top = max( ( max(data_f), max(data_r) ) ) bot = min( ( min(data_f), min(data_r) ) ) else : top = float(n_max) bot = float(n_min) step = ( top - bot ) / float(steps) lake_overlaps = [] lake_forward = [] lake_reverse = [] lake_bg_overlaps = [] lake_bg_forward = [] lake_bg_reverse = [] X = top - numpy.arange( bot, top+step, step ) for i,n in enumerate( X ) : forward = pique.findregions( data_f, n ) reverse = pique.findregions( data_r, n ) envelope = pique.overlaps( forward, reverse ) lake_overlaps.append( envelope ) lake_forward.append( forward ) lake_reverse.append( reverse ) forward = pique.findregions( b_f, n ) reverse = pique.findregions( b_r, n ) envelope = pique.overlaps( forward, reverse ) lake_bg_overlaps.append( envelope ) lake_bg_forward.append( forward ) lake_bg_reverse.append( reverse ) if i%10 == 0 :
data_ff = pique.mask( data_ff, is_elements ) data_rr = pique.mask( data_rr, is_elements ) b_ff = pique.mask( b_ff, is_elements ) b_rr = pique.mask( b_rr, is_elements ) # run the filter pique.msg( 'running filters...' ) data_f = pique.filterset( data_ff, 300, l_thresh ) data_r = pique.filterset( data_rr, 300, l_thresh ) b_f = pique.filterset( b_ff, 300, l_thresh ) b_r = pique.filterset( b_rr, 300, l_thresh ) # find the peaks pique.msg( 'finding peaks...' ) forward = pique.findregions( data_f, n_thresh ) reverse = pique.findregions( data_r, n_thresh ) envelope = pique.overlaps( forward, reverse ) # delete peaks that aren't above the control threshold pique.msg( 'removing peaks that are lost in the background...' ) weeds = [] for peak in envelope : fstart = peak['forward']['start'] fstop = peak['forward']['stop'] rstart = peak['reverse']['start'] rstop = peak['reverse']['stop'] a = float(sum(data_ff[fstart:fstop]) + sum(data_rr[rstart:rstop]) ) b = float(sum( b_f[fstart:fstop]) + sum( b_r[rstart:rstop]) ) if b != 0 :
data_ff = pique.mask(data_ff, is_elements) data_rr = pique.mask(data_rr, is_elements) b_ff = pique.mask(b_ff, is_elements) b_rr = pique.mask(b_rr, is_elements) # run the filter pique.msg('running filters...') data_f = pique.filterset(data_ff, 300, l_thresh) data_r = pique.filterset(data_rr, 300, l_thresh) b_f = pique.filterset(b_ff, 300, l_thresh) b_r = pique.filterset(b_rr, 300, l_thresh) # find the peaks pique.msg('finding peaks...') forward = pique.findregions(data_f, n_thresh) reverse = pique.findregions(data_r, n_thresh) envelope = pique.overlaps(forward, reverse) # delete peaks that aren't above the control threshold pique.msg('removing peaks that are lost in the background...') weeds = [] for peak in envelope: fstart = peak['forward']['start'] fstop = peak['forward']['stop'] rstart = peak['reverse']['start'] rstop = peak['reverse']['stop'] a = float(sum(data_ff[fstart:fstop]) + sum(data_rr[rstart:rstop])) b = float(sum(b_f[fstart:fstop]) + sum(b_r[rstart:rstop])) if b != 0: