中大五院为占位，呼研所已可以正常导出
This commit is contained in:
parent
85f2408f13
commit
40fdda6497
@ -21,7 +21,7 @@ todo: 使用mask 屏蔽无用区间
|
||||
"""
|
||||
|
||||
from pathlib import Path
|
||||
|
||||
import shutil
|
||||
import draw_tools
|
||||
import utils
|
||||
import numpy as np
|
||||
@ -30,7 +30,7 @@ import os
|
||||
from matplotlib import pyplot as plt
|
||||
os.environ['DISPLAY'] = "localhost:10.0"
|
||||
|
||||
def process_one_signal(samp_id):
|
||||
def process_one_signal(samp_id, show=False):
|
||||
signal_path = list((org_signal_root_path / f"{samp_id}").glob("OrgBCG_Sync_*.txt"))
|
||||
if not signal_path:
|
||||
raise FileNotFoundError(f"OrgBCG_Sync file not found for sample ID: {samp_id}")
|
||||
@ -43,6 +43,10 @@ def process_one_signal(samp_id):
|
||||
label_path = list(label_path)[0]
|
||||
print(f"Processing Label_corrected file: {label_path}")
|
||||
|
||||
# 保存处理后的数据和标签
|
||||
save_samp_path = save_path / f"{samp_id}"
|
||||
save_samp_path.mkdir(parents=True, exist_ok=True)
|
||||
|
||||
signal_data_raw = utils.read_signal_txt(signal_path)
|
||||
signal_length = len(signal_data_raw)
|
||||
print(f"signal_length: {signal_length}")
|
||||
@ -137,7 +141,8 @@ def process_one_signal(samp_id):
|
||||
movement_mask=resp_movement_mask,
|
||||
movement_list=resp_movement_position_list,
|
||||
sampling_rate=resp_fs,
|
||||
**resp_movement_revise_conf
|
||||
**resp_movement_revise_conf,
|
||||
verbose=False
|
||||
)
|
||||
print(f"After revise, resp_movement_mask_shape: {resp_movement_mask.shape}, num_movement: {np.sum(resp_movement_mask == 1)}, count_movement_positions: {len(resp_movement_position_list)}")
|
||||
else:
|
||||
@ -152,7 +157,8 @@ def process_one_signal(samp_id):
|
||||
movement_mask=resp_movement_mask,
|
||||
movement_list=resp_movement_position_list,
|
||||
sampling_rate=resp_fs,
|
||||
**resp_amp_change_conf)
|
||||
**resp_amp_change_conf,
|
||||
verbose=True)
|
||||
print(f"amp_change_mask_shape: {resp_amp_change_mask.shape}, num_amp_change: {np.sum(resp_amp_change_mask == 1)}, count_amp_change_positions: {len(resp_amp_change_list)}")
|
||||
else:
|
||||
resp_amp_change_mask = None
|
||||
@ -202,7 +208,7 @@ def process_one_signal(samp_id):
|
||||
signal_data_raw = utils.downsample_signal_fast(original_signal=signal_data_raw, original_fs=signal_fs, target_fs=100)
|
||||
signal_fs = 100
|
||||
|
||||
draw_tools.draw_signal_with_mask(samp_id=samp_id,
|
||||
draw_tools.draw_signal_with_mask(samp_id=samp_id,
|
||||
signal_data=signal_data,
|
||||
signal_fs=signal_fs,
|
||||
resp_data=resp_data,
|
||||
@ -216,7 +222,35 @@ def process_one_signal(samp_id):
|
||||
resp_sa_mask=event_mask,
|
||||
bcg_low_amp_mask=bcg_low_amp_mask,
|
||||
bcg_movement_mask=bcg_movement_mask,
|
||||
bcg_change_mask=bcg_amp_change_mask)
|
||||
bcg_change_mask=bcg_amp_change_mask,
|
||||
show=show,
|
||||
save_path=save_samp_path / f"{samp_id}_Signal_Plots.png")
|
||||
|
||||
|
||||
|
||||
|
||||
# 复制事件文件 到保存路径
|
||||
sa_label_save_name = f"{samp_id}" + label_path.name
|
||||
shutil.copyfile(label_path, save_samp_path / sa_label_save_name)
|
||||
|
||||
# 新建一个dataframe，分别是秒数、SA标签，SA质量标签，禁用标签，Resp低幅值标签，Resp体动标签，Resp幅值突变标签，Bcg低幅值标签，Bcg体动标签，Bcg幅值突变标签
|
||||
save_dict = {
|
||||
"Second": np.arange(signal_second),
|
||||
"SA_Label": event_mask,
|
||||
"SA_Score": score_mask,
|
||||
"Disable_Label": manual_disable_mask,
|
||||
"Resp_LowAmp_Label": resp_low_amp_mask if resp_low_amp_mask is not None else np.zeros(signal_second, dtype=int),
|
||||
"Resp_Movement_Label": resp_movement_mask if resp_movement_mask is not None else np.zeros(signal_second, dtype=int),
|
||||
"Resp_AmpChange_Label": resp_amp_change_mask if resp_amp_change_mask is not None else np.zeros(signal_second, dtype=int),
|
||||
"Bcg_LowAmp_Label": bcg_low_amp_mask if bcg_low_amp_mask is not None else np.zeros(signal_second, dtype=int),
|
||||
"Bcg_Movement_Label": bcg_movement_mask if bcg_movement_mask is not None else np.zeros(signal_second, dtype=int),
|
||||
"Bcg_AmpChange_Label": bcg_amp_change_mask if bcg_amp_change_mask is not None else np.zeros(signal_second, dtype=int)
