"""proc.py """ # This file has been replaced by jupyter/IntensityMatrix_Resizing.ipynb from pyms.GCMS.IO.ANDI import ANDI_reader # read the raw data andi_file = "data/gc01_0812_066.cdf" data =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))