def svilen(self, id=None, *args, **kwargs):
from pyqlb.nstats.well import accepted_peaks
from pyqlb.nstats.peaks import cluster_2d, peak_times, fam_widths
from pyqlb.factory import QLNumpyObjectFactory
from qtools.lib.mplot import svilen, cleanup, render as plt_render
qlwell = self.__qlwell_from_threshold_form(id)
self.__set_threshold_context(qlwell)
well_path = self.__well_path()
# oh shit
factory = QLNumpyObjectFactory()
raw_well = factory.parse_well(well_path)
crap, crap, gold, crap = cluster_2d(accepted_peaks(qlwell), c.fam_threshold,
c.vic_threshold)
times = peak_times(gold)
widths = fam_widths(gold)
title = "VIC+/FAM- droplet traces (accepted events)"
ranges = [(int(t-(w*2)), int(t+(w*2))) for t, w in zip(times, widths)]
if c.fam_threshold == 0 or c.vic_threshold == 0:
ranges = []
title = "%s (no events in quadrant)" % title
elif len(ranges) > 100:
ranges = ranges[:100]
title = "%s (truncated at first 100)" % title
fig = svilen(title, raw_well.samples, ranges, widths)
response.content_type = 'image/png'
imgdata = plt_render(fig, dpi=72)
cleanup(fig)
return imgdata
def stats_for_qlp_well_path(qlp_path, well_name, compute_clusters=False, override_thresholds=None):
"""
Return statistics about a well, given a path to a QLP file with the well metrics and the name
of the well to look at in the plate.
Structure is a bit legacy and can be massaged more.
:param qlp_path: The path to the QLP file.
:param well_name: The name of the
:param compute_clusters: Whether to compute clusters in addition to basic statistics.
:param override_thresholds: If not None, use the supplied thresholds to determine statistics,
such as concentration, clusters, S-value, etc.
:return: A 2-tuple (statistics, clusters). (TODO: document this more)
"""
from pyqlb.factory import QLNumpyObjectFactory
factory = QLNumpyObjectFactory()
plate = factory.parse_plate(qlp_path)
well = plate.analyzed_wells.get(well_name.upper(), None)
if not well:
return None
else:
return stats_for_qlp_well(well, compute_clusters=compute_clusters, override_thresholds=override_thresholds)
import re
import os
import numpy
from optparse import OptionParser
from pyqlb.nstats.peaks import *
def qlpdir(path):
"""
# Maybe this exists?
# """
scQLPs = "c:/Users/rrymer/Documents/Data/"
return "%s/%s" % (scQLPs, path)
factory = QLNumpyObjectFactory()
#plate = factory.parse_plate(qlpdir('EvaGreenPPEDNRwBGDNAAttempt3.qlp'))
##Lightweight plate
class LWPlate(object):
def add_well(self, well, fulldata):
# Should throw an exception if wellname exists, but have not figure out perl exception handling yet
if fulldata:
self.well_list[well.name] = well
else:
self.well_list[well.name] = ""
def wells(self):
print self
import csv
import argparse
import matplotlib.pyplot as plt
import matplotlib.mlab as mlab
from scipy import optimize
from pylab import *
from pyqlb.nstats.peaks import *
def qlpdir(path):
"""
# Maybe this exists?
# """
scQLPs = "c:/Users/rrymer/Documents/Data/"
return "%s/%s" % (scQLPs, path)
factory = QLNumpyObjectFactory() #not sure what this does
#Lightweight plate, collects all the wells to be analyzed by plate
class LWPlate( object ):
def add_well( self, well, fulldata ):
# Should throw an exception if wellname exists, but have not figure out perl exception handling yet
if fulldata:
self.well_list[well.name] = well
else:
self.well_list[well.name] = ""
def wells(self):
print self
return( self.well_list )
def __init__(self, filename, platename):
# -*- coding: utf-8 -*-
"""
Created on Wed Nov 20 13:44:44 2013
@author: rrymer
"""
from pyqlb.factory import QLNumpyObjectFactory
from pyqlb.nstats.peaks import fam_amplitudes
import numpy as np
factory = QLNumpyObjectFactory()
class LWPlate(object):
def add_well(self, well, fulldata):
# Should throw an exception if wellname exists, but have not figure out perl exception handling yet
if fulldata:
self.well_list[well.name] = well
else:
self.well_list[well.name] = ""
def wells(self):
print self
return self.well_list
def __init__(self, filename, platename):
self.filename = filename
self.platename = platename
self.well_list = {}
def __init__(self, *args, **kwargs):
super(TestColorCal, self).__init__(*args, **kwargs)
factory = QLNumpyObjectFactory()
self.vic = factory.parse_plate(local('colorcal_vic.qlp'))
self.hex = factory.parse_plate(local('colorcal_hex.qlp'))
def setUp(self):
factory = QLNumpyObjectFactory()
self.plate = factory.parse_plate(local('colorcomp.qlp'))
# -*- coding: utf-8 -*-
"""
Created on Wed Nov 20 13:44:44 2013
@author: rrymer
"""
from pyqlb.factory import QLNumpyObjectFactory
from pyqlb.nstats.peaks import fam_amplitudes
import numpy as np
factory = QLNumpyObjectFactory()
class LWPlate(object):
def add_well(self, well, fulldata):
# Should throw an exception if wellname exists, but have not figure out perl exception handling yet
if fulldata:
self.well_list[well.name] = well
else:
self.well_list[well.name] = ""
def wells(self):
print self
return (self.well_list)
def __init__(self, filename, platename):
self.filename = filename
self.platename = platename
self.well_list = {}
