Change quantitative properties to add units to name

spec/ndx-patterned-ogen.extensions.yaml

@@ -6,98 +6,140 @@ groups:
       - name: description
         dtype: text
         doc: Description of the scanning or scanless method for shaping optogenetic light. Examples include diffraction limited points, 3D shot, disks, etc.
-        required: false
+    datasets:
       - name: sweep_size
         dtype: numeric
         doc:
-          Size of the scanning sweep pattern in micrometers. If a scalar is provided, the sweep pattern is
+          Size of the scanning sweep pattern (default in micrometers). If a scalar is provided, the sweep pattern is
           assumed to be a circle (for 2D patterns) with diameter 'sweep_size'.
           If 'sweep_size' is a two dimensional array, the the sweep pattern is assumed to be a
           rectangle, with dimensions [width, height].
-        required: false
+        quantity: "?"
+        dims:
+        - diameter
+        - width, height
+        shape:
+        - - 1
+        - - 2
+        attributes:
+        - name: unit
+          value: micrometers
+          doc: unit of measure of the scanning sweep pattern size, fixed to micrometers
+          dtype: text
       - name: sweep_mask
         dtype: numeric
         doc:
           Scanning sweep pattern designated using a mask of size [width, height] for 2D stimulation,
           where for a given pixel a value of 1 indicates stimulation, and a
           value of 0 indicates no stimulation.
-        required: false
+        quantity: "?"        
+        dims:
+        - num_rows
+        - num_cols
+        shape:
+        - 
+        -
   - neurodata_type_def: OptogeneticStimulus3DPattern
     neurodata_type_inc: LabMetaData
     doc: Container to store the information about a generic 3D stimulus pattern (spatial information).
     attributes:
       - name: description
         dtype: text
         doc: Description of the scanning or scanless method for shaping optogenetic light. Examples include diffraction limited points, 3D shot, disks, etc.
-        required: false
+    datasets:
       - name: sweep_size
         dtype: numeric
         doc:
-          Size of the scanning sweep pattern in micrometers. If a scalar is provided, the sweep pattern is
+          Size of the scanning sweep pattern (default in micrometers). If a scalar is provided, the sweep pattern is
           assumed to be a cylinder (for 3D patterns), with diameter 'sweep_size'.
           If 'sweep_size' is a three dimensional array, the the sweep pattern is assumed to be a
           cuboid, with dimensions [width, height, depth].
-        required: false
+        quantity: "?"        
+        dims:
+        - diameter
+        - width, height, depth
+        shape:
+        - - 1
+        - - 3
+        attributes:
+        - name: unit
+          value: micrometers
+          doc: unit of measure of the scanning sweep pattern size, fixed to micrometers
+          dtype: text
       - name: sweep_mask
         dtype: numeric
         doc:
           Scanning sweep pattern designated using a mask of size [width,height, depth] for 3D stimulation,
           where for a given pixel a value of 1 indicates stimulation, and a
           value of 0 indicates no stimulation.
-        required: false
+        quantity: "?"        
+        dims:
+        - num_rows
+        - num_cols
+        - num_planes
+        shape:
+        - 
+        -
+        -
   - neurodata_type_def: SpiralScanning
     neurodata_type_inc: LabMetaData
     doc: Container to store the parameters defining a spiral scanning pattern.
-    attributes:
+    datasets:
       - name: diameter
         dtype: numeric
         doc: Spiral diameter (in micrometers).
-        required: true
+        attributes:
+        - name: unit
+          value: micrometers
+          doc: unit of measure of the spiral diameter, fixed to micrometers
+          dtype: text
       - name: number_of_revolutions
         dtype: numeric
         doc: Number of turns within a spiral.
-        required: true
-      - name: description
-        dtype: text
-        doc: Describe any additional details about the pattern.
-        required: false
       - name: height
         dtype: numeric
         doc: Spiral height of each sweep (in micrometers).
+        quantity: "?"
+        attributes:
+        - name: unit
+          value: micrometers
+          doc: unit of measure of the spiral height, fixed to micrometers
+          dtype: text
+    attributes:
+      - name: description
+        dtype: text
+        doc: Describe any additional details about the pattern.
         required: false
   - neurodata_type_def: TemporalFocusing
     neurodata_type_inc: LabMetaData
     doc: Container to store the parameters defining a temporal focusing beam-shaping.
-    attributes:
+    datasets:
       - name: lateral_point_spread_function
         dtype: text
         doc:
           Estimated lateral spatial profile or point spread function, expressed as
           mean [um] ± s.d [um].
-        required: true
       - name: axial_point_spread_function
         dtype: text
         doc:
           Estimated axial spatial profile or point spread function, expressed as mean
           [um] ± s.d [um].
-        required: true
+    attributes:
       - name: description
         dtype: text
         doc: Describe any additional details about the pattern.
         required: false
   - neurodata_type_def: PatternedOptogeneticStimulusSite
     neurodata_type_inc: OptogeneticStimulusSite
     doc: Patterned optogenetic stimulus site.
-    attributes:
+    datasets:
       - name: effector
         dtype: text
         doc: Light-activated effector protein expressed by the targeted cell (e.g., ChR2).
-        required: true
     links:
       - name: light_source
-        target_type: LightSource
+        target_type: Device
         doc: Light source used to apply photostimulation.
-        required: true
       - name: spatial_light_modulator
         target_type: Device
         doc: Spatial light modulator used to generate photostimulation pattern.
@@ -110,10 +152,15 @@ groups:
         dtype: text
