feat(mesoscope): add native schema v2 mapping

README.md

@@ -205,3 +205,4 @@ acquisition.write_standard_file(output_directory=job_settings.output_directory,
 #### Individual mappers
 
 [FIP (Fiber photometry)](src/aind_metadata_mapper/fip/README.md)
+[Mesoscope](src/aind_metadata_mapper/mesoscope/README.md)

docs/source/aind_metadata_mapper.mesoscope.rst

@@ -4,18 +4,10 @@ aind\_metadata\_mapper.mesoscope package
 Submodules
 ----------
 
-aind\_metadata\_mapper.mesoscope.models module
+aind\_metadata\_mapper.mesoscope.mapper module
 ----------------------------------------------
 
-.. automodule:: aind_metadata_mapper.mesoscope.models
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-aind\_metadata\_mapper.mesoscope.session module
------------------------------------------------
-
-.. automodule:: aind_metadata_mapper.mesoscope.session
+.. automodule:: aind_metadata_mapper.mesoscope.mapper
    :members:
    :undoc-members:
    :show-inheritance:

src/aind_metadata_mapper/mapper_registry.py

@@ -4,7 +4,9 @@
 """
 
 from aind_metadata_mapper.fip.mapper import FIPMapper
+from aind_metadata_mapper.mesoscope.mapper import MesoscopeMapper
 
 registry = {
     "fip": FIPMapper,
+    "mesoscope": MesoscopeMapper,
 }

src/aind_metadata_mapper/mesoscope/README.md

@@ -0,0 +1,62 @@
+# Mesoscope mapper
+
+This mapper transforms extractor-produced `mesoscope.json` into
+`acquisition_mesoscope.json` for `GatherMetadataJob`.
+
+## Input contract
+
+The mapper consumes the `aind-metadata-extractor` `MesoscopeExtractModel`,
+including `tiff_header`, `session_metadata`, `camstim_epchs`,
+`camstim_session_type`, and `job_settings`.
+
+`job_settings.instrument_id` is required. Preparation should populate this
+field from the raw `rig.json` `rig_id` when that full instrument identifier is
+available. The session or platform alias such as `MESO.2` must not be promoted
+to `Acquisition.instrument_id`.
+
+## Current mapping
+
+The mapper emits one `ImagingConfig` for the mesoscope stream. It uses the
+explicit `job_settings.instrument_id` value for `Acquisition.instrument_id` and
+preserves the platform or session alias such as `MESO.2` for
+`ImagingConfig.device_name`, matching current production upgrade outputs.
+
+Plane power preserves the legacy percent values. Calculated milliwatt values
+are not mapped.
+
+Naive timestamps are interpreted in `America/Los_Angeles`, while aware timestamps
+are preserved. Acquisition bounds span the recorded stream and stimulus epochs
+without altering their individual timestamps.
+
+The mapper writes the acquisition coordinate system through the
+`coordinate_system` field so that it remains compatible with the declared
+`aind-data-schema>=2.7.1,<3` dependency floor. Version 2.7.1 does not expose
+`global_coordinate_system`.
+
+Behavior, Eye, and Face camera names are normalized to upgrader-style assembly
+names such as `Behavior camera assembly`.
+
+Missing `stimulus_modalities` are normalized to `Visual`, and omitted
+visual-stimulation parameter defaults (`stimulus_type` and `notes`) are filled
+from the historical mesoscope Camstim producer contract. This keeps native
+mapper output aligned with legacy and upgraded production metadata without
+overwriting any values that are already supplied by extraction.
+
+## Inherited limits
+
+The nested `Unknown Detector`, `Laser`, and `Ophys Channel` values are
+deliberate scientific compatibility defaults inherited from the legacy mapper
+and upgrader outputs. Detector and channel-index inference are not included.
+
+## Sources
+
+The implementation follows these sources:
+
+- Legacy mapper:
+  `v0.29.3:src/aind_metadata_mapper/mesoscope/session.py`
+- Legacy Camstim producer contract:
+  `v0.29.3:src/aind_metadata_mapper/stimulus/camstim.py`
+- Released upgrader precedent:
+  `v0.17.12:src/aind_metadata_upgrader/session/v1v2.py`
+- Extractor contract:
+  `aind_metadata_extractor/models/mesoscope.py`

src/aind_metadata_mapper/mesoscope/__init__.py

@@ -0,0 +1,5 @@
+"""Mesoscope mapper module."""
+
+from aind_metadata_mapper.mesoscope.mapper import MesoscopeMapper
+
+__all__ = ["MesoscopeMapper"]