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Fix slm requirement in Python API #15

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Jun 28, 2024
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3 changes: 3 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -168,3 +168,6 @@ cython_debug/

# Mac finder
.DS_Store

# PyCharm
.idea/
19 changes: 19 additions & 0 deletions spec/ndx-patterned-ogen.extensions.yaml
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
groups:

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Also added spacing between type definitions here in the spec to make them easier to visually identify

- neurodata_type_def: OptogeneticStimulus2DPattern
neurodata_type_inc: LabMetaData
doc: Container to store the information about a generic 2D stimulus pattern (spatial information).
Expand Down Expand Up @@ -34,6 +35,8 @@ groups:
shape:
-
-


- neurodata_type_def: OptogeneticStimulus3DPattern
neurodata_type_inc: LabMetaData
doc: Container to store the information about a generic 3D stimulus pattern (spatial information).
Expand Down Expand Up @@ -71,6 +74,8 @@ groups:
-
-
-


- neurodata_type_def: SpiralScanning
neurodata_type_inc: LabMetaData
doc: Container to store the parameters defining a spiral scanning pattern.
Expand All @@ -89,6 +94,8 @@ groups:
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.
Expand All @@ -107,6 +114,8 @@ groups:
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.
Expand All @@ -122,6 +131,8 @@ groups:
target_type: Device
doc: Spatial light modulator used to generate photostimulation pattern.
required: false


- neurodata_type_def: SpatialLightModulator2D
neurodata_type_inc: Device
doc: 2D spatial light modulator used in the experiment.
Expand All @@ -138,6 +149,8 @@ groups:
- width, height
shape:
- 2


- neurodata_type_def: SpatialLightModulator3D
neurodata_type_inc: Device
doc: 3D spatial light modulator used in the experiment.
Expand All @@ -154,6 +167,8 @@ groups:
- width, height, depth
shape:
- 3


- neurodata_type_def: LightSource
neurodata_type_inc: Device
doc: Light source used in the experiment.
Expand Down Expand Up @@ -189,6 +204,8 @@ groups:
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.
Expand All @@ -200,6 +217,8 @@ groups:
neurodata_type_inc: DynamicTableRegion
doc: A table region referencing a PlaneSegmentation object storing segmented ROIs that receive photostimulation.
quantity: "?"


- neurodata_type_def: PatternedOptogeneticStimulusTable
neurodata_type_inc: TimeIntervals
doc: Table to hold all patterned optogenetic stimulus onsets.
Expand Down
1 change: 1 addition & 0 deletions src/pynwb/ndx_patterned_ogen/patterned_ogen.py
Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,7 @@ class PatternedOptogeneticStimulusSite(OptogeneticStimulusSite):
"name": "spatial_light_modulator",
"type": Device,
"doc": "Spatial light modulator used to generate photostimulation pattern.",
"default": None,
},
{"name": "light_source", "type": Device, "doc": "Light source used to apply photostimulation."},
)
Expand Down
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