sm.engine.msm_basic package¶

Submodules¶

Functions for creating isotope images from a mass spectrometry dataset

sm.engine.msm_basic.formula_imager.compute_sf_images(sf_peak_imgs)[source]¶

Group isotope images for the same formula

sf_peak_imgs : pyspark.rdd.RDD: RDD of sum formula, (local peak id, sparse matrix of intensities)

sm.engine.msm_basic.formula_imager.compute_sf_peak_images(ds, sf_sp_intens)[source]¶

Combine all pixel intensities for the same formula into isotope images represented as sparse matrices

ds : engine.dataset.Dataset sf_sp_intens : pyspark.rdd.RDD

RDD of (sum formula index, peak local index), (spectrum id, intensity)

: pyspark.rdd.RDD: RDD of sum formula, (local peak id, sparse matrix of intensities)

sm.engine.msm_basic.formula_imager.sample_spectra(sc, ds, formulas)[source]¶

Find formulas for which non-zero intensities in some spectra exist

sc : pyspark.SparkContext ds : engine.dataset.Dataset formulas : engine.formulas.Formulas

: pyspark.rdd.RDD: RDD of (sum formula index, peak local index), (spectrum id, intensity)

sm.engine.msm_basic.formula_imager_segm.compute_sf_images(sc, ds, sf_peak_df, ppm)[source]¶

Compute isotopic images for all formula

sm.engine.msm_basic.formula_imager_segm.find_mz_segments(spectra, sf_peak_df, ppm)[source]¶

sm.engine.msm_basic.formula_imager_segm.gen_iso_peak_images(sc, ds, sf_peak_df, segm_spectra, peaks_per_sp_segm, ppm)[source]¶

sm.engine.msm_basic.formula_imager_segm.gen_iso_sf_images(iso_peak_images, shape)[source]¶