From bf8143dcd94f0af9d5b1dc640efd908239be0705 Mon Sep 17 00:00:00 2001 From: Saskia de Vries Date: Wed, 8 Jan 2025 09:46:02 -0800 Subject: [PATCH 1/4] objects in arena --- src/aind_data_schema/core/session.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/aind_data_schema/core/session.py b/src/aind_data_schema/core/session.py index 6c0f1c6c2..f5549ca18 100644 --- a/src/aind_data_schema/core/session.py +++ b/src/aind_data_schema/core/session.py @@ -47,6 +47,7 @@ class StimulusModality(str, Enum): """Types of stimulus modalities""" AUDITORY = "Auditory" + FREE_MOVING = "Free moving" OLFACTORY = "Olfactory" OPTOGENETICS = "Optogenetics" NONE = "None" @@ -63,6 +64,7 @@ class FiberConnectionConfig(AindModel): patch_cord_output_power: Decimal = Field(..., title="Output power (uW)") output_power_unit: PowerUnit = Field(default=PowerUnit.UW, title="Output power unit") fiber_name: str = Field(..., title="Fiber name (must match procedure)") + channels: Optional[List[Channel]] = Field(default=None, title="Channels") class TriggerType(str, Enum): @@ -523,6 +525,7 @@ class StimulusEpoch(AindModel): light_source_config: Optional[List[LIGHT_SOURCE_CONFIGS]] = Field( default=[], title="Light source config", description="Light sources for stimulation" ) + objects_in_arena: Optional[List[str]] = Field(default=None, title="Objects in arena") output_parameters: AindGenericType = Field(default=AindGeneric(), title="Performance metrics") reward_consumed_during_epoch: Optional[Decimal] = Field(default=None, title="Reward consumed during training (uL)") reward_consumed_unit: VolumeUnit = Field(default=VolumeUnit.UL, title="Reward consumed unit") @@ -537,7 +540,7 @@ class Session(AindCoreModel): _DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/session.py" describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL}) - schema_version: SkipValidation[Literal["1.1.1"]] = Field(default="1.1.1") + schema_version: SkipValidation[Literal["1.0.3"]] = Field(default="1.0.3") protocol_id: List[str] = Field(default=[], title="Protocol ID", description="DOI for protocols.io") experimenter_full_name: List[str] = Field( ..., From 0cef5d5545b2bb32a17636458d4882993571d9c4 Mon Sep 17 00:00:00 2001 From: Saskia de Vries Date: Wed, 8 Jan 2025 12:54:26 -0800 Subject: [PATCH 2/4] examples --- examples/bergamo_ophys_session.json | 3 ++- examples/ephys_session.json | 4 +++- examples/mri_session.json | 2 +- examples/multiplane_ophys_session.json | 2 +- examples/ophys_session.json | 8 +++++--- 5 files changed, 12 insertions(+), 7 deletions(-) diff --git a/examples/bergamo_ophys_session.json b/examples/bergamo_ophys_session.json index ea5c8b9cf..7f01a3f04 100644 --- a/examples/bergamo_ophys_session.json +++ b/examples/bergamo_ophys_session.json @@ -1,6 +1,6 @@ { "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py", - "schema_version": "1.1.1", + "schema_version": "1.0.3", "protocol_id": [], "experimenter_full_name": [ "John Doe" @@ -153,6 +153,7 @@ "stimulus_device_names": [], "speaker_config": null, "light_source_config": [], + "objects_in_arena": null, "output_parameters": {}, "reward_consumed_during_epoch": null, "reward_consumed_unit": "microliter", diff --git a/examples/ephys_session.json b/examples/ephys_session.json index 6d6e42a52..918a4014f 100644 --- a/examples/ephys_session.json +++ b/examples/ephys_session.json @@ -1,6 +1,6 @@ { "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py", - "schema_version": "1.1.1", + "schema_version": "1.0.3", "protocol_id": [], "experimenter_full_name": [ "Max Quibble", @@ -326,6 +326,7 @@ "stimulus_device_names": [], "speaker_config": null, "light_source_config": [], + "objects_in_arena": null, "output_parameters": {}, "reward_consumed_during_epoch": null, "reward_consumed_unit": "microliter", @@ -368,6 +369,7 @@ "stimulus_device_names": [], "speaker_config": null, "light_source_config": [], + "objects_in_arena": null, "output_parameters": {}, "reward_consumed_during_epoch": null, "reward_consumed_unit": "microliter", diff --git a/examples/mri_session.json b/examples/mri_session.json index a2a0ce0f2..caf6fa6ea 100644 --- a/examples/mri_session.json +++ b/examples/mri_session.json @@ -1,6 +1,6 @@ { "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py", - "schema_version": "1.1.1", + "schema_version": "1.0.3", "protocol_id": [ "dx.doi.org/10.57824/protocols.io.bh7kl4n6" ], diff --git a/examples/multiplane_ophys_session.json b/examples/multiplane_ophys_session.json index 9d833a96c..835e023b3 100644 --- a/examples/multiplane_ophys_session.json +++ b/examples/multiplane_ophys_session.json @@ -1,6 +1,6 @@ { "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py", - "schema_version": "1.1.1", + "schema_version": "1.0.3", "protocol_id": [], "experimenter_full_name": [ "John Doe" diff --git a/examples/ophys_session.json b/examples/ophys_session.json index 