From a1ae933c0adeddce610719fe45994a862b157b3d Mon Sep 17 00:00:00 2001
From: David Rotermund <54365609+davrot@users.noreply.github.com>
Date: Tue, 27 Feb 2024 21:55:27 +0100
Subject: [PATCH] Add files via upload

---
 new_pipeline/config.json        | 8 +++++---
 new_pipeline/stage_4_process.py | 7 ++++---
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/new_pipeline/config.json b/new_pipeline/config.json
index bc41ec3..5c13528 100644
--- a/new_pipeline/config.json
+++ b/new_pipeline/config.json
@@ -1,7 +1,7 @@
 {
     "basic_path": "/data_1/robert",
-    "recoding_data": "2020-12-08",
-    "mouse_identifier": "M3399M",
+    "recoding_data": "2021-10-05",
+    "mouse_identifier": "M3879M",
     "raw_path": "raw",
     "export_path": "output",
     "ref_image_path": "ref_images",
@@ -20,12 +20,14 @@
     ],
     // binning
     "binning_enable": true,
-    "binning_at_the_end": false,
+    "binning_at_the_end": true,
     "binning_kernel_size": 4,
     "binning_stride": 4,
     "binning_divisor_override": 1,
     // alignment
     "alignment_batch_size": 200,
+    "rotation_stabilization_threshold_factor": 3.0, // >= 1.0
+    "rotation_stabilization_threshold_border": 0.9, // <= 1.0
     // Heart beat detection
     "lower_freqency_bandpass": 5.0, // Hz
     "upper_freqency_bandpass": 14.0, // Hz
diff --git a/new_pipeline/stage_4_process.py b/new_pipeline/stage_4_process.py
index 14045ff..d8b31a3 100644
--- a/new_pipeline/stage_4_process.py
+++ b/new_pipeline/stage_4_process.py
@@ -1,6 +1,5 @@
-# TODO: Problem 1: Rotation over time instable
-# TODO: Problem 2: I am only processing trials with one part
-# The latter on is no real problem. I just need an example...
+# TODO: I am only processing trials with one part
+# The latter one is no real problem. I just need an example...
 
 import numpy as np
 import torch
@@ -432,6 +431,7 @@ def process_trial(
         image_alignment=image_alignment,
         batch_size=config["alignment_batch_size"],
         fill_value=-100.0,
+        config=config,
     )
 
     mylogger.info(
@@ -468,6 +468,7 @@ def process_trial(
         image_alignment=image_alignment,
         batch_size=config["alignment_batch_size"],
         fill_value=-100.0,
+        config=config,
     )
 
     mylogger.info(