def convertTifs(pathDir):
allTifs = locate("*c*.tif", pathDir)
for f1 in allTifs:
f2 = f1[:-4] + '.jpg'
cmd = "convert " + f1 + " " + f2
call(cmd.split(), shell=False)
return True
def convertTifs(pathDir):
allTifs = locate("*c*.tif",pathDir)
for f1 in allTifs:
f2 = f1[:-4]+'.jpg'
cmd = "convert " + f1 + " " + f2
call(cmd.split(),shell=False)
return True
def __init__(self,exptDir):
self.exptDir = exptDir
self.dateStamp = os.path.split(self.exptDir)[1]
self.allcsv = locate("*_EXPT_RESULTS.csv",self.exptDir)
self.allcsv.sort()
self.destDir = exptDir
self.outFullFile, self.outShortFile = self.makeOutFiles()
self.nameCircInt_dict = collections.defaultdict(list)
self.nameRingInt_dict = collections.defaultdict(list)
def drawFigures(pathDir):
pklDir = os.path.join(os.path.split(pathDir)[0],'pklFiles')
pklFiles = locate('*.pkl',pklDir)
#combineExptPlots(pathDir,pklDir,radPlotDir)
for pklF in pklFiles:
print pklF
exptType = os.path.split(pklF)[1].split('.')[0]
plotType1 = RadialPlotFigure(pathDir,exptType)
fnameTag1 = 'radProfile.stdev'
plotType1.drawRadialProfile('.meanLineProfile.dict.pkl',fnameTag1)
plotType2 = RadialPlotFigure(pathDir,exptType)
fnameTag2 = 'radProfile.reduced.stdev'
plotType2.drawRadialProfile('.meanLineProfile.reduced.stdev.dict.pkl',fnameTag2)
def drawFigures(pathDir):
pklDir = os.path.join(os.path.split(pathDir)[0], 'pklFiles')
pklFiles = locate('*.pkl', pklDir)
#combineExptPlots(pathDir,pklDir,radPlotDir)
for pklF in pklFiles:
print pklF
exptType = os.path.split(pklF)[1].split('.')[0]
plotType1 = RadialPlotFigure(pathDir, exptType)
fnameTag1 = 'radProfile.stdev'
plotType1.drawRadialProfile('.meanLineProfile.dict.pkl', fnameTag1)
plotType2 = RadialPlotFigure(pathDir, exptType)
fnameTag2 = 'radProfile.reduced.stdev'
plotType2.drawRadialProfile('.meanLineProfile.reduced.stdev.dict.pkl',
fnameTag2)
def summarize_fld(dateStamp,pathDir,destDir,typeVal='count'):
"""
Summary of flds; This typically would be the count density/field;
"""
def _skip(f):
skip = ['offset','maxProj','proj','dict','tflds']
for word in skip:
if word in f: return False
return True
def _checkChannel(f):
ch = 'default'
if '561' in f: ch = '561'
if '647' in f: ch = '647'
if '561_647' in f: ch = '561_647'
if 'c1.tif' in f: ch = '561' #Must take precautions
if 'c2.tif' in f: ch = '647'
if 'c3.tif' in f: ch = '561_647'
return ch
def _summary(ch,listToWrite,ofile):
ofile.write('\n CHANNEL \t '+ch+'\n')
for l in listToWrite:
ofile.write('\t'.join(l)+'\n')
return True
if typeVal == 'count':
out_long = os.path.join(destDir,dateStamp+'_flds.long.count.summary.csv')
out_short = os.path.join(destDir,dateStamp+'_flds.short.count.summary.csv')
if typeVal == 'intensity':
out_long = os.path.join(destDir,dateStamp+'_flds.intensity.long.summary.csv')
out_short = os.path.join(destDir,dateStamp+'_flds.intensity.short.summary.csv')
ofile_long = open(out_long,'w')
if typeVal == 'count': header = '\t'.join(['FULL PATH','SUBDIR','CH','PEAK COUNT'])
if typeVal == 'intensity': header = '\t'.join(['FULL PATH', 'SUBDIR','CH','MEAN PEAK INTENSITY'])
ofile_long.write(header+'\n')
ofile_short = open(out_short,'w')
if typeVal == 'count': header = '\t'.join(['FULL PATH','SUBDIR','CH','AVERAGE PEAK COUNT', 'STDEV PEAK COUNT'])
if typeVal == 'intensity': header = '\t'.join(['FULL PATH','SUBDIR','CH', 'AVERAGE of MEAN PEAK INTENSITY','STDEV MEAN INTENSITY'])
ofile_short.write(header)
list_561 = list()
list_647 = list()
list_561_647 = list()
list_default = list()
dict_561 = collections.defaultdict(list)
dict_647 = collections.defaultdict(list)
dict_561_647 = collections.defaultdict(list)
dict_default = collections.defaultdict(list)
pattern = "*fld*.tif.png*.pkl"
allfPkl = locate(pattern, pathDir)
fList = [f for f in allfPkl if not _skip(f)]
for f in fList:
print "Loading file : %s"%(os.path.split(f)[1])
with open(f) as ifile:
peakInfo = pickle.load(ifile)
if typeVal == 'count': colVal = len(peakInfo) #Just this for now. Simples
if typeVal == 'intensity': colVal = getMeanIntensity(peakInfo)
exptPath,fname = os.path.split(f)
expt = os.path.split(exptPath)[1]
ch = _checkChannel(fname)
if ch == '561':
list_561.append([f,expt,ch,str(colVal)])
dict_561[expt].append([exptPath,expt,colVal])
elif ch == '647':
list_647.append([f,expt,ch,str(colVal)])
dict_647[expt].append([exptPath,expt,colVal])
elif ch == '561_647':
list_561_647.append([f,expt,ch,str(colVal)])
dict_561_647[expt].append([exptPath,expt,colVal])
elif ch == 'default':
list_default = list()
dict_default[expt].append([exptPath,expt,colVal])
else: raise SystemExit("Something wrong with Channels")
_summary('561',list_561,ofile_long)
_summary('647',list_647,ofile_long)
_summary('561_647',list_561_647,ofile_long)
_summary('default',list_default,ofile_long)
ofile_long.close()
list_561 = list()
list_647 = list()
list_561_647 = list()
list_ch = [list(),list(),list()]
list_default = list()
for idx,d in enumerate([dict_561,dict_647,dict_561_647]):
for expt,val in d.items():
exptPath = val[0][0]
colValL = zip(*val)[2]
avgPeaks,stdPeaks = np.mean(colValL),np.std(colValL)
list_ch[idx].append([exptPath,expt,str(idx+1),str(avgPeaks),str(stdPeaks)])
_summary('561',list_ch[0],ofile_short)
_summary('647',list_ch[1],ofile_short)
_summary('561_647',list_ch[2],ofile_short)
ofile_short.close()
return True