-        line_rate=line_rate,
-        dwell_time=dwell_time,
+        line_rate_in_Hz=line_rate_in_Hz,
+        dwell_time_in_s=dwell_time_in_s,
     )
     return line_scanning
 
@@ -107,14 +107,14 @@ def mock_RasterScanning(
     name: Optional[str] = None,
     description: str = "A mock instance of a RasterScanning type to be used for rapid testing.",
     scan_pattern: Optional[str] = "bidirectional",
-    dwell_time: Optional[float] = 0.0005,
+    dwell_time_in_s: Optional[float] = 1.0e-6,
 ) -> ndx_microscopy.RasterScanning:
     """Raster scanning method with grid-like point-by-point or line-by-line acquisition."""
     raster_scanning = ndx_microscopy.RasterScanning(
         name=name or name_generator("RasterScanning"),
         description=description,
         scan_pattern=scan_pattern,
-        dwell_time=dwell_time,
+        dwell_time_in_s=dwell_time_in_s,
     )
     return raster_scanning
 
@@ -123,14 +123,14 @@ def mock_ResonantScanning(
     *,
     name: Optional[str] = None,
     description: str = "A mock instance of a ResonantScanning type to be used for rapid testing.",
-    resonant_frequency: Optional[float] = 8000.0,
+    resonant_frequency_in_Hz: Optional[float] = 8000.0,
     resonant_amplitude: Optional[float] = 1.5,
 ) -> ndx_microscopy.ResonantScanning:
     """Resonant scanning method using a rapidly oscillating mirror for high-speed imaging."""
     resonant_scanning = ndx_microscopy.ResonantScanning(
         name=name or name_generator("ResonantScanning"),
         description=description,
-        resonant_frequency=resonant_frequency,
+        resonant_frequency_in_Hz=resonant_frequency_in_Hz,
         resonant_amplitude=resonant_amplitude,
     )
     return resonant_scanning
@@ -142,15 +142,15 @@ def mock_TemporalFocusing(
     description: str = "A mock instance of a TemporalFocusing type to be used for rapid testing.",
     lateral_point_spread_function_in_um: str = "0.5 ± 0.1",
     axial_point_spread_function_in_um: str = "2.0 ± 0.3",
-    pulse_duration: Optional[float] = 0.0000001,  # 100 nanoseconds
+    pulse_duration_in_s: Optional[float] = 0.0000001,  # 100 nanoseconds
 ) -> ndx_microscopy.TemporalFocusing:
     """Temporal focusing scanning method for depth-resolved imaging."""
     temporal_focusing = ndx_microscopy.TemporalFocusing(
         name=name or name_generator("TemporalFocusing"),
         description=description,
         lateral_point_spread_function_in_um=lateral_point_spread_function_in_um,
         axial_point_spread_function_in_um=axial_point_spread_function_in_um,
-        pulse_duration=pulse_duration,
+        pulse_duration_in_s=pulse_duration_in_s,
     )
     return temporal_focusing
 
@@ -160,14 +160,14 @@ def mock_LightSheet(
     name: Optional[str] = None,
     description: str = "A mock instance of a LightSheet type to be used for rapid testing.",
     sheet_thickness_in_um: Optional[float] = 5.0,
-    illumination_angle: Optional[float] = 45.0,
+    illumination_angle_in_degrees: Optional[float] = 45.0,
 ) -> ndx_microscopy.LightSheet:
     """Light sheet method."""
     light_sheet = ndx_microscopy.LightSheet(
         name=name or name_generator("LightSheet"),
         description=description,
         sheet_thickness_in_um=sheet_thickness_in_um,
-        illumination_angle=illumination_angle,
+        illumination_angle_in_degrees=illumination_angle_in_degrees,
     )
     return light_sheet
 
