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An example of parallel processing of data. Shows how to loop over all ICs in an intensity matrix, and perform noise smoothing on each IC (in parallel). Please see User Guide for instructions how to run this example on multiple CPUs
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | """proc.py """ from pyms.GCMS.IO.ANDI import ANDI_reader from pyms.IntensityMatrix import build_intensity_matrix_i from pyms.Noise.Window import window_smooth # read the raw data as a GCMS_data object andi_file = "data/gc01_0812_066.cdf" data = ANDI_reader(andi_file) # build the intensity matrix im = build_intensity_matrix_i(data) # get the size of the intensity matrix n_scan, n_mz = im.size print("Size of the intensity matrix is (n_scans, n_mz):", n_scan, n_mz) # loop over all m/z values, fetch the corresponding IC, and perform # noise smoothing for ii in im.iter_ic_indices(): print(ii+1,) ic = im.get_ic_at_index(ii) ic_smooth = window_smooth(ic, window=7) |