Change quantitative properties to add units to name (#6)

* add new spec (not working for the stimulated_rois)

* tests not working

* fix testing

* define what is required

* improve tutorial

* add explaination for stimulus table

* add testing for power,frequency and pulse_width as 1D arrays

* set defaults for power,frequency and pulse_width

* add schema diagram

* remove unnecessary imports

* add targeted_rois (required) and segmented_rois (optional)

* remove unnecessary imports

* remove old schema

* update schema

* minor fixes

* add elements to __all__ to count as used

* add exception to ruff

* remove space

* adjust to proper sentences

* Update spec/ndx-patterned-ogen.extensions.yaml

Co-authored-by: Cody Baker <[email protected]>

* Update spec/ndx-patterned-ogen.extensions.yaml

Co-authored-by: Cody Baker <[email protected]>

* Update spec/ndx-patterned-ogen.extensions.yaml

Co-authored-by: Cody Baker <[email protected]>

* Update spec/ndx-patterned-ogen.extensions.yaml

Co-authored-by: Cody Baker <[email protected]>

* Update spec/ndx-patterned-ogen.extensions.yaml

Co-authored-by: Cody Baker <[email protected]>

* Update spec/ndx-patterned-ogen.extensions.yaml

Co-authored-by: Cody Baker <[email protected]>

* Update spec/ndx-patterned-ogen.extensions.yaml

Co-authored-by: Cody Baker <[email protected]>

* Update spec/ndx-patterned-ogen.extensions.yaml

Co-authored-by: Cody Baker <[email protected]>

* Improve readability of doc strings

* targeted_rois defined as table region

* add example for slm model and filter_description

* split SLM in 2 device SLM2D and SLM3D

* split OgenPattern in 2D and 3D

* update tutorial and schema

* minor fixes

* update schema

* set sweeep_size and sweep_mask as datasets

* set SpiralScanning and TemporalFocusing properties as datasets

* set effector as dataset

* set spatial_resolution as dataset

* set all LightSource properties as datasets except "model"