         doc: The model specification of the spatial light modulator (e.g. 'X15213 series', from Hamamatsu).
         required: false
+    datasets:
       - name: spatial_resolution
         dtype: numeric
         doc: Resolution of spatial light modulator (in pixels), formatted as [width, height].
-        required: false
+        quantity: "?"
+        dims:
+        - width, height
+        shape:
+        - 2
   - neurodata_type_def: SpatialLightModulator3D
     neurodata_type_inc: Device
     doc: 3D spatial light modulator used in the experiment.
@@ -122,45 +169,80 @@ groups:
         dtype: text
         doc: The model specification of the spatial light modulator (e.g. 'NeuraLight 3D Ultra', from Bruker).
         required: false
+    datasets:
       - name: spatial_resolution
         dtype: numeric
         doc: Resolution of spatial light modulator (in pixels), formatted as [width, height, depth].
-        required: false
+        quantity: "?"
+        dims:
+        - width, height, depth
+        shape:
+        - 3
   - neurodata_type_def: LightSource
     neurodata_type_inc: Device
     doc: Light source used in the experiment.
-    attributes:
+    datasets:
       - name: stimulation_wavelength
         dtype: numeric
         doc: Excitation wavelength of stimulation light (nanometers).
-        required: true
-      - name: model
-        dtype: text
-        doc: Model of light source device.
-        required: false
+        attributes:
+        - name: unit
+          value: nanometers
+          doc: unit of measure of wavelength which is fixed to nanometers
+          dtype: text
       - name: filter_description
         dtype: text
         doc: Filter used to obtain the excitation wavelength of stimulation light, e.g. 'Short pass at 1040 nm'.
-        required: false
+        quantity: "?"
       - name: peak_power
         dtype: numeric
         doc: Incident power of stimulation device (in Watts).
-        required: false
+        quantity: "?"
+        attributes:
+        - name: unit
+          value: Watts
+          doc: unit of measure of power which is fixed to Watts
+          dtype: text
       - name: peak_pulse_energy
         dtype: numeric
         doc: If device is pulsed light source, pulse energy (in Joules).
-        required: false
+        attributes:
+        - name: unit
+          value: Joules
+          doc: unit of measure of energy which is fixed to Joules
+          dtype: text
+        quantity: "?"
       - name: intensity
         dtype: numeric
         doc: Intensity of the excitation in W/m^2, if known.
-        required: false
+        quantity: "?"
+        attributes:
+        - name: unit
+          value: W/m^2
+          doc: unit of measure of intensity which is fixed to Watts per square meters
+          dtype: text        
       - name: exposure_time
         dtype: numeric
         doc: Exposure time of the sample (in sec).
-        required: false
+        quantity: "?"
+        attributes:
+        - name: unit
+          value: seconds
+          doc: unit of measure of exposure time which is fixed to seconds
+          dtype: text   
       - name: pulse_rate
         dtype: numeric
         doc: If device is pulsed light source, pulse rate (in Hz) used for stimulation.
+        quantity: "?"
+        attributes:
+        - name: unit
+          value: Hz
+          doc: unit of measure of rate which is fixed to Hertz
+          dtype: text   
+    attributes:
+      - name: model
+        dtype: text
+        doc: Model of light source device.
         required: false
   - neurodata_type_def: OptogeneticStimulusTarget
     neurodata_type_inc: LabMetaData
@@ -169,46 +251,55 @@ groups:
       - name: targeted_rois
         neurodata_type_inc: DynamicTableRegion
         doc: A table region referencing a PlaneSegmentation object storing targeted ROIs.
-        required: true
       - name: segmented_rois
         neurodata_type_inc: DynamicTableRegion
         doc: A table region referencing a PlaneSegmentation object storing segmented ROIs that receive photostimulation.
-        required: false
+        quantity: "?"
   - neurodata_type_def: PatternedOptogeneticStimulusTable
     neurodata_type_inc: TimeIntervals
     doc: Table to hold all patterned optogenetic stimulus onsets.
-    quantity: "?"
     datasets:
       - name: power
         neurodata_type_inc: VectorData
-        doc: Power (in Watts) applied to each target during patterned photostimulation.
-        required: true
+        doc: Power applied to each target during patterned photostimulation, in W.
+        attributes:
+        - name: unit
+          value: Watts
+          doc: unit of measure of power which is fixed to Watts
+          dtype: text
       - name: targets
         neurodata_type_inc: VectorData
         dtype:
           target_type: OptogeneticStimulusTarget
           reftype: object
         doc: Targeted rois for the stimulus onset.
-        required: true
       - name: stimulus_pattern
         neurodata_type_inc: VectorData
         dtype:
           target_type: LabMetaData
           reftype: object
         doc: Link to the stimulus pattern.
-        required: true
       - name: stimulus_site
         neurodata_type_inc: VectorData
         dtype:
           target_type: PatternedOptogeneticStimulusSite
           reftype: object
         doc: Link to the stimulus site.
-        required: true
       - name: frequency
         neurodata_type_inc: VectorData
-        doc: Frequency of stimulation if the stimulus delivered is pulsed (in Hz).
-        required: false
+        doc: Frequency of stimulation if the stimulus delivered is pulsed, in Hz.
+        quantity: "?"
+        attributes:
+        - name: unit
+          value: Hertz
+          doc: unit of measure of frequency which is fixed to Hertz
+          dtype: text
       - name: pulse_width
         neurodata_type_inc: VectorData
         doc: Pulse width of stimulation if the stimulus delivered is pulsed, in seconds/phase.
-        required: false
+        quantity: "?"
+        attributes:
+        - name: unit
+          value: seconds/phase
+          doc: unit of measure of power which is fixed to seconds/phase
+          dtype: text