@@ -177,15 +177,15 @@ def mock_RandomAccessScanning(
     name: Optional[str] = None,
     description: str = "A mock instance of a RandomAccessScanning type to be used for rapid testing.",
     max_scan_points: Optional[int] = 1000,
-    dwell_time: Optional[float] = 0.0001,
+    dwell_time_in_s: Optional[float] = 1.0e-6,
     scanning_pattern: Optional[str] = "spiral",
 ) -> ndx_microscopy.RandomAccessScanning:
     """Random access scanning method for targeted, high-speed imaging of specific regions."""
     random_access_scanning = ndx_microscopy.RandomAccessScanning(
         name=name or name_generator("RandomAccessScanning"),
         description=description,
         max_scan_points=max_scan_points,
-        dwell_time=dwell_time,
+        dwell_time_in_s=dwell_time_in_s,
         scanning_pattern=scanning_pattern,
     )
     return random_access_scanning

src/pynwb/tests/test_constructors.py

@@ -73,8 +73,8 @@ def test_constructor_line_scanning():
     line_scanning = mock_LineScanning()
     assert line_scanning.description == "A mock instance of a LineScanning type to be used for rapid testing."
     assert line_scanning.scan_direction == "horizontal"
-    assert line_scanning.line_rate == 500.0
-    assert line_scanning.dwell_time == 0.001
+    assert line_scanning.line_rate_in_Hz == 1000.0
+    assert line_scanning.dwell_time_in_s == 1e-6
     assert isinstance(line_scanning, LineScanning)
     assert isinstance(line_scanning, ImagingModality)  # Test inheritance
 
@@ -84,7 +84,7 @@ def test_constructor_raster_scanning():
     raster_scanning = mock_RasterScanning()
     assert raster_scanning.description == "A mock instance of a RasterScanning type to be used for rapid testing."
     assert raster_scanning.scan_pattern == "bidirectional"
-    assert raster_scanning.dwell_time == 0.0005
+    assert raster_scanning.dwell_time_in_s == 1.0e-6
     assert isinstance(raster_scanning, RasterScanning)
     assert isinstance(raster_scanning, ImagingModality)  # Test inheritance
 
@@ -93,7 +93,7 @@ def test_constructor_resonant_scanning():
     """Test constructor for ResonantScanning class."""
     resonant_scanning = mock_ResonantScanning()
     assert resonant_scanning.description == "A mock instance of a ResonantScanning type to be used for rapid testing."
-    assert resonant_scanning.resonant_frequency == 8000.0
+    assert resonant_scanning.resonant_frequency_in_Hz == 8000.0
     assert resonant_scanning.resonant_amplitude == 1.5
     assert isinstance(resonant_scanning, ResonantScanning)
     assert isinstance(resonant_scanning, ImagingModality)  # Test inheritance
@@ -105,7 +105,7 @@ def test_constructor_temporal_focusing():
     assert temporal_focusing.description == "A mock instance of a TemporalFocusing type to be used for rapid testing."
     assert temporal_focusing.lateral_point_spread_function_in_um == "0.5 ± 0.1"
     assert temporal_focusing.axial_point_spread_function_in_um == "2.0 ± 0.3"
-    assert temporal_focusing.pulse_duration == 0.0000001
+    assert temporal_focusing.pulse_duration_in_s == 0.0000001
     assert isinstance(temporal_focusing, TemporalFocusing)
     assert isinstance(temporal_focusing, ImagingModality)  # Test inheritance
 
@@ -115,7 +115,7 @@ def test_constructor_light_sheet():
     light_sheet = mock_LightSheet()
     assert light_sheet.description == "A mock instance of a LightSheet type to be used for rapid testing."
     assert light_sheet.sheet_thickness_in_um == 5.0
-    assert light_sheet.illumination_angle == 45.0
+    assert light_sheet.illumination_angle_in_degrees == 45.0
     assert isinstance(light_sheet, LightSheet)
     assert isinstance(light_sheet, ImagingModality)  # Test inheritance
 
@@ -128,7 +128,7 @@ def test_constructor_random_access_scanning():
         == "A mock instance of a RandomAccessScanning type to be used for rapid testing."
     )
     assert random_access_scanning.max_scan_points == 1000
-    assert random_access_scanning.dwell_time == 0.0001
+    assert random_access_scanning.dwell_time_in_s == 1.0e-6
     assert random_access_scanning.scanning_pattern == "spiral"
     assert isinstance(random_access_scanning, RandomAccessScanning)
     assert isinstance(random_access_scanning, ImagingModality)  # Test inheritance