|
||||
}
|
||||
|
||||
mask_label_save_name = f"{samp_id}_Processed_Labels.csv"
|
||||
utils.save_process_label(save_path=save_samp_path / mask_label_save_name, save_dict=save_dict)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -229,13 +263,21 @@ if __name__ == '__main__':
|
||||
conf = utils.load_dataset_conf(yaml_path)
|
||||
select_ids = conf["select_ids"]
|
||||
root_path = Path(conf["root_path"])
|
||||
save_path = Path(conf["save_path"])
|
||||
|
||||
print(f"select_ids: {select_ids}")
|
||||
print(f"root_path: {root_path}")
|
||||
print(f"save_path: {save_path}")
|
||||
|
||||
org_signal_root_path = root_path / "OrgBCG_Aligned"
|
||||
label_root_path = root_path / "Label"
|
||||
|
||||
all_samp_disable_df = utils.read_disable_excel(disable_df_path)
|
||||
|
||||
process_one_signal(select_ids[0])
|
||||
process_one_signal(select_ids[9], show=True)
|
||||
|
||||
# for samp_id in select_ids:
|
||||
# print(f"Processing sample ID: {samp_id}")
|
||||
# process_one_signal(samp_id, show=False)
|
||||
# print(f"Finished processing sample ID: {samp_id}\n\n")
|
||||
|
||||
|
||||
277
ZD5Y_process.py
Normal file
277
ZD5Y_process.py
Normal file
@ -0,0 +1,277 @@
|
||||
"""
|
||||
本脚本完成对呼研所数据的处理，包含以下功能：
|
||||
1. 数据读取与预处理
|
||||
从传入路径中，进行数据和标签的读取，并进行初步的预处理
|
||||
预处理包括为数据进行滤波、去噪等操作
|
||||
2. 数据清洗与异常值处理
|
||||
3. 输出清晰后的统计信息
|
||||
4. 数据保存
|
||||
将处理后的数据保存到指定路径，便于后续使用
|
||||
主要是保存切分后的数据位置和标签
|
||||
5. 可视化
|
||||
提供数据处理前后的可视化对比，帮助理解数据变化
|
||||
绘制多条可用性趋势图，展示数据的可用区间、体动区间、低幅值区间等
|
||||
|
||||
todo: 使用mask 屏蔽无用区间
|
||||
|
||||
|
||||
# 低幅值区间规则标定与剔除
|
||||
# 高幅值连续体动规则标定与剔除
|
||||
# 手动标定不可用区间提剔除
|
||||
"""
|
||||
|
||||
from pathlib import Path
|
||||
import shutil
|
||||
import draw_tools
|
||||
import utils
|
||||
import numpy as np
|
||||
import signal_method
|
||||
import os
|
||||
from matplotlib import pyplot as plt
|
||||
os.environ['DISPLAY'] = "localhost:10.0"
|
||||
|
||||
def process_one_signal(samp_id, show=False):
|
||||
signal_path = list((org_signal_root_path / f"{samp_id}").glob("OrgBCG_Sync_*.txt"))
|
||||
if not signal_path:
|
||||
raise FileNotFoundError(f"OrgBCG_Sync file not found for sample ID: {samp_id}")
|
||||
signal_path = signal_path[0]
|
||||
print(f"Processing OrgBCG_Sync signal file: {signal_path}")
|
||||
|
||||
label_path = (label_root_path / f"{samp_id}").glob("SA Label_corrected.csv")
|
||||
if not label_path:
|
||||
raise FileNotFoundError(f"Label_corrected file not found for sample ID: {samp_id}")
|
||||
label_path = list(label_path)[0]
|
||||
print(f"Processing Label_corrected file: {label_path}")
|
||||
|
||||
signal_data_raw = utils.read_signal_txt(signal_path)
|
||||
signal_length = len(signal_data_raw)
|
||||
print(f"signal_length: {signal_length}")
|
||||
signal_fs = int(signal_path.stem.split("_")[-1])
|
||||
print(f"signal_fs: {signal_fs}")
|
||||
signal_second = signal_length // signal_fs
|
||||
print(f"signal_second: {signal_second}")
|
||||
|
||||
# 根据采样率进行截断
|
||||
signal_data_raw = signal_data_raw[:signal_second * signal_fs]
|
||||
|
||||
# 滤波
|
||||
# 50Hz陷波滤波器
|
||||
# signal_data = utils.butterworth(data=signal_data, _type="bandpass", low_cut=0.5, high_cut=45, order=10, sample_rate=signal_fs)
|
||||
print("Applying 50Hz notch filter...")
|
||||
signal_data = utils.notch_filter(data=signal_data_raw, notch_freq=50.0, quality_factor=30.0, sample_rate=signal_fs)
|
||||
|
||||
resp_data_0 = utils.butterworth(data=signal_data, _type="lowpass", low_cut=50, order=10, sample_rate=signal_fs)
|
||||
resp_fs = conf["resp"]["downsample_fs_1"]
|
||||
resp_data_1 = utils.downsample_signal_fast(original_signal=resp_data_0, original_fs=signal_fs, target_fs=resp_fs)
|
||||
resp_data_1 = utils.average_filter(raw_data=resp_data_1, sample_rate=resp_fs, window_size_sec=20)
|
||||
resp_data_2 = utils.butterworth(data=resp_data_1, _type=conf["resp_filter"]["filter_type"],
|
||||
low_cut=conf["resp_filter"]["low_cut"],
|
||||
high_cut=conf["resp_filter"]["high_cut"], order=conf["resp_filter"]["order"],
|
||||
sample_rate=resp_fs)
|
||||
print("Begin plotting signal data...")