08f9f8d83..ca2d07dc7 100644 --- a/examples/ophys_session.json +++ b/examples/ophys_session.json @@ -1,6 +1,6 @@ { "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py", - "schema_version": "1.1.1", + "schema_version": "1.0.3", "protocol_id": [], "experimenter_full_name": [ "John Doe" @@ -57,13 +57,15 @@ "patch_cord_name": "Patch Cord A", "patch_cord_output_power": "40", "output_power_unit": "microwatt", - "fiber_name": "Fiber A" + "fiber_name": "Fiber A", + "channels": null }, { "patch_cord_name": "Patch Cord B", "patch_cord_output_power": "43", "output_power_unit": "microwatt", - "fiber_name": "Fiber B" + "fiber_name": "Fiber B", + "channels": null } ], "fiber_modules": [], From eeddd8f4568c325e2123b3027c35660d5cb332ee Mon Sep 17 00:00:00 2001 From: Saskia de Vries Date: Wed, 8 Jan 2025 13:40:16 -0800 Subject: [PATCH 3/4] fixed goofs --- src/aind_data_schema/core/session.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/aind_data_schema/core/session.py b/src/aind_data_schema/core/session.py index f5549ca18..5ffcf7e35 100644 --- a/src/aind_data_schema/core/session.py +++ b/src/aind_data_schema/core/session.py @@ -64,7 +64,6 @@ class FiberConnectionConfig(AindModel): patch_cord_output_power: Decimal = Field(..., title="Output power (uW)") output_power_unit: PowerUnit = Field(default=PowerUnit.UW, title="Output power unit") fiber_name: str = Field(..., title="Fiber name (must match procedure)") - channels: Optional[List[Channel]] = Field(default=None, title="Channels") class TriggerType(str, Enum): @@ -540,7 +539,7 @@ class Session(AindCoreModel): _DESCRIBED_BY_URL = AindCoreModel._DESCRIBED_BY_BASE_URL.default + "aind_data_schema/core/session.py" describedBy: str = Field(default=_DESCRIBED_BY_URL, json_schema_extra={"const": _DESCRIBED_BY_URL}) - schema_version: SkipValidation[Literal["1.0.3"]] = Field(default="1.0.3") + schema_version: SkipValidation[Literal["1.1.1"]] = Field(default="1.1.1") protocol_id: List[str] = Field(default=[], title="Protocol ID", description="DOI for protocols.io") experimenter_full_name: List[str] = Field( ..., From 824c3b2caf5f08ea505e6fcf2291d9c662af3736 Mon Sep 17 00:00:00 2001 From: Saskia de Vries Date: Wed, 8 Jan 2025 14:54:29 -0800 Subject: [PATCH 4/4] examples --- examples/bergamo_ophys_session.json | 2 +- examples/ephys_session.json | 2 +- examples/mri_session.json | 2 +- examples/multiplane_ophys_session.json | 2 +- examples/ophys_session.json | 8 +++----- 5 files changed, 7 insertions(+), 9 deletions(-) diff --git a/examples/bergamo_ophys_session.json b/examples/bergamo_ophys_session.json index 7f01a3f04..b5910b473 100644 --- a/examples/bergamo_ophys_session.json +++ b/examples/bergamo_ophys_session.json @@ -1,6 +1,6 @@ { "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py", - "schema_version": "1.0.3", + "schema_version": "1.1.1", "protocol_id": [], "experimenter_full_name": [ "John Doe" diff --git a/examples/ephys_session.json b/examples/ephys_session.json index 918a4014f..603462f54 100644 --- a/examples/ephys_session.json +++ b/examples/ephys_session.json @@ -1,6 +1,6 @@ { "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py", - "schema_version": "1.0.3", + "schema_version": "1.1.1", "protocol_id": [], "experimenter_full_name": [ "Max Quibble", diff --git a/examples/mri_session.json b/examples/mri_session.json index caf6fa6ea..a2a0ce0f2 100644 --- a/examples/mri_session.json +++ b/examples/mri_session.json @@ -1,6 +1,6 @@ { "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py", - "schema_version": "1.0.3", + "schema_version": "1.1.1", "protocol_id": [ "dx.doi.org/10.57824/protocols.io.bh7kl4n6" ], diff --git a/examples/multiplane_ophys_session.json b/examples/multiplane_ophys_session.json index 835e023b3..9d833a96c 100644 --- a/examples/multiplane_ophys_session.json +++ b/examples/multiplane_ophys_session.json @@ -1,6 +1,6 @@ { "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py", - "schema_version": "1.0.3", + "schema_version": "1.1.1", "protocol_id": [], "experimenter_full_name": [ "John Doe" diff --git a/examples/ophys_session.json b/examples/ophys_session.json index ca2d07dc7..08f9f8d83 100644 --- a/examples/ophys_session.json +++ b/examples/ophys_session.json @@ -1,6 +1,6 @@ { "describedBy": "https://raw.githubusercontent.com/AllenNeuralDynamics/aind-data-schema/main/src/aind_data_schema/core/session.py", - "schema_version": "1.0.3", + "schema_version": "1.1.1", "protocol_id": [], "experimenter_full_name": [ "John Doe" @@ -57,15 +57,13 @@ "patch_cord_name": "Patch Cord A", "patch_cord_output_power": "40", "output_power_unit": "microwatt", - "fiber_name": "Fiber A", - "channels": null + "fiber_name": "Fiber A" }, { "patch_cord_name": "Patch Cord B", "patch_cord_output_power": "43", "output_power_unit": "microwatt", - "fiber_name": "Fiber B", - "channels": null + "fiber_name": "Fiber B" } ], "fiber_modules": [],