Np24: micromanipulator coordinate input

CHANGELOG.md

@@ -1,6 +1,10 @@
 Changelog
 =========
 
+UNRELEASED
+------
+* added: Neuropixel coordinate registration tool for NP2.4
+
 8.30.0
 ------
 * added: Online Plots are stored as PNG and added to Alyx as a Session Note

iblrig/ephys.py

@@ -1,12 +1,13 @@
 import argparse
-import string
 
 import numpy as np
 
 from iblatlas import atlas
+from ibllib.ephys.spikes import create_insertion
 from iblrig.base_tasks import EmptySession
 from iblrig.transfer_experiments import EphysCopier
 from iblutil.util import setup_logger
+from one.webclient import no_cache as no_cache_context
 
 
 def prepare_ephys_session_cmd():
@@ -37,7 +38,7 @@ def prepare_ephys_session(subject_name: str, nprobes: int = 2):
     copier.initialize_experiment(nprobes=nprobes)
 
 
-def neuropixel24_micromanipulator_coordinates(ref_shank, pname, ba=None, shank_spacings_um=(0, 200, 400, 600)):
+def neuropixel24_micromanipulator_coordinates(ref_shank, pname, ba=None, shank_spacings_um=(0, 200, 400, 600), pivot_shank='a'):
     """
     Provide the micro-manipulator coordinates of the first shank.
 
@@ -50,13 +51,22 @@ def neuropixel24_micromanipulator_coordinates(ref_shank, pname, ba=None, shank_s
     :param shank_spacings_um: list of shank spacings in micrometers
     :return:
     """
-    # this only works if the roll is 0, ie. the probe is facing upwards
-    assert ref_shank['roll'] == 0
+    ref_shank['roll'] = 0  # this is a constant and has no nmeaning for 4 shanks probes
+    if pivot_shank == 'd':
+        shank_letters = 'dcba'
+        spacing_sign = -1
+    elif pivot_shank == 'a':
+        shank_letters = 'abcd'
+        spacing_sign = 1
+    else:
+        raise ValueError("reference_shank parameter should be either 'a' or 'd'")
+
     ba = atlas.NeedlesAtlas() if ba is None else ba
     trajectories = {}
     for i, d in enumerate(shank_spacings_um):
-        x = ref_shank['x'] + np.sin(ref_shank['phi'] / 180 * np.pi) * d
-        y = ref_shank['y'] - np.cos(ref_shank['phi'] / 180 * np.pi) * d
+        spacing_multiplier = d * spacing_sign  # flip the direction if reference_shank is 'd'
+        x = ref_shank['x'] + np.sin(ref_shank['phi'] / 180 * np.pi) * spacing_multiplier
+        y = ref_shank['y'] - np.cos(ref_shank['phi'] / 180 * np.pi) * spacing_multiplier
         shank = {
             'x': x,
             'y': y,
@@ -72,5 +82,31 @@ def neuropixel24_micromanipulator_coordinates(ref_shank, pname, ba=None, shank_s
             xyz_ref = xyz_entry
         shank['z'] = xyz_entry[2] * 1e6
         shank['depth'] = ref_shank['depth'] + (xyz_entry[2] - xyz_ref[2]) * 1e6
-        trajectories[f'{pname}{string.ascii_lowercase[i]}'] = shank
+        trajectories[f'{pname}{shank_letters[i]}'] = shank
     return trajectories
+
+
+def register_micromanipulator_coordinates(alyx=None, trajectories=None, eid=None, metadata=None):
+    assert alyx is not None, 'An alyx client is required to register/create micromanipulator coordinates'
+    assert eid is not None, 'An session ID is required to register/create micromanipulator coordinates'
+    # if we do not have access to the fileName or any of the metadata, it will be patched later
+    metadata = {'neuropixelVersion': 'NP2.4', 'fileName': None, 'serial': -1} if metadata is None else metadata
+    rest_trajectories = {}
+    rest_insertions = {}
+    with no_cache_context(alyx):
+        traj_extra = {}
+        for pname, traj in trajectories.items():
+            _, rest_insertions[pname] = create_insertion(alyx, metadata, pname, eid=eid)
+            pid = rest_insertions[pname]['id']
+            traj_extra['probe_insertion'] = pid
+            traj_extra['chronic_insertion'] = None
+            traj_extra['provenance'] = 'Micro-manipulator'
+            traj_extra['coordinate_system'] = 'Needles-Allen'
+            rest_trajectory = alyx.rest('trajectories', 'list', probe_insertion=pid, provenance='Micro-manipulator')
+            if len(rest_trajectory) == 0:
+                rest_trajectories[pname] = alyx.rest('trajectories', 'create', data=traj | traj_extra)
+            else:
+                rest_trajectories[pname] = alyx.rest(
+                    'trajectories', 'update', id=rest_trajectory[0]['id'], data=traj | traj_extra
+                )
+    return rest_insertions, rest_trajectories