|
||||
|
||||
|
||||
# fig = plt.figure(figsize=(12, 8))
|
||||
# # 绘制三个图raw_data、resp_data_1、resp_data_2
|
||||
# ax0 = fig.add_subplot(3, 1, 1)
|
||||
# ax0.plot(np.linspace(0, len(signal_data) // signal_fs, len(signal_data)), signal_data, color='blue')
|
||||
# ax0.set_title('Raw Signal Data')
|
||||
# ax1 = fig.add_subplot(3, 1, 2, sharex=ax0)
|
||||
# ax1.plot(np.linspace(0, len(resp_data_1) // resp_fs, len(resp_data_1)), resp_data_1, color='orange')
|
||||
# ax1.set_title('Resp Data after Average Filtering')
|
||||
# ax2 = fig.add_subplot(3, 1, 3, sharex=ax0)
|
||||
# ax2.plot(np.linspace(0, len(resp_data_1) // resp_fs, len(resp_data_2)), resp_data_2, color='green')
|
||||
# ax2.set_title('Resp Data after Butterworth Filtering')
|
||||
# plt.tight_layout()
|
||||
# plt.show()
|
||||
|
||||
bcg_data = utils.butterworth(data=signal_data, _type=conf["bcg_filter"]["filter_type"],
|
||||
low_cut=conf["bcg_filter"]["low_cut"],
|
||||
high_cut=conf["bcg_filter"]["high_cut"], order=conf["bcg_filter"]["order"],
|
||||
sample_rate=signal_fs)
|
||||
|
||||
# 降采样
|
||||
old_resp_fs = resp_fs
|
||||
resp_fs = conf["resp"]["downsample_fs_2"]
|
||||
resp_data = utils.downsample_signal_fast(original_signal=resp_data_2, original_fs=old_resp_fs, target_fs=resp_fs)
|
||||
bcg_fs = conf["bcg"]["downsample_fs"]
|
||||
bcg_data = utils.downsample_signal_fast(original_signal=bcg_data, original_fs=signal_fs, target_fs=bcg_fs)
|
||||
|
||||
label_data = utils.read_label_csv(path=label_path)
|
||||
event_mask, score_mask = utils.generate_event_mask(signal_second=signal_second, event_df=label_data)
|
||||
|
||||
manual_disable_mask = utils.generate_disable_mask(signal_second=signal_second, disable_df=all_samp_disable_df[
|
||||
all_samp_disable_df["id"] == samp_id])
|
||||
print(f"disable_mask_shape: {manual_disable_mask.shape}, num_disable: {np.sum(manual_disable_mask == 0)}")
|
||||
|
||||
# 分析Resp的低幅值区间
|
||||
resp_low_amp_conf = conf.get("resp_low_amp", None)
|
||||
if resp_low_amp_conf is not None:
|
||||
resp_low_amp_mask, resp_low_amp_position_list = signal_method.detect_low_amplitude_signal(
|
||||
signal_data=resp_data,
|
||||
sampling_rate=resp_fs,
|
||||
**resp_low_amp_conf
|
||||
)
|
||||
print(f"resp_low_amp_mask_shape: {resp_low_amp_mask.shape}, num_low_amp: {np.sum(resp_low_amp_mask == 1)}, count_low_amp_positions: {len(resp_low_amp_position_list)}")
|
||||
else:
|
||||
resp_low_amp_mask, resp_low_amp_position_list = None, None
|
||||
print("resp_low_amp_mask is None")
|
||||
|
||||
# 分析Resp的高幅值伪迹区间
|
||||
resp_movement_conf = conf.get("resp_movement", None)
|
||||
if resp_movement_conf is not None:
|
||||
raw_resp_movement_mask, resp_movement_mask, raw_resp_movement_position_list, resp_movement_position_list = signal_method.detect_movement(
|
||||
signal_data=resp_data,
|
||||
sampling_rate=resp_fs,
|
||||
**resp_movement_conf
|
||||
)
|
||||
print(f"resp_movement_mask_shape: {resp_movement_mask.shape}, num_movement: {np.sum(resp_movement_mask == 1)}, count_movement_positions: {len(resp_movement_position_list)}")
|
||||
else:
|
||||
resp_movement_mask, resp_movement_position_list = None, None
|
||||
print("resp_movement_mask is None")
|
||||
|
||||
resp_movement_revise_conf = conf.get("resp_movement_revise", None)
|
||||
if resp_movement_mask is not None and resp_movement_revise_conf is not None:
|
||||
resp_movement_mask, resp_movement_position_list = signal_method.movement_revise(
|
||||
signal_data=resp_data,
|
||||
movement_mask=resp_movement_mask,
|
||||
movement_list=resp_movement_position_list,
|
||||
sampling_rate=resp_fs,
|
||||
**resp_movement_revise_conf,
|
||||
verbose=False
|
||||
)
|
||||
print(f"After revise, resp_movement_mask_shape: {resp_movement_mask.shape}, num_movement: {np.sum(resp_movement_mask == 1)}, count_movement_positions: {len(resp_movement_position_list)}")
|
||||
else:
|
||||
print("resp_movement_mask revise is skipped")
|
||||
|
||||
|
||||
# 分析Resp的幅值突变区间
|
||||
resp_amp_change_conf = conf.get("resp_amp_change", None)
|
||||
if resp_amp_change_conf is not None and resp_movement_mask is not None:
|
||||
resp_amp_change_mask, resp_amp_change_list = signal_method.position_based_sleep_recognition_v3(
|
||||
signal_data=resp_data,
|
||||
movement_mask=resp_movement_mask,
|
||||
movement_list=resp_movement_position_list,
|
||||
sampling_rate=resp_fs,
|
