def test():
pathDir = '/home/jaggu/marcotte_project/boulgakov/microscope/2015-Oct/2015-10-27_forHopper'
outputDirname = "output_2015-11-02"
outputDir = os.path.join(pathDir,outputDirname)
destDir = '/home/jaggu/marcotte_project/current/project2/jaggu/dataAnalysis/microscope1/2015-Oct/2015-10-27'
trackPhotometryFile = 'track_photometries_nx8t5v.csv'
trackFile = os.path.join(outputDir,trackPhotometryFile)
#category_trackDetails_ch1 = makeIntensityCategory(trackFile,ch=1)
#category_trackDetails_ch2 = makeIntensityCategory(trackFile,ch=2)
#print "Categories Dictionaries pickled"
category_dict_ch1 = loadPkl('category_trackDetails.ch1.dict.pkl',pathDir)
category_dict_ch2 = loadPkl('category_trackDetails.ch2.dict.pkl',pathDir)
print "Categories Dictionaries loaded "
desired_category = getDesiredCategory('staggered')
desired_categoryList_ch1 = getIntensityList_category(category_dict_ch1,desired_category)
desired_categoryList_ch2 = getIntensityList_category(category_dict_ch2,desired_category)
writeCountsFile([desired_categoryList_ch1,desired_categoryList_ch2])
print "Peptide track counts and intensity file created"
edmanframe_ch1 = 3
edmanframe_ch2 = 4
allCounts_ch1 = [item[1] for item in desired_categoryList_ch1]
allCounts_ch2 = [item[1] for item in desired_categoryList_ch2]
eff1_ch1,eff2_ch1 = calculateEdmanEfficiency(allCounts_ch1,edmanframe_ch1)
eff1_ch2,eff2_ch2 = calculateEdmanEfficiency(allCounts_ch2,edmanframe_ch2)
print "Overall Edman efficiency - \n Ch1 : ",eff1_ch1,eff2_ch1," \n Ch2 : ",eff1_ch2,eff2_ch2
def countTracks(self, pickle_exists=False,nbrframes=7,nbrchannels=2):
trackFile = self.trackFile
if pickle_exists:
category_dict_ch1 = loadPkl('category_trackDetails.ch1.dict.pkl',self.pathDir)
category_dict_ch2 = loadPkl('category_trackDetails.ch2.dict.pkl',self.pathDir)
print "Categories Dictionaries loaded "
else:
category_dict_ch1,category_peakDetails_ch1 = peptracks.makeIntensityCategory(trackFile,ch=1)
category_dict_ch2,category_peakDetails_ch2 = peptracks.makeIntensityCategory(trackFile,ch=2)
self.pickle_categoryDict(category_dict_ch1,'category_trackDetails.ch',1)
self.pickle_categoryDict(category_dict_ch2,'category_trackDetails.ch',2)
self.pickle_categoryDict(category_peakDetails_ch1,'category_peakDetails.ch',1)
self.pickle_categoryDict(category_peakDetails_ch2,'category_peakDetails.ch',2)
print "Categories Dictionaries pickled"
return category_dict_ch1, category_dict_ch2
