Merge pull request #1 from kushalbakshi/tutorial-fix

Updates to the tutorial and devcontainer

.devcontainer/Dockerfile

@@ -42,7 +42,7 @@ ENV DJ_HOST fakeservices.datajoint.io
 ENV DJ_USER root
 ENV DJ_PASS simple
 
-ENV DATA_MOUNTPOINT /workspaces/element-electrode-localization/example_data
+ENV EPHYS_ROOT_DATA_DIR /workspaces/element-electrode-localization/example_data
 ENV DATABASE_PREFIX neuro_
 
 USER vscode

.devcontainer/devcontainer.json

@@ -6,8 +6,8 @@
 	"remoteEnv": {
 		"LOCAL_WORKSPACE_FOLDER": "${localWorkspaceFolder}"
 	},
-	"onCreateCommand": "mkdir -p ${DATA_MOUNTPOINT} && pip install -e .",
-	"postStartCommand": "docker volume prune -f ",
+	"onCreateCommand": "mkdir -p ${EPHYS_ROOT_DATA_DIR} && pip install -e .",
+	"postStartCommand": "docker volume prune -f && s3fs ${DJ_PUBLIC_S3_LOCATION} ${EPHYS_ROOT_DATA_DIR} -o nonempty,multipart_size=530,endpoint=us-east-1,url=http://s3.amazonaws.com,public_bucket=1",
 	"hostRequirements": {
 		"cpus": 4,
 		"memory": "8gb",

.devcontainer/docker-compose.yaml

@@ -8,6 +8,8 @@ services:
       dockerfile: ./.devcontainer/Dockerfile
     extra_hosts:
       - fakeservices.datajoint.io:127.0.0.1
+    environment:
+      - DJ_PUBLIC_S3_LOCATION=djhub.vathes.datapub.elements:/workflow-array-ephys-benchmark/v2
     devices:
       - /dev/fuse
     cap_add:

.gitignore

@@ -73,6 +73,9 @@ dj_local_c*.json
 temp*
 *nwb
 
-#mkdocs documentation
+# mkdocs documentation
 site
 docs/src/tutorials/*ipynb
+
+# Codespaces
+example_data/*

element_electrode_localization/version.py

@@ -1,2 +1,3 @@
 """Package metadata."""
+
 __version__ = "0.2.0"

notebooks/tutorial_pipeline.py

@@ -3,6 +3,7 @@
 import datajoint as dj
 from element_animal import subject
 from element_animal.subject import Subject
+from element_interface.utils import find_full_path
 from element_array_ephys import probe, ephys_acute as ephys
 from element_lab import lab
 from element_lab.lab import Lab, Location, Project, Protocol, Source, User
@@ -20,12 +21,27 @@
     "DATABASE_PREFIX", dj.config["custom"].get("database.prefix", "")
 )
 
-if "custom" not in dj.config:
-    dj.config["custom"] = {}
+dj.config["custom"]["ephys_root_data_dir"] = os.getenv(
+    "EPHYS_ROOT_DATA_DIR", dj.config["custom"].get("ephys_root_data_dir", "")
+)
 
 db_prefix = dj.config["custom"].get("database.prefix", "")
 
 
+# Declare functions for retrieving data
+def get_ephys_root_data_dir():
+    """Retrieve ephys root data directory."""
+    ephys_root_dirs = dj.config.get("custom", {}).get("ephys_root_data_dir", None)
+    if not ephys_root_dirs:
+        return None
+    elif isinstance(ephys_root_dirs, (str, pathlib.Path)):
+        return [ephys_root_dirs]
+    elif isinstance(ephys_root_dirs, list):
+        return ephys_root_dirs
+    else:
+        raise TypeError("`ephys_root_data_dir` must be a string, pathlib, or list")
+
+
 @lab.schema
 class SkullReference(dj.Lookup):
     definition = """
@@ -44,8 +60,29 @@ class SkullReference(dj.Lookup):
 
 ephys.activate(db_prefix + "ephys", db_prefix + "probe", linking_module=__name__)
 ProbeInsertion = ephys.ProbeInsertion
+
 electrode_localization.activate(
-    db_prefix + "electrode_localization",
-    db_prefix + "coordinate_framework",
-    linking_module=__name__,
+    db_prefix + "electrode_localization", db_prefix + "ccf", linking_module=__name__
 )
+
+ccf_id = 0  # Atlas ID
+voxel_resolution = 100
+
+nrrd_filepath = find_full_path(
+    get_ephys_root_data_dir(), f"annotation_{voxel_resolution}.nrrd"
+)
+ontology_csv_filepath = find_full_path(get_ephys_root_data_dir(), "query.csv")
+
+
+if (
+    not (coordinate_framework.CCF & {"ccf_id": ccf_id})
+    and nrrd_filepath.exists()
+    and ontology_csv_filepath.exists()
+):
+    coordinate_framework.load_ccf_annotation(
+        ccf_id=ccf_id,
+        version_name="ccf_2017",
+        voxel_resolution=voxel_resolution,
+        nrrd_filepath=nrrd_filepath,
+        ontology_csv_filepath=ontology_csv_filepath,
+    )