||||
**resp_amp_change_conf)
|
||||
print(f"amp_change_mask_shape: {resp_amp_change_mask.shape}, num_amp_change: {np.sum(resp_amp_change_mask == 1)}, count_amp_change_positions: {len(resp_amp_change_list)}")
|
||||
else:
|
||||
resp_amp_change_mask = None
|
||||
print("amp_change_mask is None")
|
||||
|
||||
|
||||
|
||||
# 分析Bcg的低幅值区间
|
||||
bcg_low_amp_conf = conf.get("bcg_low_amp", None)
|
||||
if bcg_low_amp_conf is not None:
|
||||
bcg_low_amp_mask, bcg_low_amp_position_list = signal_method.detect_low_amplitude_signal(
|
||||
signal_data=bcg_data,
|
||||
sampling_rate=bcg_fs,
|
||||
**bcg_low_amp_conf
|
||||
)
|
||||
print(f"bcg_low_amp_mask_shape: {bcg_low_amp_mask.shape}, num_low_amp: {np.sum(bcg_low_amp_mask == 1)}, count_low_amp_positions: {len(bcg_low_amp_position_list)}")
|
||||
else:
|
||||
bcg_low_amp_mask, bcg_low_amp_position_list = None, None
|
||||
print("bcg_low_amp_mask is None")
|
||||
# 分析Bcg的高幅值伪迹区间
|
||||
bcg_movement_conf = conf.get("bcg_movement", None)
|
||||
if bcg_movement_conf is not None:
|
||||
raw_bcg_movement_mask, bcg_movement_mask, raw_bcg_movement_position_list, bcg_movement_position_list = signal_method.detect_movement(
|
||||
signal_data=bcg_data,
|
||||
sampling_rate=bcg_fs,
|
||||
**bcg_movement_conf
|
||||
)
|
||||
print(f"bcg_movement_mask_shape: {bcg_movement_mask.shape}, num_movement: {np.sum(bcg_movement_mask == 1)}, count_movement_positions: {len(bcg_movement_position_list)}")
|
||||
else:
|
||||
bcg_movement_mask = None
|
||||
print("bcg_movement_mask is None")
|
||||
# 分析Bcg的幅值突变区间
|
||||
if bcg_movement_mask is not None:
|
||||
bcg_amp_change_mask, bcg_amp_change_list = signal_method.position_based_sleep_recognition_v2(
|
||||
signal_data=bcg_data,
|
||||
movement_mask=bcg_movement_mask,
|
||||
sampling_rate=bcg_fs)
|
||||
print(f"bcg_amp_change_mask_shape: {bcg_amp_change_mask.shape}, num_amp_change: {np.sum(bcg_amp_change_mask == 1)}, count_amp_change_positions: {len(bcg_amp_change_list)}")
|
||||
else:
|
||||
bcg_amp_change_mask = None
|
||||
print("bcg_amp_change_mask is None")
|
||||
|
||||
|
||||
# 如果signal_data采样率过，进行降采样
|
||||
if signal_fs == 1000:
|
||||
signal_data = utils.downsample_signal_fast(original_signal=signal_data, original_fs=signal_fs, target_fs=100)
|
||||
signal_data_raw = utils.downsample_signal_fast(original_signal=signal_data_raw, original_fs=signal_fs, target_fs=100)
|
||||
signal_fs = 100
|
||||
if show:
|
||||
draw_tools.draw_signal_with_mask(samp_id=samp_id,
|
||||
signal_data=signal_data,
|
||||
signal_fs=signal_fs,
|
||||
resp_data=resp_data,
|
||||
resp_fs=resp_fs,
|
||||
bcg_data=bcg_data,
|
||||
bcg_fs=bcg_fs,
|
||||
signal_disable_mask=manual_disable_mask,
|
||||
resp_low_amp_mask=resp_low_amp_mask,
|
||||
resp_movement_mask=resp_movement_mask,
|
||||
resp_change_mask=resp_amp_change_mask,
|
||||
resp_sa_mask=event_mask,
|
||||
bcg_low_amp_mask=bcg_low_amp_mask,
|
||||
bcg_movement_mask=bcg_movement_mask,
|
||||
bcg_change_mask=bcg_amp_change_mask)
|
||||
|
||||
|
||||
# 保存处理后的数据和标签
|
||||
save_samp_path = save_path / f"{samp_id}"
|
||||
save_samp_path.mkdir(parents=True, exist_ok=True)
|
||||
|
||||
# 复制事件文件 到保存路径
|
||||
sa_label_save_name = f"{samp_id}" + label_path.name
|
||||
shutil.copyfile(label_path, save_samp_path / sa_label_save_name)
|
||||
|
||||
# 新建一个dataframe，分别是秒数、SA标签，SA质量标签，禁用标签，Resp低幅值标签，Resp体动标签，Resp幅值突变标签，Bcg低幅值标签，Bcg体动标签，Bcg幅值突变标签
|
||||
save_dict = {
|
||||
"Second": np.arange(signal_second),
|
||||
"SA_Label": event_mask,
|
||||
"SA_Score": score_mask,
|
||||
"Disable_Label": manual_disable_mask,
|
||||
"Resp_LowAmp_Label": resp_low_amp_mask if resp_low_amp_mask is not None else np.zeros(signal_second, dtype=int),
|
||||
"Resp_Movement_Label": resp_movement_mask if resp_movement_mask is not None else np.zeros(signal_second, dtype=int),
|
||||
"Resp_AmpChange_Label": resp_amp_change_mask if resp_amp_change_mask is not None else np.zeros(signal_second, dtype=int),
|
||||
"Bcg_LowAmp_Label": bcg_low_amp_mask if bcg_low_amp_mask is not None else np.zeros(signal_second, dtype=int),
|
||||
"Bcg_Movement_Label": bcg_movement_mask if bcg_movement_mask is not None else np.zeros(signal_second, dtype=int),
|
||||
"Bcg_AmpChange_Label": bcg_amp_change_mask if bcg_amp_change_mask is not None else np.zeros(signal_second, dtype=int)
|
||||
}
|
||||
|
||||
mask_label_save_name = f"{samp_id}_Processed_Labels.csv"
|
||||
utils.save_process_label(save_path=save_samp_path / mask_label_save_name, save_dict=save_dict)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
yaml_path = Path("./dataset_config/ZD5Y_config.yaml")
|
||||
disable_df_path = Path("./排除区间.xlsx")
|
||||
|
||||
conf = utils.load_dataset_conf(yaml_path)
|
||||
select_ids = conf["select_ids"]
|
||||
root_path = Path(conf["root_path"])
|
||||
save_path = Path(conf["save_path"])
|
||||
|
||||
print(f"select_ids: {select_ids}")
|
||||
print(f"root_path: {root_path}")
|
||||
print(f"save_path: {save_path}")
|
||||
|
||||
org_signal_root_path = root_path / "OrgBCG_Aligned"
|
||||
label_root_path = root_path / "Label"
|
||||
|
||||
all_samp_disable_df = utils.read_disable_excel(disable_df_path)
|
||||
|
||||
process_one_signal(select_ids[1], show=True)
|
||||
|
||||
# for samp_id in select_ids:
|
||||
# print(f"Processing sample ID: {samp_id}")
|
||||
# process_one_signal(samp_id, show=False)
|
||||
# print(f"Finished processing sample ID: {samp_id}\n\n")
|
||||
@ -11,6 +11,7 @@ select_ids:
|
||||
- 960
|
||||
|
||||
root_path: /mnt/disk_wd/marques_dataset/DataCombine2023/HYS
|
||||
save_path: /mnt/disk_code/marques/dataprepare/output/HYS
|
||||
|
||||
resp:
|
||||
downsample_fs_1: 100
|
||||
@ -32,25 +33,25 @@ resp_low_amp:
|
||||
resp_movement:
|
||||
window_size_sec: 20
|
||||
stride_sec: 1
|
||||
std_median_multiplier: 5
|
||||
std_median_multiplier: 4
|
||||
compare_intervals_sec:
|
||||
- 60
|
||||
- 120
|
||||
# - 180
|
||||
interval_multiplier: 3.5
|
||||
interval_multiplier: 3
|
||||
merge_gap_sec: 30
|
||||
min_duration_sec: 1
|
||||
|
||||
resp_movement_revise:
|
||||
up_interval_multiplier: 3
|
||||
down_interval_multiplier: 1.5
|
||||
down_interval_multiplier: 2
|
||||
compare_intervals_sec: 30
|
||||
merge_gap_sec: 10
|
||||
min_duration_sec: 1
|
||||
|
||||
resp_amp_change:
|
||||
mav_calc_window_sec: 5
|
||||
threshold_amplitude: 0.1
|
||||
mav_calc_window_sec: 1
|
||||
threshold_amplitude: 0.25
|
||||
threshold_energy: 0.4
|
||||
|
||||
|
||||
|
||||
88
dataset_config/ZD5Y_config.yaml
Normal file
88
dataset_config/ZD5Y_config.yaml
Normal file
@ -0,0 +1,88 @@
|
||||
select_ids:
|
||||
- 3103
|
||||
- 3105
|
||||
- 3106
|
||||
- 3107
|
||||
- 3108
|
||||
- 3110
|
||||
- 3203
|
||||
- 3204
|
||||
- 3205
|
||||
- 3207
|
||||
- 3208
|
||||
- 3209
|
||||
- 3212
|
||||
- 3301
|
||||
- 3303
|
||||
- 3307
|
||||
- 3403
|
||||
- 3504
|
||||
|
||||
root_path: /mnt/disk_wd/marques_dataset/DataCombine2023/ZD5Y
|
||||
save_path: /mnt/disk_code/marques/dataprepare/output/ZD5Y
|
||||
|
||||
resp:
|
||||
downsample_fs_1: 100
|
||||
downsample_fs_2: 10
|
||||
|
||||
resp_filter:
|
||||
filter_type: bandpass
|
||||
low_cut: 0.01
|
||||
high_cut: 0.7
|
||||
order: 3
|
||||
|
||||
resp_low_amp:
|
||||
window_size_sec: 30
|
||||
stride_sec:
|
||||
amplitude_threshold: 3
|
||||
merge_gap_sec: 60
|
||||
min_duration_sec: 60
|
||||
|
||||
resp_movement:
|
||||
window_size_sec: 20
|
||||
stride_sec: 1
|
||||
std_median_multiplier: 5
|
||||
compare_intervals_sec:
|
||||
- 60
|
||||
- 120
|
||||
# - 180
|
||||
interval_multiplier: 3.5
|
||||
merge_gap_sec: 30
|
||||
min_duration_sec: 1
|
||||
|
||||
resp_movement_revise:
|
||||
up_interval_multiplier: 3
|
||||
down_interval_multiplier: 2
|
||||
compare_intervals_sec: 30
|
||||
merge_gap_sec: 10
|
||||
min_duration_sec: 1
|
||||
|
||||
resp_amp_change:
|
||||
mav_calc_window_sec: 1
|
||||
threshold_amplitude: 0.25
|
||||
threshold_energy: 0.4
|
||||
|
||||
|
||||
bcg:
|
||||
downsample_fs: 100
|
||||
|
||||
bcg_filter:
|
||||
filter_type: bandpass
|
||||
low_cut: 1
|
||||
high_cut: 10
|
||||
order: 10
|
||||
|
||||
bcg_low_amp:
|
||||
window_size_sec: 1
|
||||
stride_sec:
|
||||
amplitude_threshold: 8
|
||||
merge_gap_sec: 20
|
||||
min_duration_sec: 3
|
||||
|
||||
|
||||
bcg_movement:
|
||||
window_size_sec: 2
|
||||
stride_sec:
|
||||
merge_gap_sec: 20
|
||||
min_duration_sec: 4
|
||||
|
||||
@ -178,7 +178,7 @@ def draw_signal_metrics(bcg_origin_signal, resp_origin_signal, bcg_no_movement_s
|
||||
|
||||
def draw_signal_with_mask(samp_id, signal_data, resp_data, bcg_data, signal_fs, resp_fs, bcg_fs,
|
||||
signal_disable_mask, resp_low_amp_mask, resp_movement_mask, resp_change_mask,
|
||||
resp_sa_mask, bcg_low_amp_mask, bcg_movement_mask, bcg_change_mask
