UniDec
Universal Deconvolution of Mass and Ion Mobility Spectra
Variables
UniDec.unidec_modules.auto_peak Namespace Reference

Variables

string __author__ = 'Michael.Marty'
 
string file = "C:\\cprog\\UniDecDemo\\MTM_ADH_5_rawdata.txt"
 
tuple data = np.loadtxt(file, skiprows=10)
 
tuple thresh = auto_noise_level(data)
 
tuple avgbs = average_bin_size(data)
 
int window = fwhm/avgbs/4
 
tuple cwtdat = np.transpose([data[:, 0], cwt])
 
tuple peaks = peakdetect(cwtdat, None, window * 2., thresh)
 
int zm = 1
 
list ivals = peaks[:, 1]
 
tuple maxpos = np.argmax(ivals)
 
list mins = []
 
tuple x = np.abs(zm - zm[maxpos])
 
tuple diffs = np.diff(x)
 
tuple minpos = np.argmin(diffs)
 
tuple minval = np.average(x[minpos:minpos + 2])
 
int mass = 1
 
list mz = peaks[maxpos, 0]
 
tuple charge = np.round(mass / mz)
 
 tolerance = charge*fwhm
 
tuple vec = np.array([mass, ivals[maxpos], mz, charge, diffs[minpos], tolerance, zm[maxpos], False])
 
tuple sindex = np.argsort(mins[:, 4])
 
list peakassignments = []
 
list row = mins[i]
 
list swaps = []
 
list topmass = row[0]
 
list topcharge = row[3]
 
tuple zms = np.abs(row[6] - mins[:, 6])
 
list newmass = mins[j, 2]
 
int newspot = 0
 
tuple swaprows = deepcopy(mins[newspot:j])
 
list boo1 = mins[:, 7]
 
list y = mins[boo1, 4]
 
tuple m = np.array(m)
 

Variable Documentation

string UniDec.unidec_modules.auto_peak.__author__ = 'Michael.Marty'
tuple UniDec.unidec_modules.auto_peak.avgbs = average_bin_size(data)
list UniDec.unidec_modules.auto_peak.boo1 = mins[:, 7]
tuple UniDec.unidec_modules.auto_peak.charge = np.round(mass / mz)
tuple UniDec.unidec_modules.auto_peak.cwtdat = np.transpose([data[:, 0], cwt])
tuple UniDec.unidec_modules.auto_peak.data = np.loadtxt(file, skiprows=10)
tuple UniDec.unidec_modules.auto_peak.diffs = np.diff(x)
string UniDec.unidec_modules.auto_peak.file = "C:\\cprog\\UniDecDemo\\MTM_ADH_5_rawdata.txt"
list UniDec.unidec_modules.auto_peak.ivals = peaks[:, 1]
tuple UniDec.unidec_modules.auto_peak.m = np.array(m)
int UniDec.unidec_modules.auto_peak.mass = 1
tuple UniDec.unidec_modules.auto_peak.maxpos = np.argmax(ivals)
tuple UniDec.unidec_modules.auto_peak.minpos = np.argmin(diffs)
list UniDec.unidec_modules.auto_peak.mins = []
tuple UniDec.unidec_modules.auto_peak.minval = np.average(x[minpos:minpos + 2])
list UniDec.unidec_modules.auto_peak.mz = peaks[maxpos, 0]
list UniDec.unidec_modules.auto_peak.newmass = mins[j, 2]
UniDec.unidec_modules.auto_peak.newspot = 0
list UniDec.unidec_modules.auto_peak.peakassignments = []
tuple UniDec.unidec_modules.auto_peak.peaks = peakdetect(cwtdat, None, window * 2., thresh)
list UniDec.unidec_modules.auto_peak.row = mins[i]
tuple UniDec.unidec_modules.auto_peak.sindex = np.argsort(mins[:, 4])
tuple UniDec.unidec_modules.auto_peak.swaprows = deepcopy(mins[newspot:j])
list UniDec.unidec_modules.auto_peak.swaps = []
tuple UniDec.unidec_modules.auto_peak.thresh = auto_noise_level(data)
list UniDec.unidec_modules.auto_peak.tolerance = charge*fwhm
list UniDec.unidec_modules.auto_peak.topcharge = row[3]
list UniDec.unidec_modules.auto_peak.topmass = row[0]
int UniDec.unidec_modules.auto_peak.vec = np.array([mass, ivals[maxpos], mz, charge, diffs[minpos], tolerance, zm[maxpos], False])
int UniDec.unidec_modules.auto_peak.window = fwhm/avgbs/4
list UniDec.unidec_modules.auto_peak.x = np.abs(zm - zm[maxpos])
list UniDec.unidec_modules.auto_peak.y = mins[boo1, 4]
int UniDec.unidec_modules.auto_peak.zm = 1
tuple UniDec.unidec_modules.auto_peak.zms = np.abs(row[6] - mins[:, 6])