From 17bf2410c9a809b61ace0f146c12f7a28cba826d Mon Sep 17 00:00:00 2001
From: Kat Schelonka <kschelon@gmail.com>
Date: Fri, 28 Feb 2020 15:14:22 -0800
Subject: [PATCH] GH #900: Compute display lag

Previously the BehaviorOphysLimsApi did not compute
monitor delay, but added a default value of 0.351.
This updates the default to 0.215, which is the
average of monitor delay for a large number of recent
datasets.

Additionally use the OphysTimeAligner methods to
compute the display lag, which is used in the
OphysTimeSync job to produce corrected timestamps
in the LIMS pipeline.
---
 allensdk/internal/api/behavior_ophys_api.py      | 7 +++++--
 allensdk/internal/brain_observatory/time_sync.py | 2 +-
 2 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/allensdk/internal/api/behavior_ophys_api.py b/allensdk/internal/api/behavior_ophys_api.py
index 53bbd5fbd..268073bc9 100644
--- a/allensdk/internal/api/behavior_ophys_api.py
+++ b/allensdk/internal/api/behavior_ophys_api.py
@@ -10,6 +10,7 @@
 from allensdk.internal.api.ophys_lims_api import OphysLimsApi
 from allensdk.brain_observatory.behavior.sync import (
     get_sync_data, get_stimulus_rebase_function, frame_time_offset)
+from allensdk.internal.brain_observatory.time_sync import OphysTimeAligner
 from allensdk.brain_observatory.behavior.stimulus_processing import get_stimulus_presentations, get_stimulus_templates, get_stimulus_metadata
 from allensdk.brain_observatory.behavior.metadata_processing import get_task_parameters
 from allensdk.brain_observatory.behavior.running_processing import get_running_df
@@ -38,8 +39,10 @@ def get_sync_data(self):
 
     @memoize
     def get_stimulus_timestamps(self):
-        monitor_delay = .0351
-        return self.get_sync_data()['stimulus_times_no_delay'] + monitor_delay
+        sync_path = self.get_sync_file()
+        timestamps, _, _ = (OphysTimeAligner(sync_file=sync_path)
+                            .corrected_stim_timestamps)
+        return timestamps
 
     @memoize
     def get_ophys_timestamps(self):
diff --git a/allensdk/internal/brain_observatory/time_sync.py b/allensdk/internal/brain_observatory/time_sync.py
index d7aa449b6..3133fb3e8 100644
--- a/allensdk/internal/brain_observatory/time_sync.py
+++ b/allensdk/internal/brain_observatory/time_sync.py
@@ -15,7 +15,7 @@
 REG_PHOTODIODE_MAX = 2.1 # seconds
 PHOTODIODE_ANOMALY_THRESHOLD = 0.5 # seconds
 LONG_STIM_THRESHOLD = 0.2 # seconds
-ASSUMED_DELAY = 0.0351 # seconds
+ASSUMED_DELAY = 0.0215 # seconds
 MAX_MONITOR_DELAY = 0.07 # seconds
 
 VERSION_1_KEYS = {