|
||||
resp_sa_mask, bcg_low_amp_mask, bcg_movement_mask, bcg_change_mask, show=False, save_path=None
|
||||
):
|
||||
# 第一行绘制去工频噪声的原始信号，右侧为不可用区间标记，左侧为信号幅值纵坐标
|
||||
# 第二行绘制呼吸分量，右侧低幅值、高幅值、幅值变换标记、SA标签，左侧为呼吸幅值纵坐标
|
||||
@ -292,10 +292,12 @@ def draw_signal_with_mask(samp_id, signal_data, resp_data, bcg_data, signal_fs,
|
||||
ax0_twin.callbacks.connect('ylim_changed', on_lims_change)
|
||||
ax1_twin.callbacks.connect('ylim_changed', on_lims_change)
|
||||
ax2_twin.callbacks.connect('ylim_changed', on_lims_change)
|
||||
|
||||
|
||||
plt.tight_layout()
|
||||
plt.show()
|
||||
|
||||
if save_path is not None:
|
||||
plt.savefig(save_path, dpi=300)
|
||||
if show:
|
||||
plt.show()
|
||||
|
||||
|
||||
|
||||
|
||||
@ -169,7 +169,7 @@ def detect_movement(signal_data, sampling_rate, window_size_sec=2, stride_sec=No
|
||||
|
||||
|
||||
def movement_revise(signal_data, sampling_rate, movement_mask, movement_list, up_interval_multiplier: float,
|
||||
down_interval_multiplier: float, compare_intervals_sec, merge_gap_sec, min_duration_sec):
|
||||
down_interval_multiplier: float, compare_intervals_sec, merge_gap_sec, min_duration_sec, verbose=False):
|
||||
"""
|
||||
基于标准差对已有体动掩码进行修正。 用于大尺度的体动检测后的位置精细修正
|
||||
|
||||
@ -189,13 +189,13 @@ def movement_revise(signal_data, sampling_rate, movement_mask, movement_list, up
|
||||
compare_size = int(compare_intervals_sec // (stride_size / sampling_rate))
|
||||
|
||||
_, mav = calc_mav_by_slide_windows(signal_data, movement_mask=None, low_amp_mask=None, sampling_rate=sampling_rate,
|
||||
window_second=2, step_second=1,
|
||||
inner_window_second=1)
|
||||
window_second=4, step_second=1,
|
||||
inner_window_second=4)
|
||||
|
||||
# 往左右两边取compare_size个点的mav，取平均值
|
||||
for start, end in movement_list:
|
||||
left_points = start - 5
|
||||
right_points = end + 10
|
||||
left_points = start - 20
|
||||
right_points = end + 20
|
||||
|
||||
left_values = collect_values(arr=mav, index=left_points, step=-1, limit=compare_size, mask=movement_mask)
|
||||
right_values = collect_values(arr=mav, index=right_points, step=1, limit=compare_size, mask=movement_mask)
|
||||
@ -203,28 +203,58 @@ def movement_revise(signal_data, sampling_rate, movement_mask, movement_list, up
|
||||
left_value_metrics = np.median(left_values) if len(left_values) > 0 else 0
|
||||
right_value_metrics = np.median(right_values) if len(right_values) > 0 else 0
|
||||
|
||||
if left_value_metrics == 0:
|
||||
value_metrics = right_value_metrics
|
||||
elif right_value_metrics == 0:
|
||||
value_metrics = left_value_metrics
|
||||
else:
|
||||
value_metrics = np.mean([left_value_metrics, right_value_metrics])
|
||||
# if left_value_metrics == 0:
|
||||
# value_metrics = right_value_metrics
|
||||
# elif right_value_metrics == 0:
|
||||
# value_metrics = left_value_metrics
|
||||
# else:
|
||||
# value_metrics = np.mean([left_value_metrics, right_value_metrics])
|
||||
|
||||
if left_value_metrics == 0:
|
||||
left_value_metrics = right_value_metrics
|
||||
elif right_value_metrics == 0:
|
||||
right_value_metrics = left_value_metrics
|
||||
|
||||
if verbose:
|
||||
print(f"Revising movement from index {start} to {end}, left_metric: {left_value_metrics:.2f}, right_metric: {right_value_metrics:.2f}")
|
||||
|
||||
# 逐秒遍历mav，判断是否需要修正
|
||||
# print(f"Revising movement from index {start} to {end}, left_mean: {left_value_mean:.2f}, right_mean: {right_value_mean:.2f}, mean: {value_mean:.2f}")
|
||||
for i in range(left_points, right_points):
|
||||
if i < 0 or i >= len(mav):
|
||||
continue
|
||||
# print(f"Index {i}, mav: {mav[i]:.2f}, left_mean: {left_value_mean:.2f}, right_mean: {right_value_mean:.2f}, mean: {value_mean:.2f}")
|
||||
if mav[i] > (value_metrics * up_interval_multiplier):
|
||||
if i < start:
|
||||
value_metrics = left_value_metrics
|
||||
elif i > end:
|
||||
value_metrics = right_value_metrics
|
||||
else:
|
||||
value_metrics = (left_value_metrics + right_value_metrics) / 2
|
||||
|
||||
if mav[i] > (value_metrics * up_interval_multiplier) and movement_mask[i] == 0:
|
||||
movement_mask[i] = 1
|
||||
# print(f"Movement revised at index {i}, mav: {mav[i]:.2f}, threshold: {value_mean * up_interval_multiplier:.2f}")
|
||||
elif mav[i] < (value_metrics * down_interval_multiplier):
|
||||
if verbose:
|
||||
print(f"Normal revised at index {i}, mav: {mav[i]:.2f}, threshold: {value_metrics * up_interval_multiplier:.2f}")
