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(