* update tutorial

* set segmented_rois default

* change required:false to quantity:'?' for dataset

* remove unnecessary class definition

* add unit, shape and dims

* update tutorial and mock_fun accordingly

* minor fixes

* Apply suggestions from code review

* add unit measure in the name of the attribute

---------

Co-authored-by: Cody Baker <[email protected]>

Author: alessandratrapani

spec/ndx-patterned-ogen.extensions.yaml

@@ -6,81 +6,103 @@ 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
-      - name: sweep_size
+      - name: sweep_size_in_um
         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
+        dims:
+          - diameter
+          - width, height
+        shape:
+          - - 1
+          - - 2
+    datasets:
       - 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
-      - name: sweep_size
+      - name: sweep_size_in_um
         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
+        dims:
+          - diameter
+          - width, height, depth
+        shape:
+          - - 1
+          - - 3
+    datasets:
       - 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:
-      - name: diameter
+      - name: diameter_in_um
         dtype: numeric
         doc: Spiral diameter (in micrometers).
-        required: true
       - name: number_of_revolutions
         dtype: numeric
         doc: Number of turns within a spiral.
-        required: true
+      - name: height_in_um
+        dtype: numeric
+        doc: Spiral height of each sweep (in micrometers).
+        required: false
       - 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).
-        required: false
   - neurodata_type_def: TemporalFocusing
     neurodata_type_inc: LabMetaData
     doc: Container to store the parameters defining a temporal focusing beam-shaping.
     attributes:
-      - name: lateral_point_spread_function
+      - name: lateral_point_spread_function_in_um
         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
+      - 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].
-        required: true
       - name: description
         dtype: text
         doc: Describe any additional details about the pattern.
@@ -92,12 +114,10 @@ groups:
       - 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 +130,14 @@ groups:
         dtype: text
         doc: The model specification of the spatial light modulator (e.g. 'X15213 series', from Hamamatsu).
         required: false
-      - name: spatial_resolution
+      - name: spatial_resolution_in_px
         dtype: numeric
         doc: Resolution of spatial light modulator (in pixels), formatted as [width, height].
         required: false
+        dims:
+          - width, height
+        shape:
+          - 2
   - neurodata_type_def: SpatialLightModulator3D
     neurodata_type_inc: Device
     doc: 3D spatial light modulator used in the experiment.
@@ -122,105 +146,133 @@ groups:
         dtype: text
         doc: The model specification of the spatial light modulator (e.g. 'NeuraLight 3D Ultra', from Bruker).
         required: false
-      - name: spatial_resolution
+      - name: spatial_resolution_in_px
         dtype: numeric
         doc: Resolution of spatial light modulator (in pixels), formatted as [width, height, depth].
         required: false
+        dims:
+          - width, height, depth
+        shape:
+          - 3
   - neurodata_type_def: LightSource
     neurodata_type_inc: Device
     doc: Light source used in the experiment.
     attributes:
-      - name: stimulation_wavelength
+      - name: stimulation_wavelength_in_nm
         dtype: numeric
         doc: Excitation wavelength of stimulation light (nanometers).
-        required: true
-      - name: model
-        dtype: text
-        doc: Model of light source device.
-        required: false
       - 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
-      - name: peak_power
+      - name: peak_power_in_W
         dtype: numeric
         doc: Incident power of stimulation device (in Watts).
         required: false
-      - name: peak_pulse_energy
+      - name: peak_pulse_energy_in_J
         dtype: numeric
         doc: If device is pulsed light source, pulse energy (in Joules).
         required: false
-      - name: intensity
+      - name: intensity_in_W_per_m2
         dtype: numeric
         doc: Intensity of the excitation in W/m^2, if known.
         required: false
-      - name: exposure_time
+      - name: exposure_time_in_s
         dtype: numeric
         doc: Exposure time of the sample (in sec).
         required: false
-      - name: pulse_rate
+      - name: pulse_rate_in_Hz
         dtype: numeric
         doc: If device is pulsed light source, pulse rate (in Hz) used for stimulation.
         required: false
+      - name: model
+        dtype: text
+        doc: Model of light source device.
+        required: false
   - neurodata_type_def: OptogeneticStimulusTarget
     neurodata_type_inc: LabMetaData
     doc: Container to store the targated rois in a photostimulation experiment.
     datasets:
       - 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) defined as a scalar. All rois in target receive the same photostimulation power.
         quantity: "?"
+        attributes:
+          - name: unit
+            value: Watts
+            doc: Unit of measure of power, fixed to Watts.
+            dtype: text
       - name: power_per_roi
         neurodata_type_inc: VectorData
         doc: Power (in Watts) defined as an array. Each power value refers to each roi in target.
         quantity: "?"
+        attributes:
+          - name: unit
+            value: Watts
+            doc: Unit of measure of power, 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 (in Hz) defined as a scalar. All rois in target receive the photostimulation at the same frequency.
         quantity: "?"
+        attributes:
+          - name: unit
+            value: Hertz
+            doc: Unit of measure of frequency, fixed to Hertz.
+            dtype: text
       - name: frequency_per_roi
         neurodata_type_inc: VectorData
         doc: Frequency (in Hz) defined as an array. Each frequency value refers to each roi in target.
         quantity: "?"
+        attributes:
+          - name: unit
+            value: Hertz
+            doc: Unit of measure of frequency, fixed to Hertz.
+            dtype: text
       - name: pulse_width
         neurodata_type_inc: VectorData
         doc: Pulse Width (in sec/phase) defined as a scalar. All rois in target receive the photostimulation with the same pulse width.
         quantity: "?"
+        attributes:
+          - name: unit
+            value: seconds/phase
+            doc: Unit of measure of power, fixed to seconds per phase.
+            dtype: text
       - name: pulse_width_per_roi
         neurodata_type_inc: VectorData
         doc: Pulse Width (in sec/phase) defined as an array. Each pulse width value refers to each roi in target.
         quantity: "?"
+        attributes:
+          - name: unit
+            value: seconds/phase
+            doc: Unit of measure of power, fixed to seconds per 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__ = [