|
||||
elif mav[i] < (value_metrics * down_interval_multiplier) and movement_mask[i] == 1:
|
||||
movement_mask[i] = 0
|
||||
# print(f"Movement revised at index {i}, mav: {mav[i]:.2f}, threshold: {value_mean * down_interval_multiplier:.2f}")
|
||||
# else:
|
||||
# print(f"No revision at index {i}, mav: {mav[i]:.2f}, up_threshold: {value_mean * up_interval_multiplier:.2f}, down_threshold: {value_mean * down_interval_multiplier:.2f}")
|
||||
#
|
||||
if verbose:
|
||||
print(f"Movement revised at index {i}, mav: {mav[i]:.2f}, threshold: {value_metrics * down_interval_multiplier:.2f}")
|
||||
else:
|
||||
if verbose:
|
||||
print(f"No revision at index {i}, mav: {mav[i]:.2f}, up_threshold: {value_metrics * up_interval_multiplier:.2f}, down_threshold: {value_metrics * down_interval_multiplier:.2f}")
|
||||
#
|
||||
# 逐秒遍历mav，判断是否需要修正
|
||||
# print(f"Revising movement from index {start} to {end}, left_mean: {left_value_mean:.2f}, right_mean: {right_value_mean:.2f}, mean: {value_mean:.2f}")
|
||||
# for i in range(left_points, right_points):
|
||||
# if i < 0 or i >= len(mav):
|
||||
# continue
|
||||
# # print(f"Index {i}, mav: {mav[i]:.2f}, left_mean: {left_value_mean:.2f}, right_mean: {right_value_mean:.2f}, mean: {value_mean:.2f}")
|
||||
# if mav[i] > (value_metrics * up_interval_multiplier):
|
||||
# movement_mask[i] = 1
|
||||
# # print(f"Movement revised at index {i}, mav: {mav[i]:.2f}, threshold: {value_mean * up_interval_multiplier:.2f}")
|
||||
# elif mav[i] < (value_metrics * down_interval_multiplier):
|
||||
# movement_mask[i] = 0
|
||||
# # print(f"Movement revised at index {i}, mav: {mav[i]:.2f}, threshold: {value_mean * down_interval_multiplier:.2f}")
|
||||
# # else:
|
||||
# # print(f"No revision at index {i}, mav: {mav[i]:.2f}, up_threshold: {value_mean * up_interval_multiplier:.2f}, down_threshold: {value_mean * down_interval_multiplier:.2f}")
|
||||
# #
|
||||
# 如果需要合并间隔小的体动状态
|
||||
if merge_gap_sec > 0:
|
||||
movement_mask = merge_short_gaps(movement_mask, time_points, merge_gap_sec)
|
||||
@ -520,7 +550,7 @@ def position_based_sleep_recognition_v2(signal_data, movement_mask, sampling_rat
|
||||
|
||||
|
||||
def position_based_sleep_recognition_v3(signal_data, movement_mask, movement_list, sampling_rate, mav_calc_window_sec,
|
||||
threshold_amplitude, threshold_energy):
|
||||
threshold_amplitude, threshold_energy, verbose=False):
|
||||
"""
|
||||
|
||||
:param threshold_energy:
|
||||
@ -569,9 +599,18 @@ def position_based_sleep_recognition_v3(signal_data, movement_mask, movement_lis
|
||||
|
||||
def calc_mav_by_quantiles(data_segment):
|
||||
# 先计算所有的mav值
|
||||
if len(data_segment) % (mav_calc_window_sec * sampling_rate) != 0:
|
||||
data_segment = data_segment[:-(len(data_segment) % (mav_calc_window_sec * sampling_rate))]
|
||||
|
||||
mav_values = np.nanmax(data_segment.reshape(-1, mav_calc_window_sec * sampling_rate), axis=0) - np.nanmin(
|
||||
data_segment.reshape(-1, mav_calc_window_sec * sampling_rate))
|
||||
# 计算分位数
|
||||
q20 = np.nanpercentile(mav_values, 20)
|
||||
q80 = np.nanpercentile(mav_values, 80)
|
||||
|
||||
mav_values = mav_values[(mav_values >= q20) & (mav_values <= q80)]
|
||||
mav = np.nanmean(mav_values)
|
||||
return mav
|
||||
|
||||
position_changes = np.zeros(len(signal_data) // sampling_rate, dtype=int)
|
||||
position_change_list = []
|
||||
@ -579,14 +618,17 @@ def position_based_sleep_recognition_v3(signal_data, movement_mask, movement_lis
|
||||
pre_valid_start = valid_list[0][0] * sampling_rate
|
||||
pre_valid_end = valid_list[0][1] * sampling_rate
|
||||
|
||||
print(f"Total movement segments to analyze: {len(movement_list)}")
|
||||
print(f"Total valid segments available: {len(valid_list)}")
|
||||
if verbose:
|
||||
print(f"Total movement segments to analyze: {len(movement_list)}")
|
||||
print(f"Total valid segments available: {len(valid_list)}")
|
||||
|
||||
for i in range(len(movement_list)):
|
||||
print(f"Analyzing movement segment {i + 1}/{len(movement_list)}")
|
||||
if verbose:
|
||||
print(f"Analyzing movement segment {i + 1}/{len(movement_list)}")
|
||||
|
||||
if i + 1 >= len(valid_list):
|
||||
print("No more valid segments to compare. Ending analysis.")
|
||||
if verbose:
|
||||
print("No more valid segments to compare. Ending analysis.")
|
||||
break
|
||||
|
||||
next_valid_start = valid_list[i + 1][0] * sampling_rate
|
||||
@ -597,25 +639,33 @@ def position_based_sleep_recognition_v3(signal_data, movement_mask, movement_lis
|
||||
|
||||
# 避免过短的片段
|
||||
if movement_end - movement_start <= sampling_rate: # 小于1秒的片段不考虑
|
||||
print(
|
||||
f"Skipping movement segment {i + 1} due to insufficient length. movement start: {movement_start}, movement end: {movement_end}")
|
||||
if verbose:
|
||||
print(
|
||||
f"Skipping movement segment {i + 1} due to insufficient length. movement start: {movement_start}, movement end: {movement_end}")
|
||||
continue
|
||||
|
||||
# 计算前后片段的幅值和能量
|
||||
left_mav = clac_mav(signal_data_no_movement[pre_valid_start:pre_valid_end])
|
||||
right_mav = clac_mav(signal_data_no_movement[next_valid_start:next_valid_end])
|
||||
left_energy = clac_energy(signal_data_no_movement[pre_valid_start:pre_valid_end])
|
||||
right_energy = clac_energy(signal_data_no_movement[next_valid_start:next_valid_end])
|
||||
# left_mav = clac_mav(signal_data_no_movement[pre_valid_start:pre_valid_end])
|
||||
# right_mav = clac_mav(signal_data_no_movement[next_valid_start:next_valid_end])
|
||||
# left_energy = clac_energy(signal_data_no_movement[pre_valid_start:pre_valid_end])
|
||||
# right_energy = clac_energy(signal_data_no_movement[next_valid_start:next_valid_end])
|
||||
|
||||
left_mav = calc_mav_by_quantiles(signal_data_no_movement[pre_valid_start:pre_valid_end])
|
||||
right_mav = calc_mav_by_quantiles(signal_data_no_movement[next_valid_start:next_valid_end])
|
||||
|
||||
|
||||
# 计算幅值指标的变化率
|
||||
amplitude_change = abs(right_mav - left_mav) / max(left_mav, 1e-6)
|
||||
# 计算能量指标的变化率
|
||||
energy_change = abs(right_energy - left_energy) / max(left_energy, 1e-6)
|
||||
# # 计算能量指标的变化率
|
||||
# energy_change = abs(right_energy - left_energy) / max(left_energy, 1e-6)
|
||||
|
||||
significant_change = (amplitude_change > threshold_amplitude) and (energy_change > threshold_energy)
|
||||
# significant_change = (amplitude_change > threshold_amplitude) and (energy_change > threshold_energy)
|
||||
significant_change = (amplitude_change > threshold_amplitude)
|
||||
if significant_change:
|
||||
print(
|
||||
f"Significant position change detected between segments {movement_start} and {movement_end}: left:{pre_valid_start}to{pre_valid_end} left_mav={left_mav:.2f}, right_mav={right_mav:.2f}, amplitude_change={amplitude_change:.2f}, left_energy={left_energy:.2f}, right_energy={right_energy:.2f}, energy_change={energy_change:.2f}")
|
||||
# print(
|
||||
# f"Significant position change detected between segments {movement_start} and {movement_end}: left:{pre_valid_start}to{pre_valid_end} left_mav={left_mav:.2f}, right_mav={right_mav:.2f}, amplitude_change={amplitude_change:.2f}, left_energy={left_energy:.2f}, right_energy={right_energy:.2f}, energy_change={energy_change:.2f}")
|
||||
if verbose:
|
||||
print(f"Significant position change detected between segments {movement_start} and {movement_end}: left:{pre_valid_start}to{pre_valid_end} left_mav={left_mav:.2f}, right_mav={right_mav:.2f}, amplitude_change={amplitude_change:.2f}")
|
||||
# 记录姿势变化发生的时间点 用当前分割的体动的起始位置和结束位置表示
|
||||
position_changes[movement_start:movement_end] = 1
|
||||
position_change_list.append(movement_list[i])
|
||||
@ -624,8 +674,11 @@ def position_based_sleep_recognition_v3(signal_data, movement_mask, movement_lis
|
||||
pre_valid_end = next_valid_end
|
||||
|
||||
else:
|
||||
print(
|
||||
f"No significant position change between segments {movement_start} and {movement_end}: left:{pre_valid_start}to{pre_valid_end} left_mav={left_mav:.2f}, right_mav={right_mav:.2f}, amplitude_change={amplitude_change:.2f}, left_energy={left_energy:.2f}, right_energy={right_energy:.2f}, energy_change={energy_change:.2f}")
|
||||
# print(
|
||||
# f"No significant position change between segments {movement_start} and {movement_end}: left:{pre_valid_start}to{pre_valid_end} left_mav={left_mav:.2f}, right_mav={right_mav:.2f}, amplitude_change={amplitude_change:.2f}, left_energy={left_energy:.2f}, right_energy={right_energy:.2f}, energy_change={energy_change:.2f}")
|
||||
if verbose:
|
||||
print(f"No significant position change between segments {movement_start} and {movement_end}: left:{pre_valid_start}to{pre_valid_end} left_mav={left_mav:.2f}, right_mav={right_mav:.2f}, amplitude_change={amplitude_change:.2f}")
|
||||
|
||||
# 仅更新前片段
|
||||
pre_valid_start = pre_valid_start
|
||||
pre_valid_end = next_valid_end
|
||||
|
||||
@ -2,5 +2,6 @@ from .HYS_FileReader import read_label_csv, read_signal_txt, read_disable_excel
|
||||
from .operation_tools import load_dataset_conf, generate_disable_mask, generate_event_mask, event_mask_2_list
|
||||
from .operation_tools import merge_short_gaps, remove_short_durations
|
||||
from .operation_tools import collect_values
|
||||
from .operation_tools import save_process_label
|
||||
from .event_map import E2N
|
||||
from .signal_process import butterworth, average_filter, downsample_signal_fast, notch_filter, bessel
|
||||
@ -238,3 +238,8 @@ def collect_values(arr: np.ndarray, index: int, step: int, limit: int, mask=None
|
||||
count += 1
|
||||
index += step
|
||||
return values
|
||||
|
||||
|
||||
def save_process_label(save_path: Path, save_dict: dict):
|
||||
save_df = pd.DataFrame(save_dict)
|
||||
save_df.to_csv(save_path, index=False)
|
||||
|
||||
Loading…
Reference in New Issue
Block a user