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David Rotermund 2024-02-27 21:55:27 +01:00 committed by GitHub
parent aafa3a3783
commit a1ae933c0a
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2 changed files with 9 additions and 6 deletions
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8
new_pipeline/config.json
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@ -1,7 +1,7 @@
{ {
"basic_path": "/data_1/robert", "basic_path": "/data_1/robert",
"recoding_data": "2020-12-08", "recoding_data": "2021-10-05",
"mouse_identifier": "M3399M", "mouse_identifier": "M3879M",
"raw_path": "raw", "raw_path": "raw",
"export_path": "output", "export_path": "output",
"ref_image_path": "ref_images", "ref_image_path": "ref_images",
@ -20,12 +20,14 @@
], ],
// binning // binning
"binning_enable": true, "binning_enable": true,
"binning_at_the_end": false, "binning_at_the_end": true,
"binning_kernel_size": 4, "binning_kernel_size": 4,
"binning_stride": 4, "binning_stride": 4,
"binning_divisor_override": 1, "binning_divisor_override": 1,
// alignment // alignment
"alignment_batch_size": 200, "alignment_batch_size": 200,
"rotation_stabilization_threshold_factor": 3.0, // >= 1.0
"rotation_stabilization_threshold_border": 0.9, // <= 1.0
// Heart beat detection // Heart beat detection
"lower_freqency_bandpass": 5.0, // Hz "lower_freqency_bandpass": 5.0, // Hz
"upper_freqency_bandpass": 14.0, // Hz "upper_freqency_bandpass": 14.0, // Hz

7
new_pipeline/stage_4_process.py
View file

@ -1,6 +1,5 @@
# TODO: Problem 1: Rotation over time instable # TODO: I am only processing trials with one part
# TODO: Problem 2: I am only processing trials with one part # The latter one is no real problem. I just need an example...
# The latter on is no real problem. I just need an example...
import numpy as np import numpy as np
import torch import torch
@ -432,6 +431,7 @@ def process_trial(
image_alignment=image_alignment, image_alignment=image_alignment,
batch_size=config["alignment_batch_size"], batch_size=config["alignment_batch_size"],
fill_value=-100.0, fill_value=-100.0,
config=config,
) )
mylogger.info( mylogger.info(
@ -468,6 +468,7 @@ def process_trial(
image_alignment=image_alignment, image_alignment=image_alignment,
batch_size=config["alignment_batch_size"], batch_size=config["alignment_batch_size"],
fill_value=-100.0, fill_value=-100.0,
config=config,
) )
mylogger.info( mylogger.info(