Merge pull request #201 from AllenNeuralDynamics/release-v0.20.0

Release v0.20.0

docs/source/conf.py

@@ -2,9 +2,10 @@
 #
 # For the full list of built-in configuration values, see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
-from pathlib import Path
 from datetime import date
 from os.path import abspath, dirname
+from pathlib import Path
+
 from aind_metadata_mapper import __version__ as package_version
 
 INSTITUTE_NAME = "Allen Institute for Neural Dynamics"

pyproject.toml

@@ -61,6 +61,10 @@ mesoscope = [
     "aind-metadata-mapper[bergamo]",
     "pillow >= 10.4.0",
     "tifffile==2024.2.12 ; python_version >= '3.9'",
+    "numpy >= 1.26.4",
+    "h5py >= 3.11.0",
+    "scipy >= 1.11.0",
+    "pandas >= 2.2.2",
 ]
 
 openephys = [

src/aind_metadata_mapper/__init__.py

@@ -1,3 +1,3 @@
 """Init package"""
 
-__version__ = "0.19.0"
+__version__ = "0.20.0"

src/aind_metadata_mapper/bruker/models.py

@@ -1,4 +1,5 @@
 """Module defining JobSettings for Bruker ETL"""
+
 from pathlib import Path
 from typing import List, Literal, Optional, Union
 

src/aind_metadata_mapper/bruker/session.py

@@ -1,4 +1,5 @@
 """Sets up the MRI ingest ETL"""
+
 import argparse
 import json
 import logging

src/aind_metadata_mapper/gather_metadata.py

@@ -174,7 +174,11 @@ def get_funding_info(domain: str, url_path: str, project_name: str):
                 funding_info = []
             investigators = set()
             for f in funding_info:
-                project_fundees = f.get("fundee", "").split(",")
+                project_fundees = (
+                    ""
+                    if f.get("fundee", None) is None
+                    else f.get("fundee", "").split(",")
+                )
                 pid_names = [
                     PIDName(name=p.strip()).model_dump_json()
                     for p in project_fundees

src/aind_metadata_mapper/mesoscope/data_description.py

@@ -0,0 +1,23 @@
+""" example data description """
+
+from datetime import datetime, timezone
+
+from aind_data_schema.core.data_description import Funding, RawDataDescription
+from aind_data_schema_models.modalities import Modality
+from aind_data_schema_models.organizations import Organization
+from aind_data_schema_models.pid_names import PIDName
+from aind_data_schema_models.platforms import Platform
+
+d = RawDataDescription(
+    modality=[Modality.POPHYS, Modality.BEHAVIOR_VIDEOS, Modality.BEHAVIOR],
+    platform=Platform.MULTIPLANE_OPHYS,
+    subject_id="12345",
+    creation_time=datetime(2022, 2, 21, 16, 30, 1, tzinfo=timezone.utc),
+    institution=Organization.AIND,
+    investigators=[PIDName(name="Jane Smith")],
+    funding_source=[Funding(funder=Organization.AI)],
+)
+
+serialized = d.model_dump_json()
+deserialized = RawDataDescription.model_validate_json(serialized)
+deserialized.write_standard_file()

src/aind_metadata_mapper/mesoscope/models.py

@@ -2,29 +2,57 @@
 
 from datetime import datetime
 from pathlib import Path
-from typing import List, Literal, Union
+from typing import List, Literal, Optional
 
-from pydantic import Field
+from pydantic import Field, field_validator
 
 from aind_metadata_mapper.core_models import BaseJobSettings
 
 
 class JobSettings(BaseJobSettings):
     """Data to be entered by the user."""
 
-    job_settings_name: Literal["Mesoscope"] = "Mesoscope"
-    # TODO: Can probably put this as part of input_source
-    behavior_source: Union[Path, str]
-    session_start_time: datetime
-    session_end_time: datetime
-    subject_id: str
-    project: str
-    iacuc_protocol: str = "2115"
-    magnification: str = "16x"
-    fov_coordinate_ml: float = 1.5
-    fov_coordinate_ap: float = 1.5
-    fov_reference: str = "Bregma"
+    job_settings_name: Literal["Mesoscope"] = Field(
+        default="Mesoscope", title="Name of the job settings"
+    )
+    input_source: Path = Field(..., title="Path to the input source")
+    session_id: str = Field(..., title="ID of the session")
+    behavior_source: Path = Field(..., title="Path to the behavior source")
+    make_camsitm_dir: bool = Field(
+        default=False, title="Make camsitm directory"
+    )
+    output_directory: Path = Field(..., title="Path to the output directory")
+    session_start_time: datetime = Field(
+        ..., title="Start time of the session"
+    )
+    session_end_time: datetime = Field(..., title="End time of the session")
+    subject_id: str = Field(..., title="ID of the subject")
+    project: str = Field(..., title="Name of the project")
+    iacuc_protocol: str = Field(default="2115", title="IACUC protocol number")
+    magnification: str = Field(default="16x", title="Magnification")
+    fov_coordinate_ml: float = Field(
+        default=1.5, title="Coordinate in ML direction"
+    )
+    fov_coordinate_ap: float = Field(
+        default=1.5, title="Coordinate in AL direction"
+    )
+    fov_reference: str = Field(
+        default="Bregma", title="Reference point for the FOV"
+    )
     experimenter_full_name: List[str] = Field(
-        ..., title="Full name of the experimenter"
+        title="Full name of the experimenter"
+    )
+    mouse_platform_name: str = Field(
+        default="disc", title="Name of the mouse platform"
     )
-    mouse_platform_name: str = "disc"
+    optional_output: Optional[Path] = Field(
+        default=None, title="Optional output path"
+    )
+
+    @field_validator("input_source", "behavior_source", "output_directory")
+    @classmethod
+    def validate_path_is_dir(cls, v):
+        """Validate that the input source is a directory"""
+        if not v.is_dir():
+            raise ValueError(f"{v} is not a directory")
+        return v