def GetFrameStats(data, inRunningSum, inRunningVoiceSum, inRunningCount): Ndata = len(data) voicefilter = filters.mult(filters.hpf(Ndata, 80), filters.lpf(Ndata, 1000)) (voicedata, voicefreq) = filters.apply(data, voicefilter) maxVal = max([abs(d) for d in data]) outRunningCount = inRunningCount + Ndata outRunningSum = inRunningSum + sum([abs(d) for d in data]) outRunningVoiceSum = inRunningVoiceSum + sum([abs(d) for d in voicedata]) outRunningAvg = outRunningSum / outRunningCount outRunningVoiceAvg = outRunningVoiceSum / outRunningCount voiceMax = max([abs(d) for d in voicedata]) return (maxVal, voicedata, voiceMax, outRunningCount, outRunningSum, outRunningAvg, outRunningVoiceSum, outRunningVoiceAvg)
def main( options=None, args=None ):
"""The main method"""
global COLORS
if options.scriptMode:
matplotlib.use( 'Agg' )
import pylab
thisFigure = pylab.figure( )
if options.outputFile:
thisFigure.set_size_inches((
float( options.width ) / options.dpi,
float( options.height ) / options.dpi ))
pylab.subplots_adjust( left = 0.6 / options.width * options.dpi,
right = 1.0 - 0.2 / options.width * options.dpi,
top = 1.0 - 0.45 / options.height * options.dpi,
bottom = 0.5 / options.height * options.dpi )
barOffset = options.lineWidth / 2
barAlpha = options.markerAlpha * 2 / 3
rawFiles = [ ]
rawTypes = [ '.csv', '.mzdata', '.mzxml', '.mzxml.xml',
'.json', '.json.gz' ]
for i in range( len( args )-1, -1, -1 ):
arg = args[ i ]
try:
# check the extension to see if this is xmass input data
for type_ in rawTypes:
if arg.lower( ).endswith( type_ ):
rawFiles.append( args.pop( i ))
continue
except ValueError:
pass
if rawFiles:
for r in rawFiles:
ref = mzlib.RawData( )
if not ( ref.read( r )):
sys.stderr.write( "Error: Unable to load data from '%s'" % r )
sys.exit( -1 )
if options.shortFilename:
filename = os.path.basename( r )
else:
filename = r
# apply any filters
if options.mass:
ref.onlyMz( options.mass, options.massWindow )
if options.maxTime or options.minTime:
if options.maxTime:
ref.onlyScans( options.minTime, options.maxTime )
else:
ref.onlyScans( options.minTime )
rt = [ scan[ "retentionTime" ] for scan in ref if scan[ "msLevel" ] == 1 ]
if options.bpc:
yAxis = ref.bpc( 1 )
else:
yAxis = ref.tic( 1 )
if filters:
if options.lpfThreshold and options.hpfThreshold:
yAxis = filters.bpf( yAxis, options.hpfThreshold, options.lpfThreshold )
elif options.lpfThreshold:
yAxis = filters.lpf( yAxis, options.lpfThreshold )
elif options.hpfThreshold:
yAxis = filters.hpf( yAxis, options.hpfThreshold )
if options.normalize:
if len( yAxis ):
max_ = max( yAxis )
if max_:
yAxis = [ x / max_ for x in yAxis ]
if options.normalize:
label = filename + " (normalized)"
else:
label = filename
pylab.plot( rt, yAxis, COLORS['ref'][0] , alpha = options.markerAlpha,
linewidth=options.lineWidth,
label = label )
COLORS['ref'] = COLORS['ref'][1:] + [ COLORS['ref'][0]]
if not options.scriptMode:
def findMedian( sortedArray ):
arrayLen = len( sortedArray )
if arrayLen % 2:
median = sortedArray[ arrayLen // 2 ] * sortedArray[ arrayLen // 2 + 1 ]
else:
median = sortedArray[ arrayLen // 2 ]
return median
array = list( yAxis );
array.sort( )
median = findMedian( array )
q1 = findMedian( array[ : len( array ) // 2 ])
q3 = findMedian( array[ int( math.ceil( len( array ) / 2.0 )) : ])
min_ = min( yAxis )
max_ = max( yAxis )
print( "Plot statistics for %s:" % label )
print( "\tRange: %g (%g - %g)" % ( max_ - min_, min_, max_ ))
print( "\tMean: %g" % numerical.mean( yAxis ))
print( "\tMedian: %g" % median )
print( "\tInterquartile Range: %g (%g - %g)" % ( q3 - q1, q1, q3 ))
print( "\tStandard Deviation: %g" % numerical.std( yAxis ))
print( "\tVariance: %g" % numerical.var( yAxis ))
