import time
import cwt
import commonfn
start_time = time.time()
param_set={
"mzML_files",
"min_highest_I",
"num_threads",
"library",
"RT_shift",
"pos/neg mode",
"ms1_ppm",
}
param_dict=commonfn.read_param(param_set)
mzML_files=sorted(glob.glob(param_dict["mzML_files"]))
num_threads=int(param_dict["num_threads"])
ispos=True if param_dict['pos/neg mode']=='pos' else False
ms1ppm=float(param_dict['ms1_ppm'])/1e6
min_group_size=2#int(param_dict["min_group_size"])
min_highest_I=float(param_dict["min_highest_I"])
group_I_threshold=min_highest_I#float(param_dict["group_I_threshold"])
lib_types=param_dict["library"].splitlines()
RT_shift=float(param_dict['RT_shift'])
import collections
import operator
import math
from bisect import bisect_left
import sys
import concurrent.futures
import os
import glob
from multiprocessing import freeze_support
import time
import commonfn
Peak = commonfn.Peak
param_dict = commonfn.read_param({"length_of_ion_chromatogram"})
peak_w = [int(x) for x in param_dict["length_of_ion_chromatogram"].split()]
min_feat_height = 1
min_auc = min_feat_height * 2
Coef = collections.namedtuple('Coef', ('rt sc coef'))
def findridge0(wave_scales, wave_sqrt, rerun, rerunw, EIC):
eic_dict = {rt: i for rt, i in EIC}
rt_all = sorted(eic_dict)
eic_rt = set()
for x, y in eic_dict.items():
pos = bisect_left(rt_all, x)