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:
