will delete the unwanted files

build_pipeline.py

@@ -7,8 +7,7 @@
 import element_interface
 
 dj.config['database.host'] = 'database.eflab.org:3306'
-dj.config['database.username'] = 'maria'
-dj.config['database.password'] = 'Spike@Thr200'
+
 
 experiment_dir = '/mnt/lab/data01/OpenEphys'
 db_prefix = 'lab_npx_'

element_array_ephys/ephys.py

@@ -413,10 +413,12 @@ def make(self, key):
                 for channel_idx, channel_info in channel2electrode_map.items()
             ]
         elif acq_software == "Open Ephys":
-            #print(session_dir)
+            print("Hey Im Here!!")
+            print(session_dir)
             dataset = openephys.OpenEphys(session_dir)
-            #print(dataset.probes.items())
+            print(dataset.probes.items())
             for serial_number, probe_data in dataset.probes.items():
+                print(f"Serial Number is {str(serial_number)} while inserted probeserial is: {inserted_probe_serial_number}")
                 if str(serial_number) == inserted_probe_serial_number:
                     break
             else:

populate_ephys.py

@@ -0,0 +1,103 @@
+## Imports
+import matplotlib.pyplot as plt
+import numpy as np
+import pandas as pd
+from pathlib import Path
+import os
+# import numcodecs
+import datajoint as dj
+
+## Database specifics
+experiment_dir = '/mnt/lab/data01/OpenEphys'
+db_prefix = 'lab_npx_'
+
+dj.config['database.host'] = 'database.eflab.org:3306'
+dj.config["enable_python_native_blobs"] = True
+dj.config['custom'] = {'database_prefix': db_prefix,'ephys_root_data_dir': experiment_dir}
+
+
+from build_pipeline import Subject, Session, Recording, probe, ephys, ephys_report
+
+def get_key():
+    while True:
+        # Get user inputs
+        animal_id = input("Enter animal_id: ").strip()
+        session = input("Enter session: ").strip()
+        insertion_number = input("Enter insertion number: ").strip()
+
+        # Print and confirm
+        print("\nYou entered:")
+        print(f"  animal_id     : {animal_id}")
+        print(f"  session       : {session}")
+        print(f"  insertion number       : {insertion_number}")
+        confirm = input("Are these the correct inputs? (yes/no): ").strip().lower()
+
+
+        # safety check to confirm the inputs 
+        if confirm == "yes":
+            break
+        else:
+            print("Let's try again...\n")
+
+        # Pick Probe
+        print("\nNow let's choose a probe:")
+        print(probe.Probe())
+        probes = probe.Probe.fetch(format="frame")
+        print(probes)
+        probe_idx = input("pick the index of your choice")
+        print(probe.iloc(3))
+
+    key = {'animal_id' : int(animal_id), 'session': int(session), 'insertion_number' : int(insertion_number)}
+    print(f'processing key: {key}')
+    return key , probe_idx
+
+
+def populate_ephys(key,probe_idx):
+    ''' 
+    A function that correctly checks and populates the Ephys schema with all its subsequent tables.
+    '''
+
+
+# TODO choose a different probe when they exist
+    ephys.ProbeInsertion.insert1(
+    dict(
+        key,
+        probe=(probe.Probe()).fetch('probe')[probe_idx],
+        ), skip_duplicates=True
+    )
+
+    ephys.EphysRecording().populate(key, display_progress=True)
+
+
+
+    key['paramset_idx']=3
+    file_path = (ephys.EphysRecording.EphysFile() & key).fetch('file_path')
+    ks_path = file_path[0]+'/kilosort4/sorter_output'
+    ephys.ClusteringTask.insert1(
+        dict(
+            key,
+            task_mode="load",  # load or trigger
+            clustering_output_dir=ks_path,
+        ), skip_duplicates=True
+    )
+
+    ephys.Clustering.populate(key, display_progress=True)
+    ephys.CuratedClustering.populate(key, display_progress=True)
+    ephys.QualityMetrics.populate(key, display_progress=True)
+
+
+
+
+def main():
+    key = get_key()
+    print(f"Populating the Ephys schema for key:\n {key} ... ")
+    populate_ephys(key)
+
+
+if __name__ == "__main__":
+    main()
+
+
+
+
+