From 4e5e3d3c01974a196bc56a97cd9326dd64385ce0 Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabilar@datajoint.com>
Date: Tue, 8 Aug 2023 14:54:44 -0500
Subject: [PATCH] Revert "Remove pipeline script"

This reverts commit bada53eaf47cd8c2250d764f1638921a349f9f2c.
---
 notebooks/tutorial_pipeline.py | 48 ++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 notebooks/tutorial_pipeline.py

diff --git a/notebooks/tutorial_pipeline.py b/notebooks/tutorial_pipeline.py
new file mode 100644
index 00000000..a31c076b
--- /dev/null
+++ b/notebooks/tutorial_pipeline.py
@@ -0,0 +1,48 @@
+import datajoint as dj
+from element_animal import subject
+from element_animal.subject import Subject
+from element_calcium_imaging import imaging, scan, imaging_report, db_prefix, plotting
+from element_lab import lab
+from element_lab.lab import Lab, Location, Project, Protocol, Source, User
+from element_lab.lab import Device as Equipment
+from element_lab.lab import User as Experimenter
+from element_session import session_with_datetime as session
+from element_session.session_with_datetime import Session
+import element_interface
+import pathlib
+
+
+# Declare functions for retrieving data
+def get_imaging_root_data_dir():
+    """Retrieve imaging root data directory."""
+    imaging_root_dirs = dj.config.get("custom", {}).get("imaging_root_data_dir", None)
+    if not imaging_root_dirs:
+        return None
+    elif isinstance(imaging_root_dirs, (str, pathlib.Path)):
+        return [imaging_root_dirs]
+    elif isinstance(imaging_root_dirs, list):
+        return imaging_root_dirs
+    else:
+        raise TypeError("`imaging_root_data_dir` must be a string, pathlib, or list")
+
+
+def get_image_files(scan_key, file_type: str):
+    """Retrieve the list of absolute paths associated with a given Scan."""
+    # Folder structure: root / subject / session / .tif or .sbx or .nd2
+    session_dir = element_interface.utils.find_full_path(
+        get_imaging_root_data_dir(),
+        (session.SessionDirectory & scan_key).fetch1("session_dir"),
+    )
+
+    filepaths = [fp.as_posix() for fp in session_dir.glob(file_type)]
+
+    if not filepaths:
+        raise FileNotFoundError(f"No {file_type} file found in {session_dir}")
+    return filepaths
+
+
+# Activate schemas
+lab.activate(db_prefix + "lab")
+subject.activate(db_prefix + "subject", linking_module=__name__)
+session.activate(db_prefix + "session", linking_module=__name__)
+imaging.activate(db_prefix + "imaging", db_prefix + "scan", linking_module=__name__)