"""proc.py
"""
# This file has been replaced by jupyter/IntensityMatrix_Resizing.ipynb
from pyms.GCMS.IO.ANDI import ANDI_reader
# read the raw data
andi_file = "data/gc01_0812_066.cdf"
data = ANDI_reader(andi_file)
# info about raw data
data.info()
# trim data between scans 1000 and 2000
data.trim(1000, 2000)
# info about trimmed raw data
data.info()
# reload
data = ANDI_reader(andi_file)
# trim data between retention times, 6.5 minutes to 21 minutes
data.trim("6.5m", "21m")
# info about trimmed raw data
data.info()
from pyms.Display import Display
from pyms.GCMS.IO.ANDI import ANDI_reader
from pyms.IntensityMatrix import build_intensity_matrix_i
from pyms.Noise.SavitzkyGolay import savitzky_golay
from pyms.Peak.Function import peak_sum_area
from pyms.TopHat import tophat
data_directory = pathlib.Path(".").resolve().parent.parent / "pyms-data"
# Change this if the data files are stored in a different location
output_directory = pathlib.Path(".").resolve() / "output"
# read raw data
andi_file = data_directory / "data/gc01_0812_066.cdf"
data = ANDI_reader(andi_file)
data.trim(4101, 4350)
# Build Intensity Matrix
real_im = build_intensity_matrix_i(data)
n_scan, n_mz = real_im.size
# perform necessary pre filtering
for ii in range(n_mz):
ic = real_im.get_ic_at_index(ii)
ic_smooth = savitzky_golay(ic)
ic_bc = tophat(ic_smooth, struct="1.5m")
real_im.set_ic_at_index(ii, ic_bc)
# Detect Peaks
peak_list = BillerBiemann(real_im, points=3, scans=2)
from pyms.Noise.SavitzkyGolay import savitzky_golay
from pyms.TopHat import tophat
from pyms.Peak.List.IO import store_peaks
from pyms.BillerBiemann import (
BillerBiemann,
rel_threshold,
num_ions_threshold,
)
# read in raw data
andi_file = "gc01_0812_066.cdf"
data = ANDI_reader(andi_file)
data.trim("500s", "2000s")
# Build Intensity Matrix
im = build_intensity_matrix_i(data)
n_scan, n_mz = im.size
# perform necessary pre filtering
for ii in range(n_mz):
ic = im.get_ic_at_index(ii)
ic_smooth = savitzky_golay(ic)
ic_bc = tophat(ic_smooth, struct="1.5m")
im.set_ic_at_index(ii, ic_bc)
# Detect Peaks
peak_list = BillerBiemann(im, points=9, scans=2)
print("Number of peaks found: ", len(peak_list))