src/pynwb/ndx_patterned_ogen/__init__.py

@@ -1,5 +1,5 @@
 import os
-from pynwb import load_namespaces
+from pynwb import load_namespaces, get_class
 
 try:
     from importlib.resources import files
@@ -14,22 +14,24 @@
 # If that path does not exist, we are likely running in editable mode. Use the local path instead
 if not os.path.exists(__spec_path):
     __spec_path = __location_of_this_file.parent.parent.parent / "spec" / "ndx-patterned-ogen.namespace.yaml"
+
+load_namespaces(str(__spec_path))
+
+SpatialLightModulator2D = get_class('SpatialLightModulator2D', 'ndx-patterned-ogen')
+SpatialLightModulator3D = get_class('SpatialLightModulator3D', 'ndx-patterned-ogen')
+LightSource = get_class('LightSource', 'ndx-patterned-ogen')
+OptogeneticStimulus2DPattern = get_class('OptogeneticStimulus2DPattern', 'ndx-patterned-ogen')
+OptogeneticStimulus3DPattern = get_class('OptogeneticStimulus3DPattern', 'ndx-patterned-ogen')
+SpiralScanning = get_class('SpiralScanning', 'ndx-patterned-ogen')
+TemporalFocusing = get_class('TemporalFocusing', 'ndx-patterned-ogen')
 
 # Load the namespace
-load_namespaces(str(__spec_path))
 
 from .patterned_ogen import (
-    SpatialLightModulator3D,
-    SpatialLightModulator2D,
-    LightSource,
     PatternedOptogeneticStimulusSite,
     PatternedOptogeneticStimulusTable,
-    OptogeneticStimulus2DPattern,
-    OptogeneticStimulus3DPattern,
     OptogeneticStimulusSite,
     OptogeneticStimulusTarget,
-    SpiralScanning,
-    TemporalFocusing,
 )
 
 __all__ = [