import os,sys
import fcm
from PositivityLib import *
import matplotlib.pyplot as plt

if not os.path.isdir("eqapol-11c-1"):
    raise Exception("The data directory eqapol-11c-1 is not present")

## define the file list
stimulationList = "CMVpp65"

fileList = os.listdir("eqapol-11c-1")
filePathList = [os.path.join(os.getcwd(),"eqapol-11c-1",fn) for fn in fileList]

## load the fcs files and append them to a list
fcsList = []
for filePath in filePathList:
    fcsData = fcm.loadFCS(filePath,auto_comp=False,transform=None)
    fcsData.logicle(scale_max=1e05)
    fcsList.append(fcsData)

## define variables
channelDict = {'FSC':0,'SSC':3,'CD57':8,'CD4':7,'dump':17,'CD3':16,'CD27':15,'TNFa':14,'CD8':13,'IL2':12,
               'CD45RO':11, 'CD107':10, 'IFNg':9}

## find the positivity threshold
posControlFile = 'G69019FF_SEB_CD4.fcs'
negControlFile = 'G69019FF_Costim_CD4.fcs'
beta = 0.8
cytokine = 'IL2'
positiveEvents = get_events(posControlFile,fileList,fcsList)
negativeEvents = get_events(negControlFile,fileList,fcsList)
fResults = get_positivity_threshold(negativeEvents,positiveEvents,channelDict[cytokine],beta=beta)
print fResults['threshold']

## get the percentages, counts, and indices of positive events
percentages,counts,idx = get_cytokine_positive_events(channelDict[cytokine],fResults['threshold'],
                                                      fileList,fcsList)
## plot the results
fig = plt.figure(figsize=(8,6))
ax = fig.add_subplot(111)
create_plot(fig,ax,'G69019FF_CMVpp65_CD4.fcs',cytokine,channelDict,fileList,fcsList,fResults,percentages,counts,idx)
plt.savefig("positivity_%s.png"%cytokine)