# The following section of code is specific to the OmicsDP data formats.
# You can safely delete this section if you are using this software outside
# of that environment.
# BEGIN READING DLTs
for arg in args:
scan = numerical.empty( 0, numerical.uint64 ) # scan number
barRt = numerical.empty( 0, numerical.float64 ) # retention time
barIntensity = numerical.empty( 0, numerical.float64 )
barNoise = numerical.empty( 0, numerical.float64 )
labels = [ ]
try:
f = open( arg )
lines = DictReader( f )
except IOError:
sys.stderr.write("Error: unable to read file '%s'\n" % arg )
sys.exit( -1 )
if options.shortFilename:
filename = os.path.basename( arg )
else:
filename = arg
for line in lines:
try:
scanValue = int( line[ 'Scan' ])
rtValue = float( line[ 'RT(min)'] )
mzValue = float( line[ 'M/Z' ] )
noiseValue = float( line[ 'LC_Noise' ] )
intValue = float( line[ 'Int' ] )
if ( rtValue < options.minTime or
( options.maxTime and rtValue > options.maxTime )):
continue
if ((( not noiseValue ) or
intValue/noiseValue < options.filterLevel ) or
( options.mass and
abs( options.mass - mzValue ) > options.massWindow )):
if options.verbosity:
sys.stderr.write( "Dropping line %s" % ( line ))
continue
# using plot( ) produces a more responsive graph than vlines( )
if len( scan ) and scanValue == scan[ -1 ]:
if options.bpc:
if intValue > barIntensity[ -2 ]:
barIntensity[ -2 ] = intValue
barNoise[ -2 ] = noiseValue
labels[ -1 ] = "(%.2f," % ( mzValue - 0.005 ) #truncate, don't round
else:
barIntensity[ -2 ] += intValue
barNoise[ -2 ] += noiseValue
labels[ -1 ] += " %.2f," % ( mzValue - 0.005 ) #truncate, don't round
else:
# appending [0, value, 0] allows us to plot a bar graph using lines
barRt = numerical.append( barRt, [ rtValue, rtValue, rtValue ])
barIntensity = numerical.append( barIntensity, [ 0, intValue, 0 ])
barNoise = numerical.append( barNoise, [ 0, noiseValue, 0 ])
scan = numerical.append( scan, scanValue )
if ( len( labels )):
labels[ -1 ] = labels[ -1 ][ :-1 ] + ')' # replace the last , with )
labels.append( "(%.2f," % ( mzValue - 0.005 )) #truncate, don't round
except ( ValueError, IndexError ):
if options.verbosity:
sys.stderr.write( "Skipping line %s" % ( line ))
if ( len( labels )):
labels[ -1 ] = labels[ -1 ][ :-1 ] + ')' # replace the last , with )
if options.normalize:
if len( barIntensity ):
max_ = max( barIntensity )
if max_:
barIntensity /= max_
barNoise /= max_
if options.massLabels:
for i in xrange( len( labels )):
pylab.annotate( labels[ i ], ( barRt[ 3 * i + 1 ], barIntensity[ 3 * i + 1 ]),
size=9)
# calculate alpha based on which file this is in the list
alpha = ( options.markerAlpha - options.markerAlpha *
( args.index( arg ) / float( len( args ))) * 0.75 )
if options.showPeaks:
if not options.removeNoise:
barIntensity += barNoise
if options.normalize:
label = label = ( "%s - intensity (%d peaks, normalized)" %
( filename, len( barIntensity )/3))
else:
label = label = ( "%s - intensity (%d peaks)" %
( filename, len( barIntensity )/3))
pylab.plot( barRt, barIntensity, COLORS['intensity'][0] ,
linewidth = options.lineWidth*2, alpha = alpha, label = label )
if options.connectPeaks:
pylab.plot( barRt[ 2::3 ], barIntensity[ 1::3 ], COLORS['intensity'][0],
alpha = alpha, linewidth=options.lineWidth )
COLORS['intensity'] = COLORS['intensity'][1:] + [ COLORS['intensity'][0]]
if options.showNoise:
if options.normalize:
label = ( "%s - noise (%d points, normalized)" % ( filename, len( barNoise )/3))
else:
label = ( "%s - noise (%d points)" % ( filename, len( barNoise )/3))
pylab.plot( barRt[ 2::3 ], barNoise[ 1::3 ], COLORS['noise'][0], alpha = alpha,
linewidth=options.lineWidth, label = label)
COLORS['noise'] = COLORS['noise'][1:] + [ COLORS['noise'][0]]
if len( barRt ):
#draw a horizontal black line at 0
pylab.plot( [barRt[1], barRt[-2]], [0,0], 'k', linewidth=options.lineWidth )
f.close( )
# END READING DLTs
if options.showLegend:
legend = pylab.legend( loc="upper left", prop=FontProperties( size='small' ))
pylab.grid( )
axes = thisFigure.get_axes( )[ 0 ]
axes.set_xlabel( "Time (min)" )
axes.set_ylabel( "Intensity" )
axes.ticklabel_format( style="scientific", axis="y", scilimits=(3,3) )
if not len( rawFiles ):
if ( options.bpc ):
axes.set_title( "Base Peaks" )
else:
axes.set_title( "Peaks" )
elif options.bpc:
if options.mass:
axes.set_title(
"Selected Base Peak Chromatogram (M/Z: %f, Tolerance: %f)" %
( options.mass, options.massWindow ))
else:
axes.set_title( "Base Peak Chromatogram" )
else:
if options.mass:
axes.set_title(
"Selected Ion Chromatogram (M/Z: %f, Tolerance: %f)" %
( options.mass, options.massWindow ))
else:
axes.set_title( "Total Ion Chromatogram" )
if options.outputFile:
thisFigure.savefig( options.outputFile, dpi=options.dpi )
if not options.scriptMode:
pylab.show( )
